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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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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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Nadan S, Taylor MB, Page NA. Circulation of classic and recombinant human astroviruses detected in South Africa: 2009 to 2014. J Clin Virol 2020; 135:104719. [PMID: 33388529 DOI: 10.1016/j.jcv.2020.104719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/13/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA). METHODS Astroviruses detected in stool specimens collected from hospitalised children were investigated retrospectively. Astroviruses were characterised using type-specific RT-PCR, partial nucleotide sequence analyses in ORF1 and ORF2 and whole genome sequencing. Different genotypes were compared with clinical features to investigate genotype-related associations. The Vesikari severity scale (VSS) was evaluated for scoring astrovirus diarrhoeal infections. RESULTS Of 405 astroviruses detected, 49.9 % (202/405) were characterised into 32 genotypes comprising 66.3 % (134/202) putative-recombinants and 33.7 % (68/202) classic strains. No trends by year of collection, age or site were observed. Whole genome analysis in eight strains revealed that genotypes assigned by partial nucleotide sequence analyses to five astroviruses were incorrect. Bivariate analyses showed there were no significant associations between genotypes and clinical symptoms or severity of infection. A comparison of Vesikari parameters with astrovirus-positive proxy values demonstrated that Vesikari scores for duration of diarrhoea and admission temperatures would result in a milder infection rating in astrovirus-positive cases. CONCLUSIONS Diverse genotypes co-circulated with putative-recombinants predominating. Astrovirus classification was complicated by the lack of a consistent characterisation system and reliable reference database. The VSS should be used cautiously to rate astrovirus diarrhoea. While surveillance in communities and out-patient clinics must be continued, screening for human astroviruses in alternate hosts is needed to determine the reservoir species.
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Affiliation(s)
- Sandrama Nadan
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa.
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa; National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa
| | - Nicola A Page
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa; Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa
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4
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Wu L, Teng Z, Lin Q, Liu J, Wu H, Kuang X, Cui X, Wang W, Cui X, Yuan ZA, Zhang X, Xie Y. Epidemiology and Genetic Characterization of Classical Human Astrovirus Infection in Shanghai, 2015-2016. Front Microbiol 2020; 11:570541. [PMID: 33101242 PMCID: PMC7546348 DOI: 10.3389/fmicb.2020.570541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Abstract
Objective Human astroviruses (HAstVs) are single-stranded RNA viruses of the Astroviridae family. Infection of classic HAstVs is one of the most common causes of acute viral gastroenteritis (infectious viral diarrhea). There is a lack of data on the prevalence and genetic characterization of classic HAstVs in acute viral gastroenteritis in the whole population. This study aimed to investigate the epidemiological trend, genotypes, viral co-infections, and viral loads of classic HAstVs in Shanghai, China, from January 2015 to December 2016. Methods A total of 6,051 non-redundant stool samples were collected in outpatients with acute diarrhea in Shanghai from January 2015 to December 2016. One-step real-time RT-PCR was used for screening viral diarrhea, including rotavirus A, rotavirus B, rotavirus C, norovirus genotype I and II, classic human astroviruses, and sapovirus. Real-time PCR was used for screening human enteric adenoviruses. Conventional RT-PCR was used for the amplification of viral fragments for genotyping. PCR products were sequenced and used for the construction of phylogenetic trees. Results The detection rate of classic HAstVs was 1.55% (94/6,051). The prevalence of HAstV infection displayed a typical winter/spring (December to March) seasonality and was highest in the 5–14 age group. Eighty-six samples were genotyped, which revealed HAstV-1 as the most prevalent genotype, followed by HAstV-5, HAstV-4, HAstV- 2, HAstV-8, and HAstV-3. There was a dramatic rise in the prevalence of HAstV-4 from December 2015 to March 2016, and the viral loads of HAstV-4 were significantly higher than those of other genotypes. Among the mixed infection samples, noroviruses were found to be the most frequently co-infected enteric viruses with HAstV. Conclusion Multiple genotypes of classic HAstVs circulated in Shanghai from January 2015 to December 2016. For the first time, HAstV-3\4\5\8 were detected in Shanghai.
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Affiliation(s)
- Limeng Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.,Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Zheng Teng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Qingneng Lin
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Huanyu Wu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaozhou Kuang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoqing Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Wei Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoxian Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zheng-An Yuan
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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5
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Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada. Viruses 2020; 12:v12101096. [PMID: 32998356 PMCID: PMC7600043 DOI: 10.3390/v12101096] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 02/04/2023] Open
Abstract
In this study, we aimed to molecularly characterize 14 whole genome sequences of chicken astrovirus (CAstV) isolated from samples obtained from white chick syndrome (WCS) outbreaks in Western Canada during the period of 2014–2019. Genome sequence comparisons showed all these sequences correspond to the novel Biv group from which no confirmed representatives were published in GenBank. Molecular recombination analyses using recombination detection software (i.e., RDP5 and SimPlot) and phylogenetic analyses suggest multiple past recombination events in open reading frame (ORF)1a, ORF1b, and ORF2. Our findings suggest that recombination events and the accumulation of point mutations may have contributed to the substantial genetic variation observed in CAstV and evidenced by the current seven antigenic sub-clusters hitherto described. This is the first paper that describes recombination events in CAstV following analysis of complete CAstV sequences originated in Canada.
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Barbosa G, Caetano A, Dábilla N, Franco F, Silva‐Sales M, Fiaccadori F, Souza M. Classical human astroviruses in symptomatic and asymptomatic children of Goiás, Brazil: Positivity rates, viral loads, and molecular characterization. J Med Virol 2020; 92:1053-1058. [DOI: 10.1002/jmv.25679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/09/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Gabriela Barbosa
- Laboratory of Virology and Cell Culture, Instituto de Patologia Tropical e Saúde PúblicaUniversidade Federal de GoiásGoiânia Brazil
| | - Amanda Caetano
- Laboratory of Virology and Cell Culture, Instituto de Patologia Tropical e Saúde PúblicaUniversidade Federal de GoiásGoiânia Brazil
| | - Nathânia Dábilla
- Laboratory of Virology and Cell Culture, Instituto de Patologia Tropical e Saúde PúblicaUniversidade Federal de GoiásGoiânia Brazil
| | - Fernanda Franco
- Laboratory of Virology and Cell Culture, Instituto de Patologia Tropical e Saúde PúblicaUniversidade Federal de GoiásGoiânia Brazil
| | - Marcelle Silva‐Sales
- Laboratory of Virology and Cell Culture, Instituto de Patologia Tropical e Saúde PúblicaUniversidade Federal de GoiásGoiânia Brazil
| | - Fabíola Fiaccadori
- Laboratory of Virology and Cell Culture, Instituto de Patologia Tropical e Saúde PúblicaUniversidade Federal de GoiásGoiânia Brazil
| | - Menira Souza
- Laboratory of Virology and Cell Culture, Instituto de Patologia Tropical e Saúde PúblicaUniversidade Federal de GoiásGoiânia Brazil
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Zhou N, Zhou L, Wang B. Molecular Evolution of Classic Human Astrovirus, as Revealed by the Analysis of the Capsid Protein Gene. Viruses 2019; 11:v11080707. [PMID: 31374999 PMCID: PMC6722597 DOI: 10.3390/v11080707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/17/2023] Open
Abstract
Classic human astroviruses (HAstV) are major global viral agents for gastroenteritis, but the molecular characteristics of classic HAstVs are not well understood. Here, we presented the molecular evolution of all classic HAstV serotypes by the analysis of the capsid protein sequences. Our results show that classic HAstVs can be divided into four groups with the most recent common ancestor (TMRCA) of 749. The overall evolutionary rate of classic HAstVs on the capsid gene was 4.509 × 10−4 substitutions/site/year, and most of the serotypes present a clock-like evolution with an amino acid accumulation of mutations over time. The mean effective population size of classic HAstVs is in a downward trend, and some positive and more than 500 negative selection sites were determined. Taken together, these results reveal that classic HAstVs evolve at the intra-serotype level with high genetic heterogeneity and are driven by strong purifying selection. Long-term surveillance of classic HAstVs are needed to enrich the genomic data for further analysis.
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Affiliation(s)
- Nan Zhou
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China.
| | - Lu Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, Jiangsu, China.
| | - Bei Wang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology and Statistics, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China.
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8
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Guo K, Li LL, Zhang Q, Yu JM, Ye Y. Diversified Variants of Astrovirus MLB2 in Patients Following Hematopoietic Stem Cell Transplantation and the Evolutionary Rates and Patterns of the Virus. Evol Bioinform Online 2019; 15:1176934319864922. [PMID: 31360058 PMCID: PMC6637835 DOI: 10.1177/1176934319864922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/03/2022] Open
Abstract
We assessed the quasispecies heterogeneity of a human astrovirus MLB2 (HAstV-MLB2-YJMGK) in immunocompromised patients following hematopoietic stem cell transplantation and performed genetic and evolutionary analyses of HAstV isolates circulating worldwide. The result showed that the virus had diversified variants and a strong positive selection in the patient, indicating that such patients may be a reservoir for astrovirus. The time to the most recent common ancestor of MLB2 and classic HAstVs was around 1800 years, and it has a decline in effective population size of HAstVs in the late 100 years.
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Affiliation(s)
- Ke Guo
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Li-Li Li
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Qing Zhang
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jie-Mei Yu
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yan Ye
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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9
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Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings. Emerg Microbes Infect 2018; 7:71. [PMID: 29674726 PMCID: PMC5908792 DOI: 10.1038/s41426-018-0074-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/26/2018] [Accepted: 03/17/2018] [Indexed: 11/09/2022]
Abstract
Astroviruses are recognized as a leading cause of gastroenteritis in humans and animals. They are also associated with extra-intestinal diseases, such as hepatitis in ducklings, nephritis in chickens, and encephalitis in cattle. In February 2017, a fatal infection of goslings characterized by visceral urate deposition was reported in the Shandong province, China. Our systematic investigation led to the isolation of an astrovirus, designated AAstV/Goose/CHN/2017/SD01, and similar disease was reproduced by experimental infection of healthy goslings, fulfilling Koch's postulates. The isolated astrovirus replicated well and resulted in 100% mortality of goose embryos. Complete genome sequence analysis revealed that the isolate was genetically distinct from known astroviruses and closely related to members of the avastrovirus genogroup II. Experimental infection showed that the isolate was highly pathogenic in goslings, causing clinical signs, growth repression and in many cases mortality. Histopathological examination indicated that lesions occurred mainly in the kidneys of infected birds. However, virus-specific genomic RNA was detected in all representative tissues, and virus shedding was detected up to 12 days after inoculation, suggesting that the isolate was able to spread systemically and replicate efficiently in vivo. Collectively, our study demonstrates, for the first time, the etiological role of a genetically distinct astrovirus in the fatal infection of goslings.
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10
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De Grazia S, Lanave G, Bonura F, Urone N, Cappa V, Li Muli S, Pepe A, Gellért A, Banyai K, Martella V, Giammanco GM. Molecular evolutionary analysis of type-1 human astroviruses identifies putative sites under selection pressure on the capsid protein. INFECTION GENETICS AND EVOLUTION 2017; 58:199-208. [PMID: 29288011 DOI: 10.1016/j.meegid.2017.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/06/2017] [Accepted: 12/22/2017] [Indexed: 12/23/2022]
Abstract
Human astroviruses (HAstV) are important enteric pathogens that can be classified into eight sero/genotypes (HAstV-1 to -8). Although the various HAstV types show global spread, type-1 strains tend to be predominant. Molecular analysis of the genomic region encoding the capsid protein (ORF2) has revealed discrete sequence variation, with different lineages within each HAstV type and at least three major lineages have been identified within HAstV-1. Longitudinal epidemiological surveillance has revealed temporal shift of the various HAstV-1 lineages. Metadata analysis of HAstV-1 sequences available in the databases also revealed temporal shifts of the circulation of HAstV-1 lineages, suggesting possible antigenic-related mechanisms of selection at the sub-genotype level. By comparison of HAstV-1 capsid sequences, lineage-defining residues under positive selection were identified. Structural analysis of HAstV-1 capsid allowed identifying at least six residues exposed on the virion surface. Two residues were located in the VP34 (shell region) whilst four residues were mapped in the VP25/27 (protruding region) of HAstV capsid protein, in proximity of the putative receptor binding S site. These findings suggest that mechanisms similar to those observed and/or hypothesized for other enteric viruses are also shaping the evolution of HAstVs, with intra-typic diversification being a possible mechanism to decrease the antigenic pressure to which these viruses are exposed.
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Affiliation(s)
- Simona De Grazia
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Floriana Bonura
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Noemi Urone
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Vincenzo Cappa
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Sara Li Muli
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Arcangelo Pepe
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Akos Gellért
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest H-1143, Hungary
| | - Krisztian Banyai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest H-1143, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Giovanni M Giammanco
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
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11
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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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12
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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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13
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Cortez V, Meliopoulos VA, Karlsson EA, Hargest V, Johnson C, Schultz-Cherry S. Astrovirus Biology and Pathogenesis. Annu Rev Virol 2017; 4:327-348. [PMID: 28715976 DOI: 10.1146/annurev-virology-101416-041742] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Astroviruses are nonenveloped, positive-sense single-stranded RNA viruses that cause gastrointestinal illness. Although a leading cause of pediatric diarrhea, human astroviruses are among the least characterized enteric RNA viruses. However, by using in vitro methods and animal models to characterize virus-host interactions, researchers have discovered several important properties of astroviruses, including the ability of the astrovirus capsid to act as an enterotoxin, disrupting the gut epithelial barrier. Improved animal models are needed to study this phenomenon, along with the pathogenesis of astroviruses, particularly in those strains that can cause extraintestinal disease. Much like for other enteric viruses, the current dogma states that astroviruses infect in a species-specific manner; however, this assumption is being challenged by growing evidence that these viruses have potential to cross species barriers. This review summarizes these remarkable facets of astrovirus biology, highlighting critical steps toward increasing our understanding of this unique enteric pathogen.
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Affiliation(s)
- Valerie Cortez
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Victoria A Meliopoulos
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Erik A Karlsson
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Virginia Hargest
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , , .,Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163
| | - Cydney Johnson
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; , , , , ,
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14
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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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15
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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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16
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Han HJ, Wen HL, Zhao L, Liu JW, Luo LM, Zhou CM, Qin XR, Zhu YL, Liu MM, Qi R, Li WQ, Yu H, Yu XJ. Novel coronaviruses, astroviruses, adenoviruses and circoviruses in insectivorous bats from northern China. Zoonoses Public Health 2017; 64:636-646. [PMID: 28371451 PMCID: PMC7165899 DOI: 10.1111/zph.12358] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 11/29/2022]
Abstract
Bats are considered as the reservoirs of several emerging infectious disease, and novel viruses are continually found in bats all around the world. Studies conducted in southern China found that bats carried a variety of viruses. However, few studies have been conducted on bats in northern China, which harbours a diversity of endemic insectivorous bats. It is important to understand the prevalence and diversity of viruses circulating in bats in northern China. In this study, a total of 145 insectivorous bats representing six species were collected from northern China and screened with degenerate primers for viruses belonging to six families, including coronaviruses, astroviruses, hantaviruses, paramyxoviruses, adenoviruses and circoviruses. Our study found that four of the viruses screened for were positive and the overall detection rates for astroviruses, coronaviruses, adenoviruses and circoviruses in bats were 21.4%, 15.9%, 20% and 37.2%, respectively. In addition, we found that bats in northern China harboured a diversity of novel viruses. Common Serotine (Eptesicus serotinu), Fringed long‐footed Myotis (Myotis fimriatus) and Peking Myotis (Myotis pequinius) were investigated in China for the first time. Our study provided new information on the ecology and phylogeny of bat‐borne viruses.
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Affiliation(s)
- H-J Han
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - H-L Wen
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - L Zhao
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - J-W Liu
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - L-M Luo
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - C-M Zhou
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - X-R Qin
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - Y-L Zhu
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - M-M Liu
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - R Qi
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - W-Q Li
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - H Yu
- Schools of Medicine, Fudan University, Shanghai, China
| | - X-J Yu
- Wuhan University School of Health Sciences, Wuhan, Hubei, China.,Departments of Pathology and Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
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17
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Vu DL, Bosch A, Pintó RM, Guix S. Epidemiology of Classic and Novel Human Astrovirus: Gastroenteritis and Beyond. Viruses 2017; 9:v9020033. [PMID: 28218712 PMCID: PMC5332952 DOI: 10.3390/v9020033] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/20/2022] Open
Abstract
Since they were identified in 1975, human astroviruses have been considered one of the most important agents of viral acute gastroenteritis in children. However, highly divergent astroviruses infecting humans have been recently discovered and associated with extra-intestinal infections. The report of cases of fatal meningitis and encephalitis, especially in immunocompromised individuals, has broadened their disease spectrum. Although zoonotic transmission among animal and human astroviruses has not been clearly recognized, the genetic similarity between some human and animal viruses makes it likely to occur. This review provides an update on the epidemiology of both classic and novel human astroviruses, and a comprehensive view on confirmed or potential association between astrovirus and human disease.
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Affiliation(s)
- Diem-Lan Vu
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
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18
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Chamings A, Hewson KA, O'Rourke D, Ignjatovic J, Noormohammadi AH. High-resolution melt curve analysis to confirm the presence of co-circulating isolates of avian nephritis virus in commercial chicken flocks. Avian Pathol 2016; 44:443-51. [PMID: 26365395 DOI: 10.1080/03079457.2015.1085648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Avian Nephritis Virus (ANV) has been implicated in poor growth and renal disease of young chickens. This paper describes the development of a reverse-transcriptase polymerase chain reaction for the detection of ANV in commercial meat chickens and the use of high-resolution melt curves to detect the presence of genetically different ANVs. Pooled cloacal swabs from both healthy and ill commercial chicken broiler flocks were tested for the presence of ANV using a combination of polymerase chain reaction, molecular cloning, high-resolution melt curve analysis and sequencing. Except for one, all specimens were found to contain two genetically different ANVs. Phylogenetic analysis of the capsid amino acid sequences revealed the presence of four of six groups of ANV identified previously in other countries as well as in two novel groups of ANV. Phylogenetic analysis of nucleotide sequences of partial polymerase, capsid and 3' untranslated regions reveal that the genes of individual ANV virus isolates have different ancestors. This was shown to be due to a template-switching event in the capsid gene that resulted in the 3' end of the capsid gene and the 3' untranslated region of one ANV isolate being transferred to another ANV. These results reveal that infection of chicken flocks with multiple ANV isolates is common and this needs to be taken into consideration in diagnosis of ANV using molecular techniques and in future epidemiological investigations.
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Affiliation(s)
- A Chamings
- a Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences , The University of Melbourne, Werribee , Melbourne , Victoria , Australia
| | - K A Hewson
- a Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences , The University of Melbourne, Werribee , Melbourne , Victoria , Australia
| | - D O'Rourke
- a Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences , The University of Melbourne, Werribee , Melbourne , Victoria , Australia
| | - J Ignjatovic
- a Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences , The University of Melbourne, Werribee , Melbourne , Victoria , Australia
| | - A H Noormohammadi
- a Asia Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences , The University of Melbourne, Werribee , Melbourne , Victoria , Australia
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19
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Mihalov-Kovács E, Martella V, Lanave G, Bodnar L, Fehér E, Marton S, Kemenesi G, Jakab F, Bányai K. Genome analysis of canine astroviruses reveals genetic heterogeneity and suggests possible inter-species transmission. Virus Res 2016; 232:162-170. [PMID: 27965150 PMCID: PMC7114541 DOI: 10.1016/j.virusres.2016.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/10/2016] [Accepted: 12/07/2016] [Indexed: 02/04/2023]
Abstract
We sequenced the genome of several canine astroviruses. Genetic heterogeneity was detected among strains. A novel strain related to mink astrovirus was identified.
Canine astrovirus RNA was detected in the stools of 17/63 (26.9%) samples, using either a broadly reactive consensus RT-PCR for astroviruses or random RT-PCR coupled with massive deep sequencing. The complete or nearly complete genome sequence of five canine astroviruses was reconstructed that allowed mapping the genome organization and to investigate the genetic diversity of these viruses. The genome was about 6.6 kb in length and contained three open reading frames (ORFs) flanked by a 5′ UTR, and a 3′ UTR plus a poly-A tail. ORF1a and ORF1b overlapped by 43 nucleotides while the ORF2 overlapped by 8 nucleotides with the 3′ end of ORF1b. Upon genome comparison, four strains (HUN/2012/2, HUN/2012/6, HUN/2012/115, and HUN/2012/135) were more related genetically to each other and to UK canine astroviruses (88–96% nt identity), whilst strain HUN/2012/126 was more divergent (75–76% nt identity). In the ORF1b and ORF2, strains HUN/2012/2, HUN/2012/6, and HUN/2012/135 were related genetically to other canine astroviruses identified formerly in Europe and China, whereas strain HUN/2012/126 was related genetically to a divergent canine astrovirus strain, ITA/2010/Zoid. For one canine astrovirus, HUN/2012/8, only a 3.2 kb portion of the genome, at the 3′ end, could be determined. Interestingly, this strain possessed unique genetic signatures (including a longer ORF1b/ORF2 overlap and a longer 3′UTR) and it was divergent in both ORF1b and ORF2 from all other canine astroviruses, with the highest nucleotide sequence identity (68% and 63%, respectively) to a mink astrovirus, thus suggesting a possible event of interspecies transmission. The genetic heterogeneity of canine astroviruses may pose a challenge for the diagnostics and for future prophylaxis strategies.
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Affiliation(s)
- Eszter Mihalov-Kovács
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, H-1143, Hungary
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Universitá Aldo Moro di Bari, S.p. per Casamassima km 3, 70010 Valenzano, Italy
| | - Gianvito Lanave
- Dipartimento di Medicina Veterinaria, Universitá Aldo Moro di Bari, S.p. per Casamassima km 3, 70010 Valenzano, Italy
| | - Livia Bodnar
- Dipartimento di Medicina Veterinaria, Universitá Aldo Moro di Bari, S.p. per Casamassima km 3, 70010 Valenzano, Italy
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, H-1143, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, H-1143, Hungary
| | - Gábor Kemenesi
- Virological Research Group, Faculty of Sciences, Institute of Biology, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Ferenc Jakab
- Virological Research Group, Faculty of Sciences, Institute of Biology, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, H-1143, Hungary.
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20
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Zhou N, Lin X, Wang S, Wang H, Bi Z, Wang P, Chen P, Tao Z, Song L, Song Y, Xu A. Molecular characterization of classic human astrovirus in eastern China, as revealed by environmental sewage surveillance. J Appl Microbiol 2016; 120:1436-44. [DOI: 10.1111/jam.13109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 01/20/2023]
Affiliation(s)
- N. Zhou
- School of Public Health; Shandong University; Jinan China
| | - X. Lin
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - S. Wang
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - H. Wang
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - Z. Bi
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - P. Wang
- School of Public Health; Shandong University; Jinan China
| | - P. Chen
- School of Public Health; Shandong University; Jinan China
| | - Z. Tao
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - L. Song
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
| | - Y. Song
- School of Public Health; Shandong University; Jinan China
| | - A. Xu
- School of Public Health; Shandong University; Jinan China
- Academy of Preventive Medicine; Shandong University; Jinan China
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention; Shandong Center for Disease Control and Prevention; Jinan China
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21
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Temporal variation in the distribution of type-1 human astrovirus lineages in a settled population over 14 years. Arch Virol 2016; 161:1633-7. [DOI: 10.1007/s00705-016-2798-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 02/14/2016] [Indexed: 11/27/2022]
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22
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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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23
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Deciphering the Diversities of Astroviruses and Noroviruses in Wastewater Treatment Plant Effluents by a High-Throughput Sequencing Method. Appl Environ Microbiol 2015; 81:7215-22. [PMID: 26253673 DOI: 10.1128/aem.02076-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/30/2015] [Indexed: 11/20/2022] Open
Abstract
Although clinical epidemiology lists human enteric viruses to be among the primary causes of acute gastroenteritis in the human population, their circulation in the environment remains poorly investigated. These viruses are excreted by the human population into sewers and may be released into rivers through the effluents of wastewater treatment plants (WWTPs). In order to evaluate the viral diversity and loads in WWTP effluents of the Paris, France, urban area, which includes about 9 million inhabitants (approximately 15% of the French population), the seasonal occurrence of astroviruses and noroviruses in 100 WWTP effluent samples was investigated over 1 year. The coupling of these measurements with a high-throughput sequencing approach allowed the specific estimation of the diversity of human astroviruses (human astrovirus genotype 1 [HAstV-1], HAstV-2, HAstV-5, and HAstV-6), 7 genotypes of noroviruses (NoVs) of genogroup I (NoV GI.1 to NoV GI.6 and NoV GI.8), and 16 genotypes of NoVs of genogroup II (NoV GII.1 to NoV GII.7, NoV GII.9, NoV GII.12 to NoV GII.17, NoV GII.20, and NoV GII.21) in effluent samples. Comparison of the viral diversity in WWTP effluents to the viral diversity found by analysis of clinical data obtained throughout France underlined the consistency between the identified genotypes. However, some genotypes were locally present in effluents and were not found in the analysis of the clinical data. These findings could highlight an underestimation of the diversity of enteric viruses circulating in the human population. Consequently, analysis of WWTP effluents could allow the exploration of viral diversity not only in environmental waters but also in a human population linked to a sewerage network in order to better comprehend viral epidemiology and to forecast seasonal outbreaks.
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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: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/02/2015] [Accepted: 03/09/2015] [Indexed: 11/30/2022]
Abstract
Human astroviruses (HAstVs) are important enteric pathogens and can be classified genetically and antigenically into eight types. During molecular surveillance for HAstVs in Italy, sequence analysis of the diagnostic region C (about 400 nucleotide in length), located on the capsid (ORF2) gene, identified a novel type-3 strain. Upon sequencing of the full-length ORF2, the type-3 HAstV strain was characterized as a novel ORF2 genetic lineage, designated as 3c. By converse, in the ORF1b the virus was more similar to type-1 HAstVs, rather than to type-3 strains, suggesting a recombination nature, with the crossover site being mapped to the ORF1b/ORF2 junction region. Region C sequences of similar type-3 HAstV identified from European and extra-European countries were retrieved in the databases, suggesting the global distribution of this novel type-3 lineage.
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Affiliation(s)
- Maria Cristina Medici
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.
| | - Fabio Tummolo
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Krisztián Banyai
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Elisabetta Bonerba
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Carlo Chezzi
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Maria Cristina Arcangeletti
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Flora De Conto
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Adriana Calderaro
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
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25
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Mladenova Z, Steyer A, Steyer AF, Ganesh B, Petrov P, Tchervenjakova T, Iturriza-Gomara M. Aetiology of acute paediatric gastroenteritis in Bulgaria during summer months: prevalence of viral infections. J Med Microbiol 2015; 64:272-282. [PMID: 25596126 DOI: 10.1099/jmm.0.000018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Paediatric acute gastroenteritis is a global public health problem. Comprehensive laboratory investigation for viral, bacterial and parasitic agents is helpful for improving management of acute gastroenteritis in health care settings and for monitoring and controlling the spread of these infections. Our study aimed to investigate the role of various pathogens in infantile diarrhoea in Bulgaria outside the classical winter epidemics of rotavirus and norovirus. Stool samples from 115 hospitalized children aged 0-3 years collected during summer months were tested for presence of 14 infectious agents - group A rotavirus, astrovirus, Giardia, Cryptosporidium and Entamoeba using ELISAs; norovirus by real-time RT-PCR; picobirnavirus and sapovirus by RT-PCR; adenovirus using PCR, and Salmonella, Shigella, Escherichia coli, Yersinia and Campylobacter using standard bacterial cultures. Infectious origin was established in a total of 92 cases and 23 samples remained negative. A single pathogen was found in 67 stools, of which rotaviruses were the most prevalent (56.7 %), followed by noroviruses (19.4 %), enteric adenoviruses (7.5 %), astroviruses (6.0 %), bacteria and parasites (4.5 % each) and sapoviruses (1.4 %). Rotavirus predominant genotypes were G4P[8] (46.3 %) and G2P[4] (21.4 %); for astroviruses, type 1a was the most common, while the GII.4/2006b variant was the most prevalent among noroviruses. Bacteria were observed in five cases, with Salmonella sp. as the most prevalent, while parasites were found in ten stool samples, with Giardia intestinalis in five cases. The results demonstrated high morbidity associated with viral infections and that rotavirus and norovirus remain the most common pathogens associated with severe gastroenteritis during summer months in Bulgaria, a country with a temperate climate, and significant molecular diversity among circulating virus strains.
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Affiliation(s)
- Zornitsa Mladenova
- (former) Department of Virology, National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Andrej Steyer
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | | | - Balasubramanian Ganesh
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Petar Petrov
- Infectious Ward, University Hospital 'St Anna', Sofia, Bulgaria
| | - Tanja Tchervenjakova
- Infectious Wards 1 and 2, Specialized Hospital for Infectious and Parasitic Diseases 'Prof. Ivan Kirov', Sofia, Bulgaria
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