Department of Microbiology, Haukeland University Hospital, Bergen, Norway.
Ulvik municipality, Ulvik, Norway.
mSphere. 2024 Aug 28;9(8):e0011424. doi: 10.1128/msphere.00114-24. Epub 2024 Aug 7.
Sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes throughout the COVID-19 pandemic has generated a wealth of data on viral evolution across populations, but only a few studies have so far explored SARS-CoV-2 evolution across large connected transmission networks. Here, we couple data from SARS-CoV-2 sequencing with contact tracing data from an outbreak with a single origin in a rural Norwegian community where samples from all exposed persons were collected prospectively. A total of 134 nasopharyngeal samples were positive by PCR. Among the 121 retrievable genomes, 81 were identical to the genome of the introductor, thus demonstrating that genomics beyond clustering genotypically similar viral genomes to confirm relatedness offers limited additional value to manual contact tracing. In the cases where mutations were discovered, five small genetic clusters were identified. We observed a household secondary attack rate of 77%, with 92% of household members infected among households with secondary transmission, suggesting that SARS-CoV-2 introduction into large families is likely to affect all household members.
In outbreak investigations, obtaining a full overview of infected individuals within a population is seldom achieved. We here present an example where a single introduction of B1.1.7 SARS-CoV-2 within a rural community allowed for tracing of the virus from an introductor via dissemination through larger gatherings into households. The outbreak occurred before widespread vaccination, allowing for a "natural" outbreak development with community lockdown. We show through sequencing that the virus can infect up to five consecutive persons without gaining mutations, thereby showing that contact tracing seems more important than sequencing for local outbreak investigations in settings with few alternative introductory transmission pathways. We also show how larger households where a child introduced transmission appeared more likely to promote further spread of the virus compared to households with an adult as the primary introductor.
整个 COVID-19 大流行期间对严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 基因组进行测序，产生了大量有关人群中病毒进化的资料，但迄今为止，只有少数研究探索了跨越大型连续传播网络的 SARS-CoV-2 进化。在这里，我们将 SARS-CoV-2 测序数据与来自挪威农村社区单一来源暴发的接触者追踪数据相结合，在该社区中前瞻性地收集了所有暴露者的样本。总共 134 份鼻咽样本 PCR 检测呈阳性。在可回收的 121 个基因组中，有 81 个与引入者的基因组完全相同，这表明除了通过聚类对遗传上相似的病毒基因组进行基因分型以确认亲缘关系之外，基因组学对人工接触者追踪提供的附加价值有限。在发现突变的情况下，确定了五个小的遗传簇。我们观察到家庭二次攻击率为 77%，在有二次传播的家庭中，92%的家庭成员感染，这表明 SARS-CoV-2 引入大家庭可能会影响所有家庭成员。
在暴发调查中，很少能全面了解人群中的受感染者。我们在此介绍一个示例，即 B1.1.7 SARS-CoV-2 在农村社区的单一引入允许通过较大规模的聚会传播将病毒从引入者追踪到家庭。暴发发生在广泛接种疫苗之前，允许在社区封锁下进行“自然”暴发发展。通过测序我们表明，病毒可以在没有获得突变的情况下感染多达连续五个人，这表明在引入途径较少的情况下，接触者追踪对于当地暴发调查似乎比测序更为重要。我们还表明，与成人作为主要引入者的家庭相比，有孩子引入传播的大家庭更有可能促进病毒的进一步传播。
