1
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Ijeomah IM, Temitope FOC, Lander DC, Sheriff AT, Uwem GE, Bernard OA, Oluseyi OA, Elijah OI, Toluwani AG, Arthur OO, Toluwanimi AE, Bolutife PO, Damilola OG, Titilola OO, Oluwadamilola GA, Muhammad AI, Omotosho KI, Johnson AA, Jelle M, Olubusuyi AM. Classic human astrovirus 4, 8, MLB-3, and likely new genotype 5 sublineage in stool samples of children in Nigeria. J Med Virol 2024; 96:e29489. [PMID: 38402605 DOI: 10.1002/jmv.29489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Human astrovirus (HAstV) is a nonenveloped RNA virus and has been implicated in acute gastroenteritis among children and elderly. However, there exists a substantial dearth of information on HAstV strains circulating in Nigeria. Viral-like particles were purified from archived 254 stool samples of children with acute flaccid paralysis between January and December 2020 from five states in Nigeria, using the NetoVIR protocol. Extracted viral RNA and DNA were subjected to a reverse transcription step and subsequent random polymerase chain reaction amplification. Library preparation and Illumina sequencing were performed. Using the virome paired-end reads pipeline, raw reads were processed into genomic contigs. Phylogenetic and pairwise identity analysis of the recovered HAstV genomes was performed. Six near-complete genome sequences of HAstV were identified and classified as HAstV4 (n = 1), HAstV5 (n = 1), HAstV8 (n = 1), and MLB-3 (n = 3). The HAstV5 belonged to a yet unclassified sublineage, which we tentatively named HAstV-5d. Phylogenetic analysis of open reading frames 1a, 1b, and 2 suggested recombination events inside the MAstV1 species. Furthermore, phylogenetic analysis implied a geographic linkage between the HAstV5 strain from this study with two strains from Cameroon across all the genomic regions. We report for the first time the circulation of HAstV genotypes 4, 8, and MLB-3 in Nigeria and present data suggestive for the existence of a new sublineage of HAstV5. To further understand the burden, diversity, and evolution of HAstV, increased research interest as well as robust HAstV surveillance in Nigeria is essential.
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Affiliation(s)
- Ifeorah M Ijeomah
- Department of Medical Laboratory Sciences and Center for Translation and Implementation Research, University of Nigeria Enugu Campus, Enugu, Nigeria
| | - Faleye O C Temitope
- Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - De Coninck Lander
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Agbaje T Sheriff
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - George E Uwem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University Ede, Ede, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Ede, Nigeria
| | - Onoja A Bernard
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olayinka A Oluseyi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oni I Elijah
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ajileye G Toluwani
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oragwa O Arthur
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Jos, Jos, Nigeria
| | - Akinleye E Toluwanimi
- Phytomedicine Unit, Department of Pharmacognosy, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Popoola O Bolutife
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Osasona G Damilola
- Department of Medical Laboratory Sciences, Faculty of Basic Medical Sciences, Osun State and Hospitals Management Board, Redeemer's University Ede, Ado-Ekiti, Nigeria
| | - Olayinka O Titilola
- National Polio Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Ahmed I Muhammad
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Komolafe I Omotosho
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Ede, Nigeria
| | - Adeniji A Johnson
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Matthijnssens Jelle
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Adewumi M Olubusuyi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
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2
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Li J, Yang L, Wang K, Gao Z, Li P, Lin Y, Jia L, Wang Q, Song H, Li P. Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols. Virol J 2023; 20:263. [PMID: 37964283 PMCID: PMC10647158 DOI: 10.1186/s12985-023-02224-7] [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: 06/16/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023] Open
Abstract
Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38-100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV.
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Affiliation(s)
- Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Zhiyong Gao
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Yanfeng Lin
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, China.
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
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3
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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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4
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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: 0] [Impact Index Per Article: 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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5
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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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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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Luchs A, Tardy K, Tahmasebi R, Morillo SG, Milagres FADP, Morais VDS, Brustulin R, Teles MDAR, de Azevedo LS, de Souza EV, Medeiros RS, de Souza YFVP, Araújo ELL, Witkin SS, Deng X, Delwart E, Sabino EC, Leal E, da Costa AC. Human astrovirus types 1, 4 and 5 circulating among children with acute gastroenteritis in a rural Brazilian state, 2010-2016. Arch Virol 2021; 166:3165-3172. [PMID: 34417874 DOI: 10.1007/s00705-021-05206-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/22/2021] [Indexed: 11/30/2022]
Abstract
This study combined conventional epidemiology of human astroviruses. From 2010 to 2016, 232 stool samples from children under 5 years of age were screened using NGS and conventional RT-PCR followed by genetic analysis in order to investigate the genotypic diversity of classical human astrovirus (HAstV) circulating in Tocantins State, Brazil. HAstV was detected in 16 cases (6.9%). Seven specimens (43.7%; 7/16) were positive according RT-PCR and next-generation sequencing (NGS) to investigate the molecular to both NGS and RT-PCR. NGS and RT-PCR individually revealed six (37.5%; 6/16) and three (18.8%; 3/16) additional positive samples, respectively. Sequencing of the HAstV-positive samples revealed HAstV-1a (9/16), HAstV-4c (3/16), and HAstV-5c (4/16) lineages.
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Affiliation(s)
- Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil.
| | - Kaelan Tardy
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Roozbeh Tahmasebi
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Simone Guadagnucci Morillo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | - Vanessa Dos Santos Morais
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Rafael Brustulin
- Universidade Federal do Tocantins, Tocantins, Brazil.,Laboratório Central de Saúde Pública do Tocantins (Lacen-TO), Tocantins, Brazil
| | | | - Lais Sampaio de Azevedo
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Ellen Viana de Souza
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | - Roberta Salzone Medeiros
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brazil
| | | | - Emerson Luiz Lima Araújo
- Coordenação Geral de Laboratórios de Saúde Pública, Departamento de Articulação Estratégica de Vigilância em Saúde da Secretaria de Vigilância em Saúde do Ministério da Saúde do Brasil (CGLAB/DAEVS/SVS-MS), Brasília, Brazil
| | - Steven S Witkin
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, USA
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil
| | - Elcio Leal
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, nº 470, São Paulo, SP, 05403-000, Brazil.
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Nagai M, Okabayashi T, Akagami M, Matsuu A, Fujimoto Y, Hashem MA, Mekata H, Nakao R, Matsuno K, Katayama Y, Oba M, Omatsu T, Asai T, Nakagawa K, Ito H, Madarame H, Kawai K, Ito T, Nonaka N, Tsukiyama-Kohara K, Inoshima Y, Mizutani T, Misawa N. Metagenomic identification, sequencing, and genome analysis of porcine hepe-astroviruses (bastroviruses) in porcine feces in Japan. INFECTION GENETICS AND EVOLUTION 2020; 88:104664. [PMID: 33333290 DOI: 10.1016/j.meegid.2020.104664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 11/29/2022]
Abstract
Recently, hepe-astrovirus-like RNA viruses named bastroviruses (BastVs), have been found in human, pig, bat, and rat fecal samples. In this study, we determined nearly complete genome sequences of four BastVs in the feces of healthy pigs. Genetic characterization revealed that these porcine BastVs (PBastVs) and BastVs from other animals including humans, had the same genome organization, that is, they contained three predicted conserved domains of viral methyltransferase, RNA helicase, and RdRp in the nonstructural ORF1 and the astrovirus capsid domain in the structural ORF2. Phylogenetic analyses using RNA-dependent RNA polymerase and the capsid region revealed that PBastVs branched with bat and rat BastVs; however, the groups formed by each host were distantly related to human BastVs. Pairwise amino acid sequence comparison demonstrated that PBastVs shared 95.2-98.6% and 76.1-95.5% sequence identity among each other in the ORF1 and ORF2 regions, respectively; the sequence identities between PBastVs and BastVs from other animals were 21.4-42.5% and 9.1-20.6% in the ORF1 and ORF2 regions, respectively. This suggested that BastVs were derived from a common ancestor but evolved independently in each host population during a prolonged period. Putative recombination events were identified in the PBastV genome, suggesting that PBastVs gain sequence diversity and flexibility through recombination events. In an analysis of previously obtained metagenomic data, PBastV sequence reads were detected in 7.3% (23/315) of fecal samples from pigs indicating that PBastVs are distributed among pig populations in Japan.
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Affiliation(s)
- Makoto Nagai
- Department of Large Animal Clinic, Azabu University, Veterinary Teaching Hospital, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Tamaki Okabayashi
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan; Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Masataka Akagami
- Kenpoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan
| | - Aya Matsuu
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Yoshikazu Fujimoto
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Md Abul Hashem
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan
| | - Hirohisa Mekata
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
| | - Keita Matsuno
- Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Hokkaido, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tetsuo Asai
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keisuke Nakagawa
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroshi Ito
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Hiroo Madarame
- Department of Large Animal Clinic, Azabu University, Veterinary Teaching Hospital, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Kazuhiro Kawai
- Department of Large Animal Clinic, Azabu University, Veterinary Teaching Hospital, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Toshihiro Ito
- Department of Joint Veterinary Medicine, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan; Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Nariaki Nonaka
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, Japan; Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Yasuo Inoshima
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), 1-1 Yanagido, Gifu 501-1193, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
| | - Naoaki Misawa
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan; Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.
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Amimo JO, Machuka EM, Abworo EO, Vlasova AN, Pelle R. Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms. Viruses 2020; 12:v12111262. [PMID: 33167568 PMCID: PMC7694451 DOI: 10.3390/v12111262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.
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Affiliation(s)
- Joshua O. Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, P.O. Box 29053, Nairobi 00625, Kenya
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, 1168 Madison Avenue, Wooster, OH 44961, USA;
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
- Correspondence:
| | - Eunice M. Machuka
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
| | - Edward O. Abworo
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, 1168 Madison Avenue, Wooster, OH 44961, USA;
| | - Roger Pelle
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (E.M.M.); (E.O.A.); (R.P.)
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10
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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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11
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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: 69] [Impact Index Per Article: 13.8] [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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12
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Wan CH, Chen CT, Cheng LF, Liu RC, Shi SH, Fu GH, Fu QL, Chen HM, Huang Y. A novel group of avian Avastrovirus in domestic geese, China. J Vet Med Sci 2018; 80:798-801. [PMID: 29553061 PMCID: PMC5989025 DOI: 10.1292/jvms.18-0013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Using an ORF1b-based astrovirus-specfic reverse transcription (RT)-PCR assay, a novel astrovirus-like was detected from domestic geese in China. Pairwise comparisons and phylogenetic
analyzes suggested that a novel group of goose astrovirus, different with previously known astroviruses in the genus Avastrovirus, was found circulating in geese. This study
has expanded our understanding about the role of domestic waterfowls as reservoirs for diverse astroviruses.
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Affiliation(s)
- Chun-He Wan
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Cui-Teng Chen
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Long-Fei Cheng
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Rong-Chang Liu
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Shao-Hua Shi
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Guang-Hua Fu
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Qiu-Ling Fu
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Hong-Mei Chen
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yu Huang
- Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fujian Animal Diseases Control Technology Development Center, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
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13
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Detection and genetic characterization of classic human astroviruses in Brazil, 2010-2012. Arch Virol 2018; 163:1293-1297. [DOI: 10.1007/s00705-018-3728-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/02/2018] [Indexed: 12/22/2022]
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14
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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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15
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Zhou H, Liu L, Li R, Qin Y, Fang Q, Balasubramaniam VR, Wang G, Wei Z, Ouyang K, Huang W, Chen Y. Detection and genetic characterization of canine astroviruses in pet dogs in Guangxi, China. Virol J 2017; 14:156. [PMID: 28814340 PMCID: PMC5559842 DOI: 10.1186/s12985-017-0823-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/08/2017] [Indexed: 12/12/2022] Open
Abstract
Background Astroviruses (AstVs) have been reported to infect and cause gastroenteritis in most animal species. Human AstVs were regarded the causative agent of viral diarrhea in children. In dogs, little is known about the epidemiology and clinical significance of AstV infection. Findings In this study, we collected and tested 253 rectal swabs from pet dogs; of which 64 samples (25.3%) tested positive for AstVs with diarrhea and 15 more samples (5.9%) also was identified as AstVs, however without any clinical signs. Phylogenetic analysis of 39 partial ORF1b sequences from these samples revealed that they are similar to AstVs, which can be subdivided into three lineages. Interestingly, out of the 39 isolates sequenced, 16 isolates are shown to be in the Mamastrovirus 5/canine astrovirus (CAstV) lineage and the remaining 23 isolates displayed higher similarities with known porcine astrovirus (PoAstV) 5 and 2. Further, analysis of 13 capsid sequences from these isolates showed that they are closely clustered with Chinese or Italy CAstV isolates. Conclusions The findings indicate that CAstVs commonly circulate in pet dogs, and our sequencing results have shown the genomic diversity of CAstVs leading to increasing number of clusters.
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Affiliation(s)
- Huabo Zhou
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China.,Huabo Pet Hospital, No.1 Anji Road, Nanning, 53004, People's Republic of China
| | - Lin Liu
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Ruikai Li
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Yifeng Qin
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Qingli Fang
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Vinod Rmt Balasubramaniam
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Subang Jaya, Selangor, Malaysia
| | - Guojun Wang
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Zuzhang Wei
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Kang Ouyang
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Weijian Huang
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China
| | - Ying Chen
- College of Animal Science and Technology, Guangxi University, No.100 Daxue Road, Nanning, 530004, People's Republic of China.
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16
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Astrovirus infection in hospitalized children: Molecular, clinical and epidemiological features. J Clin Virol 2017; 94:79-85. [PMID: 28772169 DOI: 10.1016/j.jcv.2017.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/19/2017] [Accepted: 07/24/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND Astrovirus (HAstV) is a common viral pathogen that causes gastroenteritis worldwide. It is classified into eight classical human types (HAstV-1/8) and seven other less prevalent types, described as HAstV VA1, VA2, VA3, VA4, MLB-1, MLB-2 and MLB-3. During outbreaks, the elderly and children are the most affected, and the spread of the virus is associated with person-to-person contact, food ingestion and contaminated water. OBJECTIVES The aim of the present study was to investigate the prevalence of infection and genetic diversity of HAstV strains. Samples were collected from children with acute gastroenteritis admitted to a large pediatric hospital during a surveillance period of three years (2008-2011) in Belém city, Pará State, Amazon Region, Northern Brazil. STUDY DESIGN Screening and genotyping tests were conducted using RT-PCR to detect the classical and non-classical HAstV types using specific primers. A semi-nested RT-PCR protocol was developed to improve viral detection in samples with a low viral load. RESULTS The overall positivity observed in this study was 3.9% (19/483). The age distribution showed a high prevalence of positive cases in children under one year old (5.3%). We found vomiting associated with 75% of the positive cases, fever with 82.3%, and dehydration with 76.9%. Most patients with positive cases demonstrated two to five days of diarrhea, two to three episodes of vomiting during hospitalization, and three bowel movements per day. Co-infection with HAstV and norovirus was observed in three cases (15.8%), and no pattern of seasonality or any relationship between the HAstV positivity rate and climate variables was observed. Eighteen positive samples (94.7%-18/19) were genotyped based on the ORF 2 region, and the greatest prevalence was of HAstV-1a (66.6%-12/18), followed by HAstV-2 (22.2%-4/18, comprising two type-2b and two type-2c genotypes), HAstV-3c (5.6%-1/18) and HAstV-4c (5.6%-1/18). No non-classical types were detected in the clinical samples analyzed. CONCLUSIONS The present study showed that although HAstV infections occur at low frequency, they are involved in severe pediatric cases of acute gastroenteritis presenting with a high diversity of strains, including the lineages 3c and 4c, which were never before detected in Brazil.
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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: 113] [Impact Index Per Article: 16.1] [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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18
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Lopez F, Lizasoain A, Victoria M, Papalardo C, Castro S, Arreseigor E, López P, Colina R. Epidemiology and genetic diversity of classic human astrovirus among hospitalized children with acute gastroenteritis in Uruguay. J Med Virol 2017; 89:1775-1781. [PMID: 28500748 DOI: 10.1002/jmv.24854] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 04/26/2017] [Indexed: 01/24/2023]
Abstract
Classic Human Astrovirus (Classic HAstV) are one of the most important causes of pediatric acute gastroenteritis (AGE), after rotaviruses and arguably caliciviruses. The aim of this study was to determine the molecular epidemiology of Classic HAstV from 175 clinical samples, being 153 stools and 22 vomits, collected from pediatric hospitalized patients with AGE in Salto city, Uruguay, from January 2011 to December 2012. Classic HAstV were detected and genotyped by using a qualitative Retro Transcription-Polimerase Chain Reaction (RT-PCR) directed to the Open Reading Frame-2 (ORF2) region C. Amplicons were sequenced and phylogenetic analyses were carried out in order to determine genotypes and lineages. Classic HAstV were detected in 18 out of 175 analyzed samples (10.3%) and 14 of them (78.0%) were successfully sequenced being 6 (42.8%) classified as HAstV-1 (1a lineage), 4 (28.6%) as HAstV-2 (2c lineage), and 4 (28.6%) as HAstV-3 (3c lineage). A higher detection of Classic HAstV infections was observed in autumn for both years of surveillance, and the majority of the positive cases were observed in 2011. The group of children between 2 and 5 years old presented the higher percentage of infections. To our knowledge, the present study represents the first report of astrovirus from acute gastroenteritis cases in Uruguay, evidencing its role as a relevant etiologic agent in severe cases of this disease.
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Affiliation(s)
- Fernando Lopez
- Molecular Virology Laboratory, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Andrés Lizasoain
- Molecular Virology Laboratory, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Matías Victoria
- Department of Mathematics and Statistics CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Cecilia Papalardo
- Department of Mathematics and Statistics CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Sebastian Castro
- Department of Mathematics and Statistics CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - Edit Arreseigor
- Pediatric Unit, Medical-Surgical Society of Salto, Salto, Uruguay
| | | | - Rodney Colina
- Molecular Virology Laboratory, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
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19
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Donato C, Vijaykrishna D. The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses. Viruses 2017; 9:v9050102. [PMID: 28489047 PMCID: PMC5454415 DOI: 10.3390/v9050102] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 01/23/2023] Open
Abstract
Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.
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Affiliation(s)
- Celeste Donato
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
| | - Dhanasekaran Vijaykrishna
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
- Duke-NUS Medical School, Singapore 169857, Singapore.
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20
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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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21
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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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22
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Lizasoain A, Tort L, García M, Gómez M, Leite J, Miagostovich M, Cristina J, Colina R, Victoria M. Environmental assessment reveals the presence of MLB-1 human astrovirus in Uruguay. J Appl Microbiol 2015; 119:859-67. [DOI: 10.1111/jam.12856] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/12/2015] [Accepted: 05/14/2015] [Indexed: 11/28/2022]
Affiliation(s)
- A. Lizasoain
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - L.F.L. Tort
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - M. García
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - M.M. Gómez
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Oswaldo Cruz Foundation; Rio de Janeiro Brazil
| | - J.P.G. Leite
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Oswaldo Cruz Foundation; Rio de Janeiro Brazil
| | - M.P. Miagostovich
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Oswaldo Cruz Foundation; Rio de Janeiro Brazil
| | - J. Cristina
- Laboratory of Molecular Virology; Nuclear Investigation Center; School of Sciences; Universidad de la República; Montevideo Uruguay
| | - R. Colina
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - M. Victoria
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
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23
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Medici MC, Tummolo F, Grazia SD, Calderaro A, Conto FD, Terio V, Chironna M, Bonura F, Pucci M, Bányai K, Martella V, Giammanco GM. Epidemiological dynamics of norovirus GII.4 variant New Orleans 2009. J Gen Virol 2015; 96:2919-2927. [PMID: 26025873 DOI: 10.1099/vir.0.000204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Norovirus (NoV) is one of the major causes of diarrhoeal disease with epidemic, outbreak and sporadic patterns in humans of all ages worldwide. NoVs of genotype GII.4 cause nearly 80-90 % of all NoV infections in humans. Periodically, some GII.4 strains become predominant, generating major pandemic variants. Retrospective analysis of the GII.4 NoV strains detected in Italy between 2007 and 2013 indicated that the pandemic variant New Orleans 2009 emerged in Italy in the late 2009, became predominant in 2010-2011 and continued to circulate in a sporadic fashion until April 2013. Upon phylogenetic analysis based on the small diagnostic regions A and C, the late New Orleans 2009 NoVs circulating during 2011-2013 appeared to be genetically different from the early New Orleans 2009 strains that circulated in 2010. For a selection of strains, a 3.2 kb genome portion at the 3' end was sequenced. In the partial ORF1 and in the full-length ORF2 and ORF3, the 2011-2013 New Orleans NoVs comprised at least three distinct genetic subclusters. By comparison with sequences retrieved from the databases, these subclusters were also found to circulate globally, suggesting that the local circulation reflected repeated introductions of different strains, rather than local selection of novel viruses. Phylogenetic subclustering did not correlate with changes in residues located in predicted putative capsid epitopes, although several changes affected the P2 domain in epitopes A, C, D and E.
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Affiliation(s)
- Maria Cristina Medici
- Unità di Microbiologia e Virologia, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Parma, Parma, Italy
| | - Fabio Tummolo
- Unità di Microbiologia e Virologia, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Parma, Parma, Italy
| | - Simona De Grazia
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile G. D'Alessandro, Università di Palermo, Palermo, Italy
| | - Adriana Calderaro
- Unità di Microbiologia e Virologia, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Parma, Parma, Italy
| | - Flora De Conto
- Unità di Microbiologia e Virologia, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Parma, Parma, Italy
| | - Valentina Terio
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Maria Chironna
- Dipartimento di Scienze Biomediche ed Oncologia Umana, Sezione di Igiene e Medicina Preventiva, Policlinico di Bari, Bari, Italy
| | - Floriana Bonura
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile G. D'Alessandro, Università di Palermo, Palermo, Italy
| | - Marzia Pucci
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile G. D'Alessandro, Università di Palermo, Palermo, Italy
| | - Kristián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni Maurizio Giammanco
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile G. D'Alessandro, Università di Palermo, Palermo, Italy
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24
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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: 21] [Impact Index Per Article: 2.3] [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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25
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Lizasoain A, Tort LFL, García M, Gómez MM, Cristina J, Leite JPG, Miagostovich MP, Victoria M, Colina R. Environmental Assessment of Classical Human Astrovirus in Uruguay. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:142-148. [PMID: 25680829 DOI: 10.1007/s12560-015-9186-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/07/2015] [Indexed: 06/04/2023]
Abstract
The aim of this study was to determine the molecular epidemiology of classical human astrovirus (HAstV) strains in sewage samples from four Uruguayan cities: Bella Unión, Salto, Paysandú, and Fray Bentos, located in the Northwestern region of the country. Overall, 96 sewage samples were collected biweekly between March 2011 and February 2012 and were subject to ultracentrifugation methodology in order to concentrate the viruses. RT-PCR directed to the ORF2 genome region was performed followed by sequencing and phylogenetic analysis. Forty-three (45 %) out of 96 analyzed samples were positive for HAstV (Mamastrovirus 1) and 31 of them were successfully sequenced being 21 (49 %) of them classified as HAstV-1 genotype (1a lineage) and 10 (23 %) as HAstV-2 genotype (eight strains belonging to the 2d lineage and two strains to the 2c lineage). The 1a lineage circulated throughout the year, while the 2d lineage only in the coldest months (June to October). Strikingly, the 2c lineage was detected only in Salto city during March 2011. In this city it was observed the highest frequency of HAstV and the greatest genetic diversity, probably due to its role as high touristic spot with an important influx of visitants from others regions of Uruguay and also from other countries. This study constitutes the first report in Uruguay that describes the phylogenetic diversity and genotype distribution of HAstV strains circulating in the Northwestern region evidencing a high frequency and also the presence of several different lineages.
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Affiliation(s)
- A Lizasoain
- Laboratorio de Virología Molecular. Regional Norte - CENUR Noroeste, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
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26
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Martella V, Pinto P, Tummolo F, De Grazia S, Giammanco GM, Medici MC, Ganesh B, L'Homme Y, Farkas T, Jakab F, Bányai K. Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system. Arch Virol 2014; 159:3185-96. [PMID: 25326755 DOI: 10.1007/s00705-014-2153-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/16/2014] [Indexed: 11/26/2022]
Abstract
Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5' or 3' end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.
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Affiliation(s)
- Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy,
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27
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Abstract
Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.
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Affiliation(s)
- Albert Bosch
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Microbiology and Institute of Nutrition and Food Safety, University of Barcelona, Barcelona, Spain
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28
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Recombination analysis based on the HAstV-2 and HAstV-4 complete genomes. INFECTION GENETICS AND EVOLUTION 2014; 22:94-102. [PMID: 24462746 DOI: 10.1016/j.meegid.2014.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/11/2014] [Accepted: 01/13/2014] [Indexed: 11/21/2022]
Abstract
Complete genome sequences of previously unstudied human astrovirus subgenotypes - HAstV-2a and HAstV-2c - and two isolates of a rare genotype HAstV-4 have been determined. These isolates were recovered from fecal samples of young children hospitalized with acute intestinal infections in Novosibirsk (Russia). Three of the four sequenced isolates (HAstV-2a, HAstV-2c, and HAstV-4) are recombinants. It has been shown that all known HAstV-2 genomes have emerged via recombination; the HAstV-1 and HAstV-4 genotypes contain both recombinant and non-recombinant isolates; and all HAstV-3, HAstV-5, and HAstV-6 whole-genome sequences display no reliable signs of recombination. The average mutation accumulation rate has been determined based on an extended ORF2 fragment and amounts to 1.0×10(-3) substitutions per site per year. The evolutionary chronology of current HAstV genotypes has been reconstructed.
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