Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing.
Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing.
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DOI：
10.1371/journal.ppat.1010636
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发表时间：
2022-10
期刊：
影响因子：
6.7
通讯作者：
中科院分区：
文献类型：
--
作者：
基于水的流行病学（WBE）是追踪SARS-COV-2谱系在社区中出现和传播的有效方法。从2021年初开始，我们实施了一种靶向方法来扩增和测序SARS-COV-2的受体结合结构域（RBD），以表征污水处理厂中存在的病毒谱系。在2021年期间，我们在美国3个州的9个污水处理厂的患者样本中重复检测到从未观察到的多种SARS-COV-2 RBD谱系。这些隐藏的谱系在RBD中含有4至24个氨基酸取代，并且在下水道中间歇性地观察到，其中它们被发现长达14个月。这些谱系中的许多氨基酸取代发生在关注的Omicron变体（VOC）中也突变的残基处，通常具有相同的取代。其中一个下水道包含一个似乎来自Alpha VOC的谱系，但大多数谱系似乎来自VOC前的SARS-COV-2谱系。具体来说，来自纽约市的几个神秘血统似乎来自一个最有可能在2020年初分化的共同祖先。虽然这些神秘谱系的来源尚未得到解决，但它们似乎越来越有可能来自长期患者感染或动物宿主。我们的研究结果表明，SARS-COV-2的遗传多样性大于通常通过常规SARS-COV-2监测观察到的。废水采样可能比患者采样更全面地捕获SARS-CoV-2遗传多样性，并可以在更广泛的人群中出现之前揭示新的VOC。在COVID-19大流行期间，基于废水的流行病学已成为有效的公共卫生工具。由于许多受感染的个体通过粪便排出SARS-CoV-2，因此对废水进行了监测，以揭示样本来源的下水道中的感染趋势。在这里，我们报告了从美国3个不同州获得的废水样品中发现的新型SARS-CoV-2谱系。这些谱系在长达14个月的时间内间歇性地出现在特定的下水道中，但通常不会在最初发现它们的下水道之外被发现。其中许多谱系可能在2020年初发生了分歧。虽然这些谱系彼此有相当大的重叠，但它们从未在世界任何地方的患者中观察到。虽然废水谱系与免疫功能低下患者长期感染中观察到的谱系有相似之处，但不能排除动物宿主作为潜在来源。
Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread of SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify and sequence the receptor binding domain (RBD) of SARS-COV-2 to characterize viral lineages present in sewersheds. Over the course of 2021, we reproducibly detected multiple SARS-COV-2 RBD lineages that have never been observed in patient samples in 9 sewersheds located in 3 states in the USA. These cryptic lineages contained between 4 to 24 amino acid substitutions in the RBD and were observed intermittently in the sewersheds in which they were found for as long as 14 months. Many of the amino acid substitutions in these lineages occurred at residues also mutated in the Omicron variant of concern (VOC), often with the same substitutions. One of the sewersheds contained a lineage that appeared to be derived from the Alpha VOC, but the majority of the lineages appeared to be derived from pre-VOC SARS-COV-2 lineages. Specifically, several of the cryptic lineages from New York City appeared to be derived from a common ancestor that most likely diverged in early 2020. While the source of these cryptic lineages has not been resolved, it seems increasingly likely that they were derived from long-term patient infections or animal reservoirs. Our findings demonstrate that SARS-COV-2 genetic diversity is greater than what is commonly observed through routine SARS-CoV-2 surveillance. Wastewater sampling may more fully capture SARS-CoV-2 genetic diversity than patient sampling and could reveal new VOCs before they emerge in the wider human population. During the COVID-19 pandemic, wastewater-based epidemiology has become an effective public health tool. Because many infected individuals shed SARS-CoV-2 in feces, wastewater has been monitored to reveal infection trends in the sewersheds from which the samples were derived. Here we report novel SARS-CoV-2 lineages in wastewater samples obtained from 3 different states in the USA. These lineages appeared in specific sewersheds intermittently over periods of up to 14 months, but generally have not been detected beyond the sewersheds in which they were initially found. Many of these lineages may have diverged in early 2020. Although these lineages share considerable overlap with each other, they have never been observed in patients anywhere in the world. While the wastewater lineages have similarities with lineages observed in long-term infections of immunocompromised patients, animal reservoirs cannot be ruled out as a potential source.
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影响因子：
16.6
作者：
Greaney AJ;Starr TN;Barnes CO;Weisblum Y;Schmidt F;Caskey M;Gaebler C;Cho A;Agudelo M;Finkin S;Wang Z;Poston D;Muecksch F;Hatziioannou T;Bieniasz PD;Robbiani DF;Nussenzweig MC;Bjorkman PJ;Bloom JD
通讯作者：
Bloom JD
影响因子：
5.3
作者：
Cotten M;Lule Bugembe D;Kaleebu P;V T Phan M
通讯作者：
V T Phan M
影响因子：
7.7
作者：
Gawish R;Starkl P;Pimenov L;Hladik A;Lakovits K;Oberndorfer F;Cronin SJ;Ohradanova-Repic A;Wirnsberger G;Agerer B;Endler L;Capraz T;Perthold JW;Cikes D;Koglgruber R;Hagelkruys A;Montserrat N;Mirazimi A;Boon L;Stockinger H;Bergthaler A;Oostenbrink C;Penninger JM;Knapp S
通讯作者：
Knapp S
DOI：
10.3390/v14020217
发表时间：
2022-01-23
期刊：
Viruses
影响因子：
--
作者：
Dezordi FZ;Neto AMDS;Campos TL;Jeronimo PMC;Aksenen CF;Almeida SP;Wallau GL;On Behalf Of The Fiocruz Covid-Genomic Surveillance Network
通讯作者：
On Behalf Of The Fiocruz Covid-Genomic Surveillance Network
影响因子：
64.5
作者：
Korber, Bette;Fischer, Will M.;Montefiori, David C.
通讯作者：
Montefiori, David C.