PUBLICATIONS SPOTLIGHT

PUBLICATIONS

Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023

Burgueño A, Giovanetti M, Fonseca V, Morel N, Lima M, Castro E, Guimarães N, Iani F, Bormida V, Cortinas M, Ramas V, Coppola L, Bento A, Franco L, Rico J, Lourenço J, Junior Alcantara L, Chiparelli H, Emerging Microbes & Infections (2024), 13(1):. doi: 10.1080/22221751.2024.2332672.:

Mapping the Dynamics of Dengue Serotypes in the 2023 Epidemic: Insights from Spatial-Temporal Analysis and Emergence of the Cosmopolitan DENV-2 Genotype in Ribeirão Preto, São Paulo, Brazil

Carmo S, Torres P, Roque D, Santos E, Elias M, Sampaio S, Giovanetti M, Fonseca V, Alcantara L, Gentil D, Giomo D, Kashima S, Passos L, International Journal of Health Science (2024), 4(28):2-9. doi: 10.22533/at.ed.1594282419035.:

DENV-1 genotype V circulation during the nonepidemic period in the Northeast of São Paulo State endemic area

de La-Roque D, Santos E, Oliveira R, Slavov S, Rodrigues E, Fonseca V, Martins A, Giomo D, Torres P, Gentil D, Catoia E, Chiquito N, Medeiros A, Yamamoto A, Passos L, Calado R, Barros C, Elias M, Sampaio S, Giovanetti M, Junior Alcantara L, Covas D, Kashima S, Journal of Medical Virology (2024), 96(3):. doi: 10.1002/jmv.29526.:

Resurgence of Dengue Virus Serotype 3 in Minas Gerais, Brazil: A Case Report

Adelino T, Lima M, Guimarães N, Xavier J, Fonseca V, Tomé L, Pereira M, Machado V, Alcantara L, Iani F, Giovanetti M, Pathogens (2024), 13(3):202. doi: 10.3390/pathogens13030202.:

Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population

Rodrigues E, Slavov S, de La Roque D, Santos E, Borges J, Evaristo M, da Costa P, de Matos Maçonetto J, Marques A, Baccarin A, Oliveira R, Junior W, Benincasa B, de Andrade da Cruz L, Lima A, Ribeiro G, Viala V, de Lima L, Martins A, dos Santos Barros C, Marqueze E, de Souza Todao Bernardino J, Grotto R, Souza-Neto J, Fonseca V, Nogueira M, Fukumasu H, Coutinho L, Calado R, Covas D, Giovanetti M, Alcantara L, Sampaio S, Elias M, Kashima S, Microorganisms (2024), 12(3):449. doi: 10.3390/microorganisms12030449.:

Evidence of Zika Virus Reinfection by Genome Diversity and Antibody Response Analysis, Brazil

da Costa Castilho M, de Filippis A, Machado L, de Lima Calvanti T, Lima M, Fonseca V, Giovanetti M, Docena C, Neto A, Bôtto-Menezes C, Kara E, de La Barrera R, Modjarrad K, Giozza S, Pereira G, Alcantara L, Broutet N, Calvet G, Wallau G, Franca R, Emerging Infectious Diseases (2024), 30(2):. doi: 10.3201/eid3002.230122.:

Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay

Vazquez C, Fonseca V, de la Fuente A, Gonzalez S, Fleitas F, Lima M, Guimarães N, Iani F, Rojas A, Alfonso T, Cantero C, Barrios J, Villalba S, Ortega M, Torales J, Gamarra M, Aquino C, Franco L, Rico J, Alcantara L, Giovanetti M, Viruses (2024), 16(1):83. doi: 10.3390/v16010083.:

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, 793–802 (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:

Associations of inter-annual rainfall decreases with subsequent HIV outcomes for persons with HIV on antiretroviral therapy in Southern Africa: a collaborative analysis of cohort studies

Trickey A, Johnson LF, Fung F, Bonifacio R, Iwuji C, Biraro S, Bosomprah S, Chirimuta L, Euvrard J, Fatti G, Fox MP, Von Groote P, Gumulira J, Howard G, Jennings L, Kiragga A, Muula G, Tanser F, Wagener T, Low A, Vickerman P, BMC Infect Dis (2024), doi: 10.1186/s12879-023-08902-9:

Convergence of HIV and non-communicable disease epidemics: geospatial mapping of the unmet health needs in an HIV hyperendemic community in South Africa

Cuadros DF, Devi C, Singh U, Olivier S, Castle AC, Moosa Y, Edwards JA, Kim HY, Siedner MJ, Wong EB, Tanser F, BMJ Glob Health (2024), 9(1):e012730. doi: 10.1136/bmjgh-2023-012730:

Effect of a male-targeted digital decision support application aimed at increasing linkage to HIV care among men: Findings from the HITS cluster randomized clinical trial in rural South Africa

Kim HY, Inghels M, Mathenjwa T, Shahmanesh M, Seeley J, Matthews P, Wyke S, McGrath N, Adeagbo O, Gareta D, Yapa HM, Zuma T, Dobra A, Blandford A, Bärnighausen T, Tanser F, medRxiv [Preprint] (2024), 2024.03.15.24304373. doi: 10.1101/2024.03.15.24304373:

The impact of a conditional financial incentive on linkage to HIV care: Findings from the HITS cluster randomized clinical trial in rural South Africa

Kim HY, Inghels M, Mathenjwa T, Shahmanesh M, Seeley J, Matthews P, McGrath N, Adeagbo O, Gareta D, Yapa HM, Zuma T, Dobra A, Bärnighausen T, Tanser F, medRxiv [Preprint] (2024), 2024.03.15.24304278. doi: 10.1101/2024.03.15.24304278:

HIV transmission dynamics and population-wide drug resistance in rural South Africa

Kemp SA, Kamelian K, Cuadros DF; PANGEA Consortium; Vukuzazi Team; Cheng MTK, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong EB, Tanser F, Siedner MJ, Gupta RK, Nat Commun. (2024), 15(1):3644. doi: 10.1038/s41467-024-47254-z:

Population impacts of conditional financial incentives and a male-targeted digital decision support application on the HIV treatment cascade in rural KwaZulu Natal: findings from the HITS cluster randomized clinical trial

Inghels M, Kim HY, Mathenjwa T, Shahmanesh M, Seeley J, Wyke S, Matthews P, Adeagbo O, Gareta D, McGrath N, Yapa HM, Blandford A, Zuma T, Dobra A, Bärnighausen T, Tanser F, J Int AIDS Soc. (2024), 27(5):e26248. doi: 10.1002/jia2.26248:

Geospatial and temporal mapping of detectable HIV-1 viral loads amid dolutegravir rollout in KwaZulu-Natal, South Africa. PLOS Glob Public Health

Gounder L, Tomita A, Lessells R, Moodley S, Francois KL, Khan A, Pillay M, Manyana SC, Govender S, Govender K, Moodley P, Parboosing R, Msomi N, Tanser F, Naidoo K, Chimukangara B, PLOS Glob Public Health (2024), 4(5):e0003224. doi: 10.1371/journal.pgph.0003224:

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 - Preprint

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 - Preprint

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: