Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.
Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.
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DOI：
10.1126/science.abl9551
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发表时间：
2021-12-17
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英国的严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）疫苗接种率很高，超过80%的成年人。随着免疫力的减弱和社会距离的放松，更多传染性变异对疾病和严重疾病的发病率有何影响？Elliott等人使用了REACT-1研究的逆转录PCR数据，结果显示，随着Alpha变异（B.1.1.7）被Delta变异（B.1.617.2）所取代，呈指数传播。在调整了年龄和其他变量后，2020年6月和7月，新变种的疫苗有效性平均为55%。尽管夏季大流行的增长速度较慢，但尽管成人疫苗接种水平很高，但秋季室内混合的增加似乎仍将维持德尔塔变种的传播。在英国，由于尚未接种疫苗的年轻人群感染，SARS-CoV-2 Delta变体呈指数增长。尽管疫苗接种水平很高，但严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）感染的流行率继续推高发病率和住院率，在许多人群中，由德尔塔病毒谱系引起的病例比例在增加。随着疫苗接种计划在全球范围内的推广和社会距离的放松，未来的SARS-CoV-2趋势是不确定的。自2020年5月以来，社区传播实时评估-1 （REACT-1）研究一直在追踪COVID-19大流行在英格兰的传播。这项研究包括在每月2到3周的时间里，从10万或更多的人身上获得一份用于逆转录聚合酶链反应（RT-PCR）的自我喉咙和鼻子拭子，该研究基于英国5岁及以上人口的随机样本。除了关于拭子阳性的信息外，我们还收集了有关潜在风险因素和（自2021年1月以来）疫苗接种史的人口统计学和其他数据。流行率估计是加权的，以代表整个英格兰人口。在这里，我们使用reaction -1第12轮（2021年5月20日至6月7日）和第13轮（2021年6月24日至7月12日）的RT-PCR拭子阳性数据分析了流行趋势及其驱动因素。响应率，定义为我们收到有效棉签结果的受邀者的百分比，在所有轮次中分别为20.4%和13.4%和11.7%。随着第三波疫情在英国爆发，我们观察到持续的指数增长，第12轮的繁殖数R估计为1.44(95%可信区间1.20,1.73)，第13轮的繁殖数R估计为1.19(1.06,1.32)，对应于第12轮的平均翻倍时间为11天（7.23天），第13轮的平均翻倍时间为25天（15.5 - 50天）。这导致平均加权患病率从第12轮（108,911份有效拭子中135份阳性）的0.15%（0.12%,0.18%）增加到第13轮（98,233份中527份阳性）的0.63%（0.57%,0.69%）。轮间和轮内的快速增长似乎是由Delta变体完全取代Alpha变体以及在年轻，接种疫苗较少的年龄组中的高患病率所驱动的：在13至17岁的人群中，我们观察到在第12轮[0.16%(0.08%,0.31%)]和第13轮[1.56%(1.25%,1.95%)]之间加权患病率增加了9倍。在第13轮中，报告未接种疫苗者的加权患病率[1.21%(1.03%,1.41%)]比报告接种过两剂疫苗者的加权患病率[0.40%(0.34%,0.48%)]高出3倍；然而，44%的感染发生在两次接种疫苗的个体中，这反映了尽管总体接种水平很高，但两次接种后疫苗对感染的有效性（VE）并不完善。在18至64岁的参与者中，根据自我报告的疫苗接种状况，我们估计在第13轮中，感染的VE（根据年龄、性别、地区、种族和多重剥夺指数进行调整）为49%(95%置信区间为22%，67%)，当仅考虑强阳性[周期阈值（Ct）值低于27]时，VE上升至58%（33%,73%）。对于同一年龄组，我们估计对有症状感染的校正VE为59%(23%,78%)，即在检测前一个月报告一种或多种常见COVID-19症状（发烧、嗅觉或味觉丧失或改变、新的持续咳嗽）的患者。除年龄外，种族、家庭规模和当地贫困程度共同导致棉签阳性流行率较高的风险。从2021年5月底到7月初，在英格兰，疫苗接种运动非常成功，疫苗接种率很高，感染呈指数级增长——由Delta变异驱动——在年轻、未接种疫苗的个体中感染率很高。尽管2021年夏季北半球的增长速度较慢（或流行率水平或下降），但德尔塔病毒变体存在下的混合增加可能解释了2021年秋季出现的重新增长，即使在疫苗接种水平较高的人群中也是如此。主要和左上：反应-1第12轮至第13轮的Delta变体完全取代Alpha，以及根据自我报告的疫苗状况随机抽样的5岁及以上英格兰人口中SARS-CoV-2感染的加权流行率。右下：经年龄、性别、多重剥夺指数、地区和种族调整后的VE。2021年初夏，由于德尔塔病毒变体，许多国家的严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）感染呈上升趋势。我们在英国社区传播实时评估-1 （REACT-1）研究中评估了逆转录聚合酶链反应拭子阳性。在2021年6月和7月期间，我们观察到持续的指数增长，平均翻倍时间为25天，这是由于Delta变体完全取代Alpha变体以及年轻，接种疫苗较少的年龄的高患病率所驱动的。未接种人群的患病率[1.21%(95%可信区间1.03%,1.41%)]是两次接种人群患病率[0.40%(95%可信区间0.34%,0.48%)]的3倍。然而，在调整了年龄和其他变量后，在英格兰，在这一时期，两次接种疫苗的人的疫苗有效性估计在50%到60%之间。在德尔塔存在的情况下，社会混合的增加有可能导致感染的持续增长，即使在高水平的疫苗接种中也是如此。
The United Kingdom has high rates of vaccination for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exceeding 80% of adults. As immunity wanes and social distancing is relaxed, how are rates of illness and severe disease affected by more infectious variants? Elliott et al. used reverse transcription PCR data from the REACT-1 study, which showed exponential transmission as the Alpha variant (B.1.1.7) was replaced by the Delta variant (B.1.617.2). After adjusting for age and other variables, vaccine effectiveness for the new variant averaged 55% in June and July of 2020. Despite the slower growth of the pandemic in the summer, it looks as if increased indoor mixing in the autumn will sustain transmission of the Delta variant despite high levels of adult vaccination. —CA The SARS-CoV-2 Delta variant increased exponentially in the United Kingdom driven by infection in the young, not yet vaccinated, population. The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to drive rates of illness and hospitalizations despite high levels of vaccination, with the proportion of cases caused by the Delta lineage increasing in many populations. As vaccination programs roll out globally and social distancing is relaxed, future SARS-CoV-2 trends are uncertain. The Real-time Assessment of Community Transmission–1 (REACT-1) study has been tracking the spread of the COVID-19 pandemic in England since May 2020. The study involves obtaining a self-administered throat and nose swab for reverse transcription polymerase chain reaction (RT-PCR) from ~100,000 or more people during 2 to 3 weeks each month, based on random samples of the population in England at ages 5 years and above. As well as information on swab positivity, we collect demographic and other data on potential risk factors and (since January 2021) vaccination history. Prevalence estimates are weighted to be representative of the population of England as a whole. Here, we analyzed prevalence trends and their drivers using RT-PCR swab positivity data from REACT-1 round 12 (between 20 May and 7 June 2021) and round 13 (between 24 June and 12 July 2021). Response rates, defined as the percentage of invitees from whom we received a valid swab result, were 20.4% across all rounds and 13.4% and 11.7% for rounds 12 and 13, respectively. We observed sustained exponential growth as the third wave in England took hold, with reproduction number R estimated at 1.44 (95% credible interval 1.20, 1.73) in round 12 and 1.19 (1.06, 1.32) in round 13, corresponding to an average doubling time of 11 days (7, 23 days) in round 12 and 25 days (15, >50 days) in round 13. This resulted in an increase in average weighted prevalence from 0.15% (0.12%, 0.18%) in round 12 (based on 135 positives out of 108,911 valid swabs) to 0.63% (0.57%, 0.69%) in round 13 (527 positives out of 98,233). The rapid growth across and within rounds appears to have been driven by complete replacement of the Alpha variant by Delta, and by the high prevalence in younger, less-vaccinated age groups: Among those aged 13 to 17 years, we observed an increase in weighted prevalence by a factor of 9 between round 12 [0.16% (0.08%, 0.31%)] and round 13 [1.56% (1.25%, 1.95%)]. In round 13, weighted prevalence among those who reported being unvaccinated [1.21% (1.03%, 1.41%)] was greater than for those who reported having had two doses of vaccine [0.40% (0.34%, 0.48%)] by a factor of 3; however, 44% of infections occurred in doubly vaccinated individuals, reflecting imperfect vaccine effectiveness (VE) against infection after two doses despite high overall levels of vaccination. Among participants aged 18 to 64 years, on the basis of self-reported vaccination status, we estimated VE against infection (adjusted for age, sex, region, ethnicity, and index of multiple deprivation) of 49% (95% confidence interval 22%, 67%) in round 13, rising to 58% (33%, 73%) when only strong positives [cycle threshold (Ct) values below 27] were considered. For the same age group, we estimated adjusted VE of 59% (23%, 78%) against symptomatic infection—that is, among those reporting one or more common COVID-19 symptoms in the month prior to testing (fever, loss or change of sense of smell or taste, new persistent cough). Ethnicity, household size, and local levels of deprivation, in addition to age, jointly contributed to the risk of higher prevalence of swab positivity. From the end of May to the beginning of July 2021 in England, where there was a highly successful vaccination campaign with high vaccine uptake, infections were increasing exponentially—driven by the Delta variant—with high infection prevalence among younger, unvaccinated individuals. Despite slower growth (or level or declining prevalence) during summer 2021 in the Northern Hemisphere, increased mixing in the presence of the Delta variant likely explains renewed growth that occurred in autumn 2021, even in populations with high levels of vaccination. Main and top left: Complete replacement of Alpha by the Delta variant from REACT-1 round 12 to round 13 and weighted prevalence of SARS-CoV-2 infection among a random sample of the population of England ages 5 years and above by self-reported vaccine status. Bottom right: VE adjusted for age, sex, index of multiple deprivation, region, and ethnicity. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.
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