Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022
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基因组监测确定 2020-2022 年美国威斯康星州当地大学人群中 SARS-CoV-2 的传播模式
DOI：
10.1101/2022.07.06.22277014
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发表时间：
2022
影响因子：
3.9
通讯作者：
S. Bhattacharyya
中科院分区：
文献类型：
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作者：
A. Ramaiah;M. Khubbar;A. Bauer;Samantha J. Scott;J. Lentz;K. Akinyemi;Addie Skillman;Josh Weiner;Nandhakumar Balakrishnan;S. Bhattacharyya
随着当前的冠状病毒病2019年(新冠肺炎)大流行进入第三个年头，严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)的新变种继续出现。了解SARS-CoV-2在大学人群中的传播对于在高等教育环境中进行有效干预至关重要，这种干预将在大流行期间为公共卫生政策提供信息。在这项研究中，我们对来自美国威斯康星州两所大学人群近20个月的1717份SARS-CoV-2阳性鼻咽/鼻拭子样本中的537份进行了全基因组测序。我们观察到病毒序列分布在15个分支的57个谱系/亚谱系中，其中大部分来自21K(Omicron，36.13%)和21J(Delta，30.91%)。近40%(213个)的序列是Omicron，其中BA.1及其8个后代占91%，其余属于BA.2及其6个后代。对这两所大学的独立序列分析显示，在SARS-CoV-2变异株的循环中存在显著差异。对密切相关的菌株进行的基因组分析以及系统发育簇已经确定，潜在的病毒传播发生在大学内部和大学之间，以及大学和当地社区之间。虽然这项研究提高了我们对当地大学中流行变种的不同传播模式的理解，但扩大基因组监测能力将有助于地方司法机构识别新出现的SARS-CoV-2变种，如BA.4和BA.5，并改善以数据为导向的公共卫生缓解和政策努力。
Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the current coronavirus disease 2019 (COVID-19) pandemic extends into its third year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in a higher education setting that will inform pubic health policy during pandemics. In this study, we performed whole-genome sequencing of 537 of 1,717 SARS-CoV-2 positive nasopharyngeal/nasal swab samples collected for nearly 20 months from the two university populations in Wisconsin, United States. We observed that the viral sequences were distributed into 57 lineages/sub-lineages belonging to 15 clades of which the majority were from 21K (Omicron, 36.13%) and 21J (Delta, 30.91%). Nearly 40% (213) of the sequences were Omicron of which BA.1 and its eight descendent lineages account for 91%, while the remaining belong to BA.2 and its six descendent lineages. The independent analysis of these two universities sequences revealed significant differences in circulating the SARS-CoV-2 variants. The genome-based analysis of closely-related strains along with phylogenetic clusters had identified that potential virus transmission occurred within as well as between universities, and between the university and local community. Although this study improves our understanding of distinct transmission patterns of circulating variants in local universities, expanding the genomic surveillance capacity will aid local jurisdictions in identifying emerging SARS-CoV-2 variants like BA.4 and BA.5, and improve data-driven public health mitigation and policy efforts.