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Tolman ER, Beatty CD, Kohli MK, Abbott J, Bybee SM, Frandsen PB, Stephen Gosnell J, Guralnick R, Kalkman VJ, Newton LG, Suvorov A, Ware JL. A molecular phylogeny of the Petaluridae (Odonata: Anisoptera): A 160-Million-Year-Old story of drift and extinction. Mol Phylogenet Evol 2024; 200:108185. [PMID: 39209047 DOI: 10.1016/j.ympev.2024.108185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/12/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Petaluridae (Odonata: Anisoptera) is a relict dragonfly family, having diverged from its sister family in the Jurassic, of eleven species that are notable among odonates (dragonflies and damselflies) for their exclusive use of fen and bog habitats, their burrowing behavior as nymphs, large body size as adults, and extended lifespans. To date, several nodes within this family remain unresolved, limiting the study of the evolution of this peculiar family. Using an anchored hybrid enrichment dataset of over 900 loci we reconstructed the species tree of Petaluridae. To estimate the temporal origin of the genera within this family, we used a set of well-vetted fossils and a relaxed molecular clock model in a divergence time estimation analysis. We estimate that Petaluridae originated in the early Cretaceous and confirm the existence of monophyletic Gondwanan and Laurasian clades within the family. Our relaxed molecular clock analysis estimated that these clades diverged from their MRCA approximately 160 mya. Extant lineages within this family were identified to have persisted from 6 (Uropetala) to 120 million years (Phenes). Our biogeographical analyses focusing on a set of key regions suggest that divergence within Petaluridae is largely correlated with continental drift, the exposure of land bridges, and the development of mountain ranges. Our results support the hypothesis that species within Petaluridae have persisted for tens of millions of years, with little fossil evidence to suggest widespread extinction in the family, despite optimal conditions for the fossilization of nymphs. Petaluridae appear to be a rare example of habitat specialists that have persisted for tens of millions of years.
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Affiliation(s)
- Ethan R Tolman
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Department of Biological Sciences, Virginia Tech, Blacksburg, VA; Conservation Connection Foundation, Boise, ID.
| | - Christopher D Beatty
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Program for Conservation Genomics, Department of Biology, Stanford University
| | - Manpreet K Kohli
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Conservation Connection Foundation, Boise, ID; Department of Natural Sciences, Baruch College, New York
| | - John Abbott
- Alabama Museum of Natural History and Department of Research and Collections, The University of Alabama
| | - Seth M Bybee
- Department of Biology and Monte L. Bean Museum, Brigham Young University, Provo, UT
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT
| | - J Stephen Gosnell
- Department of Natural Sciences, Baruch College, New York; PhD Program in Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, Room 4315, New York, 10016
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - V J Kalkman
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden
| | - Lacie G Newton
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA
| | - Jessica L Ware
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024
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Kumar M, Mahapatra DM. First reporting of BA.1* and BA.2* recombinant SARS-CoV-2 lineage XAP from Indian wastewaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174756. [PMID: 39004359 DOI: 10.1016/j.scitotenv.2024.174756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Tracking new variants of SARS-CoV-2 is vital for managing COVID-19 spread and allocating resources. Domestic antigen testing has created surveillance gaps that make it hard to identify new viral variants. We conducted whole genome sequencing of wastewater viral genes from major and minor treatment facilities in Dehradun from March 2022 onwards. Based on our analysis, the samples that achieved higher sequencing depth and covered >90 % of the viral genome uncovered a major variant pattern resembling the XAP recombinant lineage that is reported for the first time in the City of Dehradun, Uttrakhand and is the first ever records in India as on date. This novel XAP recombinant lineage had 9, 2, 30, 1, 2, 5, 1, 1, 1 aminoacid changes (total 54 mutations) in Orf1a, Orf1b, S, E, M, N, Orf3a, Orf6 and Orf8 regions of the gene respectively that shares 49 mutations common to the ancestral lineages BA.1* and BA.2*, with 6 unique mutations. Subsequent comparison and analysis of the clinical sequence data from the region post-detection of this rare and unusual variant showed no causalities infected with the newly detected XAP lineage. These findings are indicative of future alarming situation with plausible threats of fresh spur of Omicron variant led infections in the urban community.
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Affiliation(s)
- Manish Kumar
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterrey, Eugenio Garza Sada 2501 Sur, Monterrey 64849, Mexico; School of Advance Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand 248007, India.
| | - Durga Madhab Mahapatra
- School of Advance Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand 248007, India; Department of Biological and Ecological Engineering, School of Engineering, Oregon State University, Corvallis, OR, USA
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3
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Gill EE, Jia B, Murall CL, Poujol R, Anwar MZ, John NS, Richardsson J, Hobb A, Olabode AS, Lepsa A, Duggan AT, Tyler AD, N'Guessan A, Kachru A, Chan B, Yoshida C, Yung CK, Bujold D, Andric D, Su E, Griffiths EJ, Van Domselaar G, Jolly GW, Ward HKE, Feher H, Baker J, Simpson JT, Uddin J, Ragoussis J, Eubank J, Fritz JH, Gálvez JH, Fang K, Cullion K, Rivera L, Xiang L, Croxen MA, Shiell M, Prystajecky N, Quirion PO, Bajari R, Rich S, Mubareka S, Moreira S, Cain S, Sutcliffe SG, Kraemer SA, Alturmessov Y, Joly Y, Fiume M, Snutch TP, Bell C, Lopez-Correa C, Hussin JG, Joy JB, Colijn C, Gordon PMK, Hsiao WWL, Poon AFY, Knox NC, Courtot M, Stein L, Otto SP, Bourque G, Shapiro BJ, Brinkman FSL. The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. Microb Genom 2024; 10:001293. [PMID: 39401061 PMCID: PMC11472881 DOI: 10.1099/mgen.0.001293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/20/2024] [Indexed: 10/15/2024] Open
Abstract
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform the public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This portal has been coupled with other resources, such as Viral AI, and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this portal (https://virusseq-dataportal.ca/), including its contextual data not available elsewhere, and the Duotang (https://covarr-net.github.io/duotang/duotang.html), a web platform that presents key genomic epidemiology and modelling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the portal (COVID-MVP, CoVizu), are all open source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.
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Affiliation(s)
- Erin E. Gill
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Baofeng Jia
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Carmen Lia Murall
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Raphaël Poujol
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
| | - Muhammad Zohaib Anwar
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Nithu Sara John
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | | | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | | | - Ana T. Duggan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Andrea D. Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Arnaud N'Guessan
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Atul Kachru
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Brandon Chan
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Systems, Toronto, ON, Canada
| | - David Bujold
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Dusan Andric
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Edmund Su
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Emma J. Griffiths
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Gordon W. Jolly
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Henrich Feher
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jared Baker
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Jaser Uddin
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Jon Eubank
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jörg H. Fritz
- Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada
| | | | | | - Kim Cullion
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Linda Xiang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Matthew A. Croxen
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | | | - Natalie Prystajecky
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Rosita Bajari
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Samantha Rich
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Scott Cain
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Steven G. Sutcliffe
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Susanne A. Kraemer
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada
| | | | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
| | - CPHLN Consortium**
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- DNAstack, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Indoc Systems, Toronto, ON, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Sunnybrook Research Institute, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Université de Montréal, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Mila-Québec AI institute, Montréal, QC, Canada
- Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada
- Department of Medical BioPhysics, University of Toronto, ON, Canada
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - CanCOGeN Consortium**
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- DNAstack, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Indoc Systems, Toronto, ON, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Sunnybrook Research Institute, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Université de Montréal, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Mila-Québec AI institute, Montréal, QC, Canada
- Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada
- Department of Medical BioPhysics, University of Toronto, ON, Canada
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - VirusSeq Data Portal Academic and Health Network**
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- DNAstack, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Indoc Systems, Toronto, ON, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Sunnybrook Research Institute, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Université de Montréal, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Mila-Québec AI institute, Montréal, QC, Canada
- Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada
- Department of Medical BioPhysics, University of Toronto, ON, Canada
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Terrance P. Snutch
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Cindy Bell
- Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada
| | | | - Julie G. Hussin
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Mila-Québec AI institute, Montréal, QC, Canada
| | - Jeffrey B. Joy
- Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Paul M. K. Gordon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada
| | - William W. L. Hsiao
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Mélanie Courtot
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical BioPhysics, University of Toronto, ON, Canada
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Sarah P. Otto
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - CPHLN consortium
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- DNAstack, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Indoc Systems, Toronto, ON, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Sunnybrook Research Institute, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Université de Montréal, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Mila-Québec AI institute, Montréal, QC, Canada
- Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada
- Department of Medical BioPhysics, University of Toronto, ON, Canada
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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4
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Chwa JS, Shin Y, Lee Y, Fabrizio T, Congrave-Wilson Z, Cheng WA, Jumarang J, Kim M, Webby R, Bender JM, Pannaraj PS. SARS-CoV-2 Variants May Affect Saliva RT-PCR Assay Sensitivity. J Appl Lab Med 2024:jfae095. [PMID: 39246012 DOI: 10.1093/jalm/jfae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/09/2024] [Indexed: 09/10/2024]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants demonstrate predilection for different regions of the respiratory tract. While saliva-based reverse transcription-polymerase chain reaction (RT-PCR) testing is a convenient, cost-effective alternative to nasopharyngeal swabs (NPS), few studies to date have investigated whether saliva sensitivity differs across variants of concern. METHODS SARS-CoV-2 RT-PCR was performed on paired NPS and saliva specimens collected from individuals with acute coronavirus disease 2019 (COVID-19) symptoms or exposure to a COVID-19 household contact. Viral genome sequencing of NPS specimens and Los Angeles County surveillance data were used to determine the variant of infection. Saliva sensitivity was calculated using NPS-positive RT-PCR as the reference standard. Factors contributing to the likelihood of saliva SARS-CoV-2 RT-PCR positivity were evaluated with univariate and multivariable analyses. RESULTS Between June 2020 and December 2022, 548 saliva samples paired with SARS-CoV-2 positive NPS samples were tested by RT-PCR. Overall, saliva sensitivity for SARS-CoV-2 detection was 61.7% (95% CI, 57.6%-65.7%). Sensitivity was highest with Delta infection (79.6%) compared to pre-Delta (58.5%) and Omicron (61.5%) (P = 0.003 and 0.01, respectively). Saliva sensitivity was higher in symptomatic individuals across all variants compared to asymptomatic cases [pre-Delta 80.6% vs 48.3% (P < 0.001), Delta 100% vs 72.5% (P = 0.03), Omicron 78.7% vs 51.2% (P < 0.001)]. Infection with Delta, symptoms, and high NPS viral load were independently associated with 2.99-, 3.45-, and 4.0-fold higher odds of SARS-CoV-2 detection by saliva-based RT-PCR (P = 0.004, <0.001, and <0.001), respectively. CONCLUSIONS As new variants emerge, evaluating saliva-based testing approaches may be crucial to ensure effective virus detection.
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Affiliation(s)
- Jason S Chwa
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Yunho Shin
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Yesun Lee
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Thomas Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Zion Congrave-Wilson
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Wesley A Cheng
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Jaycee Jumarang
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Minjun Kim
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
| | - Richard Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, United States
| | - Jeffrey M Bender
- Department of Pediatrics, City of Hope Comprehensive Cancer Center, Duarte, California, United States
| | - Pia S Pannaraj
- Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, California, United States
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5
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Li X, Trovão NS. The evolutionary and transmission dynamics of HIV-1 CRF08_BC. PLoS One 2024; 19:e0310027. [PMID: 39241052 PMCID: PMC11379155 DOI: 10.1371/journal.pone.0310027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/22/2024] [Indexed: 09/08/2024] Open
Abstract
HIV-1 CRF08_BC is a significant subtype in China, though its origin and spread remain incompletely understood. Previous studies using partial genomic data have provided insights but lack comprehensive analysis. Here, we investigate the early evolutionary and spatiotemporal dynamics of HIV-1 CRF08_BC in China and Myanmar using near-complete genome sequences. We analyzed 28 near-complete HIV-1 CRF08_BC genomes from China and Myanmar (1997-2013). Phylogenetic, molecular clock, and Bayesian discrete trait analyses were performed to infer the virus's origin, spread, and associated risk groups. Based on Bayesian time-scaled inference with the best-fitting combination of models determined by marginal likelihood estimation (MLE), we inferred the time to the most recent common ancestor (TMRCA) and evolutionary rate of HIV-1 CRF08_BC to be at 3 October 1991 (95% HPD: 22 February1989-27 November 1993) and 2.30 × 10-3 substitutions per site per year (95% HPD: 1.96 × 10-3-2.63 × 10-3), respectively. Our analysis suggests that HIV-1 CRF08_BC originated in Yunnan Province, China, among injecting drug users, and subsequently spread to other regions. This study provides valuable insights into the early dynamics of HIV-1 CRF08_BC through combined genomic and epidemiological data, which may inform effective prevention and mitigation efforts. However, the limited genomic data influenced the extent of our findings, and challenges in collecting accurate risk group information during surveillance were evident.
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Affiliation(s)
- Xingguang Li
- Ningbo No.2 Hospital, Ningbo, China
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, China
| | - Nídia S Trovão
- National Institutes of Health, Fogarty International Center, Bethesda, Maryland, United States of America
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6
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Costacurta F, Dodaro A, Bante D, Schöppe H, Peng JY, Sprenger B, He X, Moghadasi SA, Egger LM, Fleischmann J, Pavan M, Bassani D, Menin S, Rauch S, Krismer L, Sauerwein A, Heberle A, Rabensteiner T, Ho J, Harris RS, Stefan E, Schneider R, Dunzendorfer-Matt T, Naschberger A, Wang D, Kaserer T, Moro S, von Laer D, Heilmann E. A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system. PLoS Pathog 2024; 20:e1012522. [PMID: 39259728 PMCID: PMC11407635 DOI: 10.1371/journal.ppat.1012522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 09/17/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024] Open
Abstract
Nirmatrelvir was the first protease inhibitor specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available protease inhibitors (nirmatrelvir and ensitrelvir) with cell-based, biochemical and SARS-CoV-2 replicon assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease inhibitor resistance mechanisms and show the relevance of specific mutations, thereby informing treatment decisions.
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Affiliation(s)
- Francesco Costacurta
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Andrea Dodaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - David Bante
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Helge Schöppe
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Ju-Yi Peng
- Department of Infectious Diseases and Vaccines Research, MRL, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Bernhard Sprenger
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Xi He
- Department of Infectious Diseases and Vaccines Research, MRL, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lisa Maria Egger
- Institute of Molecular Biochemistry, Biocentre, Medical University of Innsbruck, Innsbruck, Austria
| | - Jakob Fleischmann
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Tyrol, Austria
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Silvia Menin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Stefanie Rauch
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Laura Krismer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Anna Sauerwein
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Anne Heberle
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Toni Rabensteiner
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Joses Ho
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States of America
| | - Eduard Stefan
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Tyrol, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Tyrol, Austria
| | - Rainer Schneider
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | | | - Andreas Naschberger
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dai Wang
- Department of Infectious Diseases and Vaccines Research, MRL, Merck & Co., Inc., Rahway, New Jersey, United States of America
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padova, Italy
| | - Dorothee von Laer
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Emmanuel Heilmann
- Institute of Virology, Medical University of Innsbruck, Innsbruck, Tyrol, Austria
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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7
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El Moussaoui M, Bontems S, Meex C, Hayette MP, Lejeune M, Hong SL, Dellicour S, Moutschen M, Cambisano N, Renotte N, Bours V, Darcis G, Artesi M, Durkin K. Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection. Virus Evol 2024; 10:veae073. [PMID: 39399151 PMCID: PMC11470753 DOI: 10.1093/ve/veae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/18/2024] [Accepted: 08/29/2024] [Indexed: 10/15/2024] Open
Abstract
Accumulating evidence points to persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunocompromised individuals as a source of novel lineages. While intrahost evolution of the virus in chronically infected patients has previously been reported, existing knowledge is primarily based on samples from the nasopharynx. In this study, we investigate the intrahost evolution and genetic diversity that accumulated during a prolonged SARS-CoV-2 infection with the Omicron BF.7 sublineage, which is estimated to have persisted for >1 year in an immunosuppressed patient. Based on the sequencing of eight samples collected at six time points, we identified 87 intrahost single-nucleotide variants, 2 indels, and a 362-bp deletion. Our analysis revealed distinct viral genotypes in the nasopharyngeal (NP), endotracheal aspirate, and bronchoalveolar lavage samples. This suggests that NP samples may not offer a comprehensive representation of the overall intrahost viral diversity. Our findings not only demonstrate that the Omicron BF.7 sublineage can further diverge from its already exceptionally mutated state but also highlight that patients chronically infected with SARS-CoV-2 can develop genetically specific viral populations across distinct anatomic compartments. This provides novel insights into the intricate nature of viral diversity and evolution dynamics in persistent infections.
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Affiliation(s)
- Majdouline El Moussaoui
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Sebastien Bontems
- Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Cecile Meex
- Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Marie-Pierre Hayette
- Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Marie Lejeune
- Department of Hematology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 49 Herestraat, Leuven 3000, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 50 Avenue Franklin Roosevelt, Bruxelles 1050, Belgium
| | - Michel Moutschen
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Nadine Cambisano
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Nathalie Renotte
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Vincent Bours
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Gilles Darcis
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Maria Artesi
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Keith Durkin
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
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8
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Brochu HN, Song K, Zhang Q, Zeng Q, Shafi A, Robinson M, Humphrey J, Croy B, Peavy L, Perera M, Parker S, Pruitt J, Munroe J, Ghatti R, Urban TJ, Harris AB, Alfego D, Norvell B, Levandoski M, Krueger B, Williams JD, Boles D, Nye MB, Dale SE, Sapeta M, Petropoulos CJ, Meltzer J, Eisenberg M, Cohen O, Letovsky S, Iyer LK. A program for real-time surveillance of SARS-CoV-2 genetics. Sci Rep 2024; 14:20249. [PMID: 39215120 PMCID: PMC11364650 DOI: 10.1038/s41598-024-70697-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The COVID-19 pandemic brought forth an urgent need for widespread genomic surveillance for rapid detection and monitoring of emerging SARS-CoV-2 variants. It necessitated design, development, and deployment of a nationwide infrastructure designed for sequestration, consolidation, and characterization of patient samples that disseminates de-identified information to public authorities in tight turnaround times. Here, we describe our development of such an infrastructure, which sequenced 594,832 high coverage SARS-CoV-2 genomes from isolates we collected in the United States (U.S.) from March 13th 2020 to July 3rd 2023. Our sequencing protocol ('Virseq') utilizes wet and dry lab procedures to generate mutation-resistant sequencing of the entire SARS-CoV-2 genome, capturing all major lineages. We also characterize 379 clinically relevant SARS-CoV-2 multi-strain co-infections and ensure robust detection of emerging lineages via simulation. The modular infrastructure, sequencing, and analysis capabilities we describe support the U.S. Centers for Disease Control and Prevention national surveillance program and serve as a model for rapid response to emerging pandemics at a national scale.
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Affiliation(s)
- Hayden N Brochu
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Kuncheng Song
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Qimin Zhang
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Qiandong Zeng
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Adib Shafi
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Matthew Robinson
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Jake Humphrey
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Bobbi Croy
- Labcorp Information Technology, Burlington, NC, 27215, USA
| | - Lydia Peavy
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Minoli Perera
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Scott Parker
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - John Pruitt
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Jason Munroe
- Labcorp Consumer Genetics Department, Burlington, NC, 27215, USA
| | | | - Thomas J Urban
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Ayla B Harris
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - David Alfego
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Brian Norvell
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Michael Levandoski
- Labcorp Research and Development, Burlington, NC, 27215, USA
- Q2 Solutions, an IQVIA Business, Durham, NC, 27703, USA
| | - Brian Krueger
- Labcorp Research and Development, Burlington, NC, 27215, USA
- BaseX Scientific, LLC, Chapel Hill, NC, 27516, USA
| | | | - Deborah Boles
- Labcorp Research and Development, Burlington, NC, 27215, USA
| | - Melinda B Nye
- Labcorp Center for Esoteric Testing, Burlington, NC, 27215, USA
| | - Suzanne E Dale
- Labcorp Center for Esoteric Testing, Burlington, NC, 27215, USA
| | - Michael Sapeta
- Labcorp Center for Esoteric Testing, Burlington, NC, 27215, USA
| | | | | | | | - Oren Cohen
- Labcorp Drug Development, Burlington, NC, 27215, USA
- Fortrea Inc, Durham, NC, 27703, USA
| | - Stanley Letovsky
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA
| | - Lakshmanan K Iyer
- Labcorp Center for Excellence in Data Science, AI and Bioinformatics, Burlington, NC, 27215, USA.
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9
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Nanduri S, Black A, Bedford T, Huddleston J. Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579374. [PMID: 39253501 PMCID: PMC11383015 DOI: 10.1101/2024.02.07.579374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis (PCA), multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS embeddings accurately represented pairwise genetic distances including the intermediate placement of recombinant SARS-CoV-2 lineages between parental lineages. Clusters from t-SNE embeddings accurately recapitulated known phylogenetic clades, H3N2 reassortment groups, and SARS-CoV-2 recombinant lineages. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.
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Affiliation(s)
- Sravani Nanduri
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Allison Black
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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10
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Khurana MP, Curran-Sebastian J, Scheidwasser N, Morgenstern C, Rasmussen M, Fonager J, Stegger M, Tang MHE, Juul JL, Escobar-Herrera LA, Møller FT, Albertsen M, Kraemer MUG, du Plessis L, Jokelainen P, Lehmann S, Krause TG, Ullum H, Duchêne DA, Mortensen LH, Bhatt S. High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark. Nat Commun 2024; 15:7123. [PMID: 39164246 PMCID: PMC11335946 DOI: 10.1038/s41467-024-51371-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged < 15 and > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.
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Affiliation(s)
- Mark P Khurana
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Jacob Curran-Sebastian
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Neil Scheidwasser
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Christian Morgenstern
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research and Development Laboratory, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Man-Hung Eric Tang
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas L Juul
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Pikka Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Sune Lehmann
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tyra G Krause
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut Copenhagen, Copenhagen, Denmark
| | | | - David A Duchêne
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Laust H Mortensen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Statistics Denmark, Copenhagen, Denmark
| | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
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11
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Bajić V, Schulmann VH, Nowick K. mtDNA "nomenclutter" and its consequences on the interpretation of genetic data. BMC Ecol Evol 2024; 24:110. [PMID: 39160470 PMCID: PMC11331612 DOI: 10.1186/s12862-024-02288-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 07/11/2024] [Indexed: 08/21/2024] Open
Abstract
Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g., "macro-haplogroups") vary across studies, as they depend on the sample quality, technical factors of haplogroup calling, the aims of the study, and the researchers' understanding of the mtDNA haplogroup nomenclature. Retention of historical nomenclature coupled with a growing number of newly described mtDNA lineages results in increasingly complex and inconsistent nomenclature that does not reflect phylogeny well. This "clutter" leaves room for grouping errors and inconsistencies across scientific publications, especially when the haplogroup names are used as a proxy for secondary groupings, and represents a source for scientific misinterpretation. Here we explore the effects of phylogenetically insensitive secondary mtDNA haplogroup groupings, and the lack of standardized secondary haplogroup groupings on downstream analyses and interpretation of genetic data. We demonstrate that frequency-based analyses produce inconsistent results when different secondary mtDNA groupings are applied, and thus allow for vastly different interpretations of the same genetic data. The lack of guidelines and recommendations on how to choose appropriate secondary haplogroup groupings presents an issue for the interpretation of results, as well as their comparison and reproducibility across studies. To reduce biases originating from arbitrarily defined secondary nomenclature-based groupings, we suggest that future updates of mtDNA phylogenies aimed for the use in mtDNA haplogroup nomenclature should also provide well-defined and standardized sets of phylogenetically meaningful algorithm-based secondary haplogroup groupings such as "macro-haplogroups", "meso-haplogroups", and "micro-haplogroups". Ideally, each of the secondary haplogroup grouping levels should be informative about different human population history events. Those phylogenetically informative levels of haplogroup groupings can be easily defined using TreeCluster, and then implemented into haplogroup callers such as HaploGrep3. This would foster reproducibility across studies, provide a grouping standard for population-based studies, and reduce errors associated with haplogroup nomenclatures in future studies.
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Affiliation(s)
- Vladimir Bajić
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany.
| | | | - Katja Nowick
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany.
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12
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Tang L, Guo Z, Lu X, Zhao J, Li Y, Yang K. Wastewater multiplex PCR amplicon sequencing revealed community transmission of SARS-CoV-2 lineages during the outbreak of infection in Chinese Mainland. Heliyon 2024; 10:e35332. [PMID: 39166043 PMCID: PMC11334792 DOI: 10.1016/j.heliyon.2024.e35332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
During the COVID-19, wastewater-based epidemiology (WBE) has become a powerful epidemic surveillance tool widely used worldwide. However, the development and application of this technology in Chinese Mainland are relatively lagging. Herein, we for the first time monitored the community circulation of SARS-CoV-2 lineages using WBE methods in Chinese Mainland. During the peak period of infection outbreak at the end of 2022, six precious sewage samples were collected from the manhole in the student dormitory area on Wangjiang Campus of Sichuan University. RT-qPCR revealed that the six sewage samples were all positive for SARS-CoV-2 RNA. Multiplex PCR amplicon sequencing of the sewage samples reflected the local transmission of SARS-CoV-2 variants. The results of two deconvolution methods indicate that the main virus lineages have clear evolutionary genetic correlations. Furthermore, the sampling time is consistent with the timeline of concern for these virus lineages, as well as the timeline of uploading the nucleic acid sequences from the corresponding lineages in Sichuan to the database. These results demonstrate the reliability of the sewage sequencing results. Multiplex PCR amplicon sequencing is by far the most powerful analytical tool of WBE, enabling quantitative detection of virus lineages transmission and evolution at the community level.
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Affiliation(s)
| | | | - Xiaoyi Lu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Junqiao Zhao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Yonghong Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
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13
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Goya S, Ruis C, Neher RA, Meijer A, Aziz A, Hinrichs AS, von Gottberg A, Roemer C, Amoako DG, Acuña D, McBroome J, Otieno JR, Bhiman JN, Everatt J, Muñoz-Escalante JC, Ramaekers K, Duggan K, Presser LD, Urbanska L, Venter M, Wolter N, Peret TC, Salimi V, Potdar V, Borges V, Viegas M. Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level. Emerg Infect Dis 2024; 30:1631-1641. [PMID: 39043393 PMCID: PMC11286072 DOI: 10.3201/eid3008.240209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
A globally implemented unified phylogenetic classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. We formulated global consensus of HRSV classification on the basis of the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality curated dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to GenBank and GISAID (https://www.gisaid.org) public sequence databases through March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B and provided guidelines for defining prospective lineages. Our classification demonstrated robustness in its applicability to both complete and partial genomes. We envision that this unified HRSV classification proposal will strengthen HRSV molecular epidemiology on a global scale.
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Affiliation(s)
| | | | | | - Adam Meijer
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Ammar Aziz
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Angie S. Hinrichs
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Anne von Gottberg
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Cornelius Roemer
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | | | - Dolores Acuña
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Jakob McBroome
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - James R. Otieno
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Jinal N. Bhiman
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Josie Everatt
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Juan C. Muñoz-Escalante
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | | | - Kate Duggan
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Lance D. Presser
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Laura Urbanska
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Marietjie Venter
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Nicole Wolter
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Teresa C.T. Peret
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Vahid Salimi
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Varsha Potdar
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Vítor Borges
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
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14
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Goldberg AR, Langwig KE, Brown KL, Marano JM, Rai P, King KM, Sharp AK, Ceci A, Kailing CD, Kailing MJ, Briggs R, Urbano MG, Roby C, Brown AM, Weger-Lucarelli J, Finkielstein CV, Hoyt JR. Widespread exposure to SARS-CoV-2 in wildlife communities. Nat Commun 2024; 15:6210. [PMID: 39075057 PMCID: PMC11286844 DOI: 10.1038/s41467-024-49891-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/20/2024] [Indexed: 07/31/2024] Open
Abstract
Pervasive SARS-CoV-2 infections in humans have led to multiple transmission events to animals. While SARS-CoV-2 has a potential broad wildlife host range, most documented infections have been in captive animals and a single wildlife species, the white-tailed deer. The full extent of SARS-CoV-2 exposure among wildlife communities and the factors that influence wildlife transmission risk remain unknown. We sampled 23 species of wildlife for SARS-CoV-2 and examined the effects of urbanization and human use on seropositivity. Here, we document positive detections of SARS-CoV-2 RNA in six species, including the deer mouse, Virginia opossum, raccoon, groundhog, Eastern cottontail, and Eastern red bat between May 2022-September 2023 across Virginia and Washington, D.C., USA. In addition, we found that sites with high human activity had three times higher seroprevalence than low human-use areas. We obtained SARS-CoV-2 genomic sequences from nine individuals of six species which were assigned to seven Pango lineages of the Omicron variant. The close match to variants circulating in humans at the time suggests at least seven recent human-to-animal transmission events. Our data support that exposure to SARS-CoV-2 has been widespread in wildlife communities and suggests that areas with high human activity may serve as points of contact for cross-species transmission.
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Affiliation(s)
- Amanda R Goldberg
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Kate E Langwig
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Katherine L Brown
- Virginia Tech Carilion School of Medicine, Virginia Tech, Roanoke, VA, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, USA
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Jeffrey M Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, USA
| | - Pallavi Rai
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Kelsie M King
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Amanda K Sharp
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Alessandro Ceci
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | | | - Macy J Kailing
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Russell Briggs
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Matthew G Urbano
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Clinton Roby
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA
| | - Anne M Brown
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
- Data Services, University Libraries, Virginia Tech, Blacksburg, VA, USA
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, USA
- Academy of Integrated Science, Virginia Tech, Blacksburg, VA, USA
| | - James Weger-Lucarelli
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, USA
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Carla V Finkielstein
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
- Virginia Tech Carilion School of Medicine, Virginia Tech, Roanoke, VA, USA.
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, USA.
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA.
- Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, USA.
- Academy of Integrated Science, Virginia Tech, Blacksburg, VA, USA.
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
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15
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Ryder R, Smith E, Borthwick D, Elder J, Panditrao M, Morales C, Wadford DA. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses 2024; 16:1209. [PMID: 39205183 PMCID: PMC11359944 DOI: 10.3390/v16081209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in California to describe regional and statewide trends in prevalence. Many of these recombinant genomes, such as those belonging to the XZ lineage or novel recombinant lineages, likely originated within the state of California. We discuss the challenges and limitations surrounding Pango lineage assignments, the use of publicly available sequence data, and adequate sample sizes for epidemiologic analyses. Although these challenges will continue as SARS-CoV-2 sequencing volumes decrease globally, this study enhances our understanding of SARS-CoV-2 recombinant genomes to date while providing a foundation for future insights into emerging recombinant lineages.
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Affiliation(s)
- Rahil Ryder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Emily Smith
- Theiagen Genomics, Highlands Ranch, CO 80129, USA;
| | - Deva Borthwick
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Jesse Elder
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Mayuri Panditrao
- COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
| | - Christina Morales
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A. Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA
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16
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Ye Y, Shum MH, Wu I, Chau C, Zhao N, Smith DK, Wu JT, Lam TT. F1ALA: ultrafast and memory-efficient ancestral lineage annotation applied to the huge SARS-CoV-2 phylogeny. Virus Evol 2024; 10:veae056. [PMID: 39247558 PMCID: PMC11378316 DOI: 10.1093/ve/veae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/19/2024] [Accepted: 07/24/2024] [Indexed: 09/10/2024] Open
Abstract
The unprecedentedly large size of the global SARS-CoV-2 phylogeny makes any computation on the tree difficult. Lineage identification (e.g. the PANGO nomenclature for SARS-CoV-2) and assignment are key to track the virus evolution. It requires annotating clade roots of lineages to unlabeled ancestral nodes in a phylogenetic tree. Then the lineage labels of descendant samples under these clade roots can be inferred to be the corresponding lineages. This is the ancestral lineage annotation problem, and matUtils (a package in pUShER) and PastML are commonly used methods. However, their computational tractability is a challenge and their accuracy needs further exploration in huge SARS-CoV-2 phylogenies. We have developed an efficient and accurate method, called "F1ALA", that utilizes the F1-score to evaluate the confidence with which a specific ancestral node can be annotated as the clade root of a lineage, given the lineage labels of a set of taxa in a rooted tree. Compared to these methods, F1ALA achieved roughly an order of magnitude faster yet with ∼12% of their memory usage when annotating 2277 PANGO lineages in a phylogeny of 5.26 million taxa. F1ALA allows real-time lineage tracking to be performed on a laptop computer. F1ALA outperformed matUtils (pUShER) with statistical significance, and had comparable accuracy to PastML in tests on empirical and simulated data. F1ALA enables a tree refinement by pruning taxa with inconsistent labels to their closest annotation nodes and re-inserting them back to the pruned tree to improve a SARS-CoV-2 phylogeny with both higher log-likelihood and lower parsimony score. Given the ultrafast speed and high accuracy, we anticipated that F1ALA will also be useful for large phylogenies of other viruses. Codes and benchmark datasets are publicly available at https://github.com/id-bioinfo/F1ALA.
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Affiliation(s)
- Yongtao Ye
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Marcus H Shum
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Isaac Wu
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Carlos Chau
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Ningqi Zhao
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Joseph T Wu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Tommy T Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong 515063, P. R. China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong 518045, P. R. China
- Centre for Immunology & Infection, 17W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
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17
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Bonetti Franceschi V, Volz E. Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2. Wellcome Open Res 2024; 9:85. [PMID: 39132669 PMCID: PMC11316176 DOI: 10.12688/wellcomeopenres.20704.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Background Large-scale sequencing of SARS-CoV-2 has enabled the study of viral evolution during the COVID-19 pandemic. Some viral mutations may be advantageous to viral replication within hosts but detrimental to transmission, thus carrying a transient fitness advantage. By affecting the number of descendants, persistence times and growth rates of associated clades, these mutations generate localised imbalance in phylogenies. Quantifying these features in closely-related clades with and without recurring mutations can elucidate the tradeoffs between within-host replication and between-host transmission. Methods We implemented a novel phylogenetic clustering algorithm ( mlscluster, https://github.com/mrc-ide/mlscluster) to systematically explore time-scaled phylogenies for mutations under transient/multilevel selection. We applied this method to a SARS-CoV-2 time-calibrated phylogeny with >1.2 million sequences from England, and characterised these recurrent mutations that may influence transmission fitness across PANGO-lineages and genomic regions using Poisson regressions and summary statistics. Results We found no major differences across two epidemic stages (before and after Omicron), PANGO-lineages, and genomic regions. However, spike, nucleocapsid, and ORF3a were proportionally more enriched for transmission fitness polymorphisms (TFP)-homoplasies than other proteins. We provide a catalog of SARS-CoV-2 sites under multilevel selection, which can guide experimental investigations within and beyond the spike protein. Conclusions This study provides empirical evidence for the existence of important tradeoffs between within-host replication and between-host transmission shaping the fitness landscape of SARS-CoV-2. This method may be used as a fast and scalable means to shortlist large sequence databases for sites under putative multilevel selection which may warrant subsequent confirmatory analyses and experimental confirmation.
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Affiliation(s)
- Vinicius Bonetti Franceschi
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
| | - Erik Volz
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
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18
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Kumbhari A, Cheng TNH, Ananthakrishnan AN, Kochar B, Burke KE, Shannon K, Lau H, Xavier RJ, Smillie CS. Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases. Cell Host Microbe 2024; 32:1147-1162.e12. [PMID: 38917808 PMCID: PMC11239293 DOI: 10.1016/j.chom.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/16/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Gut bacteria are implicated in inflammatory bowel disease (IBD), but the strains driving these associations are unknown. Large-scale studies of microbiome evolution could reveal the imprint of disease on gut bacteria, thus pinpointing the strains and genes that may underlie inflammation. Here, we use stool metagenomes of thousands of IBD patients and healthy controls to reconstruct 140,000 strain genotypes, revealing hundreds of lineages enriched in IBD. We demonstrate that these strains are ancient, taxonomically diverse, and ubiquitous in humans. Moreover, disease-associated strains outcompete their healthy counterparts during inflammation, implying long-term adaptation to disease. Strain genetic differences map onto known axes of inflammation, including oxidative stress, nutrient biosynthesis, and immune evasion. Lastly, the loss of health-associated strains of Eggerthella lenta was predictive of fecal calprotectin, a biomarker of disease severity. Our work identifies reservoirs of strain diversity that may impact inflammatory disease and can be extended to other microbiome-associated diseases.
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Affiliation(s)
- Adarsh Kumbhari
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas N H Cheng
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Bharati Kochar
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Kristin E Burke
- Department of Medicine, Harvard Medical School, Boston, MA, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin Shannon
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Helena Lau
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Smillie
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA.
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19
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Ly-Trong N, Bielow C, De Maio N, Minh BQ. CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era. Mol Biol Evol 2024; 41:msae134. [PMID: 38934791 PMCID: PMC11232695 DOI: 10.1093/molbev/msae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/15/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and scalability, here we present two key components: (i) CMAPLE software, a highly optimized C++ reimplementation of MAPLE with many new features and advancements, and (ii) CMAPLE library, a suite of application programming interfaces to facilitate the integration of the CMAPLE algorithm into existing phylogenetic inference packages. Notably, we have successfully integrated CMAPLE into the widely used IQ-TREE 2 software, enabling its rapid adoption in the scientific community. These advancements serve as a vital step toward better preparedness for future pandemics, offering researchers powerful tools for large-scale pathogen genomic analysis.
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Affiliation(s)
- Nhan Ly-Trong
- School of Computing, College of Engineering, Computing and Cybernetics, Australian National University, Canberra, ACT 2600, Australia
| | - Chris Bielow
- Bioinformatics Solution Center, Freie Universität Berlin, 14195 Berlin, Germany
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Bui Quang Minh
- School of Computing, College of Engineering, Computing and Cybernetics, Australian National University, Canberra, ACT 2600, Australia
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20
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Iglhaut C, Pečerska J, Gil M, Anisimova M. Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels. Mol Biol Evol 2024; 41:msae109. [PMID: 38842253 PMCID: PMC11221656 DOI: 10.1093/molbev/msae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024] Open
Abstract
Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.
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Affiliation(s)
- Clara Iglhaut
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Faculty of Mathematics and Science, University of Zurich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jūlija Pečerska
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Manuel Gil
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Anisimova
- Institute of Computational Life Science, Zurich University of Applied Science, Wädenswil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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21
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Ma W, Fu H, Jian F, Cao Y, Li M. Distinct SARS-CoV-2 populational immune backgrounds tolerate divergent RBD evolutionary preferences. Natl Sci Rev 2024; 11:nwae196. [PMID: 39071101 PMCID: PMC11275455 DOI: 10.1093/nsr/nwae196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 07/30/2024] Open
Abstract
Immune evasion is a pivotal force shaping the evolution of viruses. Nonetheless, the extent to which virus evolution varies among populations with diverse immune backgrounds remains an unsolved mystery. Prior to the widespread SARS-CoV-2 infections in December 2022 and January 2023, the Chinese population possessed a markedly distinct (less potent) immune background due to its low infection rate, compared to countries experiencing multiple infection waves, presenting an unprecedented opportunity to investigate how the virus has evolved under different immune contexts. We compared the mutation spectrum and functional potential of the newly derived mutations that occurred in BA.5.2.48, BF.7.14 and BA.5.2.49-variants prevalent in China-with their counterparts in other countries. We found that the emerging mutations in the receptor-binding-domain region in these lineages were more widely dispersed and evenly distributed across different epitopes. These mutations led to a higher angiotensin-converting enzyme 2 (ACE2) binding affinity and reduced potential for immune evasion compared to their counterparts in other countries. These findings suggest a milder immune pressure and less evident immune imprinting within the Chinese population. Despite the emergence of numerous immune-evading variants in China, none of them outcompeted the original strain until the arrival of the XBB variant, which had stronger immune evasion and subsequently outcompeted all circulating variants. Our findings demonstrated that the continuously changing immune background led to varying evolutionary pressures on SARS-CoV-2. Thus, in addition to viral genome surveillance, immune background surveillance is also imperative for predicting forthcoming mutations and understanding how these variants spread in the population.
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Affiliation(s)
- Wentai Ma
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoyi Fu
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
- Changping Laboratory, Beijing 102206, China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Jiang Y, McDonald D, Perry D, Knight R, Mirarab S. Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinformatics 2024; 40:btae361. [PMID: 38870525 PMCID: PMC11193062 DOI: 10.1093/bioinformatics/btae361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 04/09/2024] [Accepted: 06/12/2024] [Indexed: 06/15/2024] Open
Abstract
MOTIVATION Phylogenetic placement of a query sequence on a backbone tree is increasingly used across biomedical sciences to identify the content of a sample from its DNA content. The accuracy of such analyses depends on the density of the backbone tree, making it crucial that placement methods scale to very large trees. Moreover, a new paradigm has been recently proposed to place sequences on the species tree using single-gene data. The goal is to better characterize the samples and to enable combined analyses of marker-gene (e.g., 16S rRNA gene amplicon) and genome-wide data. The recent method DEPP enables performing such analyses using metric learning. However, metric learning is hampered by a need to compute and save a quadratically growing matrix of pairwise distances during training. Thus, the training phase of DEPP does not scale to more than roughly 10 000 backbone species, a problem that we faced when trying to use our recently released Greengenes2 (GG2) reference tree containing 331 270 species. RESULTS This paper explores divide-and-conquer for training ensembles of DEPP models, culminating in a method called C-DEPP. While divide-and-conquer has been extensively used in phylogenetics, applying divide-and-conquer to data-hungry machine-learning methods needs nuance. C-DEPP uses carefully crafted techniques to enable quasi-linear scaling while maintaining accuracy. C-DEPP enables placing 20 million 16S fragments on the GG2 reference tree in 41 h of computation. AVAILABILITY AND IMPLEMENTATION The dataset and C-DEPP software are freely available at https://github.com/yueyujiang/dataset_cdepp/.
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Affiliation(s)
- Yueyu Jiang
- Electrical and Computer Engineering Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Daniel McDonald
- Pediatrics Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Daniela Perry
- Pediatrics Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Rob Knight
- Pediatrics Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
| | - Siavash Mirarab
- Electrical and Computer Engineering Department, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, United States
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23
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Vasylyeva TI, Havens JL, Wang JC, Luoma E, Hassler GW, Amin H, Di Lonardo S, Taki F, Omoregie E, Hughes S, Wertheim JO. The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021. PLoS Pathog 2024; 20:e1012288. [PMID: 38900824 PMCID: PMC11218943 DOI: 10.1371/journal.ppat.1012288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/02/2024] [Accepted: 05/25/2024] [Indexed: 06/22/2024] Open
Abstract
Socio-economic disparities were associated with disproportionate viral incidence between neighborhoods of New York City (NYC) during the first wave of SARS-CoV-2. We investigated how these disparities affected the co-circulation of SARS-CoV-2 variants during the second wave in NYC. We tested for correlation between the prevalence, in late 2020/early 2021, of Alpha, Iota, Iota with E484K mutation (Iota-E484K), and B.1-like genomes and pre-existing immunity (seropositivity) in NYC neighborhoods. In the context of varying seroprevalence we described socio-economic profiles of neighborhoods and performed migration and lineage persistence analyses using a Bayesian phylogeographical framework. Seropositivity was greater in areas with high poverty and a larger proportion of Black and Hispanic or Latino residents. Seropositivity was positively correlated with the proportion of Iota-E484K and Iota genomes, and negatively correlated with the proportion of Alpha and B.1-like genomes. The proportion of persisting Alpha lineages declined over time in locations with high seroprevalence, whereas the proportion of persisting Iota-E484K lineages remained the same in high seroprevalence areas. During the second wave, the geographic variation of standing immunity, due to disproportionate disease burden during the first wave of SARS-CoV-2 in NYC, allowed for the immune evasive Iota-E484K variant, but not the more transmissible Alpha variant, to circulate in locations with high pre-existing immunity.
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Affiliation(s)
- Tetyana I. Vasylyeva
- Department of Population Health and Disease Prevention, University of California Irvine, Irvine, California, United States of America
| | - Jennifer L. Havens
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Jade C. Wang
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Elizabeth Luoma
- Bureau of Communicable Disease, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Gabriel W. Hassler
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Helly Amin
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Steve Di Lonardo
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Faten Taki
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Enoma Omoregie
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Scott Hughes
- New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
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24
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Gupta A, Mirarab S, Turakhia Y. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596098. [PMID: 38854139 PMCID: PMC11160643 DOI: 10.1101/2024.05.27.596098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.
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Affiliation(s)
- Anshu Gupta
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
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25
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Gill EE, Jia B, Murall CL, Poujol R, Anwar MZ, John NS, Richardsson J, Hobb A, Olabode AS, Lepsa A, Duggan AT, Tyler AD, N’Guessan A, Kachru A, Chan B, Yoshida C, Yung CK, Bujold D, Andric D, Su E, Griffiths EJ, Van Domselaar G, Jolly GW, Ward HK, Feher H, Baker J, Simpson JT, Uddin J, Ragoussis J, Eubank J, Fritz JH, Gálvez JH, Fang K, Cullion K, Rivera L, Xiang L, Croxen MA, Shiell M, Prystajecky N, Quirion PO, Bajari R, Rich S, Mubareka S, Moreira S, Cain S, Sutcliffe SG, Kraemer SA, Joly Y, Alturmessov Y, consortium CPHLN, consortium C, Fiume M, Snutch TP, Bell C, Lopez-Correa C, Hussin JG, Joy JB, Colijn C, Gordon PM, Hsiao WW, Poon AF, Knox NC, Courtot M, Stein L, Otto SP, Bourque G, Shapiro BJ, Brinkman FS. The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. ARXIV 2024:arXiv:2405.04734v1. [PMID: 38764594 PMCID: PMC11100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This Portal has been coupled with other resources like Viral AI and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this Portal, including its contextual data not available elsewhere, and the 'Duotang', a web platform that presents key genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.
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Affiliation(s)
- Erin E. Gill
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Baofeng Jia
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Carmen Lia Murall
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Raphaël Poujol
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
| | - Muhammad Zohaib Anwar
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Nithu Sara John
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | | | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, ON Canada
| | | | - Ana T. Duggan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Andrea D. Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Arnaud N’Guessan
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Atul Kachru
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Brandon Chan
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Systems, Toronto, ON, Canada
| | - David Bujold
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Dusan Andric
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Edmund Su
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Emma J. Griffiths
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Gordon W. Jolly
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Henrich Feher
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jared Baker
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Jaser Uddin
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Jon Eubank
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jörg H. Fritz
- Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada
| | | | | | - Kim Cullion
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Linda Xiang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Matthew A. Croxen
- Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children’s Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | | | - Natalie Prystajecky
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Rosita Bajari
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Samantha Rich
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Scott Cain
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Steven G. Sutcliffe
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Susanne A. Kraemer
- McGill Genome Centre, McGill University, Montréal, QC, Canada
- Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada
| | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
| | | | | | | | | | | | - Terrance P. Snutch
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Cindy Bell
- Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada
| | | | - Julie G. Hussin
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
- Research Centre, Montréal Heart Institute, Montréal, QC, Canada
- Mila-Québec AI institute, Montréal, QC, Canada
| | - Jeffrey B. Joy
- Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Paul M.K. Gordon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada
| | - William W.L. Hsiao
- Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Art F.Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, ON Canada
| | - Natalie C. Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Mélanie Courtot
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical BioPhysics, University of Toronto, ON, Canada
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Sarah P. Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver BC Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Fiona S.L. Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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26
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Aljabali AAA, Obeid MA, El-Tanani M, Mishra V, Mishra Y, Tambuwala MM. Precision epidemiology at the nexus of mathematics and nanotechnology: Unraveling the dance of viral dynamics. Gene 2024; 905:148174. [PMID: 38242374 DOI: 10.1016/j.gene.2024.148174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The intersection of mathematical modeling, nanotechnology, and epidemiology marks a paradigm shift in our battle against infectious diseases, aligning with the focus of the journal on the regulation, expression, function, and evolution of genes in diverse biological contexts. This exploration navigates the intricate dance of viral transmission dynamics, highlighting mathematical models as dual tools of insight and precision instruments, a theme relevant to the diverse sections of Gene. In the context of virology, ethical considerations loom large, necessitating robust frameworks to protect individual rights, an aspect essential in infectious disease research. Global collaboration emerges as a critical pillar in our response to emerging infectious diseases, fortified by the predictive prowess of mathematical models enriched by nanotechnology. The synergy of interdisciplinary collaboration, training the next generation to bridge mathematical rigor, biology, and epidemiology, promises accelerated discoveries and robust models that account for real-world complexities, fostering innovation and exploration in the field. In this intricate review, mathematical modeling in viral transmission dynamics and epidemiology serves as a guiding beacon, illuminating the path toward precision interventions, global preparedness, and the collective endeavor to safeguard human health, resonating with the aim of advancing knowledge in gene regulation and expression.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan.
| | - Mohammad A Obeid
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan
| | - Mohamed El-Tanani
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Yachana Mishra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, United Kingdom.
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585703. [PMID: 38746108 PMCID: PMC11092427 DOI: 10.1101/2024.03.19.585703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app .
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28
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. ARXIV 2024:arXiv:2403.12684v2. [PMID: 38745695 PMCID: PMC11092678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Malancha Karmakar
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
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29
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Fountain-Jones NM, Vanhaeften R, Williamson J, Maskell J, Chua ILJ, Charleston M, Cooley L. Effect of molnupiravir on SARS-CoV-2 evolution in immunocompromised patients: a retrospective observational study. THE LANCET. MICROBE 2024; 5:e452-e458. [PMID: 38527471 DOI: 10.1016/s2666-5247(23)00393-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 03/27/2024]
Abstract
INTRODUCTION Continued SARS-CoV-2 infection among immunocompromised individuals is likely to play a role in generating genomic diversity and the emergence of novel variants. Antiviral treatments such as molnupiravir are used to mitigate severe COVID-19 outcomes, but the extended effects of these drugs on viral evolution in patients with chronic infections remain uncertain. This study investigates how molnupiravir affects SARS-CoV-2 evolution in immunocompromised patients with prolonged infections. METHODS The study included five immunocompromised patients treated with molnupiravir and four patients not treated with molnupiravir (two immunocompromised and two non-immunocompromised). We selected patients who had been infected by similar SARS-CoV-2 variants and with high-quality genomes across timepoints to allow comparison between groups. Throat and nasopharyngeal samples were collected in patients up to 44 days post treatment and were sequenced using tiled amplicon sequencing followed by variant calling. The UShER pipeline and University of California Santa Cruz genome viewer provided insights into the global context of variants. Treated and untreated patients were compared, and mutation profiles were visualised to understand the impact of molnupiravir on viral evolution. FINDINGS Patients treated with molnupiravir showed a large increase in low-to-mid-frequency variants in as little as 10 days after treatment, whereas no such change was observed in untreated patients. Some of these variants became fixed in the viral population, including non-synonymous mutations in the spike protein. The variants were distributed across the genome and included unique mutations not commonly found in global omicron genomes. Notably, G-to-A and C-to-T mutations dominated the mutational profile of treated patients, persisting up to 44 days post treatment. INTERPRETATION Molnupiravir treatment in immunocompromised patients led to the accumulation of a distinctive pattern of mutations beyond the recommended 5 days of treatment. Treated patients maintained persistent PCR positivity for the duration of monitoring, indicating clear potential for transmission and subsequent emergence of novel variants. FUNDING Australian Research Council.
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Affiliation(s)
- Nicholas M Fountain-Jones
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia; School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia.
| | | | - Jan Williamson
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Janelle Maskell
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia
| | - I-Ly J Chua
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Michael Charleston
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Louise Cooley
- Pathology Department, Royal Hobart Hospital, Hobart, TAS, Australia; School of Medicine, University of Tasmania, Hobart, TAS, Australia
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30
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Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Bashton M, Batty EM, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Carr RAA, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Molina Mora JA, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C, de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z. Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591666. [PMID: 38746185 PMCID: PMC11092452 DOI: 10.1101/2024.04.29.591666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 3,960,704 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of March 2023, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. Phase 2 of our project will address the fact that the data in the public archives is heavily geographically biased towards the Global North. We therefore have contributed new raw data to ENA/SRA from many countries including Ghana, Thailand, Laos, Sri Lanka, India, Argentina and Singapore. We will incorporate these, along with all public raw data submitted between March 2023 and the current day, into an updated set of assemblies, and phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.
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Affiliation(s)
- Martin Hunt
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Angie S Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - Daniel Anderson
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Lily Karim
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
| | - Bethany L Dearlove
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Jeff Knaggs
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Bede Constantinides
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Philip W Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Teresa Street
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
| | - Sheila Lumley
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Infectious Diseases and Microbiology, John Radcliffe Hospital, Oxford, UK
| | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christopher Ruis
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nicola de Maio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
| | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Dominic S Y Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Martin Avaro
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Reuben Ayivor-Djanie
- Laboratory for Medical Biotechnology and Biomanufacturing, International Centre for Genetic Engineering and Biotechnology, Tristie, Italy
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Elizabeth M Batty
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Denise De Belder
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Estefania Benedetti
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Andreas Bergthaler
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Stefan A Boers
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Rosina Afua Ampomah Carr
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, Ann Arbor, MI, USA
| | - Facundo Cuba
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Maria Elena Dattero
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok 10700, Thailand
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kwabena Obeng Duedu
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- College of Life Sciences, Birmingham City University, Birmingham, UK
| | - Lukas Endler
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna 1090, Austria
| | - Ilka Engelmann
- Pathogenesis and Control of Chronic and Emerging Infections, Univ Montpellier, INSERM, Etablissement Français du Sang, Virology Laboratory, CHU Montpellier, Montpellier, France
| | - Ngiambudulu M Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Etienne Z Gnimpieba
- Biomedical Engineering Department, University of South Dakota, Sioux Falls, SD 57107
| | - Soraya Groc
- Virology Laboratory, CHU Montpellier, Montpellier, France
| | - Jones Gyamfi
- Department of Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK
| | - Dennis Heemskerk
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nei-Yuan Hsiao
- Divison of Medical Virology, University of Cape Town and National Health Laboratory Service
| | - Matthew Huska
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | | | - Hanna Jarva
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Bani Jolly
- Karkinos Healthcare Private Limited (KHPL), Aurbis Business Parks, Bellandur, Bengaluru, Karnataka, 560103, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | | | - Ravi Kant
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
- Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, Medical University of Gdansk, 81-519 Gdynia, Poland
| | | | - Satu Kurkela
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maija Lappalainen
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marie Lataretu
- Genome Competence Center (MF1), Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Tapfumanei Mashe
- Health System Strengthening Unit, World Health Organisation, Harare, Zimbabwe
| | - Juthathip Mongkolsapaya
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Jose Arturo Molina Mora
- Centro de investigación en Enfermedades Tropicales & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Bernard Mvula
- Public Health Institute of Malawi, Ministry of Health, Malawi
| | - Niranjan Nagarajan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Joyce M Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Joana Paula da Paixão
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Marcus Panning
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tomas Poklepovich
- Unidad Operativa Centro Nacional de Genómica y Bioinformática, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Peter K Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Diyanath Ranasinghe
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Mara Russo
- Servicio de Virus Respiratorios, Instituto Nacional Enfermedades Infecciosas, ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - James Emmanuel San
- Duke Human Vaccine Institute, Duke University, Durham, NC 27710
- University of KwaZulu Natal, Durban, South Africa, 4001
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- Vishwanath Cancer Care Foundation (VCCF), Neelkanth Business Park Kirol Village, West Mumbai, Maharashtra, 400086, India
| | - Gavin Screaton
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tarja Sironen
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Darren Smith
- The Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Teemu Smura
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chayaporn Suphavilai
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
| | - Bryan Tegomoh
- Centre de Coordination des Opérations d'Urgences de Santé Publique, Ministere de Sante Publique, Cameroun
- University of California, Berkeley, Berkeley, California, USA
- Nebraska Department of Health and Human Services, Lincoln, Nebraska, USA
| | - Olli Vapalahti
- Department of Veterinary Biosciences, University of Helsinki, 00014 Helsinki, Finland
- Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Robert J Wilkinson
- Francis Crick Institute, London, UK
- Centre for Infectious Diseases Research in Africa, University of Cape Town
- Imperial College London, UK
| | | | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, South Africa
| | - Timothy Ea Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Russell Corbett-Detig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA
| | - Zamin Iqbal
- European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, UK
- Milner Centre for Evolution, University of Bath, UK
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31
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Santos JD, Sobral D, Pinheiro M, Isidro J, Bogaardt C, Pinto M, Eusébio R, Santos A, Mamede R, Horton DL, Gomes JP, Borges V. INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance. Genome Med 2024; 16:61. [PMID: 38659008 PMCID: PMC11044337 DOI: 10.1186/s13073-024-01334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. RESULTS The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. CONCLUSIONS The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
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Affiliation(s)
- João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Carlijn Bogaardt
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rodrigo Eusébio
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - André Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rafael Mamede
- Faculdade de Medicina, Instituto de Microbiologia, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel L Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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Wagner C, Kistler KE, Perchetti GA, Baker N, Frisbie LA, Torres LM, Aragona F, Yun C, Figgins M, Greninger AL, Cox A, Oltean HN, Roychoudhury P, Bedford T. Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution. Nat Commun 2024; 15:3207. [PMID: 38615031 PMCID: PMC11016114 DOI: 10.1038/s41467-024-47599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024] Open
Abstract
Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones. Indeed, ORF8 is truncated more frequently and knockouts circulate for longer than for any other gene. Using a global phylogeny, we find evidence of positive selection to explain this phenomenon: nonsense mutations resulting in shortened protein products occur more frequently and are associated with faster clade growth rates than synonymous mutations in ORF8. Loss of ORF8 is also associated with reduced clinical severity, highlighting the diverse clinical impacts of SARS-CoV-2 evolution.
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Affiliation(s)
- Cassia Wagner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Kathryn E Kistler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Noah Baker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Frank Aragona
- Washington State Department of Health, Shoreline, WA, USA
| | - Cory Yun
- Washington State Department of Health, Shoreline, WA, USA
| | - Marlin Figgins
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alex Cox
- Washington State Department of Health, Shoreline, WA, USA
| | - Hanna N Oltean
- Washington State Department of Health, Shoreline, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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33
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Sultana A, Bienzle D, Weese S, Pickering B, Kruczkiewicz P, Smith G, Pinette M, Lung O. Whole-genome sequencing of SARS-CoV-2 from the initial cases of domestic cat infections in Canada. Microbiol Resour Announc 2024; 13:e0129523. [PMID: 38411070 PMCID: PMC11008122 DOI: 10.1128/mra.01295-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/16/2024] [Indexed: 02/28/2024] Open
Abstract
Two cat nasal swabs from Canada's earliest confirmed SARS-CoV-2 positive domestic cats were sequenced to over 99% SARS-CoV-2 genome coverage. One cat had lineage A.23.1 SARS-CoV-2 not reported before in animals. Both sequences have multiple spike gene mutations and clustered closely with human-derived sequences in the global SARS-CoV-2 phylogenetic tree.
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Affiliation(s)
- Asma Sultana
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | - Dorothee Bienzle
- Ontario Veterinary College, Centre for Public Health and Zoonoses, University of Guelph, Ontario, Guelph, Canada
| | - Scott Weese
- Ontario Veterinary College, Centre for Public Health and Zoonoses, University of Guelph, Ontario, Guelph, Canada
| | - Brad Pickering
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peter Kruczkiewicz
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | - Greg Smith
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | - Mathieu Pinette
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | - Oliver Lung
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
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34
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Schöll M, Höhn C, Boucsein J, Moek F, Plath J, an der Heiden M, Huska M, Kröger S, Paraskevopoulou S, Siffczyk C, Buchholz U, Lachmann R. Bus Riding as Amplification Mechanism for SARS-CoV-2 Transmission, Germany, 2021 1. Emerg Infect Dis 2024; 30:711-720. [PMID: 38526123 PMCID: PMC10977817 DOI: 10.3201/eid3004.231299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
To examine the risk associated with bus riding and identify transmission chains, we investigated a COVID-19 outbreak in Germany in 2021 that involved index case-patients among bus-riding students. We used routine surveillance data, performed laboratory analyses, interviewed case-patients, and conducted a cohort study. We identified 191 case-patients, 65 (34%) of whom were elementary schoolchildren. A phylogenetically unique strain and epidemiologic analyses provided a link between air travelers and cases among bus company staff, schoolchildren, other bus passengers, and their respective household members. The attack rate among bus-riding children at 1 school was ≈4 times higher than among children not taking a bus to that school. The outbreak exemplifies how an airborne agent may be transmitted effectively through (multiple) short (<20 minutes) public transport journeys and may rapidly affect many persons.
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Affiliation(s)
| | | | - Johannes Boucsein
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
| | - Felix Moek
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
| | - Jasper Plath
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
| | - Maria an der Heiden
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
| | - Matthew Huska
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
| | - Stefan Kröger
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
| | - Sofia Paraskevopoulou
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
| | - Claudia Siffczyk
- Robert Koch Institute, Berlin, Germany (M. Schöll, J. Boucsein, F. Moek, M. an der Heiden, M. Huska, S. Kröger, S. Paraskevopoulou, C. Siffczyk, U. Buchholz, R. Lachmann)
- European Centre for Disease Prevention and Control, Stockholm, Sweden (M. Schöll, J. Boucsein, F. Moek)
- Public Health Authority Main-Kinzig-Kreis, Hesse, Germany (C. Höhn, J. Plath)
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35
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Yu Q, Ascensao JA, Okada T, Boyd O, Volz E, Hallatschek O. Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England. PLoS Pathog 2024; 20:e1012090. [PMID: 38620033 PMCID: PMC11045146 DOI: 10.1371/journal.ppat.1012090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 04/25/2024] [Accepted: 03/03/2024] [Indexed: 04/17/2024] Open
Abstract
Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and this is expected to substantially impact disease epidemiology and evolution. However, we don't yet have an understanding of how genetic drift changes over time or across locations. Furthermore, noise that results from data collection can potentially confound estimates of genetic drift. To address this challenge, we develop and validate a method to jointly infer genetic drift and measurement noise from time-series lineage frequency data. Our method is highly scalable to increasingly large genomic datasets, which overcomes a limitation in commonly used phylogenetic methods. We apply this method to over 490,000 SARS-CoV-2 genomic sequences from England collected between March 2020 and December 2021 by the COVID-19 Genomics UK (COG-UK) consortium and separately infer the strength of genetic drift for pre-B.1.177, B.1.177, Alpha, and Delta. We find that even after correcting for measurement noise, the strength of genetic drift is consistently, throughout time, higher than that expected from the observed number of COVID-19 positive individuals in England by 1 to 3 orders of magnitude, which cannot be explained by literature values of superspreading. Our estimates of genetic drift suggest low and time-varying establishment probabilities for new mutations, inform the parametrization of SARS-CoV-2 evolutionary models, and motivate future studies of the potential mechanisms for increased stochasticity in this system.
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Affiliation(s)
- QinQin Yu
- Department of Physics, University of California, Berkeley, California, United States of America
| | - Joao A. Ascensao
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Takashi Okada
- Department of Physics, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- RIKEN iTHEMS, Wako, Saitama, Japan
| | | | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley, California, United States of America
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
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36
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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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37
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Cahuantzi R, Lythgoe KA, Hall I, Pellis L, House T. Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods. Proc Natl Acad Sci U S A 2024; 121:e2317284121. [PMID: 38478692 PMCID: PMC10962941 DOI: 10.1073/pnas.2317284121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/05/2024] [Indexed: 03/21/2024] Open
Abstract
Since its emergence in late 2019, SARS-CoV-2 has diversified into a large number of lineages and caused multiple waves of infection globally. Novel lineages have the potential to spread rapidly and internationally if they have higher intrinsic transmissibility and/or can evade host immune responses, as has been seen with the Alpha, Delta, and Omicron variants of concern. They can also cause increased mortality and morbidity if they have increased virulence, as was seen for Alpha and Delta. Phylogenetic methods provide the "gold standard" for representing the global diversity of SARS-CoV-2 and to identify newly emerging lineages. However, these methods are computationally expensive, struggle when datasets get too large, and require manual curation to designate new lineages. These challenges provide a motivation to develop complementary methods that can incorporate all of the genetic data available without down-sampling to extract meaningful information rapidly and with minimal curation. In this paper, we demonstrate the utility of using algorithmic approaches based on word-statistics to represent whole sequences, bringing speed, scalability, and interpretability to the construction of genetic topologies. While not serving as a substitute for current phylogenetic analyses, the proposed methods can be used as a complementary, and fully automatable, approach to identify and confirm new emerging variants.
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Affiliation(s)
- Roberto Cahuantzi
- Department of Mathematics, The University of Manchester, ManchesterM13 9PL, United Kingdom
- United Kingdom Health Security Agency, University of Oxford, OxfordOX3 7LF, United Kingdom
| | - Katrina A. Lythgoe
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
- Big Data Institute, University of Oxford, OxfordOX3 7LF, United Kingdom
- Pandemic Sciences Institute, University of Oxford, OxfordOX3 7LF, United Kingdom
| | - Ian Hall
- Department of Mathematics, The University of Manchester, ManchesterM13 9PL, United Kingdom
| | - Lorenzo Pellis
- Department of Mathematics, The University of Manchester, ManchesterM13 9PL, United Kingdom
| | - Thomas House
- Department of Mathematics, The University of Manchester, ManchesterM13 9PL, United Kingdom
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38
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de Oliveira Martins L, Mather AE, Page AJ. Scalable neighbour search and alignment with uvaia. PeerJ 2024; 12:e16890. [PMID: 38464752 PMCID: PMC10924453 DOI: 10.7717/peerj.16890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 01/15/2024] [Indexed: 03/12/2024] Open
Abstract
Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by using measures of sequence similarity which consider partially ambiguous sites, allowing for more ambiguous sequences to be included in the analysis if needed. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but could also lead to improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.
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Affiliation(s)
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich, United Kingdom
- University of East Anglia, Norwich, United Kingdom
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39
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Jahshan Z, Yavits L. ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment. Bioinformatics 2024; 40:btae093. [PMID: 38374486 PMCID: PMC10913383 DOI: 10.1093/bioinformatics/btae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/04/2024] [Accepted: 02/18/2024] [Indexed: 02/21/2024] Open
Abstract
MOTIVATION Rapid spread of viral diseases such as Coronavirus disease 2019 (COVID-19) highlights an urgent need for efficient surveillance of virus mutation and transmission dynamics, which requires fast, inexpensive and accurate viral lineage assignment. The first two goals might be achieved through low-coverage whole-genome sequencing (LC-WGS) which enables rapid genome sequencing at scale and at reduced costs. Unfortunately, LC-WGS significantly diminishes the genomic details, rendering accurate lineage assignment very challenging. RESULTS We present ViTAL, a novel deep learning algorithm specifically designed to perform lineage assignment of low coverage-sequenced genomes. ViTAL utilizes a combination of MinHash for genomic feature extraction and Vision Transformer for fine-grain genome classification and lineage assignment. We show that ViTAL outperforms state-of-the-art tools across diverse coverage levels, reaching up to 87.7% lineage assignment accuracy at 1× coverage where state-of-the-art tools such as UShER and Kraken2 achieve the accuracy of 5.4% and 27.4% respectively. ViTAL achieves comparable accuracy results with up to 8× lower coverage than state-of-the-art tools. We explore ViTAL's ability to identify the lineages of novel genomes, i.e. genomes the Vision Transformer was not trained on. We show how ViTAL can be applied to preliminary phylogenetic placement of novel variants. AVAILABILITY AND IMPLEMENTATION The data underlying this article are available in https://github.com/zuherJahshan/vital and can be accessed with 10.5281/zenodo.10688110.
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Affiliation(s)
- Zuher Jahshan
- EnICS Labs, Engineering Department, Bar-Ilan University, Ramat Gan, Tel Aviv 5290002, Israel
| | - Leonid Yavits
- EnICS Labs, Engineering Department, Bar-Ilan University, Ramat Gan, Tel Aviv 5290002, Israel
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40
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Gräf T, Martinez AA, Bello G, Dellicour S, Lemey P, Colizza V, Mazzoli M, Poletto C, Cardoso VLO, da Silva AF, Motta FC, Resende PC, Siqueira MM, Franco L, Gresh L, Gabastou JM, Rodriguez A, Vicari A, Aldighieri S, Mendez-Rico J, Leite JA. Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean. Nat Commun 2024; 15:1837. [PMID: 38418815 PMCID: PMC10902334 DOI: 10.1038/s41467-024-46143-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.
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Affiliation(s)
- Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba, Brazil.
| | - Alexander A Martinez
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
- National Research System (SNI), National Secretary of Research, Technology and Innovation (SENACYT), Panama City, Panama
- Department of Microbiology and Immunology, University of Panama, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de Arbovírus e Vírus Hemorrágicos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Mattia Mazzoli
- Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Chiara Poletto
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
| | - Vanessa Leiko Oikawa Cardoso
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, FIOCRUZ-Bahia, Salvador, Brazil
| | | | - Fernando Couto Motta
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marilda M Siqueira
- Laboratório de Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leticia Franco
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Lionel Gresh
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jean-Marc Gabastou
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Angel Rodriguez
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Andrea Vicari
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Sylvain Aldighieri
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Jairo Mendez-Rico
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA
| | - Juliana Almeida Leite
- Infectious Hazards Management Unit, Health Emergencies Department, Pan American Health Organization, Washington D.C., USA.
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Standing JF, Buggiotti L, Guerra-Assuncao JA, Woodall M, Ellis S, Agyeman AA, Miller C, Okechukwu M, Kirkpatrick E, Jacobs AI, Williams CA, Roy S, Martin-Bernal LM, Williams R, Smith CM, Sanderson T, Ashford FB, Emmanuel B, Afzal ZM, Shields A, Richter AG, Dorward J, Gbinigie O, Van Hecke O, Lown M, Francis N, Jani B, Richards DB, Rahman NM, Yu LM, Thomas NPB, Hart ND, Evans P, Andersson M, Hayward G, Hood K, Nguyen-Van-Tam JS, Little P, Hobbs FDR, Khoo S, Butler C, Lowe DM, Breuer J. Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients. Nat Commun 2024; 15:1652. [PMID: 38396069 PMCID: PMC10891158 DOI: 10.1038/s41467-024-45641-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Viral clearance, antibody response and the mutagenic effect of molnupiravir has not been elucidated in at-risk populations. Non-hospitalised participants within 5 days of SARS-CoV-2 symptoms randomised to receive molnupiravir (n = 253) or Usual Care (n = 324) were recruited to study viral and antibody dynamics and the effect of molnupiravir on viral whole genome sequence from 1437 viral genomes. Molnupiravir accelerates viral load decline, but virus is detectable by Day 5 in most cases. At Day 14 (9 days post-treatment), molnupiravir is associated with significantly higher viral persistence and significantly lower anti-SARS-CoV-2 spike antibody titres compared to Usual Care. Serial sequencing reveals increased mutagenesis with molnupiravir treatment. Persistence of detectable viral RNA at Day 14 in the molnupiravir group is associated with higher transition mutations following treatment cessation. Viral viability at Day 14 is similar in both groups with post-molnupiravir treated samples cultured up to 9 days post cessation of treatment. The current 5-day molnupiravir course is too short. Longer courses should be tested to reduce the risk of potentially transmissible molnupiravir-mutated variants being generated. Trial registration: ISRCTN30448031.
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Affiliation(s)
- Joseph F Standing
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Great Ormond Street Hospital for Children NHS Trust, London, UK.
| | - Laura Buggiotti
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Jose Afonso Guerra-Assuncao
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Maximillian Woodall
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Samuel Ellis
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Akosua A Agyeman
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charles Miller
- Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Mercy Okechukwu
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emily Kirkpatrick
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Amy I Jacobs
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charlotte A Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sunando Roy
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz M Martin-Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Claire M Smith
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Fiona B Ashford
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Beena Emmanuel
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Zaheer M Afzal
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Adrian Shields
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Alex G Richter
- Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Jienchi Dorward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Oghenekome Gbinigie
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Oliver Van Hecke
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Mark Lown
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Nick Francis
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - Bhautesh Jani
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Duncan B Richards
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Najib M Rahman
- Respiratory Trials Unit and Oxford NIHR Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ly-Mee Yu
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Nigel D Hart
- School of Medicine, Dentistry and Biomedical Sciences. Queen's University Belfast, Belfast, UK
| | - Philip Evans
- APEx (Exeter Collaboration for Academic Primary Care), University of Exeter Medical School, Exeter, UK
- National Institute of Health and Care Research, Clinical Research Network, University of Leeds, Leeds, UK
| | | | - Gail Hayward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Kerenza Hood
- Centre for Trials Research, Cardiff University, Wales, UK
| | | | - Paul Little
- Primary Care Research Centre, University of Southampton, Southampton, UK
| | - F D Richard Hobbs
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Saye Khoo
- Department of Pharmacology, University of Liverpool and Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Christopher Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - David M Lowe
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Trust, London, UK
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42
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McBroome J, de Bernardi Schneider A, Roemer C, Wolfinger MT, Hinrichs AS, O'Toole AN, Ruis C, Turakhia Y, Rambaut A, Corbett-Detig R. A framework for automated scalable designation of viral pathogen lineages from genomic data. Nat Microbiol 2024; 9:550-560. [PMID: 38316930 PMCID: PMC10847047 DOI: 10.1038/s41564-023-01587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024]
Abstract
Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.
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Affiliation(s)
- Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Adriano de Bernardi Schneider
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
- RNA Forecast e.U., Vienna, Austria
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Aine Niamh O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
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43
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Ye Y, Shum MH, Tsui JL, Yu G, Smith DK, Zhu H, Wu JT, Guan Y, Lam TTY. Robust expansion of phylogeny for fast-growing genome sequence data. PLoS Comput Biol 2024; 20:e1011871. [PMID: 38330139 PMCID: PMC10898724 DOI: 10.1371/journal.pcbi.1011871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/27/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of de novo inference. 'TIPars' was developed for such challenge integrating parsimony analysis with pre-computed ancestral sequences. It took about 21 seconds to insert 100 SARS-CoV-2 genomes into a 100k-taxa reference tree using 1.4 gigabytes. Benchmarking on four datasets, TIPars achieved the highest accuracy for phylogenies of moderately similar sequences. For highly similar and divergent scenarios, fully parsimony-based and likelihood-based phylogenetic placement methods performed the best respectively while TIPars was the second best. TIPars accomplished efficient and accurate expansion of phylogenies of both similar and divergent sequences, which would have broad biological applications beyond SARS-CoV-2. TIPars is accessible from https://tipars.hku.hk/ and source codes are available at https://github.com/id-bioinfo/TIPars.
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Affiliation(s)
- Yongtao Ye
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Marcus H Shum
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Joseph L Tsui
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - David K Smith
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong, P. R. China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, P. R. China
| | - Joseph T Wu
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong, P. R. China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, P. R. China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, P. R. China
- Laboratory of Data Discovery for Health Limited, 19W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
- Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou, Guangdong, P. R. China
- EKIH (Gewuzhikang) Pathogen Research Institute, Futian District, Shenzhen City, Guangdong, P. R. China
- Centre for Immunology & Infection Limited, 17W Hong Kong Science & Technology Parks, Hong Kong SAR, P. R. China
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44
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Ma B, Gong H, Xu Q, Gao Y, Guan A, Wang H, Hua K, Luo R, Jin H. Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses. Virus Evol 2024; 10:veae005. [PMID: 38361823 PMCID: PMC10868571 DOI: 10.1093/ve/veae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/06/2024] [Accepted: 01/22/2024] [Indexed: 02/17/2024] Open
Abstract
Understanding phylogenetic relationships among species is essential for many biological studies, which call for an accurate phylogenetic tree to understand major evolutionary transitions. The phylogenetic analyses present a major challenge in estimation accuracy and computational efficiency, especially recently facing a wave of severe emerging infectious disease outbreaks. Here, we introduced a novel, efficient framework called Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) for new sample placement for viruses. In this study, a brand-new recoding method called Frequency Vector Recoding was implemented to approximate the phylogenetic distance, and the Phylogenetic Simulated Annealing Search algorithm was developed to match the recoded distance matrix with the phylogenetic tree. Meanwhile, the indel (insertion/deletion) was heuristically introduced to foreign sequence recognition for the first time. Here, we compared the Bd-RPC with the recent placement software (PAGAN2, EPA-ng, TreeBeST) and evaluated it in Alphacoronavirus, Alphaherpesvirinae, and Betacoronavirus by using Split and Robinson-Foulds distances. The comparisons showed that Bd-RPC maintained the highest precision with great efficiency, demonstrating good performance in new sample placement on all three virus genera. Finally, a user-friendly website (http://www.bd-rpc.xyz) is available for users to classify new samples instantly and facilitate exploration of the phylogenetic research in viruses, and the Bd-RPC is available on GitHub (http://github.com/Bin-Ma/bd-rpc).
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Affiliation(s)
- Bin Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Huimin Gong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Qianshuai Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Yuan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Aohan Guan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Haoyu Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Kexin Hua
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei 430070, China
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45
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Harari S, Miller D, Fleishon S, Burstein D, Stern A. Using big sequencing data to identify chronic SARS-Coronavirus-2 infections. Nat Commun 2024; 15:648. [PMID: 38245511 PMCID: PMC10799923 DOI: 10.1038/s41467-024-44803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants. One leading hypothesis suggests these variants may have emerged during chronic infections of immunocompromised individuals, but limited data from these cases hinders comprehensive analyses. Here, we harnessed millions of SARS-CoV-2 genomes to identify potential chronic infections and used language models (LM) to infer chronic-associated mutations. First, we mined the SARS-CoV-2 phylogeny and identified chronic-like clades with identical metadata (location, age, and sex) spanning over 21 days, suggesting a prolonged infection. We inferred 271 chronic-like clades, which exhibited characteristics similar to confirmed chronic infections. Chronic-associated mutations were often high-fitness immune-evasive mutations located in the spike receptor-binding domain (RBD), yet a minority were unique to chronic infections and absent in global settings. The probability of observing high-fitness RBD mutations was 10-20 times higher in chronic infections than in global transmission chains. The majority of RBD mutations in BA.1/BA.2 chronic-like clades bore predictive value, i.e., went on to display global success. Finally, we used our LM to infer hundreds of additional chronic-like clades in the absence of metadata. Our approach allows mining extensive sequencing data and providing insights into future evolutionary patterns of SARS-CoV-2.
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Affiliation(s)
- Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Shay Fleishon
- Israeli Health Intelligence Agency, Public Health Division, Ministry of Health, Jerusalem, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
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46
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de Bernardi Schneider A, Su M, Hinrichs AS, Wang J, Amin H, Bell J, Wadford DA, O’Toole Á, Scher E, Perry MD, Turakhia Y, De Maio N, Hughes S, Corbett-Detig R. SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method. Virus Evol 2024; 10:vead085. [PMID: 38361813 PMCID: PMC10868549 DOI: 10.1093/ve/vead085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine-learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome. In a preliminary study, we observed that pangoLEARN (decision tree model), while substantially faster than pUShER, offered less consistency across different versions of pangolin v3. Here, we expand upon this analysis to include v3 and v4 of pangolin, which moved the default algorithm for lineage assignment from pangoLEARN in v3 to pUShER in v4, and perform a thorough analysis confirming that pUShER is not only more stable across versions but also more accurate. Our findings suggest that future lineage assignment algorithms for various pathogens should consider the value of phylogenetic placement.
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Affiliation(s)
- Adriano de Bernardi Schneider
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michelle Su
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jade Wang
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - Helly Amin
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - John Bell
- California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA
| | - Debra A Wadford
- California Department of Public Health (CDPH), VRDL/COVIDNet, Richmond, CA 94804, USA
| | - Áine O’Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Emily Scher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Marc D Perry
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Scott Hughes
- Department of Health and Mental Hygiene, New York City Public Health Laboratory, New York, NY 10016, USA
| | - Russ Corbett-Detig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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47
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Kodsi IA, Rayes DE, Koweyes J, Khoury CA, Rahy K, Thoumi S, Chamoun M, Haddad H, Mokhbat J, Tokajian S. Tracking SARS-CoV-2 variants during the 2023 flu season and beyond in Lebanon. Virus Res 2024; 339:199289. [PMID: 38036064 PMCID: PMC10704499 DOI: 10.1016/j.virusres.2023.199289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Early SARS-CoV-2 variant detection relies on testing and genomic surveillance. The Omicron variant (B.1.1.529) has quickly become the dominant type among the previous circulating variants worldwide. Several subvariants have emerged exhibiting greater infectivity and immune evasion. In this study we aimed at studying the prevalence of the Omicron subvariants during the flu season and beyond in Lebanon through genomic screening and at determining the overall standing and trajectory of the pandemic in the country. METHODS A total of 155 SARS-CoV-2 RNA samples were sequenced, using Nanopore sequencing technology. RESULTS Nanopore sequencing of 155 genomes revealed their distribution over 39 Omicron variants. XBB.1.5 (23.29 %) was the most common, followed by XBB.1.9.1 (10.96 %) and XBB.1.42 (7.5 %). The first batch collected between September and November 2022, included the BA.2.75.2, BA.5.2, BA.5.2.20, BA.5.2.25 and BQ.1.1.5 lineages. Between December 2022 and January 2023, those lineages were replaced by BA.2.75.5, BN.1, BN.1.4, BQ.1, BQ.1.1, BQ.1.1.23, CH.1.1, CM.4 and XBK. Starting February 2023, we observed a gradual emergence and dominance of the recombinant XBB and its sub-lineages (XBB.1, XBB.1.5, XBB.1.5.2, XBB.1.5.3, XBB.1.9, XBB.1.9.1, XBB.1.9.2, XBB.1.16, XBB.1.22 and XBB.1.42). CONCLUSIONS The timely detection and characterization of SARS-CoV-2 variants is important to reduce transmission through established disease control measures and to avoid introductions into animal populations that could lead to serious public health implications.
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Affiliation(s)
- Ibrahim Al Kodsi
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Douaa El Rayes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon
| | - Kelven Rahy
- School of Medicine, Lebanese American University, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University, Lebanon
| | | | - Hoda Haddad
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Jacques Mokhbat
- Clinical Microbiology laboratory, Lebanese American University Medical Center Rizk Hospital, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Lebanon.
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48
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Aßmann E, Agrawal S, Orschler L, Böttcher S, Lackner S, Hölzer M. Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data. Gigascience 2024; 13:giae051. [PMID: 39115959 PMCID: PMC11308188 DOI: 10.1093/gigascience/giae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 04/30/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from wastewater samples has emerged as a valuable tool for detecting the presence and relative abundances of SARS-CoV-2 variants in a community. By analyzing the viral genetic material present in wastewater, researchers and public health authorities can gain early insights into the spread of virus lineages and emerging mutations. Constructing reference datasets from known SARS-CoV-2 lineages and their mutation profiles has become state-of-the-art for assigning viral lineages and their relative abundances from wastewater sequencing data. However, selecting reference sequences or mutations directly affects the predictive power. RESULTS Here, we show the impact of a mutation- and sequence-based reference reconstruction for SARS-CoV-2 abundance estimation. We benchmark 3 datasets: (i) synthetic "spike-in"' mixtures; (ii) German wastewater samples from early 2021, mainly comprising Alpha; and (iii) samples obtained from wastewater at an international airport in Germany from the end of 2021, including first signals of Omicron. The 2 approaches differ in sublineage detection, with the marker mutation-based method, in particular, being challenged by the increasing number of mutations and lineages. However, the estimations of both approaches depend on selecting representative references and optimized parameter settings. By performing parameter escalation experiments, we demonstrate the effects of reference size and alternative allele frequency cutoffs for abundance estimation. We show how different parameter settings can lead to different results for our test datasets and illustrate the effects of virus lineage composition of wastewater samples and references. CONCLUSIONS Our study highlights current computational challenges, focusing on the general reference design, which directly impacts abundance allocations. We illustrate advantages and disadvantages that may be relevant for further developments in the wastewater community and in the context of defining robust quality metrics.
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Affiliation(s)
- Eva Aßmann
- Genome Competence Center (MF1), Robert Koch Institute, Berlin 13353, Germany
- Center for Artificial Intelligence in Public Health Research (ZKI-PH), Robert Koch Institute, Berlin 13353, Germany
| | - Shelesh Agrawal
- Chair of Water and Environmental Biotechnology, Institute IWAR, Department of Civil and Environmental Engineering Sciences, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Laura Orschler
- Chair of Water and Environmental Biotechnology, Institute IWAR, Department of Civil and Environmental Engineering Sciences, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Sindy Böttcher
- Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin 13353, Germany
| | - Susanne Lackner
- Chair of Water and Environmental Biotechnology, Institute IWAR, Department of Civil and Environmental Engineering Sciences, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Berlin 13353, Germany
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49
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Bi H, You R, Bian X, Li P, Zhao X, You Z. A magnetic control enrichment technique combined with terahertz metamaterial biosensor for detecting SARS-CoV-2 spike protein. Biosens Bioelectron 2024; 243:115763. [PMID: 37890389 DOI: 10.1016/j.bios.2023.115763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023]
Abstract
The highly contagious SARS-CoV-2 virus, responsible for the COVID-19 pandemic continues to pose significant challenges to public health. Developing new methods for early detection and diagnosis is crucial in combatting the disease, mitigating its impact and be prepared for future challenges in pandemic diseases. In this study, we propose a terahertz (THz) biosensing technology that capitalizes on the properties of THz metamaterial in conjunction with magnetic nanoparticles. This approach can accurately identify the SARS-CoV-2 spike protein by pinpointing its location on the THz resonance sources grooved surface. The magnetic nanoparticles are employed to selectively bind with target molecules, and migrate towards the THz metamaterial unit cell when exposed to an applied magnetic field. The presence of target molecules in to the metamaterial variation in the frequency, amplitude, and phase of the resonance response, thus enabling swift, accurate and sensitive detection. To assess the effectiveness of the proposed technique, we have conducted a comparative analysis between real samples on platforms controlled by magnetic manipulation and those without the control. It was confirmed that the proposed THz sensing method demonstrated a linear detection range spanning from 0.005 ng mL-1 to 1000 ng mL-1 with a detection limit of 0.002 ng mL-1. Furthermore, it exhibited a frequency shift of 24 GHz and a stability index of 95%. The THz biosensing technique may pave a new avenue in identifying and preempting the spread of potential pandemic diseases.
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Affiliation(s)
- Hao Bi
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China
| | - Rui You
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China.
| | - Xiaomeng Bian
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China
| | - Peng Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China.
| | - Xiaoguang Zhao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China.
| | - Zheng You
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China
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50
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Hinrichs A, Ye C, Turakhia Y, Corbett-Detig R. The ongoing evolution of UShER during the SARS-CoV-2 pandemic. Nat Genet 2024; 56:4-7. [PMID: 38155331 DOI: 10.1038/s41588-023-01622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Affiliation(s)
- Angie Hinrichs
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Cheng Ye
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, USA
| | - Russell Corbett-Detig
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
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