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Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
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Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- 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
| | - Peter De Hoff
- 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
| | - Willi Cheung
- 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
| | - Anelizze Castro-Martinez
- 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
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- 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
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- 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
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- 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
- 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
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
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Bittremieux W, Avalon NE, Thomas SP, Kakhkhorov SA, Aksenov AA, Gomes PWP, Aceves CM, Caraballo-Rodríguez AM, Gauglitz JM, Gerwick WH, Huan T, Jarmusch AK, Kaddurah-Daouk RF, Kang KB, Kim HW, Kondić T, Mannochio-Russo H, Meehan MJ, Melnik AV, Nothias LF, O'Donovan C, Panitchpakdi M, Petras D, Schmid R, Schymanski EL, van der Hooft JJJ, Weldon KC, Yang H, Xing S, Zemlin J, Wang M, Dorrestein PC. Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics. Nat Commun 2023; 14:8488. [PMID: 38123557 PMCID: PMC10733301 DOI: 10.1038/s41467-023-44035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or "suspects," were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer's brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
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Affiliation(s)
- Wout Bittremieux
- Department of Computer Science, University of Antwerp, 2020, Antwerpen, Belgium.
| | - Nicole E Avalon
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sydney P Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sarvar A Kakhkhorov
- Laboratory of Physical and Chemical Methods of Research, Center for Advanced Technologies, Tashkent, 100174, Uzbekistan
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
- Arome Science inc., Farmington, CT, 06032, USA
| | - Paulo Wender P Gomes
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, 27709, USA
| | - Rima F Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, 27701, USA
- Department of Medicine, Duke University, Durham, NC, 27710, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, 27710, USA
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, 04310, Korea
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, Goyang, 10326, Korea
| | - Todor Kondić
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Helena Mannochio-Russo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, 14800-901, Brazil
| | - Michael J Meehan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexey V Melnik
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
- Arome Science inc., Farmington, CT, 06032, USA
| | - Louis-Felix Nothias
- Université Côte d'Azur, CNRS, ICN, Nice, France
- Interdisciplinary Institute for Artificial Intelligence (3iA) Côte d'Azur, Nice, France
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Morgan Panitchpakdi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, 72076, Tuebingen, Germany
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92507, USA
| | - Robin Schmid
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Heejung Yang
- Laboratory of Natural Products Chemistry, College of Pharmacy, Kangwon National University, Chuncheon, 24341, Korea
| | - Shipei Xing
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, 92507, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, 92093, USA.
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Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 2023; 41:1656. [PMID: 37853256 DOI: 10.1038/s41587-023-02025-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kiana A West
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Candace L Williams
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole C Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edgar Diaz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kate E Sprecher
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniela Vargas-Robles
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela
| | - Dana Withrow
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, MT, USA
| | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lucas Maciel Mauriz Marques
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Juliano Geraldo Amaral
- Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Rodrigo Moreira Silva
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Flavio Protasio Veras
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Rene Donizeti Ribeiro Oliveira
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Paulo Louzada-Junior
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Robert H Mills
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Paulina K Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Rima Kaddurah Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Curt Wittenberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Terkeltaub
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- San Diego VA Healthcare System, San Diego, CA, USA
| | - Megan M Doty
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Jae H Kim
- Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kyung E Rhee
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julia Beauchamp-Walters
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mark Manary
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Monica Guma
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, 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.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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4
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Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S, Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat Methods 2023; 20:512-522. [PMID: 36823332 PMCID: PMC10399614 DOI: 10.1038/s41592-023-01769-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.
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Affiliation(s)
- Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Alaa Abdel Latif
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia L Mullen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Manar Alkuzweny
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ginger Tsueng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Haag
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karina Zaiets
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marco Cano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xinghua Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Zhongchao Qian
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rachel Sattler
- Skaggs Graduate School of Biological and Chemical Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Raphael T C Lee
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
| | - Lucas Freitas
- GISAID Global Data Science Initiative, Munich, Germany
- Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative, Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore, Singapore
- National Centre for Infectious Diseases, Ministry of Health, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Marc A Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Scripps Research Translational Institute, La Jolla, CA, USA
| | - Laura D Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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5
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Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol 2022; 40:1774-1779. [PMID: 35798960 PMCID: PMC10277029 DOI: 10.1038/s41587-022-01368-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 05/20/2022] [Indexed: 01/30/2023]
Abstract
Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.
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Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kiana A West
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Wout Bittremieux
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Candace L Williams
- Beckman Center for Conservation Research, San Diego Zoo Wildlife Alliance, Escondido, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole C Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cameron Martino
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Tara Schwartz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gregory Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Edgar Diaz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kate E Sprecher
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Daniela Vargas-Robles
- Servicio Autónomo Centro Amazónico de Investigación y Control de Enfermedades Tropicales Simón Bolívar, Puerto Ayacucho, Amazonas, Venezuela
| | - Dana Withrow
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lourdes Herrera
- Department of Pediatrics, Billings Clinic, Billings, MT, USA
| | - Barry J Bradford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Lucas Maciel Mauriz Marques
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Juliano Geraldo Amaral
- Multidisciplinary Health Institute, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Rodrigo Moreira Silva
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Flavio Protasio Veras
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medicinal School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Rene Donizeti Ribeiro Oliveira
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Paulo Louzada-Junior
- Department of Internal Medicine, Ribeirão Preto Medical School, Center of Research in Inflammatory Diseases, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Robert H Mills
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Paulina K Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Stephanie L Servetas
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Rima Kaddurah Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
- Department of Medicine, Duke University, Durham, NC, USA
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Curt Wittenberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Terkeltaub
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- San Diego VA Healthcare System, San Diego, CA, USA
| | - Megan M Doty
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Neonatology, Department of Pediatrics, Kapi'olani Medical Center for Women and Children, John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Jae H Kim
- Division of Neonatology, Perinatal Institute, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kyung E Rhee
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julia Beauchamp-Walters
- Division of Pediatric Hospital Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kenneth P Wright
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences; Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Mark Manary
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Michelli F Oliveira
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Sao Paolo, Brazil
| | - Monica Guma
- Division of Rheumatology, Allergy & Immunology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, 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.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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6
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 2022; 609:101-108. [PMID: 35798029 PMCID: PMC9433318 DOI: 10.1038/s41586-022-05049-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/29/2022] [Indexed: 11/23/2022]
Abstract
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 biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. 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 developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified 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. Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- 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
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- 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
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- 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
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- 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
- 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
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- 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
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- 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
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- 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
- 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
- Office of the UC San Diego Health CEO, University of California, San Diego, USA
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- 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
- 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
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- 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.
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7
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Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou J, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S, Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Res Sq 2022:rs.3.rs-1723829. [PMID: 35794893 PMCID: PMC9258294 DOI: 10.21203/rs.3.rs-1723829/v1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The emergence of SARS-CoV-2 variants of concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info, a platform that currently tracks over 40 million combinations of PANGO lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials, and the general public. We describe the interpretable and opinionated visualizations in the variant and location focussed reports available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data, and the server infrastructure that enables widespread data dissemination via a high performance API that can be accessed using an R package. We present a case study that illustrates how outbreak.info can be used for genomic surveillance and as a hypothesis generation tool to understand the ongoing pandemic at varying geographic and temporal scales. With an emphasis on scalability, interactivity, interpretability, and reusability, outbreak.info provides a template to enable genomic surveillance at a global and localized scale.
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Affiliation(s)
- Karthik Gangavarapu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Alaa Abdel Latif
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Julia L. Mullen
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manar Alkuzweny
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ginger Tsueng
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Emily Haag
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christine M. Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karina Zaiets
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marco Cano
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jerry Zhou
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zhongchao Qian
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rachel Sattler
- Skaggs Graduate School of Biological and Chemical Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Raphael TC Lee
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore
| | - Lucas Freitas
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Sebastian Maurer-Stroh
- GISAID Global Data Science Initiative (GISAID), Munich, Germany
- Bioinformatics Institute & ID Labs, Agency for Science Technology and Research, Singapore
- National Centre for Infectious Diseases, Ministry of Health, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Marc A. Suchard
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Chunlei Wu
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew I. Su
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Laura D. Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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8
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022:2021.12.21.21268143. [PMID: 35411350 PMCID: PMC8996633 DOI: 10.1101/2021.12.21.21268143] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- 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
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M. Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- 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
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- 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
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- 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
- 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
| | | | | | - Dismas B. Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C. Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L. Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- 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
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- 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
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K. Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R. MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T. Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- 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
- 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
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K. Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C. Laurent
- 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
- 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
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- 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
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9
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022. [PMID: 35411350 DOI: 10.1101/2022.01.27.22269965] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
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.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- 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
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- 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
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- 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
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- 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
- 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
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- 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
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- 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
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- 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
- 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
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- 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
- 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
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- 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
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10
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Jarmusch AK, Wang M, Aceves CM, Advani RS, Aguirre S, Aksenov AA, Aleti G, Aron AT, Bauermeister A, Bolleddu S, Bouslimani A, Caraballo Rodriguez AM, Chaar R, Coras R, Elijah EO, Ernst M, Gauglitz JM, Gentry EC, Husband M, Jarmusch SA, Jones KL, Kamenik Z, Le Gouellec A, Lu A, McCall LI, McPhail KL, Meehan MJ, Melnik AV, Menezes RC, Montoya Giraldo YA, Nguyen NH, Nothias LF, Nothias-Esposito M, Panitchpakdi M, Petras D, Quinn RA, Sikora N, van der Hooft JJJ, Vargas F, Vrbanac A, Weldon KC, Knight R, Bandeira N, Dorrestein PC. ReDU: a framework to find and reanalyze public mass spectrometry data. Nat Methods 2020; 17:901-904. [PMID: 32807955 DOI: 10.1038/s41592-020-0916-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 07/10/2020] [Indexed: 11/09/2022]
Abstract
We present ReDU ( https://redu.ucsd.edu/ ), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one's own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking.
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Affiliation(s)
- Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rohit S Advani
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shaden Aguirre
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Gajender Aleti
- Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Sanjana Bolleddu
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andres Mauricio Caraballo Rodriguez
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rama Chaar
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Roxana Coras
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Makhai Husband
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Scott A Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK
| | - Kenneth L Jones
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Zdenek Kamenik
- Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic
| | - Audrey Le Gouellec
- TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France
| | - Aileen Lu
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Michael J Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Riya C Menezes
- Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yessica Alejandra Montoya Giraldo
- Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
| | - Ngoc Hung Nguyen
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA
| | - Nicole Sikora
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Alison Vrbanac
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, 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
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. .,Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
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11
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Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 2020; 15:1954-1991. [PMID: 32405051 DOI: 10.1038/s41596-020-0317-5] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.
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Affiliation(s)
- Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Christine M Aceves
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Irina Koester
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center of Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Catherine Roullier
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Kunyang Sun
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Richard M Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Cristopher A Boya P
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Martin H Christian
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | | | | | - Randy Mojica-Flores
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Departamento de Química, Universidad Autónoma de Chiriquí (UNACHI), David, Chiriquí, Panama
| | - Johant Lakey-Beitia
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Victor Vásquez-Chaves
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Yilue Zhang
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Angela I Calderón
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Nicole Tayler
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Fidele Tugizimana
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- International R&D Division, Omnia Group (Pty) Ltd., Johannesburg, South Africa
| | - Nombuso Ndlovu
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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12
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Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC. Mass spectrometry searches using MASST. Nat Biotechnol 2020; 38:23-26. [PMID: 31894142 PMCID: PMC7236533 DOI: 10.1038/s41587-019-0375-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Ometa Labs LLC, San Diego, CA, USA
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelly Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ricardo da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robert Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth Brown
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Francesca Di Ottavio
- Faculty of Bioscience and Technology for Food, Agriculture, and Environment, University of Teramo, Teramo, TE, Italy
| | - Nicole Sikora
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emmanuel O Elijah
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lara Labarta-Bajo
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Shabnam Shalapour
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kathleen E Kyle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Sara P Puckett
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Jeramie D Watrous
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Carolina S Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Elina I Zúñiga
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Marcy J Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Rohit Loomba
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,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
| | - Nuno Bandeira
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. .,Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC. Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages. Food Chem 2019; 302:125290. [PMID: 31404873 DOI: 10.1016/j.foodchem.2019.125290] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 10/26/2022]
Abstract
In our daily lives, we consume foods that have been transported, stored, prepared, cooked, or otherwise processed by ourselves or others. Food storage and preparation have drastic effects on the chemical composition of foods. Untargeted mass spectrometry analysis of food samples has the potential to increase our chemical understanding of these processes by detecting a broad spectrum of chemicals. We performed a time-based analysis of the chemical changes in foods during common preparations, such as fermentation, brewing, and ripening, using untargeted mass spectrometry and molecular networking. The data analysis workflow presented implements an approach to study changes in food chemistry that can reveal global alterations in chemical profiles, identify changes in abundance, as well as identify specific chemicals and their transformation products. The data generated in this study are publicly available, enabling the replication and re-analysis of these data in isolation, and serve as a baseline dataset for future investigations.
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Affiliation(s)
- Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States.
| | - Christine M Aceves
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Gajender Aleti
- Mammalian Genomics, J. Craig Venter Institute, San Diego, United States
| | - Jehad Almaliti
- Scripps Institution of Oceanography, University of California, San Diego, United States; Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Elizabeth A Brown
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Anaamika Campeau
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Pharmacology, University of California, San Diego, United States
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Rama Chaar
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alyssa M Demko
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Francesca Di Ottavio
- Faculty of Bioscience and Technology for Food, Agriculture, and Environment, University of Teramo, TE, Italy
| | - Emmanuel Elijah
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - L Paige Ferguson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Xavier Holmes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Alan K Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Lingjing Jiang
- Department of Family Medicine and Public Health, University of California, San Diego, United States
| | - Kyo Bin Kang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Irina Koester
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Brian Kwan
- Department of Family Medicine and Public Health, University of California, San Diego, United States
| | - Jie Li
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Yueying Li
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States
| | - Carlos Molina-Santiago
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071 Málaga, Spain
| | - Bohan Ni
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Aaron L Oom
- Department of Medicine, University of California, San Diego, United States
| | - Morgan W Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States; Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Robert Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Katharina Spengler
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Bahar Teke
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Anupriya Tripathi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Sabah Ul-Hasan
- School of Natural Sciences, University of California Merced, Merced, CA 95343, United States
| | - Justin J J van der Hooft
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Fernando Vargas
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Alison Vrbanac
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Anthony Q Vu
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, United States
| | - Steven C Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Kelly Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Center for Microbiome Innovation, University of California, San Diego, United States
| | - Kayla Wilson
- Scripps Institution of Oceanography, University of California, San Diego, United States
| | - Jacob M Wozniak
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Pharmacology, University of California, San Diego, United States
| | - Michael Yoon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States
| | - Nuno Bandeira
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Department of Computer Science and Engineering, University of California, San Diego, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, United States; Departments of Pharmacology and Pediatrics, University of California, San Diego, United States.
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