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Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing.
Published in:
Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-96934-z
By:
- Singh, Lavanya;
- Anyaneji, Ugochukwu J.;
- Ndifon, Wilfred;
- Turok, Neil;
- Mattison, Stacey A.;
- Lessells, Richard;
- Sinayskiy, Ilya;
- San, Emmanuel J.;
- Tegally, Houriiyah;
- Barnett, Shaun;
- Lorimer, Trevor;
- Petruccione, Francesco;
- de Oliveira, Tulio
Publication type:
Article
Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021.
Published in:
Emerging Infectious Diseases, 2022, v. 28, n. 5, p. 1021, doi. 10.3201/eid2805.220121
By:
- Bbosa, Nicholas;
- Ssemwanga, Deogratius;
- Namagembe, Hamidah;
- Kiiza, Ronald;
- Kiconco, Jocelyn;
- Kayiwa, John;
- Lutalo, Tom;
- Lutwama, Julius;
- Ssekagiri, Alfred;
- Ssewanyana, Isaac;
- Nabadda, Susan;
- Kyobe-Bbosa, Henry;
- Giandhari, Jennifer;
- Pillay, Sureshnee;
- Ramphal, Upasana;
- Ramphal, Yajna;
- Naidoo, Yeshnee;
- Tshiabuila, Derek;
- Tegally, Houriiyah;
- San, Emmanuel J.
Publication type:
Article
Author Correction: Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection.
Published in:
2022
By:
- Khan, Khadija;
- Karim, Farina;
- Ganga, Yashica;
- Bernstein, Mallory;
- Jule, Zesuliwe;
- Reedoy, Kajal;
- Cele, Sandile;
- Lustig, Gila;
- Amoako, Daniel;
- Wolter, Nicole;
- Samsunder, Natasha;
- Sivro, Aida;
- San, James Emmanuel;
- Giandhari, Jennifer;
- Tegally, Houriiyah;
- Pillay, Sureshnee;
- Naidoo, Yeshnee;
- Mazibuko, Matilda;
- Miya, Yoliswa;
- Ngcobo, Nokuthula
Publication type:
Correction Notice
Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-32396-9
By:
- Khan, Khadija;
- Karim, Farina;
- Ganga, Yashica;
- Bernstein, Mallory;
- Jule, Zesuliwe;
- Reedoy, Kajal;
- Cele, Sandile;
- Lustig, Gila;
- Amoako, Daniel;
- Wolter, Nicole;
- Samsunder, Natasha;
- Sivro, Aida;
- San, James Emmanuel;
- Giandhari, Jennifer;
- Tegally, Houriiyah;
- Pillay, Sureshnee;
- Naidoo, Yeshnee;
- Mazibuko, Matilda;
- Miya, Yoliswa;
- Ngcobo, Nokuthula
Publication type:
Article
Unlocking the efficiency of genomics laboratories with robotic liquid-handling.
Published in:
BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-07137-1
By:
- Tegally, Houriiyah;
- San, James Emmanuel;
- Giandhari, Jennifer;
- de Oliveira, Tulio
Publication type:
Article
Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.
Published in:
Journal of Medical Virology, 2022, v. 94, n. 8, p. 3676, doi. 10.1002/jmv.27797
By:
- Subramoney, Kathleen;
- Mtileni, Nkhensani;
- Bharuthram, Avani;
- Davis, Ashlyn;
- Kalenga, Beauty;
- Rikhotso, Mikateko;
- Maphahlele, Mpho;
- Giandhari, Jennifer;
- Naidoo, Yeshnee;
- Pillay, Sureshnee;
- Ramphal, Upasana;
- Ramphal, Yajna;
- Tegally, Houriiyah;
- Wilkinson, Eduan;
- Mohale, Thabo;
- Ismail, Arshad;
- Mashishi, Bonolo;
- Mbenenge, Nonhlanhla;
- de Oliveira, Tulio;
- Makatini, Zinhle
Publication type:
Article
Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic.
Published in:
Virus Evolution, 2022, v. 8, n. 1, p. 1, doi. 10.1093/ve/veac024
By:
- Giovanetti, Marta;
- Fonseca, Vagner;
- Wilkinson, Eduan;
- Tegally, Houriiyah;
- San, Emmanuel James;
- Althaus, Christian L;
- Xavier, Joilson;
- Slavov, Svetoslav Nanev;
- Viala, Vincent Louis;
- Lima, Alex Ranieri Jerônimo;
- Ribeiro, Gabriela;
- Souza-Neto, Jayme A;
- Fukumasu, Heidge;
- Coutinho, Luiz Lehmann;
- Cunha, Rivaldo Venancio da;
- Freitas, Carla;
- Melo, Carlos F Campelo de A e;
- Araújo, Wildo Navegantes de;
- Said, Rodrigo Fabiano Do Carmo;
- Almiron, Maria
Publication type:
Article
Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.
Published in:
Virus Evolution, 2021, v. 7, n. 1, p. 1, doi. 10.1093/ve/veab041
By:
- San, James E;
- Ngcapu, Sinaye;
- Kanzi, Aquillah M;
- Tegally, Houriiyah;
- Fonseca, Vagner;
- Giandhari, Jennifer;
- Wilkinson, Eduan;
- Nelson, Chase W;
- Smidt, Werner;
- Kiran, Anmol M;
- Chimukangara, Benjamin;
- Pillay, Sureshnee;
- Singh, Lavanya;
- Fish, Maryam;
- Gazy, Inbal;
- Martin, Darren P;
- Khanyile, Khulekani;
- Lessells, Richard;
- Oliveira, Tulio de
Publication type:
Article
Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29579-9
By:
- Scheepers, Cathrine;
- Everatt, Josie;
- Amoako, Daniel G.;
- Tegally, Houriiyah;
- Wibmer, Constantinos Kurt;
- Mnguni, Anele;
- Ismail, Arshad;
- Mahlangu, Boitshoko;
- Lambson, Bronwen E.;
- Martin, Darren P.;
- Wilkinson, Eduan;
- San, James Emmanuel;
- Giandhari, Jennifer;
- Manamela, Nelia;
- Ntuli, Noxolo;
- Kgagudi, Prudence;
- Cele, Sandile;
- Richardson, Simone I.;
- Pillay, Sureshnee;
- Mohale, Thabo
Publication type:
Article
SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.
Published in:
PLoS ONE, 2023, v. 17, n. 5, p. 1, doi. 10.1371/journal.pone.0286373
By:
- Subramoney, Kathleen;
- Mtileni, Nkhensani;
- Davis, Ashlyn;
- Giandhari, Jennifer;
- Tegally, Houriiyah;
- Wilkinson, Eduan;
- Naidoo, Yeshnee;
- Ramphal, Yajna;
- Pillay, Sureshnee;
- Ramphal, Upasana;
- Simane, Andiswa;
- Reddy, Bhaveshan;
- Mashishi, Bonolo;
- Mbenenge, Nonhlanhla;
- de Oliveira, Tulio;
- Fielding, Burtram C.;
- Treurnicht, Florette K.
Publication type:
Article
Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing.
Published in:
PLoS ONE, 2023, v. 17, n. 4, p. 1, doi. 10.1371/journal.pone.0283219
By:
- Pillay, Sureshnee;
- San, James Emmanuel;
- Tshiabuila, Derek;
- Naidoo, Yeshnee;
- Pillay, Yusasha;
- Maharaj, Akhil;
- Anyaneji, Ugochukwu J.;
- Wilkinson, Eduan;
- Tegally, Houriiyah;
- Lessells, Richard J.;
- Baxter, Cheryl;
- de Oliveira, Tulio;
- Giandhari, Jennifer
Publication type:
Article
Impacts of climate change-related human migration on infectious diseases.
Published in:
Nature Climate Change, 2024, v. 14, n. 8, p. 793, doi. 10.1038/s41558-024-02078-z
By:
- Tsui, Joseph L.-H.;
- Pena, Rosario Evans;
- Moir, Monika;
- Inward, Rhys P. D.;
- Wilkinson, Eduan;
- San, James Emmanuel;
- Poongavanan, Jenicca;
- Bajaj, Sumali;
- Gutierrez, Bernardo;
- Dasgupta, Abhishek;
- de Oliveira, Tulio;
- Kraemer, Moritz U. G.;
- Tegally, Houriiyah;
- Sambaturu, Prathyush
Publication type:
Article
Discovering novel driver mutations from pan-cancer analysis of mutational and gene expression profiles.
Published in:
PLoS ONE, 2020, v. 15, n. 11, p. 1, doi. 10.1371/journal.pone.0242780
By:
- Tegally, Houriiyah;
- Kensler, Kevin H.;
- Mungloo-Dilmohamud, Zahra;
- Ghoorah, Anisah W.;
- Rebbeck, Timothy R.;
- Baichoo, Shakuntala
Publication type:
Article
A new lineage nomenclature to aid genomic surveillance of dengue virus.
Published in:
PLoS Biology, 2024, v. 22, n. 9, p. 1, doi. 10.1371/journal.pbio.3002834
By:
- Hill, Verity;
- Cleemput, Sara;
- Pereira, James Siqueira;
- Gifford, Robert J.;
- Fonseca, Vagner;
- Tegally, Houriiyah;
- Brito, Anderson F.;
- Ribeiro, Gabriela;
- de Souza, Vinicius Carius;
- Brcko, Isabela Carvalho;
- Ribeiro, Igor Santana;
- De Lima, Iago Trezena Tavares;
- Slavov, Svetoslav Nanev;
- Sampaio, Sandra Coccuzzo;
- Elias, Maria Carolina;
- Tran, Vi Thuy;
- Kien, Duong Thi Hue;
- Huynh, Tuyen;
- Yacoub, Sophie;
- Dieng, Idrissa
Publication type:
Article
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.
Published in:
Molecular Biology & Evolution, 2022, v. 39, n. 4, p. 1, doi. 10.1093/molbev/msac061
By:
- Martin, Darren P.;
- Lytras, Spyros;
- Lucaci, Alexander G.;
- Maier, Wolfgang;
- Grüning, Björn;
- Shank, Stephen D.;
- Weaver, Steven;
- MacLean, Oscar A.;
- Orton, Richard J.;
- Lemey, Philippe;
- Boni, Maciej F.;
- Tegally, Houriiyah;
- Harkins, Gordon W.;
- Scheepers, Cathrine;
- Bhiman, Jinal N.;
- Everatt, Josie;
- Amoako, Daniel G.;
- San, James Emmanuel;
- Giandhari, Jennifer;
- Sigal, Alex
Publication type:
Article
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
Published in:
PLoS Biology, 2021, v. 19, n. 5, p. 1, doi. 10.1371/journal.pbio.3001236
By:
- Vogels, Chantal B. F.;
- Breban, Mallery I.;
- Ott, Isabel M.;
- Alpert, Tara;
- Petrone, Mary E.;
- Watkins, Anne E.;
- Kalinich, Chaney C.;
- Earnest, Rebecca;
- Rothman, Jessica E.;
- Goes de Jesus, Jaqueline;
- Morales Claro, Ingra;
- Magalhães Ferreira, Giulia;
- Crispim, Myuki A. E.;
- Singh, Lavanya;
- Tegally, Houriiyah;
- Anyaneji, Ugochukwu J.;
- Hodcroft, Emma B.;
- Mason, Christopher E.;
- Khullar, Gaurav;
- Metti, Jessica
Publication type:
Article
Understanding the Transmission Dynamics of the Chikungunya Virus in Africa.
Published in:
Pathogens, 2024, v. 13, n. 7, p. 605, doi. 10.3390/pathogens13070605
By:
- Ramphal, Yajna;
- Tegally, Houriiyah;
- San, James Emmanuel;
- Reichmuth, Martina Larissa;
- Hofstra, Marije;
- Wilkinson, Eduan;
- Baxter, Cheryl;
- de Oliveira, Tulio;
- Moir, Monika
Publication type:
Article
Correction: Subramoney et al. Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages. Viruses 2023, 15 , 1194.
Published in:
2023
By:
- Subramoney, Kathleen;
- Mtileni, Nkhensani;
- Giandhari, Jennifer;
- Naidoo, Yeshnee;
- Ramphal, Yajna;
- Pillay, Sureshnee;
- Ramphal, Upasana;
- Maharaj, Akhil;
- Tshiabuila, Derek;
- Tegally, Houriiyah;
- Wilkinson, Eduan;
- Oliveira, Tulio de;
- Fielding, Burtram C.;
- Treurnicht, Florette K.
Publication type:
Correction Notice
Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages.
Published in:
Viruses (1999-4915), 2023, v. 15, n. 5, p. 1194, doi. 10.3390/v15051194
By:
- Subramoney, Kathleen;
- Mtileni, Nkhensani;
- Giandhari, Jennifer;
- Naidoo, Yeshnee;
- Ramphal, Yajna;
- Pillay, Sureshnee;
- Ramphal, Upasana;
- Maharaj, Akhil;
- Tshiabuila, Derek;
- Tegally, Houriiyah;
- Wilkinson, Eduan;
- de Oliveira, Tulio;
- Fielding, Burtram C.;
- Treurnicht, Florette K.
Publication type:
Article
SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic.
Published in:
Viruses (1999-4915), 2022, v. 14, n. 9, p. 1878, doi. 10.3390/v14091878
By:
- Roshdy, Wael H.;
- Khalifa, Mohamed K.;
- San, James Emmanuel;
- Tegally, Houriiyah;
- Wilkinson, Eduan;
- Showky, Shymaa;
- Martin, Darren Patrick;
- Moir, Monika;
- Naguib, Amel;
- Elguindy, Nancy;
- Gomaa, Mokhtar R.;
- Fahim, Manal;
- Abu Elsood, Hanaa;
- Mohsen, Amira;
- Galal, Ramy;
- Hassany, Mohamed;
- Lessells, Richard J.;
- Al-Karmalawy, Ahmed A.;
- EL-Shesheny, Rabeh;
- Kandeil, Ahmed M.
Publication type:
Article
Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
Published in:
Viruses (1999-4915), 2021, v. 13, n. 3, p. 526, doi. 10.3390/v13030526
By:
- Engelbrecht, Susan;
- Delaney, Kayla;
- Kleinhans, Bronwyn;
- Wilkinson, Eduan;
- Tegally, Houriiyah;
- Stander, Tania;
- van Zyl, Gert;
- Preiser, Wolfgang;
- de Oliveira, Tulio;
- de Arruda, Luciana Barros;
- Campos, Fabrício S.;
- da Fonseca, Flavio Guimaraes
Publication type:
Article
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.
Published in:
PLoS Biology, 2022, v. 20, n. 8, p. 1, doi. 10.1371/journal.pbio.3001769
By:
- Happi, Christian;
- Adetifa, Ifedayo;
- Mbala, Placide;
- Njouom, Richard;
- Nakoune, Emmanuel;
- Happi, Anise;
- Ndodo, Nnaemeka;
- Ayansola, Oyeronke;
- Mboowa, Gerald;
- Bedford, Trevor;
- Neher, Richard A.;
- Roemer, Cornelius;
- Hodcroft, Emma;
- Tegally, Houriiyah;
- O'Toole, Áine;
- Rambaut, Andrew;
- Pybus, Oliver;
- Kraemer, Moritz U. G.;
- Wilkinson, Eduan;
- Isidro, Joana
Publication type:
Article
Reply to Molldrem.
Published in:
2023
By:
- Maponga, Tongai G;
- Jeffries, Montenique;
- Tegally, Houriiyah;
- Sutherland, Andrew;
- Wilkinson, Eduan;
- Lessells, Richard J;
- Msomi, Nokukhanya;
- Zyl, Gert van;
- Oliveira, Tulio de;
- Preiser, Wolfgang
Publication type:
Letter to the Editor
Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection With accumulation of mutations in a patient with poorly controlled Human Immunodeficiency Virus infection.
Published in:
Clinical Infectious Diseases, 2023, v. 76, n. 3, p. e522, doi. 10.1093/cid/ciac548
By:
- Maponga, Tongai G;
- Jeffries, Montenique;
- Tegally, Houriiyah;
- Sutherland, Andrew;
- Wilkinson, Eduan;
- Lessells, Richard J;
- Msomi, Nokukhanya;
- Zyl, Gert van;
- Oliveira, Tulio de;
- Preiser, Wolfgang
Publication type:
Article
Insights into SARS‐CoV‐2 in Angola during the COVID‐19 peak: Molecular epidemiology and genome surveillance.
Published in:
Influenza & Other Respiratory Viruses, 2023, v. 17, n. 9, p. 1, doi. 10.1111/irv.13198
By:
- Francisco, Ngiambudulu M.;
- van Wyk, Stephanie;
- Moir, Monika;
- San, James Emmanuel;
- Sebastião, Cruz S.;
- Tegally, Houriiyah;
- Xavier, Joicymara;
- Maharaj, Akhil;
- Neto, Zoraima;
- Afonso, Pedro;
- Jandondo, Domingos;
- Paixão, Joana;
- Miranda, Julio;
- David, Kumbelembe;
- Inglês, Luzia;
- Pereira, Amilton;
- Paulo, Agostinho;
- Carralero, Raisa Rivas;
- Freitas, Helga Reis;
- Mufinda, Franco
Publication type:
Article
SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021.
Published in:
Frontiers in Virology, 2022, p. 1, doi. 10.3389/fviro.2022.935131
By:
- Mwangi, Peter;
- Okendo, Javan;
- Mogotsi, Milton;
- Ogunbayo, Ayodeji;
- Adelabu, Olusesan;
- Sondlane, Hlengiwe;
- Maotoana, Makgotso;
- Mahomed, Lutfiyya;
- Morobadi, Molefi Daniel;
- Vawda, Sabeehah;
- von Gottberg, Anne;
- Bhiman, Jinal;
- Tegally, Houriiyah;
- Wilkinson, Eduan;
- Giandhari, Jennifer;
- Pillay, Sureshnee;
- Naidoo, Yeshnee;
- Ramphal, Upasana;
- de Oliveira, Tulio;
- Bester, Armand
Publication type:
Article
Escape from recognition of SARS-CoV-2 variant spike epitopes but overall preservation of T cell immunity.
Published in:
Science Translational Medicine, 2022, v. 14, n. 631, p. 1, doi. 10.1126/scitranslmed.abj6824
By:
- Riou, Catherine;
- Keeton, Roanne;
- Moyo-Gwete, Thandeka;
- Hermanus, Tandile;
- Kgagudi, Prudence;
- Baguma, Richard;
- Valley-Omar, Ziyaad;
- Smith, Mikhail;
- Tegally, Houriiyah;
- Doolabh, Deelan;
- Iranzadeh, Arash;
- Tyers, Lynn;
- Mutavhatsindi, Hygon;
- Tincho, Marius B.;
- Benede, Ntombi;
- Marais, Gert;
- Chinhoyi, Lionel R.;
- Mennen, Mathilda;
- Skelem, Sango;
- du Bruyn, Elsa
Publication type:
Article
SARS-CoV-2 Genomic Epidemiology Dashboards: A Review of Functionality and Technological Frameworks for the Public Health Response.
Published in:
Genes, 2024, v. 15, n. 7, p. 876, doi. 10.3390/genes15070876
By:
- Sitharam, Nikita;
- Tegally, Houriiyah;
- Silva, Danilo de Castro;
- Baxter, Cheryl;
- de Oliveira, Tulio;
- Xavier, Joicymara S.
Publication type:
Article
Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022.
Published in:
Genes, 2023, v. 14, n. 3, p. 705, doi. 10.3390/genes14030705
By:
- Sisay, Abay;
- Tshiabuila, Derek;
- van Wyk, Stephanie;
- Tesfaye, Abraham;
- Mboowa, Gerald;
- Oyola, Samuel O.;
- Tesema, Sofonias Kifle;
- Baxter, Cheryl;
- Martin, Darren;
- Lessells, Richard;
- Tegally, Houriiyah;
- Moir, Monika;
- Giandhari, Jennifer;
- Pillay, Sureshnee;
- Singh, Lavanya;
- Ramphal, Yajna;
- Maharaj, Arisha;
- Pillay, Yusasha;
- Maharaj, Akhil;
- Naidoo, Yeshnee
Publication type:
Article
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic.
Published in:
Genes, 2020, v. 11, n. 8, p. 949, doi. 10.3390/genes11080949
By:
- Pillay, Sureshnee;
- Giandhari, Jennifer;
- Tegally, Houriiyah;
- Wilkinson, Eduan;
- Chimukangara, Benjamin;
- Lessells, Richard;
- Moosa, Yunus;
- Mattison, Stacey;
- Gazy, Inbal;
- Fish, Maryam;
- Singh, Lavanya;
- Khanyile, Khulekani Sedwell;
- San, James Emmanuel;
- Fonseca, Vagner;
- Giovanetti, Marta;
- Alcantara, Luiz Carlos;
- de Oliveira, Tulio
Publication type:
Article

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