@article{Wolter2022a,
abstract = {Early data indicated that infection with Omicron BA.1 sub-lineage was associated with a lower risk of hospitalisation and severe illness, compared to Delta infection. Recently, the BA.2 sub-lineage has increased in many areas globally. We aimed to assess the severity of BA.2 infections compared to BA.1 in South Africa. We performed data linkages for (i) national COVID-19 case data, (ii) SARS-CoV-2 laboratory test data, and (iii) COVID-19 hospitalisations data, nationally. For cases identified using TaqPath COVID-19 PCR, infections were designated as S-gene target failure (SGTF, proxy for BA.1) or S-gene positive (proxy for BA.2). Disease severity was assessed using multivariable logistic regression models comparing individuals with S-gene positive infection to SGTF-infected individuals diagnosed between 1 December 2021 to 20 January 2022. From week 49 (starting 5 December 2021) through week 4 (ending 29 January 2022), the proportion of S-gene positive infections increased from 3{\%} (931/31,271) to 80{\%} (2,425/3,031). The odds of being admitted to hospital did not differ between individuals with S-gene positive (BA.2 proxy) infection compared to SGTF (BA.1 proxy) infection (adjusted odds ratio (aOR) 0.96, 95{\%} confidence interval (CI) 0.85-1.09). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ for individuals with S-gene positive infection compared to SGTF infection (aOR 0.91, 95{\%}CI 0.68-1.22). These data suggest that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar. {\#}{\#}{\#} Competing Interest Statement CC has received grant support from South African Medical Research Council, UK Foreign, Commonwealth and Development Office and Wellcome Trust, US Centers for Disease Control and Prevention and Sanofi Pasteur. NW has received grant support from Sanofi Pasteur and the Bill and Melinda Gates Foundation. AvG has received grant support from US Centers for Disease Control and Prevention, Africa Centres for Disease Control and Prevention, African Society for Laboratory Medicine (ASLM), South African Medical Research Council, WHO AFRO, The Fleming Fund and Wellcome Trust. RW declares personal shareholding in the following companies: Adcock Ingram Holdings Ltd, Dischem Pharmacies Ltd, Discovery Ltd, Netcare Ltd, Aspen Pharmacare Holdings Ltd. All other authors declare no conflict of interest. {\#}{\#}{\#} Funding Statement This study was funded by the South African Medical Research Council with funds received from the National Department of Health. Sequencing activities for NICD are supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (grant number 5 U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub-award from the Bill and Melinda Gates Foundation grant number INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); and the UK Department of Health and Social Care and managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. This research was also supported by The Coronavirus Aid, Relief, and Economic Security Act (CARES ACT) through the Centers for Disease Control and Prevention (CDC) and the COVID International Task Force (ITF) funds through the CDC under the terms of a subcontract with the African Field Epidemiology Network (AFENET) AF-NICD-001/2021. Screening for SGTF at UCT was supported by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). {\#}{\#}{\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval was obtained from the Human Research Ethics Committee (Medical) of University of the Witwatersrand for the collection of COVID-19 case and test data as part of essential communicable disease surveillance (M210752), and for the DATCOV surveillance programme (M2010108). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data used in this manuscript are available upon reasonable request. Proposals should be directed to cherylc{\{}at{\}}nicd.ac.za.},
author = {Wolter, Nicole and Jassat, Waasila and author Group, DATCOV-Gen and von Gottberg, Anne and Cohen, Cheryl},
doi = {10.1101/2022.02.17.22271030},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wolter et al. - 2022 - Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa.pdf:pdf},
journal = {medRxiv},
keywords = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {feb},
pages = {2022.02.17.22271030},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa}},
url = {https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1 https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1.abstract},
year = {2022}
}

{"_id":"qJXvAdJoT6pAwTWdL","bibbaseid":"wolter-jassat-authorgroup-vongottberg-cohen-clinicalseverityofomicronsublineageba2comparedtoba1insouthafrica-2022","author_short":["Wolter, N.","Jassat, W.","author Group, D.","von Gottberg, A.","Cohen, C."],"bibdata":{"bibtype":"article","type":"article","abstract":"Early data indicated that infection with Omicron BA.1 sub-lineage was associated with a lower risk of hospitalisation and severe illness, compared to Delta infection. Recently, the BA.2 sub-lineage has increased in many areas globally. We aimed to assess the severity of BA.2 infections compared to BA.1 in South Africa. We performed data linkages for (i) national COVID-19 case data, (ii) SARS-CoV-2 laboratory test data, and (iii) COVID-19 hospitalisations data, nationally. For cases identified using TaqPath COVID-19 PCR, infections were designated as S-gene target failure (SGTF, proxy for BA.1) or S-gene positive (proxy for BA.2). Disease severity was assessed using multivariable logistic regression models comparing individuals with S-gene positive infection to SGTF-infected individuals diagnosed between 1 December 2021 to 20 January 2022. From week 49 (starting 5 December 2021) through week 4 (ending 29 January 2022), the proportion of S-gene positive infections increased from 3% (931/31,271) to 80% (2,425/3,031). The odds of being admitted to hospital did not differ between individuals with S-gene positive (BA.2 proxy) infection compared to SGTF (BA.1 proxy) infection (adjusted odds ratio (aOR) 0.96, 95% confidence interval (CI) 0.85-1.09). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ for individuals with S-gene positive infection compared to SGTF infection (aOR 0.91, 95%CI 0.68-1.22). These data suggest that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar. ### Competing Interest Statement CC has received grant support from South African Medical Research Council, UK Foreign, Commonwealth and Development Office and Wellcome Trust, US Centers for Disease Control and Prevention and Sanofi Pasteur. NW has received grant support from Sanofi Pasteur and the Bill and Melinda Gates Foundation. AvG has received grant support from US Centers for Disease Control and Prevention, Africa Centres for Disease Control and Prevention, African Society for Laboratory Medicine (ASLM), South African Medical Research Council, WHO AFRO, The Fleming Fund and Wellcome Trust. RW declares personal shareholding in the following companies: Adcock Ingram Holdings Ltd, Dischem Pharmacies Ltd, Discovery Ltd, Netcare Ltd, Aspen Pharmacare Holdings Ltd. All other authors declare no conflict of interest. ### Funding Statement This study was funded by the South African Medical Research Council with funds received from the National Department of Health. Sequencing activities for NICD are supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (grant number 5 U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub-award from the Bill and Melinda Gates Foundation grant number INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); and the UK Department of Health and Social Care and managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. This research was also supported by The Coronavirus Aid, Relief, and Economic Security Act (CARES ACT) through the Centers for Disease Control and Prevention (CDC) and the COVID International Task Force (ITF) funds through the CDC under the terms of a subcontract with the African Field Epidemiology Network (AFENET) AF-NICD-001/2021. Screening for SGTF at UCT was supported by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval was obtained from the Human Research Ethics Committee (Medical) of University of the Witwatersrand for the collection of COVID-19 case and test data as part of essential communicable disease surveillance (M210752), and for the DATCOV surveillance programme (M2010108). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data used in this manuscript are available upon reasonable request. Proposals should be directed to cherylc\\at\\nicd.ac.za.","author":[{"propositions":[],"lastnames":["Wolter"],"firstnames":["Nicole"],"suffixes":[]},{"propositions":[],"lastnames":["Jassat"],"firstnames":["Waasila"],"suffixes":[]},{"propositions":["author"],"lastnames":["Group"],"firstnames":["DATCOV-Gen"],"suffixes":[]},{"propositions":["von"],"lastnames":["Gottberg"],"firstnames":["Anne"],"suffixes":[]},{"propositions":[],"lastnames":["Cohen"],"firstnames":["Cheryl"],"suffixes":[]}],"doi":"10.1101/2022.02.17.22271030","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wolter et al. - 2022 - Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa.pdf:pdf","journal":"medRxiv","keywords":"OA,fund_ack,genomics_fund_ack,original","mendeley-tags":"OA,fund_ack,genomics_fund_ack,original","month":"feb","pages":"2022.02.17.22271030","publisher":"Cold Spring Harbor Laboratory Press","title":"Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa","url":"https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1 https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1.abstract","year":"2022","bibtex":"@article{Wolter2022a,\r\nabstract = {Early data indicated that infection with Omicron BA.1 sub-lineage was associated with a lower risk of hospitalisation and severe illness, compared to Delta infection. Recently, the BA.2 sub-lineage has increased in many areas globally. We aimed to assess the severity of BA.2 infections compared to BA.1 in South Africa. We performed data linkages for (i) national COVID-19 case data, (ii) SARS-CoV-2 laboratory test data, and (iii) COVID-19 hospitalisations data, nationally. For cases identified using TaqPath COVID-19 PCR, infections were designated as S-gene target failure (SGTF, proxy for BA.1) or S-gene positive (proxy for BA.2). Disease severity was assessed using multivariable logistic regression models comparing individuals with S-gene positive infection to SGTF-infected individuals diagnosed between 1 December 2021 to 20 January 2022. From week 49 (starting 5 December 2021) through week 4 (ending 29 January 2022), the proportion of S-gene positive infections increased from 3{\\%} (931/31,271) to 80{\\%} (2,425/3,031). The odds of being admitted to hospital did not differ between individuals with S-gene positive (BA.2 proxy) infection compared to SGTF (BA.1 proxy) infection (adjusted odds ratio (aOR) 0.96, 95{\\%} confidence interval (CI) 0.85-1.09). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ for individuals with S-gene positive infection compared to SGTF infection (aOR 0.91, 95{\\%}CI 0.68-1.22). These data suggest that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar. {\\#}{\\#}{\\#} Competing Interest Statement CC has received grant support from South African Medical Research Council, UK Foreign, Commonwealth and Development Office and Wellcome Trust, US Centers for Disease Control and Prevention and Sanofi Pasteur. NW has received grant support from Sanofi Pasteur and the Bill and Melinda Gates Foundation. AvG has received grant support from US Centers for Disease Control and Prevention, Africa Centres for Disease Control and Prevention, African Society for Laboratory Medicine (ASLM), South African Medical Research Council, WHO AFRO, The Fleming Fund and Wellcome Trust. RW declares personal shareholding in the following companies: Adcock Ingram Holdings Ltd, Dischem Pharmacies Ltd, Discovery Ltd, Netcare Ltd, Aspen Pharmacare Holdings Ltd. All other authors declare no conflict of interest. {\\#}{\\#}{\\#} Funding Statement This study was funded by the South African Medical Research Council with funds received from the National Department of Health. Sequencing activities for NICD are supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention (grant number 5 U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub-award from the Bill and Melinda Gates Foundation grant number INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); and the UK Department of Health and Social Care and managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. This research was also supported by The Coronavirus Aid, Relief, and Economic Security Act (CARES ACT) through the Centers for Disease Control and Prevention (CDC) and the COVID International Task Force (ITF) funds through the CDC under the terms of a subcontract with the African Field Epidemiology Network (AFENET) AF-NICD-001/2021. Screening for SGTF at UCT was supported by the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), which is supported by core funding from the Wellcome Trust (203135/Z/16/Z and 222754). {\\#}{\\#}{\\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval was obtained from the Human Research Ethics Committee (Medical) of University of the Witwatersrand for the collection of COVID-19 case and test data as part of essential communicable disease surveillance (M210752), and for the DATCOV surveillance programme (M2010108). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data used in this manuscript are available upon reasonable request. Proposals should be directed to cherylc{\\{}at{\\}}nicd.ac.za.},\r\nauthor = {Wolter, Nicole and Jassat, Waasila and author Group, DATCOV-Gen and von Gottberg, Anne and Cohen, Cheryl},\r\ndoi = {10.1101/2022.02.17.22271030},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wolter et al. - 2022 - Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa.pdf:pdf},\r\njournal = {medRxiv},\r\nkeywords = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmendeley-tags = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmonth = {feb},\r\npages = {2022.02.17.22271030},\r\npublisher = {Cold Spring Harbor Laboratory Press},\r\ntitle = {{Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa}},\r\nurl = {https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1 https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1.abstract},\r\nyear = {2022}\r\n}\r\n","author_short":["Wolter, N.","Jassat, W.","author Group, D.","von Gottberg, A.","Cohen, C."],"key":"Wolter2022a","id":"Wolter2022a","bibbaseid":"wolter-jassat-authorgroup-vongottberg-cohen-clinicalseverityofomicronsublineageba2comparedtoba1insouthafrica-2022","role":"author","urls":{"Paper":"https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1 https://www.medrxiv.org/content/10.1101/2022.02.17.22271030v1.abstract"},"keyword":["OA","fund_ack","genomics_fund_ack","original"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://drive.google.com/uc?export=download&id=1-JLqZ7RwZ3VC2d6ErLGHAtOeMRS_7GCz","dataSources":["Krmt6gt9ktB2s6ARh","y6ojaHcuarkmc4yRQ"],"keywords":["oa","fund_ack","genomics_fund_ack","original"],"search_terms":["clinical","severity","omicron","sub","lineage","compared","south","africa","wolter","jassat","author group","von gottberg","cohen"],"title":"Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa","year":2022}