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      Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

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          Abstract

          Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens.

          ABSTRACT

          Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

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          A pneumonia outbreak associated with a new coronavirus of probable bat origin

          Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.
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            A new coronavirus associated with human respiratory disease in China

            Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health 1–3 . Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing 4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China 5 . This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
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              The species Severe acute respiratory syndrome-related coronavirus : classifying 2019-nCoV and naming it SARS-CoV-2

              The present outbreak of a coronavirus-associated acute respiratory disease called coronavirus disease 19 (COVID-19) is the third documented spillover of an animal coronavirus to humans in only two decades that has resulted in a major epidemic. The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the classification of viruses and taxon nomenclature of the family Coronaviridae, has assessed the placement of the human pathogen, tentatively named 2019-nCoV, within the Coronaviridae. Based on phylogeny, taxonomy and established practice, the CSG recognizes this virus as forming a sister clade to the prototype human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus, and designates it as SARS-CoV-2. In order to facilitate communication, the CSG proposes to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date. While the full spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined, the independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying viruses at the species level to complement research focused on individual pathogenic viruses of immediate significance. This will improve our understanding of virus–host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                mBio
                mBio
                mbio
                mbio
                mBio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                12 January 2021
                Jan-Feb 2021
                : 12
                : 1
                : e02698-20
                Affiliations
                [a ]Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
                [b ]Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
                [c ]EcoHealth Alliance, New York, New York, USA
                [d ]Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
                [e ]Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
                [f ]Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
                [g ]Gothenburg Natural History Museum, Gothenburg, Sweden
                [h ]Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
                [i ]Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, Sarawak, Malaysia
                [j ]Florida State University, Tallahassee, Florida, USA
                [k ]Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
                [l ]Bucknell University, Lewisburg, Pennsylvania, USA
                [m ]Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
                [n ]Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
                [o ]Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
                [p ]Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
                [q ]University of Vermont, Burlington, Vermont, USA
                Albert Einstein College of Medicine
                Author notes
                Address correspondence to Cody W. Thompson, cwthomp@ 123456umich.edu , or Kendra L. Phelps, phelps@ 123456ecohealthalliance.org .

                Cody W. Thompson and Kendra L. Phelps contributed equally as first authors. First author order was determined based on best out of three rounds of “rock-paper-scissors.”

                Author information
                https://orcid.org/0000-0002-6686-6056
                https://orcid.org/0000-0002-3120-4802
                https://orcid.org/0000-0001-8111-4779
                Article
                mBio02698-20
                10.1128/mBio.02698-20
                7844540
                33436435
                998853c5-f67c-446d-9df0-8bd7ed456aa7
                Copyright © 2021 Thompson et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Page count
                supplementary-material: 3, Figures: 1, Tables: 1, Equations: 0, References: 194, Pages: 20, Words: 15687
                Funding
                Funded by: National Science Foundation (NSF), https://doi.org/10.13039/100000001;
                Award ID: NSF2033482
                Award Recipient :
                Funded by: National Science Foundation (NSF), https://doi.org/10.13039/100000001;
                Award ID: NSF2033482
                Award Recipient :
                Funded by: DOD | Defense Threat Reduction Agency (DTRA), https://doi.org/10.13039/100000774;
                Award ID: HDTRA11710064
                Award Recipient :
                Funded by: National Science Foundation (NSF), https://orcid.org/0000-0003-2639-7520;
                Award ID: DBI-1547229
                Award Recipient :
                Categories
                Minireview
                Host-Microbe Biology
                Custom metadata
                January/February 2021

                Life sciences
                biorepositories,coronaviruses,extended specimen,holistic specimen,museums,zoonoses
                Life sciences
                biorepositories, coronaviruses, extended specimen, holistic specimen, museums, zoonoses

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