Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
Sci Total Environ. 2022 Nov 25;849:157546. doi: 10.1016/j.scitotenv.2022.157546. Epub 2022 Jul 30.
Although SARS-CoV-2 can cause severe illness and death, a percentage of the infected population is asymptomatic. This, along with other factors, such as insufficient diagnostic testing and underreporting due to self-testing, contributes to the silent transmission of SARS-CoV-2 and highlights the importance of implementing additional surveillance tools. The fecal shedding of the virus from infected individuals enables its detection in community wastewater, and this has become a valuable public health tool worldwide as it allows the monitoring of the disease on a populational scale. Here, we monitored the presence of SARS-CoV-2 and its dynamic genomic changes in wastewater sampled from two metropolitan areas in Arkansas during major surges of COVID-19 cases and assessed how the viral titers in these samples related to the clinical case counts between late April 2020 and January 2022. The levels of SARS-CoV-2 RNA were quantified by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) using a set of TaqMan assays targeting three different viral genes (encoding ORF1ab polyprotein, surface glycoprotein, and nucleocapsid phosphoprotein). An allele-specific RT-qPCR approach was used to screen the samples for SARS-CoV-2 mutations. The identity and genetic diversity of the virus were further investigated through amplicon-based RNA sequencing, and SARS-CoV-2 variants of concern were detected in wastewater samples throughout the duration of this study. Our data show how changes in the virus genome can affect the sensitivity of specific RT-qPCR assays used in COVID-19 testing with the surge of new variants. A significant association was observed between viral titers in wastewater and recorded number of COVID-19 cases in the areas studied, except when assays failed to detect targets due to the presence of particular variants. These findings support the use of wastewater surveillance as a reliable complementary tool for monitoring SARS-CoV-2 and its genetic variants at the community level.
虽然 SARS-CoV-2 可导致严重疾病和死亡，但部分受感染人群无症状。再加上其他因素，如诊断检测不足和因自我检测导致的漏报，导致 SARS-CoV-2 静默传播，突显了实施额外监测工具的重要性。受感染个体的病毒粪便排放使其在社区废水中被检测到，这已成为全球有价值的公共卫生工具，因为它可在人群范围内监测疾病。在此，我们在阿肯色州两个大都市区采集的废水样本中监测了 SARS-CoV-2 的存在及其动态基因组变化，并评估了这些样本中的病毒滴度与 2020 年 4 月底至 2022 年 1 月之间的临床病例数之间的关系。通过使用针对三个不同病毒基因（编码 ORF1ab 多蛋白、表面糖蛋白和核衣壳磷蛋白）的 TaqMan 测定，通过逆转录定量聚合酶链反应（RT-qPCR）定量 SARS-CoV-2 RNA。采用等位基因特异性 RT-qPCR 方法筛选样品中的 SARS-CoV-2 突变。通过基于扩增子的 RNA 测序进一步研究病毒的身份和遗传多样性，并在整个研究过程中在废水样本中检测到 SARS-CoV-2 关注变体。我们的数据显示了病毒基因组的变化如何影响用于 COVID-19 检测的特定 RT-qPCR 检测的灵敏度，特别是在新变体激增的情况下。在研究区域中，观察到废水中的病毒滴度与记录的 COVID-19 病例数之间存在显著关联，除了由于特定变体的存在而导致测定未能检测到靶标时。这些发现支持将废水监测用作在社区层面监测 SARS-CoV-2 及其遗传变体的可靠补充工具。
