Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, USA.
Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
Lancet Microbe. 2024 Apr;5(4):e335-e344. doi: 10.1016/S2666-5247(23)00372-5. Epub 2024 Mar 11.
The origin of novel SARS-CoV-2 spike sequences found in wastewater, without corresponding detection in clinical specimens, remains unclear. We sought to determine the origin of one such cryptic wastewater lineage by tracking and characterising its persistence and genomic evolution over time.
We first detected a cryptic lineage, WI-CL-001, in municipal wastewater in Wisconsin, USA, in January, 2022. To determine the source of WI-CL-001, we systematically sampled wastewater from targeted sub-sewershed lines and maintenance holes using compositing autosamplers. Viral concentrations in wastewater samples over time were measured by RT digital PCR. In addition to using metagenomic 12s rRNA sequencing to determine the virus's host species, we also sequenced SARS-CoV-2 spike receptor binding domains, and, where possible, whole viral genomes to identify and characterise the evolution of this lineage.
We traced WI-CL-001 to its source at a single commercial building. There we detected the cryptic lineage at concentrations as high as 2·7 × 10 genome copies per L. The majority of 12s rRNA sequences detected in wastewater leaving the identified source building were human. Additionally, we generated over 100 viral receptor binding domain and whole-genome sequences from wastewater samples containing the cryptic lineage collected over the 13 consecutive months this virus was detectable (January, 2022, to January, 2023). These sequences contained a combination of fixed nucleotide substitutions characteristic of Pango lineage B.1.234, which circulated in humans in Wisconsin at low levels from October, 2020, to February, 2021. Despite this, mutations in the spike gene and elsewhere resembled those subsequently found in omicron variants.
We propose that prolonged detection of WI-CL-001 in wastewater indicates persistent shedding of SARS-CoV-2 from a single human initially infected by an ancestral B.1.234 virus. The accumulation of convergent omicron-like mutations in WI-CL-001's ancestral B.1.234 genome probably reflects persistent infection and extensive within-host evolution. People who shed cryptic lineages could be an important source of highly divergent viruses that sporadically emerge and spread.
The Rockefeller Foundation, Wisconsin Department of Health Services, Centers for Disease Control and Prevention, National Institute on Drug Abuse, and the Center for Research on Influenza Pathogenesis and Transmission.
在废水样本中发现的新型 SARS-CoV-2 刺突序列的起源，而在临床样本中未检测到，其仍不清楚。我们试图通过跟踪和描述其随时间的持久性和基因组进化，来确定这种隐匿性废水谱系的起源。
我们首先于 2022 年 1 月在美国威斯康星州的市政废水中检测到一个隐匿谱系，WI-CL-001。为了确定 WI-CL-001 的来源，我们使用组合自动采样器系统地从靶向次下水道线和维护孔中采集废水样本。随着时间的推移，通过 RT 数字 PCR 测量废水样本中的病毒浓度。除了使用宏基因组 12s rRNA 测序来确定病毒的宿主种类外，我们还测序了 SARS-CoV-2 刺突受体结合结构域，并且在可能的情况下，对整个病毒基因组进行测序，以鉴定和描述该谱系的进化。
我们追溯到 WI-CL-001 的单一商业建筑来源。在那里，我们检测到该隐匿谱系的浓度高达 2.7×10 基因组拷贝/升。从确定的来源建筑物中流出的废水中检测到的大多数 12s rRNA 序列是人类的。此外，我们从 2022 年 1 月至 2023 年 1 月期间检测到该隐匿谱系的 13 个连续月份的废水样本中生成了 100 多个病毒受体结合域和全基因组序列。这些序列包含了 Pango 谱系 B.1.234 的特征性固定核苷酸取代的组合，该谱系于 2020 年 10 月至 2021 年 2 月在威斯康星州的人类中低水平传播。尽管如此，刺突基因和其他地方的突变与随后在 omicron 变体中发现的突变相似。
我们提出，WI-CL-001 在废水中的持续检测表明，最初由祖先 B.1.234 病毒感染的单个人类持续排出 SARS-CoV-2。在 WI-CL-001 的祖先 B.1.234 基因组中积累的类似 omicron 的趋同突变可能反映了持续感染和广泛的宿主内进化。隐匿谱系的感染者可能是高度变异病毒的重要来源，这些病毒偶尔会出现并传播。
洛克菲勒基金会、威斯康星州卫生服务部、疾病控制与预防中心、国家药物滥用研究所和流感发病和传播研究中心。
