Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.

COVID-19 / epidemiology Humans RNA, Viral / analysis SARS-CoV-2 / classification Sequence Analysis, RNA Wastewater / virology Wastewater-Based Epidemiological Monitoring

Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
09 2022
Historique:
received: 21 12 2021
accepted: 29 06 2022
pubmed: 8 7 2022
medline: 9 9 2022
entrez: 7 7 2022
Statut: ppublish

Résumé

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases

Identifiants

DOI: 10.1038/s41586-022-05049-6 PMID: 35798029 PMC: PMC9433318
pubmed: 35798029
doi: 10.1038/s41586-022-05049-6
pii: 10.1038/s41586-022-05049-6
pmc: PMC9433318
doi:

Substances chimiques

RNA, Viral 0
Waste Water 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

101-108

Subventions

Organisme : NIAID NIH HHS
ID : U19 AI135995
Pays : United States
Organisme : NCCIH NIH HHS
ID : DP1 AT010885
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR002550
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI151812
Pays : United States
Organisme : NIAID NIH HHS
ID : T32 AI007244
Pays : United States
Organisme : NIH HHS
ID : S10 OD026929
Pays : United States

Commentaires et corrections

Type : UpdateOf

Informations de copyright

© 2022. The Author(s).

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Auteurs

Smruthi Karthikeyan (S)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0001-6226-4536

Joshua I Levy (JI)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Peter De Hoff (P)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA.

Greg Humphrey (G)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Amanda Birmingham (A)

Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA.

Kristen Jepsen (K)

Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.

Sawyer Farmer (S)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Helena M Tubb (HM)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Tommy Valles (T)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Caitlin E Tribelhorn (CE)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Rebecca Tsai (R)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Stefan Aigner (S)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Shashank Sathe (S)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Niema Moshiri (N)

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

Benjamin Henson (B)

Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.

Adam M Mark (AM)

Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA.

Abbas Hakim (A)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA.

Nathan A Baer (NA)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Tom Barber (T)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Pedro Belda-Ferre (P)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Marisol Chacón (M)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Willi Cheung (W)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA.

Evelyn S Cresini (ES)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Emily R Eisner (ER)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Alma L Lastrella (AL)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Elijah S Lawrence (ES)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Clarisse A Marotz (CA)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Toan T Ngo (TT)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Tyler Ostrander (T)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Ashley Plascencia (A)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Rodolfo A Salido (RA)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Phoebe Seaver (P)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Elizabeth W Smoot (EW)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.

Daniel McDonald (D)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0003-0876-9060

Robert M Neuhard (RM)

Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.
Return to Learn, University of California San Diego, La Jolla, CA, USA.

Angela L Scioscia (AL)

Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA.

Alysson M Satterlund (AM)

Student Affairs, University of California San Diego, La Jolla, CA, USA.

Elizabeth H Simmons (EH)

Academic Affairs, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-0646-3458

Dismas B Abelman (DB)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

David Brenner (D)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Judith C Bruner (JC)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Anne Buckley (A)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Michael Ellison (M)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Jeffrey Gattas (J)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Steven L Gonias (SL)

Department of Pathology, University of California San Diego, La Jolla, CA, USA.

Matt Hale (M)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Faith Hawkins (F)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Lydia Ikeda (L)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Hemlata Jhaveri (H)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Ted Johnson (T)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Vince Kellen (V)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Brendan Kremer (B)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Gary Matthews (G)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Ronald W McLawhon (RW)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Pierre Ouillet (P)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Daniel Park (D)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Allorah Pradenas (A)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Sharon Reed (S)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Lindsay Riggs (L)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Alison Sanders (A)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Bradley Sollenberger (B)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Angela Song (A)

Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.
Return to Learn, University of California San Diego, La Jolla, CA, USA.

Benjamin White (B)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Terri Winbush (T)

Return to Learn, University of California San Diego, La Jolla, CA, USA.

Christine M Aceves (CM)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Catelyn Anderson (C)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Karthik Gangavarapu (K)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Emory Hufbauer (E)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Ezra Kurzban (E)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Justin Lee (J)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Nathaniel L Matteson (NL)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Edyth Parker (E)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Sarah A Perkins (SA)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
ORCID: 0000-0002-0557-3102

Karthik S Ramesh (KS)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Refugio Robles-Sikisaka (R)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Madison A Schwab (MA)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
ORCID: 0000-0003-0748-1858

Emily Spencer (E)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Shirlee Wohl (S)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Laura Nicholson (L)

Scripps Health, San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-1761-0951

Ian H McHardy (IH)

Scripps Health, San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-2121-5460

David P Dimmock (DP)

Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
ORCID: 0000-0001-6690-2523

Charlotte A Hobbs (CA)

Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.

Omid Bakhtar (O)

Sharp Healthcare, San Diego, CA, USA.

Aaron Harding (A)

Sharp Healthcare, San Diego, CA, USA.

Art Mendoza (A)

Sharp Healthcare, San Diego, CA, USA.

Alexandre Bolze (A)

Helix, San Mateo, CA, USA.
ORCID: 0000-0001-7399-2766

David Becker (D)

Helix, San Mateo, CA, USA.

Elizabeth T Cirulli (ET)

Helix, San Mateo, CA, USA.

Magnus Isaksson (M)

Helix, San Mateo, CA, USA.
ORCID: 0000-0001-6278-0522

Kelly M Schiabor Barrett (KM)

Helix, San Mateo, CA, USA.
ORCID: 0000-0001-6194-787X

Nicole L Washington (NL)

Helix, San Mateo, CA, USA.
ORCID: 0000-0001-8936-9143

John D Malone (JD)

County of San Diego Health and Human Services Agency, San Diego, CA, USA.

Ashleigh Murphy Schafer (AM)

County of San Diego Health and Human Services Agency, San Diego, CA, USA.

Nikos Gurfield (N)

County of San Diego Health and Human Services Agency, San Diego, CA, USA.

Sarah Stous (S)

County of San Diego Health and Human Services Agency, San Diego, CA, USA.

Rebecca Fielding-Miller (R)

Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.
Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA.

Richard S Garfein (RS)

Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.

Tommi Gaines (T)

Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA.

Cheryl Anderson (C)

Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.

Natasha K Martin (NK)

Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA.

Robert Schooley (R)

Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0002-2498-8426

Brett Austin (B)

Sharp Healthcare, San Diego, CA, USA.

Duncan R MacCannell (DR)

Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA.

Stephen F Kingsmore (SF)

Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.

William Lee (W)

Helix, San Mateo, CA, USA.

Seema Shah (S)

County of San Diego Health and Human Services Agency, San Diego, CA, USA.

Eric McDonald (E)

County of San Diego Health and Human Services Agency, San Diego, CA, USA.

Alexander T Yu (AT)

COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA.

Mark Zeller (M)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Kathleen M Fisch (KM)

Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA.

Christopher Longhurst (C)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA.

Patty Maysent (P)

Office of the UC San Diego Health CEO, University of California San Diego, La Jolla, CA, USA.

David Pride (D)

Department of Pathology, University of California San Diego, La Jolla, CA, USA.
Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Pradeep K Khosla (PK)

Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

Louise C Laurent (LC)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.

Gene W Yeo (GW)

Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.

Kristian G Andersen (KG)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
ORCID: 0000-0001-6431-5982

Rob Knight (R)

Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
ORCID: 0000-0002-0975-9019

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Classifications MeSH

questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Wastewater sequencing reveals early cryptic...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Wastewater sequencing reveals early cryptic...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN viral › Wastewater sequencing reveals early cryptic...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Wastewater sequencing reveals early cryptic...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Wastewater sequencing reveals early cryptic...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Pollution de l'environnement › Déchets › Eaux usées › Wastewater sequencing reveals early cryptic...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Surveillance épidémiologique › Surveillance épidémiologique fondée sur les eaux usées › Wastewater sequencing reveals early cryptic...