1
|
Dickey AM, Smith TPL, Clawson ML, Heaton MP, Workman AM. Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns. F1000Res 2021; 9:1449. [PMID: 35035904 PMCID: PMC8749911 DOI: 10.12688/f1000research.27898.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination of TMEM154 haplotypes which encodes lysine (K35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so. A2 subgroups 1 and 2 are associated with host TMEM154 genotypes; subgroup 1 with the K35/K35 genotype and subgroup 2 with the E35/E35 genotype. Methods: Sequence variation within and among full-length assemblies of SRLV subtype A2 subgroups 1 and 2 was analyzed to identify genome-scale recombination patterns and subgroup-specific variants. Results: Consensus viral genomes were assembled from 23 infected sheep, including animals of assorted TMEM154 genotypes comprised of haplotypes 1, 2, or 3. Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional sub-structure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes. Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined consensus genomes. After accounting for recombination, 413 subgroup diagnostic single nucleotide polymorphisms (SNPs) were identified. Conclusions: The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir for producing viral genomes representing recombination between A2 subgroups 1 and 2.
Collapse
Affiliation(s)
- Aaron M. Dickey
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Timothy P. L. Smith
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael L. Clawson
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael P. Heaton
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Aspen M. Workman
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| |
Collapse
|
2
|
Dickey AM, Smith TPL, Clawson ML, Heaton MP, Workman AM. Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns. F1000Res 2020; 9:1449. [PMID: 35035904 PMCID: PMC8749911 DOI: 10.12688/f1000research.27898.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 01/08/2024] Open
Abstract
Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination of TMEM154 haplotypes which encodes lysine (K35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so. A2 subgroups 1 and 2 are associated with host TMEM154 genotypes; subgroup 1 with the K35/K35 genotype and subgroup 2 with the E35/E35 genotype. Methods: Sequence variation within and among full-length assemblies of SRLV subtype A2 subgroups 1 and 2 was analyzed to identify genome-scale recombination patterns and subgroup-specific variants. Results: Consensus viral genomes were assembled from 23 infected sheep, including animals of assorted TMEM154 genotypes comprised of haplotypes 1, 2, or 3. Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional sub-structure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes. Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined consensus genomes. After accounting for recombination, 413 subgroup diagnostic single nucleotide polymorphisms (SNPs) were identified. Conclusions: The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir for producing viral genomes representing recombination between A2 subgroups 1 and 2.
Collapse
Affiliation(s)
- Aaron M. Dickey
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Timothy P. L. Smith
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael L. Clawson
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael P. Heaton
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Aspen M. Workman
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| |
Collapse
|
3
|
Russell GC, Zadoks RN, Willoughby K, Bachofen C. Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture. Microb Genom 2020; 6:e000343. [PMID: 32160141 PMCID: PMC7276709 DOI: 10.1099/mgen.0.000343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/07/2020] [Indexed: 12/25/2022] Open
Abstract
Bovine viral diarrhoea (BVD) is an important disease of cattle, with significant impacts on animal health and welfare. The wide host range of the causative pestiviruses may lead to formation of virus reservoirs in other ruminant or wildlife species, presenting a concern for the long-term success of BVD eradication campaigns. It is likely that the quasispecies nature of these RNA viruses contributes to their interspecies transmission by providing genetic plasticity. Understanding the spectrum of sequence variants present in persistently infected (PI) animals is, therefore, essential for studies of virus transmission. To analyse quasispecies diversity without amplification bias, we extracted viral RNA from the serum of a PI cow, and from cell culture fluid after three passages of the same virus in culture, to produce cDNA without amplification. Sequencing of this material using Illumina 250 bp paired-read technology produced full-length virus consensus sequences from both sources and demonstrated the quasispecies diversity of this pestivirus A genotype 1a field strain within serum and after culture. We report the distribution and diversity of over 800 SNPs and provide evidence for a loss of diversity after only three passages in cell culture, implying that cultured viruses cannot be used to understand quasispecies diversity and may not provide reliable molecular markers for source tracing or transmission studies. Additionally, both serum and cultured viruses could be sequenced as a set of 25 overlapping PCR amplicons that demonstrated the same consensus sequences and the presence of many of the same quasispecies variants. The observation that aspects of the quasispecies structure revealed by massively parallel sequencing are also detected after PCR and Sanger sequencing suggests that this approach may be useful for small or difficult to analyse samples.
Collapse
Affiliation(s)
- George C. Russell
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Ruth N. Zadoks
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
- Present address: Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Kim Willoughby
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
| | - Claudia Bachofen
- Moredun Research Institute, Pentlands Science Park, Midlothian EH26 0PZ, UK
- Present address: Institute of Virology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, CH-8057 Zürich, Switzerland
| |
Collapse
|
6
|
Yeşilbağ K, Alpay G, Becher P. Variability and Global Distribution of Subgenotypes of Bovine Viral Diarrhea Virus. Viruses 2017; 9:v9060128. [PMID: 28587150 PMCID: PMC5490805 DOI: 10.3390/v9060128] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/03/2022] Open
Abstract
Bovine viral diarrhea virus (BVDV) is a globally-distributed agent responsible for numerous clinical syndromes that lead to major economic losses. Two species, BVDV-1 and BVDV-2, discriminated on the basis of genetic and antigenic differences, are classified in the genus Pestivirus within the Flaviviridae family and distributed on all of the continents. BVDV-1 can be segregated into at least twenty-one subgenotypes (1a–1u), while four subgenotypes have been described for BVDV-2 (2a–2d). With respect to published sequences, the number of virus isolates described for BVDV-1 (88.2%) is considerably higher than for BVDV-2 (11.8%). The most frequently-reported BVDV-1 subgenotype are 1b, followed by 1a and 1c. The highest number of various BVDV subgenotypes has been documented in European countries, indicating greater genetic diversity of the virus on this continent. Current segregation of BVDV field isolates and the designation of subgenotypes are not harmonized. While the species BVDV-1 and BVDV-2 can be clearly differentiated independently from the portion of the genome being compared, analysis of different genomic regions can result in inconsistent assignment of some BVDV isolates to defined subgenotypes. To avoid non-conformities the authors recommend the development of a harmonized system for subdivision of BVDV isolates into defined subgenotypes.
Collapse
Affiliation(s)
- Kadir Yeşilbağ
- Department of Virology, Faculty of Veterinary Medicine, Uludag University, TR-16059 Bursa, Turkey.
| | - Gizem Alpay
- Department of Virology, Faculty of Veterinary Medicine, Uludag University, TR-16059 Bursa, Turkey.
| | - Paul Becher
- Institute for Virology, Department of Infectious Diseases, University of Veterinary Medicine, D-30559 Hannover, Germany.
| |
Collapse
|
8
|
Workman AM, Heaton MP, Harhay GP, Smith TPL, Grotelueschen DM, Sjeklocha D, Brodersen B, Petersen JL, Chitko-McKown CG. Resolving Bovine viral diarrhea virus subtypes from persistently infected U.S. beef calves with complete genome sequence. J Vet Diagn Invest 2016; 28:519-28. [PMID: 27400958 DOI: 10.1177/1040638716654943] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bovine viral diarrhea virus (BVDV) is classified into 2 genotypes, BVDV-1 and BVDV-2, each of which contains distinct subtypes with genetic and antigenic variation. To effectively control BVDV by vaccination, it is important to know which subtypes of the virus are circulating and how their prevalence is changing over time. Accordingly, the purpose of our study was to estimate the current prevalence and diversity of BVDV subtypes from persistently infected (PI) beef calves in the central United States. Phylogenetic analysis of the 5'-UTR (5' untranslated region) for 119 virus strains revealed that a majority (82%) belonged to genotype 1b, and the remaining strains were distributed between genotypes 1a (9%) and 2 (8%); however, BVDV-2 subtypes could not be confidently resolved. Therefore, to better define the variability of U.S. BVDV isolates and further investigate the division of BVDV-2 isolates into subtypes, complete genome sequences were obtained for these isolates as well as representatives of BVDV-1a and -1b. Phylogenetic analyses of the complete coding sequence provided more conclusive genetic classification and revealed that U.S. BVDV-2 isolates belong to at least 3 distinct genetic groups that are statistically supported by both complete and individual coding gene analyses. These results show that a more complex set of BVDV-2 subtypes has been circulating in this region than was previously thought.
Collapse
Affiliation(s)
- Aspen M Workman
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - Michael P Heaton
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - Gregory P Harhay
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - Dale M Grotelueschen
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - David Sjeklocha
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - Bruce Brodersen
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - Jessica L Petersen
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| | - Carol G Chitko-McKown
- U.S. Meat Animal Research Center, Clay Center, NE (Workman, Heaton, Harhay, Smith, Chitko-McKown)Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Clay Center, NE (Grotelueschen)Cattle Empire LLC, Satanta, KS (Sjeklocha)Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences (Brodersen), University of Nebraska-Lincoln, Lincoln, NEDepartment of Animal Science (Petersen), University of Nebraska-Lincoln, Lincoln, NE
| |
Collapse
|
9
|
Ochirkhuu N, Konnai S, Odbileg R, Odzaya B, Gansukh S, Murata S, Ohashi K. Molecular detection and characterization of bovine viral diarrhea virus in Mongolian cattle and yaks. Arch Virol 2016; 161:2279-83. [PMID: 27206573 DOI: 10.1007/s00705-016-2890-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/08/2016] [Indexed: 11/26/2022]
Abstract
Bovine viral diarrhea virus (BVDV) is classified into two species, namely, Bovine viral diarrhea virus 1 and Bovine viral diarrhea virus 2, and affects cattle worldwide, resulting in significant economic loss. The prevalence of BVDV-1 and BVDV-2 infections and its genotypes in Mongolian animals has not been studied. In this study, we surveyed BVDV infection in dairy cattle and yaks from Bornuur and Bulgan counties by RT-PCR, and the average infection rate in the sampling sites was 15.8 % and 20.0 %, respectively. In addition, molecular features of the 5'-UTR region of the BVDV genome in Mongolian cattle and yaks were identified as belonging to the subtypes BVDV-1a and BVDV-2a, respectively. Determining the prevalence, geographical distribution, and molecular diversity of BVDV-1 and BVDV-2 in various host species in Mongolia is important for further studies and process control programs.
Collapse
Affiliation(s)
- Nyamsuren Ochirkhuu
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
| | - Satoru Konnai
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
| | - Raadan Odbileg
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolia University of Life Science, Khan-Uul district, Zaisan, 17042, Ulaanbaatar, Mongolia
| | - Battogtokh Odzaya
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolia University of Life Science, Khan-Uul district, Zaisan, 17042, Ulaanbaatar, Mongolia
| | - Shura Gansukh
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolia University of Life Science, Khan-Uul district, Zaisan, 17042, Ulaanbaatar, Mongolia
| | - Shiro Murata
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan
| | - Kazuhiko Ohashi
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan.
| |
Collapse
|