Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.

Journal

medRxiv : the preprint server for health sciences
Titre abrégé: medRxiv
Pays: United States
ID NLM: 101767986

Informations de publication

Date de publication:
04 Apr 2022
Historique:
entrez: 12 4 2022
pubmed: 13 4 2022
medline: 13 4 2022
Statut: epublish

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/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Identifiants

DOI: 10.1101/2021.12.21.21268143 PMID: 35411350 PMC: PMC8996633
pubmed: 35411350
doi: 10.1101/2021.12.21.21268143
pmc: PMC8996633
pii:
doi:

Types de publication

Preprint

Langues

eng

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 : UpdateIn

Références

Lancet Gastroenterol Hepatol. 2020 May;5(5):434-435
pubmed: 32199469
Nat Rev Microbiol. 2021 Jul;19(7):409-424
pubmed: 34075212
Nat Rev Genet. 2021 Jul;22(7):415-426
pubmed: 33948037
Lancet Reg Health Am. 2023 Feb 20;19:100449
pubmed: 36844610
Bioinformatics. 2022 Mar 28;38(7):1809-1815
pubmed: 35104309
mBio. 2021 Jan 19;12(1):
pubmed: 33468686
Lancet Microbe. 2021 Jan;2(1):e13-e22
pubmed: 33521734
JAMA. 2020 Nov 3;324(17):1727-1728
pubmed: 32991681
Water Res. 2020 Aug 15;181:115942
pubmed: 32425251
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nat Med. 2020 Apr;26(4):502-505
pubmed: 32284613
Am J Prev Med. 2020 Sep;59(3):326-332
pubmed: 32703702
mSystems. 2021 Mar 2;6(2):
pubmed: 33653938
Nat Commun. 2022 Nov 16;13(1):7003
pubmed: 36385137
Lancet Infect Dis. 2022 Feb;22(2):183-195
pubmed: 34756186
J Mach Learn Res. 2016 Apr;17:
pubmed: 27375369
mSystems. 2021 Aug 31;6(4):e0079321
pubmed: 34374562
Nat Microbiol. 2019 Jan;4(1):10-19
pubmed: 30546099
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Clin Infect Dis. 2021 Nov 2;73(9):1735-1741
pubmed: 33462589
Nat Med. 2019 Feb;25(2):206-211
pubmed: 30728537
Nat Microbiol. 2022 Aug;7(8):1151-1160
pubmed: 35851854
Nat Genet. 2021 Jun;53(6):809-816
pubmed: 33972780
Health Aff (Millwood). 2021 Jun;40(6):870-878
pubmed: 33979192
Mol Biol Evol. 2021 Dec 9;38(12):5819-5824
pubmed: 34469548
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Genome Biol. 2019 Jan 8;20(1):8
pubmed: 30621750
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Nat Biotechnol. 2020 Oct;38(10):1164-1167
pubmed: 32948856
Sci Total Environ. 2021 Mar 1;758:143578
pubmed: 33221007

Auteurs

Smruthi Karthikeyan (S)

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

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.

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)

Student Health and Well-Being, 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.

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.

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.

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.

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)

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

Ian H Mchardy (IH)

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

David P Dimmock (DP)

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

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.

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.

Kelly M Schiabor Barrett (KMS)

Helix, San Mateo, CA, USA.

Nicole L Washington (NL)

Helix, San Mateo, CA, USA.

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)

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

Robert Schooley (R)

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

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)

Center for Computational Biology and Bioinformatics, 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.

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, California, USA.

Patty Maysent (P)

Office of the UC San Diego Health CEO, University of California, San Diego.

David Pride (D)

Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA.

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.

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.
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA.

Kristian G Andersen (KG)

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

Rob Knight (R)

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

Classifications MeSH