PUBLICATIONS SPOTLIGHT

PUBLICATIONS

Influência de variáveis climáticas na dinâmica vetorial de arboviroses no Brasil

Santos F, Guimarães R, Fonseca V, Xavier J, BIOINFO (2026), 6:3

Faecal Coliforms and Escherichia coli Contamination in Drinking Water Sources in Cholera Hotspot Areas of Lusaka District, Zambia: A Cross-Sectional Study

Ng’ombe H, Luchen C, Phiri B, Ngosa D, Kapikila R, Sakanya S, Sakala C, Mbewe N, Liswaniso F, Chilengi R, Wilkinson E, Liebenberg L, Khan W, Thomson N, Sack D, Bosomprah S, Chisenga C, Microorganisms (2026), 14:420

Cross-platform protocol for HTLV-1 whole-genome sequencing using nanopore and Illumina technologies

Lima A, de Moraes L, Amorim R, Cucco M, Silva R, Giovanetti M, Rego F, Araújo T, Fonseca V, Khouri R, Alcantara L, Santos L, Barreto F, Next Research (2026), 3:101110

Spatiotemporal patterns of Rift Valley fever virus in Africa: a retrospective genomic epidemiology and phylodynamic modelling study

Juma J, Tegally H, Konongoi S, Roesel K, Sang R, de Oliveira T, Njenga M, Christoffels A, Bett B, Dellicour S, Oyola S, The Lancet Microbe (2026), 7:101251

Robust mission-driven responses to infectious disease threats delivered by the Abbott pandemic defense coalition

Rodgers M, Averhoff F, Berg M, Anderson M, Strobel C, Inostroza J, Moy J, Mera J, Utz P, Weaver S, Chiu C, De Arcos J, Anzinger J, Henrys J, Hernandez-Ortiz J, Torres K, Mendes-Correa M, Gonçalves N, Kallas E, Mboup S, N’jai A, Mbanya J, de Oliveira T, Kaleebu P, El-Sayed M, Alkhazashvili M, Khan E, Khan R, Suputtamongkol Y, Osorio J, Cloherty G, International Journal of Infectious Diseases (2026), 162:108162

CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation

Tagliamonte M, Sharma A, Riva A, Moir M, Salemi M, Baxter C, de Oliveira T, Mavian C, Wilkinson E, Bioinformatics (2026), 42:

Ancient Pathogen Genomics in Africa – Current Evidence and Future Directions

Vukovikj M, Mavian C, Wang H, Gifford R, de Oliveira T, Schlebusch C, Preprints.org (2026), :

Chikungunya virus

Ramphal Y, de Oliveira T, Nature Ecology & Evolution (2026), 10:610-610

Re-emergence of DENV-3 in Paraguay After Two Decades: A Genomic and Epidemiological Investigation

Cantero C, Vazquez C, Gonzalez S, Rojas A, Fleitas F, Barrios J, Gomez de la Fuente A, Villalba S, Torales M, Ijeda A, Fonseca V, Junior Alcantara L, Giovanetti M, Emerging Microbes & Infections (2026), :

Alignment-free viral sequence classification at scale

van Zyl D, Dunaiski M, Tegally H, Baxter C, de Oliveira T, Xavier J, Riley C, Winters A, Naranbhai V, Made F, Karim S, Otwombe K, Abimiku A, Osawe S, Onyemata J, Dakum P, Murtala-Ibrahim F, Andrew N, Musa A, Adenekan T, Ewerem K, Etuk V, de Oliveira T, Baxter C, Wilkinson E, Tegally H, Poongavanan J, Parker M, Silva D, Xavier J, Stafford K, Charurat M, Blanco N, O’Connor T, Fitzpatrick M, Sajadi M, Lawal O, Xiong C, Luo W, Wu X, BMC Genomics (2025), 26:389

Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review

Moir M, Sitharam N, Hofstra L, Dor G, Mwanyika G, Ramphal Y, Reichmuth M, San J, Gifford R, Wilkinson E, Tshiabuila D, Preiser W, Konou A, Bitew M, Onoja A, Paganotti G, Abera A, Maror J, Kayiwa J, Abuelmaali S, Lusamaki E, de Oliveira T, Alcantara L, Holmes E, Padane A, Musa A, Abera A, Campbell A, Ssemaganda A, Ahouidi A, Muianga A, Samson A, Onoja A, Alemu B, Foka C, Baxter C, van Zyl D, de Castro Silva D, Martin D, Wilkinson E, Kouma E, Simo F, Mwanyika G, Godebo G, D’or G, Tegally H, Omara I, Maror J, Poonagavan J, Juma J, Oludele J, Xavier J, Lourenco J, Fokam J, Maeka K, Singh L, Chabuka L, Issaka M, Hofstra M, Giovanetti M, Faye M, Koffi M, Owusu M, Dikongo M, Alimohamed M, Bitew M, Moir M, Kraemer M, Sitharam N, Jerome N, Mbhele N, Miantsatian Andry N, Tomori O, Magalutcheemee R, Guimaraes R, Oyola S, Abuelmaali S, Golubchik T, Fonseca V, Preiser W, Ramphal Y, Venter M, Burt F, Baxter C, Lessells R, de Oliveira T, Tegally H, The Lancet Microbe (2025), 6:101176

Differences in HIV risk factors between South African adolescents and adult women and their association with sexually transmitted infections

Mkhize P, Mehou-Loko C, Maphumulo N, Radzey N, Abrahams A, Sibeko S, Harryparsad R, Manhanzva M, Meyer B, Radebe P, Liebenberg L, Ngcapu S, Ahmed N, Busakwe F, Mqaba N, Archary D, Sivro A, Samsunder N, Potloane D, Horsnell W, Jordan C, Abdool Karim Q, Bekker L, Passmore J, Jaspan H, Humphries H, Masson L, Sexually Transmitted Infections (2025), 101:174-182

Effect of the vaginal live biotherapeutic LACTIN-V (Lactobacillus crispatus CTV-05) on vaginal microbiota and genital tract inflammation among women at high risk of HIV acquisition in South Africa: a phase 2, randomised, placebo-controlled trial

Hemmerling A, Mitchell C, Demby S, Ghebremichael M, Elsherbini J, Xu J, Xulu N, Shih J, Dong K, Govender V, Pillay V, Ismail N, Casillas G, Moodley J, Bergerat A, Brunner T, Liebenberg L, Ngcapu S, Mbano I, Lagenaur L, Parks T, Ndung’u T, Kwon D, Cohen C, The Lancet Microbe (2025), 6:101037

Circulating Short-Chain Fatty Acids: Association with Vaginal Microbiota, Genital Inflammation, and HIV Acquisition

Shivakoti R, Letsoalo M, Lewis L, Mckinnon L, Passmore J, Karim S, Liebenberg L, AIDS Research and Human Retroviruses (2025), 41:559-566

Advancing the course of HIV genomics research in Africa

Agamah F, Arbuthnot P, Tindana P, Munung N, Kasule M, Ghansah A, Mosepele M, Gaolathe T, Kekitiinwa A, Nduati E, Jumare J, Gómez-Olivé F, Liebenberg L, Dandara C, Osawe S, Julius R, Muzambi T, Natus T, Omumbo J, Mayne E, Abimiku A, Richardson S, Matshaba M, Skelton M, BMJ Global Health (2025), 10:e019094

Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial)

Chetty C, Mafunda N, Happel A, Khan A, Cooley Demidkina B, Yende-Zuma N, Saidi Y, Mahabeer Polliah A, Lewis L, Osman F, Radebe P, Passmore J, Kwon D, Ravel J, Ngcapu S, Liebenberg L, Symul L, Holmes S, Mitchell C, Potloane D, Contemporary Clinical Trials Communications (2025), 48:101554

Reemergence of yellow fever virus in forest and periurban settings in Brazil

das Graças Dantas Andrade V, Ribeiro Adelino T, Fonseca V, Melo Farias Moreno K, Ribeiro Tomé L, Pereira L, Lima de La-Roque D, Bispo de Filippis A, Garkauskas Ramos D, Brock Ramalho D, de Lima Furtado K, Borges G, Martins L, Frutuoso L, Oliveira Lamounier L, Guimarães N, Sayuri Sato Barros P, Souza de Almeida P, de Souza da Silva P, Giesbrecht Pinheiro R, Guerino Stabeli R, Moreira da Silva Chagas S, Sousa Pietra Pedroso S, Kashima S, Gonçalves Penante S, Santini de Oliveira M, Lemes da Silva V, Van Voorhis W, Holmes E, Lourenço J, de Melo Iani F, Simões Jorge Júnior A, Giovanetti M, Junior Alcantara L, Communications Medicine (2025), 6:35

Detection of Lymphocytic Choriomeningitis Virus in House Mouse (Mus musculus) in Brazil

Cavalcanti G, Fernandes J, Santos F, Teixeira B, Guterres A, Brignone J, Levis S, Lucio C, Costa-Neto S, Fonseca V, Giovanetti M, Alcantara L, D’Andrea P, de Lemos E, Oliveira R, Viruses (2025), 17:1544

VAMPIRE: ALGORITMO PARA ANÁLISE DE DADOS DE NGS E IDENTIFICAÇÃO DE VARIANTES GENÉTICAS DO SISTEMA SANGUÍNEO RH

Galdino D, Rodrigues E, Lenz A, Chagas L, Laroque D, Santos F, Kashima S, Calado R, Fonseca V, Frias D, Hematology, Transfusion and Cell Therapy (2025), 47:105690

Genomic surveillance of SARS-CoV-2 in the State of Mato Grosso, Midwest Brazil

da Silva S, Vasconcelos K, Almeida J, Guimarães N, Tomé L, Fonseca V, Júnior D, Giovanetti M, de Oliveira E, Alcântara L, Gene Reports (2025), 41:102361

Uncovering DENV, CHIKV, and ZIKV in Urban Wastewater in Brazil Through Genomic and Molecular Screening

de Araujo J, Carvalho A, Adelino T, Iani F, Guimaraes N, Santos S, Leal C, Natividade M, Lima M, Almada M, Bertuce A, Guerra A, Costa M, Saia F, Fonseca V, Giovanetti M, Frutuoso L, Alcantara L, Microorganisms (2025), 13:2164

FUNIN – a fungal glycoside hydrolases 32 enzyme database for developing optimized inulinases

Palmeira L, Quintanilha-Peixoto G, da Costa A, de Carvalho Cardoso E, Uetanabaro A, da Silva Sousa J, Silva D, Guimarães R, Bortolini D, Xavier J, Andrade B, Góes-Neto A, International Journal of Biological Macromolecules (2025), 318:145050

Understanding the emergence expansion and impact of oropouche virus

Santos S, Adelino T, Cella E, Slavov S, Kashima S, Ciccozzi M, Tomé L, Guimarães N, Iani F, Alcantara L, Fonseca V, Giovanetti M, Discover Viruses (2025), 2:

Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples

de Campos G, Clemente L, Lima A, Cella E, Fonseca V, Ximenez J, Nishiyama M, de Carvalho E, Sampaio S, Giovanetti M, Elias M, Slavov S, Virology Journal (2025), 22:

Establishing a dengue genomic monitoring in Cuba: uncovering virus dynamics to enhance local response

Pérez M, Álvarez M, Perez L, Benitez A, Serrano S, Adelino T, Fonseca V, Resik S, Kouri V, Gresh L, Franco L, Rico J, Lourenço J, Alcantara L, Giovanetti M, Guzman M, IJID Regions (2025), 16:100683

Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa

Dor G, Wilkinson E, Martin DP, Moir M, Tshiabuila D, Kekana D, Ntozini B, Joseph R, Iranzadeh A, Nyaga MM, Goedhals D, Maponga T, Maritz J, Laguda-Akingba O, Ramphal Y, MacIntyre C, Chabuka L, Pillay S, Giandhari J, Baxter C, Hsiao NY, Preiser W, Bhiman JN, Davies MA, Venter M, Treurnicht FK, Wolter N, Williamson C, von Gottberg A, Lessells R, Tegally H, de Oliveira T, Nature Communications (2025), 28;16(1):4937. doi: 10.1038/s41467-025-60081-0:

Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023

Chabuka L, Choga W, Mavian C, Moir M, Morgenstern C, Tegaly H, Sharma A, Wilkinson E, Naidoo Y, Inward R, Bhatt S, WilliamWint G, Khan K, Bogoch I, Kraemer M, Lourenço J, Baxter C, Tagliamonte M, Salemi M, Lessells R, Mitambo C, Chitatanga R, Bitilinyu-Bango J, Chiwaula M, Chavula Y, Bukhu M, Manda H, Chitenje M, Malolo I, Mwanyongo A, Mvula B, Nyenje M, de Oliveira T, Kagoli M, Emerging Infectious Diseases (2025), 31(6):. doi: 10.3201/eid3106.240930.:

Importance of outbreak response research in bridging knowledge gaps on emerging infectious diseases

Breiman R, Osoro E, Reithinger R, Wang D, Diamond M, Van Voorhis W, Wasserheit J, Rabinowitz P, Mboup S, Hemingway-Foday J, de Oliveira T, Boon A, Schieffelin J, Sempowski G, Moody M, Vasilakis N, Hanley K, Nasimiyu C, Situma S, Ngere I, Kyobe Bosa H, Nyakarahuka L, Bakamutumaho B, Woodson S, Njenga M, BMJ Global Health (2025), 10(6):e018297. doi: 10.1136/bmjgh-2024-018297.:

Artificial intelligence for modelling infectious disease epidemics

Kraemer M, Tsui J, Chang S, Lytras S, Khurana M, Vanderslott S, Bajaj S, Scheidwasser N, Curran-Sebastian J, Semenova E, Zhang M, Unwin H, Watson O, Mills C, Dasgupta A, Ferretti L, Scarpino S, Koua E, Morgan O, Tegally H, Paquet U, Moutsianas L, Fraser C, Ferguson N, Topol E, Duchêne D, Stadler T, Kingori P, Parker M, Dominici F, Shadbolt N, Suchard M, Ratmann O, Flaxman S, Holmes E, Gomez-Rodriguez M, Schölkopf B, Donnelly C, Pybus O, Cauchemez S, Bhatt S, Nature (2025), :

Spatiotemporal disease suitability prediction for Oropouche virus and the role of vectors across the Americas

Poongavanan J, Dunaiski M, D’or G, Kraemer M, Giovanetti M, Lim A, Brady O, Baxter C, Fonseca V, Alcantara L, de Oliveira T, Tegally H, medRxiv (2025), doi: 10.1101/2025.02.28.25323068.: