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.:.
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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.:.
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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:.
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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:.
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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:.
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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:.
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A new lineage nomenclature to aid genomic surveillance of dengue virus.
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:.
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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:.
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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
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:.
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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:.
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An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal .
Padane A, Tegally H, Ramphal Y, Ndiaye S, Sarr M, Diop M, Diedhiou CK, Mboup A, Diouf N, Souare A, Diagne ND, Aza-Gnandji M, Dabo NA, Dia YA, Diaw NA, Leye N, Diaw PA, Ambroise A, Cisse B, Diallo AS, Diop O, Diallo AA, Ndoye S, Sanko TJ, Baxter C, Wilkinson E, James SE, Tshiabuila D, Naidoo Y, Pillay S, Lessells R, Cisse K, Leye A, Mbaye A, Kania D, Traore I, Kagone ST, Tinto B, Ouedraogo A, Lourenco J, Giovanetti M, Giandhari J, de Oliveira T, Mboup S, medrxiv (2023), MEDRXIV-2023-298527v1:.
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Will climate change amplify epidemics and give rise to pandemics?.
de Oliveira T, Tegally H, Science (2023), 381,6660, DOI: 10.1126/science.adk4500:.
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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:.
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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:.
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Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1.
Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, COVID-19 Genomics UK (COG-UK) consortium¶, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG, Science (2023), 381(6655):336-343. doi: 10.1126/science.adg6605.:.
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Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages.
Subramoney K, Mtileni N, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Maharaj A, Tshiabuila D, Tegally H, Wilkinson E, de Oliveira T, Fielding BC, Treurnicht FK, Viruses (2023), 15(5):1194. doi: 10.3390/v15051194:.
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SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.
Subramoney K, Mtileni N, Davis A, Giandhari J, Tegally H, Wilkinson E, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Simane A, Reddy B, Mashishi B, Mbenenge N, de Oliveira T, Fielding BC, Treurnicht FK, PLoS One (2023), 18(5):e0286373. doi: 10.1371/journal.pone.0286373:.
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Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.
Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, de Oliveira T, Giandhari J, PLoS ONE (2023), 18(4):e0283219. doi: 10.1371/journal.pone.0283219:.
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Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay.
Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Junior Alcantara LC, medRXiV (2023), doi:10.1101/2023.04.16.23288635:.
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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:.
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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:.
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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:.
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Global disparities in SARS-CoV-2 genomic surveillance. .
Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C; Bulgarian SARS-CoV-2 sequencing group; Communicable Diseases Genomics Network (Australia and New Zealand); COVID-19 Impact Project; Danish Covid-19 Genome Consortium; Fiocruz COVID-19 Genomic Surveillance Network; GISAID core curation team; Network for Genomic Surveillance in South Africa (NGS-SA); Swiss SARS-CoV-2 Sequencing Consortium, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR., Nature Communications (2022), 16;13(1):7003. doi: 10.1038/s41467-022-33713-y.:.
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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:.
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Impact of intra-host immune adaptations on the evolution of SARS-CoV-2 S protein among individuals with SARS-CoV-2 infections in South Africa, 2020 to 2022..
Subramoney K, Mtileni N, Davis A, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Tegally H, Wilkinson E, Simane A, Reddy B, Mashishi B, Mbenenge N, de Oliveira T, Fielding B, Treurnicht F, Authorea Preprints (2022), DOI: 10.22541/au.166305249.90395426/v1 :.
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Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.
Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O'Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Freitas L, Resende PC, Lee RTC, Maurer-Stroh S, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T, PLoS Biology (2022), doi: 10.1371/journal.pbio.3001769.:.
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Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, Iani FCM, de Carvalho Pereira G, Vazquez C, Sanabria GME, Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Paola Oliveira de Lima L, Martins AJ, Renata Dos Santos Barros C, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, Reboredo de Oliveira da Silva L, Gómez MKA, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Figueredo GPM, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Giacomini MP, Marques NQ, Riediger IN, Raboni S, Mattoso G, Cataneo AD, Zanluca C, Duarte Dos Santos CN, Assato PA, Allan da Silva da Costa F, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said RF, Campelo de A E Melo CF, Almiron M, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, Junior de Alcantara LC, Covas DT, Nature Microbiology (2022), doi: 10.1038/s41564-022-01191-z:.
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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:.
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Building genomic sequencing capacity in Africa to respond to the SARS-CoV-2 pandemic.
de Oliveira T, Wilkinson E, Baxter C, Tegally H, Giandhari J, Naidoo Y, Pillay S, Science (2022), https://www.science.org/content/resource/pandemic-preparedness-changing-world-fostering-global-collaboration, 2022:.
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Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection..
Khan K, Karim F, Ganga Y, Bernstein M, Jule Z, Reedoy K, Cele S, Lustig G, Amoako D, Wolter N, Samsunder N, Sivro A, San JE, Giandhari J, Tegally H, Pillay S, Naidoo Y, Mazibuko M, Miya Y, Ngcobo N, Manickchund N, Magula N, Karim QA, von Gottberg A, Abdool Karim SS, Hanekom W, Gosnell BI; COMMIT-KZN Team, Lessells RJ, de Oliveira T, Moosa MS, Sigal A, Nature Communications (2022), doi: 10.1038/s41467-022-32396-9:.
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Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.
Subramoney K, Mtileni N, Bharuthram A, Davis A, Kalenga B, Rikhotso M, Maphahlele M, Giandhari J, Naidoo Y, Pillay S, Ramphal U, Ramphal Y, Tegally H, Wilkinson E, Mohale T, Ismail A, Mashishi B, Mbenenge N, de Oliveira T, Makatini Z, Fielding BC, Treurnicht FK, J Med Virol. (2022), 4(8):3676-3684. doi: 10.1002/jmv.27797:.
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Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.
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Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.
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Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic.
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Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function.
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Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing.
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Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.
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Persistent SARS-CoV-2 infection with accumulation of mutations in a patient with poorly controlled HIV infection.
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Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.
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Omicron infection of vaccinated individuals enhances neutralizing immunity against the Delta variant. .
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T cell responses to SARS-CoV-2 spike cross-recognize Omicron.
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Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests.
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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
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HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens..
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Escape from recognition of SARS-CoV-2 Beta variant spike epitopes but overall preservation of T cell immunity.
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Track Omicron’s spread with molecular data.
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SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer
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Rapid replacement of the Beta variant by the Delta variant in South Africa.
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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
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Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL.
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Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing.
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Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
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Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.
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Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2.
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Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection.
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Cross-Reactive Neutralizing Antibody Responses Elicited by SARS-CoV-2 501Y.V2 (B.1.351).
Moyo-Gwete T, Madzivhandila M, Makhado Z, Ayres F, Mhlanga D, Oosthuysen B, Lambson EB, Kgagudi P, Tegally H, Iranzadeh A, Doolabh D, Tyers L, Chinhoyi RL, Mennen M, Skelm S, Wibmer K C, Bhiman N J, Ueckermann V, Rossouw T, Boswell M, de Oliveira T, Williamson T, Burgers W, Ntusi N, Morris L, Moore P, NEJM (2021), DOI: 10.1056/NEJMc2104192:.
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Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T, Viruses (2021), 22;13(3):526. doi: 10.3390/v13030526:.
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Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma..
Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Bernstein M, Balazs AB, Gosnell BI, Hanekom W, Moosa MS; NGS-SA; COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A., Nature (2021), DOI: 10.1038/s41586-021-03471-w:.
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A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa.
de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R, medRxiv (2021), :.
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Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa.
Madhi SA, Baillie VL, Cutland CL, Voysey M, KoenAL, Fairlie L, Padayachee SD, Dheda K, Barnabas SL, Bhorat QE, Briner C, Kwatra G, Ahmed K, Aley P, Bhikha S, Bhiman JN, Bhorat AE, du plessis J, Esmail A, Groenewald M, Horne E, Hwa S-H, Jose A, Lambe T, Laubscher M, Malahleha M, Masenya M, Masilela M, McKenzie S, Molapo K, Moultrie A, Oelofse S, Pate Fl, Pillay S, Rhead S, Rodel H, Rossouw L, Taoushanis C, Tegally H, Thombrayil A, van Eck S, Wibmer C, Durham NM, Kelly EJ, Villafana T, Gilbert S, Pollard AJ, de Oliveira T, Moore PL, Sigal A, Izu A, NGS-SA, Wits VIDA COVID vaccine trial group
, NEJM (2021), https://doi.org/10.1056/NEJMoa2102214:.
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Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenco J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T, Nature (2021), https://doi.org/10.1038/s41586-021-03402-9:.
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Sixteen novel lineages of SARS-CoV-2 in South Africa.
Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01255-3:.
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Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma.
Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Balazs AB, Gosnell BI, Hanekom W, Moosa MYS, NGS-SA, COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A, medRxiv (2021), 250224v1-Sigal:.
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Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.12.21.20248640:.
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High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity.
San EJ, Ngcapu S, Kanzi A, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile KS, Lessells R, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.11.15.20231993:.
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Unlocking the efficiency of genomics laboratories with robotic liquid-handling.
Tegally H, San JE, Giandhari J, de Oliveira T, BMC Genomics (2020), 729:https://doi.org/10.1186/s12864-020-07137-1.
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A genomics network established to respond rapidly to public health threats in South Africa.
Msomi N, Mlisana K, Willianson C, Bhiman JN, Goedhals D, Engelbrecht S, Van Zyl G, Preiser W, Hardie D, Hsiao M, Mulder N, Martin D, Christoffels A, York D, Giandhari J, Wilkinson E, Pillay S, Tegally H, James SE, Kanzi A, Lessells RJ, de Oliveira T, Lancet Microbe (2020), https://doi.org/10.1016/S2666-5247(20)30116-6:.
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Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic.
Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, de Oliveira T, Genes (2020), doi: https://doi.org/10.3390/genes11080949:11(8), 949.
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Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, Petruccione F, de Oliveira T, IJID (2020), doi: https://doi.org/10.1016/j.ijid.2020.11.128:.
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