Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis.
Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis.
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DOI：
10.1016/s1473-3099(22)00001-9
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发表时间：
2022-05
期刊：
影响因子：
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通讯作者：
Thompson RN
中科院分区：
文献类型：
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作者：
Hart WS;Miller E;Andrews NJ;Waight P;Maini PK;Funk S;Thompson RN
2021年5月，Delta(B.1.617.2)SARS-CoV-2变种在英国占主导地位，2021年12月被Omicron(B.1.1.529)变种取代。与阿尔法变种相比，三角洲变种与遗传性增加有关，阿尔法变种在2020年12月至2021年5月期间是英国的主要变种。为了了解传播和干预措施的有效性，我们的目的是调查Delta变种的产生时间(在感染者-感染者对中感染之间的间隔)是否比阿尔法变种的产生时间更短，即传播发生得更快。在这项流行病学分析中，我们分析了英国健康安全局(UKHSA)正在进行的一项预期家庭研究的传播数据。在一个指示病例的聚合酶链式反应检测呈阳性后，家庭被招募到研究中，并使用基因组测序来确定相关变异。通过将数学传播模型与数据相匹配，我们估计了阿尔法和德尔塔变种的固有世代时间(假设在感染过程中易感个体的持续供应)和家庭世代时间(反映研究家庭中实现的传播，占易耗尽的家庭)。在2021年2月至8月期间，UKHSA招募了227个家庭，包括559名参与者。在2月至5月招募的131个家庭(334名参与者中的243人感染)中检测到阿尔法变种或认为其对感染负责，5月至8月在96个家庭(225名参与者中的174人感染)中检测到或被认为对三角洲变种负责。Delta变异的平均固有生成时间(4.7d，95%可信区间[CI]4.1~5.6%)比α变异(5.5d，4.7~6.5%)短，后验概率为92%。与阿尔法变异(4·5天，3·7-5·4)相比，增量变异(3.2d，95%可信区间2·5~4.2d)的平均世代时间缩短28%(95%可信区间0~48%)，后验概率为97.5%。德尔塔变种在家庭中的传播速度比阿尔法变种更快，这可以归因于家庭中易感个体更快地耗尽，以及可能减少固有的世代时间。如果病毒迅速传播，接触者追踪、检测和隔离等干预措施可能不那么有效。国家健康研究所、英国健康安全局、工程和物理科学研究理事会以及英国研究和创新。
In May, 2021, the delta (B.1.617.2) SARS-CoV-2 variant became dominant in the UK, superseded by the omicron (B.1.1.529) variant in December, 2021. The delta variant is associated with increased transmissibility compared with the alpha variant, which was the dominant variant in the UK between December, 2020, and May, 2021. To understand transmission and the effectiveness of interventions, we aimed to investigate whether the delta variant generation time (the interval between infections in infector–infectee pairs) is shorter—ie, transmissions are happening more quickly—than that of the alpha variant. In this epidemiological analysis, we analysed transmission data from an ongoing UK Health Security Agency (UKHSA) prospective household study. Households were recruited to the study after an index case had a positive PCR test and genomic sequencing was used to determine the variant responsible. By fitting a mathematical transmission model to the data, we estimated the intrinsic generation time (which assumes a constant supply of susceptible individuals throughout infection) and the household generation time (which reflects realised transmission in the study households, accounting for susceptible depletion) for the alpha and delta variants. Between February and August, 2021, 227 households consisting of 559 participants were recruited to the UKHSA study. The alpha variant was detected or assumed to be responsible for infections in 131 households (243 infections in 334 participants) recruited in February–May, and the delta variant in 96 households (174 infections in 225 participants) in May–August. The mean intrinsic generation time was shorter for the delta variant (4·7 days, 95% credible interval [CI] 4·1–5·6) than the alpha variant (5·5 days, 4·7–6·5), with 92% posterior probability. The mean household generation time was 28% (95% CI 0–48%) shorter for the delta variant (3·2 days, 95% CI 2·5–4·2) than the alpha variant (4·5 days, 3·7–5·4), with 97·5% posterior probability. The delta variant transmits more quickly in households than the alpha variant, which can be attributed to faster depletion of susceptible individuals in households and a possible decrease in the intrinsic generation time. Interventions such as contact tracing, testing, and isolation might be less effective if transmission of the virus occurs quickly. National Institute for Health Research, UK Health Security Agency, Engineering and Physical Sciences Research Council, and UK Research and Innovation.