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Sawant P, Kulkarni A, Mane R, Patil R, Lavania M. Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India. Front Cell Infect Microbiol 2023; 13:1258660. [PMID: 37965252 PMCID: PMC10642067 DOI: 10.3389/fcimb.2023.1258660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023] Open
Abstract
RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to Astroviridae in both species, while Reoviridae and Picornaviridae were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.
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Affiliation(s)
- Pradeep Sawant
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajkumar Mane
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Renu Patil
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
| | - Mallika Lavania
- Enteric Viruses Group, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, India
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Nelsen A, Knudsen D, Hause BM. Identification of a Novel Astrovirus Associated with Bovine Respiratory Disease. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/8512021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Astroviruses (AstVs) cause gastrointestinal disease in mammals and avians. Emerging evidence suggests that some AstVs have extraintestinal tissue tropism, with AstVs detected in the liver, kidney, central nervous system, and the respiratory tract variably associated with disease. In cattle, AstV infection has been linked to gastroenteric or neurologic disease. Here, metagenomic sequencing of a lung from a bovine with respiratory disease identified a novel AstV with a predicted capsid-encoding ORF2 amino acid sequence with 66% identity to caprine astrovirus (CAstV G2.1). A quantitative reverse transcription PCR (qRT-PCR) targeting ORF2 found four out of 49 (8%) lungs and one out of 48 (2%) enteric samples obtained from bovine diagnostic submissions positive for the novel bovine astrovirus (BAstV). In two strongly qRT-PCR-positive lung samples, intense novel BAstV nucleic acid signals were mainly localized in the cytoplasm of alveolar macrophages and mononuclear cells using RNAscope® in situ hybridization (ISH). Genetic analysis of two novel BAstV genomes determined from qRT-PCR positive samples found high similarity for ORF1ab nucleotide sequence (92.1% and 93.9%) to BAstV strain BSRI-1, while ORF2 nucleotide sequence was most similar to CAstV G2.1 (74.6% and 77.6%). Phylogenetic analysis of the novel BAstV sequences found a close genetic relationship to the single BAstV (BSRI-1) previously identified from a bovine respiratory sample as well as bovine and caprine AstVs identified from various tissues. Further research is needed to determine the clinical significance of BAstV in respiratory diseases.
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Affiliation(s)
- April Nelsen
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - David Knudsen
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, USA
| | - Ben M. Hause
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
- Animal Disease Research and Diagnostic Laboratory, South Dakota State University, Brookings, South Dakota, USA
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Zhu J, Wang C, Zhang L, Zhu T, Li H, Wang Y, Xue K, Qi M, Peng Q, Chen Y, Hu C, Chen X, Chen J, Chen H, Guo A. Isolation of BVDV-1a, 1m, and 1v strains from diarrheal calf in china and identification of its genome sequence and cattle virulence. Front Vet Sci 2022; 9:1008107. [PMID: 36467650 PMCID: PMC9709263 DOI: 10.3389/fvets.2022.1008107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/10/2022] [Indexed: 08/25/2023] Open
Abstract
Bovine viral diarrhea virus (BVDV) is an important livestock viral pathogen responsible for causing significant economic losses. The emerging and novel BVDV isolates are clinically and biologically important, as there are highly antigenic diverse and pathogenic differences among BVDV genotypes. However, no study has yet compared the virulence of predominant genotype isolates (BVDV-1a, 1b, and 1m) in China and the emerging genotype isolate BVDV-1v. The serological relationship among these genotypes has not yet been described. In this study, we isolated three BVDV isolates from calves with severe diarrhea, characterized as BVDV-1a, 1m, and novel 1v, based on multiple genomic regions [including 5-untranslated region (5'-UTR), Npro, and E2] and the phylogenetic analysis of nearly complete genomes. For the novel genotype, genetic variation analysis of the E2 protein of the BVDV-1v HB-03 strain indicates multiple amino acid mutation sites, including potential host cell-binding sites and neutralizing epitopes. Recombination analysis of the BVDV-1v HB-03 strain hinted at the possible occurrence of cross-genotypes (among 1m, 1o, and 1q) and cross-geographical region transmission events. To compare the pathogenic characters and virulence among these BVDV-1 genotypes, newborn calves uninfected with common pathogens were infected intranasally with BVDV isolates. The calves infected with the three genotype isolates show different symptom severities (diarrhea, fever, slowing weight gain, virus shedding, leukopenia, viremia, and immune-related tissue damage). In addition, these infected calves also showed bovine respiratory disease complexes (BRDCs), such as nasal discharge, coughing, abnormal breathing, and lung damage. Based on assessing different parameters, BVDV-1m HB-01 is identified as a highly virulent strain, and BVDV-1a HN-03 and BVDV-1v HB-03 are both identified as moderately virulent strains. Furthermore, the cross-neutralization test demonstrated the antigenic diversity among these Chinese genotypes (1a, 1m, and 1v). Our findings illustrated the genetic evolution characteristics of the emerging genotype and the pathogenic mechanism and antigenic diversity of different genotype strains, These findings also provided an excellent vaccine candidate strain and a suitable BVDV challenge strain for the comprehensive prevention and control of BVDV.
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Affiliation(s)
- Jie Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chen Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lina Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Tingting Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Hanxiong Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yunqiu Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Kaili Xue
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | | | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, China
- Key Laboratory of Ruminant Bio-Products of Ministry of Agriculture and Rural Affairs, Huazhong Agriculture University, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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Wang J, Xu C, Zeng M, Tang C. Diversity of Astrovirus in Goats in Southwest China and Identification of Two Novel Caprine Astroviruses. Microbiol Spectr 2022; 10:e0121822. [PMID: 35862967 PMCID: PMC9430535 DOI: 10.1128/spectrum.01218-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/03/2022] [Indexed: 11/20/2022] Open
Abstract
A total of 232 goat fecal samples (124 diarrheic and 108 nondiarrheic) collected from 12 farms in Southwest China were tested for astrovirus using RT-PCR. A total of 16.9% (21/124) of diarrheic and 20.4% (22/108) of nondiarrheic samples were astrovirus-positive, and no statistical difference was found in the detection rate between healthy and sick goats. Furthermore, 28 obtained complete ORF2 sequences could be classified into six genotypes according to the species classification criteria of the International Committee on Taxonomy of Viruses (ICTV). It is worth noting that, in addition to four known caprine astrovirus genotypes (MAstV-33, MAstV-34, Caprine Astrovirus G5.1, and Caprine Astrovirus G3.1), MAstV-13 and MAstV-24 genotypes were identified in goats. Interestingly, five of 19 ORF2 sequences in the Caprine Astrovirus G3.1 genotype showed possible intragenotypic recombination events. Furthermore, nearly complete caprine astrovirus genomes of MAstV-13 and MAstV-24 genotypes were obtained. The genome of the SWUN/ECJK3/2021 strain shared the highest similarity (62.0% to 73.9%) with astrovirus in MAstV-13, and clustered in the so-called human-mink-ovine (HMO) clade, which contained the majority of the neurotropic astrovirus strains. Moreover, the SWUN/LJK2-2/2020 strain showed the highest similarity (69.7% to 78.6%) and the closest genetic relationship to the known porcine and bovine astroviruses in MAstV-24. In conclusion, this study confirmed six genotypes of astrovirus circulating among goats in Southwest China, including MAstV-13 and MAstV-24 genotypes. These findings enhance our knowledge of the prevalence and diversity of astroviruses. IMPORTANCE Caprine astrovirus is a newly emerging virus, and information regarding its prevalence and molecular characteristics remains limited. In this study, six genotypes of astrovirus, including MAstV-13 and MAstV-24, were identified in goats, adding two novel caprine astrovirus genotypes to the four previously known genotypes, thereby enriching the diversity of the caprine astrovirus. Moreover, genomes of MAstV-13 SWUN/ECJK3/2021 and MAstV-24 SWUN/LJK2-2/2020 strains were obtained from goats, which aids in the understanding of the infection spectrum and host range of the two genotypes. This study is the first to demonstrate the presence of neurotropic-like astrovirus (MAstV-13) in goats, which has significant implications for the diagnosis of neurological diseases in goats.
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Affiliation(s)
- Jiayi Wang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Chenxia Xu
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Mengting Zeng
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Chengdu, China
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Qin YF, Gong QL, Zhang M, Sun ZY, Wang W, Wei XY, Chen Y, Zhang Y, Zhao Q, Jiang J. Prevalence of bovine rotavirus among Bovidae in China during 1984-2021: A systematic review and meta-analysis. Microb Pathog 2022; 169:105661. [PMID: 35817280 DOI: 10.1016/j.micpath.2022.105661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 06/20/2022] [Accepted: 06/26/2022] [Indexed: 11/28/2022]
Abstract
Bovine rotavirus (BRV) is a potential zoonotic intestinal pathogen that brings a serious threat to calf health, and has resulted in huge economic losses to China's breeding industry. Here, a systematic review and meta-analysis was conducted to estimate the prevalence of BRV among Bovidae from 1984 to 2021 in China. A total of 64 publications on BRV investigation in China were screened from the databases Chinese National Knowledge Infrastructure (CNKI), Wan Fang Database, Technology Periodical Database (VIP), PubMed, and ScienceDirect. The random-effect model was used to calculate the pooled prevalence of BRV, and the analyzed data were derived from 25 provinces in China. The estimated pooled prevalence of BRV in China was 35.7% (8176/17,292). In addition, the prevalence of BRV in Southwestern China (77.1%; 2924/3600) was significantly higher than that in other regions of China. Regarding geographic and climatic factors, the prevalence of BRV in the subgroup of latitude 30-35° (76.8%; 3303/4659) was significantly higher than that in the subgroup of latitude less than 30° (37.0%; 485/1275) or more than 35° (32.6%; 1703/5722), while the prevalence of BRV in the subgroup of longitude 100-105° (75.4%; 2513/3849) was significantly higher than that in the subgroup of longitude less than 100° (32.6%; 619/2255) or more than 105° (48.9%; 2359/5552). Rainfall was positively correlated with the prevalence of BRV, whereas temperature was negatively correlated with the positive rate of BRV (P < 0.05). Our data showed that the prevalence of BRV was strongly correlated with geographical and climatic conditions. Thus, we recommend that the corresponding prevention and control programs should be formulated according to different geographical conditions. The strengthening of BRV surveillance in areas with high altitude, low temperature, and heavy rainfall may contribute to the decrease of the incidence of BRV infection among Bovidae herds in China.
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Affiliation(s)
- Yi-Feng Qin
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China; College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, 130118, China
| | - Qing-Long Gong
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, 130118, China
| | - Miao Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Zheng-Yao Sun
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, 266109, China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, China
| | - Xin-Yu Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, China
| | - Yu Chen
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, 163319, China
| | - Yuan Zhang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, Jilin Province, 130118, China.
| | - Quan Zhao
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China.
| | - Jing Jiang
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, 130600, China.
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