Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater

Smyth, Davida S.; Trujillo, Mónica; Gregory, Devon A.; Cheung, Kristen; Gao, Anna; Graham, Maddie; Guan, Yue; Guldenpfennig, Caitlyn; Kannoly, Sherin; Kubota, Nanami; Lyddon, Terri D.; Rushford, Clayton; San, Kaung Myat; Sompanya, Geena; Spagnolo, Fabrizio; Suarez, Reinier; Teixeiro, Emma; Daniëls, Mark A.; Johnson, Marc C.; Dennehy, John J.

doi:10.1101/2021.07.26.21261142

Cited by 35 publications

(47 citation statements)

References 55 publications

(45 reference statements)

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“…This “chain reaction” of host jumping could potentially lead to remarkably high diversity in the adaptation to ACE2 from various host species. Consistent with this possibility, numerous mutations were identified in the spike protein of SARS-CoV-2 RNA fragment amplified from wastewater samples ( Smyth et al, 2021 ).…”

Section: Discussionmentioning

confidence: 75%

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

Cai

Shan

Wang

et al. 2021

Journal of Genetics and Genomics

236

230

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The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of host-jumping. The molecular spectrum of mutations ( i.e. , the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients, but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.

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Section: Discussionmentioning

confidence: 75%

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

Cai

Shan

Wang

et al. 2021

Journal of Genetics and Genomics

236

230

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“…Using a relatively conservative SNV calling pipeline and lineage detection method, we tracked the spread of SARS-CoV-2 lineages in wastewater between March 2020 and July 2021 across three cities in the province of Quebec. Although WW sequencing could be used to detect novel mutations or variant lineages not found in clinical samples (Smyth et al 2021), here we focused on identifying known variants. Consistent with a similar study in the US, we found that sequencing coverage in WW was dependent on viral load, as measured by the qPCR cycle threshold (Ct) value (Baaijens et al 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Recent studies in the United States have shown that the dominant SARS-CoV-2 variants observed in clinical samples are largely mirrored in wastewater sequences (Crits-Christoph et al 2021; Baaijens et al 2021). Wastewater also has the potential to capture mutations and variant lineages not observed in human clinical samples, potentially including animal reservoirs (Smyth et al 2021). However, more studies are required to assess the sensitivity and spatio-temporal resolution of wastewater sequencing in comparison to clinical sequencing.…”

Section: Introductionmentioning

confidence: 99%

Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada

N’Guessan

Tsitouras

Sanchez-Quete

et al. 2022

Preprint

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Wastewater-based epidemiology has emerged as a promising tool to monitor pathogens in a population, particularly when clinical diagnostic capacities become overwhelmed. During the ongoing COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), several jurisdictions have tracked viral concentrations in wastewater to inform public health authorities. While some studies have also sequenced SARS-CoV-2 genomes from wastewater, there have been relatively few direct comparisons between viral genetic diversity in wastewater and matched clinical samples from the same region and time period. Here we report sequencing and inference of SARS-CoV-2 mutations and variant lineages (including variants of concern) in 936 wastewater samples and thousands of matched clinical sequences collected between March 2020 and July 2021 in the cities of Montreal, Quebec City, and Laval, representing almost half the population of the Canadian province of Quebec. We benchmarked our sequencing and variant-calling methods on known viral genome sequences to establish thresholds for inferring variants in wastewater with confidence. We found that variant frequency estimates in wastewater and clinical samples are correlated over time in each city, with similar dates of first detection. Across all variant lineages, wastewater detection is more concordant with targeted outbreak sequencing than with semi-random clinical swab sampling. Most variants were first observed in clinical and outbreak data due to higher sequencing rate. However, wastewater sequencing is highly efficient, detecting more variants for a given sampling effort. This shows the potential for wastewater sequencing to provide useful public health data, especially at places or times when sufficient clinical sampling is infrequent or infeasible.

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“…Wastewater-based surveillance is a complementary, cost-effective approach to clinical sequencing, which has gained significant attention throughout the COVID-19 pandemic (Jahn et al 2021; Hillary et al 2021; Peccia et al 2020; Smyth et al 2021; Mishra et al 2021). Given that SARS-CoV-2 is shed in faeces by more than 50% of infected people (Foladori et al 2020), it can be recovered from wastewater, its RNA extracted, and its presence and quantity in a wastewater catchment determined using RT-qPCR (Farkas et al 2020), with trends generally tracking the rise and fall of corresponding clinical cases (Peccia et al 2020; Hillary et al 2021; Wade et al 2020).…”

Section: Introductionmentioning

confidence: 99%

“…More recently, the recovery of SARS-CoV-2 genomes from wastewater has opened up the possibility of detecting and tracking circulating SARS-CoV-2 variants (Jahn et al 2021; Hillary et al 2021; Peccia et al 2020; Smyth et al 2021; Brown et al 2021). Such an approach is particularly attractive for population-level insights during periods of high prevalence, especially if capacity constraints reduce the proportion of sequenced positive RT-qPCR tests.…”

Section: Introductionmentioning

confidence: 99%

City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants

Brunner

Brown

Bassano

et al. 2022

Preprint

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Genomic surveillance of SARS-CoV-2 has been essential to provide an evidence base for public health decisions throughout the SARS-CoV-2 pandemic. Sequencing data from clinical cases has provided data crucial to understanding disease transmission and the detection, surveillance, and containment of outbreaks of novel variants, which continue to pose fresh challenges. However, genomic wastewater surveillance can provide important complementary information by providing estimates of variant frequencies which do not suffer from sampling bias, and capturing all variants circulating in a population. Here we show that genomic SARS-CoV-2 wastewater surveillance can detect fine-scale differences within urban centres, specifically within the city of Liverpool, UK, during the emergence of Alpha and Delta variants between November 2020 and June 2021. Overall, the correspondence between wastewater and clinical variant frequencies demonstrates the reliability of wastewater surveillance. Yet, discrepancies between the two approaches in when the Alpha variant was first detected emphasises that wastewater monitoring can also capture missing information resulting from asymptomatic cases or communities less engaged with testing programmes, as found by a simultaneous surge testing effort across the city.

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Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater

Cited by 35 publications

References 55 publications

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Québec, Canada

City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants

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