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      A novel defective recombinant porcine enterovirus G virus carrying a porcine torovirus papain-like cysteine protease gene and a putative anti-apoptosis gene in place of viral structural protein genes

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          Abstract

          Enterovirus G (EV-G) belongs to the family of Picornaviridae. Two types of recombinant porcine EV-Gs carrying papain-like cysteine protease (PLCP) gene of porcine torovirus, a virus in Coronaviridae, are reported. Type 1 recombinant EV-Gs are detected in pig feces in Japan, USA, and Belgium and carry the PLPC gene at the junction site of 2C/3A genes, while PLPC gene replaces the viral structural genes in type 2 recombinant EV-G detected in pig feces in a Chinese farm. We identified a novel type 2 recombinant EV-G carrying the PLCP gene with flanking sequences in place of the viral structural genes in pig feces in Japan. The ~0.3 kb-long upstream flanking sequence had no sequence homology with any proteins deposited in GenBank, while the downstream ~0.9 kb-long flanking sequence included a domain having high amino acid sequence homology with a baculoviral inhibitor of apoptosis repeat superfamily. The pig feces, where the novel type 2 recombinant EV-G was detected, also carried type 1 recombinant EV-G. The amount of type 1 and type 2 recombinant EV-G genomes was almost same in the pig feces. Although the phylogenetic analysis suggested that these two recombinant EV-Gs have independently evolved, type 1 recombinant EV-G might have served as a helper virus by providing viral structural proteins for dissemination of the type 2 recombinant EV-G.

          Highlights

          • •

            A novel type 2 recombinant EV-G was discovered in pig feces in Japan.

          • •

            Type 2 recombinant EV-G carried the PLCP torovirus gene with unknown flanking genes, in place of the viral structural proteins.

          • •

            Amount of type 2 recombinant EV-G in the pig feces was almost same with type 1.

          • •

            Type 2 recombinant EV-G belonged to be a different cluster from the cluster of type 1.

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          Most cited references22

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          Why do RNA viruses recombine?

          Etienne Simon-Loriere, Edward C. Holmes (2011)
          Key Points RNA viruses are able to undergo two forms of recombination: RNA recombination, which (in principle) can occur in any type of RNA virus, and reassortment, which is restricted to those viruses with segmented genomes. Rates of RNA recombination vary markedly among RNA viruses. Some viruses, particularly those with negative-sense single-stranded genomes, exhibit such low rates of recombination that they are effectively clonal. By contrast, some positive-sense single-stranded RNA viruses and some retroviruses such as HIV exhibit high rates of recombination that can exceed the rates of mutation when measured per nucleotide. Although recombination is often argued to represent a form of sexual reproduction, there is little evidence that recombination in RNA viruses evolved as a way of creating advantageous genotypes or removing deleterious mutations. In particular, there is no association between recombination frequency and the burden of a deleterious mutation. Similarly, there is little evidence that recombination could have been selected as a form of genetic repair. The strongest association for rates of recombination in RNA viruses is with genome structure. Hence, negative-sense single-stranded RNA viruses may recombine at low rates because of the restrictive association of genomic RNA in a ribonucleoprotein complex, as well as a lack of substrates for template switching, whereas some retroviruses recombine rapidly because their virions contain two genome copies and template switching between these copies is an inevitable part of the viral replication cycle. We therefore hypothesize that recombination in RNA viruses is a mechanistic by-product of the processivity of the viral polymerase that is used in replication, and that it varies with genome structure.
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            Is Open Access

            ICTV Virus Taxonomy Profile: Picornaviridae

            R Zell, E Delwart, A. E. Gorbalenya … (2017)
            The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains >30 genera and >75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal–oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www.ictv.global/report/picornaviridae.
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              Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences

              Marcos PÉREZ-LOSADA, Miguel Arenas, Juan Carlos Galán … (2014)
              Highlights • Recombination is very relevant in generating genetic variability in viral populations. • Viral recombination has important consequences for different areas of research. These include molecular biology, virology and evolutionary biology. It also impacts the daily practice of clinicians and public health officials. • Here we review three important aspects of viral recombination: (i) molecular mechanisms of model DNA- and RNA-viruses, (ii) methods for detection, characterization and quantification in viral populations, (iii) its impact on the evolutionary analysis of viral populations.
              Article 0 comments Cited 133 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Makoto Nagai
                Tetsuya Mizutani
                Journal
                Journal ID (nlm-ta): Infect Genet Evol
                Journal ID (iso-abbrev): Infect. Genet. Evol
                Title: Infection, Genetics and Evolution
                Publisher: Published by Elsevier B.V.
                ISSN (Print): 1567-1348
                ISSN (Electronic): 1567-7257
                Publication date PMC-release: 22 July 2019
                Publication date (Print): November 2019
                Publication date (Electronic): 22 July 2019
                Volume: 75
                Page: 103975
                Affiliations
                [a ]Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
                [b ]Azabu University, Sagamihara, Kanagawa, Japan
                [c ]Osaka Medical College, Osaka, Japan
                [d ]Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
                [e ]Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, Japan
                [f ]Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States of America
                Author notes
                [* ]Corresponding author to: T. Mizutani, Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan. tmizutan@ 123456cc.tuat.ac.jp
                [** ]Correspondence to: M. Nagai, Azabu University, Sagamihara, Kanagawa 252-5201, Japan. m-nagai@ 123456cc.tuat.ac.jp
                Article
                Publisher ID: S1567-1348(19)30193-5 Publisher ID: 103975
                DOI: 10.1016/j.meegid.2019.103975
                PMC ID: 7105976
                PubMed ID: 31344488
                SO-VID: a6c7f78f-acbd-43d0-8ab8-3f7de6b58a98
                Copyright © © 2019 Published by Elsevier B.V.
                License:

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                Date received : 18 April 2019
                Date revision received : 17 July 2019
                Date accepted : 19 July 2019
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
                Keywords: enterovirus,torovirus,recombination
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: enterovirus, torovirus, recombination

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