Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, Raquel, Moyo, Sikhulile, Amoako, Daniel G., Tegally, Houriiyah, Scheepers, Cathrine, Althaus, Christian L., Anyaneji, Ugochukwu J., Bester, Phillip A., Boni, Maciej F., Chand, Mohammed, Choga, Wonderful T., Colquhoun, Rachel, Davids, Michaela, Deforche, Koen, Doolabh, Deelan, du Plessis, Louis, Engelbrecht, Susan, Everatt, Josie, Giandhari, Jennifer, Giovanetti, Marta, Hardie, Diana, Hill, Verity, Hsiao, Nei-Yuan, Iranzadeh, Arash, Ismail, Arshad, Joseph, Charity, Joseph, Rageema, Koopile, Legodile, Kosakovsky Pond, Sergei L., Kraemer, Moritz U. G., Kuate-Lere, Lesego, Laguda-Akingba, Oluwakemi, Lesetedi-Mafoko, Onalethatha, Lessells, Richard J., Lockman, Shahin, Lucaci, Alexander G., Maharaj, Arisha, Mahlangu, Boitshoko, Maponga, Tongai, Mahlakwane, Kamela, Makatini, Zinhle, Marais, Gert, Maruapula, Dorcas, Masupu, Kereng, Matshaba, Mogomotsi, Mayaphi, Simnikiwe, Mbhele, Nokuzola, Mbulawa, Mpaphi B., Mendes, Adriano, Mlisana, Koleka, Mnguni, Anele, Mohale, Thabo, Moir, Monika, Moruisi, Kgomotso, Mosepele, Mosepele, Motsatsi, Gerald, Motswaledi, Modisa S., Mphoyakgosi, Thongbotho, Msomi, Nokukhanya, Mwangi, Peter N., Naidoo, Yeshnee, Ntuli, Noxolo, Nyaga, Martin, Olubayo, Lucier, Pillay, Sureshnee, Radibe, Botshelo, Ramphal, Yajna, Ramphal, Upasana, San, James E., Scott, Lesley, Shapiro, Roger, Singh, Lavanya, Smith-Lawrence, Pamela, Stevens, Wendy, Strydom, Amy, Subramoney, Kathleen, Tebeila, Naume, Tshiabuila, Derek, Tsui, Joseph, van Wyk, Stephanie, Weaver, Steven, Wibmer, Constantinos K., Wilkinson, Eduan, Wolter, Nicole, Zarebski, Alexander E., Zuze, Boitumelo, Goedhals, Dominique, Preiser, Wolfgang, Treurnicht, Florette, Venter, Marietje, Williamson, Carolyn, Pybus, Oliver G., Bhiman, Jinal, Glass, Allison, Martin, Darren P., Rambaut, Andrew, Gaseitsiwe, Simani, von Gottberg, Anne, de Oliveira, Tulio
Published in Nature (London) (24.03.2022)
Published in Nature (London) (24.03.2022)
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Unlocking the efficiency of genomics laboratories with robotic liquid-handling
Tegally, Houriiyah, San, James Emmanuel, Giandhari, Jennifer, de Oliveira, Tulio
Published in BMC genomics (20.10.2020)
Published in BMC genomics (20.10.2020)
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Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization
Cele, Sandile, Jackson, Laurelle, Khoury, David S., Khan, Khadija, Moyo-Gwete, Thandeka, Tegally, Houriiyah, San, James Emmanuel, Cromer, Deborah, Scheepers, Cathrine, Amoako, Daniel G., Karim, Farina, Bernstein, Mallory, Lustig, Gila, Archary, Derseree, Smith, Muneerah, Ganga, Yashica, Jule, Zesuliwe, Reedoy, Kajal, Hwa, Shi-Hsia, Giandhari, Jennifer, Blackburn, Jonathan M., Gosnell, Bernadett I., Abdool Karim, Salim S., Hanekom, Willem, von Gottberg, Anne, Bhiman, Jinal N., Lessells, Richard J., Moosa, Mahomed-Yunus S., Davenport, Miles P., de Oliveira, Tulio, Moore, Penny L., Sigal, Alex
Published in Nature (London) (24.02.2022)
Published in Nature (London) (24.02.2022)
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Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, Houriiyah, Wilkinson, Eduan, Giovanetti, Marta, Iranzadeh, Arash, Fonseca, Vagner, Giandhari, Jennifer, Doolabh, Deelan, Pillay, Sureshnee, San, Emmanuel James, Msomi, Nokukhanya, Mlisana, Koleka, von Gottberg, Anne, Walaza, Sibongile, Allam, Mushal, Ismail, Arshad, Mohale, Thabo, Glass, Allison J., Engelbrecht, Susan, Van Zyl, Gert, Preiser, Wolfgang, Petruccione, Francesco, Sigal, Alex, Hardie, Diana, Marais, Gert, Hsiao, Nei-yuan, Korsman, Stephen, Davies, Mary-Ann, Tyers, Lynn, Mudau, Innocent, York, Denis, Maslo, Caroline, Goedhals, Dominique, Abrahams, Shareef, Laguda-Akingba, Oluwakemi, Alisoltani-Dehkordi, Arghavan, Godzik, Adam, Wibmer, Constantinos Kurt, Sewell, Bryan Trevor, Lourenço, José, Alcantara, Luiz Carlos Junior, Kosakovsky Pond, Sergei L., Weaver, Steven, Martin, Darren, Lessells, Richard J., Bhiman, Jinal N., Williamson, Carolyn, de Oliveira, Tulio
Published in Nature (London) (15.04.2021)
Published in Nature (London) (15.04.2021)
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Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally, Houriiyah, Moir, Monika, Everatt, Josie, Giovanetti, Marta, Scheepers, Cathrine, Wilkinson, Eduan, Subramoney, Kathleen, Makatini, Zinhle, Moyo, Sikhulile, Amoako, Daniel G., Baxter, Cheryl, Althaus, Christian L., Anyaneji, Ugochukwu J., Kekana, Dikeledi, Viana, Raquel, Giandhari, Jennifer, Lessells, Richard J., Maponga, Tongai, Maruapula, Dorcas, Choga, Wonderful, Matshaba, Mogomotsi, Mbulawa, Mpaphi B., Msomi, Nokukhanya, Naidoo, Yeshnee, Pillay, Sureshnee, Sanko, Tomasz Janusz, San, James E., Scott, Lesley, Singh, Lavanya, Magini, Nonkululeko A., Smith-Lawrence, Pamela, Stevens, Wendy, Dor, Graeme, Tshiabuila, Derek, Wolter, Nicole, Preiser, Wolfgang, Treurnicht, Florette K., Venter, Marietjie, Chiloane, Georginah, McIntyre, Caitlyn, O’Toole, Aine, Ruis, Christopher, Peacock, Thomas P., Roemer, Cornelius, Kosakovsky Pond, Sergei L., Williamson, Carolyn, Pybus, Oliver G., Bhiman, Jinal N., Glass, Allison, Martin, Darren P., Jackson, Ben, Rambaut, Andrew, Laguda-Akingba, Oluwakemi, Gaseitsiwe, Simani, von Gottberg, Anne, de Oliveira, Tulio
Published in Nature medicine (01.09.2022)
Published in Nature medicine (01.09.2022)
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Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Cele, Sandile, Gazy, Inbal, Jackson, Laurelle, Hwa, Shi-Hsia, Tegally, Houriiyah, Lustig, Gila, Giandhari, Jennifer, Pillay, Sureshnee, Wilkinson, Eduan, Naidoo, Yeshnee, Karim, Farina, Ganga, Yashica, Khan, Khadija, Bernstein, Mallory, Balazs, Alejandro B., Gosnell, Bernadett I., Hanekom, Willem, Moosa, Mahomed-Yunus S., Lessells, Richard J., de Oliveira, Tulio, Sigal, Alex
Published in Nature (London) (06.05.2021)
Published in Nature (London) (06.05.2021)
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Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection
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, Manickchund, Nithendra, Magula, Nombulelo, Karim, Quarraisha Abdool, von Gottberg, Anne, Abdool Karim, Salim S., Hanekom, Willem, Gosnell, Bernadett I., Lessells, Richard J., de Oliveira, Tulio, Moosa, Mahomed-Yunus S., Sigal, Alex
Published in Nature communications (10.08.2022)
Published in Nature communications (10.08.2022)
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SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape
Cele, Sandile, Karim, Farina, Lustig, Gila, San, James Emmanuel, Hermanus, Tandile, Tegally, Houriiyah, Snyman, Jumari, Moyo-Gwete, Thandeka, Wilkinson, Eduan, Bernstein, Mallory, Khan, Khadija, Hwa, Shi-Hsia, Tilles, Sasha W., Singh, Lavanya, Giandhari, Jennifer, Mthabela, Ntombifuthi, Mazibuko, Matilda, Ganga, Yashica, Gosnell, Bernadett I., Karim, Salim S. Abdool, Hanekom, Willem, Van Voorhis, Wesley C., Ndung’u, Thumbi, Lessells, Richard J., Moore, Penny L., Moosa, Mahomed-Yunus S., de Oliveira, Tulio, Sigal, Alex
Published in Cell host & microbe (09.02.2022)
Published in Cell host & microbe (09.02.2022)
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Omicron infection enhances Delta antibody immunity in vaccinated persons
Khan, Khadija, Karim, Farina, Cele, Sandile, Reedoy, Kajal, San, James Emmanuel, Lustig, Gila, Tegally, Houriiyah, Rosenberg, Yuval, Bernstein, Mallory, Jule, Zesuliwe, Ganga, Yashica, Ngcobo, Nokuthula, Mazibuko, Matilda, Mthabela, Ntombifuthi, Mhlane, Zoey, Mbatha, Nikiwe, Miya, Yoliswa, Giandhari, Jennifer, Ramphal, Yajna, Naidoo, Taryn, Sivro, Aida, Samsunder, Natasha, Kharsany, Ayesha B. M., Amoako, Daniel, Bhiman, Jinal N., Manickchund, Nithendra, Abdool Karim, Quarraisha, Magula, Nombulelo, Abdool Karim, Salim S., Gray, Glenda, Hanekom, Willem, von Gottberg, Anne, Milo, Ron, Gosnell, Bernadett I., Lessells, Richard J., Moore, Penny L., de Oliveira, Tulio, Moosa, Mahomed-Yunus S., Sigal, Alex
Published in Nature (London) (14.07.2022)
Published in Nature (London) (14.07.2022)
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Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase
Siedner, Mark J., Moorhouse, Michelle A., Simmons, Bryony, de Oliveira, Tulio, Lessells, Richard, Giandhari, Jennifer, Kemp, Stephen A., Chimukangara, Benjamin, Akpomiemie, Godspower, Serenata, Celicia M., Venter, Willem D. F., Hill, Andrew, Gupta, Ravindra K.
Published in Nature communications (01.12.2020)
Published in Nature communications (01.12.2020)
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Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq
Tshiabuila, Derek, Giandhari, Jennifer, Pillay, Sureshnee, Ramphal, Upasana, Ramphal, Yajna, Maharaj, Arisha, Anyaneji, Ugochukwu Jacob, Naidoo, Yeshnee, Tegally, Houriiyah, San, Emmanuel James, Wilkinson, Eduan, Lessells, Richard J, de Oliveira, Tulio
Published in BMC genomics (22.04.2022)
Published in BMC genomics (22.04.2022)
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Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report
Giandhari, Jennifer, Pillay, Sureshnee, Wilkinson, Eduan, Tegally, Houriiyah, Sinayskiy, Ilya, Schuld, Maria, Lourenço, José, Chimukangara, Benjamin, Lessells, Richard, Moosa, Yunus, Gazy, Inbal, Fish, Maryam, Singh, Lavanya, Sedwell Khanyile, Khulekani, Fonseca, Vagner, Giovanetti, Marta, Carlos Junior Alcantara, Luiz, Petruccione, Francesco, de Oliveira, Tulio
Published in International journal of infectious diseases (01.02.2021)
Published in International journal of infectious diseases (01.02.2021)
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Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage
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, Ramphal, Upasana, Naidoo, Yeshnee, Khumalo, Zamantungwa T., Kwatra, Gaurav, Gray, Glenda, Bekker, Linda-Gail, Madhi, Shabir A., Baillie, Vicky, Van Voorhis, Wesley C., Treurnicht, Florette K., Venter, Marietjie, Mlisana, Koleka, Wolter, Nicole, Sigal, Alex, Williamson, Carolyn, Hsiao, Nei-yuan, Msomi, Nokukhanya, Maponga, Tongai, Preiser, Wolfgang, Makatini, Zinhle, Lessells, Richard, Moore, Penny L., de Oliveira, Tulio, von Gottberg, Anne, Bhiman, Jinal N.
Published in Nature communications (08.04.2022)
Published in Nature communications (08.04.2022)
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Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing
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
Published in PloS one (26.04.2023)
Published in PloS one (26.04.2023)
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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, 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
Published in PloS one (30.05.2023)
Published in PloS one (30.05.2023)
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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, Wilkinson, Eduan, de Oliveira, Tulio, Kaleebu, Pontiano
Published in Emerging infectious diseases (01.05.2022)
Published in Emerging infectious diseases (01.05.2022)
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Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
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, Jr, Luiz Carlos, de Oliveira, Tulio
Published in Genes (17.08.2020)
Published in Genes (17.08.2020)
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Hwa, Shi-Hsia, Snyman, Jumari, Bernstein, Mallory, Ganga, Yashica, Cele, Sandile, Muema, Daniel, Tan, Chee Wah, Khan, Khadija, Karim, Farina, Hanekom, Willem, Bernstein, Leslie, Kaufmann, Stefan H E, Wang, Lin-Fa, Ndung’u, Thumbi, Sigal, Alex
Published in The Journal of infectious diseases (11.01.2023)
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HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre study (DTG RESIST)
Egger, Matthias, Sauermann, Mamatha, Loosli, Tom, Hossmann, Stefanie, Riedo, Selma, Beerenwinkel, Niko, Jaquet, Antoine, Minga, Albert, Ross, Jeremy, Giandhari, Jennifer, Kouyos, Roger D, Lessells, Richard
Published in BMJ open (21.08.2024)
Published in BMJ open (21.08.2024)
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Persistent Hepatitis B Viraemia with Polymerase Mutations among HIV/HBV Co-Infected Patients on HBV-Active ART in KwaZulu-Natal, South Africa
Msomi, Nokukhanya, Parboosing, Raveen, Wilkinson, Eduan, Giandhari, Jennifer, Govender, Kerusha, Chimukangara, Benjamin, Mlisana, Koleka P
Published in Viruses (10.04.2022)
Published in Viruses (10.04.2022)
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