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Evolutionary dynamics and molecular adaptation of Rift Valley fever virus across human and non-human outbreaks in Africa.
Omara I, Juma J, Tshiabuila D, Dor G, Wilkinson E, Baxter C, Tegally H, Moir M, Oyola S, de Oliveira T, Neurosurgical focus: Video (2026), 2:V1.

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:btaf665.

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:.

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.

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 (2025), 42:.

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.:.

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.:.

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.:.

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.:.

“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.:.

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.:.

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:.

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:.

Insights into SARS?CoV?2 in Angola during the COVID?19 peak: Molecular epidemiology and genome surveillance.
Francisco N, van Wyk S, Moir M, San J, Sebastião C, Tegally H, Xavier J, Maharaj A, Neto Z, Afonso P, Jandondo D, Paixão J, Miranda J, David K, Inglês L, Pereira A, Paulo A, Carralero R, Freitas H, Mufinda F, Lutucuta S, Ghafari M, Giovanetti M, Giandhari J, Pillay S, Naidoo Y, Singh L, Tshiabuila D, Martin D, Chabuka L, Choga W, Wanjohi D, Mwangi S, Pillay Y, Kebede Y, Shumba E, Ondoa P, Baxter C, Wilkinson E, Tessema S, Katzourakis A, Lessells R, de Oliveira T, Morais J, Influenza and Other Respiratory Viruses (2023), 17:e13198.

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:.

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:.

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:.

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:.

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:.

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:.

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:.