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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [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: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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Reczyńska D, Zalewska M, Czopowicz M, Kaba J, Zwierzchowski L, Bagnicka E. Acute Phase Protein Levels as An Auxiliary Tool in Diagnosing Viral Diseases in Ruminants-A Review. Viruses 2018; 10:E502. [PMID: 30223561 PMCID: PMC6165172 DOI: 10.3390/v10090502] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/20/2022] Open
Abstract
We examined acute phase protein (APP) concentrations in viral infections of dairy ruminants and assessed the potential role of characteristic patterns of APP changes in auxiliary diagnosing viral diseases. All viruses reviewed are common causes of farm animal diseases. APPs are among the first agents of immunity, and their concentrations could be diagnostically relevant. In the most common ruminant viral diseases, elevated serum amyloid A (SAA) and haptoglobin (Hp) levels in blood serum have been observed. However, since these proteins are the main APPs in many viral infections, it is impossible to use their levels for diagnosing particular infections. Decreased Cp and albumin expression could help differentiate the bluetongue virus infection from other diseases. Lastly, analysis of SAA levels in blood serum and milk could be helpful in diagnosing small ruminant lentivirus infection. While promising, APP levels can only be considered as an auxiliary tool in diagnosing viral diseases in ruminants.
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Affiliation(s)
- Daria Reczyńska
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Postepu 36A str., 05-552 Jastrzębiec, Poland.
| | - Magdalena Zalewska
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Postepu 36A str., 05-552 Jastrzębiec, Poland.
| | - Michał Czopowicz
- Laboratory of Veterinary Epidemiology and Economics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska str. 159c., 02-776 Warsaw, Poland.
| | - Jarosław Kaba
- Laboratory of Veterinary Epidemiology and Economics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska str. 159c., 02-776 Warsaw, Poland.
| | - Lech Zwierzchowski
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Postepu 36A str., 05-552 Jastrzębiec, Poland.
| | - Emilia Bagnicka
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Postepu 36A str., 05-552 Jastrzębiec, Poland.
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Weber MN, Bauermann FV, Canal CW, Bayles DO, Neill JD, Ridpath JF. Temporal dynamics of 'HoBi'-like pestivirus quasispecies in persistently infected calves generated under experimental conditions. Virus Res 2016; 227:23-33. [PMID: 27693289 DOI: 10.1016/j.virusres.2016.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 11/26/2022]
Abstract
'HoBi'-like virus is an atypical group within the Pestivirus genus that is implicated in economic losses for cattle producers due to both acute and persistent infections. Pestivirus strains exist as quasispecies (swarms of individual viruses) in infected animals and the viral populations making up the quasispecies differ widely in size and diversity in each animal. In the present study the viral quasispecies circulating in persistently infected (PI) calves, generated and maintained under experimental conditions using two different 'HoBi'-like strains, was observed over time. An increase in genetic variability and the development of certain mutations was observed over time. Mutations observed included the loss of a putative N-linked glycosylation site in the E2 region and the change of specific residues in E1/E2. It is hypothesized that these changes may be the results on continued adaption of the pestivirus to individual hosts. This is the first study characterizing variation in the viral swarms of animals persistently infected with HoBi-like viruses over time. Studies of the shifts in PI viral swarms will contribute to our understanding of the host and viral mechanisms that function in the maintenance of pestivirus persistent infections.
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Affiliation(s)
- Matheus N Weber
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9090, CEP 91-540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernando V Bauermann
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), 1920 Dayton Av., Zip Code 50010, Ames, IA, United States
| | - Cláudio W Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9090, CEP 91-540-000, Porto Alegre, Rio Grande do Sul, Brazil
| | - Darrell O Bayles
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), 1920 Dayton Av., Zip Code 50010, Ames, IA, United States
| | - John D Neill
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), 1920 Dayton Av., Zip Code 50010, Ames, IA, United States
| | - Julia F Ridpath
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), 1920 Dayton Av., Zip Code 50010, Ames, IA, United States.
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Kane SE, Holler LD, Braun LJ, Neill JD, Young DB, Ridpath JF, Chase CCL. Bovine viral diarrhea virus outbreak in a beef cow herd in South Dakota. J Am Vet Med Assoc 2016; 246:1358-62. [PMID: 26043135 DOI: 10.2460/javma.246.12.1358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
CASE DESCRIPTION 136 pregnant beef cows were purchased in the fall of 2003. The following spring, 128 cows calved as expected; 8 cows were believed to have aborted with the fetuses unavailable for evaluation. Of the 128 calves born, 8 died within 2 weeks after birth and 9 were born with congenital abnormalities. CLINICAL FINDINGS Cows and their calves were evaluated for bovine viral diarrhea virus (BVDV) infection. Forty-four of 120 calves, but 0 cows, tested positive for BVDV antigen by immunohistochemical staining of ear notch specimens. TREATMENT AND OUTCOME Five BVDV test-positive calves died shortly after weaning, and the remaining 39 BVDV test-positive calves were moved to an isolated feedlot and retested for BVDV at 5 to 6 months of age; 36 had positive results, which indicated that they were persistently infected (PI) with BVDV, whereas 3 had negative results, which indicated that they were transiently infected with BVDV at the time of the first test. All PI calves were infected with the same BVDV type 2a strain. As yearlings, 17 of the 36 PI calves died peracutely with lesions consistent with mucosal disease, 6 died without gross lesions, and 2 were euthanized because of chronic ill thrift. The remaining 11 PI calves appeared healthy and were sold for slaughter. Screening of the following year's calf crop for BVDV by use of immunohistochemical staining of ear-notch specimens yielded negative results for all calves. CLINICAL RELEVANCE Introduction of BVDV into a naïve cow herd resulted in a loss of 44% of the calf crop subsequent to reproductive loss, poor thrift, and mucosal disease.
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Weber MN, Bauermann FV, Bayles DO, Canal CW, Neill JD, Ridpath JF. Comparison of 'HoBi'-like viral populations among persistent infected calves generated under experimental conditions and to inoculum virus. Virology 2016; 492:225-31. [PMID: 26971244 DOI: 10.1016/j.virol.2016.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 02/26/2016] [Accepted: 03/01/2016] [Indexed: 10/22/2022]
Abstract
Like other members from the Pestivirus genus, 'HoBi'-like pestiviruses cause economic losses for cattle producers due to both acute and persistent infections. The present study analyzed for the first time PI animals derived from a controlled infection with two different 'HoBi'-like strains where the animals were maintained under conditions where superinfection by other pestiviruses could be excluded. The sequence of the region coding for viral glycoproteins E1/E2 of variants within the swarms of viruses present in the PI calves and two viral inoculums used to generate them were compared. Differences in genetic composition of the viral swarms were observed suggesting that host factors can play a role in genetic variations among PIs. Moreover, PIs generated with the same inoculum showed amino acid substitutions in similar sites of the polyprotein, even in serum from PIs with different quasispecies composition, reinforcing that some specific sites in E2 are important for host adaptation.
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Affiliation(s)
- M N Weber
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - F V Bauermann
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), Ames, IA, United States
| | - D O Bayles
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), Ames, IA, United States
| | - C W Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - J D Neill
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), Ames, IA, United States
| | - J F Ridpath
- Ruminant Diseases and Immunology Research Unit, Agricultural Research Service (ARS), National Animal Disease Center (NADC), United States Department of Agriculture (USDA), Ames, IA, United States.
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Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle. PLoS One 2015; 10:e0131972. [PMID: 26132819 PMCID: PMC4488595 DOI: 10.1371/journal.pone.0131972] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/09/2015] [Indexed: 11/19/2022] Open
Abstract
Bovine viral diarrhea virus (BVDV), a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI) cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.
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Sede M, Jones LR, Moretti F, Laufer N, Quarleri J. Inter and intra-host variability of hepatitis C virus genotype 1a hypervariable envelope coding domains followed for a 4-11 year of human immunodeficiency virus coinfection and highly active antiretroviral therapy. Virology 2014; 471-473:19-28. [PMID: 25461527 DOI: 10.1016/j.virol.2014.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/13/2014] [Accepted: 09/13/2014] [Indexed: 01/25/2023]
Abstract
The evolution of hepatitis C virus (HCV) quasispecies in patients with HIV-1 coinfection is not fully understood. The HCV-1a quasispecies heterogeneity was analyzed at inter and intra-host levels along 7.6 years in 21 coinfected patients that showed different virological and immunological responses to highly active antiretroviral therapy (HAART). Two to nine serial samples were subjected to direct and clonal sequence analyses of the envelope glycoprotein 2 (E2) gene. E2-based phylogenies, intra-host HCV evolution and evolutionary rates, as well as dynamics of the quasispecies heterogeneity parameters were evaluated. Bayesian coalescent phylogenies indicated complex evolutionary histories, revealing some viral lineages that persisted along the follow up and others that were detectable at a single or some sampling times, suggesting the occurrence of emergence-extinction cycles. HCV quasispecies underwent very rapid evolution in HAART-treated patients (~3.1 × 10(-2) sub/site/year) following the recovery of the host immunocompetence irrespectively of the virological response to HAART.
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Affiliation(s)
- Mariano Sede
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Leandro Roberto Jones
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales sede Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Chubut, Argentina
| | - Franco Moretti
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Argentina
| | - Natalia Laufer
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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Chernick A, Godson DL, van der Meer F. Metadata beyond the sequence enables the phylodynamic inference of bovine viral diarrhea virus type 1a isolates from Western Canada. INFECTION GENETICS AND EVOLUTION 2014; 28:367-74. [PMID: 24424090 DOI: 10.1016/j.meegid.2014.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 01/03/2014] [Accepted: 01/04/2014] [Indexed: 11/16/2022]
Abstract
Bovine viral diarrhea virus (BVDV) has been recognized as an important pathogen of livestock in Canada. The high mutation rate of this virus leads to a great degree of diversity between isolates resulting in the ability to infer precise evolutionary relationships. Many studies have attempted to elucidate the regional and global evolution of BVDV, but so far few have applied Bayesian methods to this end. We aimed to describe the molecular epidemiology and phylodynamics of BVDV 1a isolates in Western Canada using 5'UTR and E1-E2 sequence data, collection dates and locations. Sequences were obtained from isolates submitted to a diagnostic laboratory in Saskatoon, Canada. Path sampling and stepping stone model testing were employed to identify the model that best fit the data. We found that these Western Canadian isolates share a most recent common ancestor dated near 1909. Furthermore, the E1-E2 region shows a median substitution rate about ten times greater than the 5'UTR. It was also noted that caution should be exercised when inferring phylogenetic relationships using the 5'UTR alone, as it becomes difficult to resolve relationships within major clades. Phylogeographic and population size fluctuation estimates require more thorough sampling than was performed here to be reliable. We have found that there are significant gains to be made by utilizing a Bayesian analysis and by incorporating additional types of data beyond the sequence. These include the estimation of most common recent ancestor dates and the precise inference of transmission routes. Future work will expand upon these findings by more thoroughly sampling BVDV isolates spatially and temporally and further refining the Bayesian model employed here.
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Affiliation(s)
- Adam Chernick
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N4N1, Canada.
| | - Dale L Godson
- Prairie Diagnostic Services, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N5B4, Canada
| | - Frank van der Meer
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N4N1, Canada
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Abstract
Pestiviruses cause economically important diseases among domestic ruminants and pigs, but they may also infect a wide spectrum of wild species of even-toed ungulates (Artiodactyla). Bovine viral diarrhea virus (BVDV) and Border disease virus of sheep infect their hosts either transiently or persistently. Cellular and humoral immunotolerance to the infecting strain is a unique feature of persistent infection (PI) by ruminant pestiviruses. Persistence, caused by transplacental infection early in fetal development, depends on virally encoded interferon antagonists that inactivate the host's innate immune response to the virus without globally interfering with its function against other viruses. At epidemiological equilibrium, approximately 1-2% of animals are PI. Successful BVDV control programs show that removal of PI animals results in viral extinction in the host population. The nucleotide sequences of ruminant pestiviruses change little during persistent infection. Nevertheless, they display large heterogeneity, pointing to a long history of virus-host coevolution in which avirulent strains are more successful.
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Affiliation(s)
- Matthias Schweizer
- Institute of Veterinary Virology, University of Bern, CH-3001 Bern, Switzerland; ,
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Manrique JM, Jones LR. Genetic data generated from virus-host complexes obtained by membrane co-immobilization are equivalent to data obtained from tangential filtrate virus concentrates and virus cultures. Virus Genes 2013; 48:160-7. [PMID: 24166738 DOI: 10.1007/s11262-013-0999-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
The sieving and immobilization of virus-host complexes using impact filtration (aka membrane co-immobilization or MCI) is a novel approach to the study of plankton viruses. One of the most interesting characteristics of the method is the possibility of generating data on potential viral hosts without the need of culturing hosts cells. MCI has demonstrated to be useful for studying viruses of picoalgae, but studies comparing data generated by MCI to data obtained by other techniques are lacking. In this work, Ostreococcus virus (OV) and Ostreococcus sp. sequences generated from virus-host complexes obtained by MCI were compared to sequences obtained from tangential filtration (TF) concentrates and virus cultures (VC). Statistical parsimony, phylogenetic analyses, pairwise distance comparisons, and analysis of molecular variance showed that the viral and host sequences obtained by the three methods were highly related to each other, indicating that MCI, TF, and VC produce equivalent results. Minor differences were observed among viral sequences obtained from VC and TF concentrates as well as among host sequences generated from VC and MCI. As discussed in the body of the paper, the divergence observed for cultured cells could be due to selective pressures exerted by culture conditions, whereas the correlate observed for the corresponding viral sequences could obey to a hitchhiking effect.
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Affiliation(s)
- J M Manrique
- Laboratory of Virology and Molecular Genetics, Faculty of Natural Sciences, Trelew seat, National University of Patagonia "San Juan Bosco", Av. 9 de Julio 25, 9100, Trelew, Chubut, Argentina
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Bachofen C, Vogt HR, Stalder H, Mathys T, Zanoni R, Hilbe M, Schweizer M, Peterhans E. Persistent infections after natural transmission of bovine viral diarrhoea virus from cattle to goats and among goats. Vet Res 2013; 44:32. [PMID: 23675947 PMCID: PMC3660168 DOI: 10.1186/1297-9716-44-32] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 04/23/2013] [Indexed: 11/10/2022] Open
Abstract
Bovine viral diarrhoea virus (BVDV) is an economically important pathogen of cattle worldwide. Infection of a pregnant animal may lead to persistent infection of the foetus and birth of a persistently infected (PI) calf that sheds the virus throughout its life. However, BVD viruses are not strictly species specific. BVDV has been isolated from many domesticated and wild ruminants. This is of practical importance as virus reservoirs in non-bovine hosts may hamper BVDV control in cattle. A goat given as a social companion to a BVDV PI calf gave birth to a PI goat kid. In order to test if goat to goat infections were possible, seronegative pregnant goats were exposed to the PI goat. In parallel, seronegative pregnant goats were kept together with the PI calf. Only the goat to goat transmission resulted in the birth of a next generation of BVDV PI kids whereas all goats kept together with the PI calf aborted. To our knowledge, this is the first report which shows that a PI goat cannot only transmit BVD virus to other goats but that such transmission may indeed lead to the birth of a second generation of PI goats. Genetic analyses indicated that establishment in the new host species may be associated with step-wise adaptations in the viral genome. Thus, goats have the potential to be a reservoir for BVDV. However, the PI goats showed growth retardation and anaemia and their survival under natural conditions remains questionable.
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Affiliation(s)
- Claudia Bachofen
- Institute of Veterinary Virology, University of Bern, Länggassstr, 122, P,O, Box 8466, CH-3001 Bern, Switzerland.
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Bovine viral diarrhea virus fetal persistent infection after immunization with a contaminated modified-live virus vaccine. Theriogenology 2013; 79:1184-95. [DOI: 10.1016/j.theriogenology.2013.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 02/16/2013] [Accepted: 02/17/2013] [Indexed: 11/20/2022]
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13
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Molecular biology of bovine viral diarrhea virus. Biologicals 2013; 41:2-7. [DOI: 10.1016/j.biologicals.2012.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 06/27/2012] [Accepted: 07/06/2012] [Indexed: 11/21/2022] Open
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Manrique JM, Calvo AY, Halac SR, Villafañe VE, Jones LR, Walter Helbling E. Effects of UV radiation on the taxonomic composition of natural bacterioplankton communities from Bahía Engaño (Patagonia, Argentina). JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 117:171-8. [DOI: 10.1016/j.jphotobiol.2012.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 08/23/2012] [Accepted: 09/27/2012] [Indexed: 10/27/2022]
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Muhsen M, Aoki H, Ikeda H, Fukusho A. Biological properties of bovine viral diarrhea virus quasispecies detected in the RK13 cell line. Arch Virol 2012. [PMID: 23178968 DOI: 10.1007/s00705-012-1538-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The rabbit kidney cell line RK13 has been reported to be contaminated with noncytopathogenic (ncp) bovine viral diarrhea virus (BVDV). Persistent infection was confirmed by demonstrating the stability of virus titers (10(4.6±0.5) TCID50/ml) and BVDV positive cells (71.9 ± 3.12 %), over six successive passages. Based on the "exaltation of Newcastle disease virus" (END) and reverse plaque formation methods, two types of ncp viruses were isolated, END-phenomenon-positive and negative. Isolates, RK13/E(+) and RK13/E(-), demonstrated (1) differing levels of reproducibility in cell cultures, (2) similar antigenicity against BVDV antisera, (3) identical 5'-UTR region nucleotide sequences, (4) four amino acid differences throughout the genomic open reading frame, and (5) better growth ability in primary rabbit cells than other laboratory strains when inoculated in parallel at an MOI of 0.01. Overall, the BVDV population in RK13 cells consists of at least two different END characteristic quasispecies that are adapted to cultures of rabbit origin, giving rise to naturally attenuated BVDV strains that can be used in vaccine development.
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Affiliation(s)
- Mahmod Muhsen
- Laboratory of Veterinary Hygiene, School of Veterinary Medicine, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo, 180-8602, Japan.
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Neill JD, Newcomer BW, Marley SD, Ridpath JF, Givens MD. Greater numbers of nucleotide substitutions are introduced into the genomic RNA of bovine viral diarrhea virus during acute infections of pregnant cattle than of non-pregnant cattle. Virol J 2012; 9:150. [PMID: 22867008 PMCID: PMC3487799 DOI: 10.1186/1743-422x-9-150] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 07/31/2012] [Indexed: 12/24/2022] Open
Abstract
Background Bovine viral diarrhea virus (BVDV) strains circulating in livestock herds show significant sequence variation. Conventional wisdom states that most sequence variation arises during acute infections in response to immune or other environmental pressures. A recent study showed that more nucleotide changes were introduced into the BVDV genomic RNA during the establishment of a single fetal persistent infection than following a series of acute infections of naïve cattle. However, it was not known if nucleotide changes were introduce when the virus crossed the placenta and infected the fetus or during the acute infection of the dam. Methods The sequence of the open reading frame (ORF) from viruses isolated from four acutely infected pregnant heifers following exposure to persistently infected (PI) calves was compared to the sequences of the virus from the progenitor PI calf and the virus from the resulting progeny PI calf to determine when genetic change was introduced. This was compared to genetic change found in viruses isolated from a pregnant PI cow and its PI calf, and in three viruses isolated from acutely infected, non-pregnant cattle exposed to PI calves. Results Most genetic changes previously identified between the progenitor and progeny PI viruses were in place in the acute phase viruses isolated from the dams six days post-exposure to the progenitor PI calf. Additionally, each progeny PI virus had two to three unique nucleotide substitutions that were introduced in crossing the placenta and infection of the fetus. The nucleotide sequence of two acute phase viruses isolated from steers exposed to PI calves revealed that six and seven nucleotide changes were introduced during the acute infection. The sequence of the BVDV-2 virus isolated from an acute infection of a PI calf (BVDV-1a) co-housed with a BVDV-2 PI calf had ten nucleotides that were different from the progenitor PI virus. Finally, twenty nucleotide changes were identified in the PI virus of a calf born to a PI dam. Conclusions These results demonstrate that nucleotide changes are introduced into the BVDV infecting pregnant cattle at rates of 2.3 to 8 fold higher then during the acute infection of non-pregnant animals.
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Affiliation(s)
- John D Neill
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, USDA, ARS, 1920 Dayton Ave, Ames, Iowa 50010, USA.
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17
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Manrique JM, Calvo AY, Jones LR. Phylogenetic analysis of Ostreococcus virus sequences from the Patagonian Coast. Virus Genes 2012; 45:316-26. [PMID: 22674355 DOI: 10.1007/s11262-012-0762-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 05/11/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Julieta M Manrique
- Division of Molecular Biology, Estación de Fotobiología Playa Unión, CC 15 (9103), Playa Unión, Rawson, Chubut, Argentina
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Spatial and temporal reconstruction of bovine viral diarrhea virus genotype 1 dispersion in Italy. INFECTION GENETICS AND EVOLUTION 2011; 12:324-31. [PMID: 22210133 DOI: 10.1016/j.meegid.2011.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 12/05/2011] [Accepted: 12/10/2011] [Indexed: 11/20/2022]
Abstract
Bovine viral diarrhea virus (BVDV) is a widespread and economically important pathogen of cattle; genetic typing of BVDV isolates distinguished two species, namely BVDV-1 and BVDV-2. BVDV-1 is the most widespread worldwide and it includes at least 11 subtypes. With the aim of clarifying the routes of circulation of BVDV-1 subtypes in an endemic area and in order to investigate the relationships between the genetic diversity of BVDV and its geographic distribution, a phylogenetic analysis of 5' untranslated region of Italian sequences was performed using a new Bayesian framework allowing the spatial-temporal reconstruction of the evolutionary dynamics of highly variable viruses. Our analyses suggested that different BVDV subtypes entered the North-Eastern part of Italy at different times within a time span between 23 and 7 years ago. The largest virus dispersion occurred between the mid 1990s and the early 2000s. A possible gravity-like dynamic of the infection, originating in larger animal population then following patterns of national commercial-flow, should be hypothesized.
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Neill JD, Newcomer BW, Marley SD, Ridpath JF, Givens MD. Genetic change in the open reading frame of bovine viral diarrhea virus is introduced more rapidly during the establishment of a single persistent infection than from multiple acute infections. Virus Res 2011; 158:140-5. [PMID: 21470568 DOI: 10.1016/j.virusres.2011.03.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 03/17/2011] [Accepted: 03/25/2011] [Indexed: 11/24/2022]
Abstract
Bovine viral diarrhea viruses (BVDV) are ubiquitous viral pathogens of cattle with a high degree of sequence diversity amongst strains circulating in livestock herds. The driving force behind change in sequence is not well established but the inaccurate replication of the genomic RNA by a viral RNA polymerase without proof-reading capabilities as well as immune pressure on immunodominant proteins are thought to play major roles. Additionally, it is not clear when the majority of changes are introduced, whether during acute infections with exposure to innate and adaptive immune responses or in establishment of persistent infections (PI) in utero. To examine which generates greater sequence diversity, two groups of viruses were compared. The first was six isolates of a single strain of BVDV-2 that were isolated over greater than a year's time. These viruses caused a series of severe acute (SA) BVD outbreaks over a large geographic area. Changes in nucleotide sequence were determined by comparison of the sequence of each strain to the six virus consensus sequence. The second group was composed of six BVDV strains isolated from PI calves whose dams were exposed to PI cattle. Changes were identified by comparison of the sequence of the progenitor PI virus to that of the progeny viruses from the single in vivo 'passage'. The open reading frames (ORF) of the six SA isolates were >99% identical at the nucleotide level with 30% of the changes being nonsynonymous changes. The amount of genetic change increased with time and distance from the original outbreak. Similarly, the PI viruses isolated from single passage PI calves had >99% identity with the progenitor virus. The number of nucleotide changes in these viruses was equal to or greater than that observed in the SA viruses. The majority of the nonsynonymous changes were found in the structural proteins, with 65% of these occurring in the immunodominant E2 protein. Antigenic mapping studies using a monoclonal antibody panel specific for the BVDV E2 protein showed no antigenic differences amongst the six SA viruses, nor between the progenitor and progeny type 1a and type 2 persistent viruses. However, antigenic differences were observed in the two type 1b progeny viruses that possessed the greatest number of amino acid changes. Two antibodies were found to have altered staining patterns. These results suggest that the establishment of a single persistent infection results in more rapid generation of genetic diversity in BVDV strains than a series of acute infections and may contribute to antigenic change in the absence of an immune response.
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Affiliation(s)
- John D Neill
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, USDA, ARS, Ames, IA, USA.
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20
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Ciulli S, Galletti E, Battilani M, Galligione V, Prosperi S. Analysis of variability and antigenic peptide prediction of E2 BVDV glycoprotein in a mucosal-disease affected animal. Vet Res Commun 2009; 33 Suppl 1:125-7. [DOI: 10.1007/s11259-009-9267-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Ojosnegros S, Agudo R, Sierra M, Briones C, Sierra S, González- López C, Domingo E, Cristina J. Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection. BMC Evol Biol 2008; 8:207. [PMID: 18637173 PMCID: PMC2515104 DOI: 10.1186/1471-2148-8-207] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Accepted: 07/17/2008] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The molecular events and evolutionary forces underlying lethal mutagenesis of virus (or virus extinction through an excess of mutations) are not well understood. Here we apply for the first time phylogenetic methods and Partition Analysis of Quasispecies (PAQ) to monitor genetic distances and intra-population structures of mutant spectra of foot-and-mouth disease virus (FMDV) quasispecies subjected to mutagenesis by base and nucleoside analogues. RESULTS Phylogenetic and PAQ analyses have revealed a highly dynamic variation of intrapopulation diversity of FMDV quasispecies. The population diversity first suffers striking expansions in the presence of mutagens and then compressions either when the presence of the mutagenic analogue was discontinued or when a mutation that decreased sensitivity to a mutagen was selected. The pattern of mutations found in the populations was in agreement with the behavior of the corresponding nucleotide analogues with FMDV in vitro. Mutations accumulated at preferred genomic sites, and dn/ds ratios indicate the operation of negative (or purifying) selection in populations subjected to mutagenesis. No evidence of unusually elevated genetic distances has been obtained for FMDV populations approaching extinction. CONCLUSION Phylogenetic and PAQ analysis provide adequate procedures to describe the evolution of viral sequences subjected to lethal mutagenesis. These methods define the changes of intra-population structure more precisely than mutation frequencies and Shannon entropies. PAQ is very sensitive to variations of intrapopulation genetic distances. Strong negative (or purifying) selection operates in FMDV populations subjected to enhanced mutagenesis. The quantifications provide evidence that extinction does not imply unusual increases of intrapopulation complexity, in support of the lethal defection model of virus extinction.
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Affiliation(s)
- Samuel Ojosnegros
- Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
| | - Rubén Agudo
- Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
| | - Macarena Sierra
- Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
| | - Carlos Briones
- Laboratorio de Evolución Molecular, Centro de Astrobiología (CSIC/INTA), Instituto Nacional de Técnica Aeroespacial, Ctra de Torrejón a Ajalvir, km 4, 28850 Torrejón de Ardoz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain
| | - Saleta Sierra
- Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
- Institute of Virology, University of Cologne, Fuerst-Pueckler Str. 56, D-50935 Cologne, Germany
| | - Claudia González- López
- Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
- MRC Laboratory for Molecular Cell Biology & Cell Biology Unit, University College London, Gower Street, London, WC1E 6BT, UK
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
- Laboratorio de Evolución Molecular, Centro de Astrobiología (CSIC/INTA), Instituto Nacional de Técnica Aeroespacial, Ctra de Torrejón a Ajalvir, km 4, 28850 Torrejón de Ardoz, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain
| | - Juan Cristina
- Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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Golemba MD, Parreño V, Jones LR. Simple procedures to obtain exogenous internal controls for use in RT-PCR detection of bovine pestiviruses. Mol Cell Probes 2008; 22:212-4. [PMID: 18395415 DOI: 10.1016/j.mcp.2007.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 12/31/2007] [Indexed: 10/22/2022]
Abstract
Pestiviruses are ubiquitous pathogens of cattle and frequent adventitious viruses in biologicals. Furthermore, it has been suggested that these agents might be related to infantile gastroenteritis and microencephaly. Since the virus is highly prevalent in fetal bovine serum, the risk of contamination is high in most laboratories. Thus, the implementation of detection methods in all laboratories is of worth. Despite continuous surveillance, these agents have been detected in cell lines, fetal bovine serum, live and inactivated animal and human vaccines and interferon for human use. In this report, DNA and RNA internal controls (ICs) which can be implemented in laboratories with minimal equipment are described. The developed standards can be added before RNA purification, allowing to monitor all steps of the protocol (viral RNA extraction, reverse transcription and cDNA amplification). It is shown that inhibitory effects that could lead to decreased sensitivity can be minimized by controlling the amount of mimic molecules added to the samples. A method to avoid the problem of DNA traces present in in vitro transcribed RNA preparations is provided.
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Affiliation(s)
- Marcelo D Golemba
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712) Castelar, Buenos Aires, Argentina
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23
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Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Vlasova A, Janies D, Jones LR, Ghedin E, Saif LJ. Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology 2007; 363:1-10. [PMID: 17434558 PMCID: PMC7103286 DOI: 10.1016/j.virol.2007.03.018] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 02/21/2007] [Accepted: 03/13/2007] [Indexed: 11/30/2022]
Abstract
The genetic diversity of 2 pairs (AH65 and AH187) of wild type bovine coronaviruses (BCoV) sequenced directly from nasal (respiratory) and rectal (enteric) swabs of two feedlot calves with respiratory and enteric symptoms [Hasoksuz, M., Sreevatsan, S., Cho, K.O., Hoet, A.E., Saif, L.J., 2002b. Molecular analysis of the S1 subunit of the spike glycoprotein of respiratory and enteric bovine coronavirus isolates. Virus Res. 84 (1-2), 101-109.]. was analyzed. Sequence analysis of the complete genomes revealed differences at 123 and 149 nucleotides (nt) throughout the entire genome between the respiratory and enteric strains for samples AH65 and AH187, respectively, indicating the presence of intra-host BCoV quasispecies. In addition, significant numbers of sequence ambiguities were found in the genomes of some BCoV-R and BCoV-E strains, suggesting intra-isolate quasispecies. The tissue culture (TC) passaged counterparts of AH65 respiratory BCoV (AH65-R-TC) and enteric BCoV (AH65-E-TC) were also sequenced after 14 and 15 passages and 1 plaque purification in human rectal tumor cells (HRT-18), respectively. Compared to the parental wild type strains, tissue culture passage generated 104 nt changes in the AH65-E-TC isolate but only 8 nt changes in the AH65-R-TC isolate. Particularly noteworthy, the majority of nucleotide changes in the AH65-E-TC isolate occurred at the identical positions as the mutations occurring in the AH65-R strain from the same animal. These data suggest that BCoV evolves through quasispecies development, and that enteric BCoV isolates are more prone to genetic changes and may mutate to resemble respiratory BCoV strains after tissue culture passage.
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Affiliation(s)
- Xinsheng Zhang
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA
| | - Mustafa Hasoksuz
- Istanbul University, Faculty of Veterinary Medicine, Department of Virology, Avcilar, 34320, Istanbul, Turkey
| | - David Spiro
- The Institute for Genomic Research (TIGR), Rockville, MD, USA
| | - Rebecca Halpin
- The Institute for Genomic Research (TIGR), Rockville, MD, USA
| | - Shiliang Wang
- The Institute for Genomic Research (TIGR), Rockville, MD, USA
| | - Anastasia Vlasova
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA
| | - Daniel Janies
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, OH, USA
| | - Leandro R. Jones
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712), Castelar, Buenos Aires, Argentina
| | - Elodie Ghedin
- The Institute for Genomic Research (TIGR), Rockville, MD, USA
| | - Linda J. Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA
- Corresponding author. Fax: +1 330 263 3677.
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24
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Sasaki Y, Kai A, Hayashi Y, Shinkai T, Noguchi Y, Hasegawa M, Sadamasu K, Mori K, Tabei Y, Nagashima M, Morozumi S, Yamamoto T. Multiple viral infections and genomic divergence among noroviruses during an outbreak of acute gastroenteritis. J Clin Microbiol 2006; 44:790-7. [PMID: 16517856 PMCID: PMC1393082 DOI: 10.1128/jcm.44.3.790-797.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An epidemic outbreak of both norovirus (NV) and astrovirus (ASV) occurred on a research ship surveying Tokyo Bay, causing acute gastroenteritis in 26 of its 37 crew members. The presence of viral pathogens in fecal specimens was analyzed, and noroviruses were identified by reverse transcription-PCR in 18 (48.6%) of these specimens. In addition, astroviruses were identified in 14 (37.8%) of the fecal samples from the affected crew members, and multiple viral infections of both NV and ASV were observed in 6 cases. The genogrouping of the NV-positive samples was then examined by dot blot hybridization, and it was determined that all of the isolates were from genogroup II (GII). No bacterial pathogens were subsequently isolated from fecal specimens. Furthermore, a variety of NV strains were identified by sequencing and single-stranded conformational polymorphism (SSCP) analyses of PCR products from the fecal samples. One recombinant NV isolate, Minato/14, was identified as a recombinant NV strain of GII/6 and GII/1. The other NV isolates from this outbreak were classified into three NV genotypes (GII/1 [Minato/10], GII/4 [Minato/33], and GII/5 [Minato/6]). Furthermore, ASVs in positive samples were determined to belong to serotypes 1 and 2 by sequencing analysis. Our findings thus indicate that coinfections with NV and ASV, including a number of NV genotypes, persisted during an outbreak of gastroenteritis in a closed environment.
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Affiliation(s)
- Yukiko Sasaki
- Division of Virology, Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Hyakunin-cho 3-24-1, Shinjyuku-ku, Tokyo 169-0073, Japan.
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25
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Jones LR, Zandomeni RO, Weber EL. A long distance RT-PCR able to amplify the Pestivirus genome. J Virol Methods 2006; 134:197-204. [PMID: 16497393 PMCID: PMC7112918 DOI: 10.1016/j.jviromet.2006.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 01/03/2006] [Accepted: 01/10/2006] [Indexed: 01/08/2023]
Abstract
A method to amplify long genomic regions (up to approximately 12.3 kb) from pestiviruses in one RT-PCR is described. The difficulty in designing conserved Pestivirus primers for the amplification of genomes from highly divergent isolates simply by means of overlapping segments is demonstrated using new bioinformatic tools. An alternative procedure consisting of optimizing the length of the genomic cDNA fragments and their subsequent amplification by polymerase chain reaction (PCR) using a limited set of specific primers is described. The amplification of long DNA fragments from a variety of sources, including genomic, mitochondrial, and viral DNAs as well as cDNA produced by reverse transcription (RT) has been achieved using this methodology, known as long distance PCR. In the case of viruses, it is necessary to obtain viral particles from infected cells prior to RT procedures. This work provides improvements in four steps of long distance RT-PCR (L-RT-PCR): (i) preparation of a viral stock, (ii) preparation of template RNA, (iii) reverse transcription and (iv) amplification of the cDNA by LD-PCR. The usefulness of L-RT-PCR is discussed in the light of current knowledge on pestivirus diversity. The genomic sequence of Singer_Arg reference strain obtained using this method is presented and characterized.
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Affiliation(s)
- Leandro R. Jones
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
| | - Rubén O. Zandomeni
- Instituto de Microbiología y Zoología Agrícola, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
| | - E. Laura Weber
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25, (1712) Castelar, Buenos Aires, Argentina
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26
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Jerzak G, Bernard KA, Kramer LD, Ebel GD. Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection. J Gen Virol 2005; 86:2175-2183. [PMID: 16033965 PMCID: PMC2440486 DOI: 10.1099/vir.0.81015-0] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrahost genetic diversity was analysed in naturally infected mosquitoes and birds to determine whether West Nile virus (WNV) exists in nature as a quasispecies and to quantify selective pressures within and between hosts. WNV was sampled from ten infected birds and ten infected mosquito pools collected on Long Island, NY, USA, during the peak of the 2003 WNV transmission season. A 1938 nt fragment comprising the 3' 1159 nt of the WNV envelope (E) coding region and the 5' 779 nt of the non-structural protein 1 (NS1) coding region was amplified and cloned and 20 clones per specimen were sequenced. Results from this analysis demonstrate that WNV infections are derived from a genetically diverse population of genomes in nature. The mean nucleotide diversity was 0.016 % within individual specimens and the mean percentage of clones that differed from the consensus sequence was 19.5 %. WNV sequences in mosquitoes were significantly more genetically diverse than WNV in birds. No host-dependent bias for particular types of mutations was observed and estimates of genetic diversity did not differ significantly between E and NS1 coding sequences. Non-consensus clones obtained from two avian specimens had highly similar genetic signatures, providing preliminary evidence that WNV genetic diversity may be maintained throughout the enzootic transmission cycle, rather than arising independently during each infection. Evidence of purifying selection was obtained from both intra- and interhost WNV populations. Combined, these data support the observation that WNV populations may be structured as a quasispecies and document strong purifying natural selection in WNV populations.
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Affiliation(s)
- Greta Jerzak
- The Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, 5668 State Farm Road, Slingerlands, NY 12159, USA
| | - Kristen A. Bernard
- The Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, 5668 State Farm Road, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, School of Public Health, The University at Albany, State University of New York, Albany, NY 12144-3456, USA
| | - Laura D. Kramer
- The Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, 5668 State Farm Road, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, School of Public Health, The University at Albany, State University of New York, Albany, NY 12144-3456, USA
| | - Gregory D. Ebel
- The Arbovirus Laboratories, Wadsworth Center, New York State Department of Health, 5668 State Farm Road, Slingerlands, NY 12159, USA
- Department of Biomedical Sciences, School of Public Health, The University at Albany, State University of New York, Albany, NY 12144-3456, USA
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27
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Bolin SR, Grooms DL. Origination and consequences of bovine viral diarrhea virus diversity. Vet Clin North Am Food Anim Pract 2004; 20:51-68. [PMID: 15062474 PMCID: PMC7119071 DOI: 10.1016/j.cvfa.2003.11.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The potential consequences of BVDV genetic and antigenic diversity are far ranging. The complexity of clinical presentations associated with BVDV likely arises from factors encoded by the virus genome. More importantly,prevention and control of BVDV may be complicated by diagnostic and immunization failure resulting from virus diversity. Evolutionary pressures will continue to drive further diversity, making control of BVDV challenging. Current and the potential for future BVDV strain diversity should be considered when designing BVDV control programs both at the individual farm and national herd level.
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Affiliation(s)
- Steven R. Bolin
- Department of Veterinary Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI 48824, USA
| | - Daniel L. Grooms
- Department of Large Animal Clinical Sciences, Michigan State University, A100 VTH, East Lansing, MI 48824, USA
- Corresponding author.
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28
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Ivancic J, Forcic D, Gulija TK, Zgorelec R, Repalust L, Baricevic M, Mesko-Prejac M, Mazuran R. Genetic characterization of a mumps virus isolate during passaging in the amniotic cavity of embryonated chicken eggs. Virus Res 2004; 99:121-9. [PMID: 14749177 DOI: 10.1016/j.virusres.2003.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aim of this study was the molecular characterization of a historical mumps isolate (an alleged individual sample). After RNA extraction and cDNA synthesis, selective nested PCR amplification with specific primers, automated DNA sequencing and RFLP analyses were performed. The relative ratios of the detected virus sequences were determined by GeneScan electrophoresis. Phylogenetic tree based on the 316 nucleotide region of the SH gene of the mumps virus was generated by the neighbor-joining method. Results obtained by the described molecular approach show: (a) there are two mumps virus variants, A and B, detected in the fourth passage of wild type virus in the amniotic cavity of embryonated chicken eggs (ECE); (b) variants A and B belong to different genotypes; (c) variants A and B differ in the HN and NP genes which code for amino acid sequences comprising immunogenic epitopes; (d) variant B contains one or more minor variants. We discuss whether the observed differences between the two variants are a consequence of natural heterogeneity or of laboratory contamination in the early passages.
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Affiliation(s)
- Jelena Ivancic
- Molecular Biomedicine Unit, Department of Research and Development, Institute of Immunology Inc., Rockefellerova 10, 10 000, Zagreb, Croatia.
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29
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Emmenegger EJ, Troyer RM, Kurath G. Characterization of the mutant spectra of a fish RNA virus within individual hosts during natural infections. Virus Res 2003; 96:15-25. [PMID: 12951262 DOI: 10.1016/s0168-1702(03)00169-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Infectious hematopoietic necrosis virus (IHNV) is an RNA virus that causes significant mortalities of salmonids in the Pacific Northwest of North America. RNA virus populations typically contain genetic variants that form a heterogeneous virus pool, referred to as a quasispecies or mutant spectrum. This study characterized the mutant spectra of IHNV populations within individual fish reared in different environmental settings by RT-PCR of genomic viral RNA and determination of partial glycoprotein gene sequences of molecular clones. The diversity of the mutant spectra from ten in vivo populations was low and the average mutation frequencies of duplicate populations did not significantly exceed the background mutation level expected from the methodology. In contrast, two in vitro populations contained variants with an identical mutational hot spot. These results indicated that the mutant spectra of natural IHNV populations is very homogeneous, and does not explain the different magnitudes of genetic diversity observed between the different IHNV genogroups. Overall the mutant frequency of IHNV within its host is one of the lowest reported for RNA viruses.
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