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      Multi-host dispersal of known and novel carnivore amdoparvoviruses

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          Abstract

          Amdoparvoviruses (family Parvoviridae) are ssDNA viruses that cause an immune complex-mediated wasting syndrome in carnivores. They are multi-host pathogens and cross-species infection is facilitated by the fact that viral entry is mediated by cellular Fc receptors recognizing antibody-coated viruses. We developed a pan-amdoparvovirus PCR and screened tissue samples from 666 wild carnivores (families Felidae, Canidae, and Mustelidae) from Newfoundland or Labrador (Canada) and molecularly characterized the identified strains. Fifty-four out of 666 (8.1%) animals were amdoparvovirus-positive. Infection rate was the highest in American mink (34/47, 72.3%), followed by foxes (Arctic and red foxes, 13/311, 4.2%), lynx (2/58, 3.5%), and American martens (5/156, 3.4%). No virus was detected in samples from 87 coyotes and 17 ermines. Viruses from Newfoundland were classified as Aleutian mink disease virus (AMDV). Mink harvested near AMDV-affected fur farms had higher prevalence (24/24, 100%) than other mink (10/23, 43.5%; P < 0.001) and their viruses were phylogenetically closely related to those from farms, while most viruses from other mink were in other clades. Strains from three foxes and two lynx were highly related to mink strains. This proves that farms disperse AMDV that subsequently spreads among wild mink (maintenance host) and transmits to other spillover carnivore hosts. In Labrador two novel viruses were identified, Labrador amdoparvovirus 1 (LaAV-1) found in foxes (9/261, 3.5%) and martens (5/156, 3.4%), and LaAV-2 found in one fox (0.4%). LaAV-1 fulfills all requirements to be classified as a novel species. LaAV-1 was most similar to viruses of mink and skunks (AMDV and skunk amdoparvovirus (SKAV)) while LaAV-2 was more closely related to other viruses infecting canids. LaAV-1 capsid proteins were almost indistinguishable from those of AMDV in some regions, suggesting that LaAV-1 could be a virus of mustelids that can infect foxes. While intensive farming practices provide occasions for inter-species transmission in farms, niche overlap or predation could explain cross-species transmission in the wild, but competition among sympatric species reduces the chances of direct contacts, making this an infrequent event. Pan-amdoparvovirus detection methods in wide epidemiological investigations can play a crucial role in defining amdoparvoviral ecology and evolution and discovering novel viruses.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            Clustal W and Clustal X version 2.0.

            The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
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              A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

              Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
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                Author and article information

                Contributors
                Journal
                Virus Evol
                Virus Evol
                vevolu
                Virus Evolution
                Oxford University Press
                2057-1577
                July 2020
                06 December 2020
                06 December 2020
                : 6
                : 2
                : veaa072
                Affiliations
                Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s , Newfoundland and Labrador A1B 3X9, Canada
                Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s , Newfoundland and Labrador A1B 3X9, Canada
                Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s , Newfoundland and Labrador A1B 3X9, Canada
                Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook , Newfoundland and Labrador A2H 7S1 Canada
                Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan , 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada
                Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture , PO Box 3014, Stn. B, Happy Valley-Goose Bay, Newfoundland and Labrador A0P 1E0, Canada
                Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook , Newfoundland and Labrador A2H 7S1 Canada
                Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s , Newfoundland and Labrador A1B 3X9, Canada
                Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s , Newfoundland and Labrador A1B 3X9, Canada
                Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s , Newfoundland and Labrador A1B 3X9, Canada
                Author notes
                Author information
                http://orcid.org/0000-0002-9959-128X
                http://orcid.org/0000-0002-4510-7683
                Article
                veaa072
                10.1093/ve/veaa072
                9492287
                36158990
                fddcfd77-3569-4886-8137-897de477595d
                © The Author(s) 2020. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                Page count
                Pages: 11
                Funding
                Funded by: the Joint Mink Research Committee;
                Funded by: Memorial University of Newfoundland’s University Student Summer Internship Program. E.M. and S.M.G.’s research was partially supported by funding from Memorial University of Newfoundland’s Biology Department Honours program;
                Categories
                Research Article
                AcademicSubjects/MED00860
                AcademicSubjects/SCI01130
                AcademicSubjects/SCI02285

                amdoparvovirus,aleutian mink disease virus,parvovirus,cross-species transmission,novel virus,wildlife

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