对大学校园里的 SARS-CoV-2 奥密克戎变异株进行基因组监测。
Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus.
机构信息
Department of Medicine, University of Washington, Seattle, WA, USA.
Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
出版信息
Nat Commun. 2022 Sep 6;13(1):5240. doi: 10.1038/s41467-022-32786-z.
Novel variants continue to emerge in the SARS-CoV-2 pandemic. University testing programs may provide timely epidemiologic and genomic surveillance data to inform public health responses. We conducted testing from September 2021 to February 2022 in a university population under vaccination and indoor mask mandates. A total of 3,048 of 24,393 individuals tested positive for SARS-CoV-2 by RT-PCR; whole genome sequencing identified 209 Delta and 1,730 Omicron genomes of the 1,939 total sequenced. Compared to Delta, Omicron had a shorter median serial interval between genetically identical, symptomatic infections within households (2 versus 6 days, P = 0.021). Omicron also demonstrated a greater peak reproductive number (2.4 versus 1.8), and a 1.07 (95% confidence interval: 0.58, 1.57; P < 0.0001) higher mean cycle threshold value. Despite near universal vaccination and stringent mitigation measures, Omicron rapidly displaced the Delta variant to become the predominant viral strain and led to a surge in cases in a university population.
新型变异株在 SARS-CoV-2 大流行中不断出现。大学检测计划可能提供及时的流行病学和基因组监测数据，为公共卫生应对措施提供信息。我们在接种疫苗和室内戴口罩的大学人群中进行了 2021 年 9 月至 2022 年 2 月的检测。共有 24393 人中有 3048 人通过 RT-PCR 检测出 SARS-CoV-2 阳性；对 1939 个测序的病毒基因组进行全基因组测序，确定了 209 个 Delta 和 1730 个 Omicron 基因组。与 Delta 相比，Omicron 在家中具有相同遗传特征的症状感染之间的中位序列间隔更短（2 天对 6 天，P=0.021）。Omicron 还显示出更高的峰值繁殖数（2.4 对 1.8），以及更高的平均循环阈值（1.07[95%置信区间：0.58，1.57；P<0.0001）。尽管几乎普遍接种疫苗和采取严格的缓解措施，但 Omicron 迅速取代了 Delta 变体，成为主要的病毒株，并导致大学人群中病例激增。
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