PUBLICATIONS SPOTLIGHT

PUBLICATIONS

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:

High prevalence of self-reported sexually transmitted diseases among older adults in Tanzania: results from the list experiment

Kim HY, Rohr J, Leyna GH, Killewo J, Tomita A, Tanser F, Bärnighausen T, Ann Epidemiol. (2023), S1047-2797(23)00086-8. doi: 10.1016/j.annepidem.2023.05.001:

International epidemiology Databases to Evaluate AIDS (IeDEA) Southern Africa. Abacavir safety and effectiveness in young infants with HIV in South African observational cohorts

de Waal R, Rabie H, Technau KG, Eley B, Sipambo N, Cotton M, Boulle A, Wood R, Tanser F, Fatti G, Egger M, Davies MA, Antivir Ther. (2023), 28(2):13596535231168480. doi: 10.1177/13596535231168480:

Convergence of HIV and non-communicable disease epidemics: Geospatial mapping of the unmet health needs in a HIV Hyperendemic South African community.

Cuadros DF, Devi C, Singh U, Olivier S, Castle A, Moosa Y, Edwards JA, Kim HY, Siedner MJ, Wong EB, Tanser F, medRxiv (2023), 2023.03.27.23287807. doi: 10.1101/2023.03.27.23287807:

Spatial variations in STIs among women enrolled in HIV prevention clinical trials in Durban, KwaZulu-Natal

Dassaye R, Wand H, Reddy T, Tanser F, Sartorius B, Morris N, Ramjee G, SAHARA J. (2023), (1):2193238. doi: 10.1080/17290376.2023.2193238:

HIV-1 drug resistance in people on dolutegravir-based ART: Collaborative analysis of cohort studies

Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, Monforte AD, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos R, medRxiv (2023), 5:2023.04.05.23288183. doi: 10.1101/2023.04.05.23288183:

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:

Tuberculosis drug resistance profiling based on machine learning: A literature review

Sharma A, Machado E, Lima K, Suffys P, Conceição E, The Brazilian Journal of Infectious Diseases (2022), 26:102332

Fast surveillance response reveals the introduction of a new yellow fever virus sub-lineage in 2021, in Minas Gerais, Brazil

Andrade M, Campos F, Oliveira C, Oliveira R, Campos A, Almeida M, Fonseca V, Simonini-Teixeira D, Seva A, Temponi A, Magalhaes F, Chaves D, Pereira M, Lamounier L, Menezes G, Aquino-Teixeira S, Goncalves-dos-Santos M, Bernal-Valle S, Muller N, Cardoso J, Santos E, Mares-Guia M, Albuquerque G, Romano A, Franco A, Ribeiro B, Roehe P, Abreu F, Memórias do Instituto Oswaldo Cruz (2022), 117():. doi: 10.1590/0074-02760220127.:

Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil

Dantas A, Oliveira H, Gomes C, Alves D, Infante P, Caitite R, Fritsch H, Cucco M, Silva L, Oliveira C, Bittencourt R, Amorim A, Nascimento A, Marinho F, de Medeiros D, de Oliveira M, Mistro S, de Melo F, Pereira T, Guimaraes A, Timenetsky J, Moreira P, de Oliveira S, Alcantara L, Giovanetti M, Santos L, Fonseca V, Barreto F, Campos G, Marques L, Viruses (2022), 14(11):2424. doi: 10.3390/v14112424.:

Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Brazil

Giovanetti M, Pereira L, Santiago G, Fonseca V, Mendoza M, de Oliveira C, de Moraes L, Xavier J, Tosta S, Fristch H, de Castro Barbosa E, Rodrigues E, Figueroa-Romero D, Padilla-Rojas C, Cáceres-Rey O, Mendonça A, de Bruycker Nogueira F, Venancio da Cunha R, de Filippis A, Freitas C, Peterka C, de Albuquerque C, Franco L, Méndez Rico J, Muñoz-Jordán J, Lemes da Silva V, Alcantara L, Emerging Infectious Diseases (2022), 28(8):1725-1727. doi: 10.3201/eid2808.220550.:

Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Slavov S, de La-Roque D, da Costa P, Rodrigues E, Santos E, Borges J, Evaristo M, de Matos Maçonetto J, Marques A, Milhomens J, Rós F, Fonseca V, Lima A, Ribeiro G, Lima L, Garibaldi P, Ferreira N, Moraes G, Marqueze E, Barros C, Martins A, Coutinho L, Calado R, Borges M, Elias M, Sampaio S, Giovanetti M, Alcantara L, Covas D, Kashima S, Viruses (2022), 14(10):2148. doi: 10.3390/v14102148.:

Retrospective Genomic Surveillance of Chikungunya Transmission in Minas Gerais State, Southeast Brazil

Fritsch H, Giovanetti M, Xavier J, Adelino T, Fonseca V, de Jesus J, de Jesus R, Freitas C, Peterka C, Campelo de Albuquerque C, Bispo de Filippis A, da Cunha R, Silva E, Alcantara L, Iani F, Microbiology Spectrum (2022), 10(5):. doi: 10.1128/spectrum.01285-22.:

Molecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution

Neto D, Fonseca V, Jesus R, Dutra L, Portela L, Freitas C, Fillizola E, Soares B, Abreu A, Twiari S, Azevedo V, Goes-Neto A, de Medeiros A, Lopes N, Zanotto P, Kato R, Journal of Biomolecular Structure and Dynamics (2022), 41(12):5789-5801. doi: 10.1080/07391102.2022.2097955.:

Retrospective Investigation in Horses with Encephalitis Reveals Unnoticed Circulation of West Nile Virus in Brazil

Fritsch H, Pereira F, Costa E, Fonseca V, Tosta S, Xavier J, Levy F, Oliveira C, Menezes G, Lima J, Santos L, Silva L, Nardy V, Astete M, Santos B, Aguiar N, Guedes M, Faria G, Furtini R, Drumond S, Cunha G, Souza M, Jesus R, Guimarães S, Nuno I, Santana I, Sá J, Santos G, Silva W, Guedes T, Araújo E, Said R, Albuquerque C, Peterka C, Romano A, Cunha R, Filippis A, Leal e Silva de Mello A, Giovanetti M, Alcantara L, Viruses (2022), 14(7):1540. doi: 10.3390/v14071540.:

SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves

Alcantara L, Nogueira E, Shuab G, Tosta S, Fristch H, Pimentel V, Souza-Neto J, Coutinho L, Fukumasu H, Sampaio S, Elias M, Kashima S, Slavov S, Ciccozzi M, Cella E, Lourenco J, Fonseca V, Giovanetti M, Virus Research (2022), 315():198785. doi: 10.1016/j.virusres.2022.198785.:

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.:

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: