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Albuquerque NK, Silva SP, Aragão CF, Cunha TCAS, Paiva FAS, Coelho TFSB, Cruz ACR. Virome analysis of Desmodus rotundus tissue samples from the Amazon region. BMC Genomics 2024; 25:34. [PMID: 38177994 PMCID: PMC10768307 DOI: 10.1186/s12864-023-09950-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses. RESULTS Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages. CONCLUSION This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.
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Affiliation(s)
- Nádia K Albuquerque
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
| | - Sandro P Silva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Carine F Aragão
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Tânia Cristina A S Cunha
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Francisco A S Paiva
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Taciana F S B Coelho
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil
| | - Ana Cecília R Cruz
- Institute of Biologic Science, Federal University of Pará, Augusto Corrêa Road, Belém, 66075-750, Pará, Brazil.
- Arbovirology and Hemorragic Fever Department, Evandro Chagas Institute, BR-316 Highway, Ananindeua, 67030-000, Pará, Brazil.
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López-Astacio RA, Adu OF, Lee H, Hafenstein SL, Parrish CR. The Structures and Functions of Parvovirus Capsids and Missing Pieces: the Viral DNA and Its Packaging, Asymmetrical Features, Nonprotein Components, and Receptor or Antibody Binding and Interactions. J Virol 2023; 97:e0016123. [PMID: 37367301 PMCID: PMC10373561 DOI: 10.1128/jvi.00161-23] [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] [Indexed: 06/28/2023] Open
Abstract
Parvoviruses are among the smallest and superficially simplest animal viruses, infecting a broad range of hosts, including humans, and causing some deadly infections. In 1990, the first atomic structure of the canine parvovirus (CPV) capsid revealed a 26-nm-diameter T=1 particle made up of two or three versions of a single protein, and packaging about 5,100 nucleotides of single-stranded DNA. Our structural and functional understanding of parvovirus capsids and their ligands has increased as imaging and molecular techniques have advanced, and capsid structures for most groups within the Parvoviridae family have now been determined. Despite those advances, significant questions remain unanswered about the functioning of those viral capsids and their roles in release, transmission, or cellular infection. In addition, the interactions of capsids with host receptors, antibodies, or other biological components are also still incompletely understood. The parvovirus capsid's apparent simplicity likely conceals important functions carried out by small, transient, or asymmetric structures. Here, we highlight some remaining open questions that may need to be answered to provide a more thorough understanding of how these viruses carry out their various functions. The many different members of the family Parvoviridae share a capsid architecture, and while many functions are likely similar, others may differ in detail. Many of those parvoviruses have not been experimentally examined in detail (or at all in some cases), so we, therefore, focus this minireview on the widely studied protoparvoviruses, as well as the most thoroughly investigated examples of adeno-associated viruses.
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Affiliation(s)
- Robert A. López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Oluwafemi F. Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Colin R. Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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3
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Wang Y, Sun Y, Li X, Chen R, Li W, Ji L, Zhao Q, Ji L, Yang S, Zhang W. Molecular detection and characterization of three novel parvoviruses belonging to two different subfamilies in zoo birds. Arch Virol 2023; 168:163. [PMID: 37198283 DOI: 10.1007/s00705-023-05785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/18/2023] [Indexed: 05/19/2023]
Abstract
Birds carry a large number of viruses that may cause diseases in animals or humans. At present, information about the virome of zoo birds is limited. In this study, using viral metagenomics, we investigated the fecal virome of zoo birds collected from a zoo in Nanjing, Jiangsu Province, China. Three novel parvoviruses were obtained and characterized. The genomes of the three viruses are 5,909, 4,411, and 4,233 nt in length, respectively, and contain four or five ORFs. Phylogenetic analysis showed that these three novel parvoviruses clustered with other strains and formed three different clades. Pairwise comparison of NS1 amino acid sequences showed that Bir-01-1 shared 44.30-74.92% aa sequence identity with other parvoviruses belonging to the genus Aveparvovirus, while Bir-03-1 and Bir-04-1 shared less than 66.87% and 53.09% aa sequence identity, respectively, with other parvoviruses belonging to the genus Chaphamaparvovirus. Each of these three viruses was identified as a member of a novel species based on the species demarcation criteria for parvoviruses. These findings broaden our knowledge of the genetic diversity of parvoviruses and provide epidemiological data regarding potential outbreaks of parvovirus disease in birds.
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Affiliation(s)
- Yan Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Yijie Sun
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Xin Li
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Rong Chen
- Nanjing Hongshan Forest Zoo, 210000, Nanjing, Jiangsu, People's Republic of China
| | - Wang Li
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Li Ji
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Qifan Zhao
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Likai Ji
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China.
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4
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Bovo S, Schiavo G, Bolner M, Ballan M, Fontanesi L. Mining livestock genome datasets for an unconventional characterization of animal DNA viromes. Genomics 2022; 114:110312. [DOI: 10.1016/j.ygeno.2022.110312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/16/2022] [Accepted: 02/06/2022] [Indexed: 11/04/2022]
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5
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Bitencourt MM, Bezerra AMR. Infection agents of Didelphidae (Didelphimorphia) of Brazil: an underestimated matter in zoonoses research. MAMMALIA 2021. [DOI: 10.1515/mammalia-2021-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Zoonoses are diseases or infections naturally transmissible from vertebrate animals to humans, and can be bacterial, viral or parasitic. The growth of urbanization, industrialization and the advance of agriculture and livestock facilitate the spread of infectious and parasitic agents from wild animals to the human population and to their domestic animals. Among the various reservoirs of zoonotic agents, we find that didelphid species, due to their high capacity for adaptation in urban environments, as an important study case. We reviewed the literature data on the pathogens, including with zoonotic potential of marsupial species occurring in Brazil, accounted for infections by agents that we categorized into Bacteria, Viruses, Protozoa, and Helminths. Aiming identifies possible knowledge gaps, we also surveyed the origin of studied samples and the institutions leading the researches on host didelphids. Among the hosts, the genus Didelphis in the cycles of these agents stands out. Moreover, we found that the majority of reported cases are in the Southeastern Brazil, mean the data from other Brazilian localities and didelphid species could be underestimated. Most studies took place in graduate programs of public research institutions, emphasizing the importance of the funding public research for the Brazilian scientific development.
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Affiliation(s)
- Matheus M. Bitencourt
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal do Pará , Rua Augusto Corrêa, 01, CEP 66075-110 , Belém , PA , Brazil
| | - Alexandra M. R. Bezerra
- Mastozoologia/COZOO, Museu Paraense Emilio Goeldi, Campus de Pesquisa , Av. Perimetral 1901, CEP 66077-830 , Belém , PA , Brazil
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6
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de Souza WM, Fumagalli MJ, Carrera JP, de Araujo J, Cardoso JF, de Carvalho C, Durigon EL, Queiroz LH, Faria NR, Murcia PR, Figueiredo LTM. Paramyxoviruses from neotropical bats suggest a novel genus and nephrotropism. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 95:105041. [PMID: 34411742 DOI: 10.1016/j.meegid.2021.105041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/21/2022]
Abstract
Paramyxoviruses have a broad host range and geographic distribution, including human pathogens transmitted by bats, such as Nipah and Hendra viruses. In this study, we combined high-throughput sequencing and molecular approaches to investigate the presence of paramyxoviruses in neotropical bats (Microchiroptera suborder) in Brazil. We discovered and characterized three novel paramyxoviruses in the kidney tissues of apparently healthy common vampire bats (D. rotundus) and Seba's short-tailed bats (C. perspicillata), which we tentatively named Kanhgág virus (KANV), Boe virus (BOEV), and Guató virus (GUATV). In this study, we classified these viruses as putative species into the Macrojêvirus genus, a newly proposed genus of the Orthoparamyxovirinae subfamily. Using RT-PCR, we detected these viruses in 20.9% (9 out of 43) of bats tested, and viral RNA was detected exclusively in kidney tissues. Attempts to isolate infectious virus were successful for KANV and GUATV. Our results expand the viral diversity, host range, and geographical distribution of the paramyxoviruses.
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Affiliation(s)
- William Marciel de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Marcilio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jean Paul Carrera
- Department of Zoology, University of Oxford, Oxford, UK; Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Jansen de Araujo
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Cristiano de Carvalho
- Faculty of Veterinary Medicine, São Paulo State University, Araçatuba, São Paulo, Brazil
| | - Edison Luiz Durigon
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Luzia Helena Queiroz
- Faculty of Veterinary Medicine, São Paulo State University, Araçatuba, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, UK; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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7
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Jager MC, Tomlinson JE, Lopez-Astacio RA, Parrish CR, Van de Walle GR. Small but mighty: old and new parvoviruses of veterinary significance. Virol J 2021; 18:210. [PMID: 34689822 PMCID: PMC8542416 DOI: 10.1186/s12985-021-01677-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
In line with the Latin expression "sed parva forti" meaning "small but mighty," the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.
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Affiliation(s)
- Mason C Jager
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Joy E Tomlinson
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A Lopez-Astacio
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gerlinde R Van de Walle
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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8
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Affiliation(s)
- Marcione B. De Oliveira
- Graduate Program in Zoology, National Museum, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
| | - Cibele R. Bonvicino
- Graduate Program in Zoology, National Museum, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
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9
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Vandegrift KJ, Kumar A, Sharma H, Murthy S, Kramer LD, Ostfeld R, Hudson PJ, Kapoor A. Presence of Segmented Flavivirus Infections in North America. Emerg Infect Dis 2020; 26:1810-1817. [PMID: 32687041 PMCID: PMC7392405 DOI: 10.3201/eid2608.190986] [Citation(s) in RCA: 16] [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] [Indexed: 12/31/2022] Open
Abstract
Identifying viruses in synanthropic animals is necessary for understanding the origin of many viruses that can infect humans and developing strategies to prevent new zoonotic infections. The white-footed mouse, Peromyscus leucopus, is one of the most abundant rodent species in the northeastern United States. We characterized the serum virome of 978 free-ranging P. leucopus mice caught in Pennsylvania. We identified many new viruses belonging to 26 different virus families. Among these viruses was a highly divergent segmented flavivirus whose genetic relatives were recently identified in ticks, mosquitoes, and vertebrates, including febrile humans. This novel flavi-like segmented virus was found in rodents and shares ≤70% aa identity with known viruses in the highly conserved region of the viral polymerase. Our data will enable researchers to develop molecular reagents to further characterize this virus and its relatives infecting other hosts and to curtail their spread, if necessary.
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10
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Identification of a novel bovine copiparvovirus in pooled fetal bovine serum. Virus Genes 2020; 56:522-526. [PMID: 32306155 PMCID: PMC7329774 DOI: 10.1007/s11262-020-01757-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/03/2020] [Indexed: 01/12/2023]
Abstract
A novel parvovirus was identified as a cell culture contaminant by metagenomic analysis. Droplet digital PCR (ddPCR) was used to determine viral loads in the cell culture supernatant and further analysis, by ddPCR and DNA sequencing, demonstrated that fetal bovine serum (FBS) used during cell culture was the source of the parvovirus contamination. The FBS contained ~ 50,000 copies of the novel parvovirus DNA per ml of serum. The viral DNA was resistant to DNAse digestion. Near-full length sequence of the novel parvovirus was determined. Phylogenetic analysis demonstrated that virus belongs to the Copiparvovirus genus, being most closely related to bovine parvovirus 2 (BPV2) with 41% identity with the non-structural protein NS1 and 47% identity with the virus capsid protein of BPV2. A screen of individual and pooled bovine sera identified a closely related variant of the novel virus in a second serum pool. For classification purposes, the novel virus has been designated bovine copiparvovirus species 3 isolate JB9 (bocopivirus 3-JB9).
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Yuan K, Wang D, Luan Q, Sun J, Gao Q, Jiang Z, Wang S, Han Y, Qu X, Cui Y, Qiu S, Di Y, Wang X, Song S, Wang P, Xia S, Yu Y, Liu W, Yin Y. Whole Genome Characterization and Genetic Evolution Analysis of a New Ostrich Parvovirus. Viruses 2020; 12:v12030334. [PMID: 32204363 PMCID: PMC7150892 DOI: 10.3390/v12030334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
Ostrich diseases characterized by paralysis have been breaking out in broad areas of China since 2015, causing major damage to the ostrich breeding industry in China. This report describes a parvovirus detected in ostriches from four different regions. The entire genomes of four parvovirus strains were sequenced following amplification by PCR, and we conducted comprehensive analysis of the ostrich parvovirus genome. Results showed that the length genomes of the parvovirus contained two open reading frames. Ostrich parvovirus (OsPV) is a branch of goose parvovirus (GPV). Genetic distance analysis revealed a close relationship between the parvovirus and goose parvovirus strains from China, with the closest being the 2016 goose parvovirus RC16 strain from Chongqing. This is the first report of a parvovirus in ostriches. However, whether OsPV is the pathogen of ostrich paralysis remains uncertain. This study contributes new information about the evolution and epidemiology of parvovirus in China, which provides a new way for the study of paralysis in ostriches.
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Affiliation(s)
- Kunpeng Yuan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Dongdong Wang
- Qingdao Bolong Experimental Animal Co., Ltd., Qingdao 266225, China; (D.W.); (J.S.)
| | - Qingdong Luan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Ju Sun
- Qingdao Bolong Experimental Animal Co., Ltd., Qingdao 266225, China; (D.W.); (J.S.)
| | - Qianwen Gao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Zhiyao Jiang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Shouchun Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Yijun Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Xueting Qu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Yueying Cui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Shimei Qiu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
| | - Youxia Di
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Xiaoyi Wang
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Shige Song
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Peiheng Wang
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Shilong Xia
- China Ostrich Farming and Development Association, Beijing 100026, China; (Y.D.); (X.W.); (S.S.); (P.W.); (S.X.)
| | - Yongle Yu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China;
| | - Weiquan Liu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China;
- Correspondence: (W.L.); (Y.Y.)
| | - Yanbo Yin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266019, China; (K.Y.); (Q.L.); (Q.G.); (Z.J.); (S.W.); (Y.H.); (X.Q.); (Y.C.); (S.Q.)
- Correspondence: (W.L.); (Y.Y.)
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12
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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13
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Du J, Wang W, Chan JFW, Wang G, Huang Y, Yi Y, Zhu Z, Peng R, Hu X, Wu Y, Zeng J, Zheng J, Cui X, Niu L, Zhao W, Lu G, Yuen KY, Yin F. Identification of a Novel Ichthyic Parvovirus in Marine Species in Hainan Island, China. Front Microbiol 2019; 10:2815. [PMID: 31866980 PMCID: PMC6907010 DOI: 10.3389/fmicb.2019.02815] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/20/2019] [Indexed: 01/27/2023] Open
Abstract
Parvoviruses are a diverse group of viruses that are capable of infecting a wide range of animals. In this study, we report the discovery of a novel parvovirus, tilapia parvovirus HMU-HKU, in the fecal samples of crocodiles and intestines of tilapia in Hainan Province, China. The novel parvovirus was firstly identified from crocodiles fed with tilapia using next-generation sequencing (NGS). Screening studies revealed that the prevalence of the novel parvovirus in crocodile feces samples fed on tilapia (75–86%) was apparently higher than that in crocodiles fed with chicken (4%). Further studies revealed that the prevalence of the novel parvovirus in tilapia feces samples collected at four areas in Hainan Province was between 40 and 90%. Four stains of the novel parvovirus were identified in this study based on sequence analyses of NS1 and all the four strains were found in tilapia in contrast only two of them were detected in crocodile feces. The nearly full-length genome sequence of the tilapia parvovirus HMU-HKU-1 was determined and showed less than 45.50 and 40.38% amino acid identity with other members of Parvoviridae in NS1 and VP1 genes, respectively. Phylogenetic analysis based on the complete helicase domain amino acid sequences showed that the tilapia parvovirus HMU-HKU-1 formed a relatively independent branch in the newly proposed genus Chaphamaparvovirus in the subfamily Hamaparvovirinae according to the ICTV’s most recent taxonomic criteria for Parvoviridae classification. Tilapia parvovirus HMU-HKU-1 likely represented a new species within the new genus Chaphamaparvovirus. The identification of tilapia parvovirus HMU-HKU provides further insight into the viral and genetic diversity of parvoviruses and its infections in tilapia populations need to be evaluated in terms of pathogenicity and production losses in tilapia farming.
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Affiliation(s)
- Jiang Du
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wenqi Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jasper Fuk-Woo Chan
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Gaoyu Wang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yi Huang
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yufang Yi
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Zheng Zhu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ruoyan Peng
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xiaoyuan Hu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yue Wu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jifeng Zeng
- Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research of Hainan Province, Hainan University, Haikou, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, Haikou, China
| | - Jiping Zheng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiuji Cui
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Lina Niu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Wei Zhao
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Gang Lu
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
| | - Kwok-Yung Yuen
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong
| | - Feifei Yin
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China.,Department of Pathogen Biology, Hainan Medical University, Haikou, China
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14
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Fumagalli MJ, de Souza WM, de Araujo J, Modha S, Queiroz LH, Durigon EL, Murcia PR, Figueiredo LTM. Krykféie dicistrovirus: A novel dicistrovirus in velvety free-tailed bats from Brazil. INFECTION GENETICS AND EVOLUTION 2019; 75:104036. [PMID: 31499226 DOI: 10.1016/j.meegid.2019.104036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/26/2022]
Abstract
The Dicistroviridae family comprises positive single-stranded RNA viruses that are classified into Picornavirales order. These viruses are identified in arthropod hosts, including some having devastating economic consequences. Here, we described and characterized a novel nearly complete dicistrovirus genome identified in liver samples of velvety free-tailed bats (Molossus molossus) collected in June 2010 in Araçatuba city, São Paulo State, Brazil. This novel virus presents a genome of 9262 nucleotides in length and a typical dicistrovirus genome organization. Based on our phylogenetic analysis and ICTV criteria, we propose this virus as a novel species into the Triatovirus genus. Attempts of viral propagation in Vero E6 and C6/36 cell lines were unsuccessful. The novel dicistrovirus was detected only in one out of nine liver bat samples, representing for the first time an internal organ detection from a representative of this virus family.
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Affiliation(s)
- Marcílio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - William Marciel de Souza
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jansen de Araujo
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Edison Luiz Durigon
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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15
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Pénzes JJ, de Souza WM, Agbandje-McKenna M, Gifford RJ. An Ancient Lineage of Highly Divergent Parvoviruses Infects both Vertebrate and Invertebrate Hosts. Viruses 2019; 11:v11060525. [PMID: 31174309 PMCID: PMC6631224 DOI: 10.3390/v11060525] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 12/15/2022] Open
Abstract
Chapparvoviruses (ChPVs) comprise a divergent, recently identified group of parvoviruses (family Parvoviridae), associated with nephropathy in immunocompromised laboratory mice and with prevalence in deep sequencing results of livestock showing diarrhea. Here, we investigate the biological and evolutionary characteristics of ChPVs via comparative in silico analyses, incorporating sequences derived from endogenous parvoviral elements (EPVs) as well as exogenous parvoviruses. We show that ChPVs are an ancient lineage within the Parvoviridae, clustering separately from members of both currently established subfamilies. Consistent with this, they exhibit a number of characteristic features, including several putative auxiliary protein-encoding genes, and capsid proteins with no sequence-level homology to those of other parvoviruses. Homology modeling indicates the absence of a β-A strand, normally part of the luminal side of the parvoviral capsid protein core. Our findings demonstrate that the ChPV lineage infects an exceptionally broad range of host species, including both vertebrates and invertebrates. Furthermore, we observe that ChPVs found in fish are more closely related to those from invertebrates than they are to those of amniote vertebrates. This suggests that transmission between distantly related host species may have occurred in the past and that the Parvoviridae family can no longer be divided based on host affiliation.
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Affiliation(s)
- Judit J Pénzes
- McKnight Brain Institute and Department of Biochemistry and Molecular Biology, University of Florida, 1149 Newell Dr, Gainesville, FL 32610, USA.
| | - William Marciel de Souza
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil.
| | - Mavis Agbandje-McKenna
- McKnight Brain Institute and Department of Biochemistry and Molecular Biology, University of Florida, 1149 Newell Dr, Gainesville, FL 32610, USA.
| | - Robert J Gifford
- Medical Research Council-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, UK.
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16
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Kapgate SS, Kumanan K, Vijayarani K, Barbuddhe SB. Avian parvovirus: classification, phylogeny, pathogenesis and diagnosis. Avian Pathol 2018; 47:536-545. [PMID: 30246559 DOI: 10.1080/03079457.2018.1517938] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Poultry parvoviruses identified during the early 1980s are found worldwide in intestines from young birds with enteric disease syndromes as well as healthy birds. The chicken parvovirus (ChPV) and turkey parvovirus (TuPV) belong to the Aveparvovirus genus within the subfamily Parvovirinae. Poultry parvoviruses are small, non-enveloped, single-stranded DNA viruses consisting of three open reading frames, the first two encoding the non-structural protein (NS) and nuclear phosphoprotein (NP) and the third encoding the viral capsid proteins 1 (VP1 and VP2). In contrast to other parvoviruses, the VP1-unique region does not contain the phospholipase A2 sequence motif. Recent experimental studies suggested the parvoviruses to be the candidate pathogens in cases of enteric disease syndrome. Current diagnostic methods for poultry parvovirus detection include PCR, real-time PCR, enzyme linked immunosorbent assay using recombinant VP2 or VP1 capsid proteins. Moreover, sequence-independent amplification techniques combined with next-generation sequencing platforms have allowed rapid and simultaneous detection of the parvovirus from affected and healthy birds. There is no commercial vaccine; hence, the development of an effective vaccine to control the spread of infection should be of primary importance. This review presents the current knowledge on poultry parvoviruses with emphasis on taxonomy, phylogenetic relationship, genomic analysis, epidemiology, pathogenesis and diagnostic methods.
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Affiliation(s)
- Sunil S Kapgate
- a Department of Animal Biotechnology , Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - K Kumanan
- a Department of Animal Biotechnology , Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - K Vijayarani
- a Department of Animal Biotechnology , Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - Sukhadeo B Barbuddhe
- b Meat Safety Laboratory , ICAR-National Research Centre on Meat , Chengicherla, Hyderabad , India
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17
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Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, Gifford RJ. Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus Evol 2018; 4:vey026. [PMID: 30443409 PMCID: PMC6232428 DOI: 10.1093/ve/vey026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Amdoparvoviruses (family Parvoviridae: genus Amdoparvovirus) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify endogenous parvoviral elements (EPVs) disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived EPVs in the genome of the Transcaucasian mole vole (Ellobius lutescens). We also identify four EPVs in mammal and reptile genomes that are intermediate between amdoparvoviruses and their sister genus (Protoparvovirus) in terms of their phylogenetic placement and genomic features. In particular, we identify a genome-length EPV in the genome of a pit viper (Protobothrops mucrosquamatus) that is more similar to a protoparvovirus than an amdoparvovirus in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), yet exhibits characteristically amdoparvovirus-like genome features including: (1) a putative middle ORF gene; (2) a capsid gene that lacks a phospholipase A2 domain; (3) a genome structure consistent with an amdoparvovirus-like mechanism of capsid gene expression. Our findings indicate that amdoparvovirus host range extends to rodents, and that parvovirus lineages possessing a mixture of proto- and amdoparvovirus-like characteristics have circulated in the past. In addition, we show that EPV sequences in the mole vole and pit viper encode intact, expressible replicase genes that have potentially been co-opted or exapted in these host species.
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Affiliation(s)
- Judit J Pénzes
- University of Florida McKnight Brain Institute, 1149 Newell Dr, Gainesville, USA
| | - Soledad Marsile-Medun
- Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes, France
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
| | | | - Robert James Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
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