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Hoque SA, Akari Y, Khamrin P, Phan T, Onda Y, Okitsu S, Komoto S, Hayakawa S, Komine-Aizawa S, Yuki Y, Kiyono H, Ushijima H. Epidemiology and molecular evolution of GI.1 sapovirus in the recent era. J Med Virol 2024; 96:e29904. [PMID: 39264064 DOI: 10.1002/jmv.29904] [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: 06/02/2024] [Revised: 08/25/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Sapovirus (SaV) infection is increasing worldwide. Herein, we provided evidence of a significant increase in SaV infection in Japan during 2010-2022, primarily due to the considerable (p = 0.0003) rise of the GI.1 genotype. Furthermore, we found that all major and minor SaV outbreaks in Japan, including the largest SaV outbreak in 2021-2022, were caused by the GI.1 genotype. Therefore, to get insight into the underlying molecular mechanism behind this rising trend of the SaV GI.1 type, we selected 15 SaV GI.1 outbreak strains for complete genome analysis through next-generation sequencing. Phylogenetically, our strains remained clustered in different branches in lineages I and II among the GI.1 genotype. We showed all amino acid (aa) substitutions in different open reading frames (ORFs) in these strains. Importantly, we have demonstrated that the strains involved in the largest SaV outbreak in Japan in 2021-2022 belonged to lineage II and possessed the third ORF. We have identified some unique aa mutations in these major outbreak strains in the NS1 and NS6-NS7 regions that are thought to be associated with viral pathogenicity, cell tropism, and epidemiological competence. Thus, in addition to enriching the database of SaV's complete sequences, this study provides insights into its important mutations.
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Affiliation(s)
- Sheikh A Hoque
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Yuki Akari
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, and Emerging and Re-emerging Diarrheal Viruses Research Center, Chiang Mai University, Chiang Mai, Thailand
| | - Tung Phan
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuko Onda
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Shoko Okitsu
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Satoshi Komoto
- Department of Virology, Fujita Health University School of Medicine, Toyoake, Japan
- Center for Infectious Disease Research, Research Promotion Headquarters, Fujita Health University, Toyoake, Japan
- Research Center for GLOBAL and LOCAL Infectious Diseases, Division of One Health, Oita University, Yufu, Japan
| | - Satoshi Hayakawa
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Shihoko Komine-Aizawa
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
| | - Yoshikazu Yuki
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba, Japan
- Research Institute of Disaster Medicine, Institute for Global Prominent Research, Institute for Advanced Academic Research, Chiba University, Chiba, Japan
- Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines (cMAV), Division of Gastroenterology, University of California, San Diego, California, USA
| | - Hiroshi Kiyono
- Department of Human Mucosal Vaccinology, Chiba University Hospital, Chiba, Japan
- Research Institute of Disaster Medicine, Institute for Global Prominent Research, Institute for Advanced Academic Research, Chiba University, Chiba, Japan
- Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines (cMAV), Division of Gastroenterology, University of California, San Diego, California, USA
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Nihon University School of Medicine, Division of Microbiology, Tokyo, Japan
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Álvarez ÁL, Arboleya A, Abade dos Santos FA, García-Manso A, Nicieza I, Dalton KP, Parra F, Martín-Alonso JM. Highs and Lows in Calicivirus Reverse Genetics. Viruses 2024; 16:866. [PMID: 38932159 PMCID: PMC11209508 DOI: 10.3390/v16060866] [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: 03/24/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
In virology, the term reverse genetics refers to a set of methodologies in which changes are introduced into the viral genome and their effects on the generation of infectious viral progeny and their phenotypic features are assessed. Reverse genetics emerged thanks to advances in recombinant DNA technology, which made the isolation, cloning, and modification of genes through mutagenesis possible. Most virus reverse genetics studies depend on our capacity to rescue an infectious wild-type virus progeny from cell cultures transfected with an "infectious clone". This infectious clone generally consists of a circular DNA plasmid containing a functional copy of the full-length viral genome, under the control of an appropriate polymerase promoter. For most DNA viruses, reverse genetics systems are very straightforward since DNA virus genomes are relatively easy to handle and modify and are also (with few notable exceptions) infectious per se. This is not true for RNA viruses, whose genomes need to be reverse-transcribed into cDNA before any modification can be performed. Establishing reverse genetics systems for members of the Caliciviridae has proven exceptionally challenging due to the low number of members of this family that propagate in cell culture. Despite the early successful rescue of calicivirus from a genome-length cDNA more than two decades ago, reverse genetics methods are not routine procedures that can be easily extrapolated to other members of the family. Reports of calicivirus reverse genetics systems have been few and far between. In this review, we discuss the main pitfalls, failures, and delays behind the generation of several successful calicivirus infectious clones.
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Affiliation(s)
- Ángel L. Álvarez
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Aroa Arboleya
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Fábio A. Abade dos Santos
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Nacional de Investigação Agrária e Veterinária, 2780-157 Oeiras, Portugal
| | - Alberto García-Manso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Inés Nicieza
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Kevin P. Dalton
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Francisco Parra
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
| | - José M. Martín-Alonso
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain
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3
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Liu J, Li X, Song W, Zeng X, Li H, Yang L, Wang D. The Multi-Kingdom Microbiome of Wintering Migratory Birds in Poyang Lake, China. Viruses 2024; 16:396. [PMID: 38543762 PMCID: PMC10974949 DOI: 10.3390/v16030396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Wild birds are a natural reservoir for zoonotic viruses. To clarify the role of migratory birds in viruses spread in Poyang Lake, we investigated the microbiome of 250 wild bird samples from 19 species in seven orders. The bacterial and viral content abundance and diversity were preliminarily evaluated by Kraken2 and Bracken. After de novo assembly by Megahit and Vamb, viral contigs were identified by CheckV. The reads remapped to viral contigs were quantified using Bowtie2. The bacterial microbiome composition of the samples covers 1526 genera belonging to 175 bacterial orders, while the composition of viruses covers 214 species belonging to 22 viral families. Several taxonomic biomarkers associated with avian carnivory, oral sampling, and raptor migration were identified. Additionally, 17 complete viral genomes belonging to Astroviridae, Caliciviridae, Dicistroviridae, Picornaviridae, and Tombusviridae were characterized, and their phylogenetic relationships were analyzed. This pioneering metagenomic study of migratory birds in Poyang Lake, China illuminates the diverse microbial landscape within these birds. It identifies potential pathogens, and uncovers taxonomic biomarkers relevant to varied bird habitats, feeding habits, ecological classifications, and sample types, underscoring the public health risks associated with wintering migratory birds.
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Affiliation(s)
- Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (J.L.); (X.L.); (X.Z.); (L.Y.)
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (J.L.); (X.L.); (X.Z.); (L.Y.)
| | - Wentao Song
- School of Public Health, Xiamen University, Xiamen 361005, China;
| | - Xiaoxu Zeng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (J.L.); (X.L.); (X.Z.); (L.Y.)
| | - Hui Li
- Nanchang Center for Disease Prevention and Control, Nanchang 330038, China;
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (J.L.); (X.L.); (X.Z.); (L.Y.)
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (J.L.); (X.L.); (X.Z.); (L.Y.)
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Almeida T, Lopes AM, Estruch J, Rouco C, Cavadini P, Neimanis A, Gavier-Widén D, Le Gall-Reculé G, Velarde R, Abrantes J. A new HaCV-EBHSV recombinant lagovirus circulating in European brown hares (Lepus europaeus) from Catalonia, Spain. Sci Rep 2024; 14:2872. [PMID: 38311618 PMCID: PMC10838927 DOI: 10.1038/s41598-024-53201-1] [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: 05/31/2023] [Accepted: 01/29/2024] [Indexed: 02/06/2024] Open
Abstract
In 2020/2021, several European brown hare syndrome virus (EBHSV) outbreaks were recorded in European hares (Lepus europaeus) from Catalonia, Spain. Recombination analysis combined with phylogenetic reconstruction and estimation of genetic distances of the complete coding sequences revealed that 5 strains were recombinants. The recombination breakpoint is located within the non-structural protein 2C-like RNA helicase (nucleotide position ~ 1889). For the genomic fragment upstream of the breakpoint, a non-pathogenic EBHSV-related strain (hare calicivirus, HaCV; GII.2) was the most closely related sequence; for the rest of the genome, the most similar strains were the European brown hare syndrome virus (EBHSV) strains recovered from the same 2020/2021 outbreaks, suggesting a recent origin. While the functional impact of the atypical recombination breakpoint remains undetermined, the novel recombinant strain was detected in different European brown hare populations from Catalonia, located 20-100 km apart, and seems to have caused a fatal disease both in juvenile and adult animals, confirming its viability and ability to spread and establish infection. This is the first report of a recombination event involving HaCV and EBHSV and, despite the recombination with a non-pathogenic strain, it appears to be associated with mortality in European brown hares, which warrants close monitoring.
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Affiliation(s)
- Tereza Almeida
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Ana M Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- UMIB-Unit for Multidisciplinary Research in Biomedicine, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR, Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Josep Estruch
- Wildlife Ecology & Health Group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Carlos Rouco
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Patrizia Cavadini
- WOAH Reference Laboratory for Rabbit Haemorrhagic Disease, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Aleksija Neimanis
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, 75189, Uppsala, Sweden
| | - Dolores Gavier-Widén
- Swedish Veterinary Agency (SVA), 75189, Uppsala, Sweden
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Box 7028, 75007, Uppsala, Sweden
| | - Ghislaine Le Gall-Reculé
- Avian and Rabbit Virology, Immunology and Parasitology Unit, Ploufragan-Plouzané-Niort Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (Anses), 22440, Ploufragan, France
| | - Roser Velarde
- Wildlife Ecology & Health Group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Joana Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002, Porto, Portugal.
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Ji X, Guo C, Dai Y, Chen L, Chen Y, Wang S, Sun Y. Genomic Characterization and Molecular Evolution of Sapovirus in Children under 5 Years of Age. Viruses 2024; 16:146. [PMID: 38275956 PMCID: PMC10819405 DOI: 10.3390/v16010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Sapovirus (SaV) is a type of gastroenteric virus that can cause acute gastroenteritis. It is highly contagious, particularly among children under the age of 5. In this study, a total of 712 stool samples from children under the age of 5 with acute gastroenteritis were collected. Out of these samples, 28 tested positive for SaV, resulting in a detection rate of 3.93% (28/712). Samples with Ct < 30 were collected for library construction and high-throughput sequencing, resulting in the acquisition of nine complete genomes. According to Blast, eight of them were identified as GI.1, while the remaining one was GI.6. The GI.6 strain sequence reported in our study represents the first submission of the GI.6 strain complete genome sequence from mainland China to the Genbank database, thus filling the data gap in our country. Sequence identity analysis revealed significant nucleotide variations between the two genotypes of SaV and their corresponding prototype strains. Phylogenetic and genetic evolution analyses showed no evidence of recombination events in the obtained sequences. Population dynamics analysis demonstrated potential competitive inhibition between two lineages of GI.1. Our study provides insights into the molecular epidemiological and genetic evolution characteristics of SaV prevalent in the Nantong region of China, laying the foundation for disease prevention and control, as well as pathogen tracing related to SaV in this area.
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Affiliation(s)
- Xiaolei Ji
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Chen Guo
- Department of Laboratory Medicine, Nantong Chongchuan Center for Disease Control and Prevention, 47 Zhongxiu Middle Road, Nantong 226001, China;
| | - Yaoyao Dai
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Lu Chen
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Yujia Chen
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Shifang Wang
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
| | - Yihua Sun
- Key Laboratory of Medicine, Nantong Center for Disease Control and Prevention, 189 Gongnongnan Road, Chongchuan District, Nantong 226007, China; (X.J.); (Y.D.); (L.C.); (Y.C.)
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Zhou N, Huang Y, Zhou L, Li M, Jin H. Molecular Evolution of RNA-Dependent RNA Polymerase Region in Norovirus Genogroup I. Viruses 2023; 15:166. [PMID: 36680206 PMCID: PMC9861054 DOI: 10.3390/v15010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Norovirus is the leading viral agent of gastroenteritis in humans. RNA-dependent RNA polymerase (RdRp) is essential in the replication of norovirus RNA. Here, we present a comprehensive evolutionary analysis of the norovirus GI RdRp gene. Our results show that the norovirus GI RdRp gene can be divided into three groups, and that the most recent common ancestor was 1484. The overall evolutionary rate of GI RdRp is 1.821 × 10-3 substitutions/site/year. Most of the amino acids of the GI RdRp gene were under negative selection, and only a few positively selected sites were recognized. Amino acid substitutions in the GI RdRp gene accumulated slowly over time. GI.P1, GI.P3 and GI.P6 owned the higher evolutionary rates. GI.P11 and GI.P13 had the faster accumulation rate of amino acid substitutions. GI.P2, GI.P3, GI.P4, GI.P6 and GI.P13 presented a strong linear evolution. These results reveal that the norovirus GI RdRp gene evolves conservatively, and that the molecular evolutionary characteristics of each P-genotype are diverse. Sequencing in RdRp and VP1 of norovirus should be advocated in the surveillance system to explore the effect of RdRp on norovirus activity.
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Affiliation(s)
- Nan Zhou
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yue Huang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Lu Zhou
- Department of Acute Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Mingma Li
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Hui Jin
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China
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Matsvay A, Dyachkova M, Sai A, Burskaia V, Artyushin I, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck's Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family. Microorganisms 2022; 10:1540. [PMID: 36013958 PMCID: PMC9416405 DOI: 10.3390/microorganisms10081540] [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: 06/28/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper-Temminck's stint (Calidris temminckii), preliminarily named Temminck's stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family-previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)-the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Marina Dyachkova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Anna Sai
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia;
| | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
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8
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Smertina E, Carroll AJ, Boileau J, Emmott E, Jenckel M, Vohra H, Rolland V, Hands P, Hayashi J, Neave MJ, Liu JW, Hall RN, Strive T, Frese M. Lagovirus Non-structural Protein p23: A Putative Viroporin That Interacts With Heat Shock Proteins and Uses a Disulfide Bond for Dimerization. Front Microbiol 2022; 13:923256. [PMID: 35923397 PMCID: PMC9340658 DOI: 10.3389/fmicb.2022.923256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/16/2022] [Indexed: 12/03/2022] Open
Abstract
The exact function(s) of the lagovirus non-structural protein p23 is unknown as robust cell culture systems for the Rabbit haemorrhagic disease virus (RHDV) and other lagoviruses have not been established. Instead, a range of in vitro and in silico models have been used to study p23, revealing that p23 oligomerizes, accumulates in the cytoplasm, and possesses a conserved C-terminal region with two amphipathic helices. Furthermore, the positional homologs of p23 in other caliciviruses have been shown to possess viroporin activity. Here, we report on the mechanistic details of p23 oligomerization. Site-directed mutagenesis revealed the importance of an N-terminal cysteine for dimerization. Furthermore, we identified cellular interactors of p23 using stable isotope labeling with amino acids in cell culture (SILAC)-based proteomics; heat shock proteins Hsp70 and 110 interact with p23 in transfected cells, suggesting that they ‘chaperone’ p23 proteins before their integration into cellular membranes. We investigated changes to the global transcriptome and proteome that occurred in infected rabbit liver tissue and observed changes to the misfolded protein response, calcium signaling, and the regulation of the endoplasmic reticulum (ER) network. Finally, flow cytometry studies indicate slightly elevated calcium concentrations in the cytoplasm of p23-transfected cells. Taken together, accumulating evidence suggests that p23 is a viroporin that might form calcium-conducting channels in the ER membranes.
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Affiliation(s)
- Elena Smertina
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- Centre for Invasive Species Solutions, Canberra, ACT, Australia
| | - Adam J. Carroll
- RSB/RSC Joint Mass Spectrometry Facility, Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Joseph Boileau
- RSB/RSC Joint Mass Spectrometry Facility, Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Edward Emmott
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Maria Jenckel
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Harpreet Vohra
- Imaging and Cytometry Facility, John Curtin School of Medical Research, Acton, ACT, Australia
| | - Vivien Rolland
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Philip Hands
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Junna Hayashi
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Matthew J. Neave
- Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| | - Jian-Wei Liu
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Robyn N. Hall
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
- Centre for Invasive Species Solutions, Canberra, ACT, Australia
| | - Tanja Strive
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
- Centre for Invasive Species Solutions, Canberra, ACT, Australia
| | - Michael Frese
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
- Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
- *Correspondence: Michael Frese,
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Zell R, Groth M, Selinka L, Selinka HC. Picorna-Like Viruses of the Havel River, Germany. Front Microbiol 2022; 13:865287. [PMID: 35444619 PMCID: PMC9013969 DOI: 10.3389/fmicb.2022.865287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
To improve the understanding of the virome diversity of riverine ecosystems in metropolitan areas, a metagenome analysis was performed with water collected in June 2018 from the river Havel in Berlin, Germany. After enrichment of virus particles and RNA extraction, paired-end Illumina sequencing was conducted and assignment to virus groups and families was performed. This paper focuses on picorna-like viruses, the most diverse and abundant group of viruses with impact on human, animal, and environmental health. Here, we describe altogether 166 viral sequences ranging in size from 1 to 11.5 kb. The 71 almost complete genomes are comprised of one candidate iflavirus, one picornavirus, two polycipiviruses, 27 marnaviruses, 27 dicistro-like viruses, and 13 untypeable viruses. Many partial picorna-like virus sequences up to 10.2 kb were also investigated. The sequences of the Havel picorna-like viruses represent genomes of seven of eight so far known Picornavirales families. Detection of numerous distantly related dicistroviruses suggests the existence of additional, yet unexplored virus groups with dicistronic genomes, including few viruses with unusual genome layout. Of special interest is a clade of dicistronic viruses with capsid protein-encoding sequences at the 5′-end of the genome. Also, monocistronic viruses with similarity of their polymerase and capsid proteins to those of dicistroviruses are interesting. A second protein with NTP-binding site present in the polyprotein of solinviviruses and related viruses needs further attention. The results underline the importance to study the viromes of fluvial ecosystems. So far acknowledged marnaviruses have been isolated from marine organisms. However, the present study and available sequence data suggest that rivers and limnic habitats are relevant ecosystems with circulation of marnaviruses as well as a plethora of unknown picorna-like viruses.
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Affiliation(s)
- Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marco Groth
- CF DNA Sequencing, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Lukas Selinka
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, Berlin, Germany
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Peñaflor-Téllez Y, Chávez-Munguía B, Lagunes-Guillén A, Salazar-Villatoro L, Gutiérrez-Escolano AL. The Feline Calicivirus Leader of the Capsid Protein Has the Functional Characteristics of a Viroporin. Viruses 2022; 14:v14030635. [PMID: 35337042 PMCID: PMC8955107 DOI: 10.3390/v14030635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
The leader of the capsid (LC) protein is exclusive to the Vesivirus genus, and it is needed for successful feline calicivirus (FCV) replication, as well as an efficient apoptosis induction through the mitochondrial pathway. In this work, we aimed to determine if the LC protein from the FCV is a viroporin. Although lacking in a transmembrane domain or an amphipathic helix, the LC protein from the FCV is toxic when expressed in bacteria and it oligomerizes through disulfide bonds, which are both key characteristics of viroporins. An electron microscopy analysis of LC-expressing E. coli cells suggest that the protein induces osmotic stress. Moreover, we found that the previously studied C40A LC mutant, that fails to induce apoptosis and that hinders the replication cycle, also oligomerizes but it has a reduced toxicity and fails to induce osmotic stress in bacteria. We propose that the LC protein is a viroporin that acts as a disulfide bond-dependent antimicrobial peptide, similar to the Ebola virus delta peptide.
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