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Wang X, Liu W, Hu M, He Y, Wang B, Li K, Zhang R, Zhang H, Wang T, Wang Y, Chen L, Hu X, Ren H, Song H. Coinfection of human adenovirus and recombinant human astrovirus in a case of acute gastroenteritis: A report from China. J Med Virol 2024; 96:e29940. [PMID: 39327785 DOI: 10.1002/jmv.29940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 09/03/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
Diarrhea is one of the major public health issues worldwide. Although the infections of individual enteric virus have been extensively studied, elucidation of the coinfection involving multiple viruses is still limited. In this study, we identified the coinfection of human adenovirus (HAdV) and human astrovirus (HAstV) in a child with acute gastroenteritis, analyzed their genotypes and molecular evolution characteristics. The sample was collected and identified using RT-PCR and subjected to whole-genome sequencing on the NovaSeq (Illumina) platform. Obtained sequences were assembled into the complete genome of HAdV and the ORF1 of HAstV. We conducted phylogenetic analysis using IQ-TREE software and conducted recombination analysis with the Recombination Detection Program. The sequenced HAdV was confirmed to be genotype 41, and was genetically close to some European strains. Phylogenetic analysis revealed that the HAstV was genetically close to both HAstV-2 and HAstV-4 and was different from the genotype prevalent in Shenzhen before. The recombination analysis confirmed that the sequenced HAstV strain is a recombinant of HAstV-2 and HAstV-4. Our analysis has shown that the strains in this coinfection are both uncommon variants in this geographical region, instead of dominant subtypes that have prevailed for years. This study presents a coinfection of HAdV and HAstV and conducts an evolutionary analysis on involved viruses, which reveals the genetic diversity of epidemic strains in Southern China and offers valuable insights into vaccine and medical research.
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MESH Headings
- Humans
- Coinfection/virology
- Coinfection/epidemiology
- Gastroenteritis/virology
- Phylogeny
- Mamastrovirus/genetics
- Mamastrovirus/isolation & purification
- Mamastrovirus/classification
- China/epidemiology
- Astroviridae Infections/virology
- Astroviridae Infections/epidemiology
- Adenoviruses, Human/genetics
- Adenoviruses, Human/classification
- Adenoviruses, Human/isolation & purification
- Genotype
- Adenovirus Infections, Human/virology
- Adenovirus Infections, Human/epidemiology
- Recombination, Genetic
- Genome, Viral/genetics
- Whole Genome Sequencing
- Male
- Sequence Analysis, DNA
- Child, Preschool
- Evolution, Molecular
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Affiliation(s)
- Xin Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Wanqiu Liu
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- School of Public Health, University of South China, Hengyang, China
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Mingda Hu
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yaqing He
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Boqian Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Kexin Li
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- China Medical University, Shenyang, China
| | - Rui Zhang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- China Medical University, Shenyang, China
| | - Hailong Zhang
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Tianyi Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yuxin Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- China Medical University, Shenyang, China
| | - Long Chen
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaofeng Hu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongguang Ren
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
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2
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Wei H, Kumthip K, Khamrin P, Yodmeeklin A, Jampanil N, Phengma P, Xie Z, Ukarapol N, Ushijima H, Maneekarn N. Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome. Microbiol Spectr 2023; 11:e0488822. [PMID: 37017548 PMCID: PMC10269785 DOI: 10.1128/spectrum.04888-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/08/2023] [Indexed: 04/06/2023] Open
Abstract
Human astrovirus (HAstV) strains exhibit high levels of genetic diversity, and many recombinant strains with different recombination patterns have been reported. The aims of the present study were to investigate the emergence of HAstV recombinant strains and to characterize the recombination patterns of the strains detected in pediatric patients admitted to the hospital with acute gastroenteritis in Chiang Mai, Thailand. A total of 92 archival HAstV strains detected in 2011 to 2020 were characterized regarding their open reading frame 1a (ORF1a) genotypes in comparison with their ORF1b genotypes to identify recombinant strains. The recombination breakpoints of the putative recombinant strains were determined by whole-genome sequencing and were analyzed by SimPlot and RDP software. Three HAstV strains (CMH-N178-12, CMH-S059-15, and CMH-S062-15) were found to be recombinant strains of three different HAstV genotypes, i.e., HAstV5, HAstV8, and HAstV1 within the ORF1a, ORF1b, and ORF2 regions, respectively. The CMH-N178-12 strain displayed recombination breakpoints at nucleotide positions 2681 and 4357 of ORF1a and ORF1b, respectively, whereas the other two recombinant strains, CMH-S059-15 and CMH-S062-15, displayed recombination breakpoints at nucleotide positions 2612 and 4357 of ORF1a and ORF1b, respectively. This is the first study to reveal nearly full-length genome sequences of HAstV recombinant strains with a novel recombination pattern of ORF1a-ORF1b-ORF2 genotypes. This finding may be useful as a guideline for identifying other recombinant HAstV strains in other geographical regions and may provide a better understanding of their genetic diversity, as well as basic knowledge regarding virus evolution. IMPORTANCE Recombination is one of the mechanisms that plays a crucial role in the genetic diversity and evolution of HAstV. We wished to investigate the emergence of HAstV recombinant strains and to analyze the whole-genome sequences of the putative HAstV recombinant strains detected in pediatric patients with acute gastroenteritis in 2011 to 2020. We reported 3 novel intergenotype recombinant strains of HAstV5-HAstV8-HAstV1 at the ORF1a-ORF1b-ORF2 regions of the HAstV genome. The hot spots of recombination occur frequently near the ORF1a-ORF1b and ORF1b-ORF2 junctions of the HAstV genome. The findings indicate that intergenotype recombination of HAstV occurs frequently in nature. The emergence of a novel recombinant strain allows the new virus to adapt and successfully escape from the host immune system, eventually emerging as the predominant genotype to infect human populations that lack herd immunity against novel recombinant strains. The virus may cause an outbreak and needs to be monitored continually.
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Affiliation(s)
- Hongyu Wei
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phitchakorn Phengma
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Zhenfeng Xie
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Nuthapong Ukarapol
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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Okitsu S, Khamrin P, Hikita T, Shimizu-Onda Y, Thongprachum A, Hayakawa S, Maneekarn N, Ushijima H. Molecular Epidemiology of Classic, MLB, and VA Astroviruses in Children with Acute Gastroenteritis, 2014-2021: Emergence of MLB3 Strain in Japan. Microbiol Spectr 2023; 11:e0070023. [PMID: 37140393 PMCID: PMC10269582 DOI: 10.1128/spectrum.00700-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Human astroviruses (HAstVs) are important causative pathogens of acute gastroenteritis (AGE) in children worldwide. MLB and VA HAstVs, which are genetically distinct from the previously known classic HAstVs, have been detected since 2008. To investigate the role of HAstVs in AGE, we conducted molecular detection and characterization of HAstVs circulating in children with AGE in Japan from 2014 to 2021. Out of 2,841 stool samples, HAstVs were detected in 130 (4.6%). MLB1 was the predominant genotype detected (45.4%), followed by HAstV1 (39.2%), MLB2 (7.4%), VA2 (3.1%), HAstV3 (2.3%), HAstV4, HAstV5, and MLB3 (0.8% each). The results demonstrated that HAstV infection in pediatric patients in Japan was dominated by the two major genotypes MLB1 and HAstV1, with a small proportion of other genotypes. The overall infection rates of MLB and VA HAstVs were higher than those of classic HAstVs. The HAstV1 strains detected in this study belonged solely to lineage 1a. The rare MLB3 genotype was detected for the first time in Japan. All three HAstV3 strains belonged to lineage 3c based on the ORF2 nucleotide sequence and were shown to be recombinant strains. IMPORTANCE HAstVs are one of the pathogens of viral AGE and are considered the third most common viral agents of AGE after rotavirus and norovirus. HAstVs are also suspected to be the causative agents of encephalitis or meningitis in immunocompromised patients and elderly persons. However, little is known about the epidemiology of HAstVs in Japan, especially that of MLBs and VA HAstVs. This study demonstrated epidemiological features and molecular characterization of human astroviruses encompassing a 7-year study period in Japan. This study highlights the genetic diversity of HAstV circulating in pediatric patients with acute AGE in Japan.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | | | - Yuko Shimizu-Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Aksara Thongprachum
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Wei H, Khamrin P, Kumthip K, Yodmeeklin A, Maneekarn N. Emergence of Multiple Novel Inter-Genotype Recombinant Strains of Human Astroviruses Detected in Pediatric Patients With Acute Gastroenteritis in Thailand. Front Microbiol 2021; 12:789636. [PMID: 34966371 PMCID: PMC8710764 DOI: 10.3389/fmicb.2021.789636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022] Open
Abstract
Objective: Human astrovirus (HAstV) is recognized as an important cause of acute gastroenteritis in children. Recombination between different genotypes of HAstV can contribute to diversity and evolution of the virus. This study aimed to investigate the emergence of HAstV recombinant strains in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, spanning 2011–2020. Methods: A total of 92 archival HAstV strains collected from pediatric patients with acute gastroenteritis during 2011–2020 were further characterized to identify the recombinant strains. The ORF1b and ORF2 junction region of each strain was amplified and sequenced. The obtained sequences were analyzed in comparison with the reference sequences retrieved from GenBank database. Their genotypes were assigned using MEGA X software based on the partial ORF1b (RdRp) and ORF2 (capsid) regions, and the recombination breakpoints of recombinant strains were determined by SimPlot and RDP4 analyses. Results: Five inter-genotype recombinant strains with three recombination patterns of ORF1b/ORF2 of classic HAstV, HAstV8/HAstV1, HAstV8/HAstV3, and HAstV3/HAstV2, were detected. The recombination breakpoints of all strains were located at the 3′-end region of ORF1b close to the ORF1b/ORF2 junction. Conclusion: Several novel inter-genotype recombinant strains of classic HAstV genotypes were detected in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand, during the period of 10 years from 2011 to 2020.
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Affiliation(s)
- Hongyu Wei
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Pathogenic Biology and Immunology, Youjiang Medical University for Nationalities, Baise, China
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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5
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High divergence of human astrovirus genotypes circulating in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, 2017-2020. Sci Rep 2021; 11:23266. [PMID: 34853390 PMCID: PMC8636499 DOI: 10.1038/s41598-021-02745-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/22/2021] [Indexed: 02/04/2023] Open
Abstract
Human astrovirus (HAstV) is one of the common causes of acute gastroenteritis in children. The investigation of molecular epidemiology of HAstV is essential for monitoring the emergence and/or re-emergence of new HAstV genotypes, as well as understanding the evolution of HAstV circulating in children suffering from acute gastroenteritis. The present study aimed to investigate the prevalence and distribution of HAstVs strains circulating in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand during 2017-2020. A total of 1500 fecal specimens collected from children with acute gastroenteritis were screened for HAstV by RT-PCR that targeted the partial RdRp in ORF1b and strains were characterized by sequencing and phylogenetic analysis. Of the 1500 fecal samples, 39 (2.6%) were positive for HAstV. Of these, both classic and novel HAstV genotypes, including classic HAstV1-HAstV5, novel HAstV-MLB1, MLB2, and HAstV-VA2, were detected. The data in this study revealed a high divergence of HAstV genotypes circulating in pediatric patients admitted to the hospitals with acute gastroenteritis in Chiang Mai, Thailand during 2017-2020.
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Zhu J, Qi M, Jiang C, Peng Y, Peng Q, Chen Y, Hu C, Chen J, Chen X, Chen H, Guo A. Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea. J Gen Virol 2021; 102. [PMID: 34424158 PMCID: PMC8513638 DOI: 10.1099/jgv.0.001640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.
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Affiliation(s)
- Jie Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Chuanwen Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Yongchong Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China
| | - Qingjie Peng
- Wuhan Keqian Biology Co.Ltd, Wuhan, 430070, PR China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Ruminant Bio-products of Ministry of Agriculture and and Rural Affairs, Huazhong Agriculture University, Wuhan 430070, PR China
| | - Changmin Hu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jianguo Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xi Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Wuhan Keqian Biology Co.Ltd, Wuhan, 430070, PR China
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China.,Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, 430070, PR China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, PR China.,Key Laboratory of Ruminant Bio-products of Ministry of Agriculture and and Rural Affairs, Huazhong Agriculture University, Wuhan 430070, PR China
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7
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Su CM, Cheng YC, Wang HY, Hsieh CH, Wan CH. The origin and past demography of murine astrovirus 1 in laboratory mice. J Gen Virol 2021; 102. [PMID: 33206033 DOI: 10.1099/jgv.0.001520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Astroviruses are non-enveloped, positive-sense, ssRNA viruses and often associated with gastrointestinal diseases. Murine astrovirus (MuAstV) was first confirmed in a laboratory mouse colony in 2011. Although infected mice do not present significant clinical symptoms, the virus might interfere with research results. A recent surveillance has shown that MuAstV is highly prevalent in laboratory mice. The aims of the present study were to identify and characterize MuAstV strains as well as to investigate the prevalence rate of viral RNA in laboratory mice in Taiwan, and to estimate the origin and past population demography of MuAstVs. Based on molecular surveillance, MuAstV RNA was detected in 45.7 % of laboratory mice (48/105) from seven of nine colonies. Three fully sequenced MuAstV strains, MuAstV TW1, TW2 and TW3, exhibited 89.1-94.4 % and 89.1-90.0 % nucleotide identities with the reference strains MuAstV STL1 and STL2, respectively. Phylogenetic analyses of the partial regions of the RNA-dependent RNA polymerase (RdRp) and capsid protein (CP) genes of 18 Taiwan strains along with other astroviruses revealed that there are three distinct lineages of mouse astrovirus, MuAstV1, MuAstV2 and mouse astrovirus JF755422. The mutation rates of MuAstV1 were 2.6×10-4 and 6.2×10-4 substitutions/site/year for the RdRp and CP regions, respectively. Based on the above molecular clock, the colonization of MuAstV1 in laboratory mice was between 1897 and 1912, in good agreement with the establishment of 'modern' laboratory mouse facilities. Since its initial infection, the population size of MuAstV1 has increased 15-60-fold, probably consistent with the increased use of laboratory mice. In conclusion, MuAstV1 has been associated with modern laboratory mice since the beginning, and its influence on research results may require further investigation.
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Affiliation(s)
- Chia-Ming Su
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, ROC
| | - Ying-Chien Cheng
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, ROC
| | - Hurng-Yi Wang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, ROC.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, No. 7, Chung San South Road, Taipei 10002, Taiwan, ROC
| | - Chia-Hung Hsieh
- Department of Forestry and Nature Conservation, Chinese Culture University, No. 55, Hwa Kang Road, Yang-Ming-Shan, Taipei, Taiwan, ROC
| | - Cho-Hua Wan
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, ROC
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8
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Yu JM, Wang ZH, Liu N, Zhang Q, Dong YJ, Duan ZJ. Complete genome of a novel recombinant human astrovirus and its quasispecies in patients following hematopoietic stem cell transplantation. Virus Res 2020; 288:198138. [PMID: 32827625 DOI: 10.1016/j.virusres.2020.198138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/01/2020] [Accepted: 08/17/2020] [Indexed: 12/30/2022]
Abstract
Human astroviruses (HAstVs) were first identified in 1975 and can be classified into three clades: classic HAstVs (HAstV 1-8), MLB (MLB1-3) and VA (VA1-5), with MLB and VA were newly identified. Recombination and a high mutation rate make HAstV as one of the rapidly evolving infectious agents. This study reported a novel identified recombinant human astrovirus (Y/1-CHN) and its long existence in two immunocompromised patients with diarrhea following allogeneic hematopoietic stem cell transplantation (allo-HSCT). The identified Yu/1-CHN genome contains 6801 base pairs encoding three open reading frames, with ORF1a best hit to the HAstV1 (Pune strain, 97 % nucleotide identity), while ORF1b and ORF2 best hit to HAstV-5 (DL30 strain, 99 % nucleotide identity). Possible recombination breakpoint was predicted to be located in the boundary of ORF1a and ORF1b. Different quasispecies were found in the host, and the dN/dS ratios of the S and P domains were determined to be 1.189 and 1.444, respectively, suggesting a positive selection existed. Fecal samples collected in different clinical phases from the two patients were all positive for Yu/1-CHN, suggesting a long existence of the virus in the host. It was indicated that immunocompromised patients may a reservoir for astrovirus, their excreta should be monitored even after discharge from hospital.
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Affiliation(s)
- Jie-Mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China; National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Zhen-Hua Wang
- Department of Hematology, Peking University First Hospital, Beijing 100034, China; Department of Hematology, Qingdao Municipal Hospital (Group), Qingdao, 266071, China
| | - Na Liu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Qing Zhang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Yu-Jun Dong
- Department of Hematology, Peking University First Hospital, Beijing 100034, China.
| | - Zhao-Jun Duan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China.
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9
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Li M, Yan N, Ji C, Wang M, Zhang B, Yue H, Tang C. Prevalence and genome characteristics of canine astrovirus in southwest China. J Gen Virol 2019; 99:880-889. [PMID: 29846155 DOI: 10.1099/jgv.0.001077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The aim of this study was to investigate canine astrovirus (CaAstV) infection in southwest China. We collected 107 faecal samples from domestic dogs with obvious diarrhoea. Forty-two diarrhoeic samples (39.3 %) were positive for CaAstV by RT-PCR, and 41/42 samples showed co-infection with canine coronavirus (CCoV), canine parvovirus-2 (CPV-2) and canine distemper virus (CDV). Phylogenetic analysis based on 26 CaAstV partial ORF1a and ORF1b sequences revealed that most CaAstV strains showed unique evolutionary features. Interestingly, putative recombination events were observed among four of the five complete ORF2 sequences cloned in this study, and three of the five complete ORF2 sequences formed a single unique group, suggesting that these strains could be a novel genotype. We successfully sequenced the complete genome of one CaAstV strain (designated 2017/44/CHN), which was 6628 nt in length. The features of this genome include putative recombination events in the ORF1a, ORF1b and ORF2 genes, while the ORF2 gene had a continuous insertion of 7 aa in region II compared with the other complete ORF2 sequences available in GenBank. Phylogenetic analysis showed that 2017/44/CHN formed a single group based on genome sequences, suggesting that this strain might be a novel genotype. The results of this study revealed that CaAstV circulates widely in diarrhoeic dogs in southwest China and exhibits unique evolutionary events. To the best of our knowledge, this is the first report of recombination events in CaAstV, and it contributes to further understanding of the genetic evolution of CaAstV.
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Affiliation(s)
- Mingxiang Li
- College of Life Science and Technology, Southwest University for Nationalities, No. 16, South 4th Section 1st Ring Road, Chengdu 610041, PR China
| | - Nan Yan
- College of Life Science and Technology, Southwest University for Nationalities, No. 16, South 4th Section 1st Ring Road, Chengdu 610041, PR China
| | - Conghui Ji
- Chongqing Academy of Animal Science, Rongchang, Chongqing 402460, PR China
| | - Min Wang
- College of Life Science and Technology, Southwest University for Nationalities, No. 16, South 4th Section 1st Ring Road, Chengdu 610041, PR China
| | - Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, No. 16, South 4th Section 1st Ring Road, Chengdu 610041, PR China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, No. 16, South 4th Section 1st Ring Road, Chengdu 610041, PR China
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, No. 16, South 4th Section 1st Ring Road, Chengdu 610041, PR China
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10
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Lv SL, Zhang HH, Li JY, Hu WQ, Song YT, Opriessnig T, Xiao CT. High genetic diversity and recombination events of porcine astrovirus strains identified from ill and asymptomatic pigs in 2017, Hunan Province, China. Virus Genes 2019; 55:673-681. [PMID: 31372920 DOI: 10.1007/s11262-019-01692-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022]
Abstract
Astroviruses (AstV) are associated with enteric and systemic disease in mammals and birds. Astroviruses have received increased attention recently as they have been found to be associated with sporadic neurologic disease in mammals including humans. In pigs, porcine astrovirus (PoAstV) can be widely detected and has been grouped in five genotypes (PoAstV1 to PoAstV5). In the present study, we detected multiple PoAstVs in serum samples, nasal swabs, and fecal swabs collected from pigs suffering from respiratory disease or diarrhea but also from asymptomatic pigs, indicating a wide tissue tropism of the identified PoAstV genotypes. Coinfection of different genotypes in the same pig was commonly observed, and within an individual pig a high genetic diversity was observed for viruses belonging to the same PoAstV genotype. Two complete genomes of PoAstV2-WG-R2/2017 and PoAstV4-WG-R2/2017 were successfully obtained and characterized, with genome sizes of 6396 and 6643 nucleotides, respectively. The PoAstV2-WG-R2/2017 genome showed identities of 67.2-77.4% to other known PoAstV2 genomes, and the PoAstV4-WG-R2/2017 genome showed identities of 72.8-80.5% to other known PoAstV4 genomes. The predicted spike domain of open reading frame 2 (ORF2) of these strains showed the highest genetic heterogeneity, with amino acid identities of 13.7-70.9% for PoAstV2-WG-R2/2017 to other known PoAstV2 strains, and identities of 24.4-63.3% for the PoAstV4-WG-R2/2017 to other known PoAstV4 strains. Possible recombination events were identified in each of the two sequences. Two subclades of PoAstV2 and three subclades of PoAstV4 were defined in the present analyses. The obtained data provide further evidence for extraintestinal infectivity of PoAstVs, and confirmed the high genetic diversity of PoAstVs and the coinfection potential of different PoAstV types in a single pig.
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Affiliation(s)
- Sun-Liang Lv
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, China
| | - Hui-Hui Zhang
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, China
| | - Jie-Yu Li
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, China
| | - Wen-Qin Hu
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, China
| | - Ya-Ting Song
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Chao-Ting Xiao
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha, 410082, China.
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11
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Zhou N, Zhou L, Wang B. Molecular Evolution of Classic Human Astrovirus, as Revealed by the Analysis of the Capsid Protein Gene. Viruses 2019; 11:v11080707. [PMID: 31374999 PMCID: PMC6722597 DOI: 10.3390/v11080707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/17/2023] Open
Abstract
Classic human astroviruses (HAstV) are major global viral agents for gastroenteritis, but the molecular characteristics of classic HAstVs are not well understood. Here, we presented the molecular evolution of all classic HAstV serotypes by the analysis of the capsid protein sequences. Our results show that classic HAstVs can be divided into four groups with the most recent common ancestor (TMRCA) of 749. The overall evolutionary rate of classic HAstVs on the capsid gene was 4.509 × 10−4 substitutions/site/year, and most of the serotypes present a clock-like evolution with an amino acid accumulation of mutations over time. The mean effective population size of classic HAstVs is in a downward trend, and some positive and more than 500 negative selection sites were determined. Taken together, these results reveal that classic HAstVs evolve at the intra-serotype level with high genetic heterogeneity and are driven by strong purifying selection. Long-term surveillance of classic HAstVs are needed to enrich the genomic data for further analysis.
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Affiliation(s)
- Nan Zhou
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China.
| | - Lu Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, Jiangsu, China.
| | - Bei Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China.
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12
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Guo K, Li LL, Zhang Q, Yu JM, Ye Y. Diversified Variants of Astrovirus MLB2 in Patients Following Hematopoietic Stem Cell Transplantation and the Evolutionary Rates and Patterns of the Virus. Evol Bioinform Online 2019; 15:1176934319864922. [PMID: 31360058 PMCID: PMC6637835 DOI: 10.1177/1176934319864922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/03/2022] Open
Abstract
We assessed the quasispecies heterogeneity of a human astrovirus MLB2 (HAstV-MLB2-YJMGK) in immunocompromised patients following hematopoietic stem cell transplantation and performed genetic and evolutionary analyses of HAstV isolates circulating worldwide. The result showed that the virus had diversified variants and a strong positive selection in the patient, indicating that such patients may be a reservoir for astrovirus. The time to the most recent common ancestor of MLB2 and classic HAstVs was around 1800 years, and it has a decline in effective population size of HAstVs in the late 100 years.
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Affiliation(s)
- Ke Guo
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Li-Li Li
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Qing Zhang
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jie-Mei Yu
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yan Ye
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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13
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Giannitti F, Caffarena RD, Pesavento P, Uzal FA, Maya L, Fraga M, Colina R, Castells M. The First Case of Bovine Astrovirus-Associated Encephalitis in the Southern Hemisphere (Uruguay), Uncovers Evidence of Viral Introduction to the Americas From Europe. Front Microbiol 2019; 10:1240. [PMID: 31231334 PMCID: PMC6559012 DOI: 10.3389/fmicb.2019.01240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/17/2019] [Indexed: 12/05/2022] Open
Abstract
Astrovirus species members of the Mamastrovirus genus (family Astroviridae) have been increasingly recognized as neuroinvasive pathogens in various mammals, including humans, mink, cattle, sheep, and pigs. While cases of astrovirus-associated encephalitis have been reported in North America, Europe, and Asia, their presence has never been documented in the Southern hemisphere. This paper describes a case of astrovirus-associated encephalitis in cattle in Uruguay that broadens the geographic distribution and genetic diversity of neuroinvasive astroviruses and provides phylogeographic evidence of viral introduction to the Americas from Europe. A 22-month-old Holstein steer from a farm in Colonia Department, Uruguay developed progressive neurological signs over a 3-days period before dying. Histopathological examination of the brain and proximal cervical spinal cord revealed disseminated, moderate to severe lymphocytic, histiocytic, and plasmacytic poliomeningoencephalomyelitis with neuronal necrosis. A Mamastrovirus strain in the CH13/NeuroS1 clade, that we called bovine astrovirus (BoAstV)-Neuro-Uy, was identified by reverse transcriptase PCR followed by nearly complete genome sequencing. Additionally, BoAstV was detected intralesionally in the brain by chromogenic RNA in situ hybridization within neuronal perikarya, axons and dendrites. Phylogenetic analysis of BoAstV-Neuro-Uy revealed a close relationship to neurotropic BoAstVs within the Virginia/Human-Mink-Ovine clade, which contains a growing cadre of neuroinvasive astroviruses. Analyzing the complete coding region of neuroinvasive BoAstVs sequences available in GenBank, we estimated an evolutionary rate of 4.27 × 10-4 (95% HPD 2.19–6.46 × 10-4) nucleotide substitutions/site/year. Phylogeographic analysis suggests that the common viral ancestor circulated in Europe between 1794–1940, and was introduced in Uruguay between 1849–1967, to later spread to North America and Japan.
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Affiliation(s)
- Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental INIA La Estanzuela, Colonia, Uruguay
| | - Rubén Darío Caffarena
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental INIA La Estanzuela, Colonia, Uruguay.,Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Patricia Pesavento
- Pathology, Microbiology and Immunology Department, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Francisco Alejandro Uzal
- Pathology, Microbiology and Immunology Department, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Leticia Maya
- Laboratorio de Virología Molecular, Centro Universitario Regional (CENUR) Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Martín Fraga
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental INIA La Estanzuela, Colonia, Uruguay
| | - Rodney Colina
- Laboratorio de Virología Molecular, Centro Universitario Regional (CENUR) Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Matías Castells
- Instituto Nacional de Investigación Agropecuaria (INIA), Plataforma de Investigación en Salud Animal, Estación Experimental INIA La Estanzuela, Colonia, Uruguay.,Laboratorio de Virología Molecular, Centro Universitario Regional (CENUR) Litoral Norte, Universidad de la República, Salto, Uruguay
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14
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Wohlgemuth N, Honce R, Schultz-Cherry S. Astrovirus evolution and emergence. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 69:30-37. [PMID: 30639546 PMCID: PMC7106029 DOI: 10.1016/j.meegid.2019.01.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/19/2022]
Abstract
Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown. Recombination events can lead to drastic evolutionary changes and contribute to cross-species transmission events. This work reviews the current state of research on astrovirus evolution and emergence, especially as it relates to cross-species transmission and recombination of astroviruses.
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Affiliation(s)
- Nicholas Wohlgemuth
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38105, United States
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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15
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Hata A, Kitajima M, Haramoto E, Lee S, Ihara M, Gerba CP, Tanaka H. Next-generation amplicon sequencing identifies genetically diverse human astroviruses, including recombinant strains, in environmental waters. Sci Rep 2018; 8:11837. [PMID: 30087387 PMCID: PMC6081416 DOI: 10.1038/s41598-018-30217-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023] Open
Abstract
Human astroviruses are associated with gastroenteritis and known to contaminate water environments. Three different genetic clades of astroviruses are known to infect humans and each clade consists of diverse strains. This study aimed to determine the occurrence and genetic diversity of astrovirus strains in water samples in different geographical locations, i.e., influent and effluent wastewater samples (n = 24 each) in Arizona, U.S., and groundwater (n = 37) and river water (n = 14) samples collected in the Kathmandu Valley, Nepal, using next-generation amplicon sequencing. Astrovirus strains including rare types (types 6 and 7 classical human astroviruses), emerging type (type 5 VA-astroviruses), and putative recombinants were identified. Feline astrovirus strains were collaterally identified and recombination between human and feline astroviruses was suggested. Classical- and VA-astroviruses seemed to be prevalent during cooler months, while MLB-astroviruses were identified only during warmer months. This study demonstrated the effectiveness of next-generation amplicon sequencing for identification and characterization of genetically diverse astrovirus strains in environmental water.
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Affiliation(s)
- Akihiko Hata
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan. .,Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Hokkaido, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Yamanashi, Japan
| | - Suntae Lee
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan
| | - Charles P Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, Arizona, USA
| | - Hiroaki Tanaka
- Research Center for Environmental Quality Management, Kyoto University, Shiga, Japan
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16
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Jacobsen S, Höhne M, Marques AM, Beslmüller K, Bock CT, Niendorf S. Co-circulation of classic and novel astrovirus strains in patients with acute gastroenteritis in Germany. J Infect 2018; 76:457-464. [PMID: 29454018 DOI: 10.1016/j.jinf.2018.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/12/2018] [Accepted: 02/09/2018] [Indexed: 10/18/2022]
Abstract
OBJECTIVES In order to analyze the molecular epidemiology of human astroviruses (HAstV) in Germany, a retrospective long-term study was performed to characterize circulating human astrovirus in patients with acute gastroenteritis in Germany. METHODS A total of 2877 stool samples, collected between January 2010 and December 2015 from sporadic cases and outbreaks of acute gastroenteritis were retrospectively analyzed for astrovirus. A two-step PCR algorithm was developed and used to identify and characterize human astrovirus infections. RESULTS Overall, 143 samples were astrovirus-positive (5.0%). Astrovirus infection was most frequently detectable in samples from children of 3-4 years (15%) followed by children of 1-2 years (8.6%), detection rates in adults were lower (1%-3.6%). A high number (71.3%) of co-infections, mainly with noro- or rotaviruses, were identified. Genotyping revealed that at least ten genotypes from all four human MAstV species were circulating in the study population. HAstV-1 was predominant in different age groups. Novel HAstV (MLB and VA genotypes) were also circulating in Germany. CONCLUSION Our findings give new insights into the circulation and genetic diversity of human astroviruses in patients with acute gastroenteritis. The novel HAstV-MLB and -VA genotypes could be characterized firstly in Germany while the analysis showed that these viruses have been dispersed in Germany since 2011 as a causative agent of acute gastroenteritis.
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Affiliation(s)
- Sonja Jacobsen
- Department of Infectious Diseases, Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany; Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Marina Höhne
- Department of Infectious Diseases, Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany; Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Andreas Mas Marques
- Department of Infectious Diseases, Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany; Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Klara Beslmüller
- Department of Infectious Diseases, Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany; Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - C-Thomas Bock
- Department of Infectious Diseases, Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany
| | - Sandra Niendorf
- Department of Infectious Diseases, Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany; Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353, Berlin, Germany.
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17
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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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18
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Cortez V, Meliopoulos VA, Karlsson EA, Hargest V, Johnson C, Schultz-Cherry S. Astrovirus Biology and Pathogenesis. Annu Rev Virol 2017; 4:327-348. [PMID: 28715976 DOI: 10.1146/annurev-virology-101416-041742] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Astroviruses are nonenveloped, positive-sense single-stranded RNA viruses that cause gastrointestinal illness. Although a leading cause of pediatric diarrhea, human astroviruses are among the least characterized enteric RNA viruses. However, by using in vitro methods and animal models to characterize virus-host interactions, researchers have discovered several important properties of astroviruses, including the ability of the astrovirus capsid to act as an enterotoxin, disrupting the gut epithelial barrier. Improved animal models are needed to study this phenomenon, along with the pathogenesis of astroviruses, particularly in those strains that can cause extraintestinal disease. Much like for other enteric viruses, the current dogma states that astroviruses infect in a species-specific manner; however, this assumption is being challenged by growing evidence that these viruses have potential to cross species barriers. This review summarizes these remarkable facets of astrovirus biology, highlighting critical steps toward increasing our understanding of this unique enteric pathogen.
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Affiliation(s)
- Valerie Cortez
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Victoria A Meliopoulos
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Erik A Karlsson
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Virginia Hargest
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , , .,Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Cydney Johnson
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
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19
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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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20
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Ha HJ, Lee SG, Cho HG, Jin JY, Lee JW, Paik SY. Complete genome sequencing of a recombinant strain between human astrovirus antigen types 2 and 8 isolated from South Korea. INFECTION GENETICS AND EVOLUTION 2016; 39:127-131. [PMID: 26812127 DOI: 10.1016/j.meegid.2016.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
Abstract
Human astroviruses (HAstVs) occur worldwide and are known to the causative agents of diarrhea in infants and elderly patients with immune dysfunction. This study aimed to identify recombinant HAstV strains and characterize rare genotypes. The full-length genome of a recombinant HAstV strain isolated from the stool sample of a patient with acute gastroenteritis from South Korea was amplified using three pairs of previously designed primers and seven newly designed primers. The recombinant HAstV was 6757-bp long and contained three sequential open reading frames (ORFs), designated as ORF1a (2781 bp), ORF1b (1548 bp), and ORF2 (2349 bp). Our findings suggested that a recombination event had occurred between ORF1b and ORF2 of the isolated strain, with a recombination breakpoint at 4081 bp. To our knowledge, this is the first study to reveal the complete nucleotide sequence of a recombinant HAstV strain from South Korea. Our study findings might be useful for identifying other recombinant HAstV strains and for developing vaccines against this pathogenic virus.
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Affiliation(s)
- Hyun-Ju Ha
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea.
| | - Sung-Geun Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan 570-390, Republic of Korea.
| | - Han-Gil Cho
- Division of Public Health Research, Gyeonggi Province Institute of Health and Environment, Suwon 440-290, Republic of Korea.
| | - Ji-Young Jin
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea.
| | - Jae Woong Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea.
| | - Soon-Yong Paik
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu, Seoul 06591, Republic of Korea.
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21
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Medici MC, Tummolo F, Martella V, Banyai K, Bonerba E, Chezzi C, Arcangeletti MC, De Conto F, Calderaro A. Genetic heterogeneity and recombination in type-3 human astroviruses. INFECTION GENETICS AND EVOLUTION 2015; 32:156-60. [PMID: 25784567 DOI: 10.1016/j.meegid.2015.03.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/02/2015] [Accepted: 03/09/2015] [Indexed: 11/30/2022]
Abstract
Human astroviruses (HAstVs) are important enteric pathogens and can be classified genetically and antigenically into eight types. During molecular surveillance for HAstVs in Italy, sequence analysis of the diagnostic region C (about 400 nucleotide in length), located on the capsid (ORF2) gene, identified a novel type-3 strain. Upon sequencing of the full-length ORF2, the type-3 HAstV strain was characterized as a novel ORF2 genetic lineage, designated as 3c. By converse, in the ORF1b the virus was more similar to type-1 HAstVs, rather than to type-3 strains, suggesting a recombination nature, with the crossover site being mapped to the ORF1b/ORF2 junction region. Region C sequences of similar type-3 HAstV identified from European and extra-European countries were retrieved in the databases, suggesting the global distribution of this novel type-3 lineage.
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Affiliation(s)
- Maria Cristina Medici
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.
| | - Fabio Tummolo
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Krisztián Banyai
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Elisabetta Bonerba
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Carlo Chezzi
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Maria Cristina Arcangeletti
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Flora De Conto
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Adriana Calderaro
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
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