1
|
Intrahost Selection Pressure Drives Equine Arteritis Virus Evolution during Persistent Infection in the Stallion Reproductive Tract. J Virol 2019; 93:JVI.00045-19. [PMID: 30918077 DOI: 10.1128/jvi.00045-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/12/2019] [Indexed: 12/18/2022] Open
Abstract
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a reproductive and respiratory disease of horses. Following natural infection, 10 to 70% of infected stallions can become carriers of EAV and continue to shed virus in the semen. In this study, sequential viruses isolated from nasal secretions, buffy coat cells, and semen of seven experimentally infected and two naturally infected EAV carrier stallions were deep sequenced to elucidate the intrahost microevolutionary process after a single transmission event. Analysis of variants from nasal secretions and buffy coat cells lacked extensive positive selection; however, characteristics of the mutant spectra were different in the two sample types. In contrast, the initial semen virus populations during acute infection have undergone a selective bottleneck, as reflected by the reduction in population size and diversifying selection at multiple sites in the viral genome. Furthermore, during persistent infection, extensive genome-wide purifying selection shaped variant diversity in the stallion reproductive tract. Overall, the nonstochastic nature of EAV evolution during persistent infection was driven by active intrahost selection pressure. Among the open reading frames within the viral genome, ORF3, ORF5, and the nsp2-coding region of ORF1a accumulated the majority of nucleotide substitutions during persistence, with ORF3 and ORF5 having the highest intrahost evolutionary rates. The findings presented here provide a novel insight into the evolutionary mechanisms of EAV and identified critical regions of the viral genome likely associated with the establishment and maintenance of persistent infection in the stallion reproductive tract.IMPORTANCE EAV can persist in the reproductive tract of infected stallions, and consequently, long-term carrier stallions constitute its sole natural reservoir. Previous studies demonstrated that the ampullae of the vas deferens are the primary site of viral persistence in the stallion reproductive tract and the persistence is associated with a significant inflammatory response that is unable to clear the infection. This is the first study that describes EAV full-length genomic evolution during acute and long-term persistent infection in the stallion reproductive tract using next-generation sequencing and contemporary sequence analysis techniques. The data provide novel insight into the intrahost evolution of EAV during acute and persistent infection and demonstrate that persistent infection is characterized by extensive genome-wide purifying selection and a nonstochastic evolutionary pattern mediated by intrahost selective pressure, with important nucleotide substitutions occurring in ORF1a (region encoding nsp2), ORF3, and ORF5.
Collapse
|
2
|
Lazić S, Lupulović D, Gaudaire D, Petrovic T, Lazić G, Hans A. Serological evidence of equine arteritis virus infection and phylogenetic analysis of viral isolates in semen of stallions from Serbia. BMC Vet Res 2017; 13:316. [PMID: 29115996 PMCID: PMC5678800 DOI: 10.1186/s12917-017-1226-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 10/25/2017] [Indexed: 11/26/2022] Open
Abstract
Background Equine arteritis virus (EAV) is responsible for infections in equids. It can spread easily within the horse population and has a major impact on the horse breeding industry. No EAV outbreak has ever been reported in Serbia. To determine whether EAV is nonetheless circulating there, especially in the Vojvodina region, 340 horse serum samples were subjected to serology testing to detect EAV antibodies. In parallel, semen samples from three seropositive stallions were collected to evaluate their EAV status, using RT-qPCR and virus isolation on cell culture. Results Horse sera with EAV antibodies represented 15.88% (54/340) of the tested samples, 83.23% (283/340) being negative, and just three samples (0.89%) being uninterpretable due to cytotoxicity. Only 7.2% (10/138) of horses kept by private owners on their own property were seropositive for EAV, whereas 21.8% (44/202) of horses kept on stud farms had EAV antibodies. Phylogenetic analysis showed that the Serbian EAV isolate was most closely related to isolates from the neighbouring Hungary. Conclusions EAV is circulating in the Serbian horse population, especially among the breeding population certainly due to the use of EAV shedder stallions since there is no surveillance programme in Serbia and only limited checks on racehorses. Moreover, phylogenetic analysis indicates that the EAV isolated from a Lipizzaner stallion in Serbia is closely related to isolates from Hungary, and together form a new cluster.
Collapse
Affiliation(s)
- Sava Lazić
- Scientific Veterinary Institute "Novi Sad", Novi Sad, Serbia
| | - Diana Lupulović
- Scientific Veterinary Institute "Novi Sad", Novi Sad, Serbia
| | - Delphine Gaudaire
- ANSES, Laboratory for Equine Diseases, Virology Unit, Dozulé, France
| | - Tamas Petrovic
- Scientific Veterinary Institute "Novi Sad", Novi Sad, Serbia
| | - Gospava Lazić
- Scientific Veterinary Institute "Novi Sad", Novi Sad, Serbia
| | - Aymeric Hans
- ANSES, Laboratory for Equine Diseases, Virology Unit, Dozulé, France.
| |
Collapse
|
3
|
Kuhn JH, Lauck M, Bailey AL, Shchetinin AM, Vishnevskaya TV, Bào Y, Ng TFF, LeBreton M, Schneider BS, Gillis A, Tamoufe U, Diffo JLD, Takuo JM, Kondov NO, Coffey LL, Wolfe ND, Delwart E, Clawson AN, Postnikova E, Bollinger L, Lackemeyer MG, Radoshitzky SR, Palacios G, Wada J, Shevtsova ZV, Jahrling PB, Lapin BA, Deriabin PG, Dunowska M, Alkhovsky SV, Rogers J, Friedrich TC, O'Connor DH, Goldberg TL. Reorganization and expansion of the nidoviral family Arteriviridae. Arch Virol 2016; 161:755-68. [PMID: 26608064 PMCID: PMC5573231 DOI: 10.1007/s00705-015-2672-z] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/03/2015] [Indexed: 11/30/2022]
Abstract
The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American "types" of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.
Collapse
Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
| | - Michael Lauck
- Wisconsin National Primate Research Center, Madison, WI, 53715, USA
| | - Adam L Bailey
- Wisconsin National Primate Research Center, Madison, WI, 53715, USA
| | - Alexey M Shchetinin
- D.I. Ivanovsky Institute of Virology, Federal Research Center for Epidemiology and Microbiology Named After the Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Tatyana V Vishnevskaya
- D.I. Ivanovsky Institute of Virology, Federal Research Center for Epidemiology and Microbiology Named After the Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | - Lark L Coffey
- Center for Vectorborne Diseases, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | | | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Anna N Clawson
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Elena Postnikova
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Laura Bollinger
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Matthew G Lackemeyer
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Zinaida V Shevtsova
- Scientific-Research Institute of Experimental Pathology and Therapy, Sukhumi, Autonomous Republic of Abkhazia, Georgia
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Boris A Lapin
- Scientific-Research Institute of Medical Primatology, Russian Academy of Medical Sciences, Sochi, Russia
| | - Petr G Deriabin
- D.I. Ivanovsky Institute of Virology, Federal Research Center for Epidemiology and Microbiology Named After the Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Magdalena Dunowska
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology, Federal Research Center for Epidemiology and Microbiology Named After the Honorary Academician N. F. Gamaleya, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin National Primate Research Center, Madison, WI, 53715, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, Madison, WI, 53715, USA
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Wisconsin National Primate Research Center, Madison, WI, 53715, USA.
| |
Collapse
|
4
|
Steinbach F, Westcott DG, McGowan SL, Grierson SS, Frossard JP, Choudhury B. Re-emergence of a genetic outlier strain of equine arteritis virus: Impact on phylogeny. Virus Res 2014; 202:144-50. [PMID: 25527462 PMCID: PMC7172687 DOI: 10.1016/j.virusres.2014.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/05/2014] [Accepted: 12/09/2014] [Indexed: 12/24/2022]
Abstract
Re-emergence of a “historical” EAV strain. An updated EAV phylogeny scheme. Measures to improve EAV phylogenetic analysis through harmonization.
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory and reproductive disease of equids, which is notifiable in some countries including the Great Britain (GB) and to the OIE. Herein, we present the case of a persistently infected stallion and the phylogenetic tracing of the virus strain isolated. Discussing EAV occurrence and phylogenetic analysis we review features, which may aid to harmonise and enhance the classification of EAV.
Collapse
Affiliation(s)
- F Steinbach
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - D G Westcott
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - S L McGowan
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - S S Grierson
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - J P Frossard
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom
| | - B Choudhury
- Department of Virology, Animal and Plant Health Agency, Weybridge, Surrey KT15 3NB, United Kingdom.
| |
Collapse
|
5
|
Rola J, Socha W, Zmudzinski JF. Sequence analysis of ORFs 5, 6 and 7 of equine arteritis virus during persistent infection of the stallion--a 7-year study. Vet Microbiol 2013; 164:378-82. [PMID: 23490558 DOI: 10.1016/j.vetmic.2013.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/08/2013] [Accepted: 02/15/2013] [Indexed: 11/18/2022]
Abstract
Nucleotide and amino acid sequences of ORFs 5, 6 and 7 of EAV during persistent infection in the stallion of the Malopolska breed were analysed in the study. A total of 11 blood and semen samples were collected between 2004 and 2011. The titre of specific EAV antibodies in this carrier stallion was maintained at a high level throughout the study and was equal approximately 1:128. The sequence analysis of ORF5 showed 16 variable sites including 12 with synonymous substitutions and 4 with non-synonymous substitutions. The degree of nucleotide sequence identity among the strains ranged from 98.92% to 100%, whereas amino acid homology ranged from 98.06% to 100%. Ten substitutions were identified including 7 with synonymous mutations and 3 with non-synonymous mutations in ORF6. The degree of similarities among the strains ranged from 94.55 to 100% and from 98.41% to 100% at the level of nucleotide and amino acid sequence, respectively. Only a single point mutation at position 255 of ORF7 (99.6% identity) was found in nucleotide sequences of these strains. Phylogenetic analysis showed that all strains present in the semen of this carrier stallion created a separate cluster of "quasi-species" within the second European subgroup of EAV.
Collapse
Affiliation(s)
- Jerzy Rola
- Department of Virology, National Veterinary Research Institute, Pulawy, Poland.
| | | | | |
Collapse
|
6
|
Emergence of novel equine arteritis virus (EAV) variants during persistent infection in the stallion: origin of the 2007 French EAV outbreak was linked to an EAV strain present in the semen of a persistently infected carrier stallion. Virology 2011; 423:165-74. [PMID: 22209234 DOI: 10.1016/j.virol.2011.11.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/04/2011] [Accepted: 11/30/2011] [Indexed: 11/21/2022]
Abstract
During the summer of 2007, an outbreak of equine viral arteritis (EVA) occurred in Normandy (France). After investigation, a link was suggested between an EAV carrier stallion (A) and the index premise of the outbreak. The full-length nucleotide sequence analysis of a study reference strain (F27) isolated from the lung of a foal revealed a 12,710 nucleotides EAV genome with unique molecular hallmarks in the 5'UTR leader sequence and the ORF1a sequence encoding the non-structural protein 2. The evolution of the viral population in the persistently infected Stallion A was then studied by cloning ORFs 3 and 5 of the EAV genome from four sequential semen samples which were collected between 2000 and 2007. Molecular analysis of the clones confirmed the likely implication of Stallion A in the origin of this outbreak through the yearly emergence of new variants genetically similar to the F27 strain.
Collapse
|
7
|
Lauck M, Hyeroba D, Tumukunde A, Weny G, Lank SM, Chapman CA, O'Connor DH, Friedrich TC, Goldberg TL. Novel, divergent simian hemorrhagic fever viruses in a wild Ugandan red colobus monkey discovered using direct pyrosequencing. PLoS One 2011; 6:e19056. [PMID: 21544192 PMCID: PMC3081318 DOI: 10.1371/journal.pone.0019056] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 03/26/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Simian hemorrhagic fever virus (SHFV) has caused lethal outbreaks of hemorrhagic disease in captive primates, but its distribution in wild primates has remained obscure. Here, we describe the discovery and genetic characterization by direct pyrosequencing of two novel, divergent SHFV variants co-infecting a single male red colobus monkey from Kibale National Park, Uganda. METHODOLOGY/PRINCIPAL FINDINGS The viruses were detected directly from blood plasma using pyrosequencing, without prior virus isolation and with minimal PCR amplification. The two new SHFV variants, SHFV-krc1 and SHFV-krc2 are highly divergent from each other (51.9% nucleotide sequence identity) and from the SHFV type strain LVR 42-0/M6941 (52.0% and 51.8% nucleotide sequence identity, respectively) and demonstrate greater phylogenetic diversity within SHFV than has been documented within any other arterivirus. Both new variants nevertheless have the same 3' genomic architecture as the type strain, containing three open reading frames not present in the other arteriviruses. CONCLUSIONS/SIGNIFICANCE These results represent the first documentation of SHFV in a wild primate and confirm the unusual 3' genetic architecture of SHFV relative to the other arteriviruses. They also demonstrate a degree of evolutionary divergence within SHFV that is roughly equivalent to the degree of divergence between other arterivirus species. The presence of two such highly divergent SHFV variants co-infecting a single individual represents a degree of within-host viral diversity that exceeds what has previously been reported for any arterivirus. These results expand our knowledge of the natural history and diversity of the arteriviruses and underscore the importance of wild primates as reservoirs for novel pathogens.
Collapse
Affiliation(s)
- Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David Hyeroba
- Jane Goodall Institute, Entebbe, Uganda
- Kibale EcoHealth Project, Makerere University Biological Field Station, Kanyawara, Uganda
| | - Alex Tumukunde
- Kibale EcoHealth Project, Makerere University Biological Field Station, Kanyawara, Uganda
| | - Geoffrey Weny
- Kibale EcoHealth Project, Makerere University Biological Field Station, Kanyawara, Uganda
| | - Simon M. Lank
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Colin A. Chapman
- Jane Goodall Institute, Entebbe, Uganda
- Department of Anthropology and School of Environment, McGill University, Montreal, Quebec, Canada
- Department of Biology, Makerere University, Kampala, Uganda
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
| | - Thomas C. Friedrich
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Tony L. Goldberg
- Kibale EcoHealth Project, Makerere University Biological Field Station, Kanyawara, Uganda
- Wisconsin National Primate Research Center, Madison, Wisconsin, United States of America
- Department of Biology, Makerere University, Kampala, Uganda
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
| |
Collapse
|
8
|
PRONOST S, PITEL PH, MISZCZAK F, LEGRAND L, MARCILLAUD-PITEL C, HAMON M, TAPPREST J, BALASURIYA UBR, FREYMUTH F, FORTIER G. Description of the first recorded major occurrence of equine viral arteritis in France. Equine Vet J 2010; 42:713-20. [DOI: 10.1111/j.2042-3306.2010.00109.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
9
|
Zhang J, Timoney PJ, Shuck KM, Seoul G, Go YY, Lu Z, Powell DG, Meade BJ, Balasuriya UBR. Molecular epidemiology and genetic characterization of equine arteritis virus isolates associated with the 2006-2007 multi-state disease occurrence in the USA. J Gen Virol 2010; 91:2286-301. [PMID: 20444993 DOI: 10.1099/vir.0.019737-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 2006-2007, equine viral arteritis (EVA) was confirmed for the first time in Quarter Horses in multiple states in the USA. The entire genome of an equine arteritis virus (EAV) isolate from the index premises in New Mexico was 12 731 nt in length and possessed a previously unrecorded unique 15 nt insertion in the nsp2-coding region in ORF1a and a 12 nt insertion in ORF3. Sequence analysis of additional isolates made during this disease occurrence revealed that all isolates from New Mexico, Utah, Kansas, Oklahoma and Idaho had 98.6-100.0 % (nsp2) and 97.8-100 % (ORF3) nucleotide identity and contained the unique insertions in nsp2 and ORF3, indicating that the EVA outbreaks in these states probably originated from the same strain of EAV. Sequence and phylogenetic analysis of several EAV isolates made following an EVA outbreak on another Quarter Horse farm in New Mexico in 2005 provided evidence that this outbreak may well have been the source of virus for the 2006-2007 occurrence of the disease. A virus isolate from an aborted fetus in Utah was shown to have a distinct neutralization phenotype compared with other isolates associated with the 2006-2007 EVA occurrence. Full-length genomic sequence analysis of 18 sequential isolates of EAV made from eight carrier stallions established that the virus evolved genetically during persistent infection, and the rate of genetic change varied between individual animals and the period of virus shedding.
Collapse
Affiliation(s)
- Jianqiang Zhang
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Metz GE, Serena MS, Ocampos GM, Panei CJ, Fernandez VL, Echeverría MG. Equine arteritis virus: a new isolate from the presumable first carrier stallion in Argentina and its genetic relationships among the four reported unique Argentinean strains. Arch Virol 2008; 153:2111-5. [PMID: 18937029 DOI: 10.1007/s00705-008-0224-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
Abstract
Equine arteritis virus (EAV) was isolated from a testicle of the presumable first stallion infected with EAV in Argentina. This virus isolate (named LT-LP-ARG) was confirmed by GP5-specific PCR and indirect immunofluorescence assays. The PCR product was sequenced, and the phylogenetic analysis revealed that the LT-LP-ARG strain of EAV forms a monophyletic group, together with other strains previously isolated in our laboratory (LP02 group). However, all Argentinean EAV strains belong to a polyphyletic group. We believe that the virus isolate presented in this report could be the origin of EAV infection in our country.
Collapse
Affiliation(s)
- Germán E Metz
- Department of Virology, Faculty of Veterinary Sciences, National University of La Plata, 60 and 118, CC 296, 1900, La Plata, Argentina
| | | | | | | | | | | |
Collapse
|
11
|
Mankoc S, Hostnik P, Grom J, Toplak I, Klobucar I, Kosec M, Barlic-Maganja D. Comparison of different molecular methods for assessment of equine arteritis virus (EAV) infection: a novel one-step MGB real-time RT-PCR assay, PCR-ELISA and classical RT-PCR for detection of highly diverse sequences of Slovenian EAV variants. J Virol Methods 2007; 146:341-54. [PMID: 17854913 DOI: 10.1016/j.jviromet.2007.07.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 07/23/2007] [Accepted: 07/24/2007] [Indexed: 11/17/2022]
Abstract
In the present study, a new one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) strategy with minor-groove-binder (MGB) technology for the detection of EAV from 40 semen samples of Slovenian carrier stallions was tested. A novel MGB probe (EAVMGBpr) and a reverse primer (EAV-R) based on the multiple sequence alignment of 49 different EAV strain sequences of the highly conserved ORF7 (nucleocapsid gene) were designed. The performance of the assay was compared with different molecular detection methods. Three different primer pairs targeting the ORF1b and ORF7 were used, respectively. The real-time RT-PCR assay was at least 2 log(10) more sensitive than the classical RT-PCR and at least 1 log(10) more sensitive than the primer set used in the semi-nested PCR. The specificities of the amplification reactions were confirmed with biotinylated probes in the PCR-enzyme-linked immunosorbent assay (PCR-ELISA). Under the conditions described in our study, the sensitivity of the real-time RT-PCR was found to be superior to the PCR-ELISA assay. Thus, while the PCR-ELISA method was found to be both relatively demanding and time consuming, better sensitivity coupled with high specificity and speed of the assay makes the real-time RT-PCR a valuable tool for diagnosis of EAV infection.
Collapse
Affiliation(s)
- S Mankoc
- Virology Unit, Institute for Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbiceva 60, SI-1115 Ljubljana, Slovenia.
| | | | | | | | | | | | | |
Collapse
|
12
|
Zhang J, Miszczak F, Pronost S, Fortier C, Balasuriya UBR, Zientara S, Fortier G, Timoney PJ. Genetic variation and phylogenetic analysis of 22 French isolates of equine arteritis virus. Arch Virol 2007; 152:1977-94. [PMID: 17680321 DOI: 10.1007/s00705-007-1040-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 06/27/2007] [Indexed: 10/23/2022]
Abstract
Genetic variation and phylogenetic relationships among 22 French isolates of equine arteritis virus (EAV) obtained over four breeding seasons (2001-2004) were determined by sequencing open reading frames (ORFs) 2a-7. The ORFs 2a-7 of 22 isolates differed from the prototype virulent Bucyrus strain of EAV by between 14 (99.5% identity) and 328 (88.7% identity) nucleotides, and differed from each other by between 0 (100% identity) and 346 (88.1% identity) nucleotides, confirming genetic diversity among EAV strains circulating in France. Phylogenetic analysis based on the partial ORF5 sequences (nucleotides 11296-11813) of 22 French isolates and 216 additional EAV strains available in GenBank clustered the global isolates of EAV into two distinct groups: North American and European. The latter could be further divided into two large subgroups: European subgroup 1 (EU-1) and European subgroup 2 (EU-2). Phylogenetic analysis based on 100 EAV ORF3 sequences yielded similar results. Of the 22 French EAV isolates, the 11 isolates obtained before January 28, 2003 clustered with either the EU-1 (9 isolates) or EU-2 (2 isolates) subgroup. In contrast, by the criteria used in this study, the 11 isolates obtained after January 30, 2003 belong to the North American group, strongly suggesting that these strains were recently introduced into France.
Collapse
Affiliation(s)
- J Zhang
- Maxwell H Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | | | | | | | | | | | | | | |
Collapse
|