tulio@sun.ac.za and deoliveira@ukzn.ac.za +27 (0) 31 260 4898
Background:
Prof. Tulio de Oliveira is the director of the Centre for Epidemic Response and Innovation (CERI) and the KwaZulu-Natal Research Innovation and Sequencing Plaform (KRISP). Prof. de Oliveira is a Professor of Bioinformatics at the School for Data Science and Computational Thinking, Stellenbosch University and at the Collegue of Health Sciences at University of KwaZulu-Natal.
He has received his BSc at the Federal University of Rio Grande do Sul (UFRGS), Brazil and MSc/PhD at the Nelson R Mandela School of Medicine, UKZN, South Africa. He was a Marie Curie Research Fellow at the University of Oxford, U.K. from 2004 to 2006 and a Newton Advanced Fellow at the Wellcome Trust Sanger Institute (WTSI) and at the University of Edinburgh from 2015-2019. In 2015, he became a Professor at UKZN and in 2018, Associate Professor on Global Health at the University of Washington, Seattle, USA and in 2021, he became a Professor at Stellenbosch University.
Prof. de Oliveira has worked for over 20 years with viral outbreaks, including HIV, Hepatitis B and C, Chikungunya, Dengue, SARS-CoV-2, Zika, and Yellow Fever Virus. Prof. de Oliveira has more than 300 publications, with many of them in, the top scientific journals, Nature, Science and Lancet.
Awards:
Prof. de Oliveira was included in a list of ten most important scientists by Nature in 2021. De Oliveira was also included in a list of the MIT Technology Review as one of the leaders of the ten breakthrough technologies in 2021. In 2022, he received the Gold Medal Award from the South African Medical Research Council (SAMRC). In the same year, for his contributions to society, he received the Batho Pele Platinum Award from the Government of South Africa. Prof. Tulio de Oliveira also received the German African Award from the German Chancellor Olaf Scholz in 2022. In 2023, Prof. de Oliveira has received the Discovery Lifetime Leadership Award and the Order of the Merit of Portugual with the title of Commander (ComM) (Comendador)..
Current Affiliations:
Professor on Bioinformatics: School for Data Science and Computational Thinking, Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.
Director: KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa.
Fractional Professor - College of Health Sciences, University of KwaZulu-Natal (UKZN), Durban, South Africa.
Affiliate Professor, Department of Global Health, University of Washington, Seattle, US.
Senior Research Associate, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, South Africa.
Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil.
Tegally H, Dellicour S, Poongavanan J, Mavian C, Dor G, Fonseca V, Tagliamonte M, Dunaiski M, Moir M, Wilkinson E, de Albuquerque C, Frutuoso L, , Holmes E, Baxter C, Lessells R, Kraemer M, Lourenço J, Alcantara L, de Oliveira T, Giovanetti M, (2024), ():. doi: 10.1101/2024.10.29.24316328.:.
Dengue virus importation risks in Africa: a modelling study.
Poongavanan J, Lourenço J, Tsui J, Colizza V, Ramphal Y, Baxter C, Kraemer M, Dunaiski M, de Oliveira T, Tegally H, The Lancet Planetary Health (2024), 8(12):e1043-e1054. doi: 10.1016/s2542-5196(24)00272-9.:.
Using HIV and Hepatitis C Molecular Epidemiology to Investigate Assisted Partner Services Recruitment Among People Who Inject Drugs in Kenya.
Kingston H, Chohan B, Mbogo L, Bukusi D, Monroe-Wise A, Sambai B, Omballa V, Tram K, Guthrie B, Giandhari J, Masyuko S, Bosire R, Sinkele W, de Oliveira T, Scott J, Farquhar C, Herbeck J, AIDS Research and Human Retroviruses (2024), ():. doi: 10.1089/aid.2024.0036.:.
SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study.
Dassaye R, Chetty T, Daniels B, Gaffoor Z, Spooner E, Ramraj T, Mthethwa N, Nsibande D, Pillay S, Bhana A, Magasana V, Reddy T, Mohlabi K, Moore P, Burgers W, de Oliveira T, Msomi N, Goga A, JMIR Research Protocols (2024), 13():e52713. doi: 10.2196/52713.:.
The COVID-19 pandemic in BRICS: Milestones, interventions, and molecular epidemiology.
van Wyk S, Moir M, Banerjee A, Bazykin G, Biswas N, Sitharam N, Das S, Ma W, Maitra A, Mazumder A, Karim W, Lamarca A, Li M, Nabieva E, Tegally H, San J, Vasconcelos A, Xavier J, Wilkinson E, de Oliveira T, PLOS Global Public Health (2024), 4(12):e0003023. doi: 10.1371/journal.pgph.0003023.:.
Alignment-Free Viral Sequence Classification at Scale.
van Zyl D, Dunaiski M, Tegally H, Baxter C, , de Oliveira T, Xavier J, (2024), ():. doi: 10.1101/2024.12.10.627186.:.
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana.
Choga W, Gustani-Buss E, Tegally H, Maruapula D, Yu X, Moir M, Zuze B, James S, Ndlovu N, Seru K, Motshosi P, Blenkinsop A, Gobe I, Baxter C, Manasa J, Lockman S, Shapiro R, Makhema J, Wilkinson E, Blackard J, Lemey P, Lessells R, Martin D, de Oliveira T, Gaseitsiwe S, Moyo S, Virus Evolution (2024), 10(1):. doi: 10.1093/ve/veae095.:.
Hybrid versus vaccine immunity of mRNA-1273 among people living with HIV in East and Southern Africa: a prospective cohort analysis from the multicentre CoVPN 3008 (Ubuntu) study.
Garrett N, Tapley A, Hudson A, Dadabhai S, Zhang B, Mgodi N, Andriesen J, Takalani A, Fisher L, Kee J, Magaret C, Villaran M, Hural J, Andersen-Nissen E, Ferarri G, Miner M, Le Roux B, Wilkinson E, Lessells R, de Oliveira T, Odhiambo J, Shah P, Polakowski L, Yacovone M, Samandari T, Chirenje Z, Elyanu P, Makhema J, Kamuti E, Nuwagaba-Biribonwoha H, Badal-Faesen S, Brumskine W, Coetzer S, Dawson R, Delany-Moretlwe S, Diacon A, Fry S, Gill K, Ebrahim Hoosain Z, Hosseinipour M, Inambao M, Innes C, Innes S, Kalonji D, Kasaro M, Kassim P, Kayange N, Kilembe W, Laher F, Malahleha M, Maluleke V, Mboya G, McHarry K, Mitha E, Mngadi K, Mda P, Moloantoa T, Mutuluuza C, Naicker N, Naicker V, Nana A, Nanvubya A, Nchabeleng M, Otieno W, Potgieter E, Potloane D, Punt Z, Said J, Singh Y, Tayob M, Vahed Y, Wabwire D, McElrath M, Kublin J, Bekker L, Gilbert P, Corey L, Gray G, Huang Y, Kotze P, Badal-Faesen S, Baepanye K, Bailey V, Baloyi-Oseh K, Booley M, Botha J, Brown Y, Brown V, Bunts L, Coetzer S, Cohen M, Collie S, Dawson R, Deb P, El Sahly H, El-Khorazaty J, Engelbrecht A, Gildea M, Govender D, Hanke J, Harris J, Hendricks S, Hopkinson N, Howell H, Ketter N, Khuto K, Laher Omar F, Katsidzira L, Linton K, Ludwig J, Mabilane B, Malefo M, Mamushiana N, Margineantu D, May J, Mayat F, Molitor C, Naidoo Y, Nebergall M, Nguyen A, Nikles S, Noronha B, Peda M, Phiri T, Pillay S, Pillay S, Proulx-Burns L, Rinn L, Sanders L, Sopher C, Sripathy S, Stirewalt M, Tegally H, Thiebaud S, Toledano A, Van Wyk S, Whitby S, Wilcox S, Wilkinson E, Wilvich H, Wiysonge C, Xaba N, Xulu N, eClinicalMedicine (2025), 80():103054. doi: 10.1016/j.eclinm.2024.103054.:.
Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil.
Romero-Calle D, Pedrosa-Silva F, Ribeiro Tomé L, Fonseca V, Guimarães Benevides R, de Oliveira Santos L, de Oliveira T, da Costa M, Alcantara L, de Carvalho Azevedo V, Brenig B, Venancio T, Billington C, Góes-Neto A, Microorganisms (2023), 11(7):1837. doi: 10.3390/microorganisms11071837.:.
Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay.
Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, Gomez de la Fuente A, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega M, Gamarra M, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani F, Pereira G, de Oliveira C, Schuab G, Rodrigues E, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis W, Lessels R, de Filippis A, Ojeda A, Sequera G, Montoya R, Holmes E, de Oliveira T, Rico J, Lourenço J, Fonseca V, Alcantara L, Emerging Infectious Diseases (2023), 29(9):. doi: 10.3201/eid2909.230523.:.
Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023.
Cella E, Fonseca V, Branda F, Tosta S, Moreno K, Schuab G, Ali S, Slavov S, Scarpa F, Santos L, Kashima S, Wilkinson E, Tegally H, Mavian C, Borsetti A, Caccuri F, Salemi M, de Oliveira T, Azarian T, de Filippis A, Alcantara L, Ceccarelli G, Caruso A, Colizzi V, Marcello A, Lourenço J, Ciccozzi M, Giovanetti M, International Journal of Infectious Diseases (2024), ():107262. doi: 10.1016/j.ijid.2024.107262.:.
The third era of genomics is at risk of being dismantled across the Global South.
de Oliveira T, Science (2024), 386(6718):eadt4843. doi: 10.1126/science.adt4843.:.
A new lineage nomenclature to aid genomic surveillance of dengue virus.
Hill V, Cleemput S, Pereira JS, Gifford RJ, Fonseca V, Tegally H, Brito AF, Ribeiro G, de Souza VC, Brcko IC, Ribeiro IS, De Lima ITT, Slavov SN, Sampaio SC, Elias MC, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, Lima ARJ, de Oliveira T, Grubaugh ND., PLoS Biology (2024), 22(9):e3002834. doi: 10.1371/journal.pbio.3002834.:.
Impacts of climate change-related human migration on infectious diseases.
Tsui JLH, Pena RE, Moir M, Inward RPD, Wilkinson E, San JE, Poongavanan J, Bajaj S, Gutierrez B, Dasgupta A, de Oliveira T, Kraemer MUG, Tegally H, Sambaturu P , Nature Climate Change (2024), 14, 793802 (2024). https://doi.org/10.1038/s41558-024-02078-z:.
Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours.
Godwe C, Goni OH, San JE, Sonela N, Tchakoute M, Nanfack A, Koro FK, Butel C, Vidal N, Duerr R, Martin DP, de Oliveira T, Peeters M, Altfeld M, Ayouba A, Ndung'u T, Tongo M, Virus Evolution (2024), 10(1):veae070. doi: 10.1093/ve/veae070:.
SARS-CoV-2 Genomic Epidemiology Dashboards: A Review of Functionality and Technological Frameworks for the Public Health Response.
Sitharam N, Tegally H, Silva DC, Baxter C, de Oliveira T, Xavier JS, Genes (2024), 15(7):876. doi: 10.3390/genes15070876:.
Understanding the Transmission Dynamics of the Chikungunya Virus in Africa.
Ramphal Y, Tegally H, San JE, Reichmuth ML, Hofstra M, Wilkinson E, Baxter C, Climade Consortium, de Oliveira T, Moir M, Pathogens (2024), 13(7):605. doi: 10.3390/pathogens13070605:.
Sustained Human Outbreak of a New MPXV Clade I Lineage in the Eastern Democratic Republic of the Congo.
Vakaniaki EH, Kacita C, Kinganda-Lusamaki E, O'Toole Á, Wawina-Bokalanga T, Mukadi-Bamuleka D, Amuri-Aziza A, Malyamungu-Bubala N, Mweshi-Kumbana F, Mutimbwa-Mambo L, Belesi-Siangoli F, Mujula Y, Parker E, Muswamba-Kayembe PC, Nundu SS, Lushima RS, Makangara-Cigolo JC, Mulopo-Mukanya N, Pukuta-Simbu E, Akil-Bandali P, Kavunga H, Abdramane O, Brosius I, Bangwen E, Vercauteren K, Sam-Agudu NA, Mills EJ, Tshiani-Mbaya O, Hoff NA, Rimoin AW, Hensley LE, Kindrachuk J, Baxter C, de Oliveira T, Ayouba A, Peeters M, Delaporte E, Ahuka-Mundeke S, Mohr EL, Sullivan NJ, Muyembe-Tamfum JJ, Nachega JB, Rambaut A, Liesenborghs L, Mbala-Kingebeni P, Nature Medicine (2024), doi: 10.1038/s41591-024-03130-3:.
HIV escape and resistance in the central nervous system in treatment experienced South Africans.
Collier D, Derache A, Karim F, Smit T, Adamson J, Khan K, Naidoo T, Perumal N, Brijkumar J, Giandhari J, De Oliveira T, Sigal A, Kemp S, Gupta RK, medRxiv [Preprint] (2024), :.
Disentangling seasonal introduction and establishment risk of dengue in Africa.
Poongavanan J, Lourenço J, Tsui JHL, Colizza V, Ramphal Y, Baxter C, Kraemer MOG, Dunaiski M, de Oliveira T, Tegally H, medRxiv [Preprint] (2024), https://doi.org/10.1101/2024.05.07.24306997:.
A new lineage nomenclature to aid genomic surveillance of dengue virus.
Hill V, Cleemput S, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, de Oliveira T, Grubaugh ND, medRxiv [Preprint] (2024), 2024.05.16.24307504. doi: 10.1101/2024.05.16.24307504:.
Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation.
Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MS, Sigal A, Nature Communications (2024), 15;15(1):2360:.
Managing and assembling population-scale data streams, tools and workflows to plan for future pandemics within the INFORM-Africa Consortium.
Poongavanan J, Xavier J, Dunaiski M, Tegally H, Oladejo S, Ayorinde O, Wilkinson E, Baxter C, de Oliveira T, S Afr J Sci. (2024), 119(5-6):14569. doi: 10.17159/sajs.2023/14659:.
An updated framework for SARS-CoV-2 variants reflects the unpredictability of viral evolution.
Subissi L, Otieno JR, Worp N, Attar Cohen H, Oude Munnink BB, Abu-Raddad LJ, Alm E, Barakat A, Barclay WS, Bhiman JN, Caly L, Chand M, Chen M, Cullinane A, de Oliveira T, Drosten C, Druce J, Effler P, El Masry I, Faye A, Ghedin E, Grant R, Haagmans BL, Happi C, Herring BL, Hodcroft EB, Ikejezie J, Katawera V, Kassamali ZA, Leo YS, Leung GM, Kondor RJ, Marklewitz M, Mendez-Rico J, Melhem NM, Munster V, Nahapetyan K, Naindoo D, Oh DY, Peacock TP, Peiris M, Peng Z, Poon LLM, Rambaut A, Saha S, Shen Y, Siqueira MM, Volz E, Tessema SK, Thiel V, Triki H, van der Werf S, von Eije K, Cunningham J, Koopmans MPG, von Gottberg A, Agrawal A, Van Kerkhove MD, Nature Medicine (2024), doi: 10.1038/s41591-024-02949-0:.
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Bashton M, Batty EM, Bediako Y, Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Ampomah Carr RA, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Molina Mora JA, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C; IMSSC2 Laboratory Network Consortium; de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z., bioRxiv [Preprint] (2024), 2024.04.29.591666. doi: 10.1101/2024.04.29.59166:.
Save lives in the next pandemic: ensure vaccine equity now.
Carlson C, Becker D, Happi C, O'Donoghue Z, de Oliveira T, Oyola SO, Poisot T, Seifert S, Phelan A, Nature (2024), 626(8001):952-953. doi: 10.1038/d41586-024-00545-3:.
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations.
Lustig G, Ganga Y, Rodel HE, Tegally H, Khairallah A, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Ndung'u T, Moosa MS, Archary D, de Oliveira T, Lessells R, Neher RA, Abdool Karim SS, Sigal A, Virus Evolution (2024), 10(1):vead075. doi: 10.1093/ve/vead075:.
Investing in Africa's scientific future.
de Oliveira T, Baxter C, Science (2024), ;383(6678):eadn4168. doi: 10.1126/science.adn4168:.
Climate Change and Epidemics 2023 Synthesis Report.
de Oliveira T, Baxter C, for the CLIMADE consortium , (2023), CLIMADE, Stellenbosch, South Africa. pp1-23, doi 10.25413/sun.24599043:.
NEJM Case 40-2023: A 70-Year-Old Woman with Cough and Shortness of Breath.
Gandhi RT, Castle AC, de Oliveira T, Lessells RJ, New England Journal of Medicine (2023), 389(26):2468-2476. doi: 10.1056/NEJMcpc2300910:.
Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant.
Khan K, Lustig G, Römer C, Reedoy K, Jule Z, Karim F, Ganga Y, Bernstein M, Baig Z, Jackson L, Mahlangu B, Mnguni A, Nzimande A, Stock N, Kekana D, Ntozini B, van Deventer C, Marshall T, Manickchund N, Gosnell BI, Lessells RJ, Karim QA, Abdool Karim SS, Moosa MS, de Oliveira T, von Gottberg A, Wolter N, Neher RA, Sigal A., Nature Communications (2023), 14(1):8078. doi: 10.1038/s41467-023-43703-3:.
Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection..
Choga WT, Kurusa Gasenna GK, San JE, Ookame T, Gobe I, Chand M, Phafane B, Seru K, Matshosi P, Zuze B, Ndlovu N, Matsuru T, Maruapula D, Bareng OT, Macheke K, Kuate-Lere L, Tlale L, Lesetedi O, Tau M, Mbulawa MB, Smith-Lawrence P, Matshaba M, Shapiro R, Makhema J, Martin DP, de Oliveira T, Lessells RJ, Lockman S, Gaseitsiwe S, Moyo S, Int J Infect Dis. (2023), 138:91-96. doi: 10.1016/j.ijid.2023.11.011:.
An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal .
Padane A, Tegally H, Ramphal Y, Ndiaye S, Sarr M, Diop M, Diedhiou CK, Mboup A, Diouf N, Souare A, Diagne ND, Aza-Gnandji M, Dabo NA, Dia YA, Diaw NA, Leye N, Diaw PA, Ambroise A, Cisse B, Diallo AS, Diop O, Diallo AA, Ndoye S, Sanko TJ, Baxter C, Wilkinson E, James SE, Tshiabuila D, Naidoo Y, Pillay S, Lessells R, Cisse K, Leye A, Mbaye A, Kania D, Traore I, Kagone ST, Tinto B, Ouedraogo A, Lourenco J, Giovanetti M, Giandhari J, de Oliveira T, Mboup S, medrxiv (2023), MEDRXIV-2023-298527v1:.
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil.
Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi AC, Tscha M, Soares G, Dorl GG, Marques AEML, Sousa R, Adelino TER, Xavier J, de Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonça AF, de Macêdo IL, Ribeiro de Sousa DE, Rodrigues de Toledo Costa G, Botelho de Castro M, de Souza Andrade M, de Abreu FVS, Campos FS, Iani FCM, Pereira MA, Cavalcante KRLJ, de Freitas ARR, Campelo de Albuquerque CF, Macário EM, Dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, Oliveira de Moura NF, Fabri A, Dos Santos Rodrigues CD, Dos Santos CC, Barreto de Almeida MA, Dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, Mayoral Pedroso da Silva G, Soares MRF, de Castilhos MMS, de Souza E Silva JC, Bisetto Junior A, Pouzato EG, Tanabe LS, Arita DA, Matsuo R, Dos Santos Raymundo J, Silva PCL, Santana Araújo Ferreira Silva A, Samila S, Carvalho G, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, de Almeida Medeiros DB, Cruz ACR, Venâncio da Cunha R, Van Voorhis W, Bispo de Filippis AM, Almiron M, Holmes EC, Ramos DG, Romano A, Lourenço J, Alcantara LCJ, Duarte Dos Santos CN, Science Advances (2023), 9(35):eadg9204. doi: 10.1126/sciadv.adg9204:.
Will climate change amplify epidemics and give rise to pandemics?.
de Oliveira T, Tegally H, Science (2023), 381,6660, DOI: 10.1126/science.adk4500:.
Genomic epidemiology of the cholera outbreak in Malawi 2022-2023.
Chabuka L, Choga WT, Mavian CN, Moir M, Tegally H, Wilkinson E, Naidoo Y, Inward R, Morgenstern C, Bhatt S, Wint WGR, Khan K, Bogoch II, Kraemer MUG, Baxter C, Tagliamonte M, Salemi M, Lessells RJ, Mitambo C, Chitatanga R, Bango JB, Chiwaula M, Chavula Y, Bukhu M, Manda H, Chitenje M, Malolo I, Mwanyongo A, Mvula B, Nyenje M, de Oliveira T, Kagoli M, medRxiv (2023), https://doi.org/10.1101/2023.08.22.23294324:.
Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern.
Tegally H, Wilkinson E, Tsui JL, Moir M, Martin D, Brito AF, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells RJ, Faria NR, Kraemer MUG, de Oliveira T, Cell (2023), S0092-8674(23)00641-4. doi: 10.1016/j.cell.2023.06.001:.
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.
Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, COVID-19 Genomics UK (COG-UK) consortium¶, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG, Science (2023), 381(6655):336-343. doi: 10.1126/science.adg6605.:.
Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages.
Subramoney K, Mtileni N, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Maharaj A, Tshiabuila D, Tegally H, Wilkinson E, de Oliveira T, Fielding BC, Treurnicht FK, Viruses (2023), 15(5):1194. doi: 10.3390/v15051194:.
SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.
Subramoney K, Mtileni N, Davis A, Giandhari J, Tegally H, Wilkinson E, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Simane A, Reddy B, Mashishi B, Mbenenge N, de Oliveira T, Fielding BC, Treurnicht FK, PLoS One (2023), 18(5):e0286373. doi: 10.1371/journal.pone.0286373:.
Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.
Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, de Oliveira T, Giandhari J, PLoS ONE (2023), 18(4):e0283219. doi: 10.1371/journal.pone.0283219:.
Genomic epidemiology sheds light on the recent spatio-temporal dynamics of Yellow Fever virus and the spatial corridor that fueled its ongoing emergence in southern Brazil.
Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi A, Tscha M, Soares G, Dorl G, Marques AE, Sousa RS, Adelino TER, Xavier J, Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonca AF, de Macedo IL, de Souze DER , Costa GRT, de Castro MB, Iani FCM, Pereira MA, Cavalcante KRLJ, Freitas ARR, de Albuquerque CFC, Macario EM, dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, de Moura NFB, Fabri A, Rodrigues CDS, dos Santos CC, de Almeida MAB, dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, da Silva GMP, Soares MRF, de Castilhos MMS, Silva JCS, Junior AB, Pouzato EG, Tanabe LS, Arita DA, Matsuo RM, Raymundo JS, Silva PCL, Silva ASAF, Samila S, Pereira GC, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, Medeiros DBA, Cruz ACR, Cunha RV, Voorhis WV, de Filippis AMB, Almiron MA, Holmes EC, Ramos DG, Martins AP, Lourenco JL, Alcantara LCJ, dos Santos CND, medRxiv (2023), 2023.01.13.23284525v1:.
Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay.
Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Junior Alcantara LC, medRXiV (2023), doi:10.1101/2023.04.16.23288635:.
SARS-CoV-2 Africa dashboard for real-time COVID-19 information.
Xavier JS, Moir M, Tegally H, Sitharam N, Abdool Karim W, San JE, Linhares J, Wilkinson E, Ascher DB, Baxter C, Pires DEV, de Oliveira T, Nature Microbiology (2023), 8(1):1-4. doi: 10.1038/s41564-022-01276-9:.
Advancing detection and response capacities for emerging and re-emerging pathogens in Africa.
achega JB, Nsanzimana S, Rawat A, Wilson LA, Rosenthal PJ, Siedner MJ, Varma JK, Kilmarx PH, Mutesa L, Tanner M, Binagwaho A, Forrest J, Mbala-Kingebeni P, Muyembe-Tamfum JJ, Ntoumi F, Zumla A, de Oliveira T, Mills EJ, Lancet Infect Dis. (2023), :S1473-3099(22)00723-X. doi: 10.1016/S1473-3099(22)00723-X:.
New nomenclature for mpox (monkeypox) and monkeypox virus clades.
Ulaeto D, Agafonov A, Burchfield J, Carter L, Happi C, Jakob R, Krpelanova E, Kuppalli K, Lefkowitz EJ, Mauldin MR, de Oliveira T, Onoja B, Otieno J, Rambaut A, Subissi L, Yinka-Ogunleye A, Lewis RF, Lancet Infect Dis. (2023), 23(3):273-275. doi: 10.1016/S1473-3099(23)00055-5:.
Consequences of rpoB mutations missed by the GenoType MTBDRplus assay in a programmatic setting in South Africa.
Mvelase NR, Cele LP, Singh R, Naidoo Y, Giandhari J, Wilkinson E, de Oliveira T, Swe-Han KS, Mlisana KP, Afr J Lab Med. (2023), 12(1):1975. doi: 10.4102/ajlm.v12i1.1975:.
Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique.
Ismael N, van Wyk S, Tegally H, Giandhari J, San JE, Moir M, Pillay S, Utpatel C, Singh L, Naidoo Y, Ramphal U, Mabunda N, Abílio N, Arnaldo P, Xavier J, Amoako DG, Everatt J, Ramphal Y, Maharaj A, de Araujo L, Anyaneji UJ, Tshiabuila D, Viegas S, Lessells R, Engelbrecht S, Gudo E, Jani I, Niemann S, Wilkinson E, de Oliveira T, PLOS Glob Public Health (2023), 6;3(3):e0001593. doi: 10.1371/journal.pgph.0001593:.
Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia 2020-2022.
Sisay A, Tshiabuila D, van Wyk S, Tesfaye A, Mboowa G, Oyola SO, Tesema SK, Baxter C, Martin D, Lessells R, Tegally H, Moir M, Giandhari J, Pillay S, Singh L, Ramphal Y, Maharaj A, Pillay Y, Maharaj A, Naidoo Y, Ramphal U, Chabuka L, Wilkinson E, de Oliveira T, Desta AF, San JE, Genes (2023), 13;14(3):705. doi: 10.3390/genes14030705:.
Global disparities in SARS-CoV-2 genomic surveillance. .
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C; Bulgarian SARS-CoV-2 sequencing group; Communicable Diseases Genomics Network (Australia and New Zealand); COVID-19 Impact Project; Danish Covid-19 Genome Consortium; Fiocruz COVID-19 Genomic Surveillance Network; GISAID core curation team; Network for Genomic Surveillance in South Africa (NGS-SA); Swiss SARS-CoV-2 Sequencing Consortium, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR., Nature Communications (2022), 16;13(1):7003. doi: 10.1038/s41467-022-33713-y.:.
Antiretroviral therapy adherence patterns, virological suppression, and emergence of drug resistance: A nested case-control study from Uganda and South Africa.
.
Tyagi A, Tong Y, Rabideau DJ, Reynolds Z, De Oliveira T, Lessells R, Amanyire G, Orrell C, Asiimwe S, Chimukangara B, Giandhari J, Pillay S, Haberer JE, Siedner MJ; META Study Investigators. , Antivir Ther. (), 27(5):13596535221114822. doi: 10.1177/13596535221114822:.
Ethics and governance challenges related to genomic data sharing in southern Africa: the case of SARS-CoV-2.
Moodley K, Cengiz N, Domingo A, Nair G, Obasa AE, Lessells RJ, de Oliveira T, Lancet Global Health (2022), https://doi.org/10.1016/ S2214-109X(22)00417-X:.
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.
Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri AN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang'a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O'Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR; Africa Pathogen Genomics Initiative (Africa PGI), Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E, Science (2022), eabq5358. doi: 10.1126/science.abq5358:.
Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999-2018.
Ismael N, Wilkinson E, Mahumane I, Gemusse H, Giandhari J, Bauhofer A, Vubil A, Mambo P, Singh L, Mabunda N, Bila D, Engelbrecht S, Gudo E, Lessells R, de Oliveira T, Viruses (2022), 14(9):1992. doi: 10.3390/v14091992:.
Clinical evaluation of SARS-CoV-2 rapid antigen tests during the Omicron wave in South Africa.
Samsunder N, de Vos M, Ngcapu S, Giandhari J, Lewis L, Kharsany AB, Carwood C, de Oliveira T, Karim QA, Karim SA, Naidoo K, Escadafal C, Sivro A, J Infect Dis. (2022), jiac333. doi: 10.1093/infdis/jiac333:.
Impact of intra-host immune adaptations on the evolution of SARS-CoV-2 S protein among individuals with SARS-CoV-2 infections in South Africa, 2020 to 2022..
Subramoney K, Mtileni N, Davis A, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Tegally H, Wilkinson E, Simane A, Reddy B, Mashishi B, Mbenenge N, de Oliveira T, Fielding B, Treurnicht F, Authorea Preprints (2022), DOI: 10.22541/au.166305249.90395426/v1 :.
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.
Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O'Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Freitas L, Resende PC, Lee RTC, Maurer-Stroh S, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T, PLoS Biology (2022), doi: 10.1371/journal.pbio.3001769.:.
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, Iani FCM, de Carvalho Pereira G, Vazquez C, Sanabria GME, Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Paola Oliveira de Lima L, Martins AJ, Renata Dos Santos Barros C, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, Reboredo de Oliveira da Silva L, Gómez MKA, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Figueredo GPM, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Giacomini MP, Marques NQ, Riediger IN, Raboni S, Mattoso G, Cataneo AD, Zanluca C, Duarte Dos Santos CN, Assato PA, Allan da Silva da Costa F, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said RF, Campelo de A E Melo CF, Almiron M, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, Junior de Alcantara LC, Covas DT, Nature Microbiology (2022), doi: 10.1038/s41564-022-01191-z:.
SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic.
Roshdy WH, Khalifa MK, San JE, Tegally H, Wilkinson E, Showky SM, Darren P, Moir M, Naguib AEN, Gomaa MR, Fahim MAEH, Mohsen AGR, Hassany M, Lessells R, Al-Karmalawy AA, EL-Shesheny R, Kandeil AM, Ali MA, de Oliveira T, Viruses (2022), https://www.mdpi.com/1999-4915/14/9/1878:.
Building genomic sequencing capacity in Africa to respond to the SARS-CoV-2 pandemic.
de Oliveira T, Wilkinson E, Baxter C, Tegally H, Giandhari J, Naidoo Y, Pillay S, Science (2022), https://www.science.org/content/resource/pandemic-preparedness-changing-world-fostering-global-collaboration, 2022:.
Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection..
Khan K, Karim F, Ganga Y, Bernstein M, Jule Z, Reedoy K, Cele S, Lustig G, Amoako D, Wolter N, Samsunder N, Sivro A, San JE, Giandhari J, Tegally H, Pillay S, Naidoo Y, Mazibuko M, Miya Y, Ngcobo N, Manickchund N, Magula N, Karim QA, von Gottberg A, Abdool Karim SS, Hanekom W, Gosnell BI; COMMIT-KZN Team, Lessells RJ, de Oliveira T, Moosa MS, Sigal A, Nature Communications (2022), doi: 10.1038/s41467-022-32396-9:.
Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment.
Juma J, Fonseca V, Konongoi SL, van Heusden P, Roesel K, Sang R, Bett B, Christoffels A, de Oliveira T, Oyola SO, BMC Genomics (2022), 23(1):520. doi: 10.1186/s12864-022-08764-6:.
HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy.
Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK, mBio (2022), 13(3):e0026922. doi: 10.1128/mbio.00269-22:.
Low-frequency HIV-1 drug resistance mutations in antiretroviral naive individuals in Botswana.
Maruapula D, Seatla KK, Morerinyane O, Molebatsi K, Giandhari J, de Oliveira T, Musonda RM, Leteane M, Mpoloka SW, Rowley CF, Moyo S, Gaseitsiwe S, Medicine (Baltimore) (2022), 101(28):e29577. doi: 10.1097/MD.0000000000029577:.
Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.
Subramoney K, Mtileni N, Bharuthram A, Davis A, Kalenga B, Rikhotso M, Maphahlele M, Giandhari J, Naidoo Y, Pillay S, Ramphal U, Ramphal Y, Tegally H, Wilkinson E, Mohale T, Ismail A, Mashishi B, Mbenenge N, de Oliveira T, Makatini Z, Fielding BC, Treurnicht FK, J Med Virol. (2022), 4(8):3676-3684. doi: 10.1002/jmv.27797:.
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.
Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Moyo S, Amoako D, Althaus C, Anyaneji U, Kekana D, Viana R, Giandhari J, Maponga T, Maruapula D, Choga W, Mayaphi S, Mbhele N, Gaseitsiwe S, Msomi N, Naidoo Y, Pillay S, Sanko T, San J, Scott L, Singh L, Magini N, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht F, Venter M, Davids M, Chiloane G, Mendes A, McIntyre C, O'Toole A, Ruis C, Peacock T, Roemer C, Williamson C, Pybus O, Bhiman J, Glass A, Martin D, Rambaut A, Gaseitsiwe S, von Gottberg A, Baxter C, Lessells R, de Oliveira T, Nature Medicine (2022), https://doi.org/10.1038/s41591-022-01911-2:.
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.
Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, Toole A, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T, Virological (2022), https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853:.
Tracking the 2022 monkeypox outbreak with epidemiological data in real-time.
Kraemer MUG, Tegally H, Pigott DM, Dasgupta A, Sheldon J, Wilkinson E, Schultheiss M, Han A, Oglia M, Marks S, Kanner J, OBrien K, Dandamudi S, Rader B, Sewalk K, Bento AI, Scarpino SV, de Oliveira T, Bogoch II, Katz R, Brownstein JS, , The Lancet Infectious Diseases (2022), DOI:https://doi.org/10.1016/S1473-3099(22)00359-0:.
An early warning system for emerging SARS-CoV-2 variants.
Subissi L, von Gottberg A, Thukral L, Worp N, Oude Munnink BB, Rathore S, Abu-Raddad LJ, Aguilera X, Alm E, Archer BN, Attar Cohen H, Barakat A, Barclay WS, Bhiman JN, Caly L, Chand M, Chen M, Cullinane A, de Oliveira T, Drosten C, Druce J, Effler P, El Masry I, Faye A, Gaseitsiwe S, Ghedin E, Grant R, Haagmans BL, Herring BL, Iyer SS, Kassamali Z, Kakkar M, Kondor RJ, Leite JA, Leo Y, Leung GM, Marklewitz M, Moyo S, Mendez-Rico J, Melhem NM, Munster V, Nahapetyan K, Oh D, Pavlin BI, Peacock TP, Peiris M, Peng Z, Poon LLM, Rambaut A, Sacks J, Shen Y, Siqueira MM, Tessema SK, Volz EM, Thiel V, van der Werf S, Briand S, Perkins MD, Van Kerkhove MD, Koopmans MPG, Agrawal A, Nature Medicine (2022), https://doi.org/10.1038/s41591-022-01836-w:.
Infectious diseases science in Africa takes a leading place in the world.
de Oliveira T, The Lancet (2022), https://doi.org/10.1016/S0140-6736(22)00977-1I:.
Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study.
Bekker LG, Garrett N, Goga A, Fairall L, Reddy T, Yende-Zuma N, Kassanjee R, Collie S, Sanne I, Boulle A, Seocharan I, Engelbrecht I, Davies MA, Champion J, Chen T, Bennett S, Mametja S, Semenya M, Moultrie H, de Oliveira T, Lessells R, Cohen C, Jassat W, Groome M, Von Gottberg A, Le Roux E, Khuto K, Barouch D, Mahomed H, Wolmarans M, Rousseau P, Bradshaw D, Mulder M, Opie J, Louw V, Jacobson B, Rowji P, Peter JG, Takalani A, Odhiambo J, Mayat F, Takuva S, Corey L, Gray GE, Lancet (2022), 399(10330):1141-1153. doi: 10.1016/S0140-6736(22)00007-1:.
The geography and inter-community configuration of new sexual partnership formation in a rural South African population over fourteen years (20032016).
Kim H-Y, Cuadros D, Wilkinson E, Junqueira DM, de Oliveira T, Tanser F, PLoS Global Public Health (2022), https://doi.org/10.1371/journal.pgph.0000055:.
Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.
Scheepers C, Everatt J, Amoako DG, Tegally H, Wibmer CK, Mnguni A, Ismail A, Mahlangu B, Lambson BE, Martin DP, Wilkinson E, San JE, Giandhari J, Manamela N, Ntuli N, Kgagudi P, Cele S, Richardson SI, Pillay S, Mohale T, Ramphal U, Naidoo Y, Khumalo ZT, Kwatra G, Gray G, Bekker LG, Madhi SA, Baillie V, Van Voorhis WC, Treurnicht FK, Venter M, Mlisana K, Wolter N, Sigal A, Williamson C, Hsiao NY, Msomi N, Maponga T, Preiser W, Makatini Z, Lessells R, Moore PL, de Oliveira T, von Gottberg A, Bhiman JN, Nature Commununications (2022), 13(1):1976. doi: 10.1038/s41467-022-29579-9:.
Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San JE, Rodrigues ES, Vieira Santos E, Aburjaile F, Xavier J, Fritsch H, Ribeiro Adelino TE, Pereira F, Leal A, Campos de Melo Iani F, de Carvalho Pereira G, Vazquez C, Mercedes Estigarribia Sanabria G, de Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Oliveira de Lima LP, Martins AJ, Dos Santos Barros CR, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Drummond Sampaio Corrêa Mariani P, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Brandão Nardy V, Reboredo de Oliveira da Silva L, Astete Gómez MK, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, F da Penha MP, Ortega MJ, Gómez de la Fuente A, Villalba S, Torales J, Gamarra ML, Aquino C, Martínez Figueredo GP, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Cavalheiro Maymone Gonçalves C, Debur Rossa MDC, Becker GN, Presibella MM, Marques NQ, Riediger IN, Raboni S, Coelho GM, Cataneo AHD, Zanluca C, Dos Santos CND, Assato PA, Allan da Silva da Costa F, Poleti MD, Chagas Lesbon JC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Tommasini Grotto RM, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Leonel Peterka CR, Rangel Fernandes CF, de Araújo WN, do Carmo Said RF, Almiron M, Campelo de Albuquerque E Melo CF, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, de Alcantara LCJ, Covas DT, medRxiv [Preprint] (2022), 28:2021.10.07.21264644. doi: 10.1101/2021.10.07.21264644:.
Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic.
Giovanetti M, Fonseca V, Wilkinson E, Tegally H, San EJ, Althaus CL, Xavier J, Nanev Slavov S, Viala VL, Ranieri Jerônimo Lima A, Ribeiro G, Souza-Neto JA, Fukumasu H, Lehmann Coutinho L, Venancio da Cunha R, Freitas C, Campelo de A E Melo CF, Navegantes de Araújo W, Do Carmo Said RF, Almiron M, de Oliveira T, Coccuzzo Sampaio S, Elias MC, Covas DT, Holmes EC, Lourenço J, Kashima S, de Alcantara LCJ, Virus Evolution (2022), doi: 10.1093/ve/veac024:.
Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Mol Biol Evol. (2022), doi: 10.1093/molbev/msac061:.
Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021.
Bbosa N, Ssemwanga D, Namagembe H, Kiiza R, Kiconco J, Kayiwa J, Lutalo T, Lutwama J, Ssekagiri A, Ssewanyana I, Nabadda S, Kyobe-Bbosa H, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Naidoo Y, Tshiabuila D, Tegally H, San EJ, Wilkinson E, de Oliveira T, Kaleebu P, Emerg Infect Dis (2022), doi: 10.3201/eid2805.220121:.
Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing.
Singh L, San JE, Tegally H, Brzoska PM, Anyaneji UJ, Wilkinson E, Clark L, Giandhari J, Pillay S, Lessells RJ, Martin DP, Furtado M, Kiran AM, de Oliveira T, Microb Genom. (2022), doi: 10.1099/mgen.0.000774:.
A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil..
Giovanetti M, Pereira LA, Adelino TÉR, Fonseca V, Xavier J, de Araújo Fabri A, Slavov SN, da Silva Lemos P, de Almeida Marques W, Kashima S, Lourenço J, de Oliveira T, Campelo de Albuquerque CF, Freitas C, Peterka CRL, da Cunha RV, Mendonça AF, Lemes da Silva V, Alcantara LCJ, Microbiol Spectr. (2022), e0015522. doi: 10.1128/spectrum.00155-22:.
The role of high-risk geographies in the perpetuation of the HIV epidemic in rural South Africa: A spatial molecular epidemiology study.
Cuadros DF, de Oliveira T, Graf T, Junqueira DM, Wilkinson E, Lemey P, Barnighausen T, Kim H-Y, Tanser F, PLoS Global Public Health (2022), https://doi.org/10.1371/journal.pgph.0000105:.
Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.
Tshiabuila D, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Maharaj A, Anyaneji UJ, Naidoo Y, Tegally H, San EJ, Wilkinson E, Lessells R, de Oliveira T, Research Square (2022), https://doi.org/10.21203/rs.3.rs-1249711/v1:.
Persistent SARS-CoV-2 infection with accumulation of mutations in a patient with poorly controlled HIV infection.
Maponga TG, Jeffries M, Tegally H, Sutherland A, Wilkinson E, Lessells R, Msomi N, van Zyl G, de Oliveira T, Preiser W, Clin Infect Dis. (2022), ciac548. doi: 10.1093/cid/ciac548:.
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins G, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL, bioXriv (2022), 2022.01.14.476382. doi: 10.1101/2022.01.14.476382:.
Omicron infection of vaccinated individuals enhances neutralizing immunity against the Delta variant. .
Khan K, Karim F, Cele S, San JE, Lustig G, Tegally H, Rosenberg Y, Bernstein M, Ganga Y, Jule Z, Reedoy K, Ngcobo N, Miya Y, Mazibuko M, Mthabela N, Mhlane Z, Mbatha N, Giandhari J, Ramphal Y, Naidoo T, Manickchund N, Magula N, Karim SA, Gray G, Hanekom W, von Gottberg A, Milo R, Gosnell B, Lessells R, de Oliveira T, Moore P, Moosa YS, Sigal A., medRxiv (2022), 2021.12.27.21268439. doi: 10.1101/2021.12.27.21268439:.
T cell responses to SARS-CoV-2 spike cross-recognize Omicron.
Keeton R, Tincho MB, Ngomti A, Baguma R, Benede N, Suzuki A, Khan K, Cele S, Bernstein M, Karim F, Madzorera SV, Moyo-Gwete T, Mennen M, Skelem S, Adriaanse M, Mutithu D, Aremu O, Stek C, du Bruyn E, Van Der Mescht MA, de Beer Z, de Villiers TR, Bodenstein A, van den Berg G, Mendes A, Strydom A, Venter M, Giandhari J, Naidoo Y, Pillay S, Tegally H, Grifoni A, Weiskopf D, Sette A, Wilkinson RJ, de Oliveira T, Bekker LG, Gray G, Ueckermann V, Rossouw T, Boswell MT, Bihman J, Moore PL, Sigal A, Ntusi NAB, Burgers WA, Riou C, Nature (2022), doi: 10.1038/s41586-022-04460-3:.
Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests..
Rodgers MA, Olivo A, Harris BJ, Lark C, Luo X, Berg MG, Meyer TV, Mohaimani A, Orf GS, Goldstein Y, Fox AS, Hirschhorn J, Glen WB, Nolte F, Landay A, Jennings C, Moy J, Servellita V, Chiu C, Batra R, Snell LB, Nebbia G, Douthwaite S, Tanuri A, Singh L, de Oliveira T, Ahouidi A, Mboup S, Cloherty GA, J Clin Virol. (2022), 105080. doi: 10.1016/j.jcv.2022.105080:.
HIV-1 drug resistance in adults and adolescents on protease inhibitor-based antiretroviral treatment in KwaZulu-Natal Province, South Africa.
Chimukangara B, Lessells RJ, Sartorius B, Gounder L, Manyana S, Pillay M, Singh L, Giandhari J, Govender K, Samuel R, Msomi N, Naidoo K, de Oliveira T, Moodley P, Parboosing R, J Glob Antimicrob Resist. (2021), S2213-7165(21)00249-6. doi: 10.1016/j.jgar.2021.10.023. :.
Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa..
Chimukangara B, Lessells RJ, Singh L, Grigalionyte I, Yende-Zuma N, Adams R, Dawood H, Dlamini L, Buthelezi S, Chetty S, Diallo K, Duffus WA, Mogashoa M, Hagen MB, Giandhari J, de Oliveira T, Moodley P, Padayatchi N, Naidoo K., AIDS Res Ther. (2021), 18(1):74. doi: 10.1186/s12981-021-00393-5:.
Temporal Changes in Vaginal Microbiota and Genital Tract Cytokines Among South African Women Treated for Bacterial Vaginosis.
Mtshali A, San JE, Osman F, Garrett N, Balle C, Giandhari J, Onywera H, Mngomezulu K, Mzobe G, de Oliveira T, Rompalo A, Mindel A, Abdool Karim SS, Ravel J, Passmore JS, Abdool Karim Q, Jaspan HB, Liebenberg LJP, Ngcapu S, Front Immunol. (2021), 12:730986. doi: 10.3389/fimmu.2021.730986.:.
Immunogenicity of SARS-CoV-2 infection and Ad26.CoV2.S vaccination in people living with HIV.
.
Khan K, Lustig G, Bernstein M, Archary D, Cele S, Karim F, Smith M, Ganga Y, Jule Z, Reedoy K, Miya Y, Mthabela N, Magula NP, Lessells R, de Oliveira T, Gosnell BI, Karim SA, Garrett N, Hanekom W, Gail-Bekker L, Gray G, Blackburn JM, Moosa MS, Sigal A; COMMIT-KZN Team, Clin Infect Dis. (2021), 10:ciab1008. doi: 10.1093/cid/ciab1008:.
Escape from recognition of SARS-CoV-2 Beta variant spike epitopes but overall preservation of T cell immunity.
Riou C, Keeton R, Moyo-Gwete T, Hermanus T, Kgagudi P, Baguma R, Valley-Omar Z, Smith M, Tegally H, Doolabh D, Iranzadeh A, Tyers L, Mutavhatsindi H, Tincho MB, Benede N, Marais G, Chinhoyi LR, Mennen M, Skelem S, du Bruyn E, Stek C; SA-CIN, de Oliveira T, Williamson C, Moore PL, Wilkinson RJ, Ntusi NAB, Burgers WA, Science Translational Medicine (2021), DOI: 10.1126/scitranslmed.abj6824:.
Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests.
Valley-Omar Z, Marais G, Iranzadeh A, Naidoo M, Korsman S, Maponga T, Hussey H, Davies MA, Boulle A, Doolabh D, Laubscher M, Wojno J, Deetlefs JD, Maritz J, Scott L, Msomi N, Naicker C, Tegally H, de Oliveira T, Bhiman J, Williamson C, Preiser W, Hardie D, Hsiao NY, J Virol Methods (2022), 302:114471. doi: 10.1016/j.jviromet.2022.114471:.
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T, Nature (2022), doi: 10.1038/s41586-022-04411-y:.
The political theatre of the UKs travel ban on South Africa.
Mendelson M, Venter F, Moshabela M, Gray G, Blumberg L, de Oliveira T, Madhi SA, The Lancet (2021), https://doi.org/10.1016/ S0140-6736(21)02752-5:.
Track Omicrons spread with molecular data.
Scott L, Hsiao NY, Moyo S, Singh L, Tegally H, Dor G, Maes P, Pybus OG, Kraemer MUG, Semenova E, Bhatt S, Flaxman S, Faria NR, de Oliveira T, Science (2021), DOI: 10.1126/science.abn4543
:.
Africa: tackle HIV and COVID-19 together.
Msomi N, Lessells RJ, Mlisana K, de Oliveira T, Nature (2021), 600, 33-36, doi: https://doi.org/10.1038/d41586-021-03546-8:.
SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer
BNT162b2 elicited neutralization and requires ACE2 for infection.
Cele S, Jackson L, Khoury DS, Khan K, Moyo-Gwete T, Tegally H, San JE, Cromer D, Scheepers C, Amoako DG, Karim F, Bernstein M, Lustig G, Archary D, Smith M, Ganga Y, Jule Z, Reedoy K, Hwa SH, Giandhari J, Blackburn JM, Gosnell BI, Abdool Karim SS, Hanekom W; NGS-SA; COMMIT-KZN Team, von Gottberg A, Bhiman JN, Lessells RJ, Moosa MS, Davenport MP, de Oliveira T, Moore PL, Sigal A, Nature (2021), doi: 10.1038/s41586-021-04387-1.:.
Rapid replacement of the Beta variant by the Delta variant in South Africa.
Tegally H, Wilkinson E, Althaus C, Giovanetti M, San J, Giandhari J, Pillay S, Naidoo Y, Ramphal U, Msomi N, Mlisana K, Amoako D, Everatt J, Mohale T, Nguni A, Mahlangu B, Ntuli N, Khumalo Z, Makatini Z, Wolter N, Scheepers C, Ismail A, Doolabh D, Joseph R, Strydom A, Mendes A, Davids M, Mayaphi S, Ramphal Y, Maharaj A, Karim W, Tshiabuila D, Anyaneji U, Singh L, Engelbrecht S, Fonseca V, Marais K, Korsman S, Hardie D, Hsiao N, Maponga T, van Zyl G, Marais G, Iranzadeh A, Martin D, Alcantara L, Bester P, Nyaga M, Subramoney K, Treurnicht F, Venter M, Goedhals D, Preiser W, Bhiman J, vonGottberg A, Williamson C, Lessells R, de Oliveira T, medRxiv (2021), MEDRXIV-2021-264018v1:.
The biological and clinical significance of emerging SARS- CoV-2 variants.
Tao T, Tzou1 PL, Nouhin J, Gupta RK, de Oliveira T, Pond SLK, Fera D, Shafer RW, Nature Reviews Genetics (2021), https://doi.org/10.1038/s41576-021-00408- x:.
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
.
Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri AN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang'a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O'Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LO, Tyers L, Ramuth M, Mastouri M, Aouni M, El Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T, Science (2021), DOI: 10.1126/science.abj4336:.
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
.
Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL.
, Cell (2021), https://doi.org/10.1016/j.cell.2021.09.003:.
Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing.
.
Singh L, Anyaneji UJ, Ndifon W, Turok N, Mattison SA, Lessells R, Sinayskiy I, San EJ, Tegally H, Barnett S, Lorimer T, Petruccione F, de Oliveira T.
, Scientific Reports (2021), 11(1):17793. doi: 10.1038/s41598-021-96934-z:.
Two doses of SARS-CoV-2 vaccination induce robust immune responses to emerging SARS-CoV-2 variants of concern.
Skelly DT, Harding AC, Gilbert-Jaramillo J, Knight ML, Longet S, Brown A, Adele S, Adland E, Brown H, Medawar Laboratory Team, Tipton T, Stafford L, Mentzer AJ, Johnson SA, Amini A, OPTIC, Tan TK, Schimanski L, Huang K-Y A, Rijal P, PITCH Study Group, C-MORE/PHOSP-C Group, Frater J, Goulder P, Conlon CP, Jeffery K, Dold C, Pollard AJ, Sigal A, de Oliveira T, Townsend AR, Klenerman P, Dunachie SJ, Barnes E, Carroll MW, James WS, Nature Communications (2021), https://doi.org/10.1038/s41467-021-25167-5:.
West Nile Virus in Brazil.
Costa WE, Giovanetti M, Silva Catenacci L, Fonseca V, Aburjaile FF, Chalhoub FLL, Xavier J, Campos de Melo Iani F, da Cunha E Silva Vieira MA, Freitas Henriques D, Medeiros DBA, Guedes MIMC, Senra Álvares da Silva Santos B, Gonçalves Silva AS, de Pino Albuquerque Maranhão R, da Costa Faria NR, Farinelli de Siqueira R, de Oliveira T, Ribeiro Leite Jardim Cavalcante K, Oliveira de Moura NF, Pecego Martins Romano A, Campelo de Albuquerque CF, Soares Feitosa LC, Martins Bayeux JJ, Bertoni Cavalcanti Teixeira R, Lisboa Lobato O, da Costa Silva S, Bispo de Filippis AM, Venancio da Cunha R, Lourenco J, Alcantara LCJ, Pathogens (2021), 10(7):896. doi: 10.3390/pathogens10070896:.
Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains.
Faulkner N, Ng KW, Wu MY, Harvey R, Margaritis M, Paraskevopoulou S, Houlihan C, Hussain S, Greco M, Bolland W, Warchal S, Heaney J, Rickman H, Spyer M, Frampton D, Byott M, de Oliveira T, Sigal A, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, McCauley JW, Daniels RS, Howell M, Bauer D, Nastouli E, Kassiotis G, Elife (2021), 10:e69317. doi: 10.7554/eLife.69317:.
Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil.
Tosta S, Giovanetti M, Brandão Nardy V, Reboredo de Oliveira da Silva L, Kelly Astete Gomez M, Gomes Lima J, Wanderley Cardoso C, Oliveira Silva T, Sao Pedro Leal de Souza M, Presta Dia PH, Fonseca V, de Oliveira T, Lourenco J, Carlos Junior Alcantara L, Pereira F, Leal A, PLoS Negl Trop Dis. (2021), 15(7):e0009591. doi: 10.1371/journal.pntd.0009591:.
HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens..
Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San EJ, de Oliveira T, Network for Genomic Surveillance in South Africa (NGS-SA), Gnanakaran S, Korber B, Cell Host Microbe (2022), 29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012:.
Pan-genomics of virus and its applications.
Giovanetti M, Salgado A, Fonseca V, Tosta SFO, Xavier J, de Jesus JG, Iani FCM, Adelino TER, Barreto FK, Faria NR, De Oliveira T, Alcantara LCJ., Academic Press (2020), 2020; Pages 237-250:.
Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas.
de Oliveira EC, Fonseca V, Xavier J, Adelino T, Morales Claro I, Fabri A, Macario EM, Viniski AE, Souza CLC, Costa ESG, Sousa CS, Duarte FGD, Medeiros AC, Albuquerque CFC, Cunha RV, Moura NFO, Filippis AMB, de Oliveira T, Lourenço J, Abreu AL, Alcantara LCJ, Giovanetti M
, PLoS Negl Trop Dis (2021), 2021; 15(4): e0009290. https://doi.org/10.1371/journal.pntd.0009290:.
Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.
Adelino TÉR, Giovanetti M, Fonseca V, Xavier J, de Abreu ÁS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da Silva VL, de Mello ALES, Cunha GM, Santos RH, de Oliveira EC, Júnior JAC, de Melo Iani FC, de Filippis AMB, de Abreu AL, de Jesus R, de Albuquerque CFC, Rico JM, do Carmo Said RF, Silva JA, de Moura NFO, Leite P, Frutuoso LCV, Haddad SK, Martínez A, Barreto FK, Vazquez CC, da Cunha RV, Araújo ELL, de Oliveira Tosta SF, de Araújo Fabri A, Chalhoub FLL, da Silva Lemos P, de Bruycker-Nogueira F, de Castro Lichs GG, Zardin MCSU, Segovia FMC, Gonçalves CCM, Grillo ZDCF, Slavov SN, Pereira LA, Mendonça AF, Pereira FM, de Magalhaes JJF, Dos Santos Júnior ACM, de Lima MM, Nogueira RMR, Góes-Neto A, de Carvalho Azevedo VA, Ramalho DB, Oliveira WK, Macario EM, de Medeiros AC, Pimentel V; Latin American Genomic Surveillance Arboviral Network, Holmes EC, de Oliveira T, Lourenco J, Alcantara LCJ, Nature Communications (2021), 12(1):2296. doi: 10.1038/s41467-021-22607-0.:.
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.
Giovanetti M, Cella E, Benedetti F, Rife Magalis B, Fonseca V, Fabris S, Campisi G, Ciccozzi A, Angeletti S, Borsetti A, Tambone V, Sagnelli C, Pascarella S, Riva A, Ceccarelli G, Marcello A, Azarian T, Wilkinson E, de Oliveira T, Alcantara LCJ, Cauda R, Caruso A, Dean NE, Browne C, Lourenco J, Salemi M, Zella D, Ciccozzi M, Communications Biology (2021), 4(1):489. doi: 10.1038/s42003-021-02025-0.:.
Peer-mediated HIV assisted partner services to identify and link to care HIV-positive and HCV-positive people who inject drugs: a cohort study protocol.
Monroe-Wise A, Mbogo L, Guthrie B, Bukusi D, Sambai B, Chohan B, Scott J, Cherutich P, Musyoki H, Bosire R, Dunbar M, Macharia P, Masyuko S, Wilkinson E, De Oliveira T, Ludwig-Barron N, Sinkele B, Herbeck J, Farquhar C, BMJ Open (2021), 11(4):e041083. doi: 10.1136/bmjopen-2020-041083:.
Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay.
Graf T, Vazquez C, Giovanetti M, de Bruycker-Nogueira F, Fonseca V, Claro IM, de Jesus JG, Gómez A, Xavier J, de Mendonça MCL, Villalba S, Torales J, Gamarra ML, Thézé J, de Filippis AMB, Azevedo V, de Oliveira T, Franco L, de Albuquerque CFC, Irala S, Holmes EC, Méndez Rico JA, Alcantara LCJ, Emerg Infect Dis (2021), 27(5):1393-1404. doi: 10.3201/eid2705.204244:.
Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant.
Shinde V, Bhikha S, Hoosain Z, Archary M, Bhorat Q, Fairlie L, Lalloo U, Masilela MSL, Moodley D, Hanley S, Fouche L, Louw C, Tameris M, Singh N, Goga A, Dheda K, Grobbelaar C, Kruger G, Carrim-Ganey N, Baillie V, de Oliveira T, Lombard Koen A, Lombaard JJ, Mngqibisa R, Bhorat AE, Benade G, Lalloo N, Pitsi A, Vollgraaff PL, Luabeya A, Esmail A, Petrick FG, Oommen-Jose A, Foulkes S, Ahmed K, Thombrayil A, Fries L, Cloney-Clark S, Zhu M, Bennett C, Albert G, Faust E, Plested JS, Robertson A, Neal S, Cho I, Glenn GM, Dubovsky F, Madhi SA; 2019nCoV-501 Study Group., NEJM (2021), 384(20):1899-1909. doi: 10.1056/NEJMoa2103055.:.
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhaes Ferreira G, Crispim MAE, Brazil-UK CADDE Genomic Network, Singh L, Tegally H, Anyaneji UJ; Network for Genomic Surveillance in South Africa, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND, PLoS Biology (2021), DOI: 10.1371/journal.pbio.3001236:.
Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant of interest in Brazil: Case report.
Pereira F, Tosta S, Lima MM, Reboredo de Oliveira da Silva L, Nardy VB, Gomez MKA, Lima JG, Fonseca V, de Oliveira T, Lourenco J, Alcantara LC Jr, Giovanetti M, Leal A, J Med Virol (2021), doi: 10.1002/jmv.27086:.
Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil.
Fonseca V, de Jesus R, Adelino T, Reis AB, de Souza BB, Ribeiro AA, Guimaraes NR, Livorati MTFP, Neto DFL, Kato RB, Portela LMO, Dutra LH, Freitas C, de Abreu AL, Filizzola ERM, de Medeiros AC, Iani FCM, Carvalho G, Lourenco J, de Oliveira T, Alcantara LCJ, Giovanetti M, Journal of Infection (2021), DOI:https://doi.org/10.1016/j.jinf.2021.05.014:.
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.
San JE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Nelson CW, Smidt W, Kiran AM, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Martin DP, Khanyile K, Lessells R, de Oliveira T., Virus Evolution (2021), 7(1):veab041. doi: 10.1093/ve/veab041. eCollection 2021 Jan:.
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2.
O'Toole A, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbruck L, Stadler T, Swiss Viollier Sequencing Consortium, Parisi A, Bianco A, Garcia de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha Rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), de Oliveira T, Faria N, Rambaut A, Kraemer MUG., Wellcome Open Res (2021), 6:121. doi: 10.12688/wellcomeopenres.16661.1. eCollection 2021.:.
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse.
Konings F, Perkins MD, Kuhn JH, Pallen MJ, Alm EJ, Archer BN, Barakat A, Bedford T, Bhiman JN, Caly L, Carter LL, Cullinane A, de Oliveira T, Druce J, El Masry I, Evans R, Gao GF, Gorbalenya AE, Hamblion E, Herring BL, Hodcroft E, Holmes EC, Kakkar M, Khare S, Koopmans MPG, Korber B, Leite J, MacCannell D, Marklewitz M, Maurer-Stroh S, Rico JAM, Munster VJ, Neher R, Munnink BO, Pavlin BI, Peiris M, Poon L, Pybus O, Rambaut A, Resende P, Subissi L, Thiel V, Tong S, van der Werf S, von Gottberg A, Ziebuhr J, Van Kerkhove MD, Nature Microbiology (2021), https://doi.org/10.1038/s41564-021-00932-w:.
Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection.
Karim F, Moosa MYS, Gosnell BI, Cele S, Giandhari J, Pillay S, Tegally H, Wilkinson E, San JE, Msomi N, Mlisana K, Khan K, Bernstein M, Manickchund N, Singh L, Ramphal U, COMMIT-KZN Team, Hanekom W, Lessells RJ, Sigal A, de Oliveira T, medRxiv (2021), submitted, available on KRISP website.:.
Cross-Reactive Neutralizing Antibody Responses Elicited by SARS-CoV-2 501Y.V2 (B.1.351).
Moyo-Gwete T, Madzivhandila M, Makhado Z, Ayres F, Mhlanga D, Oosthuysen B, Lambson EB, Kgagudi P, Tegally H, Iranzadeh A, Doolabh D, Tyers L, Chinhoyi RL, Mennen M, Skelm S, Wibmer K C, Bhiman N J, Ueckermann V, Rossouw T, Boswell M, de Oliveira T, Williamson T, Burgers W, Ntusi N, Morris L, Moore P, NEJM (2021), DOI: 10.1056/NEJMc2104192:.
Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T, Viruses (2021), 22;13(3):526. doi: 10.3390/v13030526:.
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma..
Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Bernstein M, Balazs AB, Gosnell BI, Hanekom W, Moosa MS; NGS-SA; COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A., Nature (2021), DOI: 10.1038/s41586-021-03471-w:.
A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa.
de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R, medRxiv (2021), :.
New SARS-CoV-2 Variants Clinical, Public Health, and Vaccine Implications.
Karim SSA, de Oliveira T, NEJM (2021), DOI: 10.1056/NEJMc2100362:.
Appropriate names for COVID-19 variants.
Karim SSA, de Oliveira T, Loots G, Science (2021), http://science.sciencemag.org/content/371/6535/1215:.
Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa.
Madhi SA, Baillie VL, Cutland CL, Voysey M, KoenAL, Fairlie L, Padayachee SD, Dheda K, Barnabas SL, Bhorat QE, Briner C, Kwatra G, Ahmed K, Aley P, Bhikha S, Bhiman JN, Bhorat AE, du plessis J, Esmail A, Groenewald M, Horne E, Hwa S-H, Jose A, Lambe T, Laubscher M, Malahleha M, Masenya M, Masilela M, McKenzie S, Molapo K, Moultrie A, Oelofse S, Pate Fl, Pillay S, Rhead S, Rodel H, Rossouw L, Taoushanis C, Tegally H, Thombrayil A, van Eck S, Wibmer C, Durham NM, Kelly EJ, Villafana T, Gilbert S, Pollard AJ, de Oliveira T, Moore PL, Sigal A, Izu A, NGS-SA, Wits VIDA COVID vaccine trial group
, NEJM (2021), https://doi.org/10.1056/NEJMoa2102214:.
Voices of Biotech Research.
Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett K, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik M, Henaff E, Huch M, Iliev I, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez M, Miura K, Molloy J, Cruz A, Platt R, Posey A, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe L, Varshney R, Wang J, Nature Biotechnology (2021), https://doi.org/10.1038/s41587-021-00847-1:.
Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenco J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T, Nature (2021), https://doi.org/10.1038/s41586-021-03402-9:.
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma.
Wibmer CK, Ayres F, Hermanus T, Madzivhandila M, Kgagudi P, Oosthuysen B, Lambson BE, de Oliveira T, Vermeulen M, van der Berg K, Rossouw T, Boswell M, Ueckermann V, Meiring S, von Gottberg A, Cohen C, Morris L, Bhiman JN, Moore PL, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01285-x:.
Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil.
Xavier J, Fonseca V, Bezerra JF, Do Monte Alves M, Mares-Guia NA, Claro IM, De Jesus R, Adelino T, Araujo E, Cavalcante KRLJ, Tosta S, De Souza TR, Moreira Da Cruz FE, De Araujo Fabri A, de Oliveira EC, De Moura NFO, Do Carmo Said RF, De Albuquerque CFC, Azevedo V, de Oliveira T, De Filippis AMB, Venancio Da Cunha R, Luz KG, Giovanetti M, Alcantara L, IJID (2021), S1201-9712(21)00037-0:.
Sixteen novel lineages of SARS-CoV-2 in South Africa.
Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01255-3:.
Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma.
Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Balazs AB, Gosnell BI, Hanekom W, Moosa MYS, NGS-SA, COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A, medRxiv (2021), 250224v1-Sigal:.
Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.12.21.20248640:.
Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase.
Siedner MJ, Moorhouse MA, Simmons B, de Oliveira T, Lessells R, Giandhari J, Kemp SA, Chimukangara B, Akpomiemie G, Serenata Cm, Venter WDF, HillA, Gupta RK, Nature Communications (2020), https://doi.org/10.1038/s41467-020-19801-x:.
HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in COVID-19 disease.
Karim F, Gazy I, Cele S, Zungu Y, Krause R, Bernstein M, Ganga Y, Rodel H, Mthabela N, Mazibuko M, Khan K, Muema D, Ramjit D, Lustig G, Ndung'u T, Hanekom W, Gosnell BI, COMMIT-KZN Team, Wong E, de Oliveira T, Moosa MYS, Leslie A, Kløverpris H, Sigal A, medRxiv (2020), doi: https://doi.org/10.1101/2020.11.23.20236828:.
High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity.
San EJ, Ngcapu S, Kanzi A, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile KS, Lessells R, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.11.15.20231993:.
Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil.
Adelino TER, Giovanetti M, Fonseca V, Xavier J, Salgado A, Nascimento V, Demarchi LH, Oliveira M, Silva V, Mello A, Muricy G, Santos R, Oliveira E, Junior JAC, Iani F, de Filippis AMB, Abreu AL, de Jesus R, Albuquerque CF, Rico J, Said R, Silva J, Moura N, Leite P, Vinhal L, Kashima S, Martinez AA, Khouri F, Vazquez C, Cunha R, Araujo E, Tosta S, Fabri A, Chalhoub F, Lemos P, de Bruycker-Nogueira F, Lichs G, Zardin M, Cardozo F, Goncalves C, Fernandez Z, Slavov S, Pereira LA, Mendonca AF, Pereira F, Magalhaes J, de Castro A, Lima M, Nogueira R, Goes A, Azevedo V, Ramalho D, Oliveira W, Medeiros A, Pimentel V, Latin American Genomic Surveillance Arboviral Network, Holmes EC, de Oliveira T, Lourenco J, Alcantara LCJ, medRxiv (2020), https://doi.org/10.1101/2020.09.01.20183301:.
Adding a Voice to the Unique Ethical Considerations in Molecular HIV Surveillance.
Mutenherwa F, Wassenaar D, de Oliveira T, The American Journal of Bioethics (2020), https://doi.org/10.1080/15265161.2020.1806399:.
Detection of Inducible Replication-Competent HIV-1 Subtype C Provirus Despite Long-Term Antiretroviral Treatment in Perinatally Infected Adolescents in Botswana.
Koofhethile CK, Moyo S, Kotokwe KP, Chang C, Mokgethi P, Muchoba L, Mokgweetsi S, Makhema J, Lockman S, Gaseitsiwe S, de Oliveira T, Essex M, Shapiro R, Kanki P, Novitsky V, AIDS Res Hum Retroviruses (2020), doi: 10.1089/AID.2020.0097:.
Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.
Kanzi AM, San JE , Chimukangara B, Wilkinson E, Ramsuran V, de Oliveira T, Frontiers in Genetics (2020), 11: 1250, https://doi.org/10.3389/fgene.2020.544162:.
Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals.
Chimukangara B, Giandhari J, Lessells J, Yende-Zuma N, Sartorius B, Samuel R, Khanyile KS, Stray-Pedersen B, Moodley P, Metzner KJ, Padayatchi N, Naidoo K, de Oliveira T, Journal of Antimicrobial Chemotherapy (2020), 75, 11:33193326, https://doi.org/10.1093/jac/dkaa343.
Unlocking the efficiency of genomics laboratories with robotic liquid-handling.
Tegally H, San JE, Giandhari J, de Oliveira T, BMC Genomics (2020), 729:https://doi.org/10.1186/s12864-020-07137-1.
Accelerating genomics-based surveillance for COVID-19 response in Africa.
Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN, Lancet Microbe (2020), https://doi.org/10.1016/S2666-5247(20)30117-8:.
A genomics network established to respond rapidly to public health threats in South Africa.
Msomi N, Mlisana K, Willianson C, Bhiman JN, Goedhals D, Engelbrecht S, Van Zyl G, Preiser W, Hardie D, Hsiao M, Mulder N, Martin D, Christoffels A, York D, Giandhari J, Wilkinson E, Pillay S, Tegally H, James SE, Kanzi A, Lessells RJ, de Oliveira T, Lancet Microbe (2020), https://doi.org/10.1016/S2666-5247(20)30116-6:.
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic.
Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, de Oliveira T, Genes (2020), doi: https://doi.org/10.3390/genes11080949:11(8), 949.
Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, Petruccione F, de Oliveira T, IJID (2020), doi: https://doi.org/10.1016/j.ijid.2020.11.128:.
Protocol: Leveraging a demographic and health surveillance system for Covid-19 Surveillance in rural KwaZulu-Natal.
Siedner MJ, Harling G, Derache A, Smit T, Khoza T, Gunda R, Mngomezulu T, Gareta D, Majozi N, Ehlers E, Dreyer J, Nxumalo S, Dayi N, Ording-Jesperson G, Ngwenya N, Wong E, Iwuji C, Shahmanesh M, Seeley J, de Oliveira T, Ndung'u T, Hanekom W, Herbst K, Wellcome Open Research (2020), 5:109:.
The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.
Xavier J, Giovanetti M, Adelino T, Fonseca V, da Costa AVB, Ribeiro AA, Felicio KN, Duarte CG, Silva MVF, Salgado A, Lima MT, de Jesus D, Fabri A, Zoboli CFS, Santos TGS, Iani F,de Filippis AMB, de Siqueira AMNT, de Abreu AL, de Azevedo V, Ramalho DBR, de Albuquerque CFC, de Oliveira T, Holmes EC, Lourenco J, Alcantara CLJ, Oliveira MAA, Emerging Microbes & Infections (2020), vol 9:.
Pervasive and non-random recombination in near full-length HIV genomes from Uganda.
Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Gomez LRE, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh-Brown AJ, Virus Evolution (2020), veaa004, https://doi.org/10.1093/ve/veaa004:.
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme A-M, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TTY, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M, Proceedings of the National Academy of Sciences (PNAS) (2020), doi:10.1073/pnas.2007295117:.
New Genomes from The Congo Basin Expand History of CRF01_AE Origin and Dissemination.
Junqueira DM, Wilkinson E, Vallari AS, Deng XD, Achari A, Yu G, McArthur C, Kaptué L, Mbanya DN, Chiu C, Cloherty G, de Oliveira T, Rodgers MA, AIDS Res Hum Retroviruses (2020), doi: 10.1089/AID.2020.0031:.
Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.
Giovanetti M, Faria NR, Lourenco J, Goes de Jesus J, Xavier J, Claro IM, Kraemer MUG, Fonseca V, Dellicour S, Theze J, da Silva Salles F, Graef T, Silveira PP, Costa de Souza V, Alves do Nascimento V, Campos de Melo Iani F, Castilho-Martins EA, Cruz LN, Wallau G, Fabri A, Levy F, Quick J, de Azevedo V, Santana Aguiar R, de Oliveira T, Botto de Menezes C, da Costa Castilho M, Matos Terra T, Souza da Silva M, Bispo de Filippis M, Luiz de Abreu A, Kleber Oliveira W, Croda J, Campelo de Albuquerque CF, Nunes MRT, Cerdeira Sabino E, Loman N, Gomes Naveca F, Pybus O, Alcantara LC., Cell Reports (2020), https://doi.org/10.1016/j.celrep.2020.01.085:.
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T, Bioinformatics (2020), btaa145, https://doi.org/10.1093/bioinformatics/btaa145:.
Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.
San EJ, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T, Front. Microbiol. (2020), https://doi.org/10.3389/fmicb.2019.03119:.
Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.
Ratmann O, Kagaayi J, Hall M, Golubchick T, Kigozi G, Xi X, Wymant C, Nakigozi G, Abeler-Dörner L, Bonsall D, Gall A, Hoppe A, Kellam P, Bazaale J, Kalibbala S, Laeyendecker O, Lessler J, Nalugoda F, Chang LW, de Oliveira T, Pillay D, Quinn TC, Reynolds SJ, Spencer SEF, Ssekubugu R, Serwadda D, Wawer MJ, Gray RH, Fraser C, Grabowski MK, on behalf of the Rakai Health Sciences Program and the Pangea HIV Consortium, Lancet HIV (2020), https://doi.org/10.1016/ S2352-3018(19)30378-9:.
Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil.
Goes de Jesus J, da Luz Wallau G, Lima Maia M, Xavier J, Oliveira Lima MA, Fonseca V, Salgado de Abreu A, Fraga de Oliveira Tosta S, Ramos do Amaral H, Andrade Barbosa Lima I, Viana Silva P, Carlos Dos Santos D, Sousa de Oliveira A, Campos de Souza S, Barreto Falcão M, Cerqueira E, Ceschini Machado L, Sobral MC, Teodoro Rezende TM, Ribeiro Pereira M, Mota Pereira F, Pereira Gusmão Maia Z, Freitas de Oliveira França R, Luiz de Abreu A, Campelo de Albuquerque E Melo CF, Rodrigues Faria N, Venâncio da Cunha R, Giovanetti M, Alcantara LCJ, PLoS ONE (2020), 15(1):e0226098. doi: 10.1371/journal.pone.0226098:.
Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases..
Pereira Gusmão Maia Z, Mota Pereira F, do Carmo Said RF, Fonseca V, Gräf T, de Bruycker Nogueira F, Brandão Nardy V, Xavier J, Lima Maia M, Abreu AL, Campelo de Albuquerque CF, Kleber Oliveira W, Croda J, de Filippis AMB, Venancio Cunha R, Lourenço J, de Oliveira T, Faria NR, Junior Alcantara LC, Giovanetti M, Emerg Microbes Infect. (2020), 9(1):53-57. doi: 10.1080/22221751.2019.1701954:.
Declines in HIV incidence among men and women in a South African population-based cohort.
Vandormael A, Akullian A, Siedner M, de Oliveira T, Bärnighausen T, Tanser F, Nature Communications (2019), 10(1):5482. doi: 10.1038/s41467-019-13473-y:.
Undetectable proviral deoxyribonucleic acid in an adolescent perinatally infected with human immunodeficiency virus-1C and on long-term antiretroviral therapy resulted in viral rebound following antiretroviral therapy termination: A case report with implications for clinical care.
Koofhethile CK, Moyo S, Kotokwe KP, Mokgethi P, Muchoba L, Mokgweetsi S, Gaolathe T, Makhema J, Shapiro R, Lockman S, Kanki P, Essex M, Gaseitsiwe S, de Oliveira T, Novitsky V, Medicine (Baltimore) (2019), 98(47):e18014. doi: 10.1097/MD.0000000000018014:.
Trends in HIV Prevention, Treatment, and Incidence in a Hyperendemic Area of KwaZulu-Natal, South Africa
.
Kharsany ABM, Cawood C, Lewis L, Yende-Zuma N, Khanyile D, Puren A, Madurai S, Baxter C, George G, Govender K, Beckett S, Samsunder N, Toledo C, Ayalew KA, Diallo K, Glenshaw M, Herman-Roloff A, Wilkinson E, de Oliveira T, Abdool Karim SS, Abdool Karim Q, JAMA Network Open (2019), 2(11):e1914378. doi:10.1001/jamanetworkopen.2019.14378:.
Yellow fever virus re-emergence and spread in Southeast Brazil, 2016-2019.
Giovanetti M, Lima de Mendonça MC, Fonseca V, Mares-Guia MA, Fabri A, Xavier J, Goes de Jesus J, Gräf T, Damasceno Dos Santos Rodrigues C, Cardoso Dos Santos C, Alves Sampaio S, Lowen Levy Chalhoub F, Bruycker Nogueira F, Theze J, Pecego Martins Romano A, Garkauskas Ramos D, Luiz de Abreu A, Kleber Oliveira W, do Carmo Said RF, Campelo de Alburque CF, de Oliveira T, Fernandes CA, Ferreira Aguiar S, Chieppe A, Carvalho Sequeira P, Rodrigues Faria N, Venâncio Cunha R, Alcantara LCJ, Bispo de Filippis AM., Journal of Virology (2019), JVI.01623-19. doi: 10.1128/JVI.01623-19:.
Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches.
Mutenherwa F, Wassenaar DR, de Oliveira T, BMC Medical Ethics (2019), 20:67, https://doi.org/10.1186/s12910-019-0403-9:.
Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era.
Fonseca V, Xavier J, San EJ, de Oliveira T, de Filippis AMB, Alcantara LCJ, Giovanetti M, Current Topics in the Epidemiology of Vector-Borne (2019), DOI: 10.5772/intechopen.88769:.
Space-time clustering of recently diagnosed tuberculosis and impact of ART scale-up: Evidence from an HIV hyper-endemic rural South African population.
Tomita A, Smith CM, Lessells RJ, Pym A, Grant AD, de Oliveira T, Tanser F
, Scientific Reports (2019), https://doi.org/10.1038/s41598-019-46455-7:.
Whole genome sequencing for drug-resistant tuberculosismanagement in South Africa: What gaps would this address andwhat are the challenges to implementation?.
Dlamini MT, Lessells R, Iketleng T, de Oliveira T, Journal of Clinical TB and Other Mycobacterial Dis (2019), https://doi.org/10.1016/j.jctube.2019.100115:.
Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.
Xavier J, Giovanetti M, Fonseca V, Thézé J, Gräf T, Fabri A, Goes de Jesus J, Lima de Mendonça MC, Damasceno Dos Santos Rodrigues C, Mares-Guia MA, Cardoso Dos Santos C, Fraga de Oliveira Tosta S, Candido D, Ribeiro Nogueira RM, Luiz de Abreu A, Kleber Oliveira W, Campelo de Albuquerque CF, Chieppe A, de Oliveira T, Brasil P, Calvet G, Carvalho Sequeira P, Rodrigues Faria N, Bispo de Filippis AM, Alcantara LCJ, PLoS One (2019), 14(6):e0217871:.
A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti M, Cuypers L, Nowé A, Abecasis A, Deforche K, Santiago GA, Siqueira IC, San EJ, Machado KCB, Azevedo V, Filippis AMB, Cunha RVD, Pybus OG, Vandamme AM, Alcantara LCJ, de Oliveira T, PLoS Negl Trop Dis (2019), 13(5):e0007231: doi: 10.1371/journal.pntd.0007231.
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O, Grabowski KM, Hall M, Golubchik T, Wymant C, Abeler-Dorner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, PANGEA Consortium and Rakai Health Sciences Program
, Nature Communications (2019), 10:1411:https://doi.org/10.1038/s41467-019-09139-4.
Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 20002016: A Pooled Sequence Analysis.
Chimukangara B, Lessells RJ, Rhee S-Y, Giandhari J, Kharsany ABM, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Karim SSA, de Oliveira T, EClinicalMedicine (Lancet) (2019), DOI:https://doi.org/10.1016/j.eclinm.2019.03.006:.
Factors influencing HIV-1 phylogenetic clustering.
Junqueira DM, Sibisi Z, Wilkinson E, de Oliveira T, Curr Opin HIV AIDS (2019), doi: 10.1097/COH.0000000000000540:.
Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018.
Hill SC, Neto de Vasconcelos J, Granja BG, Thézé J, Jandondo D, Neto Z, Mirandela M, Sebastião CDS, Cândido ALM, Clemente C, Pereira da Silva S, de Oliveira T, Pybus OG, Faria NR, Afonso JM, Emerg Infect Dis. (2019), 25(4):784-787.
The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis.
Wilkinson E, Junqueira DM, Lessells R, Engelbrecht S, van Zyl G, de Oliveira T, Salemi M, Scientific Reports (2019), 9:2640:https://doi.org/10.1038/s41598-018-37749-3.
Sociobehavioral and community predictors of unsuppressed HIV viral load: multilevel results from a hyperendemic rural South African population.
Tomita A, Vandormael A, Bärnighausen T, Phillips A, Pillay D, De Oliveira T, Tanser F, AIDS (2019), 33(3):559569.
Early detection of emergent extensively drug resistant tuberculosis (XDR-TB) by flow cytometry-based phenotyping and whole genome sequencing.
O'Donnell MR, Larsen MH, Brown TS, Jain P, Munsamy V, Wolf A, Uccellini L, Karim F, de Oliveira T, Mathema B, Jacobs WR, Pym A, Antimicrob Agents Chemother. (2019), pii: AAC.01834-18.:doi: 10.1128/AAC.01834-18.
Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research.
Mutenherwa F, Wassenaar DR, de Oliveira T, J Empir Res Hum Res Ethics (2019), 1556264618809608. doi: 10.1177/1556264618809608:.
Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa.
Rasmussen DA, Wilkinson E, Vandormael A, Tanser F, Pillay D, Stadler T, de Oliveira T, Virus Evolution (2018), 4(2): vey037:.
Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa.
Chimukangara B, Kharsany AB, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer R, Hunt G, Pillay D, Abdool SK, de Oliveira T, AIDS Research and Human Retroviruses (2019), https://doi.org/10.1089/AID.2018.0202:.
Mycobacterium tuberculosis Next-Generation Whole Genome Sequencing: Opportunities and Challenges.
Iketleng T, Lessells R, Dlamini MT, Mogashoa T, Mupfumi L, Moyo S, Gaseitsiwe S, de Oliveira T, Tuberculosis Research and Treatment (2018), https://doi.org/10.1155/2018/1298542:.
Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California.
Dalai SC, Junqueira DM, Wilkinson E, Mehra R, Kosakovsky Pond SL, Levy V, Israelski D, de Oliveira T, Katzenstein D, Front. Microbiol. (2018), https://doi.org/10.3389/fmicb.2018.02799:.
2018 update to the HIV-TRePS system: the development of new computational models to predict HIV treatment outcomes, with or without a genotype, with enhanced usability for low-income settings.
Revell AD, Wang D, Perez-Elias MJ, Wood R, Cogill D, Tempelman H, Hamers RL, Reiss P,, van Sighem AI, Rehm CA, Pozniak A, Montaner JSG, Lane HC, Larder BA, RDI Data and Study Group Collaborators: Reiss P, van Sighem A, Montaner J, Harrigan R, Rinke de Wit T, Hamers R, Sigaloff K, Agan B, Marconi V, Wegner S, Sugiura W, Zazzi M, Kaiser R, Schuelter E, Streinu-Cercel A, Alvarez-Uria G, Perez-Elias MJ, de Oliveira T, Gatell J, Lazzari E, Gazzard B, Nelson M, Pozniak A, Mandalia S, Smith C, Ruiz L, Clotet B, Staszewski S, Torti C, Lane C, Metcalf J, Rehm CA, Perez-Elias MJ, Vella S, Dettorre G, Carr A, Norris R, Hesse K, Vlahakis E, Tempelman H, Barth R, Wood R, Morrow C, Cogill D, Hoffmann C, Ene L, Dragovic G, Diaz R, Sucupira C, Sued O, Cesar C, Madero JS, Balavskrishnan P, Saravanan S, Emery S, Cooper D, Torti C, Baxter J, Monno L, Torti C, Gatell J, Clotet B, Picchio G, deBethune MP, Perez-Elias MJ, Emery S, Khabo P, Ledwaba L
, J Antimicrob Chemother (2018), 73(8):21862196.
Community engagement with HIV drug adherence in rural South Africa: a transdisciplinary approach.
Treffry-Goatley A, Lessells RJ, Moletsane R, de Oliveira T, Gaede B, BMJ Med Humanit (2018), 44:239246.
Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART.
Derache A, Iwuji CC, Danaviah S, Giandhari J, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Pillay D, Gupta RK, J Antimicrob Chemother. (2018), doi: 10.1093/jac/dky428:doi:10.1093/jac/dky428.
Impact of next generation sequencing defined HIV pre-treatment drug resistance on virological outcomes in the ANRS 12249 treatment as prevention trial.
.
Derache A, Iwuji CC, Baisley K, Danaviah S, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Porter K, Pillay D, Clin Infect Dis (2018), doi: 10.1093/cid/ciy881:.
Genomic and epidemiological monitoring of yellow fever virus transmission potential.
Faria NR, Kraemer MUG, S C Hill, J Goes de Jesus, R S Aguiar, F C M Iani, J Xavier, J Quick, L du Plessis, S Dellicour, J Thézé, R D O Carvalho, G Baele, C-H Wu, P P Silveira, M B Arruda, M A Pereira, G C Pereira, J Lourenço1, U Obolski, L Abade, T I Vasylyeva, M Giovanetti, D Yi, D J Weiss, G R W Wint, F M Shearer, S Funk, B Nikolay, Fonseca V, T E R Adelino, M A A Oliveira, M V F Silva, L Sacchetto, P O Figueiredo, I M Rezende, E M Mello, R F C Said, D A Santos, M L Ferraz, M G Brito, L F Santana, M T Menezes, R M Brindeiro, A Tanuri, F C P dos Santos, M S Cunha, J S Nogueira, I M Rocco, A C da Costa, S C V Komninakis, V Azevedo, A O Chieppe, E S M Araujo, M C L Mendonça, C C dos Santos, C D dos Santos, A M Mares-Guia, R M R Nogueira, P C Sequeira, R G Abreu, M H O Garcia, A L Abreu, O Okumoto, E G Kroon, C F C de Albuquerque, K Lewandowski, S T Pullan, M Carroll, de Oliveira T, E C Sabino, R P Souza, M A Suchard, P Lemey, G S Trindade, B P Drumond, A M B Filippis, N J Loman, S Cauchemez, Alcantara LCJ, Pybus OG , Science (2018), DOI: 10.1126/science.aat7115:.
Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data..
Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T, Bioinformatics (2019), doi: 10.1093/bioinformatics/bty695:.
Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation.
Tongo M, de Oliveira T, Martin DP, Virus Evolution (2018), Volume 4, Issue 1, 1 January 2018, vey015:.
Dolutegravir for first-line antiretroviral therapy in low-income and middle-income countries: uncertainties and opportunities for implementation and research.
Dorward J, Lessells R, Drain PK, Naidoo K, de Oliveira T, Pillay Y, Karim SSA, Garrett N, Lancet HIV (2018), https://doi.org/10.1016/S2352-3018(18)30093-6:.
Renewing Felsenstein's phylogenetic bootstrap in the era of big data.
Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Davila Felipe M, de Oliveira T, Gascuel O, Nature (2018), :doi:10.1038/s41586-018-0043-0.
Ethical issues associated with HIV phylogenetics in HIV transmission dynamics research: A review of the literature using the Emanuel Framework.
Mutenherwa F, Wassenaar DR, de Oliveira T, Developing World Bioethics (2018), https://doi.org/10.1111/dewb.12191:.
Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages.
Tongo M, Harkins GW, Dorfman JR, Tovanabutra EBS, de Oliveira T, Martin DP, Virus Evolution (2018), 4(1) doi:vey003/4877091:.
Effect of population viral load on prospective HIV incidence in a hyperendemic rural African community.
Tanser F, Vandormael A, Cuadros D, Phillips AN, de Oliveira T, Tomita A, Barnighausen T, Pillay D, Science Translational Medicine (2017), 9:eaam8012.
HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis.
Gupta RK, Gregson J, Parkin N, Haile-Selassie H, Tanuri A, Andrade Forero L, Kaleebu P, Watera C, Aghokeng A, Mutenda N, Dzangare J, Hone S, Hang ZZ, Garcia J, Garcia Z, Marchorro P, Beteta E, Giron A, Hamers R, Inzaule S, Frenkel LM, Chung MH, de Oliveira T, Pillay D, Naidoo K, Kharsany A, Kugathasan R, Cutino T, Hunt G, Avila Rios S, Doherty M, Jordan MR, Bertagnolio S., Lancet ID (2018), :http://dx.doi.org/10.1016/S1473-3099(17)30702-8.
Universal test and treat and the HIV epidemic in rural South Africa: a phase 4, open-label, community cluster randomised trial.
Iwuji CC, Orne-Gliemann J, Larmarange J, Balestre E, Thiebaut R, Tanser F, Okesola N, Makowa T, Dreyer J, Herbst K, McGrath N, Barnighausen T, Boyer S, de Oliveira T, Rekacewicz C, Bazin B, Newell ML, Pillay D, Dabis F, for the ANRS 12249 TasP Study Group, Lancet HIV (2018), :http://dx.doi.org/10.1016/S2352-3018(17)30205-9.
Longitudinal trends in the prevalence of detectable HIV viremia: Population-based evidence from rural KwaZulu-Natal, South Africa.
Vandormael A, Barnighausen T, Herbeck J, Tomita A, Phillips A, Pillay D, de Oliveira T, Tanser F, Clin Infect Dis. (2017), :doi: 10.1093/cid/cix976.
High percentage of undiagnosed HIV cases within a hyperendemic South African community: a population-based study.
Vandormael A, de Oliveira T, Tanser F, Barnighausen T, Herbeck JT, J Epidemiol Community Health (2018), :doi: 10.1136/jech-2017-209713.
Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa.
Hunt GM, Dokubo EK, Takuva S, de Oliveira T, Ledwaba J, Dube N, Moodley P, Sabatier J, Deyde V, Morris L, Raizes E, Journal of Antimicrobial Chemotherapy (2017), :https://doi.org/10.1093/jac/dkx252.
Automated profiling of the human virome from raw metagenomic data.
Moosa Y, Vilsker M, Vanden Eyden E, Fonseca V, Nooij S, Deforche K, de Oliveira T, Virus Evolution (2017), : doi: 10.1093/ve/vew036.033.
Persistent circulation of highly divergent HIV-1M lineages in the Congo Basin Region.
Tongo M, Dorfman JR, de Oliveira T, Martin DP, Virus Evolution (2017), :doi: 10.1093/ve/vew036.039.
LIKE 'OLD TWITTER': Scientists move to BlueSky - the gem - 2025-02-09
Top Genomics Labs partner with UK Foreign, Commonwealth & Development Office to strengthen surveillance in SA and UK - PRESS RELEASE - 2025-02-05
Mastercard Foundation, Stellenbosch University and the Institut Pasteur de Dakar unveil African STARS Fellowship Programme - African STAR Fellowship - 2025-01-12
Africa in the World Festival - the gem - 2024-10-31
Key Takeaways from the Grant Writing Workshop - the gem - 2024-10-31
Mastering the Art of Grant Writing - the gem - 2024-10-31
Football for Science? - the gem - 2024-10-31
Mosquito-borne diseases are surging in Europe how worried are scientists? - the gem - 2024-10-31
28th VEME is delivered as a successful workshop in Brazil 2024 - the gem - 2024-09-04
CLIMADE Keynote Summit at Global Pandemic Preparedness Summit - the gem - 2024-09-02
CERI & KRISP expands partnership with AIMS & Google DeepMind - the gem - 2024-09-01
Microbial Ecology ISME 19 - first time in Africa - the gem - 2024-09-01
Africas cholera crisis worsens amid extreme weather events - CERI News - 2024-07-08
Prioritizing Well-being in PhD Journey: Dr. Farirai Mutenherwas Path to Success - CERI News - 2024-07-08
Training Opportunity: Genomics & Bioinformatics,15-26 July 2024, CERI, South Africa - CERI news - 2024-06-30
South Africa Waits for Mpox Vaccines After Confirming Seven Severe Cases - Healthpolicy Watch - 2024-06-17
More awareness key to containing Mpox: experts amid rising cases - Sunday Times/Times Live - 2024-06-13
CERI & KRISP Newsletter Apr/May: Professor Tulio de Oliveira selected for TIME100 Health 2024 - Newsletter - 2024-05-07
Virology in Africa Conference Highlights Advances and Collaboration in Disease Management - CERI News - 2024-05-02
Professor Tulio de Oliveira selected for TIME100 Health 2024: 2nd recognition as one of worlds 100 most influential individuals - Stellenbosch Press - 2024-05-02
Celebrating Academic Excellence: Congratulations to Our Graduates! - CERI News - 2024-05-01
Why Africa is facing an uphill battle to make its own vaccines - Teh Telegraph - 2024-05-01
The bird flu virus was in US livestock for months without being detected - Wired - 2024-04-30
Meet Professor Tulio de Oliveira, forging a genomic surveillance partnership between the Wellcome Sanger Institute and South Africa - Wellcome Sanger Institute - 2024-02-29
As Pandemic Negotiations Move at Snails Pace, Scientists Urge Pathogen-Sharing Agreement - healthpolicy-watch - 2024-02-27
Climate change risks triggering a spike in infectious disease outbreaks: three reasons why - Info Nile - 2024-02-16
New Chikungunya vaccine must be tested for efficacy in West Africa, scientists say - Nature Africa - 2024-02-16
Leading UK and South African genomics labs unite to take disease surveillance beyond COVID - CERI & Sanger - 2024-02-04
Academic cooperation between Africa, Europe goes forward - University World News - 2024-02-01
Act now to stop climate change from turbo-charging infectious disease, scientists warn - The Telegraph - 2023-12-08
Climate change and epidemics: Report says what can be done - University World News - 2023-12-06
Climate Change and Epidemics 2023 Report released at COP28 - COP28 - 2023-12-03
Empowering African Scientists: CERI's Grant Writing Workshop - CERI - 2023-11-07
CLIMADE: Climate Change and Public Health in Botswana - - 2023-11-07
Lenine Liebenberg Joins CERI: A Game-Changer in Mucosal Immunology - Personal View - 2023-09-21
Devex CheckUp: This distant crisis sparked Malawis cholera outbreak - Devex - 2023-09-14
How Pakistan's massive floods sparked Malawi's record cholera outbreak - Devex - 2023-09-14
SU-led international consortium receives R101 million EU grant for epidemic research: PRESS RELEASE - Press Release - 2023-09-13
Inaugural Lecture: Two Decades of Genomics Excellence - KRISP & CERI Talks - 2023-09-05
Unveiling the power of bioinformatics: VEME workshop leaves lasting impact - VEME2023 - 2023-09-04
Sudanese Lecturer Finds Home Away from Home in South Africa Amidst Civil War - CERI & KRISP news - 2023-08-04
Professor Tulio de Oliveira Honored with 2023 Discovery Health Lifetime Leadership Award - CERI & KRISP News - 2023-08-02
Visit to Multidisciplinary Center for Infectious Diseases, Bern University - Univ Bern - 2023-05-24
Visit to the Health 2030 Genomics Centre in Geneva - Health 2023 - 2023-05-23
How Africa could protect the world from new pathogens - The Telegraph - 2023-05-03
Virus Hunters Search for Diseases Supercharged by Climate Change - Bloomberg - 2023-04-22
SA's R1.2bn biomedical research facility opens its doors at Stellenbosch University - Citizen - 2023-04-21
The Era of Pandemics: Abbott Partnership To Address Emerging Viral Threats In Africa - quicknews - 2023-04-21
Abbott and New Global Consortium Partnership Address Viral Outbreaks Caused by Climate Change - Press release - 2023-04-21
Africa strives to revamp its universities - DW - 2023-04-20
Climate Change: The Impact on Viral Outbreaks - Abbott - 2023-04-20
New R1.2bn biomedical unit a weapon against future epidemics - https://www.medicalbrief.co.za/new-r1-2bn-biomedical-unit-a-weapon-against-future-epidemics/ - 2023-04-19
This is the highest level of science inside Stellies new Biomedical Research Institute - Daily Maverick - 2023-04-19
Africa's Most Sophisticated Biomedical Research Centre Opens in South Africa - Medical Innovation - 2023-04-18
Stellenbosch University unveils R1.2-billion investment in biomedical science for Africa - Daily Maverick - 2023-04-13
Leading epidemiologist joins CERI as Director of Population Health Innovation Programme - Stellenbosch University - 2023-03-05
CERIs team photo makes Science Favorite Photos Award - Science - 2023-03-02
Opening of the Largest Genomics Facility in Africa - CERI news - 2023-03-01
Coronavirus variant XBB.1.5 rises in the United States - is it a global threat? - Nature - 2023-01-09
Covid-19 'mutation': Call for people to vaccinate and get boosters - Sunday Times - 2023-01-09
Leading WHO advisers call for 'realistic' COVID data from China at key meeting - Reuters - 2023-01-03
Postdoctoral Research Fellowship in Epidemiology, Genomics & Phylogenetics - Fellowship - 2022-12-31
Postdoctoral Research Fellowship in Epidemiology, Ecology and Climate Studies - Fellowship - 2022-12-31
Postdoctoral Research Fellowship in Spatial Epidemiology and Biostatistics - Fellowships - 2022-12-31
Postdoctoral Research Software Engineers (RSEs) - Fellowships - 2022-12-31
Monkeypox Has a New Name: Mpox - NY Times - 2022-12-02
Chancellor Scholz praises African science - DW - 2022-12-01
Why are COVID-19 cases rising in China? - CBNC TV - 2022-11-24
Embrace the hustle: African universities can make a real impact on the continent - Sunday Times - 2022-11-22
German Africa Prize won by scientists who identified Omicron - German-Africa Prize - 2022-10-25
Prof. Frank Tanser joins CERI at SU as Director of Population Health Program - CERI News - 2022-10-14
100,000 coronavirus genomes reveal COVID's evolution in Africa - nature - 2022-10-03
What are the origins of COVID-19 variants in Africa? - Pasteur Network - 2022-09-27
Majority of Covid-19 variants in Africa came from abroad - study - East Coast Radio - 2022-09-16
The Virus Hunters Trying to Prevent the Next Pandemic - TIME - 2022-09-01
Tulio de Oliveira: collaborating to boost science in Africa - the Lancet - 2022-09-01
Why Experts Want to Rename Monkeypox - New York Times - 2022-08-23
Monkeypox is now a global health emergency - Heres what it means for Africa - Independent - 2022-07-25
First case of antibody-avoiding Covid subvariant detected - Bankok Post - 2022-07-20
Omicron sub-variant BA.2.75 not dangerous as 'hyped': Expert - Economic Times - 2022-07-19
COVID-19: Reinfections amid complex mix of immunity - Spotlight - 2022-07-12
Headed in a bad direction: Omicron variant may bring second-largest US Covid wave - The Guardian - 2022-07-08
COVID-19 Subvariants Might Offer Clues About Future Waves - ADF - 2022-07-06
Rename monkeypox to remove geographic stigma, researchers say - Science - 2022-06-10
New versions of Omicron are masters of immune evasion - Science - 2022-05-10
How global heating will increase virus swapping between species - Daily Maverick - 2022-05-10
Watch | South Africa's 5th COVID Wave Is Very Different From the Earlier One' - Wire - 2022-05-09
Are COVID surges becoming more predictable? New Omicron variants offer a hint - Nature - 2022-05-06
South Africas latest surge is a possible preview of the pandemics next chapter. - New York Times - 2022-05-04
Are new Omicron subvariants a threat? Here's how scientists are keeping watch - Nature - 2022-04-15
Omicrons new sub-lineages in SA: Continued evolution of the virus entirely expected - News24 - 2022-04-13
'No cause for alarm' as scientists find two new Omicron strains in SA - News24 - 2022-04-12
Prof Tulio de Oliveira: saving lives by searching for clues in pandemics - Stellenbosch University - 2022-04-11
SAMRC Scientific Merit Awards: Prof Tulio de Oliveira is awarded a Gold Medal - SAMRC - 2022-04-01
UKZN researchers scoop the 2022 National Batho Pele Excellence Awards - News24 - 2022-03-28
In an uncertain and rapidly changing world, research universities play a critical role in building a better future - Daily Maverick - 2022-03-21
How should the world respond to the next pandemic? - The Guardian - 2022-03-18
No Real-World Evidence BA.2 Is More Severe - MedPage Today - 2022-02-26
How tracking coronavirus variants will prepare us for the next global public health threat - MIT Tech Review - 2022-02-23
Fact Check: New BA.2 variant HAS NOT caused a spike in deaths for SA - The South African - 2022-02-20
Africas first mRNA hub in Cape Town a potential game changer, says WHO boss - https://www.news24.com/health24/medical/infectious-diseases/coronavirus/pics-africas-first-mrna-hub- - 2022-02-10
Where did Omicron come from? Three key theories - Nature - 2022-01-28
South Africa Bolsters Genomics Capability to Hunt Deadly Disease - Bloomberg - 2022-01-21
How We Can Spot the Next COVID-19 Variant Even Faster - Time - 2022-01-13
Natures 10: Ten people who helped shape science in 2021 - Nature - 2021-12-15
The Variant Hunters: Inside South Africas Effort to Stanch Dangerous Mutations. - The New York Times - 2021-12-06
How South African Researchers Identified the Omicron Variant of COVID - New Yorker - 2021-11-30
CERI: Realizing the Potential of Pathogen Genomics in Africa - Illumina - 2021-09-30
The Rockefeller Foundation Supports the Launch of the Centre for Epidemic Response and Innovation To Help Prevent Future Pandemics - Rockefeller Foundation - 2021-09-23
Unethical? Unnecessary? The COVID-19 vaccine booster debate intensifies - Science - 2021-08-27
Stellenbosch University 2 Postdoctoral Positions on Pathogen Genomics, Cape Town - PostDoc - 2021-07-30
As COVID-19 collides with HIV/AIDS, the pandemic may be taking an ominous turn - LA Times - 2021-06-03
Coronavirus variants get Greek names, but will scientists use them? - Nature - 2021-06-01
Jiving with Science to get South Africans in tune with Covid-19 science - Sunday Times - 2021-05-24
Some Nations Could Wait Years for Covid Shots. That is Bad for Everyone - NY Times - 2021-03-23
Whats unique about the bodys response to the 501Y.V2 variant? Find out - Bhekisisa - 2021-03-12
We Now Can See a Virus Mutate Like Never Before - The Atlantic - 2021-03-09
Antibodies from S Africa COVID variant may offer cross-protection - Al Jazeera - 2021-03-04
A Virus Variant by Any Other Name - Please - The New York Times - 2021-03-03
Another coronavirus variant detected in SA, but no reason to panic - News24 - 2021-03-02
Coronavirus variants update: One has spread to over 90 countries, two on WHO watchlist - News24 - 2021-02-26
South African scientists on pandemics frontline - Financial Times - 2021-02-15
All These Mutant Virus Strains Need New Code Names - Wired - 2021-02-08
Worrisome New Coronavirus Strains Are Emerging. Why Now? - Wired - 2021-01-27
Fast-spreading COVID variant can elude immune responses - Nature - 2021-01-21
Alarming COVID variants show vital role of genomic surveillance - Nature - 2021-01-17
Answers to 9 crucial questions about the coronavirus variants spreading around the world - Business Insider - 2021-01-15
As Coronavirus Mutates, the World Stumbles Again to Respond - The New York Times - 2021-01-15
A bloody mess': Confusion reigns over naming of new COVID variants - Nature - 2021-01-15
Could new COVID variants undermine vaccines? Labs scramble to find out - Nature - 2021-01-14
Third concerning coronavirus variant should be a 'wake up call' to the world, experts warn - The Telegraph - 2021-01-12
WHO calls for new names for Covid variants to avoid country stigma - The Telegraph - 2021-01-12
As the coronavirus mutates, the world stumbles to respond - Brief on NY Times live blog - The New York Times - 2021-01-09
South African Covid variant may affect vaccine efficacy, warn scientists - Financial Times - 2021-01-06
Boris Johnson Tightens U.K. Lockdown, Citing Fast-Spreading Version of Virus - The New York Times - 2021-01-04
Fast-spreading virus variants raise alarms - Science - 2021-01-01
Variants put spotlight on immunocompromised patients' role in the COVID-19 pandemic - Science - 2020-12-23
KRISP produces over 1000 HIV-1 genomes in record time - SAMRC Press Release - 2020-12-03
Initial COVID-19 Infections In CT Came From Europe, Researchers Find - EWN - 2020-07-17
Scientists found who may have triggered the coronavirus crisis in Cape Town - Businesstech - 2020-07-15
SA's first Covid-19 vaccine trial brings hope - Sunday Tribune - 2020-07-12
En Afrique du Sud, des chercheurs remontent la piste du coronavirus - Le Monde - 2020-06-06
South Africa: Protecting Healthcare Workers 'Not Rocket Science' - All Africa - 2020-06-02
Full report: How 135 people at St Augustine's Hospital in Durban got COVID-19 - Bhekisisa - 2020-05-29
Three detectives', a virus and the patient who infected an entire hospital | Future Planet - Future Planet - 2020-05-27
Between two devils: Why hospitals must act fast to prevent health worker deaths - Bhekisisa - 2020-05-25
Southern Africa: COVID-19 Roundup | Back to School - All Africa - 2020-05-23
Netcare welcomes findings into Covid-19 outbreak at St Augustine's Hospital - Independent - 2020-05-20
More than 100 infections and 15 patient deaths in Covid-19 outbreak at St Augustine's Hospital - Times Live - 2020-05-20
University probe finds over 100 COVID-19 cases at St Augustine's Hospital - East Coast Radio - 2020-05-20
Investigation report reveals single source of infection caused St Augustine virus outbreak - Berea Mail - 2020-05-20
14% OF KZN COVID-19 CASES CAN BE TRACED TO ST AUGUSTINE'S HOSPITAL - REPORT - EWN - 2020-05-20
Cape Town Becomes Center of South Africa's Virus Pandemic - Bloomberg - 2020-05-16
A Lockdown may Have Averted 20,000 Deaths, Says Bio-Information Expert - Eye Witness News - 2020-05-14
The Western Cape now accounts for more than half of South Africa's coronavirus cases - Businesstech - 2020-05-14
Researcher explains how early SA lockdown has saved at least 20,000 lives - Cape Talk - 2020-05-14
Lockdown and other interventions potentially saved 20 000 lives - News24 - 2020-05-13
UKZN's Professor Tulio de Oliveira talks Covid-19 to East Coast Radio Breakfast Show - East Coast Radio - 2020-05-06
SA's confirmed Covid-19 cases rise to 5 951, with 13 deaths on Day 1 of level 4 lockdown - IOL News - 2020-05-02
Covid-19: Infections could rise by 10% per day after lockdown lifts - top scientists - News24 - 2020-05-01
Coronavirus: 27 patients on ventilators as SA edges towards the end of 'hard' lockdown - News24 - 2020-04-28
Human trials for vaccine begins - Independent on Saturday - 2020-04-25
The Pros and Cons of high-speed science - Daily Maverick - 2020-04-24
Data science sees gold rush to create COVID-19 breakthroughs - ITWeb News - 2020-04-23
SA scientists on breaking the Covid-19 code - Saturday Independent - 2020-04-21
KwaZulu-Natal researchers seeking to research Covid-19 outbreak in South Africa - Creamer Engineering News - 2020-04-20
Scientists launch fundraising campaign to support analysis of COVID-19 data in real time - Phoenix Sun - 2020-04-20
Support South Africa's COVID-19 Scientists on the Frontline - BackaBuddy - 2020-04-19
Big Data, Bioinformatics & Artificial Intelligence to fight COVID-19 epidemic in South Africa - Big Data to fight COVID-19 - 2020-04-18
Big Data presentations on COVID-19 by Profs. Salim Abdool Karim, Tulio de Oliveira, Richard Lessells and Francesco Petruccione - UKZN data@breakfast - 2020-04-17
SA government plans for Covid-19 to peak in September but questions about data remain - News24 - 2020-04-12
Public warned about 'rapid' coronavirus test kits - Daily News - 2020-04-03
Testing to be ramped up and new tests in pipeline for COVID-19 - Spotlight and Daily Maverick - 2020-03-31
Big Data update for COVID-19 in Africa: Epidemiology & Genomics - KRISP Big Data - 2020-03-20
Coronavirus testing: How it works, what it costs and when you need a test - Bhekisisa - 2020-03-11
KRISP scientists quick action lauded by Nature - Saturday Independent - 2020-02-25
Social media helped scientists with coronavirus - Independent on Saturday - 2020-02-15
Novel Coronavirus (2019-nCoV) Outbreak: Genomics & Epidemiology - KRISP Talks - 2020-02-14
KRISP Join Stanford SPARK Global Program and creates Durban SPARK Innovation Breakfast Monthly Meeting - KRISP News - 2020-01-01
New study shows 43% drop in rate of new HIV infections - KRISP & AHRI News - 2019-12-14
Science Through the Lens of Photography - KRISP News - 2019-12-12
International Virus Bioinformatics Meeting 2020 - KRISP News - 2019-11-06
Open Access Book Chapter - Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era - KRISP News - 2019-10-03
KRISP participation at BioAfrica 2019 in Review - KRISP News - 2019-10-01
KRISP Talks: Funding Opportunities: FLAIR Fellowship & SAMRC-NIH Calls 2019 - KRISP Talks - 2019-04-24
24th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) - KRISP, KULeuven & Univ. Hong Kong - 2019-03-30
NextStrain & Genome Detective Workshop, KRISP, Durban, South Africa, 24-25 January 2019 - KRISP & Univ. of Basel - 2019-01-24
In Epicenter of Global HIV Crisis, Multiple Partners and Age Disparity Part of Problem - Epoch Times - 2018-10-17
Quasi-companies in Biotechnology - Durban SPARK Innovation Breakfast, 5 Sept 2018 - Durban SPARK Innovation Breakfast - 2018-09-05
Boston, Berlin, Brazil & SPARK Global Successful model - Durban SPARK Innovation Breakfast, 1 Aug 2018 - Durban SPARK Innovation Breakfast - 2018-08-01
Nature paper: Renewing Felsenstein's phylogenetic bootstrap in the era of big data - KRISP Papers - 2018-04-18
University-Industry-Government Co-operation Needed for Entrepreneurial Success - KRISP News - 2018-04-18
3rd Durban Spark Innovation breakfast meeting - 4th April at 7h30-8h30, Durban, South Africa - KRISP News - 2018-04-04
2nd Durban Spark Innovation Breakfast Meeting - March Meeting Sparking Innovation on UKZN's Medical School Campus - UKZN News NdabaOnline - 2018-03-15
X-meeting - 13th International Conference of the AB3C, Sao Pedro, Brazil, Oct 4-6, 2017 - KRISP Training - 2017-10-04
11th Annual Workshop on Advanced Clinical Care - AIDS (AWACC), Durban, South Africa, 6-7 Sep 2017 - KRISP Training - 2017-09-06
22nd International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME), Lisbon, Portugal - KRISP Training - 2017-08-27
KRISP Newsletter - July 2017: news, videos, blogs, publications and training events - KRISP Newsletter - 2017-08-01
KRISP & SANTHE trainee wins Best Abstract at DELTAS Africa meeting - KRISP News - 2017-07-20
KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) Established - KRISP News - 2017-07-12
KRISP/SATuRN & CAPRISA 2017: HIV & TB Drug Resistance and Advanced Care Workshop - KRISP & CAPRISA - 2017-03-30
Seminar: Microbial genome-wide association studies: lessons from human GWAS - KRISP Talks - 2017-03-17
Swiss South African Symposium on Pathogen Genomics - Swiss National Science Foundation & SA NRF - 2017-02-23
Newsletter, Dec 2016: Ethics & phylogenetics, HIV transmission cycle, UNAIDS Report, Drug resistance increases in Africa - BioAfrica & SATuRN - 2016-12-15
Two manuscripts featured in the Lancet website front webpage on AIDS day. - The Lancet - 2016-12-01
UNAIDS Report 2016 - Get on the Fast-Track - The life-cycle approach to HIV - UNAIDS - 2016-11-22
More than 18 million on HIV treatment, a million more than 2015: UNAIDS 2016 Report - Reuters - 2016-11-22
10th Annual Workshop on Advanced Clinical Care - AIDS (AWACC) - AWACC - 2016-10-06
PhD Fellowship I: Genomics, Bioinformatics & Drug Resistance - CAPRISA, UKZN & MRC Flagship - 2016-08-23
PhD Fellowship II: Genomics, Bioinformatics, Epidemioloy and Phylogenetics - CAPRISA, UKZN & MRC Flagship - 2016-08-23
Social cycle aids HIV spread - Nature - 2016-07-21
Studies Offer Fresh Hope in Fight Against HIV/AIDS in South Africa. - Wall Street Journal - 2016-07-18
South Africa's bid to end AIDS - Science - 2016-06-29
21st International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) - Rega Institute & Korea University College of Medicine - 2016-03-15
Research travel grants: Doctoral or post-doctoral students to Wellcome Trust Africa Centre, South Africa - WTAC & MRC Flagship UKZN - 2015-08-15
MOLECULAR EPIDEMIOLOGY: HIV family trees reveal viral spread. - Science - 2015-06-12
Feature story: Understanding HIV through phylogenetic research - UNAIDS - 2015-06-08
HIV 2015: Using Phylogenetics to Enhance the HIV Response, New York, June 4, 2015 - New York Academy of Sciences - 2015-06-04
Seminar: Near Full Length Sequencing to Understand HIV & TB Epidemics In Africa In Real Time - KRISP Talks - 2015-04-30
Ground-breaking PhD Study helps Rural Doctors monitor HIV Drug Resistance - UKZN - 2015-04-17
Our genomics and bioinformatics research program was selected as a keynote presentation in the 1st South African Illumina User Group Meeting, 2015 - Illumina User Meeting - 2015-03-31
Doris Duke Annual Seminar for Medical Students from Harvard and UKZN - SATuRN & Harvard - 2014-10-09
Postdoc Fellowship available - HIV Genomics & Bioinformatics I - WTAC, UCL, LSHTM & UKZN - 2014-07-26
Postdoc Fellowship available - HIV Bioinformatics & Phylogenetics II - WTAC, UCL, LSHTM & UKZN - 2014-07-26
Postdoc Fellowship available - HIV & HTLV Bioinformatics & Phylogenetics III - WTAC, UKZN, FioCruz, CNPQ - 2014-07-26
SATuRN Newsletter, Jul 2014: Annual HIVDR Workshop, News, Publications & Blogs - SATuRN - 2014-07-24
Postdoctoral Research Fellows in HIV - WT Africa Centre, UCL & LSHTM - 2014-07-17
Seminar: Genomics & Bioinformatics: The need to engage biologists, mathematicians & computer scientists. - KRISP Talks - 2014-06-25
SA Medical Research Council Scientific Awards - Mail & Guardian - 2013-12-08
Heroes in the battle for health - Sunday Times - 2013-12-01
Putting the I into HIV - World Aids Day UKZN - UKZN - 2013-11-30
'An HIV-1 vaccine is possible' says Prof Thumbi Ndung'u at UKZN AIDS Day 2013 - K-RITH - 2013-11-29
A UKZN panel discussion: Bringing the 'I' into HIV - New approaches in developing person-centred interventions to fight the HIV epidemic - UKZN, CAPRISA & HEARD - 2013-11-08
16.5 million rand to convert cutting-edge HIV research in rural South Africa into national policy - Africa Centre & UKZN DVC - 2013-10-31
Multi-million rand award to UKZN scientists for Cutting-Edge HIV Research - UKZN - 2013-10-30
BioMedical research is undergoing a revolution - K-RITH - 2013-10-25
Newsletter, Oct 2013: News, blogs, manuscripts & Youtube videos! - SATuRN - 2013-10-01
BOOK REVIEW - HIV & TB Drug Resistance & Clinical Management Case Book - Southern African Journal of HIV Medicine - 2013-06-20
Bioinformatics in the tropics workshop series 2013-2014 - Bioinformatics in the Tropics - 2013-05-30
Infectious Disease Genomics and Global Health Wellcome Trust Conference - Wellcome Trust - 2013-05-24
The Network Marker - International Innovation - 2013-04-22
Case book tackles HIV and TB drug resistance - Zululand Observer - 2013-04-15
University of Pretoria and partners launch a book - University of Pretoria - 2013-03-19
Casebook aims to curb drug resistance - PretoriaNews - 2013-03-19
BOOK ON MANAGEMENT OF HIV AND TB DRUG RESISTANCE LAUNCHED - UKZNonline - 2013-03-16
Universiteit van Pretoria en vennote stel boek vry oor weerstand teen middels wat gebruik word om MIV en tuberkulose te bekamp - Universiteit van Pretoria - 2013-03-15
PRESS RELEASE: Book Launch: HIV and TB Drug Resistance & Clinical Management Case Book - Africa Centre - 2013-03-06
Invitation to the launch of the HIV and TB drug resistance & clinical management case book - University of Pretoria - 2013-03-05
18th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology, USA, 25-30 Aug 2013 - Leuven & Univ. Florida - 2013-02-27
Comminit News: Scientific Community Engagement Activities in Rural KwaZulu-Natal, South Africa - The Communication Initiative Network - 2012-11-30
'Tainted milk' from wet nurse HIV risk - Cape Argus - 2012-08-26
Local centre proves 'surrogate' HIV infection - Zululand Observer - 2012-08-24
DNA sequencing confirms HIV transmission through surrogate breastfeeding - Wellcome Trust - 2012-08-23
Breastfeeding in the spotlight - SABC - 2012-08-16
Collaboration to Undertake HIV Resistance Testing in Africa - LabMedica - 2012-08-06
Creating access to HIV/TB drug resistance testing - CAPRISA - 2012-08-01
Life Tech, SATuRN Collaborate on Dx for Antiretroviral Resistance in HIV in Africa - GenomeWeb - 2012-07-26
Life Technologies and SATuRN Collaborate to Increase Access to HIV Testing in Africa - The Wall Street Journal - 2012-07-24
BioAfrica Art & Science section is open! - BioAfrica - 2012-05-10
SATuRN Newsletter Vol. 1 Number 1, Jan-Mar 2012 - BioAfrica - 2012-04-15
Transmitted Drug Resistance Rate Remains Below 5% in South Africa - IAS - 2012-03-05
Highly Specialized Team to Tackle HIV Drug Resistance Problem in Southern Africa - UKZN - 2012-02-22
Meeting to Discuss the Growing Threat of HIV & TB Drug Resistance in South Africa and Botswana - CDC - South Africa - 2011-11-04
Believe in ART, get tested please - Die Burger - 2008-09-10
High noon in Libya - Nature - 2007-07-19
World-class scientist due to join UWC team tackling HIV/Aids treatment in SA. - Cape Times - 2007-01-14
Genetic Analysis Clears Accused Medics - Science - 2006-12-20
New evidence in Libyan HIV trial - New Scientist - 2006-12-20
Libya sentences medics to death - BBC - 2006-12-19
Medics face death while Libya uses HIV children as diplomatic pawns - The Guardian - 2006-12-17
New scientific evidence in Libya HIV death penalty case - University of Oxford - BluePrint News - 2006-12-07
New Evidence Disputes Libya Case in H.I.V. Trial - NY Times - 2006-12-07
Study backs Libya HIV case medics - BBC - 2006-12-06
Molecular HIV evidence backs accused medics - Nature - 2006-12-06
COVID-19 | News sub-variant being monitored closely - YouTube - 2023-01-10
COVID-19 in SA | SA scientists don't expect high infection or hospitalisation numbers - YouTube - 2023-01-10
Prof. de Oliveira says the world has entered an age of epidemics and pandemics - YouTube - 2022-06-08
8th SAMRC Scientific Merit Awards - Prof Tulio de Oliveira - Gold Award - YouTube - 2022-04-01
BBC: Three people across Africa who made a difference in 2021 - YouTube - 2021-12-31
Genomics Surveillance Training to 15 African Countries at CERI, 2021 - YouTube - 2021-12-24
CNN - Prof. Tulio de Oliveira First Move Julia Chatterley 23 Dec 2021 - YouTube - 2021-12-23
Genetic study indicates two novel resistance loci for severe malaria in Africa - by Zakia Jeewa and Tulio de Oliveira - 2014-08-01
Wellcome Trust Africa Centre Seminar & Twitter Q&A on HIV drug resistance in Africa, 15-Jan-2014 - by Tulio de Oliveira - 2014-01-16
Data Curation and its tenets - by Lungani Ndwandwe, Tulio de Oliveira - 2013-08-15
South African scientific excellence: South African AIDS scientist to lead UNAIDS Expert Panel - by Tulio de Oliveira - 2013-07-01
Pirate Science - an interesting website on open-access phylogenetic publications - by Tulio de Oliveira - 2013-04-28
SATuRN on the Chair of African Dreams - by Lungani Ndwandwe, Justen Manasa, Xolile Kineri, Zakhona Gumede, Astrid Treffry-Goatley, Eduan Wilkinson, Tulio de Oliveira - 2013-04-06
The Southern African Treatment Resistance Network (SATuRN) at the KZNSA Gallery - by Lungani Ndwandwe, Tulio de Oliveira - 2012-12-01
Zooming in on home-based health care givers in rural South Africa - by Lungani Ndwandwe, Tulio de Oliveira - 2012-09-13
ACiLT Practical Course on Quality Assurance of HIV-1 Drug Resistance Interpretation in Sequence Editing and Data Management Process, 7-11 May 2012 - by Justen Manasa, Tulio de Oliveira - 2012-06-01
National Strategic Plan 2012-2016: Integrating research and all sectors of society to fight HIV, STIs and TB in South Africa - by Lungani Ndwandwe, Tulio de Oliveira - 2012-04-20
Shortage of doctors in rural South Africa? - by Lungani Ndwandwe, Tulio de Oliveira - 2012-03-29
Social Worker perspective: Adolescents on Antiretroviral (ARV) therapy - a VideoBlog - by Pretty Nkosi, Nokuthula Skhosana, Lungani Ndwandwe and Tulio de Oliveira - 2012-02-10
Scientific Community Engagement Activities in rural KwaZulu-Natal, South Africa - by Tulio de Oliveira - 2012-01-22
Botswana hosted a successful HIV and TB workshop - by Tulio de Oliveira, Lungani Ndwandwe - 2011-12-01
KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).
Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira