Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study.
Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study.
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DOI：
10.1016/s0140-6736(22)00017-4
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发表时间：
2022-01-29
期刊：
影响因子：
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通讯作者：
Cohen C
中科院分区：
文献类型：
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作者：
Wolter N;Jassat W;Walaza S;Welch R;Moultrie H;Groome M;Amoako DG;Everatt J;Bhiman JN;Scheepers C;Tebeila N;Chiwandire N;du Plessis M;Govender N;Ismail A;Glass A;Mlisana K;Stevens W;Treurnicht FK;Makatini Z;Hsiao NY;Parboosing R;Wadula J;Hussey H;Davies MA;Boulle A;von Gottberg A;Cohen C
2021年11月在南非发现了SARS-CoV-2 omicron变异体，该变异体与COVID-19病例增加有关。我们的目的是使用Thermo Fisher Scientific TaqPath COVID-19 PCR检测中的S基因靶标失效（SGTF）作为替代，评估omicron变异体感染的临床严重程度。我们对南非全国COVID-19病例数据、SARS-CoV-2实验室检测数据、SARS-CoV-2基因组数据和COVID-19住院数据进行了数据链接。对于通过TaqPath PCR检测诊断为COVID-19的个体，感染被指定为SGTF或非SGTF。通过基因组测序鉴定δ变体。使用多变量logistic回归模型，我们通过比较2021年10月1日至11月30日期间诊断的SGTF与非SGTF感染个体来评估疾病严重程度和住院治疗，并通过比较2021年10月1日至11月30日期间诊断的SGTF感染个体与2021年4月1日至11月9日期间诊断的Delta变异体感染个体来进一步评估疾病严重程度。从2021年10月1日（第39周）至2021年12月6日（第49周），南非报告了161 328例COVID-19病例。通过TaqPath PCR检测诊断了38282人，并确定了29721例SGTF感染和1412例非SGTF感染。SGTF感染的比例从第39周的63例中的2例（3.2%）增加到第48周的22 455例中的21 978例（97.9%）。在控制了与住院相关的因素后，SGTF感染者的入院几率显著低于非SGTF感染者（1 - 0 547例中有256例[2.4%] vs 948例中有121例[12.8%];校正后的比值比[aOR] 0.2，95%CI 0.1 - 0.3）。在控制了与疾病严重程度相关的因素后，SGTF感染住院患者与非SGTF感染住院患者之间发生严重疾病的几率相似（42/204 [21%] vs 45/113 [40%]; aOR 0.7，95%CI 0.3 - 1.4）。在控制了与疾病严重程度相关的因素后，与早期感染δ变异体的个体相比，SGTF感染个体发生严重疾病的几率显著较低（793例中有496例[62.5%] vs 244例中有57例[23.4%]; aOR 0.3，95%CI 0.2 - 0.5）。我们的早期分析表明，在同一时间段内诊断出SGTF感染的个体与非SGTF感染的个体相比，住院的几率显著降低。SGTF感染的个体与早期感染δ变体的个体相比，严重疾病的几率显著降低。这种严重程度的降低可能是以前免疫的结果。南非医学研究理事会、南非国家卫生部、美国疾病控制和预防中心、非洲实验室医学学会、非洲疾病控制和预防中心、比尔和梅林达·盖茨基金会、惠康信托基金会和弗莱明基金会。
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. 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. 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. 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. 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.