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Zhao J, Wan W, Yu K, Lemey P, Pettersson JHO, Bi Y, Lu M, Li X, Chen Z, Zheng M, Yan G, Dai J, Li Y, Haerheng A, He N, Tu C, Suchard MA, Holmes EC, He WT, Su S. Farmed fur animals harbour viruses with zoonotic spillover potential. Nature 2024:10.1038/s41586-024-07901-3. [PMID: 39232170 DOI: 10.1038/s41586-024-07901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 08/01/2024] [Indexed: 09/06/2024]
Abstract
Animals such as raccoon dogs, mink and muskrats are farmed for fur and are sometimes used as food or medicinal products1,2, yet they are also potential reservoirs of emerging pathogens3. Here we performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission, including zoonotic spillover. Notably, we identified seven species of coronaviruses, expanding their known host range, and documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs and of bat HKU5-like coronaviruses to mink, present at a high abundance in lung tissues. Three subtypes of influenza A virus-H1N2, H5N6 and H6N2-were detected in the lungs of guinea pig, mink and muskrat, respectively. Multiple known zoonotic viruses, such as Japanese encephalitis virus and mammalian orthoreovirus4,5, were detected in guinea pigs. Raccoon dogs and mink carried the highest number of potentially high-risk viruses, while viruses from the Coronaviridae, Paramyxoviridae and Sedoreoviridae families commonly infected multiple hosts. These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses.
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Affiliation(s)
- Jin Zhao
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Wenbo Wan
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Kang Yu
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - John H-O Pettersson
- Clinical Microbiology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden
- Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, Uppsala, Sweden
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Meng Lu
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Xinxin Li
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhuohang Chen
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Mengdi Zheng
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Ge Yan
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - JianJun Dai
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yuxing Li
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Ayidana Haerheng
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Na He
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Wan-Ting He
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Shuo Su
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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2
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Wu Y, Zhao Y, Zhang X, Wei T, Peng Q, Wang J, Liu Z, Zhu Y, Shao X. Diverse amdoparvoviruses infection of farmed Asian badgers (Meles meles). Arch Virol 2024; 169:139. [PMID: 38849620 DOI: 10.1007/s00705-024-06073-9] [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: 12/07/2023] [Accepted: 04/28/2024] [Indexed: 06/09/2024]
Abstract
Amdoparvoviruses infect various carnivores, including mustelids, canids, skunks, and felids. Aleutian mink disease virus (AMDV) belongs to the prototypical species Amdoparvovirus carnivoran1. Here, we identified a novel amdoparvovirus in farmed Asian badgers (Meles meles), and we named this virus "Meles meles amdoparvovirus" (MMADV). A total of 146 clinical samples were collected from 134 individual badgers, and 30.6% (41/134) of the sampled badgers tested positive for amdoparvovirus by PCR. Viral DNA was detected in feces, blood, spleen, liver, lung, and adipose tissue from these animals. Viral sequences from eight samples were determined, five of which represented nearly full-length genome sequences (4,237-4,265 nt). Six serum samples tested positive by PCR, CIEP, and IAT, four of which had high antibody titers (> 512) against AMDV-G. Twenty-six of the 41 amdoparvovirus-positive badgers showed signs of illness, and necropsy revealed lesions in their organs. Sequence comparisons and phylogenetic analysis of the viral NS1 and VP2 genes of these badger amdoparvoviruses showed that their NS1 proteins shared 62.6%-88.8% sequence identity with known amdoparvoviruses, and they clustered phylogenetically into two related clades. The VP2 proteins shared 76.6%-97.2% identity and clustered into two clades, one of which included raccoon dog and arctic fox amdoparvovirus (RFAV), and the other of which did not include other known amdoparvoviruses. According to the NS1-protein-based criterion for parvovirus species demarcation, the MMADV isolate from farm YS should be classified as a member of a new species of the genus Amdoparvovirus. In summary, we have discovered a novel MMADV and other badger amdoparvoviruses that naturally infect Asian badgers and are possibly pathogenic in badgers.
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Affiliation(s)
- Yanhong Wu
- Jilin Agricultural Science and Technology University, Jilin, Jilin Province, 132101, China
| | - Yongqiang Zhao
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, 130112, China
| | - Xiuting Zhang
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, 130112, China
| | - Tao Wei
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, 130112, China
| | - Qianwen Peng
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, 130112, China
| | - Jianke Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, Hebei Province, 071001, China
| | - Zongyue Liu
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, 130112, China
| | - Yanzhu Zhu
- Jilin Agricultural Science and Technology University, Jilin, Jilin Province, 132101, China
| | - Xiqun Shao
- Jilin Agricultural Science and Technology University, Jilin, Jilin Province, 132101, China.
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3
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Prpić J, Kunić A, Keros T, Lojkić I, Brnić D, Jemeršić L. Absence of Hepatitis E Virus (HEV) Circulation in the Most Widespread Wild Croatian Canine Species, the Red Fox ( Vulpes vulpes) and Jackal ( Canis aureus moreoticus). Microorganisms 2023; 11:microorganisms11040834. [PMID: 37110256 PMCID: PMC10145003 DOI: 10.3390/microorganisms11040834] [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: 02/27/2023] [Revised: 03/11/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Hepatitis E virus (HEV) can infect a wide range of domestic and wild animals, and the identification of new host species is reported successively worldwide. Nevertheless, its zoonotic potential and natural transmission, especially in wildlife remains unclear, primarily due to the discrete nature of HEV infections. Since the red fox (Vulpus vulpus) is the most widespread carnivore worldwide, and has been recognized as a potential HEV reservoir, its role as a potent host species is of increasing interest. Another wild canine species, the jackal (Canis aureus moreoticus), is becoming more important within the same habitat as that of the red fox since its number and geographical distribution have been rapidly growing. Therefore, we have chosen these wild species to determine their potential role in the epidemiology and persistence of HEV in the wilderness. The main reason for this is the finding of HEV and a rather high HEV seroprevalence in wild boars sharing the same ecological niche as the wild canine species, as well as the risk of the spread of HEV through red foxes into the outskirts of cities, where possible indirect and even direct contact with people are not excluded. Therefore, our study aimed to investigate the possibility of natural HEV infection of free-living wild canines, by testing samples for the presence of HEV RNA and anti-HEV antibodies to gain better epidemiological knowledge of the disease. For this purpose, 692 red fox and 171 jackal muscle extracts and feces samples were tested. Neither HEV RNA nor anti-HEV antibodies were detected. Although HEV circulation was not detected in the tested samples, to our knowledge, these are the first results that include jackals as a growing and important omnivore wildlife species for the presence of HEV infection in Europe.
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Affiliation(s)
- Jelena Prpić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Ana Kunić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Tomislav Keros
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Ivana Lojkić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Dragan Brnić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
| | - Lorena Jemeršić
- Croatian Veterinary Institute, Savska cesta 143, 10000 Zagreb, Croatia
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Pacini MI, Mazzei M, Sgorbini M, D’Alfonso R, Papini RA. A One-Year Retrospective Analysis of Viral and Parasitological Agents in Wildlife Animals Admitted to a First Aid Hospital. Animals (Basel) 2023; 13:ani13050931. [PMID: 36899788 PMCID: PMC10000059 DOI: 10.3390/ani13050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
This study aimed to provide information on the presence and frequency of viral and parasitic agents in wildlife presented to a Veterinary Teaching Hospital in 2020-2021. Serum and faecal samples were collected from 50 rescued animals (roe deer, fallow deer, foxes, badgers, pine martens, and porcupines) and examined by serological, molecular, and parasitological techniques. Transtracheal wash (TTW) was also collected post-mortem from roe deer. Overall, the results of the different techniques showed infections with the following viral and parasitic agents: Bovine Viral Diarrhea Virus, Small Ruminant Lentiviruses, Kobuvirus, Astrovirus, Canine Adenovirus 1, Bopivirus, gastrointestinal strongyles, Capillaria, Ancylostomatidae, Toxocara canis, Trichuris vulpis, Hymenolepis, Strongyloides, Eimeria, Isospora, Dictyocaulus, Angiostrongylus vasorum, Crenosoma, Dirofilaria immitis, Neospora caninum, Giardia duodenalis, and Cryptosporidium. Sequencing (Tpi locus) identified G. duodenalis sub-assemblages AI and BIV in one roe deer and one porcupine, respectively. Adult lungworms collected from the TTW were identified as Dictyocaulus capreolus (COX1 gene). This is the first molecular identification of G. duodenalis sub-assemblage AI and D. capreolus in roe deer in Italy. These results show a wide presence of pathogens in wild populations and provide an overview of environmental health surveillance.
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Affiliation(s)
- Maria Irene Pacini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
- Correspondence:
| | - Maurizio Mazzei
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Micaela Sgorbini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Rossella D’Alfonso
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Roberto Amerigo Papini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
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5
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Miranda TDS, Schiffler FB, D'arc M, Moreira FRR, Cosentino MAC, Coimbra A, Mouta R, Medeiros G, Girardi DL, Wanderkoke V, Soares CFA, Francisco TM, Henry MD, Afonso BC, Soffiati FL, Ferreira SS, Ruiz-Miranda CR, Soares MA, Santos AFA. Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil. Virus Res 2023; 325:199017. [PMID: 36565815 DOI: 10.1016/j.virusres.2022.199017] [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: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.
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Affiliation(s)
- Thamiris Dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Déa Luiza Girardi
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Victor Wanderkoke
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Caique Ferreira Amaral Soares
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Talitha Mayumi Francisco
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Malinda Dawn Henry
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Bianca Cardozo Afonso
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | | | | | - Carlos Ramon Ruiz-Miranda
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - André Felipe Andrade Santos
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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Kim SL, Choi JH, Yi MH, Lee S, Kim M, Oh S, Lee IY, Jeon BY, Yong TS, Kim JY. Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius. Parasit Vectors 2022; 15:486. [PMID: 36564849 PMCID: PMC9789561 DOI: 10.1186/s13071-022-05608-w] [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: 08/05/2022] [Accepted: 12/03/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The striped field mouse Apodemus agrarius is a wild rodent commonly found in fields in Korea. It is a known carrier of various pathogens. Amplicon-based next-generation sequencing (NGS) targeting the 16S ribosomal RNA (rRNA) gene is the most common technique used to analyze the bacterial microbiome. Although many bacterial microbiome analyses have been attempted using feces of wild animals, only a few studies have used NGS to screen for parasites. This study aimed to rapidly detect bacterial, fungal and parasitic pathogens in the guts of A. agrarius using NGS-based metabarcoding analysis. METHODS We conducted 18S/16S rDNA-targeted high-throughput sequencing on cecal samples collected from A. agrarius (n = 48) trapped in May and October 2017. Taxa of protozoa, fungi, helminths and bacteria in the cecal content were then identified. RESULTS Among the protozoa identified, the most prevalent was Tritrichomonas sp., found in all of the cecal samples, followed by Monocercomonas sp. (95.8% prevalence; in 46/48 samples) and Giardia sp. (75% prevalence; in 36/48 samples). For helminths, Heligmosomoides sp. was the most common, found in 85.4% (41/48) of samples, followed by Hymenolepis sp. (10.4%; 5/48) and Syphacia sp. (25%; 12/48). The 16S rRNA gene analysis showed that the microbial composition of the cecal samples changed by season (P = 0.005), with the linear discriminant analysis effect size showing that in the spring Escherichia coli and Lactobacillus murinus were more abundant and Helicobacter rodentium was less abundant. Helicobacter japonicus was more abundant and Prevotella_uc was less abundant in males. The microbial composition changed based on the Heligmosomoides sp. infection status (P = 0.019); specifically, Lactobacillus gasseri and Lactobacillus intestinalis were more abundant in the Heligmosomoides sp.-positive group than in the Heligmosomoides sp.-negative group. CONCLUSIONS This study demonstrated that bacterial abundance changed based on the season and specific parasitic infection status of the trapped mice. These results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs.
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Affiliation(s)
- Soo Lim Kim
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Jun Ho Choi
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Myung-hee Yi
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Seogwon Lee
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Myungjun Kim
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Singeun Oh
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - In-Yong Lee
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Bo-Young Jeon
- grid.15444.300000 0004 0470 5454Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju, 26493 Republic of Korea
| | - Tai-Soon Yong
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Ju Yeong Kim
- grid.15444.300000 0004 0470 5454Department of Environmental Medical Biology, Institute of Tropical Medicine, and Arthropods of Medical Importance Resource Bank, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
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7
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He WT, Hou X, Zhao J, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, Li J, Lemey P, Guo D, Tu C, Holmes EC, Shi M, Su S. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell 2022; 185:1117-1129.e8. [PMID: 35298912 PMCID: PMC9942426 DOI: 10.1016/j.cell.2022.02.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.
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Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Xin Hou
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.,These authors contributed equally
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.,These authors contributed equally
| | - Jiumeng Sun
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijian He
- Agricultural College, Jinhua Polytechnic, Jinhua 320017, China
| | - Wei Si
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziqing Yan
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Xing
- MOA Key Laboratory of Animal Virology, Zhejiang University, Hangzhou 310058, China
| | - Meng Lu
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, the United States
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Wenjie Gong
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong 999077, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Deyin Guo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin 130062, China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Senior authors,Correspondence: Shuo Su (); Mang Shi (); and Edward C. Holmes ()
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China.
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China.
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Konstantinidis K, Bampali M, de Courcy Williams M, Dovrolis N, Gatzidou E, Papazilakis P, Nearchou A, Veletza S, Karakasiliotis I. Dissecting the Species-Specific Virome in Culicoides of Thrace. Front Microbiol 2022; 13:802577. [PMID: 35330767 PMCID: PMC8940260 DOI: 10.3389/fmicb.2022.802577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/31/2022] [Indexed: 12/14/2022] Open
Abstract
Biting midges (Culicoides) are vectors of arboviruses of both veterinary and medical importance. The surge of emerging and reemerging vector-borne diseases and their expansion in geographical areas affected by climate change has increased the importance of understanding their capacity to contribute to novel and emerging infectious diseases. The study of Culicoides virome is the first step in the assessment of this potential. In this study, we analyzed the RNA virome of 10 Culicoides species within the geographical area of Thrace in the southeastern part of Europe, a crossing point between Asia and Europe and important path of various arboviruses, utilizing the Ion Torrent next-generation sequencing (NGS) platform and a custom bioinformatics pipeline based on TRINITY assembler and alignment algorithms. The analysis of the RNA virome of 10 Culicoides species resulted in the identification of the genomic signatures of 14 novel RNA viruses, including three fully assembled viruses and four segmented viruses with at least one segment fully assembled, most of which were significantly divergent from previously identified related viruses from the Solemoviridae, Phasmaviridae, Phenuiviridae, Reoviridae, Chuviridae, Partitiviridae, Orthomyxoviridae, Rhabdoviridae, and Flaviviridae families. Each Culicoides species carried a species-specific set of viruses, some of which are related to viruses from other insect vectors in the same area, contributing to the idea of a virus-carrier web within the ecosystem. The identified viruses not only expand our current knowledge on the virome of Culicoides but also set the basis of the genetic diversity of such viruses in the area of southeastern Europe. Furthermore, our study highlights that such metagenomic approaches should include as many species as possible of the local virus-carrier web that interact and share the virome of a geographical area.
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Affiliation(s)
| | - Maria Bampali
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Nikolas Dovrolis
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Elisavet Gatzidou
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | | | | | - Stavroula Veletza
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Department of Medicine, Laboratory of Biology, Democritus University of Thrace, Alexandroupolis, Greece
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9
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Dong X, Hu T, Ren Y, Meng F, Li C, Zhang Q, Chen J, Song J, Wang R, Shi M, Li J, Zhao P, Li C, Tang KFJ, Cowley JA, Shi W, Huang J. A Novel Bunyavirus Discovered in Oriental Shrimp ( Penaeus chinensis). Front Microbiol 2021; 12:751112. [PMID: 34899637 PMCID: PMC8652140 DOI: 10.3389/fmicb.2021.751112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Herein, we describe a novel bunyavirus, oriental wenrivirus 1 (OWV1), discovered in moribund oriental shrimp (Penaeus chinensis) collected from a farm in China in 2016. Like most bunyaviruses, OWV1 particles were enveloped, spherical- to ovoid-shaped, and 80-115 nm in diameter. However, its genome was found to comprise four segments of (-)ssRNA. These included an L RNA segment (6,317 nt) encoding an RNA-directed RNA polymerase (RdRp) of 2,052 aa, an M RNA segment (2,978 nt) encoding a glycoprotein precursor (GPC) of 922 aa, an S1 RNA segment (1,164 nt) encoding a nucleocapsid (N) protein of 243 aa, and an S2 RNA segment (1,382 nt) encoding a putative non-structural (NSs2) protein of 401 aa. All the four OWV1 RNA segments have complementary terminal decanucleotides (5'-ACACAAAGAC and 3'-UGUGUUUCUG) identical to the genomic RNA segments of uukuviruses and similar to those of phleboviruses and tenuiviruses in the Phenuiviridae. Phylogenetic analyses revealed that the RdRp, GPC, and N proteins of OWV1 were closely related to Wēnzhōu shrimp virus 1 (WzSV-1) and Mourilyan virus (MoV) that infect black tiger shrimp (P. monodon). Phylogenetic analyses also suggested that OWV1 could be classified into a second, yet to be established, species of the Wenrivirus genus in the Phenuiviridae. These wenriviruses also clustered with Wenling crustacean virus 7 from shrimps and bunya-like brown spot virus from white-clawed crayfish. Of note there were no homologs of the NSs2 of OWV1 and MoV/WzSV-1 in GenBank, and whether other crustacean phenuiviruses also possess a similar S2 RNA segment warrants further investigation. In addition, we established a TaqMan probe-based reverse-transcription quantitative PCR method for detection of OWV1, and it was detected as 1.17 × 102-1.90 × 107 copies/ng-RNA in gills of 23 out of 32 P. chinensis samples without an obvious gross sign. However, the discovery of OWV1 highlights the expanding genomic diversity of bunyaviruses.
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Affiliation(s)
- Xuan Dong
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
| | - Tao Hu
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Yanbei Ren
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Fanzeng Meng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
| | - Chen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
| | - Qingli Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
| | - Jiayuan Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
| | - Jipeng Song
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Ruoyu Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Peng Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, China
| | - Cixiu Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Kathy F. J. Tang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
| | - Jeff A. Cowley
- Livestock and Aquaculture, CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, China
| | - Jie Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affair, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Qingdao, China
- Network of Aquaculture Centres in Asia-Pacific, Bangkok, Thailand
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10
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Canuti M, Bouchard É, Rodrigues B, Whitney HG, Hopson M, Gilroy C, Stenson G, Dufour SC, Lang AS, Verhoeven JTP. Newlavirus, a Novel, Highly Prevalent, and Highly Diverse Protoparvovirus of Foxes ( Vulpes spp.). Viruses 2021; 13:1969. [PMID: 34696399 PMCID: PMC8537079 DOI: 10.3390/v13101969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
The genus Protoparvovirus (family Parvoviridae) includes several viruses of carnivores. We describe a novel fox protoparvovirus, which we named Newlavirus as it was discovered in samples from Newfoundland and Labrador, Canada. Analysis of the full non-structural protein (NS1) sequence indicates that this virus is a previously uncharacterized species. Newlavirus showed high prevalence in foxes from both the mainland (Labrador, 54/137, 39.4%) and the island of Newfoundland (22/50, 44%) but was not detected in samples from other carnivores, including coyotes (n = 92), lynx (n = 58), martens (n = 146), mink (n = 47), ermines (n = 17), dogs (n = 48), and ringed (n = 4), harp (n = 6), bearded (n = 6), and harbor (n = 2) seals. Newlavirus was found at similar rates in stool and spleen (24/80, 30% vs. 59/152, 38.8%, p = 0.2) but at lower rates in lymph nodes (2/37, 5.4%, p < 0.01). Sequencing a fragment of approximately 750 nt of the capsid protein gene from 53 samples showed a high frequency of co-infection by more than one strain (33.9%), high genetic diversity with 13 genotypes with low sequence identities (70.5-87.8%), and no geographic segregation of strains. Given the high prevalence, high diversity, and the lack of identification in other species, foxes are likely the natural reservoir of Newlavirus, and further studies should investigate its distribution.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Émilie Bouchard
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada;
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, 3200 rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Bruce Rodrigues
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook, NL A2H 7S1, Canada;
| | - Hugh G. Whitney
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Marti Hopson
- Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PE C1A 4P3, Canada;
| | - Cornelia Gilroy
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PE C1A 4P3, Canada;
| | - Garry Stenson
- Fisheries and Oceans Canada, Government of Canada, P.O. Box 5667, St. John’s, NL A1C 5X1, Canada;
| | - Suzanne C. Dufour
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Andrew S. Lang
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Joost T. P. Verhoeven
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
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11
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Virtanen J, Zalewski A, Kołodziej-Sobocińska M, Brzeziński M, Smura T, Sironen T. Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids. Virus Evol 2021; 7:veab075. [PMID: 34548930 PMCID: PMC8449508 DOI: 10.1093/ve/veab075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/11/2022] Open
Abstract
Aleutian mink disease virus (AMDV), which causes Aleutian disease, is widely spread both in farmed mink and wild mustelids. However, only limited data are available on the role of wild animals in AMDV transmission and spread. Our aim was to shed light on AMDV transmission among wild mustelids and estimate the effect of intense farming practices on the virus circulation by studying AMDV prevalence and genetic diversity among wild mustelids in Poland. We compared AMDV seroprevalence and proportion of PCR-positive individuals in American mink, polecats, otters, stone martens, and pine martens and used the phylogenetic analysis of the NS1 region to study transmission. In addition, we used a metagenomic approach to sequence complete AMDV genomes from tissue samples. In eastern Poland, AMDV seroprevalence in wild mustelids varied from 22 per cent in otters to 62 per cent and 64 per cent in stone martens and feral mink, respectively. All studied antibody-positive mink were also PCR positive, whereas only 10, 15, and 18 per cent of antibody-positive polecats, pine martens, and stone martens, respectively, were PCR positive, suggesting lower virus persistence among these animal species as compared to feral mink. In phylogenetic analysis, most sequences from feral mink formed region-specific clusters that have most likely emerged through multiple introductions of AMDV to feral mink population over decades. However, virus spread between regions was also observed. Virus sequences derived from farmed and wild animals formed separate subclusters in the phylogenetic tree, and no signs of recent virus transmission between farmed and wild animals were observed despite the frequent inflow of farmed mink escapees to wild populations. These results provide new information about the role of different mustelid species in AMDV transmission and about virus circulation among the wild mustelids. In addition, we pinpoint gaps of knowledge, where more studies are needed to achieve a comprehensive picture of AMDV transmission.
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Affiliation(s)
| | | | | | - Marcin Brzeziński
- Faculty of Biology, University of Warsaw, ul. Miecznikowa 1, Warszawa 02-096, Poland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, Helsinki 00290, Finland
| | - Tarja Sironen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, Helsinki 00790, Finland
- Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, Helsinki 00290, Finland
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12
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Panicz R, Eljasik P, Skorupski J, Śmietana P, Stefánsson RA, von Schmalensee M, Szenejko M. Assessment of Aleutian mink disease virus (AMDV) prevalence in feral American mink in Iceland. Case study of a pending epizootiological concern in Europe. PeerJ 2021; 9:e12060. [PMID: 34616603 PMCID: PMC8451439 DOI: 10.7717/peerj.12060] [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: 03/22/2021] [Accepted: 08/04/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Recurring escapes or deliberate releases and subsequent infiltration or establishment of feral populations by individuals from fur farms have been commonly noted since the beginning of fur industry expansion. Once animals have invaded ecosystems adjacent to source farms escapees can change the demography of the feral populations through hybridization, outbreeding depression, competition and spreading of various pathogens which can decimate wild populations. In our study, we aimed to assess spread of Aleutian mink disease virus (AMDV) in the feral population of American mink (Neovison vison) in Iceland. The additional objective was to elucidate whether basic morpho-anatomical parameters (i.e., Fulton's condition factor or spleen to body weight ratio) might be used as a preliminary indicator of AMDV infection. METHODS American mink (n = 164) were captured by professional hunters in 8 regions of Iceland. The detection of AMDV in the spleen of male and female individuals was based on PCR amplification of an NS1 gene fragment. RESULTS We confirmed AMDV presence in 23.8% (n = 39) of collected samples with no significant difference in infection rate between males and females. Additionally, we revealed that the prevalence of virus in the feral population was higher closer to fur farms. However, the countrywide prevalence and direction of AMDV distribution needs to be further investigated. Comparison of condition indices in non-infected and infected animals showed significant deterioration of body and spleen parameters in the latter group. Therefore, the application of basic measurements of the American mink may be used to evaluate the health status of individuals in terms of pathogen infection. CONCLUSIONS The study shed a new light on prevalence and distribution of AMDV in the feral population of American mink in Iceland and the results might be successfully applied to develop models to infer dynamics of various pathogens, even those latently transmitted by disease-free animals.
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Affiliation(s)
- Remigiusz Panicz
- Department of Meat Technology, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology Szczecin, Szczecin, Poland
| | - Piotr Eljasik
- Department of Meat Technology, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology Szczecin, Szczecin, Poland
| | - Jakub Skorupski
- Institute of Marine and Environmental Sciences, Molecular Biology and Biotechnology Centre, University of Szczecin, Szczecin, Poland
| | - Przemysław Śmietana
- Institute of Marine and Environmental Sciences, Molecular Biology and Biotechnology Centre, University of Szczecin, Szczecin, Poland
| | | | | | - Magdalena Szenejko
- Institute of Marine and Environmental Sciences, Molecular Biology and Biotechnology Centre, University of Szczecin, Szczecin, Poland
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13
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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14
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Canuti M, McDonald E, Graham SM, Rodrigues B, Bouchard É, Neville R, Pitcher M, Whitney HG, Marshall HD, Lang AS. Multi-host dispersal of known and novel carnivore amdoparvoviruses. Virus Evol 2020; 6:veaa072. [PMID: 36158990 PMCID: PMC9492287 DOI: 10.1093/ve/veaa072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Emily McDonald
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Stephanie M Graham
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Bruce Rodrigues
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook, Newfoundland and Labrador A2H 7S1 Canada
| | - Émilie Bouchard
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Richard Neville
- 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
| | - Mac Pitcher
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook, Newfoundland and Labrador A2H 7S1 Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - H Dawn Marshall
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave, St. John’s, Newfoundland and Labrador A1B 3X9, Canada
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Skorupski J. Fifty Years of Research on European Mink Mustela lutreola L., 1761 Genetics: Where Are We Now in Studies on One of the Most Endangered Mammals? Genes (Basel) 2020; 11:E1332. [PMID: 33187363 PMCID: PMC7696698 DOI: 10.3390/genes11111332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this review is to present the current state of knowledge about the genetics of European mink Mustela lutreola L., 1761, which is one of the most endangered mammalian species in the world. This article provides a comprehensive description of the studies undertaken over the last 50 years in terms of cytogenetics, molecular genetics, genomics (including mitogenomics), population genetics of wild populations and captive stocks, phylogenetics, phylogeography, and applied genetics (including identification by genetic methods, molecular ecology, and conservation genetics). An extensive and up-to-date review and critical analysis of the available specialist literature on the topic is provided, with special reference to conservation genetics. Unresolved issues are also described, such as the standard karyotype, systematic position, and whole-genome sequencing, and hotly debated issues are addressed, like the origin of the Southwestern population of the European mink and management approaches of the most distinct populations of the species. Finally, the most urgent directions of future research, based on the research questions arising from completed studies and the implementation of conservation measures to save and restore M. lutreola populations, are outlined. The importance of the popularization of research topics related to European mink genetics among scientists is highlighted.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Adama Mickiewicza 16 St., 70-383 Szczecin, Poland; ; Tel.: +48-914-441-685
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
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16
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Cowley JA. The genomes of Mourilyan virus and Wēnzhōu shrimp virus 1 of prawns comprise 4 RNA segments. Virus Res 2020; 292:198225. [PMID: 33181202 DOI: 10.1016/j.virusres.2020.198225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/16/2022]
Abstract
Reported here is the complete genome sequence of Mourilyan virus (MoV) that infects giant tiger (Penaeus monodon) and kuruma prawns (P. japonicas) in Australia. Its genome was determined using various PCR strategies based on the sequences of 3 randomly-amplified cDNA clones to its L and M RNA segments discovered in a library generated to determine the genome sequence of gill-associated ronivirus. The sequences of PCR products and clones obtained showed the MoV genome to comprise 4 ssRNA segments (L, M, S1 and S2), as confirmed by Northern blotting using RNA from naïve and MoV-infected prawns, and by Illumina sequence analysis of semi-purified MoV. BLASTn searches identified the MoV L, M and S1 RNA segments to be homologous to Wēnzhōu shrimp virus 1 (WzSV1) segments discovered recently in a P. monodon RNA-Seq library (SRR1745808). Mapping this read library to the MoV S2 RNA segment identified WzSV1 to also possess an equivalent segment. BLASTp searches identified the putative non-structural protein (NSs2; 393-394 aa) encoded in their S2 RNA segments to have no homologs in GenBank. Possibly due to NSs2 being encoded in a discrete RNA segment rather than in ambisense relative to the N protein as in the S RNA segments of other phenuiviruses, each of 6 MoV S1 RNA segment clones sequenced possessed a variable-length (≤ 645 nt) imperfect GA-repeat extending from the N protein stop codon to the more variable ∼90 nt segment terminal sequence. Read mapping of RNA-Seq library SRR1745808 showed the WzSV1 S1 RNA segment to possess a similar GA-repeat. However, paired-read variations hindered definitive assembly of a consensus sequence. All 4 MoV and WzSV1 RNA segments terminated with a 10 nt inverted repeat sequence (5'-ACACAAAGAC.) identical to the RNA segment termini of uukuviruses. Phylogenetic analyses of MoV/WzSV1 RNA-dependant RNA polymerase (L RNA), G1G2 precursor glycoprotein (M RNA) and nucleocapsid (N) protein (S1 RNA) sequences generally clustered them with as yet unassigned crustacean/diptera bunya-like viruses on branches positioned closely to others containing tick-transmitted phenuiviruses. As genome sequences of most phenuiviruses discovered recently have originated from meta-transcriptomics studies, the data presented here showing the MoV and WzSV1 genomes to comprise more than 3 RNA segments, like the plant tenuiviruses, suggests a need to investigate the genomes of these unassigned viruses more closely.
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Affiliation(s)
- Jeff A Cowley
- Livestock & Aquaculture, CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD, 4067, Australia.
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17
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Identification of Hepatitis E Virus in the Feces of Red Foxes ( Vulpes vulpes). Animals (Basel) 2020; 10:ani10101841. [PMID: 33050408 PMCID: PMC7601027 DOI: 10.3390/ani10101841] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Orthohepeviruses, commonly known as Hepatitis E virus (HEV), is a diverse virus group belonging to the family of Hepeviridae and is responsible for acute hepatitis in humans worldwide. These viruses show a relatively strict host specificity, e.g., rodent-related, avian-related, or even bat-related virus groups. However, similar (HEV-like) viruses have been identified in carnivores; some of them form a new genetically separated group, while others show a close evolutionary relationship with the rodent-related group, thus makes the strict host-specificity questionable and the classification of these new strains uncertain. Herein, we investigated feces of red foxes, the most widespread carnivore species worldwide, to identify the Hepatitis E virus and to ascertain their evolutionary origin via sequencing. The non-invasively collected fecal samples can provide information about the presence of viruses specific to the host and viruses derived from their prey as well. The virus we detected from our samples showed a very close relationship (91% identity) with rodent-related HEV described before from common voles, whilst a more distant relationship (85%) with fox-specific HEV strains was observed. Our results strongly support “the dietary-origin” of unclassified HEV-like strains described from various predator species. Abstract Orthohepeviruses (HEV) can infect a wide range of animals, showing a relatively strict host specificity; however, its zoonotic potential, natural transmission in the wildlife are less known. Several new HEV-like viruses have been identified in various animal species, including carnivores; however, the phylogenetic relationship among these viruses is poorly resolved, since some of them were known as rodent-related so far. The red fox, the most widespread carnivore worldwide, is a known reservoir of several viruses that transmit from wildlife to humans or domestic animals; they might have a defined role in the circulation of rodent-borne HEV. In this study, we performed a HEV survey by heminested RT-PCR (Reverse Transcription PCR) on red fox fecal samples to investigate the presence of HEV in red foxes living in natural conditions, and to explore the origin of the virus via phylogenetic analysis. Out of the 26 investigated samples, HEV RNA was identified in one sample. Following Sanger sequencing, the novel sequence displayed 91% identity on the nucleotide level with recently published European common vole-HEV derived from Microtus arvalis. In contrast, it shared 85% nucleotide similarity with HEV strains described previously in red foxes. Our results strongly support “the dietary-origin” of unclassified HEV-like strains described from predators that usually prey on rodents.
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18
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Viral diversity in oral cavity from Sapajus nigritus by metagenomic analyses. Braz J Microbiol 2020; 51:1941-1951. [PMID: 32780265 DOI: 10.1007/s42770-020-00350-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/25/2020] [Indexed: 01/14/2023] Open
Abstract
Sapajus nigritus are non-human primates which are widespread in South America. They are omnivores and live in troops of up to 40 individuals. The oral cavity is one of the main entry routes for microorganisms, including viruses. Our study proposed the identification of viral sequences from oral swabs collected in a group of capuchin monkeys (n = 5) living in a public park in a fragment of Mata Atlantica in South Brazil. Samples were submitted to nucleic acid extraction and enrichment, which was followed by the construction of libraries. After high-throughput sequencing and contig assembly, we used a pipeline to identify 11 viral families, which are Herpesviridae, Parvoviridae, Papillomaviridae, Polyomaviridae, Caulimoviridae, Iridoviridae, Astroviridae, Poxviridae, and Baculoviridae, in addition to two complete viral genomes of Anelloviridae and Genomoviridae. Some of these viruses were closely related to known viruses, while other fragments are more distantly related, with 50% of identity or less to the currently available virus sequences in databases. In addition to host-related viruses, insect and small vertebrate-related viruses were also found, as well as plant-related viruses, bringing insights about their diet. In conclusion, this viral metagenomic analysis reveals, for the first time, the profile of viruses in the oral cavity of wild, free ranging capuchin monkeys.
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Nicolas de Francisco O, Esperón F, Juan-Sallés C, Ewbank AC, das Neves CG, Marco A, Neves E, Anderson N, Sacristán C. Neoplasms and novel gammaherpesviruses in critically endangered captive European minks (Mustela lutreola). Transbound Emerg Dis 2020; 68:552-564. [PMID: 32619314 DOI: 10.1111/tbed.13713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023]
Abstract
The European mink (Mustela lutreola) is a riparian mustelid, considered one of the most endangered carnivores in the world. Alpha, beta and gammaherpesviruses described in mustelids have been occasionally associated with different pathological processes. However, there is no information about the herpesviruses species infecting European minks. In this study, 141 samples of swabs (oral, conjunctival, anal), faeces and tissues from 23 animals were analysed for herpesvirus (HV) using a pan-HV-PCR assay. Two different, potentially novel, gammaherpesvirus species were identified in 12 samples from four animals (17.3%), and tentatively named Mustelid gammaherpesvirus-2 (MUGHV-2) and MuGHV-3. Gross examination was performed on dead minks (n = 11), while histopathology was performed using available samples from HV-positive individuals (n = 2), identifying several neoplasms, including B-cell lymphoma (identified by immunohistochemistry) with intralesional syncytia and intranuclear inclusion bodies characteristic of HV (n = 1), pulmonary adenocarcinoma (n = 1), and biliary (n = 1) and preputial (n = 1) cystadenomas, as well as other lesions (e.g., axonal vacuolar degeneration [n = 2] and neuritis [n = 1]). Viral particles, consistent with HVs, were observed by electron microscopy in the mink with neural lymphoma and inclusion bodies. This is the first description of neoplasms and concurrent gammaherpesvirus infection in European minks. The pathological, ultrastructural and PCR findings (MuGHV-2) in the European mink with lymphoma strongly suggest a potential role for this novel gammaherpesvirus in its pathogenesis, as it has been reported in other HV-infected species with lymphoma. The occurrence of neural lymphoma with intralesional syncytia and herpesviral inclusions is, however, unique among mammals. Further research is warranted to elucidate the potential oncogenic properties of gammaherpesviruses in European mink and their epidemiology in the wild population.
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Affiliation(s)
- Olga Nicolas de Francisco
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Roslin, UK
| | - Fernando Esperón
- Group of Epidemiology and Environmental Health, Animal Health Research Center (INIA-CISA), Valdeolmos, Madrid, Spain
| | | | - Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
| | | | - Alberto Marco
- Departament de Sanitat i d'Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra-Barcelona, Spain
| | - Elena Neves
- Group of Epidemiology and Environmental Health, Animal Health Research Center (INIA-CISA), Valdeolmos, Madrid, Spain
| | - Neil Anderson
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Roslin, UK
| | - Carlos Sacristán
- Group of Epidemiology and Environmental Health, Animal Health Research Center (INIA-CISA), Valdeolmos, Madrid, Spain.,Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
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20
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Canuti M, Todd M, Monteiro P, Van Osch K, Weir R, Schwantje H, Britton AP, Lang AS. Ecology and Infection Dynamics of Multi-Host Amdoparvoviral and Protoparvoviral Carnivore Pathogens. Pathogens 2020; 9:pathogens9020124. [PMID: 32075256 PMCID: PMC7168296 DOI: 10.3390/pathogens9020124] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Amdoparvovirus and Protoparvovirus are monophyletic viral genera that infect carnivores. We performed surveillance for and sequence analyses of parvoviruses in mustelids in insular British Columbia to investigate parvoviral maintenance and cross-species transmission among wildlife. Overall, 19.1% (49/256) of the tested animals were parvovirus-positive. Aleutian mink disease virus (AMDV) was more prevalent in mink (41.6%, 32/77) than martens (3.1%, 4/130), feline panleukopenia virus (FPV) was more prevalent in otters (27.3%, 6/22) than mink (5.2%, 4/77) or martens (2.3%, 3/130), and canine parvovirus 2 (CPV-2) was found in one mink, one otter, and zero ermines (N = 27). Viruses were endemic and bottleneck events, founder effects, and genetic drift generated regional lineages. We identified two local closely related AMDV lineages, one CPV-2 lineage, and five FPV lineages. Highly similar viruses were identified in different hosts, demonstrating cross-species transmission. The likelihood for cross-species transmission differed among viruses and some species likely represented dead-end spillover hosts. We suggest that there are principal maintenance hosts (otters for FPV, raccoons for CPV-2/FPV, mink for AMDV) that enable viral persistence and serve as sources for other susceptible species. In this multi-host system, viral and host factors affect viral persistence and distribution, shaping parvoviral ecology and evolution, with implications for insular carnivore conservation.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada
- Correspondence: (M.C.); (A.S.L.); Tel.: +1-709-864-8761 (M.C.); +1-709-864-7517 (A.S.L.)
| | - Melissa Todd
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Paige Monteiro
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Kalia Van Osch
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Richard Weir
- British Columbia Ministry of Environment and Climate Change Strategy, PO Box 9338 STN Prov Govt, Victoria, BC V8W 9M2, Canada;
| | - Helen Schwantje
- British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Wildlife Health Program, Wildlife and Habitat Branch, 2080 Labieux Rd., Nanaimo, BC V9T 6J9, Canada;
| | - Ann P. Britton
- Animal Health Center, British Columbia Ministry of Agriculture, 1767 Angus Campbell Rd., Abbotsford, BC V3G 2M3, Canada;
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada
- Correspondence: (M.C.); (A.S.L.); Tel.: +1-709-864-8761 (M.C.); +1-709-864-7517 (A.S.L.)
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21
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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22
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Gupta P, Robin VV, Dharmarajan G. Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2020; 99:65. [PMID: 33622992 PMCID: PMC7371965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/23/2020] [Accepted: 05/25/2020] [Indexed: 08/23/2024]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease mediated extinctions and wildlife epidemics. We then focus on elucidating how host-parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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Affiliation(s)
- Pooja Gupta
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29801, USA.
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23
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Mukai Y, Tomita Y, Kryukov K, Nakagawa S, Ozawa M, Matsui T, Tomonaga K, Imanishi T, Kawaoka Y, Watanabe T, Horie M. Identification of a distinct lineage of aviadenovirus from crane feces. Virus Genes 2019; 55:815-824. [PMID: 31549291 DOI: 10.1007/s11262-019-01703-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/29/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022]
Abstract
Viruses are believed to be ubiquitous; however, the diversity of viruses is largely unknown because of the bias of previous research toward pathogenic viruses. Deep sequencing is a promising and unbiased approach to detect viruses from animal-derived materials. Although cranes are known to be infected by several viruses such as influenza A viruses, previous studies targeted limited species of viruses, and thus viruses that infect cranes have not been extensively studied. In this study, we collected crane fecal samples in the Izumi plain in Japan, which is an overwintering site for cranes, and performed metagenomic shotgun sequencing analyses. We detected aviadenovirus-like sequences in the fecal samples and tentatively named the discovered virus crane-associated adenovirus 1 (CrAdV-1). We determined that our sequence accounted for approximately three-fourths of the estimated CrAdV-1 genome size (33,245 bp). The GC content of CrAdV-1 genome is 34.1%, which is considerably lower than that of other aviadenoviruses. Phylogenetic analyses revealed that CrAdV-1 clusters with members of the genus Aviadenovirus, but is distantly related to the previously identified aviadenoviruses. The protein sequence divergence between the DNA polymerase of CrAdV-1 and those of other aviadenoviruses is 45.2-46.8%. Based on these results and the species demarcation for the family Adenoviridae, we propose that CrAdV-1 be classified as a new species in the genus Aviadenovirus. Results of this study contribute to a deeper understanding of the diversity and evolution of viruses and provide additional information on viruses that infect cranes, which might lead to protection of the endangered species of cranes.
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Affiliation(s)
- Yahiro Mukai
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto, Japan
- Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yuriko Tomita
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, Tokyo, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Tokyo, Japan
| | - Makoto Ozawa
- Joint Faculty of Veterinary Medicine, Laboratory of Animal Hygiene, Kagoshima University, Kagoshima, Japan
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
- United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Tsutomu Matsui
- Kagoshima Crane Conservation Committee, Izumi, Kagoshima, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto, Japan
- Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Tokyo, Japan
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Tokiko Watanabe
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
| | - Masayuki Horie
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto, Japan.
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8507, Japan.
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24
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Wu YH, Wei T, Zhang XT, Zhao YQ, Wang JK, Cong L, Xu BZ, Shao XQ. Development and evaluation of a direct TaqMan qPCR assay for the rapid detection of diverse carnivore amdoparvoviruses. Mol Cell Probes 2019; 48:101448. [PMID: 31521579 DOI: 10.1016/j.mcp.2019.101448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 10/26/2022]
Abstract
Amdoparvoviruses infect carnivore species, including mink, raccoon dog, fox, skunk, and red panda. Amdoparvovirus infection is a major cause of morbidity and mortality in farmed minks. Here, we developed a direct TaqMan qPCR assay for detection and quantification of carnivore amdoparvoviruses by using three primers and one probe based on the conserved VP2 gene. The detection limit for Aleutian mink disease virus (AMDV) and Raccoon dog and arctic fox amdoparvovirus (RFAV) were 4.06 × 101 copies/μl and 2.93 × 101 copies/μl, respectively. Both intra- and inter-assay variability were less than 2%. Among 74 carnivore samples, the positive rates for amdoparvoviruses were 62.2% (46/74) by direct TaqMan qPCR, while only 40.5% (30/74) by SYBR Green I qPCR. This result suggests that the direct TaqMan qPCR was more sensitive than the SYBR Green I qPCR. Additionally, the direct TaqMan qPCR is a rapid and sensitive method for liquid samples at microliter level as the assay employed the direct alkaline lysis method to obtain viral DNA and, therefore, eliminated the cumbersome steps in extracting DNA. Overall, the direct TaqMan qPCR assay possessed high specificity, sensitivity, and reproducibility, indicating that it can be used as a powerful tool for detection and quantification of various carnivore amdoparvoviruses in epidemiological and pathogenesis studies.
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Affiliation(s)
- Yan-Hong Wu
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Tao Wei
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Xiu-Ting Zhang
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yong-Qiang Zhao
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Jian-Ke Wang
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Li Cong
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Bao-Zeng Xu
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
| | - Xi-Qun Shao
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
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25
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Charoenkul K, Janetanakit T, Chaiyawong S, Bunpapong N, Boonyapisitsopa S, Tangwangvivat R, Amonsin A. First detection and genetic characterization of canine Kobuvirus in domestic dogs in Thailand. BMC Vet Res 2019; 15:254. [PMID: 31324182 PMCID: PMC6642606 DOI: 10.1186/s12917-019-1994-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/04/2019] [Indexed: 11/30/2022] Open
Abstract
Background Canine Kobuvirus (CaKoV) has been detected both in healthy and diarrheic dogs and in asymptomatic wild carnivores. In this study, we conducted a survey of CaKoV at small animal hospitals in Bangkok and vicinity of Thailand during September 2016 to September 2018. Results Three hundred and seven rectal swab samples were collected from healthy dogs (n = 55) and dogs with gastroenteritis symptoms (n = 252). Of 307 swab samples tested by using one-step RT-PCR specific to 3D gene, we found CaKoV positivity at 17.59% (54/307). CaKoVs could be detected in both sick (19.44%) and healthy (9.09%) animals. In relation to age group, CaKoV could be frequently detected in younger dogs (25.45%). Our result showed no seasonal pattern of CaKoV infection in domestic dogs. In this study, we characterized CaKoVs by whole genome sequencing (n = 4) or 3D and VP1 gene sequencing (n = 8). Genetic and phylogenetic analyses showed that whole genomes of Thai CaKoVs were closely related to Chinese CaKoVs with highest 99.5% amino acid identity suggesting possible origin of CaKoVs in Thailand. Conclusions In conclusion, this study was the first to report the detection and genetic characteristics of CaKoVs in domestic dogs in Thailand. CaKoVs could be detected in both sick and healthy dogs. The virus is frequently detected in younger dogs. Thai CaKoVs were genetically closely related and grouped with Chinese CaKoVs. Our result raises the concerns to vet practitioners that diarrhea in dogs due to canine Kobuvirus infection should not be ignored. Electronic supplementary material The online version of this article (10.1186/s12917-019-1994-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kamonpan Charoenkul
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Taveesak Janetanakit
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Supassama Chaiyawong
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Napawan Bunpapong
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Supanat Boonyapisitsopa
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ratanaporn Tangwangvivat
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Alongkorn Amonsin
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand. .,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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26
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Grandjean F, Gilbert C, Razafimafondy F, Vucić M, Delaunay C, Gindre P, Bouchard J, Raimond M, Moumen B. A new bunya-like virus associated with mass mortality of white-clawed crayfish in the wild. Virology 2019; 533:115-124. [DOI: 10.1016/j.virol.2019.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/12/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023]
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27
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Optimization and evaluation of a non-invasive tool for peste des petits ruminants surveillance and control. Sci Rep 2019; 9:4742. [PMID: 30894600 PMCID: PMC6426962 DOI: 10.1038/s41598-019-41232-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/05/2019] [Indexed: 11/08/2022] Open
Abstract
Peste des petits ruminants (PPR) is a highly contagious and devastating viral disease affecting mainly sheep and goats, but also a large number of wild species within the order Artiodactyla. A better understanding of PPR transmission dynamics in multi-host systems is necessary to efficiently control the disease, in particular where wildlife and livestock co-occur. Notably, the role of wildlife in PPR epidemiology is still not clearly understood. Non-invasive strategies to detect PPR infection without the need for animal handling could greatly facilitate research on PPR epidemiology and management of the disease in atypical hosts and in complex field situations. Here, we describe optimized methods for the direct detection of PPR virus genetic material and antigen in fecal samples. We use these methods to determine the detection window of PPR in fecal samples, and compare the sensitivity of these methods to standard invasive sampling and PPR diagnostic methods using field samples collected at a wildlife-livestock interface in Africa. Our results show that quantitative reverse transcription PCR (RT-QPCR) amplification of PPRV from fecal swabs has good sensitivity in comparison to ocular swabs. Animals infected by PPRV could be identified relatively early on and during the whole course of infection based on fecal samples using RT-QPCR. Partial gene sequences could also be retrieved in some cases, from both fecal and ocular samples, providing important information about virus origin and relatedness to other PPRV strains. Non-invasive strategies for PPRV surveillance could provide important data to fill major gaps in our knowledge of the multi-host PPR epidemiology.
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28
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Parida S, Selvaraj M, Gubbins S, Pope R, Banyard A, Mahapatra M. Quantifying Levels of Peste Des Petits Ruminants (PPR) Virus in Excretions from Experimentally Infected Goats and Its Importance for Nascent PPR Eradication Programme. Viruses 2019; 11:E249. [PMID: 30871054 PMCID: PMC6466160 DOI: 10.3390/v11030249] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 02/28/2019] [Indexed: 02/02/2023] Open
Abstract
Following the successful eradication of rinderpest, the World Organization of Animal Health (OIE) and the Food and Agriculture Organisation (FAO) have set a goal to globally eradicate Peste des petits ruminants (PPR) by 2030. To support the eradication programme we have quantified the levels of PPR virus (PPRV) nucleic acid excreted in body fluids (blood, feces, saliva, nasal and eye swabs) of PPRV-infected goats to ascertain which days post-infection animals are potentially infectious, and hence direct quarantine activities. The data will also indicate optimal sample strategies to assess presence of PPR infection in the naturally infected herd. Peak PPRV nucleic acid detection in different bodily fluids was between 5 and 10 days post-infection. As such, this period must be considered the most infectious period for contact transmission, although high viral load was observed through RNA detection in nasal excretions from two days post-infection until at least two weeks post-infection. Percentage sample positivity was low both in eye swabs and saliva samples during the early stage of infection although RNA was detected as late as two weeks post-infection. From the individual animal data, PPRV was detected later post-infection in fecal material than in other body fluids and the detection was intermittent. The results from this study indicate that nasal swabs are the most appropriate to sample when considering molecular diagnosis of PPRV.
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Affiliation(s)
- Satya Parida
- The Pirbright Institute, Ash Road, Woking, Surrey GU24 0NF, UK.
| | - M Selvaraj
- The Pirbright Institute, Ash Road, Woking, Surrey GU24 0NF, UK.
| | - S Gubbins
- The Pirbright Institute, Ash Road, Woking, Surrey GU24 0NF, UK.
| | - R Pope
- The Pirbright Institute, Ash Road, Woking, Surrey GU24 0NF, UK.
| | - A Banyard
- Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, UK.
| | - Mana Mahapatra
- The Pirbright Institute, Ash Road, Woking, Surrey GU24 0NF, UK.
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29
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Virome profiling of rodents in Xinjiang Uygur Autonomous Region, China: Isolation and characterization of a new strain of Wenzhou virus. Virology 2019; 529:122-134. [PMID: 30685659 DOI: 10.1016/j.virol.2019.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 11/21/2022]
Abstract
Rodents, as the most diverse and widest distributed mammals, are a natural reservoir of many zoonotic viruses. However, little is known about the viral diversity harbored by rodents in China. Here we performed viral metagenomic analyses of 314 wild rodents covering 7 species, sampled in North-western China. We also conducted a systematic virological characterization of a new Wenzhou virus (WENV) isolate, QARn1, from a brown rat (Rattus norvegicus). Full genomic and phylogenetic analyses showed that QARn1 is a previously unidentified strain of Wenzhou mammarenavirus and forms a new branch within the Asian clade. Experimental infection of Sprague-Dawley rats with QARn1 did not present overt pathology, but specific humoral immune responses developed and mild hemorrhage and immunocyte infiltration of the lungs and thymus were observed. These observations have expanded the geographic distribution of WENV to Central Asia, and further confirm that brown rats are natural hosts of Wenzhou virus.
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30
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Stronen AV, Iacolina L, Ruiz-Gonzalez A. Rewilding and conservation genomics: How developments in (re)colonization ecology and genomics can offer mutual benefits for understanding contemporary evolution. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2018.e00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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31
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Monterroso P, Godinho R, Oliveira T, Ferreras P, Kelly MJ, Morin DJ, Waits LP, Alves PC, Mills LS. Feeding ecological knowledge: the underutilised power of faecal
DNA
approaches for carnivore diet analysis. Mamm Rev 2018. [DOI: 10.1111/mam.12144] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
| | - Raquel Godinho
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Teresa Oliveira
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM) Ronda de Toledo 12 Ciudad Real 13071 Spain
| | - Marcella J. Kelly
- Department of Fish and Wildlife ConservationVirginia Tech 146 Cheatham Hall Blacksburg VA 24061‐0321 USA
| | - Dana J. Morin
- Cooperative Wildlife Research LaboratorySouthern Illinois University 251 Lincoln Drive Carbondale IL 62901 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
| | - Paulo C. Alves
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
- Office of Research and Creative ScholarshipUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
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32
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Virtanen J, Smura T, Aaltonen K, Moisander-Jylhä AM, Knuuttila A, Vapalahti O, Sironen T. Co-circulation of highly diverse Aleutian mink disease virus strains in Finland. J Gen Virol 2018; 100:227-236. [PMID: 30526739 DOI: 10.1099/jgv.0.001187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aleutian mink disease virus (AMDV) is the causative agent of Aleutian disease (AD), which affects mink of all genotypes and also infects other mustelids such as ferrets, martens and badgers. Previous studies have investigated diversity in Finnish AMDV strains, but these studies have been restricted to small parts of the virus genome, and mostly from newly infected farms and free-ranging mustelids. Here, we investigated the diversity and evolution of Finnish AMDV strains by sequencing the complete coding sequences of 31 strains from mink originating from farms differing in their virus history, as well as from free-ranging mink. The data set was supplemented with partial genomes obtained from 26 strains. The sequences demonstrate that the Finnish AMDV strains have considerable diversity, and that the virus has been introduced to Finland in multiple events. Frequent recombination events were observed, as well as variation in the evolutionary rate in different parts of the genome and between different branches of the phylogenetic tree. Mink in the wild carry viruses with high intra-host diversity and are occasionally even co-infected by two different strains, suggesting that free-ranging mink tolerate chronic infections for extended periods of time. These findings highlight the need for further sampling to understand the mechanisms playing a role in the evolution and pathogenesis of AMDV.
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Affiliation(s)
- Jenni Virtanen
- 1Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
| | - Teemu Smura
- 2Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
| | - Kirsi Aaltonen
- 1Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
| | - Anna-Maria Moisander-Jylhä
- 1Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
| | - Anna Knuuttila
- 1Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland.,†Present address: Anna Knuuttila, Fimmic Oy, Helsinki, Finland
| | - Olli Vapalahti
- 1Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland.,2Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
| | - Tarja Sironen
- 1Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland.,2Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
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33
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Birch JM, Ullman K, Struve T, Agger JF, Hammer AS, Leijon M, Jensen HE. Investigation of the viral and bacterial microbiota in intestinal samples from mink (Neovison vison) with pre-weaning diarrhea syndrome using next generation sequencing. PLoS One 2018; 13:e0205890. [PMID: 30335814 PMCID: PMC6193705 DOI: 10.1371/journal.pone.0205890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 10/03/2018] [Indexed: 01/21/2023] Open
Abstract
Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2-3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing. In addition, we used deep sequencing to determine and compare the viral intestinal content in 31 healthy non-diarrheic and 30 diarrheic pooled samples (2-3 mink kits from the same litter per pool). The results showed high variations in composition of the bacterial species between the pools. Enterococci, staphylococci and streptococci dominated in both diarrheic and non-diarrheic pools. However, enterococci accounted for 70% of the reads in the diarrheic group compared to 50% in the non-diarrheic group and this increase was at the expense of staphylococci and streptococci which together accounted for 45% and 17% of the reads in the non-diarrheic and diarrheic group, respectively. Moreover, in the diarrheic pools there were more reads assigned to Clostridia, Escherichia-Shigella and Enterobacter compared to the non-diarrheic pools. The taxonomically categorized sequences from the virome showed that the most prevalent viruses in all pools were caliciviruses and mamastroviruses (almost exclusively type 10). However, the numbers of reads assigned to caliciviruses were almost 3 times higher in the diarrheic pools compared the non-diarrheic pools and Sapporo-like caliciviruses were more abundant than the Norwalk-like caliciviruses. The results from this study have contributed to the insight into the changes in the intestinal microbiota associated with the PWD syndrome of mink.
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Affiliation(s)
- Julie Melsted Birch
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Karin Ullman
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Tina Struve
- Kopenhagen Fur Diagnostics, Kopenhagen Fur, Glostrup, Denmark
| | - Jens Frederik Agger
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anne Sofie Hammer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mikael Leijon
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus. Virology 2018; 521:77-91. [PMID: 29886344 DOI: 10.1016/j.virol.2018.05.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/30/2018] [Indexed: 12/27/2022]
Abstract
The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials.
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35
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Xie XT, Kropinski AM, Tapscott B, Weese JS, Turner PV. Prevalence of fecal viruses and bacteriophage in Canadian farmed mink (Neovison vison). Microbiologyopen 2018; 8:e00622. [PMID: 29635866 PMCID: PMC6341152 DOI: 10.1002/mbo3.622] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/18/2017] [Accepted: 01/05/2018] [Indexed: 01/01/2023] Open
Abstract
Recent viral metagenomic studies have demonstrated the diversity of eukaryotic viruses and bacteriophage shed in the feces of domestic species. Although enteric disease is a major concern in the commercial mink farming industry, few etiologic agents have been well characterized. This study aimed to identify viruses shed in the fecal matter of clinically healthy commercial mink from 40 southern Ontario farms. Viral RNA was extracted from 67 pooled fecal samples (30 adult female mink and 37 kit) and amplified for Illumina sequencing on the NextSeq platform, and the resulting contigs were trimmed and assembled using Trimmomatic 0.36.0 and Spades 3.8.0 in iVirus (CyVerse, AZ, USA) and SeqMan NGen 12 (DNAStar, WI, USA). Identification of assembled sequences >100 bp (Geneious 10.1.3) showed an abundance of bacteriophage sequences, mainly from families Siphoviridae (53%), Podoviridae (22%), Myoviridae (20%), Inoviridae (1%), Leviviridae (0.04%), Tectiviridae (0.01%), and Microviridae (0.01%). A diverse range of vertebrate viruses were detected, of which posavirus 3, mink bocavirus, gyroviruses, and avian‐associated viruses were most abundant. Additionally, sequences from nonvertebrate viruses with water and soil‐associated amebal and algal hosts were also highly prevalent. The results of this study show that viruses shed in the fecal matter of healthy commercial mink are highly diverse and could be closely associated with diet, and that more research is necessary to determine how the detected viruses may impact mink health.
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Affiliation(s)
- Xiao-Ting Xie
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | | | - Brian Tapscott
- Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), Elora, ON, Canada
| | - J Scott Weese
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Patricia V Turner
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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Duraisamy R, Akiana J, Davoust B, Mediannikov O, Michelle C, Robert C, Parra HJ, Raoult D, Biagini P, Desnues C. Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses. Virus Genes 2018; 54:256-271. [PMID: 29476397 PMCID: PMC7088520 DOI: 10.1007/s11262-018-1543-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 02/16/2018] [Indexed: 12/27/2022]
Abstract
Most of the emerging infectious diseases reported so far originated in wildlife. Therefore, virological surveillance of animals and particularly great apes is of great interest to establish the repertory of viruses associated with healthy hosts. This will further help to identify the emergence of new viruses and predict the possibility of interspecies transmission. In this study, we performed shotgun viral metagenomics on stool samples collected from seventeen free-living wild gorillas from the Republic of the Congo. The analysis revealed the presence of novel RNA viruses (picobirnaviruses, partitivirus, and Picornavirales (posa-like and dicistrovirus-like viruses)). Among these, picobirnavirus-related sequences were abundantly covered in the stools. Based on genetic variations both in capsid and RdRp proteins of picobirnaviruses, at least 96 variants were identified and most of them were novel. Among the 96, 22 variants had a nearly complete genome or segment. A comprehensive sequence analysis identified a potential new genogroup/genetic cluster and the presence of a short linear amino acid motif (ExxRxNxxxE) in a hypothetical protein. The sequence analysis of posa-like virus and dicistrovirus showed that these two viruses were novel members in the respective viral families. In conclusion, the identification of novel RNA viruses and their genetic diversity increases our knowledge about viruses that are associated with stools of wild gorillas and contributes to the initiatives in the search for potential emerging zoonotic viruses.
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Affiliation(s)
- Raja Duraisamy
- Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
| | - Jean Akiana
- Laboratoire national de santé publique, Brazzaville, Republic of the Congo
| | - Bernard Davoust
- Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Oleg Mediannikov
- Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Catherine Robert
- Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Henri-Joseph Parra
- Laboratoire national de santé publique, Brazzaville, Republic of the Congo
| | - Didier Raoult
- Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Biagini
- Unité Mixte de Recherche 7268 ADES, Etablissement Français du Sang, Marseille, France
| | - Christelle Desnues
- Aix-Marseille Université, CNRS 7278, IRD 198, INSERM 1095, Assistance-Publique des Hôpitaux de Marseille, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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37
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Abstract
Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda ( Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.
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Krishnamurthy SR, Wang D. Extensive conservation of prokaryotic ribosomal binding sites in known and novel picobirnaviruses. Virology 2018; 516:108-114. [PMID: 29346073 DOI: 10.1016/j.virol.2018.01.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/03/2018] [Accepted: 01/05/2018] [Indexed: 12/27/2022]
Abstract
Currently, the Leviviridae and Cystoviridae are the only two recognized families of prokaryotic RNA viruses. Picobirnaviruses, which are bisegmented double-stranded RNA viruses commonly found in animal stool samples, are currently thought to be animal viruses, but have not been propagated in cell culture or in an animal model. We hypothesize that picobirnaviruses are prokaryotic RNA viruses. We identified and analyzed the genomes of 38 novel picobirnaviruses and determined that a classical bacterial sequence motif, the ribosomal binding site (RBS), is present in the 5' untranslated regions (5' UTRs) of all of the novel as well as all previously published picobirnavirus sequences. Among all viruses, enrichment of the RBS motif is only observed in viral families that infect prokaryotes and not in eukaryotic infecting viral families. These results will enable future studies to more accurately understand the biology of picobirnaviruses.
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Affiliation(s)
- Siddharth R Krishnamurthy
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA.
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Lu T, Wang Y, Ge J, Ma Q, Yan W, Zhang Y, Zhao L, Chen H. Identification and characterization of a novel B-cell epitope on Aleutian Mink Disease virus capsid protein VP2 using a monoclonal antibody. Virus Res 2017; 248:74-79. [PMID: 29278728 DOI: 10.1016/j.virusres.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 11/30/2022]
Abstract
Aleutian mink disease is caused by a highly contagious parvovirus (Aleutian mink disease virus, AMDV). This disease is one of the most commercially important infectious disease worldwide and causes considerable economic losses to mink farmers. The capsid protein VP2 is the major immunogenic antigenic protein of AMDV, and is involved in viral tropism, pathogenicity, and host selection. However, few reports have described the use of VP2-specific monoclonal antibodies (mAbs) in B-cell epitope identification and immunological detection. In this study, we produced a specific mAb, 1G5, against AMDV VP2 protein (amino acids: 200 ∼ 588) and characterized its specificity and relative affinity. Six partially overlapping truncated recombinant proteins and seven synthetized peptides were used to identify the epitopes recognized by 1G5. The results indicate that mAb 1G5 can distinguish AMDV, MEV and CPV2 with high affinity (Ka = 5.37 × 109), and the minimal linear epitope is located in amino acid residues 459EEEGWPAASGTHFED473. Sequence alignments demonstrated that the linear epitope was completely conserved among most Amdoparvoviruses except the bat parvovirus, where three substitutions (463W-463F, 466A-466G and 471F-471Y) were noted. Our results reveal that the identified epitope might be a common B-cell epitope of AMDV antibodies, and the 1G5 mAb can be used to identify the cleavage of the capsid proteins during AMDV infection. This is also the first report of a B-cell epitope on AMDV capsid protein VP2 (VP2: 459-473) using a mAb. These findings have potential applications in the development of new diagnostic tools for AMDV.
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Affiliation(s)
- Taofeng Lu
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Yuanzhi Wang
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Junwei Ge
- Veterinary Department, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, People's Republic of China
| | - Qin Ma
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Wenzhuo Yan
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Yuanyuan Zhang
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Lili Zhao
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Hongyan Chen
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China.
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Shi W, Li J, Zhou H, Gao GF. Pathogen genomic surveillance elucidates the origins, transmission and evolution of emerging viral agents in China. SCIENCE CHINA. LIFE SCIENCES 2017; 60:1317-1330. [PMID: 29270793 PMCID: PMC7088571 DOI: 10.1007/s11427-017-9211-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/01/2017] [Indexed: 02/06/2023]
Abstract
In the past twenty years, numerous novel zoonotic viral agents with pandemic potential have emerged in China, such as the severe acute respiratory syndrome (SARS) coronavirus and, more recently, the avian-origin influenza A/H7N9 virus, which have caused outbreaks among humans with high morbidity and mortality. In addition, several emerging and re-emerging viral pathogens have also been imported into China from travelers, e.g. the Middle East respiratory syndrome (MERS) coronavirus and Zika virus (ZIKV). Herein, we review these emerging viral pathogens in China and focus on how surveillance by pathogen genomics has been employed to discover and annotate novel pathogenic agents, identify natural reservoirs, monitor the transmission events and delineate their evolution and adaption to the human host. We also highlight the application of genomic sequencing in the recent Ebola epidemics in Western Africa. In summary, genomic sequencing has become a standard research tool in the field of emerging infectious diseases which has been proven invaluable in containing these viral infections and reducing burden of disease in humans and animals. Genomic surveillance of pathogenic agents will serve as a key epidemiological and research tool in the modern era of precision infectious diseases and in the future studies of virosphere.
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Affiliation(s)
- Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China.
| | - Juan Li
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong (Taishan Medical College), Taishan Medical College, Taian, 271000, China
| | - George F Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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Xu L, Wu J, Jiang T, Qin S, Xia L, Li X, He B, Tu C. Molecular detection and sequence characterization of diverse rhabdoviruses in bats, China. Virus Res 2017; 244:208-212. [PMID: 29196194 PMCID: PMC7114522 DOI: 10.1016/j.virusres.2017.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 11/22/2022]
Abstract
Three new rhabdoviruses were detected in bats, China. JHBV and BXBV found in Rhinolophus bats could be new members of the genus Vesiculovirus. Four strains of YJBV detected in Hipposideros larvatus formed a new lineage.
The Rhabdoviridae is among the most diverse families of RNA viruses and currently classified into 18 genera with some rhabdoviruses lethal to humans and other animals. Herein, we describe genetic characterization of three novel rhabdoviruses from bats in China. Of these, two viruses (Jinghong bat virus and Benxi bat virus) found in Rhinolophus bats showed a phylogenetic relationship with vesiculoviruses, and sequence analyses indicate that they represent two new species within the genus Vesiculovirus. The remaining Yangjiang bat virus found in Hipposideros larvatus bats were only distantly related to currently known rhabdoviruses.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Jianmin Wu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Shaomin Qin
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Lele Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Xingyu Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China.
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China.
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Lewandowska DW, Zagordi O, Geissberger FD, Kufner V, Schmutz S, Böni J, Metzner KJ, Trkola A, Huber M. Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. MICROBIOME 2017; 5:94. [PMID: 28789678 PMCID: PMC5549297 DOI: 10.1186/s40168-017-0317-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. RESULTS In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. CONCLUSIONS The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karin J Metzner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Moreno PS, Wagner J, Mansfield CS, Stevens M, Gilkerson JR, Kirkwood CD. Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLoS One 2017; 12:e0178433. [PMID: 28570584 PMCID: PMC5453527 DOI: 10.1371/journal.pone.0178433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/12/2017] [Indexed: 01/01/2023] Open
Abstract
The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.
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Affiliation(s)
- Paloma S. Moreno
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Josef Wagner
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Caroline S. Mansfield
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Matthew Stevens
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - James R. Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Carl D. Kirkwood
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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Canuti M, Doyle HE, P Britton A, Lang AS. Full genetic characterization and epidemiology of a novel amdoparvovirus in striped skunk (Mephitis mephitis). Emerg Microbes Infect 2017; 6:e30. [PMID: 28487558 PMCID: PMC5520478 DOI: 10.1038/emi.2017.13] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 11/09/2022]
Abstract
Amdoparvovirus is a newly defined parvoviral genus that contains four species (Carnivore amdoparvovirus 1-4), including the well-known Aleutian mink disease virus (AMDV). Amdoparvoviruses cause an immune-associated and often lethal wasting syndrome in Mustelidae and Caninae hosts. In this study, we molecularly investigated amdoparvoviruses detected in 44 striped skunks (Mephitis mephitis) found dead in and around Vancouver, British Columbia, Canada. Some of the animals exhibited pathological changes compatible with amdoparvovirus-associated disease. The nearly complete genomic sequence was obtained for seven different strains and our analyses show how this virus, which we named skunk amdoparvovirus (SKAV), should be classified as a separate species within the genus (proposed Carnivore amdoparvovirus 5). We detected co-infections, recombinant genomes, at least three separate viral lineages, and preliminary evidence for geographic segregation of lineages. Furthermore, we proved that similar viruses, only partially characterized in previous studies and labeled as AMDV, circulate in skunks from other distant areas of North America (Ontario and California) and found evidence for spillover events in mink (Neovison vison). Although SKAVs are capable of causing disease in infected animals, a high proportion of sub-clinical infections has been observed, suggesting these animals might act as asymptomatic carriers and pose a threat to wild and captive carnivores. Finally, we highlight the need for more specific diagnostic tests and further molecular investigations to clarify the epidemiology and host- and geographical distributions of amdoparvoviruses in terrestrial carnivores, especially because the whole spectrum of viral diversity in this group is likely still unknown.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B3X9, Canada
| | - Hillary E Doyle
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B3X9, Canada
| | - Ann P Britton
- Animal Health Centre, BC Ministry of Agriculture, Abbotsford, BC V3G2M3, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B3X9, Canada
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Wicker LV, Canfield PJ, Higgins DP. Potential Pathogens Reported in Species of the Family Viverridae and Their Implications for Human and Animal Health. Zoonoses Public Health 2017; 64:75-93. [PMID: 27359248 PMCID: PMC7165938 DOI: 10.1111/zph.12290] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 12/28/2022]
Abstract
The Viverridae is a family of nocturnal carnivores including civets, genets and African linsangs. While a list of known organisms isolated from a species is an essential tool for population management, this review represents the first attempt to collate published reports of organisms isolated from viverrids. A wide range of organisms, including 11 viruses, eight bacterial species, one internal arthropod species, representatives from eight genera of protozoan, 21 genera of nematode, seven genera of cestode, eight genera of trematode and six genera of external arthropod (mites, ticks and louse), have been reported in literature spanning over a century of research. Many of these are capable of infecting multiple hosts, including humans. This is of concern given the anthropogenic factors that bring humans and domestic species into close contact with viverrids, facilitating transmission and spillover of organisms between groups. These factors include trade in viverrids for human consumption, captive management in zoos, rescue centres or on commercial breeding farms, and the increasing overlap of free-ranging viverrid distribution and human settlement.
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Affiliation(s)
- L. V. Wicker
- Faculty of Veterinary ScienceThe University of SydneySydneyNSW2006Australia
- Save Vietnam's WildlifeCuc Phuong National ParkNinh BinhVietnam
| | - P. J. Canfield
- Faculty of Veterinary ScienceThe University of SydneySydneyNSW2006Australia
| | - D. P. Higgins
- Faculty of Veterinary ScienceThe University of SydneySydneyNSW2006Australia
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Candido M, Batinga MCA, Alencar ALF, de Almeida-Queiroz SR, da Glória Buzinaro M, Livonesi MC, Fernandes AM, de Sousa RLM. Molecular characterization and genetic diversity of bovine Kobuvirus, Brazil. Virus Genes 2016; 53:105-110. [PMID: 27623839 DOI: 10.1007/s11262-016-1391-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/06/2016] [Indexed: 12/01/2022]
Abstract
It is suggested that Bovine kobuvirus (BKV) is involved in the etiology of gastroenteric diseases especially among calves; however, this association remains unknown. This study evaluated 216 fecal samples from cattle with and without diarrhea symptoms obtained from different regions of Brazil. A 216 bp fragment of the BKV 3D gene was amplified by RT-PCR in 14.4 % (31/216) of the studied samples, and 17 samples were subjected to nucleotide sequencing. All positive samples were obtained from animals aged less than 5 months, and most of animals presented diarrhea (p < 0.05). Phylogenetic analyses showed that the obtained sequences were grouped within the genogroup 2 of BKV forming subclades specific for each Brazilian municipality sampled. In addition, the alignment of the sequences revealed differences of nucleotides between sequences from different locations. Our results indicate for the first time that there is a regional genotypic differentiation of BKV in Brazil.
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Affiliation(s)
- Marcelo Candido
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil.
| | - Maria Cryskely Agra Batinga
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Anna Luiza Farias Alencar
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Sabrina Ribeiro de Almeida-Queiroz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Maria da Glória Buzinaro
- Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellani, Rural, Jaboticabal, São Paulo, 14884-900, Brazil
| | - Márcia Cristina Livonesi
- Department of Clinical Analysis, Alfenas Federal University (UNIFAL), Rua Gabriel Monteiro da Silva, 700, Centro, Alfenas, Minas Gerais, 37130-000, Brazil
| | - Andrezza Maria Fernandes
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
| | - Ricardo Luiz Moro de Sousa
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Avenida Duque de Caxias Norte, 225, Jardim Elite, Pirassununga, São Paulo, 13635-900, Brazil
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PREVALENCE OF ANTIBODIES TO SELECTED VIRUSES AND PARASITES IN INTRODUCED AND ENDEMIC CARNIVORES IN WESTERN MADAGASCAR. J Wildl Dis 2016; 52:544-52. [PMID: 27195685 DOI: 10.7589/2015-03-063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introduced animals impact endemic populations through predation, competition, and disease transmission. Populations of endemic carnivores in Madagascar are declining, and pathogens transmitted from introduced species may further endanger these unique species. We assessed the exposure of introduced and endemic carnivores to common viral and parasitic pathogens in two national parks of Madagascar (Kirindy Mitea National Park and Ankarafantsika National Park) and their neighboring villages. We also identified variables associated with the presence of antibodies to these pathogens in fosa ( Cryptoprocta ferox ). Introduced and endemic species were exposed to canine parvovirus, canine herpesvirus, feline calicivirus, and Toxoplasma gondii . Domestic dogs ( Canis familiaris ) and cats ( Felis catus ) may be sources of infection for these pathogens. Prevalence of antibodies to Toxoplasma in captured fosa was >93%, and adults were more likely to be exposed than immature individuals. Our data provide a basis upon which to evaluate and manage risks of pathogen transmission between species.
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Canuti M, O’Leary KE, Hunter BD, Spearman G, Ojkic D, Whitney HG, Lang AS. Driving forces behind the evolution of the Aleutian mink disease parvovirus in the context of intensive farming. Virus Evol 2016; 2:vew004. [PMID: 27774297 PMCID: PMC4989880 DOI: 10.1093/ve/vew004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasmacytosis outbreak began on the Island of Newfoundland, and the virus has been endemic in farms since then. In this study, we evaluated the molecular epidemiology of AMDV in farmed and wild animals of Newfoundland since before the beginning of the outbreak and investigated the epidemic in a global context by studying AMDV worldwide, thereby examining its diffusion and phylogeography. Furthermore, AMDV evolution was examined in the context of intensive farming, where host population dynamics strongly influence viral evolution. Partial NS1 sequences and several complete genomes were obtained from Newfoundland viruses and analyzed along with numerous sequences from other locations worldwide that were either obtained as part of this study or from public databases. We observed very high viral diversity within Newfoundland and within single farms, where high rates of co-infection, recombinant viruses and polymorphisms were observed within single infected individuals. Worldwide, we documented a partial geographic distribution of strains, where viruses from different countries co-exist within clades but form country-specific subclades. Finally, we observed the occurrence of recombination and the predominance of negative selection pressure on AMDV proteins. A surprisingly low number of immunoepitopic sites were under diversifying pressure, possibly because AMDV gains no benefit by escaping the immune response as viral entry into target cells is mediated through interactions with antibodies, which therefore contribute to cell infection. In conclusion, the high prevalence of AMDV in farms facilitates the establishment of co-infections that can favor the occurrence of recombination and enhance viral diversity. Viruses are then exchanged between different farms and countries and can be introduced into the wild, with the rapidly evolving viruses producing many parallel lineages.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland and Labrador, A1B 3X9, Canada
| | - Kimberly E. O’Leary
- Animal Health Division, Forestry and Agrifoods Agency, P.O. Box 7400, St. John’s, Newfoundland and Labrador, A1E 3Y5, Canada
| | - Bruce D. Hunter
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Grant Spearman
- Department of Agriculture, Animal Health Laboratory, 65 River Rd., Truro, Nova Scotia, B2N 5E3, Canada and
| | - Davor Ojkic
- Animal Health Laboratory, 419 Gordon Street, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Hugh G. Whitney
- Animal Health Division, Forestry and Agrifoods Agency, P.O. Box 7400, St. John’s, Newfoundland and Labrador, A1E 3Y5, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland and Labrador, A1B 3X9, Canada
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Conceição-Neto N, Zeller M, Lefrère H, De Bruyn P, Beller L, Deboutte W, Yinda CK, Lavigne R, Maes P, Van Ranst M, Heylen E, Matthijnssens J. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci Rep 2015; 5:16532. [PMID: 26559140 PMCID: PMC4642273 DOI: 10.1038/srep16532] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/15/2015] [Indexed: 12/19/2022] Open
Abstract
A major limitation for better understanding the role of the human gut virome in health and disease is the lack of validated methods that allow high throughput virome analysis. To overcome this, we evaluated the quantitative effect of homogenisation, centrifugation, filtration, chloroform treatment and random amplification on a mock-virome (containing nine highly diverse viruses) and a bacterial mock-community (containing four faecal bacterial species) using quantitative PCR and next-generation sequencing. This resulted in an optimised protocol that was able to recover all viruses present in the mock-virome and strongly alters the ratio of viral versus bacterial and 16S rRNA genetic material in favour of viruses (from 43.2% to 96.7% viral reads and from 47.6% to 0.19% bacterial reads). Furthermore, our study indicated that most of the currently used virome protocols, using small filter pores and/or stringent centrifugation conditions may have largely overlooked large viruses present in viromes. We propose NetoVIR (Novel enrichment technique of VIRomes), which allows for a fast, reproducible and high throughput sample preparation for viral metagenomics studies, introducing minimal bias. This procedure is optimised mainly for faecal samples, but with appropriate concentration steps can also be used for other sample types with lower initial viral loads.
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Affiliation(s)
- Nádia Conceição-Neto
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical Virology, Rega Institute for Medical Research Leuven, Belgium
| | - Mark Zeller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium
| | - Hanne Lefrère
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium
| | - Pieter De Bruyn
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium
| | - Leen Beller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium
| | - Ward Deboutte
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium
| | - Claude Kwe Yinda
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical Virology, Rega Institute for Medical Research Leuven, Belgium
| | - Rob Lavigne
- KU Leuven - University of Leuven, Department of Biosystems, Laboratory of Gene Technology, Faculty of Bioscience Engineering, Belgium
| | - Piet Maes
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical Virology, Rega Institute for Medical Research Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical Virology, Rega Institute for Medical Research Leuven, Belgium
| | - Elisabeth Heylen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical Virology, Rega Institute for Medical Research Leuven, Belgium
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Canuti M, Whitney HG, Lang AS. Amdoparvoviruses in small mammals: expanding our understanding of parvovirus diversity, distribution, and pathology. Front Microbiol 2015; 6:1119. [PMID: 26528267 PMCID: PMC4600916 DOI: 10.3389/fmicb.2015.01119] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Many new viruses have been discovered recently, thanks in part to the advent of next-generation sequencing technologies. Among the Parvoviridae, three novel members of the genus Amdoparvovirus have been described in the last 4 years, expanding this genus that had contained a single species since its discovery, Aleutian mink disease virus. The increasing number of molecular and epidemiological studies on these viruses around the world also highlights the growing interest in this genus. Some aspects of amdoparvoviruses have been well characterized, however, many other aspects still need to be elucidated and the most recent reviews on this topic are outdated. We provide here an up-to-date overview of what is known and what still needs to be investigated about these scientifically and clinically relevant animal viruses.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland St. John's, NL, Canada
| | - Hugh G Whitney
- Animal Health Division, Forestry and Agrifoods Agency St. John's, NL, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland St. John's, NL, Canada
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