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1. Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant

Author

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

Subjects
Science
Abstract

Abstract Omicron BA.2.86 subvariant differs from Omicron BA.2 as well as recently circulating variants by over 30 mutations in the spike protein alone. Here we report on the isolation of the live BA.2.86 subvariant from a diagnostic swab collected in South Africa which we tested for escape from neutralizing antibodies and viral replication properties in cell culture. We found that BA.2.86 does not have significantly more escape relative to Omicron XBB.1.5 from neutralizing immunity elicited by either Omicron XBB-family subvariant infection or from residual neutralizing immunity of recently collected sera from the South African population. BA.2.86 does have extensive escape relative to ancestral virus with the D614G substitution (B.1 lineage) when neutralized by sera from pre-Omicron vaccinated individuals and relative to Omicron BA.1 when neutralized by sera from Omicron BA.1 infected individuals. BA.2.86 and XBB.1.5 show similar viral infection dynamics in the VeroE6-TMPRSS2 and H1299-ACE2 cell lines. We also investigate the relationship of BA.2.86 to BA.2 sequences. The closest BA.2 sequences are BA.2 samples from Southern Africa circulating in early 2022. Similarly, many basal BA.2.86 sequences were sampled in Southern Africa. This suggests that BA.2.86 potentially evolved in this region, and that unobserved evolution led to escape from neutralizing antibodies similar in scale to recently circulating strains of SARS-CoV-2.

Published
2023
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2. Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

Author

Cathrine Scheepers, Josie Everatt, Daniel G. Amoako, Houriiyah Tegally, Constantinos Kurt Wibmer, Anele Mnguni, Arshad Ismail, Boitshoko Mahlangu, Bronwen E. Lambson, Darren P. Martin, Eduan Wilkinson, James Emmanuel San, Jennifer Giandhari, Nelia Manamela, Noxolo Ntuli, Prudence Kgagudi, Sandile Cele, Simone I. Richardson, Sureshnee Pillay, Thabo Mohale, Upasana Ramphal, Yeshnee Naidoo, Zamantungwa T. Khumalo, Gaurav Kwatra, Glenda Gray, Linda-Gail Bekker, Shabir A. Madhi, Vicky Baillie, Wesley C. Van Voorhis, Florette K. Treurnicht, Marietjie Venter, Koleka Mlisana, Nicole Wolter, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Nokukhanya Msomi, Tongai Maponga, Wolfgang Preiser, Zinhle Makatini, Richard Lessells, Penny L. Moore, Tulio de Oliveira, Anne von Gottberg, and Jinal N. Bhiman

Subjects
Science
Abstract

The SARS-CoV-2 PANGO lineage C.1.2 has been under monitoring by global health authorities as it has spread worldwide. Here, Bhiman and colleagues characterise the emergence of the lineage, and its neutralisation sensitivity using data from vaccinees and previously infected individuals.

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

Author

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

Subjects
Models, Molecular, Recombination, Genetic, Botswana, Multidisciplinary, SARS-CoV-2, COVID-19, 610 Medicine & health, Antibodies, Neutralizing, South Africa, 360 Social problems & social services, Mutation, Spike Glycoprotein, Coronavirus, Humans, Phylogeny, Immune Evasion
Abstract

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

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

Author

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

Abstract

SummaryThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

Published
2021
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5. Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

Author

Cathrine Scheepers, Josie Everatt, Daniel G. Amoako, Houriiyah Tegally, Constantinos Kurt Wibmer, Anele Mnguni, Arshad Ismail, Boitshoko Mahlangu, Bronwen E. Lambson, Darren P. Martin, Eduan Wilkinson, James Emmanuel San, Jennifer Giandhari, Nelia Manamela, Noxolo Ntuli, Prudence Kgagudi, Sandile Cele, Simone I. Richardson, Sureshnee Pillay, Thabo Mohale, Upasana Ramphal, Yeshnee Naidoo, Zamantungwa T. Khumalo, Gaurav Kwatra, Glenda Gray, Linda-Gail Bekker, Shabir A. Madhi, Vicky Baillie, Wesley C. Van Voorhis, Florette K. Treurnicht, Marietjie Venter, Koleka Mlisana, Nicole Wolter, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Nokukhanya Msomi, Tongai Maponga, Wolfgang Preiser, Zinhle Makatini, Richard Lessells, Penny L. Moore, Tulio de Oliveira, Anne von Gottberg, and Jinal N. Bhiman

Subjects
Multidisciplinary, Neutralization Tests, SARS-CoV-2, Spike Glycoprotein, Coronavirus, General Physics and Astronomy, COVID-19, Humans, General Chemistry, Antibodies, Viral, Antibodies, Neutralizing, General Biochemistry, Genetics and Molecular Biology
Abstract

Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other countries. The initial C.1.2 detection is associated with a high substitution rate, and includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity in SARS-CoV-2 variants of concern or variants of interest. Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma from vaccinees and individuals infected with the ancestral D614G virus. In contrast, convalescent donors infected with either Beta or Delta show high plasma neutralization against C.1.2. These functional data suggest that vaccine efficacy against C.1.2 will be equivalent to Beta and Delta, and that prior infection with either Beta or Delta will likely offer protection against C.1.2.

Published
2021

6. Emergence and phenotypic characterization of C.1.2, a globally detected lineage that rapidly accumulated mutations of concern

Author

James Emmanuel San, Koleka Mlisana, Vicky L Baillie, Richard J Lessells, Tulio de Oliveira, Thabo Mohale, Zamantungwa T. H. Khumalo, Carolyn Williamson, Noxolo Ntuli, Prudence Kgagudi, Wolfgang Preiser, Wesley C. Van Voorhis, Josie Everatt, Shabir A. Madhi, Anele Mnguni, Florette K. Treurnicht, Cathrine Scheepers, Bronwen E. Lambson, Sureshnee Pillay, Nicole Wolter, Linda-Gail Bekker, Nelia P. Manamela, Penny L. Moore, Yeshnee Naidoo, Zinhle Makatini, Daniel G. Amoako, Nokukhanya Msomi, Jennifer Giandhari, Anne von Gottberg, Sandile Cele, Alex Sigal, Marietje Venter, Arshad Ismail, Houriiyah Tegally, Nei-yuan Hsiao, Eduan Wilkinson, Constantinos Kurt Wibmer, Tongai Maponga, Glenda Gray, Jinal N. Bhiman, Boitshoko Mahlangu, Gaurav Kwatra, Simone I. Richardson, Darren P. Martin, and Upasana Ramphal

Subjects
Delta, Lineage (genetic), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Biology, Beta (finance), Vaccine efficacy, Virology, Neutralization, Transmissibility (vibration), Virus
Abstract

Global genomic surveillance of SARS-CoV-2 has identified variants associated with increased transmissibility, neutralization resistance and disease severity. Here we report the emergence of the PANGO lineage C.1.2, detected at low prevalence in South Africa and eleven other countries. The emergence of C.1.2, associated with a high substitution rate, includes changes within the spike protein that have been associated with increased transmissibility or reduced neutralization sensitivity in SARS-CoV-2 VOC/VOIs. Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma from vaccinees and individuals infected with the ancestral D614G virus. In contrast, convalescent donors infected with either Beta or Delta showed high plasma neutralization against C.1.2. These functional data suggest that vaccine efficacy against C.1.2 will be equivalent to Beta and Delta, and that prior infection with either Beta or Delta will likely offer protection against C.1.2.

Published
2021
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7. Rapid replacement of the Beta variant by the Delta variant in South Africa

Author

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

Subjects
Delta, Transmission (mechanics), law, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Biology, Beta (finance), Third wave, Demography, law.invention
Abstract

The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in South Africa in late 2020 and rapidly became the dominant variant, causing over 95% of infections in the country during and after the second epidemic wave. Here we show rapid replacement of the Beta variant by the Delta variant, a highly transmissible variant of concern (VOC) that emerged in India and subsequently spread around the world. The Delta variant was imported to South Africa primarily from India, spread rapidly in large monophyletic clusters to all provinces, and became dominant within three months of introduction. This was associated with a resurgence in community transmission, leading to a third wave which was associated with a high number of deaths. We estimated a growth advantage for the Delta variant in South Africa of 0.089 (95% confidence interval [CI] 0.084-0.093) per day which corresponds to a transmission advantage of 46% (95% CI 44-48) compared to the Beta variant. These data provide additional support for the increased transmissibility of the Delta variant relative to other VOC and highlight how dynamic shifts in the distribution of variants contribute to the ongoing public health threat.

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