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Aguilera-Sepúlveda P, Llorente F, Rosenstierne MW, Bravo-Barriga D, Frontera E, Fomsgaard A, Fernández-Pinero J, Jiménez-Clavero MÁ. Detection of a new avian bornavirus in barn owl (Tyto alba) by pan-viral microarray. Vet Microbiol 2024; 289:109959. [PMID: 38134487 DOI: 10.1016/j.vetmic.2023.109959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023]
Abstract
A barn owl (Tyto alba) died with neurological signs compatible with a viral infection. After discarding other possible infections caused by circulating viruses in the area, analysis of the central nervous system using a pan-viral microarray revealed hybridization to canary bornavirus 2 (CnBV-2). Subsequent sequence analysis confirmed the presence of a virus sharing more than 83% identity with CnBV-2. Surprisingly, the new sequence corresponds to a new virus, here named Barn owl Bornavirus 1 (BoBV-1), within the Orthobornavirus serini species. Moreover, it is the first member of this species that has been detected in a non-passerine bird, indicating that Orthobornavirus serini species comprises viruses with a wider range of hosts than previously presumed. The use of this microarray has proven to be an excellent tool for viral detection in clinical samples, with capacity to detect new viral variants. This allows the diagnosis of a great range of viruses, which can cause similar disease symptoms and which identification by PCR methods might be tedious, probably unsuccessful and, in the long run, expensive. This platform is highly useful for a fast and precise viral detection, contributing to the improvement of diagnostic methods.
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Affiliation(s)
| | - Francisco Llorente
- Centro de Investigación en Sanidad Animal (CISA-INIA), CSIC, 28130 Valdeolmos, Spain
| | - Maiken Worsoe Rosenstierne
- QlifeAps, Industriparken 39-41, DK-2750 Ballerup, Denmark; Virus Research & Development Laboratory Statens Serum Institut, Copenhagen, Denmark
| | - Daniel Bravo-Barriga
- Departamento de Sanidad Animal, Grupo de Investigación en Salud Animal y Zoonosis (GISAZ), UIC Zoonosis y Enfermedades Emergentes (ENZOEM), Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Eva Frontera
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Anders Fomsgaard
- Virus Research & Development Laboratory Statens Serum Institut, Copenhagen, Denmark
| | | | - Miguel Ángel Jiménez-Clavero
- Centro de Investigación en Sanidad Animal (CISA-INIA), CSIC, 28130 Valdeolmos, Spain; CIBER of Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain.
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Onasanya AE, El-Hage C, Diaz-Méndez A, Vaz PK, Legione AR, Devlin JM, Hartley CA. Genomic diversity and natural recombination of equid gammaherpesvirus 5 isolates. Infect Genet Evol 2023; 115:105517. [PMID: 37879385 DOI: 10.1016/j.meegid.2023.105517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/09/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Equid gammaherpesvirus 5 (EHV5) is closely related to equid gammaherpesvirus 2 (EHV2). Detection of EHV5 is frequent in horse populations worldwide, but it is often without a clear and significant clinical impact. Infection in horses can often present as subclinical disease; however, it has been associated with respiratory disease, including equine multinodular pulmonary fibrosis (EMPF). Genetic heterogeneity within small regions of the EHV5 glycoprotein B (gB) sequences have been reported and multiple genotypes of this virus have been identified within individual horses, but full genome sequence data for these viruses is limited. The primary focus of this study was to assess the genomic diversity and natural recombination among EHV5 isolates. RESULTS The genome size of EHV5 prototype strain and the five EHV5 isolates cultured for this study, including four isolates from the same horse, ranged from 181,929 to 183,428 base pairs (bp), with the sizes of terminal repeat regions varying from 0 to 10 bp. The nucleotide sequence identity between the six EHV5 genomes ranged from 95.5 to 99.1%, and the estimated average nucleotide diversity between isolates was 1%. Individual genes displayed varying levels of nucleotide diversity that ranged from 0 to 19%. The analysis of nonsynonymous substitution (Ka > 0.025) revealed high diversity in eight genes. Genome analysis using RDP4 and SplitsTree programs detected evidence of past recombination events between EHV5 isolates. CONCLUSION Genomic diversity and recombination hotspots were identified among EHV5 strains. Recombination can drive genetic diversity, particularly in viruses that have a low rate of nucleotide substitutions. Therefore, the results from this study suggest that recombination is an important contributing factor to EHV5 genomic diversity. The findings from this study provide additional insights into the genetic heterogeneity of the EHV5 genome.
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Affiliation(s)
- Adepeju E Onasanya
- The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Charles El-Hage
- Centre for Equine Infectious Disease, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrés Diaz-Méndez
- The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paola K Vaz
- The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alistair R Legione
- The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joanne M Devlin
- The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Carol A Hartley
- The Asia-Pacific Centre for Animal Health, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Centre for Equine Infectious Disease, Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
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Hoffmann B, Joseph S, Patteril NAG, Caveney MR, Elizabeth SK, Muhammed R, Wernery R, Wernery U. Comparative Genome Analysis of All Nine African Horse Sickness Serotypes Isolated From Equine Fatalities in Kenya and South Africa. J Equine Vet Sci 2022; 119:104137. [PMID: 36223818 DOI: 10.1016/j.jevs.2022.104137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
African horse sickness (AHS) is a viral disease of equids, caused by a virus of the genus Orbivirus, family Reoviridae. The African horse sickness virus (AHSV) genome is made up of ten double-stranded RNA (dsRNA) segments that together code for seven structural and four nonstructural proteins. AHS is endemic in sub-Saharan countries. The efficacy and safety of inactivated AHS vaccines containing all nine serotypes, produced at the Central Veterinary Research Laboratory (CVRL) in Dubai, United Arab Emirates have been proven in the past. All nine AHSV serotypes were isolated from 102 samples collected in the last 20 years from horse fatalities in seven different area of Kenya, Africa. CVRL inactivated AHS vaccines are used in a few African countries defining the importance of this present study to compare the genome sequences of the nine AHSV serotypes isolated from horse fatalities in Kenya and nine AHSV serotypes isolated in South Africa. The hypothesized serotypes of the newly sequenced AHSV field strains from Kenya were likewise confirmed in this investigation, and they show substantial sequence homologies with recently isolated AHSV field strains.
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Affiliation(s)
- Bernd Hoffmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald - Insel Riems, Germany
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | | | | | | | - Rubeena Muhammed
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Renate Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates.
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Zhou Y, Teng Z, Chen H, Cui X, Fang F, Mou J, Jiang H, Zhang X. Virology features of a family cluster of SARS-CoV-2 infections in Shanghai, China. Biosaf Health 2021; 3:187-9. [PMID: 34095806 DOI: 10.1016/j.bsheal.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 12/02/2022] Open
Abstract
The global spread of SARS-CoV-2 is currently continuing, and the World Health Organization has announced the risk assessment of the viruses as high. In this study, we analyzed virology features of SARS-CoV-2 causing a family cluster outbreak. Among the six family members, five have been laboratory-confirmed infection of SARS-CoV-2 viruses. A total of five SARS-CoV-2 viruses have been isolated from the nasopharyngeal swabs. The complete genome of the viruses exhibited 100% nucleotide identity with each other. Only two nucleotide differences have been observed between genomes of the isolated viruses and the HCoV/Wuhan/ IVDC-HB-01/2019 strain. Therefore, SARS-CoV-2 has been confirmed as the causation of the family cluster infections.
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Ou Z, Chen Z, Zhao Y, Lu H, Liu W, Li W, Ren P, Geng C, Xiao M, Hu G, Wu D, Wang X, Liu N, Zhu S, Lu L, Li J. Genetic signatures for lineage/sublineage classification of HPV16, 18, 52 and 58 variants. Virology 2021; 553:62-9. [PMID: 33238224 DOI: 10.1016/j.virol.2020.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 11/20/2022]
Abstract
Increasing evidences indicate that high-risk HPV variants are heterogeneous in carcinogenicity and ethnic dispersion. In this work, we identified genetic signatures for convenient determination of lineage/sublineage of HPV16, 18, 52 and 58 variants. Using publicly available genomes, we found that E2 of HPV16, L2 of HPV18, L1 and LCR of HPV52, and L2, LCR and E1 of HPV58 contain the proper genetic signature for lineage/sublineage classification. Sets of hierarchical signature nucleotide positions were further confirmed for high accuracy (>95%) by classifying HPV genomes obtained from Chinese females, which included 117 HPV16 variants, 48 HPV18 variants, 117 HPV52 variants and 89 HPV58 variants. The circulation of HPV variants posing higher cancer risk in Eastern China, such as HPV16 A4 and HPV58 A3, calls for continuous surveillance in this region. The marker genes and signature nucleotide positions may facilitate cost-effective diagnostic detections of HPV variants in clinical settings.
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King J, Harder T, Beer M, Pohlmann A. Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses. BMC Infect Dis 2020; 20:648. [PMID: 32883215 PMCID: PMC7468549 DOI: 10.1186/s12879-020-05367-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Due to the frequent reassortment and zoonotic potential of influenza A viruses, rapid gain of sequence information is crucial. Alongside established next-generation sequencing protocols, the MinION sequencing device (Oxford Nanopore Technologies) has become a serious competitor for routine whole-genome sequencing. Here, we established a novel, rapid and high-throughput MinION multiplexing workflow based on a universal RT-PCR. METHODS Twelve representative influenza A virus samples of multiple subtypes were universally amplified in a one-step RT-PCR and subsequently sequenced on the MinION instrument in conjunction with a barcoding library preparation kit from the rapid family and the MinIT performing live base-calling. The identical PCR products were sequenced on an IonTorrent platform and, after final consensus assembly, all data was compared for validation. To prove the practicability of the MinION-MinIT method in human and veterinary diagnostics, we sequenced recent and historical influenza strains for further benchmarking. RESULTS The MinION-MinIT combination generated over two million reads for twelve samples in a six-hour sequencing run, from which a total of 72% classified as quality screened, trimmed and mapped influenza reads to produce full genome sequences. Identities between the datasets of > 99.9% were achieved, with 100% coverage of all segments alongside a sufficient confidence and 4492fold mean depth. From RNA extraction to finished sequences, only 14 h were required. CONCLUSIONS Overall, we developed and validated a novel and rapid multiplex workflow for influenza A virus sequencing. This protocol suits both clinical and academic settings, aiding in real time diagnostics and passive surveillance.
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Affiliation(s)
- Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany.
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Hebberecht L, Mortier V, Dauwe K, Schauvliege M, Staelens D, Demecheleer E, Stoffels K, Vanroye F, Delforge ML, Vancutsem E, Dessilly G, Vaira D, Van Laethem K, Verhofstede C. High frequency of new recombinant forms in HIV-1 transmission networks demonstrated by full genome sequencing. Infect Genet Evol 2020; 84:104365. [PMID: 32417307 DOI: 10.1016/j.meegid.2020.104365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/22/2022]
Abstract
The HIV-1 epidemic in Belgium is primarily driven by MSM. In this patient population subtype B predominates but an increasing presence of non-B subtypes has been reported. We aimed to define to what extent the increasing subtype heterogeneity in a high at risk population induces the formation and spread of new recombinant forms. The study focused on transmission networks that reflect the local transmission to an important extent. One hundred and five HIV-1 transmission clusters were identified after phylogenetic analysis of 2849 HIV-1 pol sequences generated for the purpose of baseline drug resistance testing between 2013 and 2017. Of these 105 clusters, 62 extended in size during the last two years and were therefore considered as representing ongoing transmission. These 62 clusters included 774 patients in total. From each cluster between 1 and 3 representative patients were selected for near full-length viral genome sequencing. In total, the full genome sequence of 101 patients was generated. Indications for the presence of a new recombinant form were found for 10 clusters. These 10 clusters represented 105 patients or 13.6% of the patients covered by the study. The findings clearly show that new recombinant strains highly contribute to local transmission, even in an epidemic that is largely MSM and subtype B driven. This is an evolution that needs to be monitored as reshuffling of genome fragments through recombination may influence the transmissibility of the virus and the pathology of the infection. In addition, important changes in the sequence of the viral genome may challenge the performance of tests used for diagnosis, patient monitoring and drug resistance analysis.
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Leyson C, Youk SS, Smith D, Dimitrov K, Lee DH, Larsen LE, Swayne DE, Pantin-Jackwood MJ. Pathogenicity and genomic changes of a 2016 European H5N8 highly pathogenic avian influenza virus (clade 2.3.4.4) in experimentally infected mallards and chickens. Virology 2019; 537:172-85. [PMID: 31493656 DOI: 10.1016/j.virol.2019.08.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
Abstract
Highly pathogenic avian influenza H5N8 clade 2.3.4.4 virus caused outbreaks in poultry and unusually high mortality in wild birds in 2016-2017. The pathobiology of one of these viruses was examined in mallards and chickens. High mortality and transmission to direct contacts were observed in mallards inoculated with medium and high doses of the virus. However, in chickens, high mortality occurred only when birds are given the high virus dose and no transmission was observed, indicating that the virus was better adapted to mallards. In comparison with the virus inoculum, viral sequences obtained from the chickens had a higher number of nucleotide changes but lower intra-host genomic diversity than viral sequences obtained from the mallards. These observations are consistent with population bottlenecks occurring when viruses infect and replicate in a host that it is not well adapted to. Whether these observations apply to influenza viruses in general remains to be determined.
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De Sabato L, Lelli D, Faccin F, Canziani S, Di Bartolo I, Vaccari G, Moreno A. Full genome characterization of two novel Alpha-coronavirus species from Italian bats. Virus Res 2018; 260:60-66. [PMID: 30447246 PMCID: PMC7114869 DOI: 10.1016/j.virusres.2018.11.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/07/2018] [Accepted: 11/13/2018] [Indexed: 12/27/2022]
Abstract
Coronaviruses (CoVs) have been detected worldwide in several bat species, which are considered the main reservoir. The attention to the high diversity of CoVs hosted by bats has increased during the last decade due to the high number of human infections caused by two zoonotic Beta-CoVs, SARS-CoV and MERS-CoV, that cause several respiratory diseases. Among coronaviruses, two Alpha-CoV strains (HuCoV-229E and HuCoV-NL63) cause mild respiratory disease that can change to severe disease in children, elderly and individuals affected by illnesses. Phylogenetic analysis conducted on bat Alpha-CoV strains revealed their evolutive correlation to human strains, suggesting their origin in bats. The genome of CoVs is characterized by a high frequency of mutations and recombination events, increasing their ability to switch hosts and their zoonotic potential. In this study, three strains of Alpha-CoV genera detected in Italian bats (Pipistrellus kuhlii) were fully sequenced by Next Generation Sequencing (NGS) and characterized. The complete genome analysis showed the correlation of the Italians strains with a Chinese strain detected in 2013 and, based on CoV molecular species demarcation, two new Alpha-CoV species were established. The analysis of a fragment of the RNA-dependent RNA polymerase (RdRp) showed the correlation of the Italian strains with CoVs that was only detected in the bat Pipistrellus genera (Pipistrellus kuhlii and Pipistrellus Pipistrellus) in European countries.
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Affiliation(s)
- Luca De Sabato
- Department of Sciences, University Roma Tre, Viale Guglielmo Marconi 446, 00146, Rome, Italy; Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Davide Lelli
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
| | - Francesca Faccin
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
| | - Sabrina Canziani
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Ana Moreno
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
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Moreno A, Lelli D, de Sabato L, Zaccaria G, Boni A, Sozzi E, Prosperi A, Lavazza A, Cella E, Castrucci MR, Ciccozzi M, Vaccari G. Detection and full genome characterization of two beta CoV viruses related to Middle East respiratory syndrome from bats in Italy. Virol J 2017; 14:239. [PMID: 29258555 PMCID: PMC5735805 DOI: 10.1186/s12985-017-0907-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/06/2017] [Indexed: 01/15/2023] Open
Abstract
Background Middle East respiratory syndrome coronavirus (MERS-CoV), which belongs to beta group of coronavirus, can infect multiple host species and causes severe diseases in humans. Multiple surveillance and phylogenetic studies suggest a bat origin. In this study, we describe the detection and full genome characterization of two CoVs closely related to MERS-CoV from two Italian bats, Pipistrellus kuhlii and Hypsugo savii. Methods Pool of viscera were tested by a pan-coronavirus RT-PCR. Virus isolation was attempted by inoculation in different cell lines. Full genome sequencing was performed using the Ion Torrent platform and phylogenetic trees were performed using IQtree software. Similarity plots of CoV clade c genomes were generated by using SSE v1.2. The three dimensional macromolecular structure (3DMMS) of the receptor binding domain (RBD) in the S protein was predicted by sequence-homology method using the protein data bank (PDB). Results Both samples resulted positive to the pan-coronavirus RT-PCR (IT-batCoVs) and their genome organization showed identical pattern of MERS CoV. Phylogenetic analysis showed a monophyletic group placed in the Beta2c clade formed by MERS-CoV sequences originating from humans and camels and bat-related sequences from Africa, Italy and China. The comparison of the secondary and 3DMMS of the RBD of IT-batCoVs with MERS, HKU4 and HKU5 bat sequences showed two aa deletions located in a region corresponding to the external subdomain of MERS-RBD in IT-batCoV and HKU5 RBDs. Conclusions This study reported two beta CoVs closely related to MERS that were obtained from two bats belonging to two commonly recorded species in Italy (P. kuhlii and H. savii). The analysis of the RBD showed similar structure in IT-batCoVs and HKU5 respect to HKU4 sequences. Since the RBD domain of HKU4 but not HKU5 can bind to the human DPP4 receptor for MERS-CoV, it is possible to suggest also for IT-batCoVs the absence of DPP4-binding potential. More surveillance studies are needed to better investigate the potential intermediate hosts that may play a role in the interspecies transmission of known and currently unknown coronaviruses with particular attention to the S protein and the receptor specificity and binding affinity.
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Affiliation(s)
- Ana Moreno
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy.
| | - Davide Lelli
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
| | - Luca de Sabato
- Department of Food Safety, Istituto Superiore di Sanità. Nutrition and Veterinary Public Health, Viale Regina Elena 299, 00161, Rome, Italy.,Dept. of Sciences, University Roma Tre, Viale Guglielmo Marconi 446, 00146, Rome, Italy
| | - Guendalina Zaccaria
- Department of Food Safety, Istituto Superiore di Sanità. Nutrition and Veterinary Public Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Arianna Boni
- Department of Food Safety, Istituto Superiore di Sanità. Nutrition and Veterinary Public Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Enrica Sozzi
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
| | - Alice Prosperi
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
| | - Antonio Lavazza
- Department of Virology, Istituto Zooprofilattico Sperimentale Lombardia ed Emilia Romagna, Via Antonio Bianchi 9, 25124, Brescia, Italy
| | - Eleonora Cella
- University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Maria Rita Castrucci
- Department of Food Safety, Istituto Superiore di Sanità. Nutrition and Veterinary Public Health, Viale Regina Elena 299, 00161, Rome, Italy
| | - Massimo Ciccozzi
- University Campus Bio-Medico of Rome, Via Álvaro del Portillo, 21, 00128, Rome, Italy
| | - Gabriele Vaccari
- Department of Food Safety, Istituto Superiore di Sanità. Nutrition and Veterinary Public Health, Viale Regina Elena 299, 00161, Rome, Italy
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Doan YH, Haga K, Fujimoto A, Fujii Y, Takai-Todaka R, Oka T, Kimura H, Yoshizumi S, Shigemoto N, Okamoto-Nakagawa R, Shirabe K, Shinomiya H, Sakon N, Katayama K. Genetic analysis of human rotavirus C: The appearance of Indian-Bangladeshi strain in Far East Asian countries. Infect Genet Evol 2016; 41:160-173. [PMID: 27071530 DOI: 10.1016/j.meegid.2016.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/17/2016] [Accepted: 03/25/2016] [Indexed: 11/30/2022]
Abstract
Rotaviruses C (RVCs) circulate worldwide as an enteric pathogen in both humans and animals. Most studies of their genetic diversity focus on the VP7 and VP4 genes, but the complete genomes of 18 human RVCs have been described in independent studies. The genetic background of the Far East Asian RVCs is different than other human RVCs that were found in India and Bangladesh. Recently, a RVC detected in 2010 in South Korea had genetic background similar to the Indian-Bangladeshi RVCs. This study was undertaken to determine the whole genome of eight Japanese RVCs detected in 2005-2012, and to compare them with other human and animal global RVCs to better understand the genetic background of contemporary Far East Asian RVC. By phylogenetic analysis, the human RVCs appeared to be distinct from animal RVCs. Among human RVCs, three lineage constellations had prolonged circulation. The genetic background of the Far East Asian RVC was distinguished from Indian-Bangladeshi RVC as reported earlier. However, we found one Japanese RVC in 2012 that carried the genetic background of Indian-Bangladeshi RVC, whereas the remaining seven Japanese RVCs carried the typical genetic background of Far East Asian RVC. This is the first report of the Indian-Bangladeshi RVC in Japan. With that observation and the reassortment event of human RVCs in Hungary, our study indicates that the RVCs are spreading from one region to another.
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Affiliation(s)
- Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Fujimoto
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Takai-Todaka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | | | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, Ehime, Japan
| | - Naomi Sakon
- Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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12
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De Grazia S, Giammanco GM, Dóró R, Bonura F, Marton S, Cascio A, Martella V, Bányai K. Identification of a multi-reassortant G12P[9] rotavirus with novel VP1, VP2, VP3 and NSP2 genotypes in a child with acute gastroenteritis. Infect Genet Evol 2015. [PMID: 26205691 DOI: 10.1016/j.meegid.2015.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The G12 rotavirus genotype is globally emerging to cause severe gastroenteritis in children. Common G12 rotaviruses have either a Wa-like or DS-1-like genome constellation, while some G12 strains may have unusual genome composition. In this study, we determined the full-genome sequence of a G12P[9] strain (ME848/12) detected in a child hospitalized with acute gastroenteritis in Italy in 2012. Strain ME848/12 showed a complex genetic constellation (G12-P[9]-I17-R12-C12-M11-A12-N12-T7-E6-H2), likely derived from multiple reassortment events, with the VP1, VP2, VP3 and NSP2 genes being established as novel genotypes R12, C12, M11 and N12, respectively. Gathering sequence data on human and animal rotaviruses is important to trace the complex evolutionary history of atypical RVAs.
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Affiliation(s)
- Simona De Grazia
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Giovanni M Giammanco
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Renáta Dóró
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Floriana Bonura
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Szilvia Marton
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Antonio Cascio
- Department of Human Pathology, University of Messina, Messina, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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13
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Freuling CM, Binger T, Beer M, Adu-Sarkodie Y, Schatz J, Fischer M, Hanke D, Hoffmann B, Höper D, Mettenleiter TC, Oppong SK, Drosten C, Müller T. Lagos bat virus transmission in an Eidolon helvum bat colony, Ghana. Virus Res 2015; 210:42-5. [PMID: 26191622 DOI: 10.1016/j.virusres.2015.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 11/19/2022]
Abstract
A brain sample of a straw-coloured fruit bat (Eidolon helvum) from Ghana without evident signs of disease tested positive by generic Lyssavirus RT-PCR and direct antigen staining. Sequence analysis confirmed the presence of a Lagos bat virus belonging to phylogenetic lineage A. Virus neutralization tests using the isolate with sera from the same group of bats yielded neutralizing antibodies in 74% of 567 animals. No cross-neutralization was observed against a different Lagos bat virus (lineage B).
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Affiliation(s)
- Conrad M Freuling
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany.
| | - Tabea Binger
- Institute of Virology, University of Bonn and German Centre for Infection Research, Bonn, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Germany
| | - Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Juliane Schatz
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Melina Fischer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Germany
| | - Dennis Hanke
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Germany
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Germany
| | - Thomas C Mettenleiter
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Samual K Oppong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Christian Drosten
- Institute of Virology, University of Bonn and German Centre for Infection Research, Bonn, Germany
| | - Thomas Müller
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
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14
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Deng YM, Spirason N, Iannello P, Jelley L, Lau H, Barr IG. A simplified Sanger sequencing method for full genome sequencing of multiple subtypes of human influenza A viruses. J Clin Virol 2015; 68:43-8. [PMID: 26071334 DOI: 10.1016/j.jcv.2015.04.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/20/2015] [Accepted: 04/25/2015] [Indexed: 01/31/2023]
Abstract
BACKGROUND Full genome sequencing of influenza A viruses (IAV), including those that arise from annual influenza epidemics, is undertaken to determine if reassorting has occurred or if other pathogenic traits are present. Traditionally IAV sequencing has been biased toward the major surface glycoproteins haemagglutinin and neuraminidase, while the internal genes are often ignored. Despite the development of next generation sequencing (NGS), many laboratories are still reliant on conventional Sanger sequencing to sequence IAV. OBJECTIVES To develop a minimal and robust set of primers for Sanger sequencing of the full genome of IAV currently circulating in humans. STUDY DESIGN A set of 13 primer pairs was designed that enabled amplification of the six internal genes of multiple human IAV subtypes including the recent avian influenza A(H7N9) virus from China. Specific primers were designed to amplify the HA and NA genes of each IAV subtype of interest. Each of the primers also incorporated a binding site at its 5'-end for either a forward or reverse M13 primer, such that only two M13 primers were required for all subsequent sequencing reactions. RESULTS This minimal set of primers was suitable for sequencing the six internal genes of all currently circulating human seasonal influenza A subtypes as well as the avian A(H7N9) viruses that have infected humans in China. CONCLUSIONS This streamlined Sanger sequencing protocol could be used to generate full genome sequence data more rapidly and easily than existing influenza genome sequencing protocols.
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Affiliation(s)
- Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.
| | - Natalie Spirason
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Pina Iannello
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Lauren Jelley
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Hilda Lau
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, VIDRL, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia; School of Applied and Biomedical Sciences, Federation University, Churchill, Victoria 3842, Australia
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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.
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16
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Kot W, Vogensen FK, Sørensen SJ, Hansen LH. DPS - a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque. J Virol Methods 2013; 196:152-6. [PMID: 24239631 DOI: 10.1016/j.jviromet.2013.10.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/25/2013] [Accepted: 10/29/2013] [Indexed: 01/21/2023]
Abstract
Bacteriophages (phages) coexist with bacteria in all environments and influence microbial diversity, evolution and industrial production processes. As a result of this major impact of phages on microbes, tools that allow rapid characterization of phages are needed. Today, one of the most powerful methods for characterization of phages is determination of the whole genome using high throughput sequencing approaches. Here a direct plaque sequencing (DPS) is described, which is a rapid method that allows easy full genome sequencing of DNA-containing phages using the Nextera XT™ kit. A combination of host-DNA removal followed by purification and concentration of the viral DNA, allowed the construction of Illumina-compatible sequencing libraries using the Nextera™ XT technology directly from single phage plaques without any whole genome amplification step. This method was tested on three Caudovirales phages; ϕ29 Podoviridae, P113g Siphoviridae and T4 Myovirdae, which are representative of >96% of all known phages, and were sequenced using the Illumina MiSeq platform. Successful de novo assembly of the viral genomes was possible.
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Affiliation(s)
- Witold Kot
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark.
| | - Finn K Vogensen
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
| | - Søren J Sørensen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark
| | - Lars H Hansen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark; Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, Denmark
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17
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Kvisgaard LK, Hjulsager CK, Fahnøe U, Breum SØ, Ait-Ali T, Larsen LE. A fast and robust method for full genome sequencing of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Type 1 and Type 2. J Virol Methods 2013; 193:697-705. [PMID: 23891870 DOI: 10.1016/j.jviromet.2013.07.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/03/2013] [Accepted: 07/12/2013] [Indexed: 11/21/2022]
Abstract
PRRSV is a positive-sense RNA virus with a high degree of genetic variability among isolates. For diagnostic sensitivity and vaccine design it is essential to monitor PRRSV genetic diversity. However, to date only a few full genome sequences of PRRSV isolates have been made publicly available. In the present study, fast and robust methods for long range RT-PCR amplification and subsequent next generation sequencing (NGS) were developed and validated on nine Type 1 and nine Type 2 PRRSV viruses. The methods generated robust and reliable sequences both on primary material and cell culture adapted viruses and the protocols performed well on all three NGS platforms tested (Roche 454 FLX, Illumina HiSeq2000, and Ion Torrent PGM™ Sequencer). These methods will greatly facilitate the generation of more full genome PRRSV sequences globally.
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