SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021
Since the COVID-19 outbreak emerged, SARS-CoV-2 has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. The SARS-CoV-2 pandemic in South Africa has been characterized by periods...
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Virology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fviro.2022.935131/full |
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| author | Peter Mwangi Javan Okendo Javan Okendo Milton Mogotsi Ayodeji Ogunbayo Olusesan Adelabu Hlengiwe Sondlane Makgotso Maotoana Lutfiyya Mahomed Molefi Daniel Morobadi Molefi Daniel Morobadi Sabeehah Vawda Sabeehah Vawda Anne von Gottberg Anne von Gottberg Jinal Bhiman Jinal Bhiman Houriiyah Tegally Eduan Wilkinson Jennifer Giandhari Sureshnee Pillay Yeshnee Naidoo Upasana Ramphal Tulio de Oliveira Tulio de Oliveira Tulio de Oliveira Armand Bester Armand Bester Dominique Goedhals Dominique Goedhals Dominique Goedhals Martin Nyaga |
| author_facet | Peter Mwangi Javan Okendo Javan Okendo Milton Mogotsi Ayodeji Ogunbayo Olusesan Adelabu Hlengiwe Sondlane Makgotso Maotoana Lutfiyya Mahomed Molefi Daniel Morobadi Molefi Daniel Morobadi Sabeehah Vawda Sabeehah Vawda Anne von Gottberg Anne von Gottberg Jinal Bhiman Jinal Bhiman Houriiyah Tegally Eduan Wilkinson Jennifer Giandhari Sureshnee Pillay Yeshnee Naidoo Upasana Ramphal Tulio de Oliveira Tulio de Oliveira Tulio de Oliveira Armand Bester Armand Bester Dominique Goedhals Dominique Goedhals Dominique Goedhals Martin Nyaga |
| author_sort | Peter Mwangi |
| collection | DOAJ |
| description | Since the COVID-19 outbreak emerged, SARS-CoV-2 has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. The SARS-CoV-2 pandemic in South Africa has been characterized by periods of infections with four major epidemic waves. To determine whether the variants driving the epidemic waves at the national level were also driving the epidemic waves at the local level, we performed analysis of a total of 1287 samples from qPCR confirmed SARS-CoV-2 positive individuals. The samples were subjected to viral RNA extraction, genomic amplification, and sequencing. Variant assignment of the viral sequences and mutation identification were conducted using PANGOLIN and SARS-CoV-2 genome annotator, respectively. Our analysis revealed that during the initial part of the first wave, B.1, B.1.1, B.1.1.53, B.1.1.448 and B.1.237 circulated in the Free State province, followed by Beta variant, B.1.351 later in the wave. Although most of the initially detected variants disappeared during the second wave, the Beta variant, B.1.351, persisted. Early in the third wave, the Beta variant, B.1.351, predominated but was replaced by the Delta sub-lineage, AY.45. The fourth wave was characterized by unique emergence of the Omicron sub-variant, BA.1. The data further indicates that SARS-CoV-2 variants driving the epidemic waves in the Free State at the local level correlated with the ones driving the epidemic waves at the national level. Findings from this study highlight the importance of continued genomic surveillance and monitoring of the circulating SARS-CoV-2 variants to inform public health efforts and ensure adequate control of the ongoing pandemic. |
| first_indexed | 2024-04-11T09:54:43Z |
| format | Article |
| id | doaj.art-291c42a6b3aa4017baf17b154012b068 |
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| issn | 2673-818X |
| language | English |
| last_indexed | 2024-04-11T09:54:43Z |
| publishDate | 2022-09-01 |
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| series | Frontiers in Virology |
| spelling | doaj.art-291c42a6b3aa4017baf17b154012b0682022-12-22T04:30:37ZengFrontiers Media S.A.Frontiers in Virology2673-818X2022-09-01210.3389/fviro.2022.935131935131SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021Peter Mwangi0Javan Okendo1Javan Okendo2Milton Mogotsi3Ayodeji Ogunbayo4Olusesan Adelabu5Hlengiwe Sondlane6Makgotso Maotoana7Lutfiyya Mahomed8Molefi Daniel Morobadi9Molefi Daniel Morobadi10Sabeehah Vawda11Sabeehah Vawda12Anne von Gottberg13Anne von Gottberg14Jinal Bhiman15Jinal Bhiman16Houriiyah Tegally17Eduan Wilkinson18Jennifer Giandhari19Sureshnee Pillay20Yeshnee Naidoo21Upasana Ramphal22Tulio de Oliveira23Tulio de Oliveira24Tulio de Oliveira25Armand Bester26Armand Bester27Dominique Goedhals28Dominique Goedhals29Dominique Goedhals30Martin Nyaga31Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaSystems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South AfricaCentre for Research in Therapeutic Sciences (CREATES), Strathmore University, Nairobi, KenyaNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaDivision of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaDivision of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaDivision of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaAmpath Laboratories, Pretoria, South AfricaDivision of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaDivision of Virology, National Health Laboratory Service, Bloemfontein, South AfricaNational Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South AfricaSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South AfricaNational Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South AfricaSchool of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South AfricaKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa0Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa1Centre for AIDS Program of Research in South Africa (CAPRISA), Durban, South AfricaDivision of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaDivision of Virology, National Health Laboratory Service, Bloemfontein, South AfricaDivision of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaDivision of Virology, National Health Laboratory Service, Bloemfontein, South Africa2Pathcare Vermaak, Pretoria, South AfricaNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South AfricaSince the COVID-19 outbreak emerged, SARS-CoV-2 has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. The SARS-CoV-2 pandemic in South Africa has been characterized by periods of infections with four major epidemic waves. To determine whether the variants driving the epidemic waves at the national level were also driving the epidemic waves at the local level, we performed analysis of a total of 1287 samples from qPCR confirmed SARS-CoV-2 positive individuals. The samples were subjected to viral RNA extraction, genomic amplification, and sequencing. Variant assignment of the viral sequences and mutation identification were conducted using PANGOLIN and SARS-CoV-2 genome annotator, respectively. Our analysis revealed that during the initial part of the first wave, B.1, B.1.1, B.1.1.53, B.1.1.448 and B.1.237 circulated in the Free State province, followed by Beta variant, B.1.351 later in the wave. Although most of the initially detected variants disappeared during the second wave, the Beta variant, B.1.351, persisted. Early in the third wave, the Beta variant, B.1.351, predominated but was replaced by the Delta sub-lineage, AY.45. The fourth wave was characterized by unique emergence of the Omicron sub-variant, BA.1. The data further indicates that SARS-CoV-2 variants driving the epidemic waves in the Free State at the local level correlated with the ones driving the epidemic waves at the national level. Findings from this study highlight the importance of continued genomic surveillance and monitoring of the circulating SARS-CoV-2 variants to inform public health efforts and ensure adequate control of the ongoing pandemic.https://www.frontiersin.org/articles/10.3389/fviro.2022.935131/fullBeta variantDelta variantepidemiological profileOmicron variantFree StateSARS-CoV-2 variants |
| spellingShingle | Peter Mwangi Javan Okendo Javan Okendo Milton Mogotsi Ayodeji Ogunbayo Olusesan Adelabu Hlengiwe Sondlane Makgotso Maotoana Lutfiyya Mahomed Molefi Daniel Morobadi Molefi Daniel Morobadi Sabeehah Vawda Sabeehah Vawda Anne von Gottberg Anne von Gottberg Jinal Bhiman Jinal Bhiman Houriiyah Tegally Eduan Wilkinson Jennifer Giandhari Sureshnee Pillay Yeshnee Naidoo Upasana Ramphal Tulio de Oliveira Tulio de Oliveira Tulio de Oliveira Armand Bester Armand Bester Dominique Goedhals Dominique Goedhals Dominique Goedhals Martin Nyaga SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021 Frontiers in Virology Beta variant Delta variant epidemiological profile Omicron variant Free State SARS-CoV-2 variants |
| title | SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021 |
| title_full | SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021 |
| title_fullStr | SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021 |
| title_full_unstemmed | SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021 |
| title_short | SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021 |
| title_sort | sars cov 2 variants from covid 19 positive cases in the free state province south africa from july 2020 to december 2021 |
| topic | Beta variant Delta variant epidemiological profile Omicron variant Free State SARS-CoV-2 variants |
| url | https://www.frontiersin.org/articles/10.3389/fviro.2022.935131/full |
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