TEAM
Dr Monika Moir
CERI Team

Dr Monika
Moir

Researcher
// Affiliations
Primary
CERI- Stellenbosch University
// Education
PhD Zoology
Stellenbosch University, 2020
Dr Monika Moir is a Researcher in the Data Science group at the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University. She joined CERI in 2021, where her initial work focused on genomic surveillance and the phylogenetic and phylodynamic reconstruction of SARS-CoV-2 transmission dynamics across South Africa and the broader African continent. This work contributed to understanding viral spread and informing public health responses during the COVID-19 pandemic. Her current research builds on these approaches to investigate climate-sensitive infectious diseases, with a particular focus on arthropod-borne viruses such as West Nile virus. She applies molecular epidemiology and data-driven modelling to reconstruct outbreaks and understand the drivers of disease emergence and transmission. Her research programme comprises interconnected projects aimed at strengthening outbreak detection, surveillance systems, and early warning capacity across Africa. Dr Moir is a co-lead and coordinator of CLIMADE Africa, a continent-wide working group within the Climate Amplified Diseases and Epidemics global consortium, which supports coordinated responses to climate-sensitive disease outbreaks. She is also an Associate Member of the Centre for Bioinformatics and Computational Biology and the National Institute for Theoretical and Computational Sciences at Stellenbosch University, contributing to interdisciplinary research at the interface of data science, epidemiology, and public health.
// Research Output

Publications

2026
Dynamics and ecology of a multistage 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, Campelo de Albuquerque C, Frutuoso L, Holmes E, Baxter C, Lessells R, Kraemer M, Lourenço J, Alcantara L, de Oliveira T, Giovanetti M on behalf of CLIMADE

Nature Ecology & Evolution
2026
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
2:V1
2026
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
42:btaf665
2026
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
42
2025
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
6:101176
2025
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
42
2025
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
28;16(1):4937. doi: 10.1038/s41467-025-60081-0
2025
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
31(6):. doi: 10.3201/eid3106.240930.
2025
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
31(3):. doi: 10.3201/eid3103.240996.
2025
Infectious diseases in a warming world: A call for action

Moir M, Baxter C, Tegally H, de Oliveira T

South African Journal of Science
121(3/4):. doi: 10.17159/sajs.2025/20722.
2025
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

doi: 10.1101/2024.12.18.629123.
2024
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

doi: 10.1101/2024.10.29.24316328.
2024
“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
4(12):e0003023. doi: 10.1371/journal.pgph.0003023.
2024
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
10(1):. doi: 10.1093/ve/veae095.
2024
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
14, 793–802 (2024). https://doi.org/10.1038/s41558-024-02078-z
2024
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
13(7):605. doi: 10.3390/pathogens13070605
2023
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
17:e13198
2023
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
https://doi.org/10.1101/2023.08.22.23294324
2023
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
S0092-8674(23)00641-4. doi: 10.1016/j.cell.2023.06.001
2023
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
8(1):1-4. doi: 10.1038/s41564-022-01276-9
2023
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
6;3(3):e0001593. doi: 10.1371/journal.pgph.0001593
2023
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
13;14(3):705. doi: 10.3390/genes14030705
2022
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
eabq5358. doi: 10.1126/science.abq5358
2022
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
https://www.mdpi.com/1999-4915/14/9/1878
2022
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
https://doi.org/10.1038/s41591-022-01911-2
2022
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
doi: 10.1038/s41586-022-04411-y