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2. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation

Author

Karim, Farina, Riou, Catherine, Bernstein, Mallory, Jule, Zesuliwe, Lustig, Gila, van Graan, Strauss, Keeton, Roanne S., Upton, Janine-Lee, Ganga, Yashica, Khan, Khadija, Reedoy, Kajal, Mazibuko, Matilda, Govender, Katya, Thambu, Kershnee, Ngcobo, Nokuthula, Venter, Elizabeth, Makhado, Zanele, Hanekom, Willem, von Gottberg, Anne, Hoque, Monjurul, Karim, Quarraisha Abdool, Abdool Karim, Salim S., Manickchund, Nithendra, Magula, Nombulelo, Gosnell, Bernadett I., Lessells, Richard J., Moore, Penny L., Burgers, Wendy A., de Oliveira, Tulio, Moosa, Mahomed-Yunus S., and Sigal, Alex

Published
2024
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4. Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant

Author

Khan, Khadija, Lustig, Gila, Römer, Cornelius, Reedoy, Kajal, Jule, Zesuliwe, Karim, Farina, Ganga, Yashica, Bernstein, Mallory, Baig, Zainab, Jackson, Laurelle, Mahlangu, Boitshoko, Mnguni, Anele, Nzimande, Ayanda, Stock, Nadine, Kekana, Dikeledi, Ntozini, Buhle, van Deventer, Cindy, Marshall, Terry, Manickchund, Nithendra, Gosnell, Bernadett I., Lessells, Richard J., Karim, Quarraisha Abdool, Abdool Karim, Salim S., Moosa, Mahomed-Yunus S., de Oliveira, Tulio, von Gottberg, Anne, Wolter, Nicole, Neher, Richard A., and Sigal, Alex

Published
2023
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5. The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Author

Martin, Darren P, Weaver, Steven, Tegally, Houriiyah, San, James Emmanuel, Shank, Stephen D, Wilkinson, Eduan, Lucaci, Alexander G, Giandhari, Jennifer, Naidoo, Sureshnee, Pillay, Yeshnee, Singh, Lavanya, Lessells, Richard J, NGS-SA, UK, COVID-19 Genomics, Gupta, Ravindra K, Wertheim, Joel O, Nekturenko, Anton, Murrell, Ben, Harkins, Gordon W, Lemey, Philippe, MacLean, Oscar A, Robertson, David L, de Oliveira, Tulio, and Pond, Sergei L Kosakovsky

Subjects
Biological Sciences, Evolutionary Biology, Infectious Diseases, Emerging Infectious Diseases, Genetics, Coronaviruses, Human Genome, Infection, Good Health and Well Being, Amino Acid Sequence, COVID-19, Codon, Evolution, Molecular, Genes, Viral, Genetic Drift, Host Adaptation, Humans, Immune Evasion, Mutation, Pandemics, Phylogeny, Public Health, SARS-CoV-2, NGS-SA, COVID-19 Genomics UK, COVID 19, convergent mutations, directional selection, diversifying selection, evolutionary adaptation, immune evasion, lineage-defining mutations, positive selection, recurrent mutations, transmission advantage, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three "501Y lineages" coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.

Published
2021

6. Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern

Author

Tegally, Houriiyah, Wilkinson, Eduan, Tsui, Joseph L.- H., Moir, Monika, Martin, Darren, Brito, Anderson Fernandes, Giovanetti, Marta, Khan, Kamran, Huber, Carmen, Bogoch, Isaac I., San, James Emmanuel, Poongavanan, Jenicca, Xavier, Joicymara S., Candido, Darlan da S., Romero, Filipe, Baxter, Cheryl, Pybus, Oliver G., Lessells, Richard J., Faria, Nuno R., Kraemer, Moritz U.G., and de Oliveira, Tulio

Published
2023
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8. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Author

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, and de Oliveira, Tulio

Published
2022
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9. Omicron infection enhances Delta antibody immunity in vaccinated persons

Author

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., and Sigal, Alex

Published
2022
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11. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Author

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, and de Oliveira, Tulio

Published
2022
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12. Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

Author

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., and Sigal, Alex

Published
2022
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13. Author Correction: Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection

Author

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., and Sigal, Alex

Published
2022
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15. Virologic Failure and Drug Resistance After Programmatic Switching to Dolutegravir-based First-line Antiretroviral Therapy in Malawi and Zambia

Author

Skrivankova, Veronika Whitesell, primary, Huwa, Jacqueline, additional, Muula, Guy, additional, Chiwaya, Geldert D, additional, Banda, Esau, additional, Buleya, Shameem, additional, Chihota, Belinda, additional, Chintedza, Joseph, additional, Bolton, Carolyn, additional, Tweya, Hannock, additional, Kalua, Thokozani, additional, Hossmann, Stefanie, additional, Kouyos, Roger, additional, Wandeler, Gilles, additional, Egger, Matthias, additional, and Lessells, Richard J, additional

Published
2024
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16. HIV-1 subtype-specific drug resistance on dolutegravir-based antiretroviral therapy: protocol for a multicentre longitudinal study (DTG RESIST)

Author

Egger, Matthias, primary, Sauermann, Mamatha, additional, Loosli, Tom, additional, Hossmann, Stefanie, additional, Riedo, Selma, additional, Beerenwinkel, Niko, additional, Jaquet, Antoine, additional, Minga, Albert, additional, Ross, Jeremy, additional, Giandhari, Jennifer, additional, Kouyos, Roger, additional, and Lessells, Richard J., additional

Published
2024
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17. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

Author

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., and Sigal, Alex

Published
2022
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18. Cost-effectiveness of public health strategies for COVID-19 epidemic control in South Africa: a microsimulation modelling study

Author

Reddy, Krishna P, Shebl, Fatma M, Foote, Julia H A, Harling, Guy, Scott, Justine A, Panella, Christopher, Fitzmaurice, Kieran P, Flanagan, Clare, Hyle, Emily P, Neilan, Anne M, Mohareb, Amir M, Bekker, Linda-Gail, Lessells, Richard J, Ciaranello, Andrea L, Wood, Robin, Losina, Elena, Freedberg, Kenneth A, Kazemian, Pooyan, and Siedner, Mark J

Published
2021
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20. Sixteen novel lineages of SARS-CoV-2 in South Africa

Author

Tegally, Houriiyah, Wilkinson, Eduan, Lessells, Richard J., Giandhari, Jennifer, Pillay, Sureshnee, Msomi, Nokukhanya, and Mlisana, Koleka

Subjects
Epidemics -- Genetic aspects -- Identification and classification -- Distribution -- South Africa, Company distribution practices, Biological sciences, Health
Abstract

The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90).sup.1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections.sup.2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. .sup.3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. .sup.4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. .sup.5). Interrogation of 1,365 near whole-genome sequences of SARS-CoV-2 variants isolated in South Africa during the first 6 months of the global pandemic reveals three major monophyletic lineages responsible for more than half of the infections in the country and underscores the value of integrating genomic surveillance methods to inform the national pandemic response., Author(s): Houriiyah Tegally [sup.1] , Eduan Wilkinson [sup.1] , Richard J. Lessells [sup.1] , Jennifer Giandhari [sup.1] , Sureshnee Pillay [sup.1] , Nokukhanya Msomi [sup.2] , Koleka Mlisana [sup.3] , [...]

Published
2021
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21. Detection of a SARS-CoV-2 variant of concern in South Africa

Author

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, and de Oliveira, Tulio

Published
2021
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23. Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa

Author

Chimukangara, Benjamin, Lessells, Richard J., Singh, Lavanya, Grigalionyte, Indra, Yende-Zuma, Nonhlanhla, Adams, Rochelle, Dawood, Halima, Dlamini, Linda, Buthelezi, Sibonisile, Chetty, Sheldon, Diallo, Karidia, Duffus, Wayne A., Mogashoa, Mary, Hagen, Melissa B., Giandhari, Jennifer, de Oliveira, Tulio, Moodley, Pravi, Padayatchi, Nesri, and Naidoo, Kogieleum

Published
2021
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24. COVID-19 Vaccine Uptake and Effectiveness by Time since Vaccination in the Western Cape Province, South Africa: An Observational Cohort Study during 2020–2022.

Author

Kassanjee, Reshma, Davies, Mary-Ann, Heekes, Alexa, Mahomed, Hassan, Hawkridge, Anthony J., Morden, Erna, Jacobs, Theuns, Cohen, Cheryl, Moultrie, Harry, Lessells, Richard J., Van Der Walt, Nicolette, Arendse, Juanita O., Wolter, Nicole, Walaza, Sibongile, Jassat, Waasila, von Gottberg, Anne, Hannan, Patrick L., Feikin, Daniel R., Cloete, Keith, and Boulle, Andrew

Subjects
VACCINE effectiveness, VACCINATION status, COVID-19 vaccines, BOOSTER vaccines, VACCINATION
Abstract

There are few data on the real-world effectiveness of COVID-19 vaccines and boosting in Africa, which experienced widespread SARS-CoV-2 infection before vaccine availability. We assessed the association between vaccination and severe COVID-19 in the Western Cape, South Africa, in an observational cohort study of >2 million adults during 2020–2022. We described SARS-CoV-2 testing, COVID-19 outcomes, and vaccine uptake over time. We used multivariable cox models to estimate the association of BNT162b2 and Ad26.COV2.S vaccination with COVID-19-related hospitalization and death, adjusting for demographic characteristics, underlying health conditions, socioeconomic status proxies, and healthcare utilization. We found that by the end of 2022, 41% of surviving adults had completed vaccination and 8% had received a booster dose. Recent vaccination was associated with notable reductions in severe COVID-19 during periods dominated by Delta, and Omicron BA.1/2 and BA.4/5 (sub)lineages. During the latest Omicron BA.4/5 wave, within 3 months of vaccination or boosting, BNT162b2 and Ad26.COV2.S were each 84% effective against death (95% CIs: 57–94 and 49–95, respectively). However, distinct reductions of effectiveness occurred at longer times post completing or boosting vaccination. Results highlight the importance of continued emphasis on COVID-19 vaccination and boosting for those at high risk of severe COVID-19, even in settings with widespread infection-induced immunity. [ABSTRACT FROM AUTHOR]

Published
2024
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26. Clinical outcomes with second-line dolutegravir in people with virological failure on first-line non-nucleoside reverse transcriptase inhibitor-based regimens in South Africa: a retrospective cohort study

Author

Asare, Kwabena, primary, Sookrajh, Yukteshwar, additional, van der Molen, Johan, additional, Khubone, Thokozani, additional, Lewis, Lara, additional, Lessells, Richard J, additional, Naidoo, Kogieleum, additional, Sosibo, Phelelani, additional, van Heerden, Rosemary, additional, Garrett, Nigel, additional, and Dorward, Jienchi, additional

Published
2023
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27. Clinical Outcomes After Viremia Among People Receiving Dolutegravir vs Efavirenz-Based First-line Antiretroviral Therapy in South Africa

Author

Asare, Kwabena, primary, Lewis, Lara, additional, van der Molen, Johan, additional, Sookrajh, Yukteshwar, additional, Khubone, Thokozani, additional, Moodley, Pravikrishnen, additional, Lessells, Richard J, additional, Naidoo, Kogieleum, additional, Sosibo, Phelelani, additional, Garrett, Nigel, additional, and Dorward, Jienchi, additional

Published
2023
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28. Rapid dynamic changes of FL.2 variant: a case report of COVID-19 breakthrough infection.

Author

Choga, Wonderful T., primary, Kurusa (Gasenna), Gobuiwang Khilly, additional, San, James Emmanuel, additional, Ookame, Tidimalo, additional, Gobe, Irene, additional, Chand, Mohammed, additional, Phafane, Badisa, additional, Seru, Kedumetse, additional, Matshosi, Patience, additional, Zuze, Boitumelo, additional, Ndlovu, Nokuthula, additional, Matsuru, Teko, additional, Maruapula, Dorcas, additional, Bareng, Ontlametse T., additional, Macheke, Kutlo, additional, Kuate-Lere, Lesego, additional, Tlale, Labapotswe, additional, Lesetedi, Onalethata, additional, Tau, Modiri, additional, Mbulawa, Mpaphi B., additional, Smith-Lawrence, Pamela, additional, Matshaba, Mogomotsi, additional, Shapiro, Roger, additional, Makhema, Joseph, additional, Martin, Darren P., additional, de Oliveira, Tulio, additional, Lessells, Richard J., additional, Lockman, Shahin, additional, Gaseitsiwe, Simani, additional, and Moyo, Sikhulile, additional

Published
2023
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29. Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant

Author

Khan, Khadija, primary, Lustig, Gila, additional, Reedoy, Kajal, additional, Jule, Zesuliwe, additional, Römer, Cornelius, additional, Karim, Farina, additional, Ganga, Yashica, additional, Bernstein, Mallory, additional, Baig, Zainab, additional, Mahlangu, Boitshoko, additional, Mnguni, Anele, additional, Nzimande, Ayanda, additional, Stock, Nadine, additional, Kekana, Dikeledi, additional, Ntozini, Buhle, additional, van Deventer, Cindy, additional, Marshall, Terry, additional, Manickchund, Nithendra, additional, Gosnell, Bernadett I., additional, Lessells, Richard J., additional, Abdool Karim, Quarraisha, additional, Abdool Karim, Salim S., additional, Moosa, Mahomed-Yunus S., additional, de Oliveira, Tulio, additional, von Gottberg, Anne, additional, Wolter, Nicole, additional, Neher, Richard A, additional, and Sigal, Alex, additional

Published
2023
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30. Clinical outcomes after the introduction of dolutegravir for second-line antiretroviral therapy in South Africa: a retrospective cohort study

Author

Asare, Kwabena, primary, Sookrajh, Yukteshwar, additional, van der Molen, Johan, additional, Khubone, Thokozani, additional, Lewis, Lara, additional, Lessells, Richard J, additional, Naidoo, Kogieleum, additional, Sosibo, Phelelani, additional, van Heerden, Rosemary, additional, Garrett, Nigel, additional, and Dorward, Jienchi, additional

Published
2023
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32. Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing

Author

Pillay, Sureshnee, primary, San, James Emmanuel, additional, Tshiabuila, Derek, additional, Naidoo, Yeshnee, additional, Pillay, Yusasha, additional, Maharaj, Akhil, additional, Anyaneji, Ugochukwu J., additional, Wilkinson, Eduan, additional, Tegally, Houriiyah, additional, Lessells, Richard J., additional, Baxter, Cheryl, additional, de Oliveira, Tulio, additional, and Giandhari, Jennifer, additional

Published
2023
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33. Reply to Molldrem

Author

Maponga, Tongai G, primary, Jeffries, Montenique, additional, Tegally, Houriiyah, additional, Sutherland, Andrew, additional, Wilkinson, Eduan, additional, Lessells, Richard J, additional, Msomi, Nokukhanya, additional, van Zyl, Gert, additional, de Oliveira, Tulio, additional, and Preiser, Wolfgang, additional

Published
2023
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34. SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic

Author

Roshdy, Wael H., primary, Khalifa, Mohamed K., additional, San, James Emmanuel, additional, Tegally, Houriiyah, additional, Wilkinson, Eduan, additional, Showky, Shymaa, additional, Martin, Darren Patrick, additional, Moir, Monika, additional, Naguib, Amel, additional, Elguindy, Nancy, additional, Gomaa, Mokhtar R., additional, Fahim, Manal, additional, Abu Elsood, Hanaa, additional, Mohsen, Amira, additional, Galal, Ramy, additional, Hassany, Mohamed, additional, Lessells, Richard J., additional, Al-Karmalawy, Ahmed A., additional, EL-Shesheny, Rabeh, additional, Kandeil, Ahmed M., additional, Ali, Mohamed A., additional, and de Oliveira, Tulio, additional

Published
2022
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35. Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection With accumulation of mutations in a patient with poorly controlled Human Immunodeficiency Virus infection

Author

Maponga, Tongai G, primary, Jeffries, Montenique, additional, Tegally, Houriiyah, additional, Sutherland, Andrew, additional, Wilkinson, Eduan, additional, Lessells, Richard J, additional, Msomi, Nokukhanya, additional, van Zyl, Gert, additional, de Oliveira, Tulio, additional, and Preiser, Wolfgang, additional

Published
2022
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38. SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape

Author

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, and Sigal, Alex

Published
2022
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40. Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing

Author

Singh, Lavanya, primary, San, James E., additional, Tegally, Houriiyah, additional, Brzoska, Pius M., additional, Anyaneji, Ugochukwu J., additional, Wilkinson, Eduan, additional, Clark, Lindsay, additional, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Lessells, Richard J., additional, Martin, Darren Patrick, additional, Furtado, Manohar, additional, Kiran, Anmol M., additional, and de Oliveira, Tulio, additional

Published
2022
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41. Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq

Author

Tshiabuila, Derek, primary, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Ramphal, Upasana, additional, Ramphal, Yajna, additional, Maharaj, Arisha, additional, Anyaneji, Ugochukwu Jacob, additional, Naidoo, Yeshnee, additional, Tegally, Houriiyah, additional, San, Emmanuel James, additional, Wilkinson, Eduan, additional, Lessells, Richard J., additional, and de Oliveira, Tulio, additional

Published
2022
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42. SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection

Author

Cele, Sandile, Jackson, Laurelle, Khoury, David S., Khan, Khadija, Moyo-Gwete, Thandeka, Tegally, Houriiyah, San, James Emmanuel, Cromer, Deborah, Scheepers, Cathrine, Amoako, Daniel, 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, Lessells, Richard J., Moosa, Mahomed-Yunus S., Davenport, Miles P., de Oliveira, Tulio, Moore, Penny L., and Sigal, Alex

Subjects
Article
Abstract

The emergence of SARS-CoV-2 Omicron, first identified in Botswana and South Africa, may compromise vaccine effectiveness and the ability of antibodies triggered by previous infection to protect against re-infection (1). Here we investigated whether Omicron escapes antibody neutralization in South Africans, either previously SARS-CoV-2 infected or uninfected, who were vaccinated with Pfizer BNT162b2. We also investigated if Omicron requires the ACE2 receptor to infect cells. We isolated and sequence confirmed live Omicron virus from an infected person in South Africa and compared plasma neutralization of this virus relative to an ancestral SARS-CoV-2 strain with the D614G mutation, observing that Omicron still required ACE2 to infect. For neutralization, blood samples were taken soon after vaccination, so that vaccine elicited neutralization was close to peak. Neutralization capacity of the D614G virus was much higher in infected and vaccinated versus vaccinated only participants but both groups had 22-fold Omicron escape from vaccine elicited neutralization. Previously infected and vaccinated individuals had residual neutralization predicted to confer 73% protection from symptomatic Omicron infection, while those without previous infection were predicted to retain only about 35%. Both groups were predicted to have substantial protection from severe disease. These data support the notion that high neutralization capacity elicited by a combination of infection and vaccination, and possibly boosting, could maintain reasonable effectiveness against Omicron. A waning neutralization response is likely to decrease vaccine effectiveness below these estimates. However, since protection from severe disease requires lower neutralization levels and involves T cell immunity, such protection may be maintained.

Published
2021

43. Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection With accumulation of mutations in a patient with poorly controlled Human Immunodeficiency Virus infection.

Author

Maponga, Tongai G, Jeffries, Montenique, Tegally, Houriiyah, Sutherland, Andrew, Wilkinson, Eduan, Lessells, Richard J, Msomi, Nokukhanya, Zyl, Gert van, Oliveira, Tulio de, and Preiser, Wolfgang

Subjects
HIV infections, COVID-19, GENETIC mutation, IMMUNOCOMPROMISED patients, CHRONIC diseases, WOMEN, HIGHLY active antiretroviral therapy, INFECTION, RESEARCH funding, AIDS patients
Abstract

A 22-year-old woman with uncontrolled advanced human immunodeficiency virus (HIV) infection was persistently infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) beta variant for 9 months, the virus accumulating >20 additional mutations. Antiretroviral therapy suppressed HIV and cleared SARS-CoV-2 within 6 to 9 weeks. Increased vigilance is warranted to benefit affected individuals and prevent the emergence of novel SARS-CoV-2 variants. [ABSTRACT FROM AUTHOR]

Published
2023
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44. SARS-CoV-2 Genetic diversity and lineage dynamics of in Egypt

Author

Roshdy, Wael H., primary, khalifa, Mohamed K., additional, San, James Emmanuel, additional, Tegally, Houriiyah, additional, Wilkinson, Eduan, additional, Showky, Shymaa, additional, Martin, Daren Patrick, additional, Moir, Monika, additional, Naguib, Amel, additional, Elguindy, Nancy, additional, Gomaa, Mokhtar R., additional, Fahim, Manal, additional, Elsood, Hanaa Abu, additional, Mohsen, Amira, additional, Galal, Ramy, additional, Hassany, Mohamed, additional, Lessells, Richard J, additional, Al-Karmalawy, Ahmed A., additional, EL-Shesheny, Rabeh, additional, Kandeil, Ahmed M., additional, Ali, Mohamed A., additional, and de Oliveira, Tulio, additional

Published
2022
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45. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Author

Viana, Raquel, primary, Moyo, Sikhulile, additional, Amoako, Daniel G, additional, Tegally, Houriiyah, additional, Scheepers, Cathrine, additional, Althaus, Christian L, additional, Anyaneji, Ugochukwu J, additional, Bester, Phillip A, additional, Boni, Maciej F, additional, Chand, Mohammed, additional, Choga, Wonderful T, additional, Colquhoun, Rachel, additional, Davids, Michaela, additional, Deforche, Koen, additional, Doolabh, Deelan, additional, Engelbrecht, Susan, additional, Everatt, Josie, additional, Giandhari, Jennifer, additional, Giovanetti, Marta, additional, Hardie, Diana, additional, Hill, Verity, additional, Hsiao, Nei-Yuan, additional, Iranzadeh, Arash, additional, Ismail, Arshad, additional, Joseph, Charity, additional, Joseph, Rageema, additional, Koopile, Legodile, additional, Pond, Sergei L Kosakovsky, additional, Kraemer, Moritz UG, additional, Kuate-Lere, Lesego, additional, Laguda-Akingba, Oluwakemi, additional, Lesetedi-Mafoko, Onalethatha, additional, Lessells, Richard J, additional, Lockman, Shahin, additional, Lucaci, Alexander G, additional, Maharaj, Arisha, additional, Mahlangu, Boitshoko, additional, Maponga, Tongai, additional, Mahlakwane, Kamela, additional, Makatini, Zinhle, additional, Marais, Gert, additional, Maruapula, Dorcas, additional, Masupu, Kereng, additional, Matshaba, Mogomotsi, additional, Mayaphi, Simnikiwe, additional, Mbhele, Nokuzola, additional, Mbulawa, Mpaphi B, additional, Mendes, Adriano, additional, Mlisana, Koleka, additional, Mnguni, Anele, additional, Mohale, Thabo, additional, Moir, Monika, additional, Moruisi, Kgomotso, additional, Mosepele, Mosepele, additional, Motsatsi, Gerald, additional, Motswaledi, Modisa S, additional, Mphoyakgosi, Thongbotho, additional, Msomi, Nokukhanya, additional, Mwangi, Peter N, additional, Naidoo, Yeshnee, additional, Ntuli, Noxolo, additional, Nyaga, Martin, additional, Olubayo, Lucier, additional, Pillay, Sureshnee, additional, Radibe, Botshelo, additional, Ramphal, Yajna, additional, Ramphal, Upasana, additional, San, James E, additional, Scott, Lesley, additional, Shapiro, Roger, additional, Singh, Lavanya, additional, Smith-Lawrence, Pamela, additional, Stevens, Wendy, additional, Strydom, Amy, additional, Subramoney, Kathleen, additional, Tebeila, Naume, additional, Tshiabuila, Derek, additional, Tsui, Joseph, additional, van Wyk, Stephanie, additional, Weaver, Steven, additional, Wibmer, Constantinos K, additional, Wilkinson, Eduan, additional, Wolter, Nicole, additional, Zarebski, Alexander E, additional, Zuze, Boitumelo, additional, Goedhals, Dominique, additional, Preiser, Wolfgang, additional, Treurnicht, Florette, additional, Venter, Marietje, additional, Williamson, Carolyn, additional, Pybus, Oliver G, additional, Bhiman, Jinal, additional, Glass, Allison, additional, Martin, Darren P, additional, Rambaut, Andrew, additional, Gaseitsiwe, Simani, additional, von Gottberg, Anne, additional, and de Oliveira, Tulio, additional

Published
2021
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46. Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection

Author

Choga, Wonderful T., Kurusa (Gasenna), Gobuiwang Khilly, San, James Emmanuel, Ookame, Tidimalo, Gobe, Irene, Chand, Mohammed, Phafane, Badisa, Seru, Kedumetse, Matshosi, Patience, Zuze, Boitumelo, Ndlovu, Nokuthula, Matsuru, Teko, Maruapula, Dorcas, Bareng, Ontlametse T., Macheke, Kutlo, Kuate-Lere, Lesego, Tlale, Labapotswe, Lesetedi, Onalethata, Tau, Modiri, Mbulawa, Mpaphi B., Smith-Lawrence, Pamela, Matshaba, Mogomotsi, Shapiro, Roger, Makhema, Joseph, Martin, Darren P., de Oliveira, Tulio, Lessells, Richard J., Lockman, Shahin, Gaseitsiwe, Simani, and Moyo, Sikhulile

Published
2024
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47. Rapid replacement of the Beta variant by the Delta variant in South Africa

Author

Tegally, Houriiyah, primary, Wilkinson, Eduan, additional, Althaus, Christian L., additional, Giovanetti, Marta, additional, San, James Emmanuel, additional, Giandhari, Jennifer, additional, Pillay, Sureshnee, additional, Naidoo, Yeshnee, additional, Ramphal, Upasana, additional, Msomi, Nokukhanya, additional, Mlisana, Koleka, additional, Amoako, Daniel G., additional, Everatt, Josie, additional, Mohale, Thabo, additional, Nguni, Anele, additional, Mahlangu, Boitshoko, additional, Ntuli, Noxolo, additional, Khumalo, Zamantungwa T., additional, Makatini, Zinhle, additional, Wolter, Nicole, additional, Scheepers, Cathrine, additional, Ismail, Arshad, additional, Doolabh, Deelan, additional, Joseph, Rageema, additional, Strydom, Amy, additional, Mendes, Adriano, additional, Davis, Michaela, additional, Mayaphi, Simnikiwe H., additional, Ramphal, Yajna, additional, Maharaj, Arisha, additional, Karim, Wasim Abdool, additional, Tshiabuila, Derek, additional, Anyaneji, Ugochukwu J., additional, Singh, Lavanya, additional, Engelbrecht, Susan, additional, Fonseca, Vagner, additional, Marais, Kruger, additional, Korsman, Stephen, additional, Hardie, Diana, additional, Hsiao, Nei-yuan, additional, Maponga, Tongai, additional, van Zyl, Gert, additional, Marais, Gert, additional, Iranzadeh, Arash, additional, Martin, Darren, additional, Alcantara, Luiz Carlos Junior, additional, Bester, Phillip Armand, additional, Nyaga, Martin M., additional, Subramoney, Kathleen, additional, Treurnicht, Florette K., additional, Venter, Marietjie, additional, Goedhals, Dominique, additional, Preiser, Wolfgang, additional, Bhiman, Jinal N., additional, Gottberg, Anne von, additional, Williamson, Carolyn, additional, Lessells, Richard J., additional, and de Oliveira, Tulio, additional

Published
2021
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48. Scale-up of a decentralized HIV treatment programme in rural KwaZulu-Natal, South Africa: does rapid expansion affect patient outcomes?/Mise en place elargie d'un programme decentralise de traitement du VIH dans le KwaZulu-Natal rural, Afrique du Sud: une expansion rapide affecte-elle les resultats des patients?/Ampliacion de un programa descentralizado de tratamiento del VIH ...?

Author

Mutevedzi, Portia C., Lessells, Richard J., Heller, Tom, Barnighausen, Till, Cooke, Graham S., and Newell, Marie-Louise

Subjects
Antiviral agents -- Usage -- Research, Anti-HIV agents -- Usage -- Research, HIV infection -- Patient outcomes -- Drug therapy -- Research -- Care and treatment -- Usage, Health
Abstract

Objective To describe the scale-up of a decentralized HIV treatment programme delivered through the primary health care system in rural KwaZulu-Natal, South Africa, and to assess trends in baseline characteristics and outcomes in the study population. Methods The programme started delivery of antiretroviral therapy (ART) in October 2004. Information on all patients initiated on ART was captured in the programme database and follow-up status was updated monthly. All adult patients (≥ 16 years) who initiated ART between October 2004 and September 2008 were included and stratified into 6-month groups. Clinical and sociodemographic characteristics were compared between the groups. Retention in care, mortality, loss to follow-up and virological outcomes were assessed at 12 months post-ART initiation. Findings A total of 5719 adults initiated on ART were included (67.9% female). Median baseline CD4+ lymphocyte count was 116. cells/µl (interquartile range, IQR: 53-173). There was ah increase in the proportion of women who initiated ART while pregnant but no change in other baseline characteristics over time. Overall retention in care at 12 months was 84.0% (95% confidence interval, CI: 82.6-85.3); 10.9% died (95% CI: 9.8-12.0); 3.7% were lost to follow-up (95% CI: 3.0-4.4). Mortality was highest in the first 3 months after ART initiation: 30.1 deaths per 100 person-years (95% CI: 26.3-34.5). At 12 months 23.0% had a detectable viral load (> 25 copies/ml) (95% CI: 19.5-25.5). Conclusion Outcomes were not affected by rapid expansion of this decentralized HIV treatment programme. The relatively high rates of detectable viral load highlight the need for further efforts to improve the quality of services. Une traduction en francais de ce resume figure a la fin de l'article. al final del articulo se facilita una traduccion al espanol. Objectif Decrire le passage a l'echelle superieure d'un programme decentralise de traitement du VIH delivre au travers du systeme de soins de sante primaires au KwaZulu-Natal rural, Afrique du Sud, et evaluer les tendances des caracteristiques de ligne de base et les resultats sur la population etudiee. Methodes Le programme a commence la distribution d'une therapie antiretrovirale (TAR) en octobre 2004. Les informations concernant l'ensemble des patients entamant un traitement TAR ont ete recueillies dans une base de donnees informatisee et le suivi de leur etat a ete actualise chaque mois. Tous les patients adultes (≥ 16 ans) ayant commence la TAR entre octobre 2004 et septembre 2008 ont ete inclus et stratifies en groupes de 6 mois. Les caracteristiques cliniques et sociodemographiques ont ete comparees entre les groupes. Les taux de retention sous traitement et de mortalite, ainsi que les nombres de perdus pour le suivi et les resultats virologiques ont ete evalues 12 mois apres le debut de la TAR. Resultats Au total 5 719 patients ayant initie un traitement TAR ont ete inclus (67,9 % de femmes). Le nombre moyen de lymphocytes CD4+ a la ligne de base etait de 116 cellules/µl (intervalle interquartile, IQR: 53-173). Une augmentation de la proportion de femmes ayant entame un traitement TAR alors qu'elles etaient enceintes a ete notee, mais aucun changement n'a ete observe dans le temps pour les autres caracteristiques a la ligne de base. Le taux global de retention sous traitement a 12 mois etait de 84,0 % (intervalle de confiance a 95 %, IC: 82,6-85,3); 10,9 % sont decedes (IC a 95 %: 9,8-12,0); 3.7 % ont ete perdus pour le suivi (IC a 95 %: 3,0-4,4). La mortalite a ete plus elevee durant les 3 premiers mois qui ont suivi le debut de TAR : 30,1 deces pour 100 personnes-ans (IC a 95 %: 26,3-34,5). A 12 mois, 23,0 % presentaient une charge virale detectable (> 25 copies/mi) (IC a 95 %: 19,5-25,5). Conclusion Les resultats n'ont pas ete affectes par la rapide expansion de ce programme de traitement du VIH decentralise. Les taux relativement eleves de charge virale detectable mettent en evidence la necessite de futurs efforts a mettre en place pour ameliorer la qualite des services. Objetivos Describir la ampliacion de un programa descentralizado de tratamiento del VIH a traves del sistema sanitario de atencion primaria en zonas rurales de KwaZulu-Natal, Sudafrica, y evaluar las tendencias de las caracteristicas iniciales y los resultados de la poblacion en estudio. Metodos El programa comenzo con la administracion de un tratamiento antirretroviral (ARV) en octubre de 2004. La informacion de todos los pacientes que comenzaron el tratamiento ARV se recopilo en la base de datos del programa y el seguimiento se actualizo mensualmente. Todos los pacientes adultos (≥ 16 anos) que iniciaron el tratamiento ARV entre octubre de 2004 y septiembre de 2008 se incluyeron y estratificaron en grupos de seis meses. Se compararon las caracteristicas clinicas y sociodemograficas intergrupales. A los 12 meses del inicio del tratamiento ARV se evaluo la continuidad asistencial, la perdida para el seguimiento y los resultados virologicos. Resultados Se incluyo a un total de 5719 adultos que habian iniciado el tratamiento ARV, de los que el 67,9% eran mujeres. El recuento medio inicial de linfocitos CD4 fue de 116 celulas/µl (amplitud intercuartil, AIC: 53-173). El porcentaje de mujeres que iniciaron el tratamiento ARV durante el embarazo aumento, si bien no se produjo ningun cambio en otras caracteristicas iniciales a lo largo del tiempo. La continuidad asistencial general a los 12 meses fue del 84,0% (intervalo de confianza del 95%, Ch 82; 6--85,3); el 10,9% fallecio (CI del 95%: 9; 8-12,0); el 3,7% se perdio para el seguimiento (CI del 95%: 3,0-4,4). La mortalidad fue mas elevada en los primeros tres meses posteriores al inicio del tratamiento ARV: 30,1 fallecimientos por cada 100 afios-personas (CI del 95%: 26,3-34,5). El 23,0% tenia una carga viral detectable a los 12 meses (> 25 replicas/ml) (CI del 95%: 19,5- 25,5). Conclusion Los resultados no se vieron afectados por la rapida expansion de este programa descentralizado de tratamiento del VIH. Los indices relativamente altos de la carga virica detectable ponen en evidencia la necesidad de dedicar un mayor esfuerzo en la mejora de la calidad de los servicios., Introduction South Africa is home to 5.7 million people living with h del immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS), or approximately 1 in 6 of the world's HIV+ [...]

Published
2010
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49. Additional file 1 of Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa

Author

Chimukangara, Benjamin, Lessells, Richard J., Singh, Lavanya, Grigalionyte, Indra, Yende-Zuma, Nonhlanhla, Adams, Rochelle, Dawood, Halima, Dlamini, Linda, Buthelezi, Sibonisile, Chetty, Sheldon, Diallo, Karidia, Duffus, Wayne A., Mogashoa, Mary, Hagen, Melissa B., Giandhari, Jennifer, de Oliveira, Tulio, Moodley, Pravi, Padayatchi, Nesri, and Naidoo, Kogieleum

Subjects
parasitic diseases
Abstract

Additional file 1: Figure S1. Study flow diagram from participant selection to reporting of results in the acquired HIV drug resistance study in KwaZulu-Natal (KZN) province, South Africa, May–September 2019. Table S1. Comparison of participant characteristics among samples excluded and included in final analysis in the acquired HIV drug resistance study in KwaZulu-Natal (KZN) province, South Africa, May–September 2019. Table S2. Patterns of drug class resistance among participants on first- and second-line ART in the acquired HIV drug resistance study in KwaZulu-Natal (KZN) province, South Africa, May–September 2019. Table S3. Prevalence of specific acquired drug resistance mutations in the acquired HIV drug resistance study in KwaZulu-Natal (KZN) province, South Africa, May–September 2019. Table S4. Relationship between patient characteristics and acquired drug resistance using multivariable logistic regression.

Published
2021
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50. Genomic epidemiology of SARS-CoV-2 in Mauritius reveals a new wave of infections dominated by the B.1.1.318, a variant under investigation

Author

Tegally, Houriiyah, primary, Ramuth, Magalutcheemee, additional, Amoaka, Daniel, additional, Scheepers, Cathrine, additional, Wilkinson, Eduan, additional, Giovanetti, Marta, additional, Lessells, Richard J, additional, Giandhari, Jennifer, additional, Ismail, Arshad, additional, Martin, Darren, additional, San, Emmanuel James, additional, Crawford, Margaret, additional, Daniels, Rodney S, additional, Harvey, Ruth, additional, Bahadoor, Somduthsingh, additional, Sonoo, Janaki, additional, Timol, Myriam, additional, Veerapa-Mangroo, Lovena, additional, Gottberg, Anne von, additional, Bhiman, Jinal N., additional, de Oliveira, Tulio, additional, and Manraj, Shyam, additional

Published
2021
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