PUBLICATIONS SPOTLIGHT

PUBLICATIONS

Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Lugano D, Mwangi K, Mware B, Kibet G, Osiany S, Kiritu E, Dobi P, Muli C, Njeru R, de Oliveira T, Njenga M, Routh A, Oyola S, medRxiv (2025), doi: 10.1101/2025.03.03.25323296.:

Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics

Adeniji A, Chukwuneme C, Conceição E, Ayangbenro A, Wilkinson E, Maasdorp E, de Oliveira T, Babalola O, Microbiology Spectrum (2025), doi: 10.1128/spectrum.01466-24.:

Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022–2023

Abera A, Tegally H, Tasew G, Wilkinson E, Ali A, Regasa F, Bitew M, Belachew M, Chabuka L, Mwanyika G, Tshiabuila D, Giandhari J, Pillay S, Poogavanan J, Moir M, Kraemer M, Khan K, Huber C, Tollera G, de Wit T, Baxter C, Lessells R, Wolday D, Beyene D, de Oliveira T,, Emerging Infectious Diseases (2025), 31(3):. doi: 10.3201/eid3103.240996.:

Infectious diseases in a warming world: A call for action

Moir M, Baxter C, Tegally H, de Oliveira T, South African Journal of Science (2025), 121(3/4):. doi: 10.17159/sajs.2025/20722.:

Travel-associated international spread of Oropouche virus beyond the Amazon

de Melo Iani F, Pereira F, de Oliveira E, Rodrigues J, Machado M, Fonseca V, Adelino T, Guimarães N, Tomé L, Gómez M, Nardy V, Ribeiro A, Rosewell A, Ferreira, Silva de Mello A, Fernandes B, de Albuquerque C, dos Santos Pereira D, Pimentel E, Lima F, Silva F, de Carvalho Pereira G, Tegally H, Almeida J, Moreno K, Vasconcelos K, Santos L, Silva L, Frutuoso L, Lamounier L, Costa M, de Oliveira M, dos Anjos M, Ciccozzi M, Lima M, Pereira M, Rocha M, de Souza da Silva P, Rabinowitz P, de Almeida P, Lessells R, Gazzinelli R, da Cunha R, Gonçalves S, dos Santos S, de Alcântara Belettini S, Pedroso S, Araújo S, da Silva S, Croda J, Maciel E, Van Voorhis W, Martin D, Holmes E, de Oliveira T, Lourenço J, Alcantara L, Giovanetti M, Journal of Travel Medicine (2025), doi: 10.1093/jtm/taaf018.:

Craft: A Machine Learning Approach to Dengue Subtyping

van Zyl D, Dunaiski M, Tegally H, Baxter C, de Oliveira T, Xavier J, (2025), doi: 10.1101/2025.02.10.637410.:

Identifying genomic surveillance gaps in Africa for the global public health response to West Nile Virus

Moir M, Sitharam N, Hofstra M, Dor G, Mwanyika G, Ramphal Y, Reichmuth M, James S, Gifford R, Wilkinson E, Tshiabuila D, Preiser W, Konou A, Bitew M, Onoja B, Paganotti G, Abera A, Maror J, Kayiwa J, Abuelmaali S, Lusamaki E, , Venter M, Burt F, Baxter C, Lessells R, de Oliveira T, Tegally H, (2025), doi: 10.1101/2024.12.18.629123.:

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.:

Staphylococcus aureus associated with surgical site infections in Western Kenya reveals genomic hotspots for pathogen evolution

Mogoi N, Sifuna A, Okoth P, Reva O, Malaba R, Negesa R, Nyongesa K, Osoro K, Welch M, Access Microbiology (2024), 6:000734.v4

Innovative infrastructure to access Brazilian fungal diversity using deep learning

Chaves T, Santos Xavier J, Gonçalves dos Santos A, Martins-Cunha K, Karstedt F, Kossmann T, Sourell S, Leopoldo E, Fortuna Ferreira M, Farias R, Titton M, Alves-Silva G, Bittencourt F, Bortolini D, Gumboski E, von Wangenheim A, Góes-Neto A, Drechsler-Santos E, PeerJ (2024), 12:e17686

Doing just sustainability transitions: Facing thelegitimation crisis in the Anthropocene today

van Breda J, Treffry-Goatley A, South African Journal of Science (2024), 120:19223

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 - Preprint

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.:

North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic

Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M, BMC Infectious Diseases (2024), 24(1):. doi: 10.1186/s12879-024-09658-6.:

Genomics-based timely detection of dengue virus type I genotypes I and V in Uruguay

Morel N, Giovanetti M, Fonseca V, Burgueño A, Lima M, Castro E, Guimarães N, Iani F, Bormida V, Cortinas M, Ramas V, Coppola L, Bento A, Rosewell A, Franco L, Mendez Rico J, Lourenço J, Junior Alcantara L, Chiparelli H, Heliyon (2024), 10(22):e39246. doi: 10.1016/j.heliyon.2024.e39246.:

Unraveling the Complexity of Chikungunya Virus Infection Immunological and Genetic Insights in Acute and Chronic Patients

Fritsch H, Giovanetti M, Clemente L, da Rocha Fernandes G, Fonseca V, de Lima M, Falcão M, de Jesus N, de Cerqueira E, Venâncio da Cunha R, de Oliveira Francisco M, de Siqueira I, de Oliveira C, Xavier J, Ferreira J, Queiroz F, Smith E, Tisoncik-Go J, Van Voorhis W, Rabinowitz P, Wasserheit J, Gale M, de Filippis A, Alcantara L, Genes (2024), 15(11):1365. doi: 10.3390/genes15111365.:

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.:

Fatal Oropouche Virus Infections in Nonendemic Region, Brazil, 2024

Bandeira A, Pereira F, Leal A, Santos S, Barbosa A, Souza M, de Souza D, Guimaraes N, Fonseca V, Giovanetti M, Alcantara L, Lessa A, Saavedra R, Tomé L, Iani F, Barros R, Purificação S, de Jesus J, Fonseca R, Araújo M, Emerging Infectious Diseases (2024), 30(11):. doi: 10.3201/eid3011.241132.:

Detection of Multiple Human Viruses, including Mpox, Using a Wastewater Surveillance Approach in Brazil

Calabria de Araujo J, Carvalho A, Leal C, Natividade M, Borin M, Guerra A, Carobin N, Sabino A, Almada M, Costa M, Saia F, Frutuoso L, Iani F, Adelino T, Fonseca V, Giovanetti M, Alcantara L, Pathogens (2024), 13(7):589. doi: 10.3390/pathogens13070589.:

Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022

Ferreira da Silva L, Alcantara L, Fonseca V, Frias D, Umaki Zardin M, de Castro Lichs G, Esposito A, Xavier J, Fritsch H, Lima M, de Oliveira C, Castilho de Arruda L, Maziero L, Rodrigues Barretos E, Tsuha Oshiro P, Gimenes Mendes Menezes E, de Freitas Cardoso L, Ferreira Lemos E, Lourenço J, de Albuquerque C, do Carmo Said R, Rosewell A, Ferraz Demarchi L, Croda J, Giovanetti M, Maymone Gonçalves C, Viruses (2024), 16(7):1143. doi: 10.3390/v16071143.:

Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach

Moreno K, de Andrade V, de Melo Iani F, Fonseca V, Lima M, de Castro Barbosa E, Tomé L, Guimarães N, Fritsch H, Adelino T, Oliveira Fereguetti T, Aspahan M, Gamarano Barros T, Alcantara L, Giovanetti M, Genes (2024), 15(7):922. doi: 10.3390/genes15070922.:

Tracing the evolution of the chikungunya virus in Argentina, 2016-2023: independent introductions and prominence of Latin American lineages

Fabbri C, Giovanetti M, Luppo V, Fonseca V, Garcia J, Barulli C, Feroci M, Perrone S, Casoni D, Giamperetti S, Alvarez Lopez M, Foussal M, Figueredo M, Salvatierra K, Lejona S, Ruiz Diaz N, Castro G, Bravo G, Jackel N, Sen C, Poklepovich Caride T, Franco L, Giovachini C, Mendez Rico J, Alcantara L, Morales M, Emerging Microbes & Infections (2024), 13(1):. doi: 10.1080/22221751.2024.2362941.:

Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spread

Schuab G, Tosta S, Moreno K, Fonseca V, Santos L, Slavov S, Kashima S, Ciccozzi M, Lourenço J, Cella E, de Oliveira C, Cavalcanti A, Junior Alcantara L, de Bruycker-Nogueira F, Bispo de Filippis A, Giovanetti M, The Lancet Regional Health - Americas (2024), 35():100786. doi: 10.1016/j.lana.2024.100786.:

Detection of encephalitis-causing viruses reveals predominance of chikungunya virus in the state of Bahia, Brazil

Sampaio M, do Rosário M, Martins L, Trindade L, Francisco M, Costa B, Vasconcelos G, Lima I, Macêdo Y, Carvalho F, de Santana M, Khouri R, Fritsch H, Xavier J, Fonseca V, Giovanetti M, de Mello A, Pereira F, Campos G, de Jesus P, Farias D, de Souza M, Galvão A, Costa F, Bessa M, Chagas J, Silvany C, Teles J, de Lima M, Farias T, Gräf T, de Siqueira I, International Journal of Infectious Diseases (2024), 145():107090. doi: 10.1016/j.ijid.2024.107090.:

Exploring the Chikungunya virus landscape in a dengue-endemic Brazilian area

de La Roque D, Santos E, Policastro L, da Costa P, Evaristo M, Yamamoto A, Giomo D, Torres P, Gentil D, Minto E, Slavov S, Fonseca V, dos Santos Barros C, Martins A, Calado R, Passos L, Elias M, Sampaio S, Giovanetti M, Covas D, Alcântara L, Kashima S, Journal of Infection and Public Health (2024), 17(7):102442. doi: 10.1016/j.jiph.2024.04.026.: