Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants.
Alexander Crits-Christoph,Rose S. Kantor,Matthew R. Olm,Oscar N. Whitney,Basem Al-Shayeb,Yue Clare Lou,Avi I. Flamholz,Lauren C Kennedy,Hannah D. Greenwald,Adrian Hinkle,Jonathan Hetzel,Sara Spitzer,Jeffery Koble,Asako Tan,Fred Hyde,Gary P. Schroth,Scott Kuersten,Jillian F. Banfield,Kara L. Nelson +18 more
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In this paper, the authors used a pipeline for single nucleotide variant calling in a metagenomic context, characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California.Abstract:
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.read more
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Journal ArticleDOI
Evaluation of Sampling, Analysis, and Normalization Methods for SARS-CoV-2 Concentrations in Wastewater to Assess COVID-19 Burdens in Wisconsin Communities
Shuchen Feng,Adélaïde Roguet,Jill S. McClary-Gutierrez,Ryan J. Newton,Nathan Kloczko,Jonathan G. Meiman,Sandra L. McLellan +6 more
TL;DR: The differences in the strength of SARS-CoV-2 relationships to COVID-19 incidence and the effect of normalization on these data among communities demonstrate that rigorous validation should be performed at individual sites where wastewater surveillance programs are implemented.
Journal ArticleDOI
Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium.
Ray Izquierdo-Lara,Goffe Elsinga,Leo Heijnen,Bas B. Oude Munnink,Claudia M. E. Schapendonk,David F. Nieuwenhuijse,Matthijs Kon,Lu Lu,Frank Møller Aarestrup,Samantha Lycett,Gertjan Medema,Marion Koopmans,Miranda de Graaf +12 more
TL;DR: In this paper, the authors used next-generation sequencing of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level in the Netherlands and Belgium.
Journal ArticleDOI
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
Smruthi Karthikeyan,J. Levy,Peter De Hoff,Gregory Humphrey,Amanda Birmingham,Kristen Jepsen,Sawyer Farmer,Helena M. Tubb,Tomás Mulet Valles,Caitlin E Tribelhorn,Rebecca Tsai,Stefan Aigner,Shashank Sathe,Niema Moshiri,Benjamin Henson,Adam Mark,A. Hakim,N. A. Baer,T. Barber,Pedro Belda-Ferre,Marisol Chacon,W. Cheung,Evelyn S Cresini,Emily R Eisner,Alma L. Lastrella,Elijah S. Lawrence,Clarisse Marotz,Toan Tri Dung Ngo,T. Ostrander,A. Plascencia,Rodolfo A. Salido,Phoebe Seaver,E. W. Smoot,Daniel McDonald,Robert M Neuhard,Angela L. Scioscia,Alysson M Satterlund,Elizabeth H. Simmons,Dismas B. Abelman,David Brenner,Judith C Bruner,Andrew Buckley,Michael Lee Ellison,Jeffrey Gattas,Steven L. Gonias,Matt Hale,Faith Kirkham Hawkins,Lydia Ikeda,Hemlata Jhaveri,Ted L. Johnson,Vincent J Kellen,Brendan Kremer,Gary Matthews,Ronald W. McLawhon,P. Ouillet,Daniel Park,Allorah Pradenas,Sharon L. Reed,Lindsay Riggs,Alison Sanders,Bradley Sollenberger,Angela Song,Benjamin A. White,Terri Winbush,Christine M. Aceves,C. Anderson,Karthik Gangavarapu,Emory Hufbauer,E. Kurzban,Justin Lee,Nathaniel L. Matteson,Edyth Parker,Sarah Perkins,Karthik S Ramesh,Refugio Robles-Sikisaka,M. A. Schwab,Emily Spencer,Shirlee Wohl,Laura Nicholson,Ian Howard Mchardy,David Dimmock,Charlotte A. Hobbs,Omid Bakhtar,Aaron Harding,A. D. Mendoza,Alexandre Bolze,D.S. Becker,Elizabeth T. Cirulli,Magnus Isaksson,Kelly M. Schiabor Barrett,Nicole L. Washington,John D Malone,Ashleigh Murphy Schafer,Nikos Gurfield,Sarah S Stous,Rebecca Fielding-Miller,Richard S. Garfein,Tommi L. Gaines,Cheryl Anderson,Natasha K. Martin,Robert E. Schooley,B. Austin,Duncan MacCannell,Stephen F. Kingsmore,William E. Lee,Seema Ramesh Shah,Eric McDonald,Alexander T. Yu,Mark Zeller,Kathleen M. Fisch,Christopher Evan Longhurst,Patricia Maysent,David T. Pride,Pradeep Khosla,Louise C. Laurent,Gene W. Yeo,Kristian G. Andersen,Rob Knight +117 more
TL;DR: In this paper , a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission was proposed, in the controlled environment of a large university campus and the broader context of the surrounding county.
Posted ContentDOI
Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples
Katharina Jahn,David Dreifuss,Ivan Topolsky,Anina Kull,Pravin Ganesanandamoorthy,Xavier Fernandez-Cassi,Carola Bänziger,Alexander J. devaux,Elyse Stachler,Lea Caduff,Federica Cariti,Alex Tunas Corzon,Lara Fuhrmann,Chaoran Chen,Kim Philipp Jablonski,Sarah Nadeau,Mirjam Feldkamp,Christian Beisel,Catharine Aquino,Tanja Stadler,Christoph Ort,Tamar Kohn,Timothy R. Julian,Timothy R. Julian,Timothy R. Julian,Niko Beerenwinkel +25 more
TL;DR: In this paper, the authors report a genomic analysis of SARS-CoV-2 in 48 raw wastewater samples collected from three wastewater treatment plants in Switzerland between July 9 and December 21, 2020.
Journal ArticleDOI
Evaluating recovery, cost, and throughput of different concentration methods for SARS-CoV-2 wastewater-based epidemiology.
Zachary W. LaTurner,David M. Zong,Prashant Kalvapalle,Kiara Reyes Gamas,Austen Terwilliger,Tessa Crosby,Priyanka Ali,Vasanthi Avadhanula,Haroldo Hernandez Santos,Kyle Weesner,Loren Hopkins,Pedro A. Piedra,Anthony W. Maresso,Lauren B. Stadler +13 more
TL;DR: In this article, the authors evaluated the recovery, cost, and throughput of five different concentration methods for quantifying SARS-CoV-2 virus RNA in wastewater samples and evaluated the use of a bovine coronavirus vaccine as a process control and pepper mild mottle virus as a normalization factor.
References
More filters
Journal ArticleDOI
Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal ArticleDOI
An interactive web-based dashboard to track COVID-19 in real time.
TL;DR: The outbreak of the 2019 novel coronavirus disease (COVID-19) has induced a considerable degree of fear, emotional stress and anxiety among individuals around the world.
Journal ArticleDOI
SciPy 1.0: fundamental algorithms for scientific computing in Python.
Pauli Virtanen,Ralf Gommers,Travis E. Oliphant,Matt Haberland,Matt Haberland,Tyler Reddy,David Cournapeau,Evgeni Burovski,Pearu Peterson,Warren Weckesser,Jonathan Bright,Stefan van der Walt,Matthew Brett,Joshua Wilson,K. Jarrod Millman,Nikolay Mayorov,Andrew Nelson,Eric Jones,Robert Kern,Eric B. Larson,CJ Carey,Ilhan Polat,Yu Feng,Eric Moore,Jake Vanderplas,Denis Laxalde,Josef Perktold,Robert Cimrman,Ian Henriksen,Ian Henriksen,E. A. Quintero,Charles R. Harris,Anne M. Archibald,Antônio H. Ribeiro,Fabian Pedregosa,Paul van Mulbregt,SciPy . Contributors +36 more
TL;DR: SciPy as discussed by the authors is an open-source scientific computing library for the Python programming language, which has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year.
Journal ArticleDOI
Virological assessment of hospitalized patients with COVID-2019.
Roman Wölfel,Victor M. Corman,Wolfgang Guggemos,M Seilmaier,Sabine Zange,Marcel A. Müller,Daniela Niemeyer,Terry Jones,Terry Jones,Patrick Vollmar,Camilla Rothe,Michael Hoelscher,Tobias Bleicker,Sebastian Brünink,Julia Schneider,Rosina Ehmann,Katrin Zwirglmaier,Christian Drosten,Clemens M. Wendtner +18 more
TL;DR: Detailed virological analysis of nine cases of coronavirus disease 2019 (COVID-19) provides proof of active replication of the SARS-CoV-2 virus in tissues of the upper respiratory tract.
Journal ArticleDOI
Data, disease and diplomacy: GISAID's innovative contribution to global health
TL;DR: The article finds that the Global Initiative on Sharing All Influenza Data contributes to global health in at least five ways: collating the most complete repository of high‐quality influenza data in the world; facilitating the rapid sharing of potentially pandemic virus information during recent outbreaks; supporting the World Health Organization's biannual seasonal flu vaccine strain selection process; developing informal mechanisms for conflict resolution around the sharing of virus data.
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