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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Rubinstein RJ, Reyes Y, González F, Gutiérrez L, Toval-Ruíz C, Hammond K, Bode L, Vinjé J, Vilchez S, Becker-Dreps S, Bucardo F, Vielot NA. Epidemiology of pediatric astrovirus gastroenteritis in a Nicaraguan birth cohort. medRxiv 2023:2023.08.24.23294584. [PMID: 37662285 PMCID: PMC10473812 DOI: 10.1101/2023.08.24.23294584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Astrovirus is a leading cause of acute gastroenteritis in children worldwide. However, few prospective studies have analyzed astrovirus in community-dwelling pediatric populations in low-and-middle-income countries. Methods We assessed the incidence, risk factors, clinical characteristics, genotypes, viral coinfections and seasonality of astrovirus gastroenteritis in 443 healthy Nicaraguan children born in 2017-2018, followed for 36 months. Children were recruited from maternity hospitals and birth records in an economically-diverse neighborhood of León, the second-largest city in Nicaragua. Astrovirus-positive episodes and genotypes were identified from diarrheal specimens with reverse transcription quantitative polymerase chain reaction and Sanger sequencing. Results Of 1708 total specimens tested, eighty children (18%) experienced at least 1 astrovirus episode, and 9 experienced repeat episodes, mostly during the rainy season (May-October). The incidence of astrovirus episodes was 7.8/100 child-years (95% CI: 6.2, 9.8). Genotype-specific incidence of astrovirus also exhibited seasonality. Median age of astrovirus episode onset was 16 months (IQR 9, 23). Initial astrovirus episodes were not associated with protection against future episodes during the age span studied. Astrovirus cases were exclusively breastfed for a shorter period than uninfected children, and the human milk oligosaccharide lacto-N-fucopentaose-I was more concentrated in mothers of these children. Home toilets appeared to protect against future astrovirus episodes (HR=0.19, 95% CI 0.04-0.91). Human astrovirus-5 episodes, comprising 15% of all typed episodes, were associated with longer diarrhea and more symptomatic rotavirus co-infections. Conclusion Astrovirus was a common cause of gastroenteritis in this cohort, and future studies should clarify the role of astrovirus genotype in clinical infection severity.
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Affiliation(s)
- Rebecca J Rubinstein
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yaoska Reyes
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Fredman González
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Lester Gutiérrez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Christian Toval-Ruíz
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Kelli Hammond
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lars Bode
- Department of Pediatrics, University of California San Diego
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Samuel Vilchez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Sylvia Becker-Dreps
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Filemón Bucardo
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Universidad Nacional Autónoma de Nicaragua-León, León, Nicaragua
| | - Nadja A Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Farahmand M, Khales P, Salavatiha Z, Sabaei M, Hamidzade M, Aminpanah D, Tavakoli A. Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis. Microb Pathog 2023:106209. [PMID: 37385570 DOI: 10.1016/j.micpath.2023.106209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 07/01/2023]
Abstract
AIM Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis. METHODS Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis. RESULTS Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I2 = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%). CONCLUSION The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Khales
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Salavatiha
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Milad Sabaei
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Hamidzade
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Danesh Aminpanah
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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Razizadeh MH, Pourrostami K, Kachooei A, Zarei M, Asghari M, Hamldar S, Khatami A. An annoying enteric virus: A systematic review and meta‐analysis of human astroviruses and gastrointestinal complications in children. Rev Med Virol 2022; 32:e2389. [DOI: 10.1002/rmv.2389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/22/2022] [Accepted: 07/21/2022] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kumars Pourrostami
- Department of Pediatrics School of Medicine Alborz University of Medical Sciences Karaj Iran
- Dietary Supplements and Probiotic Research Center Alborz University of Medical Sciences Karaj Iran
| | - Atefeh Kachooei
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
| | - Mohammad Zarei
- Renal Division Harvard Medical School Brigham and Women's Hospital Boston Massachusetts USA
- Harvard T.H. Chan School of Public Health John B. Little Center for Radiation Sciences Boston Massachusetts USA
| | - Milad Asghari
- Department of Microbiology Faculty of Basic Science Tabriz Branch Islamic Azad University Tabriz Iran
| | - Shahrzad Hamldar
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
| | - Alireza Khatami
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Olortegui MP, Rouhani S, Yori PP, Salas MS, Trigoso DR, Mondal D, Bodhidatta L, Platts-Mills J, Samie A, Kabir F, Lima A, Babji S, Shrestha SK, Mason CJ, Kalam A, Bessong P, Ahmed T, Mduma E, Bhutta ZA, Lima I, Ramdass R, Moulton LH, Lang D, George A, Zaidi AK, Kang G, Houpt ER, Kosek MN. Astrovirus Infection and Diarrhea in 8 Countries. Pediatrics 2018; 141:peds.2017-1326. [PMID: 29259078 PMCID: PMC9923568 DOI: 10.1542/peds.2017-1326] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Astroviruses are important drivers of viral gastroenteritis but remain understudied in community settings and low- and middle-income countries. We present data from 8 countries with high prevalence of diarrhea and undernutrition to describe astrovirus epidemiology and assess evidence for protective immunity among children 0 to 2 years of age. METHODS We used 25 898 surveillance stools and 7077 diarrheal stools contributed by 2082 children for enteropathogen testing, and longitudinal statistical analysis to describe incidence, risk factors, and protective immunity. RESULTS Thirty-five percent of children experienced astrovirus infections. Prevalence in diarrheal stools was 5.6%, and severity exceeded all enteropathogens except rotavirus. Incidence of infection and diarrhea were 2.12 and 0.88 episodes per 100 child-months, respectively. Children with astrovirus infection had 2.30 times the odds of experiencing diarrhea after adjustment for covariates (95% confidence interval [CI], 2.01-2.62; P < .001). Undernutrition was a risk factor: odds of infection and diarrhea were reduced by 10% and 13%, respectively, per increase in length-for-age z score (infection: odds ratio, 0.90 [95% CI, 0.85-0.96]; P < .001; diarrhea: odds ratio, 0.87 [95% CI, 0.79-0.96]; P = .006). Some evidence of protective immunity to infection was detected (hazard ratio, 0.84 [95% CI, 0.71-1.00], P = .052), although this was heterogeneous between sites and significant in India and Peru. CONCLUSIONS Astrovirus is an overlooked cause of diarrhea among vulnerable children worldwide. With the evidence presented here, we highlight the need for future research as well as the potential for astrovirus to be a target for vaccine development.
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Affiliation(s)
| | - Saba Rouhani
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pablo Peñataro Yori
- Asociación Benéfica PRISMA, Iquitos, Peru;,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | | | | | | | - James Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia
| | | | | | - Aldo Lima
- Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Sanjaya Kumar Shrestha
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand;,Centre for International Health, University of Bergen, Bergen, Norway
| | - Carl J. Mason
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Adil Kalam
- Aga Khan University, Naushahro Feroze, Pakistan
| | | | | | | | | | - Ila Lima
- Universidade Federal do Ceará, Fortaleza, Brazil
| | | | - Lawrence H. Moulton
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Dennis Lang
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland; and,Foundation for the National Institutes of Health, Bethesda, Maryland
| | | | | | | | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia
| | - Margaret N. Kosek
- Asociación Benéfica PRISMA, Iquitos, Peru;,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland;,Address correspondence to Margaret N. Kosek, MD, Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, MD 21205. E-mail
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De La Cruz Hernández SI, Anaya Molina Y, Gómez Santiago F, Terán Vega HL, Monroy Leyva E, Méndez Pérez H, García Lozano H. Real-time RT-PCR, a necessary tool to support the diagnosis and surveillance of rotavirus in Mexico. Diagn Microbiol Infect Dis 2018; 90:272-6. [PMID: 29329758 DOI: 10.1016/j.diagmicrobio.2017.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/08/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022]
Abstract
Rotavirus produces diarrhea in children under 5 years old. Most of those conventional methods such as polyacrylamide gel electrophoresis (PAGE) and reverse transcription-polymerase chain reaction (RT-PCR) have been used for rotavirus detection. However, these techniques need a multi-step process to get the results. In comparison with conventional methods, the real-time RT-PCR is a highly sensitive method, which allows getting the results in only one day. In this study a real-time RT-PCR assay was tested using a panel of 440 samples from patients with acute gastroenteritis, and characterized by PAGE and RT-PCR. The results show that the real-time RT-PCR detected rotavirus from 73% of rotavirus-negative samples analyzed by PAGE and RT-PCR; thus, the percentage of rotavirus-positive samples increased to 81%. The results indicate that this real-time RT-PCR should be part of a routine analysis, and as a support of the diagnosis of rotavirus in Mexico.
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zaraket H, Abou-El-Hassan H, Kreidieh K, Soudani N, Ali Z, Hammadi M, Reslan L, Ghanem S, Hajar F, Inati A, Rajab M, Fakhouri H, Ghanem B, Baasiri G, Melhem NM, Dbaibo G. Characterization of astrovirus-associated gastroenteritis in hospitalized children under five years of age. Infect Genet Evol 2017; 53:94-9. [PMID: 28536072 DOI: 10.1016/j.meegid.2017.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 11/23/2022]
Abstract
PURPOSE The aim of this study was to determine the incidence and genetic diversity of astrovirus (AstV) detected in children hospitalized for gastroenteritis (GE). METHODS A multi-center, hospital-based surveillance study was conducted across Lebanon to investigate the incidence of AstV among diarrheal hospitalizations. Viral RNA was extracted from stool samples collected between 2011 and 2013 from children, below the age of 5years, hospitalized for GE at six medical centers across Lebanon. Demographic and clinical data were collected and analyzed. RNA of eligible samples (n=739) was screened by two AstV-specific PCR assays followed by genotype-specific PCR. Sanger sequencing and phylogenetic analysis were performed for genotypic characterization. RESULTS Overall, 5.5% (41/739) of rotavirus-negative stool samples collected from hospitalized children <5years old tested positive for AstV infection. AstV infections were detected all year long. Diarrhea, dehydration, vomiting and fever were the most common symptoms associated with AstV infections. Children aged 48-59months had the highest incidence of AstV. Using the Vesikari Scoring System to assess clinical severity, 85.4% of children with AstV had a score>11, indicating severe GE. Genotype-specific PCR identified 22 classical and 4 MLB-like AstV specimens. Further sequencing and phylogenetic analysis of orf1b and orf2 genes revealed that AstV classical 1-3, 5, 6, and 8, MLB-1, VA-1 and -2 genotypes circulated in Lebanon. Recombination between classical AstV strains was detected in several cases as evident by the lack of congruency in the tree topologies of the orf1b and orf2. Two cases of mixed infections between classical and non-classical genotypic strains were recorded. CONCLUSION High genetic diversity was detected among AstVs in Lebanon. AstVs are associated with 5.5% of non-rotavirus GE-associated hospitalizations in children under five years in Lebanon.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Fischer K, Pinho Dos Reis V, Balkema-Buschmann A. Bat Astroviruses: Towards Understanding the Transmission Dynamics of a Neglected Virus Family. Viruses 2017; 9:E34. [PMID: 28230787 DOI: 10.3390/v9020034] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 01/11/2023] Open
Abstract
Bats belong to the order Chiroptera that represents the second largest order of mammals with more than 1200 species and an almost global distribution. Environmental changes and deforestation have severely influenced many ecosystems, intensifying the contact between wildlife and humans. In recent years, bats have been found to harbor a number of different viruses with zoonotic potential, as well as a great diversity of astroviruses, for which the question of zoonotic potential remains unanswered to date. Human astroviruses have been identified as the causative agent for diarrhea in children and immunocompromised patients. For a long time, astroviruses have been considered to be strictly species-specific. However, a great genetic diversity has recently been discovered among animal and human astroviruses that might indicate the potential of these viruses to cross species barriers. Furthermore, our knowledge about the tissue tropism of astroviruses has been expanded to some neurotropic strains that have recently been shown to be responsible for encephalitis in humans and livestock. This review gives an overview on what is known about astroviruses in bats, humans and livestock, especially bovines and pigs. Future research activities are suggested to unravel astrovirus infection dynamics in bat populations to further assess the zoonotic potential of these viruses.
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Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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York RL, Yousefi PA, Bogdanoff W, Haile S, Tripathi S, DuBois RM. Structural, Mechanistic, and Antigenic Characterization of the Human Astrovirus Capsid. J Virol 2015; 90:2254-63. [PMID: 26656707 DOI: 10.1128/JVI.02666-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/03/2015] [Indexed: 11/20/2022] Open
Abstract
Human astroviruses (HAstVs) are nonenveloped, positive-sense, single-stranded RNA viruses that are a leading cause of viral gastroenteritis. HAstV particles display T=3 icosahedral symmetry formed by 180 copies of the capsid protein (CP), which undergoes proteolytic maturation to generate infectious HAstV particles. Little is known about the molecular features that govern HAstV particle assembly, maturation, infectivity, and immunogenicity. Here we report the crystal structures of the two main structural domains of the HAstV CP: the core domain at 2.60-Å resolution and the spike domain at 0.95-Å resolution. Fitting of these structures into the previously determined 25-Å-resolution electron cryomicroscopy density maps of HAstV allowed us to characterize the molecular features on the surfaces of immature and mature T=3 HAstV particles. The highly electropositive inner surface of HAstV supports a model in which interaction of the HAstV CP core with viral RNA is a driving force in T=3 HAstV particle formation. Additionally, mapping of conserved residues onto the HAstV CP core and spike domains in the context of the immature and mature HAstV particles revealed dramatic changes to the exposure of conserved residues during virus maturation. Indeed, we show that antibodies raised against mature HAstV have reactivity to both the HAstV CP core and spike domains, revealing for the first time that the CP core domain is antigenic. Together, these data provide new molecular insights into HAstV that have practical applications for the development of vaccines and antiviral therapies. IMPORTANCE Astroviruses are a leading cause of viral diarrhea in young children, immunocompromised individuals, and the elderly. Despite the prevalence of astroviruses, little is known at the molecular level about how the astrovirus particle assembles and is converted into an infectious, mature virus. In this paper, we describe the high-resolution structures of the two main astrovirus capsid proteins. Fitting these structures into previously determined low-resolution maps of astrovirus allowed us to characterize the molecular surfaces of immature and mature astroviruses. Our studies provide the first evidence that astroviruses undergo viral RNA-dependent assembly. We also provide new insight into the molecular mechanisms that lead to astrovirus maturation and infectivity. Finally, we show that both capsid proteins contribute to the adaptive immune response against astrovirus. Together, these studies will help to guide the development of vaccines and antiviral drugs targeting astrovirus.
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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 Environ Virol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Bai Z, Xie H, You Q, Pickerill S, Zhang Y, Li T, Geng J, Hu L, Shan H, Di B. Isothermal cross-priming amplification implementation study. Lett Appl Microbiol 2014; 60:205-9. [DOI: 10.1111/lam.12342] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/16/2014] [Accepted: 10/17/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Z. Bai
- Guangzhou Center for Disease Control and Prevention; Guangzhou Guangdong China
| | - H. Xie
- Guangzhou Center for Disease Control and Prevention; Guangzhou Guangdong China
| | - Q. You
- Ustar Biotechnologies (Hangzhou) Co., Ltd.; Hangzhou Zhejiang China
| | - S. Pickerill
- Ustar Biotechnologies (Hangzhou) Co., Ltd.; Hangzhou Zhejiang China
| | - Y. Zhang
- Guangzhou Center for Disease Control and Prevention; Guangzhou Guangdong China
| | - T. Li
- Guangzhou Center for Disease Control and Prevention; Guangzhou Guangdong China
| | - J. Geng
- Guangzhou Center for Disease Control and Prevention; Guangzhou Guangdong China
| | - L. Hu
- Ustar Biotechnologies (Hangzhou) Co., Ltd.; Hangzhou Zhejiang China
| | - H. Shan
- ADICON Clinical Laboratory, Inc.; Hangzhou Zhejiang China
| | - B. Di
- Guangzhou Center for Disease Control and Prevention; Guangzhou Guangdong China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Liu C, Liu WH, Kan LL, Li X, Li YG, Zhao W. Production of polyclonal antibody to a recombinant non-structural protein Nsp1a of human astrovirus. J Virol Methods 2014; 209:82-5. [PMID: 25239369 DOI: 10.1016/j.jviromet.2014.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 09/02/2014] [Accepted: 09/09/2014] [Indexed: 11/17/2022]
Abstract
Human astrovirus (HAstV) are important pathogens that cause acute viral diarrhea in infants. Little is known about the mechanisms of astrovirus-induced diarrhea. Previous studies have suggested that an apoptosis inducer may be encoded in the non-structural protein (nsP1a) of astrovirus and contribute to virus-induced diarrhea. To study the biological function of nsP1a and to gain further insight into nsP1a protein-host cell interactions, good quality antibodies must be produced. The nsP1agene of HAstV-1 was cloned into a bacterial expression vector Pgex-6P-1. The recombinant plasmid Pgex-6P-nsP1a was transformed into Escherichia coli BL21 (DE3) and expressed as a fusion protein that contains N-terminal GST tags. The expressed recombinant protein was purified and used as an antigen to produce an nsP1a antiserum in rabbits. ELISA was used to detect the titer of specific antibodies. Specificity activity was detected by Western blot and immunofluorescence analysis. The titer of specific antibodies was up to 1:30,000. Western blotting and immunofluorescence analysis indicated that the polyclonal antibody could recognize specifically the HAstV-1 nsP1a protein.
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Affiliation(s)
- Chang Liu
- 1st affiliated hospital endocrinology, Liaoning Medical University, Jinzhou, 121000 Liaoning, China
| | - Wen-Hui Liu
- Liaoning Medical University, Jinzhou, 121200 Liaoning, China
| | - Li-Li Kan
- Panjin Liaohe Oilfield General Hospital, Panjin, 124010 Liaoning, China
| | - Xin Li
- Liaoning Medical University, Jinzhou, 121200 Liaoning, China
| | - Yong-gang Li
- Liaoning Medical University, Jinzhou, 121200 Liaoning, China
| | - Wei Zhao
- Liaoning Medical University, Jinzhou, 121200 Liaoning, China.
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Shaukat S, Angez M, Alam MM, Jebbink MF, Deijs M, Canuti M, Sharif S, de Vries M, Khurshid A, Mahmood T, van der Hoek L, Zaidi SSZ. Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA. Virol J 2014; 11:146. [PMID: 25112200 PMCID: PMC4254409 DOI: 10.1186/1743-422x-11-146] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Methods VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers. Results Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community. Conclusion Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-146) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan.
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Abstract
Astroviruses have been gaining widespread importance over the past few decades owing to their detection through advanced molecular techniques. The association of astrovirus-associated enteric infections have been reported from various settings among different age groups. The tremendous efforts of scientists from different countries to detect and characterize these star-like viruses in the course of surveillance has shown the emergence of novel astroviruses from varied host species, necessitating changes in the classification to update their taxonomy. The public health importance of these viruses implies new control measures are essential to reduce disease burden in developing countries.
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Mor SK, Chander Y, Marthaler D, Patnayak DP, Goyal SM. Detection and molecular characterization of Porcine astrovirus strains associated with swine diarrhea. J Vet Diagn Invest 2012; 24:1064-7. [PMID: 22956487 DOI: 10.1177/1040638712458781] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Astrovirus has been reported to be associated with diarrhea in pigs. The current study was conducted for the detection and molecular characterization of astroviruses in diarrheic pigs submitted to the Veterinary Diagnostic Laboratory, University of Minnesota. Intestinal contents from 269 pigs were examined by reverse transcription polymerase chain reaction (RT-PCR), and 62% were found positive for astroviruses. Of the positive samples, 20% were positive for astrovirus alone while astrovirus with rotavirus was detected in 58% of the samples. The remaining 22% revealed the presence of astrovirus along with Porcine hemagglutinating encephalomyelitis virus, Transmissible gastroenteritis virus, or Porcine circovirus-2. Sequencing the capsid gene of 56 randomly selected samples confirmed them to be Porcine astrovirus type 4 (PAstV-4) with 58-100% nucleotide identity within these viruses. Phylogenetic analysis revealed 2 possible subgroups. The results indicate that PAstV is present on swine farms in the United States and that it may be associated with diarrhea either alone or in combination with other enteric viruses. Further studies are needed to determine strain diversity among porcine astroviruses so that appropriate control strategies can be devised and implemented.
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Affiliation(s)
- Sunil K Mor
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108, USA
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De Grazia S, Medici MC, Pinto P, Moschidou P, Tummolo F, Calderaro A, Bonura F, Banyai K, Giammanco GM, Martella V. Genetic heterogeneity and recombination in human type 2 astroviruses. J Clin Microbiol 2012; 50:3760-4. [PMID: 22933603 DOI: 10.1128/JCM.02102-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Novel lineages of human astrovirus (HAstV) types 2, 2c, and 2d have been identified. Upon sequencing of the 3' end of the genome, the type 2c and 2d HAstVs were found to be open reading frame 1b (ORF1b)-ORF2 recombinant, with ORF1b being derived from type 3 and type 1 HAstVs, respectively. An ORF2 interlineage recombinant strain, 2c/2b, was also identified.
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Wang F, Wang YH, Peng JS, Zhou X, Tang L, Kobayashi N, Hu Q, Zhou DJ, Huang HJ, Liu MQ. Genetic characterization of Human astrovirus infection in Wuhan, People's Republic of China, 2007-2008. Can J Microbiol 2011; 57:964-8. [PMID: 22004120 DOI: 10.1139/w11-085] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human astrovirus (HAstV) was an important cause of viral gastroenteritis in infants in Wuhan city based on our previous study. The aim of the study was to investigate the nature of HAstV infection in Wuhan, People's Republic of China, especially in adults. Stool specimens were collected from 361 children and 301 adults with diarrhea from July 2007 to June 2008 and were tested for HAstV RNA by RT-PCR. The 348-bp PCR product of positive samples was further sequenced and analyzed for multiple sequence alignment and phylogenetic tree. HAstV RNA was detected in 2.33% (7/301) adults, which was significantly lower than that in children (13.57%, 49/361). HAstV-positive patients were either older than 50 years of age or younger than 3. Genetic analysis showed that the HAstV strain in adults was the same as that in children in 2007-2008. Contrarily, HAstV strains prevalent in 2007-2008 showed genetic characteristics different from those in 2004-2005 and belonged to two new groups of HAstV-1b. Thus, our data characterized HAstV infection in Wuhan 2007-2008, suggesting that HAstV infection also played an important role in adults in Wuhan, especial in patients of >50 years, and should be included for routine diagnosis in the population with diarrheal illness.
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Affiliation(s)
- Fang Wang
- Department of Pathogenic Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People's Republic of China
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Pinsky BA, Banaei N. Molecular Diagnosis of Gastrointestinal Infections. In: Persing DH, Tenover FC, Tang Y, Nolle FS, Hayden RT, van Belkum A, editors. Molecular Microbiology. Wiley; 2011. pp. 727-50. [DOI: 10.1128/9781555816834.ch48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Jeong AY, Jeong HS, Jo MY, Jung SY, Lee MS, Lee JS, Jee YM, Kim JH, Cheon DS. Molecular epidemiology and genetic diversity of human astrovirus in South Korea from 2002 to 2007. Clin Microbiol Infect 2011; 17:404-8. [PMID: 20491833 DOI: 10.1111/j.1469-0691.2010.03263.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The present study was conducted to survey the prevalence and genotypic distribution of human astrovirus (HAstV) circulating in South Korea. Of 160,027 patients with acute gastroenteritis, 2,057 (1.3%) were positive for HAstV antigen. We determined the genotypes of 187 HAstV strains collected from laboratories across the country. Genetic analysis revealed genotype 1 to be the most prevalent, accounting for 72.19% of the strains, followed by genotypes 8 (9.63%), 6 (6.95%), 4 (6.42%), 2 (3.21%) and 3 (1.60%). Our findings indicate that HAstV is less common but, even so, a potentially important viral agent of gastroenteritis in South Korea, with significant genetic diversity among circulating HAstV strains.
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Affiliation(s)
- A Y Jeong
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul, South Korea
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Jindal N, Patnayak DP, Chander Y, Ziegler AF, Goyal SM. Comparison of capsid gene sequences of turkey astrovirus-2 from poult-enteritis-syndrome-affected and apparently healthy turkeys. Arch Virol 2011; 156:969-77. [PMID: 21327787 DOI: 10.1007/s00705-011-0931-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 01/21/2011] [Indexed: 11/25/2022]
Abstract
This study was conducted to determine genetic variations in the capsid gene of turkey astrovirus-2 (TAstV-2) detected in apparently healthy and poult enteritis syndrome (PES)-affected turkeys. Capsid genes of astroviruses obtained from 30 PES-affected and 45 apparently healthy turkey flocks had sequence homologies of 73.4-100% and 72.4-100% at the nucleotide levels, respectively. The analysis of deduced amino acid sequences revealed one amino acid deletion at position 552 in 28 (93.3%) of 30 PES-affected cases. However, there were two deletions (at positions 551 and 552) in 31 (68.9%) of 45 TAstV-2 from apparently healthy flocks. The TAstV-2 (6.7%) from two PES-affected cases had two amino acid insertions each between positions 552 and 553, while TAstV-2 from 14 (31.1%) of 45 healthy flocks had two insertions at the same position. Phylogenetic analysis based on nucleotide sequences revealed that the astroviruses in this study were closely related to most of the previously published TAstV-2 isolates. The sequence homology of TAstV-2 in this study ranged from 70.4% to 99.4% at the nucleotide level with those of previously published TAstV-2 isolates. The variations at the amino acid level in the capsid gene suggest the possibility of the existence of different serotypes of turkey astrovirus. The close relationship of turkey astroviruses from apparently healthy flocks to those from PES-affected cases in capsid gene phylogeny necessitates further studies to compare complete capsid gene sequences from both types of flocks from different geographic areas for better understanding of TAstV circulating in turkeys.
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Affiliation(s)
- N Jindal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
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Pantin-Jackwood MJ, Strother KO, Mundt E, Zsak L, Day JM, Spackman E. Molecular characterization of avian astroviruses. Arch Virol 2010; 156:235-44. [PMID: 21069394 DOI: 10.1007/s00705-010-0849-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 10/21/2010] [Indexed: 10/18/2022]
Abstract
Astroviruses are frequently associated with enteric diseases in poultry, being isolated from cases of runting-stunting syndrome (RSS) of broiler chickens, poult enteritis complex (PEC), and poult enteritis mortality syndrome (PEMS) of turkeys. Currently, five types of avian astrovirus have been identified: turkey astroviruses 1 and 2 (TAstV-1, TAstV-2), avian nephritis virus (ANV), chicken astrovirus (CAstV) and duck astrovirus (DAstV). The objective of this study was to molecularly characterize the different types of avian astroviruses circulating in commercial poultry. Sequence analysis of a region of ORF2, which encodes the capsid precursor protein associated with serotype and viral pathogenesis, revealed extensive variation in amino acid sequence within each subtype: TAstV-2 (81.5%-100%), ANV (69.9%-100%), and CAstV (85.3%-97.9%). However, this region was more conserved in TAstV-1's (96.2%-100%). Furthermore, a novel astrovirus was detected in chicken samples and found to be <64% similar to ANV and <30.6% similar to CAstV. The results of this study underline the great genetic variability of avian astroviruses and indicate that there are most likely multiple serotypes of each avian astrovirus circulating in commercial poultry.
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Affiliation(s)
- M J Pantin-Jackwood
- Southeast Poultry Research Laboratory, Agricultural Research Laboratory, U.S. Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA.
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Sdiri-Loulizi K, Gharbi-Khelifi H, de Rougemont A, Hassine M, Chouchane S, Sakly N, Pothier P, Guédiche MN, Aouni M, Ambert-Balay K. Molecular epidemiology of human astrovirus and adenovirus serotypes 40/41 strains related to acute diarrhea in Tunisian children. J Med Virol 2009; 81:1895-902. [PMID: 19774695 DOI: 10.1002/jmv.21586] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human astrovirus (AstV) and adenovirus types 40 and 41 (AdV 40/41) are responsible for epidemic and endemic acute gastroenteritis in children and adults. The present study was designed to evaluate the prevalence and genetic diversity of enteric viruses in children in Tunisia. A total of 788 fecal samples were collected during a 4-year period in the region of Monastir, from children under 12 years old, hospitalized or presenting in dispensaries with symptoms of acute gastroenteritis. AstV and AdV40/41 were detected by immunoenzymatic methods and confirmed by PCR/RT-PCR and sequence analysis. Phylogenetic analyses were performed for nucleotide homology with reference strains. AstV and AdV40/41 were characterized as a causative agent in 28 (3.6%) and 18 (2.3%) of the fecal samples, respectively. Phylogenetic analysis showed that the AstVs belonged to the serotypes 3 (n = 4; 14.3%) and 1 (n = 24; 85.7%), and the enteric AdVs to the serotypes 40 (n = 1; 5.6%) and 41 (n = 17; 94.4%). This is the first report that describes the molecular epidemiology of AstV and AdV40/41 in Tunisian children. Their respective detection rate was very low, far below that of rotavirus and norovirus. The genetic diversity among these two viruses is relatively limited and varies depending on the area.
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Espinosa AC, Arias CF, Sánchez-Colón S, Mazari-Hiriart M. Comparative study of enteric viruses, coliphages and indicator bacteria for evaluating water quality in a tropical high-altitude system. Environ Health 2009; 8:49. [PMID: 19860917 PMCID: PMC2777857 DOI: 10.1186/1476-069x-8-49] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 10/27/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bacteria used as indicators for pathogenic microorganisms in water are not considered adequate as enteric virus indicators. Surface water from a tropical high-altitude system located in Mexico City that receives rainwater, treated and non-treated wastewater used for irrigation, and groundwater used for drinking, was studied. METHODS The presence of enterovirus, rotavirus, astrovirus, coliphage, coliform bacteria, and enterococci was determined during annual cycles in 2001 and 2002. Enteric viruses in concentrated water samples were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). Coliphages were detected using the double agar layer method. Bacteria analyses of the water samples were carried out by membrane filtration. RESULTS The presence of viruses and bacteria in the water used for irrigation showed no relationship between current bacterial indicator detection and viral presence. Coliphages showed strong association with indicator bacteria and enterovirus, but weak association with other enteric viruses. Enterovirus and rotavirus showed significant seasonal differences in water used for irrigation, although this was not clear for astrovirus. CONCLUSION Coliphages proved to be adequate faecal pollution indicators for the irrigation water studied. Viral presence in this tropical high-altitude system showed a similar trend to data previously reported for temperate zones.
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Affiliation(s)
- Ana C Espinosa
- Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán, 04510 México, DF, México
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av Universidad 2001, Col Chamilpa, 62210 Cuernavaca, Morelos, México
| | - Salvador Sánchez-Colón
- Consultoría Ambiental y Estadística, Cerrada de Cortés 43, Colonia Campestre Tlacopac, San Ángel, 01049 México, DF, México
| | - Marisa Mazari-Hiriart
- Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán, 04510 México, DF, México
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30
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Silva PA, Santos RAT, Costa PSS, Teixeira JMS, Giugliano LG, Andreasi MSA, Leite JPG, Schreier E, Cardoso DDDDP. The circulation of human astrovirus genotypes in the Central West Region of Brazil. Mem Inst Oswaldo Cruz 2009; 104:655-8. [DOI: 10.1590/s0074-02762009000400021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 03/31/2009] [Indexed: 11/21/2022] Open
Affiliation(s)
- Paula Andreia Silva
- Instituto de Patologia Tropical e Saúde Pública; Robert Koch-Institute, Germany
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31
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Shan T, Dai X, Guo W, Zhang W, Cui L, Yuan C, Shang X, Shen Q, Hua X. Human astrovirus infection in children with gastroenteritis in Shanghai. J Clin Virol 2009; 44:248-9. [DOI: 10.1016/j.jcv.2008.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 10/21/2022]
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Lee JI, Park SH, Kim MS, Oh YH, Yu IS, Choi BH, Lee GC, Kim MS, Jang SY, Lee CH. Surveillance of Acute Gastroenteritis in Seoul, Korea, During May 2004 and June 2007. ACTA ACUST UNITED AC 2009. [DOI: 10.4167/jbv.2009.39.4.363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jae In Lee
- Seoul Metropolitan Institue of Public Health & Environment, Seoul, Korea
| | - Sang Hun Park
- Seoul Metropolitan Institue of Public Health & Environment, Seoul, Korea
| | - Moo Sang Kim
- Seoul Metropolitan Institue of Public Health & Environment, Seoul, Korea
| | - Young Hee Oh
- Seoul Metropolitan Institue of Public Health & Environment, Seoul, Korea
| | - In Sil Yu
- Seoul Metropolitan Institue of Public Health & Environment, Seoul, Korea
| | - Byung Hyun Choi
- Seoul Metropolitan Institue of Public Health & Environment, Seoul, Korea
| | - Gyu Cheol Lee
- Water Analysis and Research Center, K-water, Daejeon, Korea
| | - Mi Suk Kim
- Department of Microbiology, Chungbuk National University, Cheongju, Korea
| | - So Young Jang
- Department of Microbiology, Chungbuk National University, Cheongju, Korea
| | - Chan Hee Lee
- Department of Microbiology, Chungbuk National University, Cheongju, Korea
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33
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Silva PA, Stark K, Mockenhaupt FP, Reither K, Weitzel T, Ignatius R, Saad E, Seidu-Korkor A, Bienzle U, Schreier E. Molecular characterization of enteric viral agents from children in northern region of Ghana. J Med Virol 2008; 80:1790-8. [DOI: 10.1002/jmv.21231] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Liu MQ, Peng JS, Tang L, Zhou Y, Yang BF, Wang YH, Wang B, Zhou DJ, Huang HJ, Ho WZ. Identification of new subtype of astrovirus type 3 from an infant with diarrhea in Wuhan, China. Virology 2008; 375:301-6. [PMID: 18308361 DOI: 10.1016/j.virol.2008.01.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 01/14/2008] [Accepted: 01/25/2008] [Indexed: 10/22/2022]
Abstract
Human astrovirus is one of the important causes for viral gastroenteritis in young children. In previous study where we examined the molecular epidemiology of human astrovirus (HAstV) infection in infants in Wuhan City, we isolated and identified a new subtype (WH1859) of HAstV genotype 3 from an infant with diarrhea. The sequence analysis of this strain showed that the complete region of ORF2 of WH1859 contains 2385-bp of nucleotides that encode 795 amino acids. Because WH1859 strain has the identity of less than 95% with the distance of more than 0.05 to the reference strains of HAstV-3, WH1859 represents a distinct subtype within HAstV-3 strains. Further studies are needed to determine the role of this new subtype strain of HAstV in viral gastroenteritis among young children.
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Affiliation(s)
- Man-Qing Liu
- Division of Virology, Wuhan Centers for Disease Prevention and Control, Wuhan 430022, Hubei, PR China
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35
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Guix S, Caballero S, Fuentes C, Bosch A, Pintó RM. Genetic analysis of the hypervariable region of the human astrovirus nsP1a coding region: design of a new RFLP typing method. J Med Virol 2008; 80:306-15. [PMID: 18098163 DOI: 10.1002/jmv.21058] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human astroviruses (HAstV) are causative agents of viral gastroenteritis worldwide. A hypervariable region (HVR) is located close to the C-terminus of the nsP1a, and recent data support the involvement of the HVR-containing nonstructural protein in viral RNA replication processes, suggesting a correlation between variability in this region and pathogenic properties. The HVR of the C-terminal nsP1a coding region of 104 wild-type and reference isolates of HAstV was sequenced. A phylogenetic analysis was performed to identify different genotypes, and a restriction fragment length polymorphism (RFLP) method was designed. An extensive nucleotide and deduced amino acid sequence variability was observed, as well as many insertions and deletions that retained the reading frame. The resultant phylogenetic tree supported the subdivision of HAstV into the two previously described major genetic groups, genogroup A and B, and the identification of 12 genotypes (9 within genogroup A, and 3 within genogroup B), which could be identified by RFLP. A correlation analysis was performed between genotype information and viral load using information from 35 clinical samples. Significant differences were observed between the viral load in clinical samples and certain HAstV genotypes that belonged to the same serotype, confirming the influence of C-terminal nsP1a variability on the viral replication phenotype. The use of the new RFLP typing method based on the HVR of the C-terminal nsP1a coding region by diagnosticians would help to understand the relationship between different genotypes and the severity of the gastroenteritis.
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Affiliation(s)
- Susana Guix
- Enteric Virus Laboratory, Department of Microbiology, University of Barcelona, Barcelona, Spain
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36
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Gabbay YB, Linhares AC, Oliveira DS, Nakamura LS, Mascarenhas JDP, Gusmão RHP, Heinemann MB, Macêdo O, Leite JPG. First detection of a human astrovirus type 8 in a child with diarrhea in Belém, Brazil: comparison with other strains worldwide and identification of possible three lineages. Mem Inst Oswaldo Cruz 2008; 102:531-4. [PMID: 17612775 DOI: 10.1590/s0074-02762007005000032] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 03/22/2007] [Indexed: 11/21/2022] Open
Abstract
This study describes the genetic relationships of the first human astrovirus type-8 (HAstV-8) detected in Belém-Brazil, during a public hospital-based study. This strain was compared with other HAstV-8 strains identified elsewhere which have sequences available at GeneBank. The regions ORF1a (primers Mon348/Mon340) and ORF2 (primers Mon269/Mon270) were analyzed by nucleotide sequencing and a high similarity rate was observed among the Belém strain and other HAstV-8 strains. In ORF1a, homology values of 93-100% were detected, and in ORF2 96-99%. Considering the sequence variation (7%) observed in ORF2 region, it was suggested that HAstV-8 strains could be divided in three different lineages.
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Affiliation(s)
- Yvone B Gabbay
- Secão de Virologia, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, PA, 67030-000, Brasil.
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37
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Resque HR, Munford V, Castilho JG, Schmich H, Caruzo TAR, Rácz ML. Molecular characterization of astrovirus in stool samples from children in São Paulo, Brazil. Mem Inst Oswaldo Cruz 2007; 102:969-74. [DOI: 10.1590/s0074-02762007000800012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2007] [Accepted: 12/19/2007] [Indexed: 12/22/2022] Open
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38
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Gabbay YB, Leite JPG, Oliveira DS, Nakamura LS, Nunes MRT, Mascarenhas JDP, Heinemann MB, Linhares AC. Molecular epidemiology of astrovirus type 1 in Belém, Brazil, as an agent of infantile gastroenteritis, over a period of 18 years (1982–2000): Identification of two possible new lineages. Virus Res 2007; 129:166-74. [PMID: 17714822 DOI: 10.1016/j.virusres.2007.07.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/12/2007] [Indexed: 12/16/2022]
Abstract
Human astroviruses (HAstV) are worldwide recognized as important viral enteropathogens during childhood. This study aims to determine the incidence, genetic diversity and intertype variability of HAstV-1 in children less than 5 years of age enrolled in several studies conducted in Belém/Pará, and São Luís/Maranhão, Brazil, from December 1982 to May 2000. Using EIA and RT-PCR, an overall positivity of 6.1% (155/2.534) was achieved, of these, 140 were positive by RT-PCR. The analysis of a 348bp ORF2 fragment revealed that HAstV-1 was the predominant genotype (85/140, 60.7%) throughout the 18 years of study. Phylogenetic analysis was performed for 81 of these strains, and 76 (93.8%) were genetically classified as HAstV-1a. The remainder of strains (n=5) were assigned to possible new lineages, 1e and 1f. Four of these five strains were detected in 1983 and 1984, and the lineage 1a circulated during 10 consecutive years (1990/2000). Genome sequence variation was found among the HAstV-1 strains involving all lineages, but only five nucleotide changes translated into aminoacid changes over this period, suggesting that HAstV-1 was very stable. The data obtained in this study should be useful for further studies at molecular level, including improvement of disease surveillance based on molecular diagnostic tools, and vaccine development.
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Affiliation(s)
- Yvone B Gabbay
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Rodovia BR 316, Km 07, S/N, Levilândia 67030-000, Ananindeua, PA, Brazil.
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39
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Brown DW, Gunning KB, Henry DM, Awdeh ZL, Brinker JP, Tzipori S, Herrmann JE. A DNA oligonucleotide microarray for detecting human astrovirus serotypes. J Virol Methods 2007; 147:86-92. [PMID: 17905448 PMCID: PMC2238180 DOI: 10.1016/j.jviromet.2007.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 07/24/2007] [Accepted: 07/30/2007] [Indexed: 11/30/2022]
Abstract
Human astroviruses have been shown in numerous studies to be an important cause of gastroenteritis in young children worldwide. The present communication addresses their characterization by use of oligonucleotide microarray hybridization. The system developed consists of an RT-PCR using primers of low degeneracy capable of detecting all eight serotypes of human astroviruses. RT-PCR products are then hybridized against a microarray consisting of short oligonucleotide probes 17-18 nucleotides in length. Cy3-labeled ssDNA targets are generated using a Cy3-labeled primer in the RT-PCR. The non-labeled strand is enzymatically digested, and the labeled target is rescued by column purification. This method of generating labeled target uses equimolar concentrations of the amplifying primers and does not compromise assay sensitivity for initial detection of the virus. Hybridization can be performed without the need for additional amplification. Although the amplicon spans a relatively conserved region of the astrovirus genome, the use of short probes enables type distinction despite such limited diversity. Probes differing by as little as a single nucleotide can be used to distinguish isolates. The microarray developed was capable of distinguishing representatives of the eight known serotypes of human astroviruses.
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Affiliation(s)
- David W Brown
- Tufts University, Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA.
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40
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Abstract
AIMS Routine procedures for monitoring viruses in water samples have not been drawn up for the water-microbiology screening panel. Enteric viruses, including astroviruses, are able to persist under environmental conditions and may cause public health problems by contaminating natural and drinking water resources. The aim of this study was to detect human astroviruses (HAstVs) from raw wastewater samples. METHODS AND RESULTS To obtain data on whether human astroviruses are shed in the environment, 35 raw sewage samples from 22 sewage plants in different regions of Baranya County, Hungary were tested for astrovirus using a polyethylene glycol method for concentration and a guanidinium thiocyanate-silica procedure for extraction of viral RNA. Reverse transcription-polymerase chain reaction (RT-PCR) with HAstV-specific primer pairs was used for amplification and the specificity of amplicons was confirmed by nucleotide sequencing and phylogenetic analysis. Among the 35 raw sewage samples, 15 (43%) contained HAstV and by sequence analysis, 10 genotype HAstV-1 and one genotype HAstV-2 were identified. CONCLUSIONS The high detection rate of astroviruses we encountered in this study provide convincing evidence that HAstVs circulate at a relatively high frequency in the Hungarian population. No correlation between the standard indicators of faecal pollution and the presence of HAstVs was found. SIGNIFICANCE AND IMPACT OF THE STUDY Our study is the first report on detection of HAstV in sewage in Hungary and suggests that HAstV might be potent indicators of viral pollution in environmental specimens.
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Affiliation(s)
- E Meleg
- Regional Laboratory of Virology, Baranya County Institute of State Public Health Service, Pécs, Hungary.
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41
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Gabbay YB, Linhares AC, Cavalcante-Pepino EL, Nakamura LS, Oliveira DS, da Silva LD, Mascarenhas JDP, Oliveira CS, Monteiro TAF, Leite JPG. Prevalence of human astrovirus genotypes associated with acute gastroenteritis among children in Belém, Brazil. J Med Virol 2007; 79:530-8. [PMID: 17385695 DOI: 10.1002/jmv.20813] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Worldwide human astroviruses (HAstV) have increasingly been recognized as causative agents of viral gastroenteritis, mainly in infants and young children. The aim of this study was to assess the epidemiology and genotype diversity of HAstVs detected in children who participated in a trial in Belém, Brazil with the rhesus human reassortant rotavirus vaccine tetravalent (RRV-TV). From April/1990 to August/1992, 624 diarrheic stool samples were tested by enzyme immunoassay (EIA) for HAstV, with a positive rate of 4.0%. Reverse transcription-polymerase chain reaction (RT-PCR) was done in 129 samples (25 positive and 104 with twice the optical density (OD) value of negative control by EIA) being 33 positive. The overall positivity yielded by both methods was 5.4% (34/624). Genotyping of the 33 positive samples was done by type-specific RT-PCR and confirmed by sequence analysis. Phylogenetic analysis was performed using a 348-bp fragment of the ORF2 region of the capsid gene. HAstV-1 was the most prevalent, accounting for 45.5% of the isolates, followed by HAstV-2 (27.3%), HAstV-3 (12.1%), HAstV-4 (12.1%), and HAstV-6 (3.0%). The monthly distribution showed that HAstV-1 was predominant in the first year of study (May/1990 to May/1991) with highest prevalence in January/1991. HAstV-2 was predominant from July to November/1991 and HAstV-4 from September to October/1990. At 24 months of age, 30.6% of children had been infected by HAstV. The clinical symptoms registered during HAstV associated-diarrhea were usually mild. These data highlight the circulation of the different HAstV genotypes in Belém during the study period.
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Affiliation(s)
- Yvone B Gabbay
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil.
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42
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Liu MQ, Yang BF, Peng JS, Zhou DJ, Tang L, Wang B, Liu Y, Sun SH, Ho WZ. Molecular epidemiology of astrovirus infection in infants in Wuhan, China. J Clin Microbiol 2007; 45:1308-9. [PMID: 17301278 PMCID: PMC1865841 DOI: 10.1128/jcm.00010-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the molecular epidemiology of astrovirus infection in 335 infants with diarrhea in Wuhan City, China. Astrovirus RNA was detected in the stool specimens of 33 children (9.87%). Genotyping analysis indicated that 23 out of 24 astroviruses identified were classified as belonging to genotype 1, with highest identity (>98%) to a Mongolian strain.
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Affiliation(s)
- Man-Qing Liu
- Wuhan Centers for Disease Prevention and Control, 24 Jiang Han Bei Road, Wuhan, Hubei 430022, People's Republic of China.
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Gabbay YB, Chamone CB, Nakamura LS, Oliveira DS, Abreu SFD, Cavalcante-Pepino EL, Mascarenhas JDP, Leite JPG, Linhares AC. Characterization of an astrovirus genotype 2 strain causing an extensive outbreak of gastroenteritis among Maxakali Indians, Southeast Brazil. J Clin Virol 2006; 37:287-92. [PMID: 16996790 DOI: 10.1016/j.jcv.2006.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Revised: 08/14/2006] [Accepted: 08/17/2006] [Indexed: 11/15/2022]
Abstract
BACKGROUND Human astroviruses (HAstVs) are a common cause of sporadic diarrhea in children but large outbreaks occur in children's day care centers, schools and in homes for the elderly. OBJECTIVES To report a large outbreak of acute gastroenteritis that occurred in January 2004 among Indians from the Maxakali Reserve in the State of Minas Gerais, Brazil. STUDY DESIGN Fecal samples from 46 Maxakali patients were collected and tested for a range of enteric pathogens. HAstVs was detected by EIA and strains were confirmed by RT-PCR and typed by direct sequencing. Clinical information was collected. RESULTS The illness which affected more than 100 children under 6 years of age was characterized by watery diarrhea, fever and vomiting. HAstV-2 was the sole enteropathogen detected in 26 (56%) of 46 samples analyzed by EIA and/or RT-PCR. The 17 positive samples sequenced were identical in a 348bp region used for phylogenetic analysis and were classified as genotype 2. CONCLUSIONS This is the first description of an outbreak of HAstV-2 gastroenteritis in a population of Brazilian Indians. The magnitude of the outbreak and the severity of the disease underscore the need to better understand the epidemiology of astrovirus and other enteric agents in these populations.
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Affiliation(s)
- Yvone Benchimol Gabbay
- Seção de Virologia, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Belém, Pará, Brazil.
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Pantin-Jackwood MJ, Spackman E, Woolcock PR. Phylogenetic analysis of Turkey astroviruses reveals evidence of recombination. Virus Genes 2006; 32:187-92. [PMID: 16604451 PMCID: PMC7089065 DOI: 10.1007/s11262-005-6875-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 08/13/2005] [Indexed: 12/04/2022]
Abstract
Sequence data was obtained from the capsid (ORF-2) and the polymerase (ORF-lb) genes of 23 turkey astrovirus (TAstV) isolates collected from commercial turkey flocks around the United States between 2003 and 2004. A high level of genetic variation was observed among the isolates, particularly in the capsid gene, where nucleotide sequence identity among them was as low as 69%. Isolates collected on the same farm, on the same day, but from different houses could have as little as 72% identity between their capsid gene sequences when compared. Phylogenetic analysis of the capsid gene revealed no clear assortment by geographic region or isolation date. The polymerase gene was more conserved with between 86 and 99% nucleotide identity and did assort in a geographic manner. Based on differing topologies of the capsid and polymerase gene phylogenetic trees, TAstV appears to undergo recombination.
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Affiliation(s)
- Mary J. Pantin-Jackwood
- Southeast Poultry Research Laboratory, Agriculture Research Service, US Department of Agriculture, 934 College Station Rd., Athens, GA 30605 USA
| | - Erica Spackman
- Southeast Poultry Research Laboratory, Agriculture Research Service, US Department of Agriculture, 934 College Station Rd., Athens, GA 30605 USA
| | - Peter R. Woolcock
- California Animal Health and Food Safety Laboratory System, University of California Davis, Davis, California 39616 USA
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45
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Zhang Z, Mitchell DK, Afflerbach C, Jakab F, Walter J, Zhang YJ, Staat MA, Azimi P, Matson DO. Quantitation of human astrovirus by real-time reverse-transcription-polymerase chain reaction to examine correlation with clinical illness. J Virol Methods 2006; 134:190-6. [PMID: 16490263 DOI: 10.1016/j.jviromet.2006.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 12/21/2005] [Accepted: 01/10/2006] [Indexed: 11/20/2022]
Abstract
Human astroviruses (HAstVs) cause gastroenteritis. Real-time, reverse-transcription-polymerase chain reaction (RT2-PCR) was developed to quantitate HAstV RNA. An 88 bp amplicon from the conserved 3' genomic region was detected by binding of SYBR Green. RT2-PCR was reproducible, with a correlation coefficient of 0.998-1.00 and PCR efficiency of 94.4-100% (mean 97%). The coefficient of variation was 0.6-2.5%, dynamic range with RNA standard up to 5 x 10(8) RNA copies (RNACN) and sensitivity 5 RNACN. Of 54 blinded, archived stool samples from children hospitalized because of gastroenteritis tested by RT-PCR, 49 (91%) agreed by RT2-PCR for HAstV-positivity (Cohen kappa=0.81, 95%CI 0.66-0.97). HAstV RNACN in stools ranged from 7.6 x 10(1) to 3.6 x 10(14)copies/0.1g. Children coinfected with rotavirus had lower RNACN (mean log 4.22/standard deviation=2.26) than those without coinfection (7.57/3.06; p=.019). Children taking infant formula also had lower RNACN (5.96/2.98) than breast-fed or weaned children (8.73/2.92; p=.027). Higher RNACN tended to occur with longer duration of diarrhea for the episode (r=0.49, p=.064), but was not associated with change in age, gender, illness day, severity or breast-feeding. RT2-PCR quantitated HAstV RNA and RNACN in stool correlates with features of clinical illness.
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Affiliation(s)
- Zhian Zhang
- Center for Pediatric Research, Eastern Virginia Medical School, 855 West Brambleton Avenue, Norfolk, VA 23510, USA
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Silva PA, Cardoso DDP, Schreier E. Molecular characterization of human astroviruses isolated in Brazil, including the complete sequences of astrovirus genotypes 4 and 5. Arch Virol 2006; 151:1405-17. [PMID: 16421636 DOI: 10.1007/s00705-005-0704-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 11/25/2005] [Indexed: 10/25/2022]
Abstract
Human astroviruses (HAstV) are recognized as an important cause of gastroenteritis in young children worldwide. This study describes the molecular characteristics of astroviruses isolated in Brazil, using RT-PCR and molecular sequencing of segments of all three viral ORFs. Genetic analysis of a 348-nucleotide segment from ORF 2 demonstrated that the Brazilian isolates belong to HAstV genotypes 1 to 5 and 8. ORF 1b sequences displayed a high degree of nucleotide identity even between different genotypes, which disfavours HAstV genotyping in this region. ORF 1a sequence analysis classified all Brazilian samples as genogroup A. The complete sequences of HAstV genotype 4 (putative serotype 4) and genotype 5 (putative serotype 5) were determined for the first time.
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Affiliation(s)
- P A Silva
- Laboratory of Virology, Institute of Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
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47
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Abstract
Human astroviruses (HAstV) are important human pathogens causing gastroenteritis worldwide. The increased recognition of astroviruses as the cause of sporadic outbreaks of disease is due to the recent availability of improved diagnostic methods. During the last decade, most epidemiological surveys have chosen astrovirus-specific RT-PCR as screening methods. In addition to serotyping by molecular techniques, new typing methods are being developed that may also identify other viral properties related to virulence. The information provided by different typing assays is required for a better understanding of both the antigenic diversity and the molecular mechanisms of pathogenicity.
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Affiliation(s)
- S Guix
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Barcelona, Spain
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Jakab F, Péterfai J, Meleg E, Bányai K, Mitchell DK, Szucs G. Comparison of clinical characteristics between astrovirus and rotavirus infections diagnosed in 1997 to 2002 in Hungary. Acta Paediatr 2005; 94:667-71. [PMID: 16188766 DOI: 10.1111/j.1651-2227.2005.tb01962.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM To determine the severity and clinical characteristics of human astrovirus (HAstV) infections among hospitalized children and compare them with children infected by rotavirus. METHODS Retrospective, case-control study of astrovirus-infected and rotavirus-infected children. Astroviruses were detected in stool samples by enzyme immunoassay and/or reverse transcriptase-polymerase chain reaction. All stool samples were tested for rotavirus and bacterial pathogens, and all negative samples were further tested for human astrovirus. Children with astrovirus-positive stool samples and complete clinical data were included in this study. RESULTS Astrovirus was detected in 29 (1.8%) children, and 63 rotavirus-infected children were included as controls. Astrovirus-infected children had shorter duration of diarrhea than rotavirus-infected children (median 4 and 6 d, respectively; p<0.05), and 79% of the astrovirus infections were associated with a short duration of vomiting (median 1 and 4 d, respectively; p<0.0001). Rotavirus-infected children had longer hospitalization (p<0.050) than astrovirus-infected children. CONCLUSION HAstV-infected children had similar symptoms to those occurring in rotavirus infection. However, astrovirus-infected patients had a significantly shorter duration of diarrhea and vomiting, and they required a shorter hospitalization. On the basis of the clinical data and severity scores, children with rotavirus infection had more severe illness.
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Affiliation(s)
- Ferenc Jakab
- Regional Laboratory of Virology, Baranya County Institute of State Public Health Service, Pécs, Hungary.
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Oliver SL, Brown DWG, Green J, Bridger JC. A chimeric bovine enteric calicivirus: evidence for genomic recombination in genogroup III of the Norovirus genus of the Caliciviridae. Virology 2004; 326:231-9. [PMID: 15302209 PMCID: PMC7172961 DOI: 10.1016/j.virol.2004.06.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Accepted: 06/04/2004] [Indexed: 11/23/2022]
Abstract
The Norovirus genus of the Caliciviridae encompasses viruses that cause outbreaks of gastroenteritis in human and viruses that have been associated with diarrhea in cattle. The two bovine noroviruses, Bo/Newbury2/76/UK and Bo/Jena/80/DE, represent two distinct genetic clusters in the newly described genogroup III. In the present study, Jena-like polymerase sequences were identified for the first time in the UK, but one of these, Bo/Thirsk10/00/UK, was a chimeric virus. Bo/Thirsk10/00/UK had a Jena-like polymerase gene but Newbury2-like capsid and ORF3 genes by comparison of their genome organization, nucleotide, and amino acid identities and phylogenetic analyses. The present study is one of few studies to clearly demonstrate the existence of chimeric genomes in the Norovirus genus and the first, to our knowledge, to identify a chimeric genome in genogroup III. It provides additional support that genomic recombination is part of the natural evolution of noroviruses and is relevant to the diagnosis and immunological control of norovirus diarrhea outbreaks.
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Affiliation(s)
- S L Oliver
- Department of Pathology and Infectious Diseases, The Royal Veterinary College, Camden, London NW1 0TU, UK.
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Jakab F, Meleg E, Bányai K, Melegh B, Tímár L, Péterfai J, Szucs G. One-year survey of astrovirus infection in children with gastroenteritis in a large hospital in Hungary: Occurrence and genetic analysis of astroviruses. J Med Virol 2004; 74:71-7. [PMID: 15258971 DOI: 10.1002/jmv.20148] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human astroviruses (HAstV) are the causative agents of viral gastroenteritis mainly in children worldwide. This study investigated the epidemiology and genotype diversity of HAstVs detected in children admitted to hospital with gastroenteritis in Hungary. Stool samples were collected from children with diarrhea at the Municipal "Szent László" Hospital, Budapest, Hungary, between January 2002 and December 2002. Of 2,758 samples, 607 were negative for both rotaviruses and bacterial pathogens and were tested for astroviruses using a reverse transcriptase-polymerase chain reaction (RT-PCR) targeting the open reading frame (ORF2), capsid region. Astrovirus was detected in 10 samples (1.6%) by RT-PCR. Astrovirus infection was more frequent among children 49 to 60 months of age. Genotyping of positive samples was performed by type-specific RT-PCR and confirmed by sequence analysis. Phylogenetic analysis was performed using a 203 nucleotide consensus length of the 3'-end of the capsid gene. Type-specific RT-PCR and sequence analysis detected genotypes 1 (50%), 4 (30%), 3 (10%), and 8 (10%) among the children admitted to hospital. Genotype 1 was the predominant genotype, but genotypes 3, 4, and 8 were also present indicating the importance of emerging genotype 8 infections. Two distinct genotype 4 variants were observed during this study. Sequence analysis confirmed type-specific RT-PCR results in the capsid region. This is the first comprehensive report on the occurrence of HAstV infections in Central/Eastern Europe.
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Affiliation(s)
- Ferenc Jakab
- Regional Laboratory of Virology, Baranya County Institute of State Public Health Service, Pécs, Hungary.
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