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Kuczera K, Orłowska A, Smreczak M, Frant M, Trębas P, Rola J. Prevalence of Astroviruses in Different Animal Species in Poland. Viruses 2024; 16:80. [PMID: 38257780 PMCID: PMC10819871 DOI: 10.3390/v16010080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Astroviruses (AstVs) are small RNA viruses characterized by a high mutation rate, the ability to recombine, and interspecies transmission, which allows them to infect a multitude of hosts including humans, companion animals, and farmed animals as well as wildlife. AstVs are stable in the environment, and their transmission is usually through the fecal-oral route or via contaminated water and food. Although direct zoonotic transmission was not confirmed, interspecies transmission events have occurred or have been indicated to occur in the past between wild and domestic animals and humans. They cause large economic losses, mainly in the poultry sector, due to gastroenteritis and mortality. In young children, they are the second most common cause of diarrhea. This study involved 166 intestine samples and pools of spleen, lymph node, and kidney samples collected from 352 wild animals, 52 pigs, and 31 companion animals. Astroviruses were detected in the intestine samples and were separately detected in pools of tissue samples prepared for individual animals using a heminested RT-PCR protocol. Amplicons were subjected to Sanger sequencing, and a phylogenetic analysis of 320 nt RNA-dependent RNA polymerase (RdRp) fragments referring to known nt sequences of astroviruses was performed. Astroviral RNA was detected in the intestine samples and/or tissue pools of red foxes (nine positive intestines and six positive tissue pools), rats (two positive intestines and three positive tissue pools), a cat (one AstV detected in an intestine sample), pigs (eight positive tissue pools), and wild boars (two positive pools of spleens, kidneys, and lymph nodes). No astroviral RNA was detected in wild mustelids, dogs, or other small wild animals including rodents. A phylogenetic analysis revealed that the astroviruses detected during this study were mostly host-specific, such as porcine, canine, and rat astroviruses that were highly homologous to the sequences of reference strains. In one of two wild boars, an AstV distinct to porcine species was found with the highest nt identity to Avastroviruses, i.e., turkey astroviruses, which suggests potential cross-species transmission of the virus, as previously described. Here, we present the first detection of astroviruses in the population of wild animals, companion animals, and pigs in Poland, confirming that astroviruses are frequent pathogens circulating in animals in the field. Our study also suggests potential cross-species transmission of Avaastrovirus to wild boars; however, further molecular characterization is needed.
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Affiliation(s)
- Konrad Kuczera
- Voivodship Veterinary Inspectorate Katowice, ul. Brynowska 25a, 40-585 Katowice, Poland;
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Marcin Smreczak
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Maciej Frant
- Department of Swine Diseases, National Veterinary Research Institute, 24-100 Puławy, Poland;
| | - Paweł Trębas
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (P.T.); (J.R.)
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Pacini MI, Mazzei M, Sgorbini M, D’Alfonso R, Papini RA. A One-Year Retrospective Analysis of Viral and Parasitological Agents in Wildlife Animals Admitted to a First Aid Hospital. Animals (Basel) 2023; 13:ani13050931. [PMID: 36899788 PMCID: PMC10000059 DOI: 10.3390/ani13050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
This study aimed to provide information on the presence and frequency of viral and parasitic agents in wildlife presented to a Veterinary Teaching Hospital in 2020-2021. Serum and faecal samples were collected from 50 rescued animals (roe deer, fallow deer, foxes, badgers, pine martens, and porcupines) and examined by serological, molecular, and parasitological techniques. Transtracheal wash (TTW) was also collected post-mortem from roe deer. Overall, the results of the different techniques showed infections with the following viral and parasitic agents: Bovine Viral Diarrhea Virus, Small Ruminant Lentiviruses, Kobuvirus, Astrovirus, Canine Adenovirus 1, Bopivirus, gastrointestinal strongyles, Capillaria, Ancylostomatidae, Toxocara canis, Trichuris vulpis, Hymenolepis, Strongyloides, Eimeria, Isospora, Dictyocaulus, Angiostrongylus vasorum, Crenosoma, Dirofilaria immitis, Neospora caninum, Giardia duodenalis, and Cryptosporidium. Sequencing (Tpi locus) identified G. duodenalis sub-assemblages AI and BIV in one roe deer and one porcupine, respectively. Adult lungworms collected from the TTW were identified as Dictyocaulus capreolus (COX1 gene). This is the first molecular identification of G. duodenalis sub-assemblage AI and D. capreolus in roe deer in Italy. These results show a wide presence of pathogens in wild populations and provide an overview of environmental health surveillance.
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Affiliation(s)
- Maria Irene Pacini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
- Correspondence:
| | - Maurizio Mazzei
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Micaela Sgorbini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Rossella D’Alfonso
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Roberto Amerigo Papini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
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Sarchese V, Fruci P, Palombieri A, Di Profio F, Robetto S, Ercolini C, Orusa R, Marsilio F, Martella V, Di Martino B. Molecular Identification and Characterization of a Genotype 3 Hepatitis E Virus (HEV) Strain Detected in a Wolf Faecal Sample, Italy. Animals (Basel) 2021; 11:ani11123465. [PMID: 34944242 PMCID: PMC8698176 DOI: 10.3390/ani11123465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 12/27/2022] Open
Abstract
Hepatitis E virus (HEV) infection is a major health problem worldwide. In developed countries, zoonotic transmission of HEV genotypes (Gt) 3 and 4 is caused by the ingestion of raw or undercooked meat of infected pigs and wild boars, the main reservoirs of HEV. However, additional animals may harbour HEV or HEV-related strains, including carnivores. In this study, we investigated the molecular epidemiology of orthohepeviruses in wild canids by screening a total of 136 archival faecal samples, collected from wolves (42) and red foxes (94) in Northwestern Italy. Orthohepevirus RNA was identified in a faecal specimen, collected from a wolf carcass in the province of La Spezia (Liguria Region, Italy). The nearly full-length (7212 nucleotides) genome of the strain HEV/81236/Wolf/2019/ITA (GenBank accession no. MZ463196) was determined by combining a sequence-independent single-primer amplification (SISPA) approach with the Oxford Nanopore Technologies sequencing platform. Upon phylogenetic analysis, the HEV detected in wolf was segregated into clade HEV-3.1, displaying the highest nucleotide (nt) identity (89.0-93.3%) to Gt3 strains belonging to subtype c. Interestingly, the wolf faecal sample also contained porcine astrovirus sequences, endorsing the hypothesis of a dietary origin of the HEV strain due to preying habits.
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Affiliation(s)
- Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (V.S.); (P.F.); (A.P.); (F.D.P.); (F.M.)
| | - Paola Fruci
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (V.S.); (P.F.); (A.P.); (F.D.P.); (F.M.)
| | - Andrea Palombieri
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (V.S.); (P.F.); (A.P.); (F.D.P.); (F.M.)
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (V.S.); (P.F.); (A.P.); (F.D.P.); (F.M.)
| | - Serena Robetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), 11020 Aosta, Italy; (S.R.); (R.O.)
| | - Carlo Ercolini
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, SC Liguria e Portualità Marittima, 19100 La Spezia, Italy;
| | - Riccardo Orusa
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), 11020 Aosta, Italy; (S.R.); (R.O.)
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (V.S.); (P.F.); (A.P.); (F.D.P.); (F.M.)
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, 70121 Valenzano, Italy;
| | - Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy; (V.S.); (P.F.); (A.P.); (F.D.P.); (F.M.)
- Correspondence:
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Epidemiological investigation and genetic characterization of porcine astrovirus genotypes 2 and 5 in Yunnan province, China. Arch Virol 2021; 167:355-366. [PMID: 34839421 PMCID: PMC8627673 DOI: 10.1007/s00705-021-05311-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/10/2021] [Indexed: 01/25/2023]
Abstract
Astroviruses (AstVs) are among the most important viruses causing diarrhea in human infants and many animals, posing a threat to public health safety and a burden on the economy. Five porcine AstV (PAstV) genotypes have been identified in various countries, including China. However, the epidemiology of PAstV in Yunnan province, China, remains unknown. In this study, 489 fecal samples from pigs in all 16 prefectures/cities of Yunnan were collected between April and August of 2020 for epidemiological investigation. The total infection rate of PAstV-2 or PAstV-5 was 39.9%, with suckling piglets having the highest infection rate (62.3%). The ORF2 genes of seven PAstV-2 and 10 PAstV-5 isolates were sequenced and phylogenetically analyzed. In addition to coinfections with PAstV-2 and PAstV-5, coinfections of PAstV with other diarrhea-inducing viruses (e.g., porcine bocavirus) were also discovered. A comparison of ORF2-encoded capsid protein sequences revealed that there were multiple insertions and deletions in the seven Yunnan PAstV-2 sequences, while point mutations, but no deletions or insertions, were found in the 10 Yunnan PAstV-5 sequences, which were very similar to the reference sequences. This is the first epidemiological investigation and genetic characterization of PAstV-2 and PAstV-5 in Yunnan province, China, demonstrating the current PAstV infection situation in Yunnan.
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Three Novel Avastroviruses Identified in Dead Wild Crows. Virol Sin 2021; 36:1673-1677. [PMID: 34460065 DOI: 10.1007/s12250-021-00416-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/27/2021] [Indexed: 10/20/2022] Open
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Phylogenetic analysis of kobuviruses and astroviruses from Korean wild boars: 2016-2018. Arch Virol 2021; 166:2591-2596. [PMID: 34244861 DOI: 10.1007/s00705-021-05164-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 10/20/2022]
Abstract
Between 2016 and 2018, the prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in Korean wild boars (n = 845) was 28.0% and 10.7%, respectively. Coinfection by both viruses was detected in 5.1% of boars. Phylogenetic analysis revealed that 134 PKoV isolates belonged to diverse lineages within the species Aichivirus C; however, one strain (WKoV16CN-8627) clustered with bovine kobuvirus (Aichivirus B). Forty-seven PAstVs belonged to lineage PAstV4, and only one strain (WAst17JN-10931) was a novel addition to lineage PAstV2. The two viruses were more prevalent in boars weighing ≤ 60 kg than in boars weighing > 61 kg.
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Amimo JO, Machuka EM, Abworo EO, Vlasova AN, Pelle R. Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms. Viruses 2020; 12:v12111262. [PMID: 33167568 PMCID: PMC7694451 DOI: 10.3390/v12111262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.
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Affiliation(s)
- Joshua O. Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O. Box 29053, Nairobi 00625, Kenya
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, 1168 Madison Avenue, Wooster, OH 44961, USA;
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
- Correspondence:
| | - Eunice M. Machuka
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
| | - Edward O. Abworo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, 1168 Madison Avenue, Wooster, OH 44961, USA;
| | - Roger Pelle
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
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Van Borm S, Vanneste K, Fu Q, Maes D, Schoos A, Vallaey E, Vandenbussche F. Increased viral read counts and metagenomic full genome characterization of porcine astrovirus 4 and Posavirus 1 in sows in a swine farm with unexplained neonatal piglet diarrhea. Virus Genes 2020; 56:696-704. [PMID: 32880793 DOI: 10.1007/s11262-020-01791-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022]
Abstract
Neonatal diarrhea in piglets may cause major losses in affected pig herds. The present study used random high-throughput RNA sequencing (metagenomic next generation sequencing, mNGS) to investigate the virome of sows from a farm with persistent neonatal piglet diarrhea in comparison to two control farms without diarrhea problems. A variety of known swine gastrointestinal viruses was detected in the control farms as well as in the problem farm (Mamastrovirus, Enterovirus, Picobirnavirus, Posavirus 1, Kobuvirus, Proprismacovirus). A substantial increase in normalized viral read counts was observed in the affected farm compared to the control farms. The increase was attributable to a single viral species in each of the sampled sows (porcine astrovirus 4 and Posavirus 1). The complete genomes of a porcine astrovirus 4 and two co-infecting Posavirus 1 were de novo assembled and characterized. The 6734 nt single-stranded RNA genome of porcine astrovirus 4 (PoAstV-4) strain Belgium/2019 contains three overlapping open reading frames (nonstructural protein 1ab, nonstructural protein 1a, capsid protein). Posavirus 1 strains Belgium/01/2019 and Belgium/02/2019 have a 9814 nt single-stranded positive-sense RNA genome encoding a single open reading frame (polyprotein precursor) containing the five expected Picornavirales-conserved protein domains. The study highlights the potential of mNGS workflows to study unexplained neonatal diarrhea in piglets and contributes to the scarce availability of both PoAstV-4 and Posavirus-1 whole genome sequences from Western Europe.
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Affiliation(s)
- Steven Van Borm
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium.
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Qiang Fu
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Dominiek Maes
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Alexandra Schoos
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
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Qin Y, Fang Q, Li X, Li F, Liu H, Wei Z, Ouyang K, Chen Y, Huang W. Molecular epidemiology and viremia of porcine astrovirus in pigs from Guangxi province of China. BMC Vet Res 2019; 15:471. [PMID: 31881886 PMCID: PMC6935060 DOI: 10.1186/s12917-019-2217-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 12/19/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Porcine astroviruses (PAstVs) are common in pigs worldwide. There are five distinct lineages with each lineage representing a different ancestral origin. Recently, multiple reports have demonstrated the evidence of extra-intestinal infection of PAstVs, but little is known about viremia. RESULTS In this study, a total of 532 fecal samples and 120 serum samples from healthy pigs were collected and tested from 2013 to 2015 in Guangxi province, China; of these 300/532 (56.4%) and 7/120 (5.8%) of fecal samples tested positive for PAstVs, respectively. Our study revealed that there was wide genetic diversity and high prevalence of the virus in the pig population. All five of the known PAstVs genotypes (1-5) prevailed in the pig population of Guangxi province and were distributed in all age groups of pigs, from suckling piglets to sows, with PAstV2 (47.7%), PAstV1 (26.2%) and PAstV5 (21.5%) seen predominantly. Phylogenetic analysis of partial ORF1b and partial capsid sequences from fecal and serum samples revealed that they were divided into the five lineages. Among these genotypes, based on partial ORF2 genes sequencing 23 strains were grouped as PAstV1, including 6 serum-derived strains, and were regarded as the causative agents of viremia in pigs. CONCLUSIONS Due to the information regarding the types of PAstV in blood is limit. This is the first report for the presence of PAstV1 in blood and PAstV3 in the feces of nursery pigs of China. This study provides a reference for understanding the prevalence and genetic evolution of PAstVs in pigs in Guangxi province, China. It also provides a new perspective for understanding of the extra-intestinal infection of PAstVs in pigs.
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Affiliation(s)
- Yifeng Qin
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Qingli Fang
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Xunjie Li
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Fakai Li
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Huan Liu
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Zuzhang Wei
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Kang Ouyang
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Ying Chen
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China.
| | - Weijian Huang
- Laboratory of animal infectious disease and immunology, College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China.
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Vilcek S, Salamunova S, Jackova A. Genetic identification of astroviruses in wild boars. J Vet Sci 2019; 20:91-94. [PMID: 30481990 PMCID: PMC6351768 DOI: 10.4142/jvs.2019.20.1.91] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/08/2018] [Accepted: 11/18/2018] [Indexed: 11/20/2022] Open
Abstract
Astroviruses are widely detected in pigs but their detection in wild boars is rather sporadic. In this study, astroviruses were detected in organ homogenates of wild boars by applying nested reverse transcriptase polymerase chain reaction, and the typing was carried out by phylogenetic analysis. Overall, 30/200 (15.0%) homogenates were positive for astroviruses. Genetic typing revealed that of 13 amplicons analyzed, 8 were typed as porcine astrovirus lineage 2 (PAstV-2), 2 as lineage 4 (PAstV-4), 2 identical sequences were grouped with chicken astrovirus, and 1 sequence belonged to a bat astrovirus lineage. This first identification of chicken and bat astroviruses in wild boars indicates interspecies transmission.
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Affiliation(s)
- Stefan Vilcek
- Department of Epizootiology and Parasitology, University of Veterinary Medicine and Pharmacy, SK-041 81 Košice, Slovakia
| | - Slavomira Salamunova
- Department of Epizootiology and Parasitology, University of Veterinary Medicine and Pharmacy, SK-041 81 Košice, Slovakia
| | - Anna Jackova
- Department of Epizootiology and Parasitology, University of Veterinary Medicine and Pharmacy, SK-041 81 Košice, Slovakia
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Boujon CL, Koch MC, Seuberlich T. The Expanding Field of Mammalian Astroviruses: Opportunities and Challenges in Clinical Virology. Adv Virus Res 2017; 99:109-137. [PMID: 29029723 DOI: 10.1016/bs.aivir.2017.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Astroviruses are best known as being one of the leading causes of diarrhea in infants and were first described in this context in 1975. In its first years, astrovirus research was mainly restricted to electron microscopy and serology studies. The ability to culture some of these viruses in vitro allowed a first consequent step forward, especially at the molecular level. Since the emergence of more powerful genetic methods, though, the face of this research field has dramatically changed and evolved. From the exponential number of discoveries of new astrovirus strains in the most varied of animal species to their association with atypical diseases, these viruses revealed a lot of surprises, and many more are probably still waiting to be uncovered. This chapter summarizes the most important knowledge about astroviruses and discusses the implication of the latest findings in this area of research.
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Conceição-Neto N, Theuns S, Cui T, Zeller M, Yinda CK, Christiaens I, Heylen E, Van Ranst M, Carpentier S, Nauwynck HJ, Matthijnssens J. Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs. Virus Evol 2017; 3:vex024. [PMID: 28924489 PMCID: PMC5591953 DOI: 10.1093/ve/vex024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Diarrhea outbreaks in pig farms have raised major concerns in Europe and USA, as they can lead to dramatic pig losses. During a suspected outbreak in Belgium of porcine epidemic diarrhea virus (PEDV), we performed viral metagenomics to assess other potential viral pathogens. Although PEDV was detected, its low abundance indicated that other viruses were involved in the outbreak. Interestingly, a porcine bocavirus and several enteroviruses were most abundant in the sample. We also observed the presence of a porcine enterovirus genome with a gene insertion, resembling a C28 peptidase gene found in toroviruses, which was confirmed using re-sequencing, bioinformatics, and proteomics approaches. Moreover, the predicted cleavage sites for the insertion suggest that this gene was being expressed as a single protein, rather than a fused protein. Recombination in enteroviruses has been reported as a major mechanism to generate genetic diversity, but gene insertions across viral families are rather uncommon. Although such inter-family recombinations are rare, our finding suggests that these events may significantly contribute to viral evolution.
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Affiliation(s)
- Nádia Conceição-Neto
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Sebastiaan Theuns
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Tingting Cui
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Mark Zeller
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Claude Kwe Yinda
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Isaura Christiaens
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Elisabeth Heylen
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,Facility for Systems Biology Based Mass Spectrometry (SYBIOMA), KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Hans J Nauwynck
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
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13
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Donato C, Vijaykrishna D. The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses. Viruses 2017; 9:v9050102. [PMID: 28489047 PMCID: PMC5454415 DOI: 10.3390/v9050102] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 01/23/2023] Open
Abstract
Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.
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Affiliation(s)
- Celeste Donato
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
| | - Dhanasekaran Vijaykrishna
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
- Duke-NUS Medical School, Singapore 169857, Singapore.
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14
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Ito M, Kuroda M, Masuda T, Akagami M, Haga K, Tsuchiaka S, Kishimoto M, Naoi Y, Sano K, Omatsu T, Katayama Y, Oba M, Aoki H, Ichimaru T, Mukono I, Ouchi Y, Yamasato H, Shirai J, Katayama K, Mizutani T, Nagai M. Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination. INFECTION GENETICS AND EVOLUTION 2017; 50:38-48. [PMID: 28189887 DOI: 10.1016/j.meegid.2017.02.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs.
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Affiliation(s)
- Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Moegi Kuroda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan
| | - Masataka Akagami
- Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Toru Ichimaru
- Department of Health and Medical Sciences, Ishikawa Prefectural Nursing University, Kahoku, Ishikawa, 929-1210, Japan
| | - Itsuro Mukono
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Yoshinao Ouchi
- Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan
| | - Hiroshi Yamasato
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan.
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15
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Diseases of the Alimentary Tract. Vet Med (Auckl) 2017. [PMCID: PMC7167529 DOI: 10.1016/b978-0-7020-5246-0.00007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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16
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Zhou W, Ullman K, Chowdry V, Reining M, Benyeda Z, Baule C, Juremalm M, Wallgren P, Schwarz L, Zhou E, Pedrero SP, Hennig-Pauka I, Segales J, Liu L. Molecular investigations on the prevalence and viral load of enteric viruses in pigs from five European countries. Vet Microbiol 2015; 182:75-81. [PMID: 26711031 PMCID: PMC7125590 DOI: 10.1016/j.vetmic.2015.10.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022]
Abstract
Porcine astrovirus type 4 was prevalent in the 49 European farms with a high viral load. Rotaviruses were mainly found in diarrheic pigs. Kobuvirus and porcine circovirus 2 were ubiquitous.
Enteric viral infections in pigs may cause diarrhea resulting in ill-thrift and substantial economic losses. This study reports the enteric infections with porcine astrovirus type 4 (PAstV4), porcine group A rotavirus (GARV), porcine group C rotavirus (GCRV), porcine circovirus type 2 (PCV2) and porcine kobuvirus (PKoV) in 419 pigs, comprising both healthy and diarrheic animals, from 49 farms in five European countries (Austria, Germany, Hungary, Spain and Sweden). Real-time RT-PCR assays were developed to test fecal samples and to compare the prevalence and viral load in relation to health status, farms of origin and age groups. The results showed that PAstV4 (70.4%) was the dominant virus species, followed by PKoV (56.7%), PCV2 (42.2%), GCRV (3%) and GARV (0.9%). Diarrheic pigs had a higher viral load of PAstV4 in the nursery and growing-finishing groups. Rotaviruses were mainly detected in diarrheic pigs, whereas PCV2 was more often detected in clinically healthy than in diarrheic pigs, suggesting that most PCV2 infections were subclinical. PAstV4, PCV2 and PKoV were considered ubiquitous in the European pig livestock and co-infections among them were frequent, independently of the disease status, in contrast to a low prevalence of classical rotavirus infections.
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Affiliation(s)
- Weiguang Zhou
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture, Hohhot, China; National Veterinary Institute (SVA), Uppsala, Sweden
| | - Karin Ullman
- National Veterinary Institute (SVA), Uppsala, Sweden
| | - Vinay Chowdry
- National Veterinary Institute (SVA), Uppsala, Sweden
| | | | | | - Claudia Baule
- National Veterinary Institute (SVA), Uppsala, Sweden
| | | | - Per Wallgren
- National Veterinary Institute (SVA), Uppsala, Sweden
| | - Lukas Schwarz
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Enmin Zhou
- College of Veterinary Medicine Northwest A&F University, Shaanxi, China
| | - Sonia Pina Pedrero
- Centre de Recerca en Sanitat Animal (CReSA)-Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Isabel Hennig-Pauka
- University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Joaquim Segales
- Centre de Recerca en Sanitat Animal (CReSA)-Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Lihong Liu
- National Veterinary Institute (SVA), Uppsala, Sweden.
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17
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Detection of a mammalian-like astrovirus in bird, European roller (Coracias garrulus). INFECTION GENETICS AND EVOLUTION 2015; 34:114-21. [DOI: 10.1016/j.meegid.2015.06.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 06/04/2015] [Accepted: 06/17/2015] [Indexed: 12/29/2022]
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18
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Detection and molecular characterization of zoonotic viruses in swine fecal samples in Italian pig herds. Arch Virol 2015. [PMID: 26215443 DOI: 10.1007/s00705-015-2538-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Gastrointestinal disease is frequent in pigs, and among the different etiological agents involved, viruses are considered the leading cause of infection in this animal species. Furthermore, about half of the newly identified swine pathogens are viruses, many of which may be transmitted to humans by direct contact or by indirect transmission pathways. In this study, the prevalence of astrovirus (AstV), group A rotavirus (RVA), norovirus (NoV) and hepatitis E virus (HEV) infections in pigs was investigated. During 2012-2014, 242 fecal samples were collected from pigs at different production stages (5 to 220 days old) on eight swine farms located in northern, central and southern Italy. Seven out of eight farms analyzed were positive for AstV, which was detected in 163 out of 242 (67.4%) samples and was the most prevalent virus; 61 of the 163 AstV-positive animals (37.4%) had diarrhea. HEV was detected on six farms and in 45 (18.6%) of the 242 samples analyzed. Twenty-three HEV-infected pigs had diarrhea (51.1%). A lower prevalence was observed for RVA, which was found in 10 of the 242 samples (4.1%) from three positive farms, and diarrhea was present only in six infected pigs (60.0%). No swine samples were found to be positive for NoV. Genetic diversity and phylogenetic relationships of some strains representative of the different viruses detected were investigated, confirming a wide heterogeneity of viral strains circulating among pigs.
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19
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Woo PCY, Lau SKP, Teng JLL, Tsang AKL, Joseph S, Xie J, Jose S, Fan RYY, Wernery U, Yuen KY. A novel astrovirus from dromedaries in the Middle East. J Gen Virol 2015; 96:2697-2707. [PMID: 26296576 DOI: 10.1099/jgv.0.000233] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent emergence of Middle East respiratory syndrome coronavirus from the Middle East and its discovery from dromedary camels has boosted interest in the search for novel viruses in dromedaries. The existence of astroviruses (AstVs) in dromedaries was previously unknown. We describe the discovery of a novel dromedary camel AstV (DcAstV) from dromedaries in Dubai. Among 215 dromedaries, DcAstV was detected in faecal samples of four [three (1.5 %) adult dromedaries and one (8.3 %) dromedary calf] by reverse transcription-PCR. Sequencing of the four DcAstV genomes and phylogenetic analysis showed that the DcAstVs formed a distinct cluster. Although DcAstV was most closely related to a recently characterized porcine AstV 2, their capsid proteins only shared 60-66 % amino acid identity, with a mean amino acid genetic distance of 0.372. Notably, the N-terminal halves of the capsid proteins of DcAstV shared ≤ 85 % amino acid identity, but the C-terminal halves only shared ≤ 49 % amino acid identity compared with the corresponding proteins in other AstVs. A high variation of the genome sequences of DcAstV was also observed, with a mean amino acid genetic distance of 0.214 for ORF2 of the four strains. Recombination analysis revealed a possible recombination event in ORF2 of strain DcAstV-274. The low Ka/Ks ratios (number of non-synonymous substitutions per non-synonymous site to number of synonymous substitutions per synonymous site) of the four ORFs in the DcAstV genomes supported the suggestion that dromedaries are the natural reservoir where AstV is stably evolving. These results suggest that AstV is a novel species of the genus Mamastrovirus in the family Astroviridae. Further studies are important to understand the pathogenic potential of DcAstV.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, PR China
| | - Susanna K P Lau
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong, PR China
| | - Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, PR China
| | - Alan K L Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong, PR China
| | - Sunitha Joseph
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Jun Xie
- Department of Microbiology, The University of Hong Kong, Hong Kong, PR China
| | - Shanty Jose
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Rachel Y Y Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong, PR China
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Kwok-Yung Yuen
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, PR China
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20
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Abstract
Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.
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Affiliation(s)
- Albert Bosch
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
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21
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Amimo JO, Okoth E, Junga JO, Ogara WO, Njahira MN, Wang Q, Vlasova AN, Saif LJ, Djikeng A. Molecular detection and genetic characterization of kobuviruses and astroviruses in asymptomatic local pigs in East Africa. Arch Virol 2013; 159:1313-9. [PMID: 24327095 PMCID: PMC4094370 DOI: 10.1007/s00705-013-1942-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 11/29/2013] [Indexed: 12/14/2022]
Abstract
In this study, swine fecal specimens (n = 251) collected from nursing and weaned piglets raised under smallholder production systems were screened for the presence of kobuviruses by RT-PCR. Porcine kobuviruses were detected in 13.1 % (33/251) of the samples. We demonstrated that porcine kobuvirus infections exist in indigenous pigs in Kenya and Uganda and that the prevalence was higher in young piglets than older pigs: nursing piglets (15 %), post-weaning (3-month-old) pigs (17 %), 4-month-old pigs (10 %). Genetic analysis of the partial RNA-dependent RNA polymerase (RdRp) region (690 nt) revealed that kobuviruses circulating in East Africa are diverse, sharing nucleotide sequence identities ranging from 89.7 to 99.1 % and 88 to 92.3 % among them and with known porcine kobuviruses, respectively. The nucleotide sequence identities between our kobuvirus strains and those of human, bovine and canine kobuviruses were 69.4-70.7 %, 73.1-74.4 % and 67-70.7 %, respectively. Additionally, upon sequencing selected samples that showed consistent 720-bp RT-PCR bands while using the same primer set, we detected porcine astroviruses in our samples belonging to type 2 and type 3 mamastroviruses. To our knowledge, this study reports the first detection and molecular analysis of both porcine kobuviruses and astroviruses in an African region. Further studies are required to determine the role of these viruses in gastrointestinal infections of pigs in this region and to determine the genetic diversity of the circulating strains to develop accurate diagnostic tools and implement appropriate control strategies.
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Affiliation(s)
- Joshua O. Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O Box 29053, Nairobi, 00625 Kenya
- Bioscience of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O Box 30709, Nairobi, 00100 Kenya
| | - Edward Okoth
- Bioscience of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O Box 30709, Nairobi, 00100 Kenya
| | - Joseph O. Junga
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O Box 29053, Nairobi, 00625 Kenya
| | - William O. Ogara
- Department of Public Health Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Nairobi, P.O Box 29053, Nairobi, 00625 Kenya
| | - Moses N. Njahira
- Bioscience of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O Box 30709, Nairobi, 00100 Kenya
| | - Qiuhong Wang
- Food Animal Health Research Program, Veterinary Preventive Medicine Department, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Veterinary Preventive Medicine Department, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Linda J. Saif
- Food Animal Health Research Program, Veterinary Preventive Medicine Department, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Avenue, Wooster, OH 44691 USA
| | - Appolinaire Djikeng
- Bioscience of Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O Box 30709, Nairobi, 00100 Kenya
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22
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Bodewes R, van der Giessen J, Haagmans BL, Osterhaus ADME, Smits SL. Identification of multiple novel viruses, including a parvovirus and a hepevirus, in feces of red foxes. J Virol 2013; 87:7758-64. [PMID: 23616657 PMCID: PMC3700315 DOI: 10.1128/jvi.00568-13] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/12/2013] [Indexed: 02/07/2023] Open
Abstract
Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands.
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23
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Carmona-Vicente N, Buesa J, Brown PA, Merga JY, Darby AC, Stavisky J, Sadler L, Gaskell RM, Dawson S, Radford AD. Phylogeny and prevalence of kobuviruses in dogs and cats in the UK. Vet Microbiol 2013; 164:246-52. [PMID: 23490561 PMCID: PMC7127238 DOI: 10.1016/j.vetmic.2013.02.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 01/12/2023]
Abstract
The kobuviruses represent an emerging genus in the Picornaviridae. Here we have used next generation sequencing and conventional approaches to identify the first canine kobuvirus (CaKoV) from outside the USA. Phylogenetic analysis suggests that a single lineage genotype of CaKoV now exists in Europe and the USA with 94% nucleotide similarity in the coding region. CaKoV was only identified in a single case from a case–control study of canine diarrhoea, suggesting this virus was not a frequent cause of disease in this population. Attempts to grow CaKoV in cell culture failed. Sequence analysis suggested CaKoV was distinct from human Aichi virus (AiV), and unlikely to pose a significant zoonotic risk. Serosurveys by ELISA, immunofluorescence and neutralisation tests, using AiV as antigen, suggested kobuvirus infection is prevalent in dogs. In addition, IgG antibody to AiV was also detected in cat sera, indicating for the first time that cats may also be susceptible to kobuvirus infection.
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Affiliation(s)
- N Carmona-Vicente
- Department of Microbiology, School of Medicine, Hospital Clínico Universitario, University of Valencia, Valencia, Spain
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24
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Brnić D, Prpić J, Keros T, Roić B, Starešina V, Jemeršić L. Porcine astrovirus viremia and high genetic variability in pigs on large holdings in Croatia. INFECTION GENETICS AND EVOLUTION 2013; 14:258-64. [PMID: 23313832 DOI: 10.1016/j.meegid.2012.12.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
Abstract
Astroviruses are emerging viral agents, primarily enteropathogenic in mammals, but recently have been acknowledged to have extra-intestinal implications in humans and mink. Porcine astrovirus is thought to be widely distributed and highly prevalent among pigs, nevertheless its clinical significance remains doubtful as it can be detected in diarrheic as well as in healthy pigs. Recent reports imply the immense genetic variability among porcine astrovirus strains with five distinct lineages being characterized so far. Herein, we report porcine astrovirus circulation in the blood of healthy pigs in different age categories bred on two large industrial holdings in Croatia, with viral RNA seroprevalence of 3.89%. These are the first extra-intestinal findings of astrovirus in pigs, indicating a more complex pathogenesis than previously thought. Partial polymerase sequences of serum-derived strains provisionally clustered into porcine astrovirus lineages 2 and 4, sharing high genetic identity with previously described porcine astrovirus strains. The results were supported by detecting porcine astrovirus strains in composite fecal samples, regardless of pig category or holding tested. Phylogenetic analysis of derived strains suggested the presence of porcine astrovirus lineages previously detected in pig sera with an additional highly genetically divergent lineage 5, reported for the first time in Europe. Moreover, the existence of possible sub lineages should not be excluded. The results obtained in the present study, contribute to knowledge of porcine astrovirus pathogenesis; even though it's possible clinical significance remains unclear. High fecal prevalence accompanied with vast genetic diversity on a relatively confined area, underscores the importance of pigs as porcine astrovirus reservoirs with eventual recombination events as a possible outcome.
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Affiliation(s)
- Dragan Brnić
- Croatian Veterinary Institute, Virology Department, Savska cesta 143, 10000 Zagreb, Croatia.
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Xiao CT, Giménez-Lirola LG, Gerber PF, Jiang YH, Halbur PG, Opriessnig T. Identification and characterization of novel porcine astroviruses (PAstVs) with high prevalence and frequent co-infection of individual pigs with multiple PAstV types. J Gen Virol 2012; 94:570-582. [PMID: 23223616 DOI: 10.1099/vir.0.048744-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many astrovirus (AstV) species are associated with enteric disease, although extraintestinal manifestations in mammalian and avian hosts have also been described. In this study, the prevalence rates of porcine AstV types 1-5 (PAstV1-PAstV5) were investigated using faecal samples from 509 pigs of which 488 (95.9%) came from farms with a history of diarrhoea. All of the five known PAstV types were found to circulate in pigs in the USA, and co-infection of a single pig with two or more PAstV types was frequently observed. A high overall prevalence of 64.0% (326/509) of PAstV RNA-positive samples was detected, with 97.2% (317/326) of the PAstV RNA-positive pigs infected with PAstV4. Further genomic sequencing and characterization of the selected isolates revealed low sequence identities (49.2-89.0%) with known PAstV strains, indicating novel types or genotypes of PAstV2, PAstV4 and PAstV5. Some new features of the genomes of the PAstVs were also discovered. The first complete genome of a PAstV3 isolate was obtained and showed identities of 50.5-55.3% with mink AstV and the novel human AstVs compared with 38.4-42.7% with other PAstV types. Phylogenetic analysis revealed that PAstV1, PAstV2 and PAstV3 were more closely related to AstVs from humans and other animals than to each other, indicating past cross-species transmission and the zoonotic potential of these PAstVs.
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Affiliation(s)
- Chao-Ting Xiao
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Priscilla F Gerber
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Yong-Hou Jiang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Patrick G Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
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Phylogenetic analysis of porcine astrovirus in domestic pigs and wild boars in South Korea. Virus Genes 2012; 46:175-81. [PMID: 22965450 PMCID: PMC7089313 DOI: 10.1007/s11262-012-0816-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 08/28/2012] [Indexed: 12/05/2022]
Abstract
Porcine astrovirus (PAstV) belongs to genetically divergent lineages within the genus Mamastrovirus. In this study, 25/129 (19.4 %) domestic pig and 1/146 (0.7 %) wild boar fecal samples tested in South Korea were positive for PAstV. Positive samples were mainly from pigs under 6 weeks old. Bayesian inference (BI) tree analysis for RNA-dependent RNA polymerase (RdRp) and capsid (ORF2) gene sequences, including Mamastrovirus and Avastrovirus, revealed a relatively geographically divergent lineage. The PAstVs of Hungary and America belong to lineage PAstV 4; those of Japan belong to PAstV 1; and those of Canada belong to PAstV 1, 2, 3, and 5, but not to 4. This study revealed that the PAstVs of Korea belong predominantly to lineage PAstV 4 and secondarily to PAstV 2. It was also observed that PAstV infections are widespread in South Korea regardless of the disease state in domestic pigs and in wild boars as well.
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Reuter G, Nemes C, Boros A, Kapusinszky B, Delwart E, Pankovics P. Porcine kobuvirus in wild boars (Sus scrofa). Arch Virol 2012; 158:281-2. [PMID: 22926717 DOI: 10.1007/s00705-012-1456-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/16/2012] [Indexed: 11/30/2022]
Abstract
Fecal samples (N = 10) from 6- to 8-week-old wild boar piglets (Sus scrofa), collected from an animal park in Hungary in April 2011, were analyzed using viral metagenomics and complete genome sequencing. Kobuvirus (genus Kobuvirus, family Picornaviridae) was detected in all (100 %) specimens, with the closest nucleotide (89 %) and amino acid (94 %) sequence identity of the strain wild boar/WB1-HUN/2011/HUN (JX177612) to the prototype porcine kobuvirus S-1-HUN (EU787450). This study suggests that genetically highly similar (practically the same geno-/serotype) porcine kobuvirus circulate in wild boars, the wildlife counterparts of domestic pigs. Wild boars could be an important host and reservoir for kobuvirus.
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Affiliation(s)
- Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Szabadság út 7., 7623, Pécs, Hungary.
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28
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Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus. J Virol 2012; 86:11024-30. [PMID: 22855485 DOI: 10.1128/jvi.01427-12] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed <39% and <31% identities to those of previously known parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.
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High throughput sequencing methods for microbiome profiling: application to food animal systems. Anim Health Res Rev 2012; 13:40-53. [PMID: 22853944 DOI: 10.1017/s1466252312000126] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the 'rare biosphere' in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.
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Boros Á, Nemes C, Pankovics P, Kapusinszky B, Delwart E, Reuter G. Porcine teschovirus in wild boars in Hungary. Arch Virol 2012; 157:1573-8. [PMID: 22569887 DOI: 10.1007/s00705-012-1327-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 03/27/2012] [Indexed: 11/27/2022]
Abstract
The genus Teschovirus, family Picornaviridae, currently includes 12 serotypes (PTV 1 to 12) isolated from swine. PTVs have been well studied in domestic pigs, but knowledge about PTVs in wild boars is deficient. Here, we report the first complete PTV genome sequence from 7 (70 %) of 10 fecal samples of wild boar piglets (Sus scrofa) by RT-PCR and pyrosequencing. Analysis of the wild boar PTV strain WB2C-TV/2011/HUN (JQ429405) showed considerable difference, especially in VP1 (66-74 % amino acid identity) compared to the available PTVs. PTV is present in wild boars, and WB2C-TV/2011/HUN represents a novel PTV genotype, provisionally named PTV-13.
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Affiliation(s)
- Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Szabadság út 7, 7623 Pécs, Hungary
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