@article{Wolter2022,
abstract = {Summary Background The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. Methods We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. Findings From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3{\textperiodcentered}2{\%}) of 63 in week 39 to 21 978 (97{\textperiodcentered}9{\%}) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2{\textperiodcentered}4{\%}] of 10 547 vs 121 [12{\textperiodcentered}8{\%}] of 948; adjusted odds ratio [aOR] 0{\textperiodcentered}2, 95{\%} CI 0{\textperiodcentered}1–0{\textperiodcentered}3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21{\%}] of 204 vs 45 [40{\%}] of 113; aOR 0{\textperiodcentered}7, 95{\%} CI 0{\textperiodcentered}3–1{\textperiodcentered}4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62{\textperiodcentered}5{\%}] of 793 vs 57 [23{\textperiodcentered}4{\%}] of 244; aOR 0{\textperiodcentered}3, 95{\%} CI 0{\textperiodcentered}2–0{\textperiodcentered}5), after controlling for factors associated with disease severity. Interpretation Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. Funding The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill {\&} Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.},
author = {Wolter, Nicole and Jassat, Waasila and Walaza, Sibongile and Welch, Richard and Moultrie, Harry and Groome, Michelle and Amoako, Daniel Gyamfi and Everatt, Josie and Bhiman, Jinal N and Scheepers, Cathrine and Tebeila, Naume and Chiwandire, Nicola and du Plessis, Mignon and Govender, Nevashan and Ismail, Arshad and Glass, Allison and Mlisana, Koleka and Stevens, Wendy and Treurnicht, Florette K and Makatini, Zinhle and Hsiao, Nei-yuan and Parboosing, Raveen and Wadula, Jeannette and Hussey, Hannah and Davies, Mary-Ann and Boulle, Andrew and von Gottberg, Anne and Cohen, Cheryl},
doi = {10.1016/S0140-6736(22)00017-4},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wolter et al. - 2022 - Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa a data linkage study.pdf:pdf},
issn = {0140-6736},
journal = {The Lancet},
keywords = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,genomics{\_}fund{\_}ack,original},
month = {jan},
number = {10323},
pages = {437--446},
pmid = {35065011},
publisher = {Elsevier},
title = {{Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study}},
url = {http://www.thelancet.com/article/S0140673622000174/fulltext http://www.thelancet.com/article/S0140673622000174/abstract https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00017-4/abstract},
volume = {399},
year = {2022}
}

{"_id":"sxrsKqmuTZ3kixCNK","bibbaseid":"wolter-jassat-walaza-welch-moultrie-groome-amoako-everatt-etal-earlyassessmentoftheclinicalseverityofthesarscov2omicronvariantinsouthafricaadatalinkagestudy-2022","author_short":["Wolter, N.","Jassat, W.","Walaza, S.","Welch, R.","Moultrie, H.","Groome, M.","Amoako, D. G.","Everatt, J.","Bhiman, J. N","Scheepers, C.","Tebeila, N.","Chiwandire, N.","du Plessis, M.","Govender, N.","Ismail, A.","Glass, A.","Mlisana, K.","Stevens, W.","Treurnicht, F. K","Makatini, Z.","Hsiao, N.","Parboosing, R.","Wadula, J.","Hussey, H.","Davies, M.","Boulle, A.","von Gottberg, A.","Cohen, C."],"bibdata":{"bibtype":"article","type":"article","abstract":"Summary Background The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. Methods We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. Findings From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3˙2%) of 63 in week 39 to 21 978 (97˙9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2˙4%] of 10 547 vs 121 [12˙8%] of 948; adjusted odds ratio [aOR] 0˙2, 95% CI 0˙1–0˙3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0˙7, 95% CI 0˙3–1˙4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62˙5%] of 793 vs 57 [23˙4%] of 244; aOR 0˙3, 95% CI 0˙2–0˙5), after controlling for factors associated with disease severity. Interpretation Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. Funding The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.","author":[{"propositions":[],"lastnames":["Wolter"],"firstnames":["Nicole"],"suffixes":[]},{"propositions":[],"lastnames":["Jassat"],"firstnames":["Waasila"],"suffixes":[]},{"propositions":[],"lastnames":["Walaza"],"firstnames":["Sibongile"],"suffixes":[]},{"propositions":[],"lastnames":["Welch"],"firstnames":["Richard"],"suffixes":[]},{"propositions":[],"lastnames":["Moultrie"],"firstnames":["Harry"],"suffixes":[]},{"propositions":[],"lastnames":["Groome"],"firstnames":["Michelle"],"suffixes":[]},{"propositions":[],"lastnames":["Amoako"],"firstnames":["Daniel","Gyamfi"],"suffixes":[]},{"propositions":[],"lastnames":["Everatt"],"firstnames":["Josie"],"suffixes":[]},{"propositions":[],"lastnames":["Bhiman"],"firstnames":["Jinal","N"],"suffixes":[]},{"propositions":[],"lastnames":["Scheepers"],"firstnames":["Cathrine"],"suffixes":[]},{"propositions":[],"lastnames":["Tebeila"],"firstnames":["Naume"],"suffixes":[]},{"propositions":[],"lastnames":["Chiwandire"],"firstnames":["Nicola"],"suffixes":[]},{"propositions":["du"],"lastnames":["Plessis"],"firstnames":["Mignon"],"suffixes":[]},{"propositions":[],"lastnames":["Govender"],"firstnames":["Nevashan"],"suffixes":[]},{"propositions":[],"lastnames":["Ismail"],"firstnames":["Arshad"],"suffixes":[]},{"propositions":[],"lastnames":["Glass"],"firstnames":["Allison"],"suffixes":[]},{"propositions":[],"lastnames":["Mlisana"],"firstnames":["Koleka"],"suffixes":[]},{"propositions":[],"lastnames":["Stevens"],"firstnames":["Wendy"],"suffixes":[]},{"propositions":[],"lastnames":["Treurnicht"],"firstnames":["Florette","K"],"suffixes":[]},{"propositions":[],"lastnames":["Makatini"],"firstnames":["Zinhle"],"suffixes":[]},{"propositions":[],"lastnames":["Hsiao"],"firstnames":["Nei-yuan"],"suffixes":[]},{"propositions":[],"lastnames":["Parboosing"],"firstnames":["Raveen"],"suffixes":[]},{"propositions":[],"lastnames":["Wadula"],"firstnames":["Jeannette"],"suffixes":[]},{"propositions":[],"lastnames":["Hussey"],"firstnames":["Hannah"],"suffixes":[]},{"propositions":[],"lastnames":["Davies"],"firstnames":["Mary-Ann"],"suffixes":[]},{"propositions":[],"lastnames":["Boulle"],"firstnames":["Andrew"],"suffixes":[]},{"propositions":["von"],"lastnames":["Gottberg"],"firstnames":["Anne"],"suffixes":[]},{"propositions":[],"lastnames":["Cohen"],"firstnames":["Cheryl"],"suffixes":[]}],"doi":"10.1016/S0140-6736(22)00017-4","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wolter et al. - 2022 - Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa a data linkage study.pdf:pdf","issn":"0140-6736","journal":"The Lancet","keywords":"OA,fund_ack,genomics_fund_ack,original","mendeley-tags":"OA,fund_ack,genomics_fund_ack,original","month":"jan","number":"10323","pages":"437–446","pmid":"35065011","publisher":"Elsevier","title":"Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study","url":"http://www.thelancet.com/article/S0140673622000174/fulltext http://www.thelancet.com/article/S0140673622000174/abstract https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00017-4/abstract","volume":"399","year":"2022","bibtex":"@article{Wolter2022,\r\nabstract = {Summary Background The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. Methods We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021. Findings From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3{\\textperiodcentered}2{\\%}) of 63 in week 39 to 21 978 (97{\\textperiodcentered}9{\\%}) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2{\\textperiodcentered}4{\\%}] of 10 547 vs 121 [12{\\textperiodcentered}8{\\%}] of 948; adjusted odds ratio [aOR] 0{\\textperiodcentered}2, 95{\\%} CI 0{\\textperiodcentered}1–0{\\textperiodcentered}3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21{\\%}] of 204 vs 45 [40{\\%}] of 113; aOR 0{\\textperiodcentered}7, 95{\\%} CI 0{\\textperiodcentered}3–1{\\textperiodcentered}4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62{\\textperiodcentered}5{\\%}] of 793 vs 57 [23{\\textperiodcentered}4{\\%}] of 244; aOR 0{\\textperiodcentered}3, 95{\\%} CI 0{\\textperiodcentered}2–0{\\textperiodcentered}5), after controlling for factors associated with disease severity. Interpretation Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity. Funding The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill {\\&} Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.},\r\nauthor = {Wolter, Nicole and Jassat, Waasila and Walaza, Sibongile and Welch, Richard and Moultrie, Harry and Groome, Michelle and Amoako, Daniel Gyamfi and Everatt, Josie and Bhiman, Jinal N and Scheepers, Cathrine and Tebeila, Naume and Chiwandire, Nicola and du Plessis, Mignon and Govender, Nevashan and Ismail, Arshad and Glass, Allison and Mlisana, Koleka and Stevens, Wendy and Treurnicht, Florette K and Makatini, Zinhle and Hsiao, Nei-yuan and Parboosing, Raveen and Wadula, Jeannette and Hussey, Hannah and Davies, Mary-Ann and Boulle, Andrew and von Gottberg, Anne and Cohen, Cheryl},\r\ndoi = {10.1016/S0140-6736(22)00017-4},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Wolter et al. - 2022 - Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa a data linkage study.pdf:pdf},\r\nissn = {0140-6736},\r\njournal = {The Lancet},\r\nkeywords = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmendeley-tags = {OA,fund{\\_}ack,genomics{\\_}fund{\\_}ack,original},\r\nmonth = {jan},\r\nnumber = {10323},\r\npages = {437--446},\r\npmid = {35065011},\r\npublisher = {Elsevier},\r\ntitle = {{Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study}},\r\nurl = {http://www.thelancet.com/article/S0140673622000174/fulltext http://www.thelancet.com/article/S0140673622000174/abstract https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00017-4/abstract},\r\nvolume = {399},\r\nyear = {2022}\r\n}\r\n","author_short":["Wolter, N.","Jassat, W.","Walaza, S.","Welch, R.","Moultrie, H.","Groome, M.","Amoako, D. 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