1
|
Vernygora O, Sullivan D, Nielsen O, Huntington KB, Rouse N, Popov VL, Lung O. Senecavirus cetus a novel picornavirus isolated from cetaceans represents a major host switching to the marine environment. NPJ VIRUSES 2024; 2:33. [PMID: 40295809 PMCID: PMC11721122 DOI: 10.1038/s44298-024-00040-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/21/2024] [Indexed: 04/30/2025]
Abstract
Senecavirus A (SVA), an emerging virus that causes vesicular disease in swine, was, until recently, the only member of the Senecavirus genus (Picornaviridae). Here, we report the isolation and complete genome sequence of two isolates of cetacean picornavirus 1 (Senecavirus cetus), a novel picornavirus species of the Senecavirus genus from dead stranded cetaceans from Alaska. One isolate was from a harbor porpoise stranded in 2017, and another from a beluga whale, stranded in 2019. Whole-genome sequencing of Senecavirus cetus strains showed a genome-wide nucleotide identity of 98.8% and a genome size of 7455 nucleotides. The Senecavirus cetus genomes are most similar to SVA with a 58.3% genome-wide pairwise nucleotide identity. Infection of eleven available cell lines from terrestrial and aquatic animals showed that beluga and sheep cells were susceptible to infection by Senecavirus cetus. Phylogenetic and ancestral state reconstruction analyses supported the novel virus being a member of the Senecavirus genus and provided the first evidence of Senecavirus-like picornavirus infecting marine mammals and likely descending from a terrestrial host ancestor. These discoveries provided important information on the evolutionary relationships and taxonomy of picornaviruses and increased our understanding of the genomic characteristics and potential host range of Senecavirus cetus.
Collapse
Affiliation(s)
- Oksana Vernygora
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB, Canada
| | - Daniel Sullivan
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ole Nielsen
- Department of Fisheries & Oceans Canada, Winnipeg, MB, Canada.
| | - Kathleen Burek Huntington
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, USA
- Alaska Veterinary Pathology Services, Eagle River, AK, USA
| | - Natalie Rouse
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, USA
- Alaska Veterinary Pathology Services, Eagle River, AK, USA
| | - Vsevolod L Popov
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Oliver Lung
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB, Canada.
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada.
| |
Collapse
|
2
|
Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
Collapse
Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
3
|
Rodrigues TCS, Nielsen O, Burek-Huntington KA, Popov VL, Raverty S, Lambourn DM, Subramaniam K, Waltzek TB. Genomic Characterization of Picornaviruses Isolated From Ribbon ( Histriophoca fasciata) and Harbor ( Phoca vitulina) Seals. Front Vet Sci 2020; 7:554716. [PMID: 33195526 PMCID: PMC7661754 DOI: 10.3389/fvets.2020.554716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
The seal picornavirus 1, species Aquamavirus A, is currently the only recognized member of the genus Aquamavirus within the family Picornaviridae. The bear picornavirus 1 was recently proposed as the second species in the genus under the name aquamavirus B. Herein, we determined the complete genomes of two novel pinniped picornaviruses, the harbor seal picornavirus (HsPV) and the ribbon seal picornavirus (RsPV). The HsPV and the RsPV were isolated in Vero.DogSLAMtag cells from samples collected from stranded harbor (Phoca vitulina) and ribbon (Histriophoca fasciata) seals. RsPV-infected Vero.DogSLAMtag cells displaying extensive cytopathic effects were processed for transmission electron microscopy and revealed non-enveloped viral particles aggregated into paracrystalline arrays in the cytoplasm. A next-generation sequencing approach was used to recover the complete genomes of the HsPV and the RsPV (6,709 and 6,683 bp, respectively). Phylogenetic and genetic analyses supported the HsPV and the RsPV as members of the Aquamavirus genus. Based on these results, RsPV represents a novel strain of Aquamavirus A, while the HsPV is a novel strain of the proposed species aquamavirus B. These discoveries provide information on the evolutionary relationships and ultrastructure of aquamaviruses and expands the known host range of those viruses. Our results underscore the importance of the application of classical virology and pathology techniques coupled with high-throughput sequencing technologies for the discovery and characterization of pathogens in wild marine mammals.
Collapse
Affiliation(s)
- Thais C S Rodrigues
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Ole Nielsen
- Department of Fisheries & Oceans Canada, Winnipeg, MB, Canada
| | | | - Vsevolod L Popov
- Center for Biodefense and Emerging Infectious Diseases, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States
| | - Stephen Raverty
- Animal Health Center, Abbotsford Agriculture Centre, Provincial Government of British Columbia, Abbotsford, BC, Canada
| | - Dyanna M Lambourn
- Marine Mammal Investigations, Washington Department of Fish and Wildlife, Lakewood, WA, United States
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Thomas B Waltzek
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| |
Collapse
|
4
|
A novel picornavirus in feces of a rainbow lorikeet (Trichoglossus moluccanus) shows a close relationship to members of the genus Avihepatovirus. Arch Virol 2019; 164:1911-1914. [PMID: 30982088 DOI: 10.1007/s00705-019-04246-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
A novel picornavirus, named "lorikeet picornavirus 1" (LoPV-1), was detected in a fecal sample from rainbow lorikeets using viral metagenomic analysis, and its complete genome sequence was determined and analyzed. The genome of LoPV-1 is 7862 nt long, including a 617-nt 5' UTR, a type IV IRES 5'UTR with an '8-like' motif, a 7032-nt polyprotein ORF, and a 213-nt 3' UTR. Phylogenetic analysis and pairwise asequence comparisons based on the amino acid sequences of P1, P2, and P3 indicated that LoPV-1 showed the closest relationship to two picornaviruses that were isolated recently from red-crowned cranes and clustered together with members of the genus Avihepatovirus.
Collapse
|