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Okitsu S, Khamrin P, Hikita T, Shimizu-Onda Y, Thongprachum A, Hayakawa S, Maneekarn N, Ushijima H. Molecular Epidemiology of Classic, MLB, and VA Astroviruses in Children with Acute Gastroenteritis, 2014-2021: Emergence of MLB3 Strain in Japan. Microbiol Spectr 2023; 11:e0070023. [PMID: 37140393 PMCID: PMC10269582 DOI: 10.1128/spectrum.00700-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Human astroviruses (HAstVs) are important causative pathogens of acute gastroenteritis (AGE) in children worldwide. MLB and VA HAstVs, which are genetically distinct from the previously known classic HAstVs, have been detected since 2008. To investigate the role of HAstVs in AGE, we conducted molecular detection and characterization of HAstVs circulating in children with AGE in Japan from 2014 to 2021. Out of 2,841 stool samples, HAstVs were detected in 130 (4.6%). MLB1 was the predominant genotype detected (45.4%), followed by HAstV1 (39.2%), MLB2 (7.4%), VA2 (3.1%), HAstV3 (2.3%), HAstV4, HAstV5, and MLB3 (0.8% each). The results demonstrated that HAstV infection in pediatric patients in Japan was dominated by the two major genotypes MLB1 and HAstV1, with a small proportion of other genotypes. The overall infection rates of MLB and VA HAstVs were higher than those of classic HAstVs. The HAstV1 strains detected in this study belonged solely to lineage 1a. The rare MLB3 genotype was detected for the first time in Japan. All three HAstV3 strains belonged to lineage 3c based on the ORF2 nucleotide sequence and were shown to be recombinant strains. IMPORTANCE HAstVs are one of the pathogens of viral AGE and are considered the third most common viral agents of AGE after rotavirus and norovirus. HAstVs are also suspected to be the causative agents of encephalitis or meningitis in immunocompromised patients and elderly persons. However, little is known about the epidemiology of HAstVs in Japan, especially that of MLBs and VA HAstVs. This study demonstrated epidemiological features and molecular characterization of human astroviruses encompassing a 7-year study period in Japan. This study highlights the genetic diversity of HAstV circulating in pediatric patients with acute AGE in Japan.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | | | - Yuko Shimizu-Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Aksara Thongprachum
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing. Viruses 2021; 13:v13081608. [PMID: 34452472 PMCID: PMC8402840 DOI: 10.3390/v13081608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.
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Rahman R, Rahman S, Afrad MMH, Talha M, Islam D, Uddin KMM, Ahmed S, Afrad MH, Faruque ASG, Hossian ME, Rahman M. Epidemiology and genetic characterization of human sapovirus among hospitalized acute diarrhea patients in Bangladesh, 2012-2015. J Med Virol 2021; 93:6220-6228. [PMID: 34081341 DOI: 10.1002/jmv.27125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/09/2022]
Abstract
Human sapovirus, which causes acute gastroenteritis, is not well studied and poorly understood. This study aims to investigate the contribution of sapovirus in diarrhea, their clinical association, and genotypic diversity. Fecal specimens (n = 871) were randomly selected from diarrheal patients who attended International Centre for Diarrhoeal Disease Research, Bangladesh hospital in Dhaka, Bangladesh during January 2012-December 2015 and tested for the presence of sapovirus RNA using real-time polymerase chain reaction. Sapovirus RNA was identified in 2.3% (n = 20) of the samples. Seventy-five percent of the sapovirus positive cases were coinfected with other pathogens, such as rotavirus, norovirus, enterotoxigenic Escherichia coli, adenovirus, Shigella spp., and Vibrio cholerae. A vast genetic diversity was observed among sapovirus with at least seven common genotypes (GI.1, GI.2, GI.7, GII.1, GII.4, GII.6, and GIV), and a new genotype GII.NA1. Some of the GI.1 strains detected were similar to GI.4 in the polymerase region sequence and were confirmed as recombinant strains. Our findings suggest that the overall contribution of sapovirus in hospitalized diarrheal illness is low but highlight enormous genetic diversity.
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Affiliation(s)
- Rajibur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Sezanur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Md M H Afrad
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Muhammad Talha
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Deen Islam
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - K M Main Uddin
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mokibul H Afrad
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Abu S G Faruque
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mohammad E Hossian
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
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Kauer RV, Koch MC, Hierweger MM, Werder S, Boujon CL, Seuberlich T. Discovery of novel astrovirus genotype species in small ruminants. PeerJ 2019; 7:e7338. [PMID: 31396439 PMCID: PMC6679648 DOI: 10.7717/peerj.7338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/23/2019] [Indexed: 01/09/2023] Open
Abstract
Astroviruses (AstV) are single-stranded, positive-sense RNA viruses, best known for causing diarrhea in humans and are also found in many other mammals; in those, the relevance in gastroenteritis remains unclear. Recently described neurotropic AstV showed associations with encephalitis in humans as well as in other mammals. In Switzerland, two different neurotropic AstV were identified in cattle, as well as one in a sheep. The high genetic similarity between the ovine and one of the bovine AstV strengthens the hypothesis of an interspecies transmission. In humans, AstV associated with encephalitis were found also in human stool samples, suggesting that in these patients the infection spreads from the gastrointestinal tract to the brain under certain conditions, such as immunosuppression. Whether a similar pathogenesis occurs in ruminants remains unknown. The aims of this study were (1) the investigation of the potential occurrence of neurotropic AstV in feces samples, (2) the discovery and analysis of so far unknown AstV in small ruminants and other ruminant species’ fecal samples and (3) the examination of a potential interspecies transmission of AstV. To achieve these aims, RNA extraction out of 164 fecal samples from different ruminant species was performed and all samples were screened for known neurotropic AstV occurring in Switzerland, as well as for various AstV using RT-PCR. Positive tested samples were submitted to next generation sequencing. The generated sequences were compared to nucleotide- and amino acid databases, virus properties were identified, and phylogenetic analyses as well as recombination analysis were performed. The excretion of neurotropic AstV in small ruminants’ feces could not be demonstrated, but this work suggests the first identification of AstV in goats as well as the discovery of multiple and highly diverse new genetic variants in small ruminants, which lead to a classification into novel genotype-species. Additionally, the prediction of multiple recombination events in four of five newly discovered full or almost full-length genome sequences suggests a plausible interspecies transmission. The findings point out the occurrence and fecal shedding of previously unknown AstV in sheep and goats and pave the way towards a better understanding of the diversity and transmission of AstV in small ruminants.
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Affiliation(s)
- Ronja V Kauer
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michel C Koch
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Melanie M Hierweger
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Simea Werder
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Céline L Boujon
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Torsten Seuberlich
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Afrad MH, Avzun T, Haque J, Haque W, Hossain ME, Rahman AR, Ahmed S, Faruque ASG, Rahman MZ, Rahman M. Detection of enteric- and non-enteric adenoviruses in gastroenteritis patients, Bangladesh, 2012-2015. J Med Virol 2018; 90:677-684. [PMID: 29244212 DOI: 10.1002/jmv.25008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 11/28/2017] [Indexed: 11/09/2022]
Abstract
Human adenoviruses (HAdVs) are common cause of nonbacterial acute gastroenteritis worldwide. Limited data exist on HAdVs molecular epidemiology associated with acute gastroenteritis in Bangladesh. We describe the genetic diversity and epidemiology of HAdVs among hospitalized diarrhea patients, including HAdV genotypes, clinical symptoms, and co-infecting enteric pathogens. Stool samples were collected from ongoing diarrhea surveillance during 2012-2015. HAdV was detected using PCR and genotyped by sequencing and phylogenetic analysis. Detailed socio-demographic and clinical information regarding each individual was recorded such as duration of diarrhea, dehydration status, vomiting, abdominal pain, fever, and severity. Of 871 fecal specimens, HAdV DNA was detected in 93 (10.7%). Among them 56% were co-infected with other known enteric viral and bacterial pathogens and 31.6% had severe gastroenteritis. The majority (55%) of HAdV positives were children <5 years of age. Two main clinical symptoms in HAdV infected patients were diarrhea and vomiting. HAdVs were detected throughout the year with low prevalence in winter (November-January). Five HAdV species (A, B, C, D, and F) including 17 different genotypes were identified during the study period, with enteric HAdV species F (HAdV-40/41) being the most dominant. However, non-enteric HAdV were also detected in substantial proportion of specimens (15% species C, 15% species D, 10.8% species A, and 4.3% species B). Our study demonstrates high genetic diversity of HAdVs including enteric and non-enteric HAdVs among diarrhea patients and provides a foundation for further clarification of the role of non-enteric HAdVs in diarrheal diseases.
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Affiliation(s)
- Mokibul Hassan Afrad
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Tasnuva Avzun
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Jahurul Haque
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Warda Haque
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mohammad Enayet Hossain
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Afm Rajibur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Abu Syed Golam Faruque
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mohammed Ziaur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
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Ito M, Kuroda M, Masuda T, Akagami M, Haga K, Tsuchiaka S, Kishimoto M, Naoi Y, Sano K, Omatsu T, Katayama Y, Oba M, Aoki H, Ichimaru T, Mukono I, Ouchi Y, Yamasato H, Shirai J, Katayama K, Mizutani T, Nagai M. Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination. INFECTION GENETICS AND EVOLUTION 2017; 50:38-48. [PMID: 28189887 DOI: 10.1016/j.meegid.2017.02.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs. Based on a phylogenetic analysis and pairwise sequence comparison, 10, 5, 15, and 6 sequences were classified as PoAstV2, PoAstV3, PoAstV4, and PoAstV5, respectively. Co-infection with two or three strains was found in individual fecal samples from eight pigs. The phylogenetic trees of ORF1a, ORF1b, and ORF2 of PoAstV2 and PoAstV4 showed differences in their topologies. The PoAstV3 and PoAstV5 strains shared high sequence identities within each genotype in all ORFs; however, one PoAstV3 strain and one PoAstV5 strain showed considerable sequence divergence from the other PoAstV3 and PoAstV5 strains, respectively, in ORF2. Recombination analysis using whole genomes revealed evidence of multiple possible intra-genotype recombination events in PoAstV2 and PoAstV4, suggesting that recombination might have contributed to the genetic diversity and played an important role in the evolution of Japanese PoAstVs.
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Affiliation(s)
- Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Moegi Kuroda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan
| | - Masataka Akagami
- Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Toru Ichimaru
- Department of Health and Medical Sciences, Ishikawa Prefectural Nursing University, Kahoku, Ishikawa, 929-1210, Japan
| | - Itsuro Mukono
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Yoshinao Ouchi
- Kenhoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan
| | - Hiroshi Yamasato
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 683-0017, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan.
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Nakamura N, Kobayashi S, Minagawa H, Matsushita T, Sugiura W, Iwatani Y. Molecular epidemiology of enteric viruses in patients with acute gastroenteritis in Aichi prefecture, Japan, 2008/09−2013/14. J Med Virol 2015; 88:1180-6. [DOI: 10.1002/jmv.24445] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Noriko Nakamura
- Aichi Prefectural Institute of Public Health; Nagoya Aichi Japan
- Nagoya University Graduate School of Medicine; Nagoya Aichi Japan
- Clinical Research Center; National Hospital Organization Nagoya Medical Center; Nagoya Aichi Japan
| | | | - Hiroko Minagawa
- Aichi Prefectural Institute of Public Health; Nagoya Aichi Japan
| | | | - Wataru Sugiura
- Nagoya University Graduate School of Medicine; Nagoya Aichi Japan
- Clinical Research Center; National Hospital Organization Nagoya Medical Center; Nagoya Aichi Japan
| | - Yasumasa Iwatani
- Nagoya University Graduate School of Medicine; Nagoya Aichi Japan
- Clinical Research Center; National Hospital Organization Nagoya Medical Center; Nagoya Aichi Japan
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Epidemiology and genetic diversity of human astrovirus infection among hospitalized patients with acute diarrhea in Bangladesh from 2010 to 2012. J Clin Virol 2013; 58:612-8. [PMID: 24183929 DOI: 10.1016/j.jcv.2013.09.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/16/2013] [Accepted: 09/30/2013] [Indexed: 01/20/2023]
Abstract
BACKGROUND Globally, human astroviruses (HAstVs) have emerged as another common cause of non-bacterial acute gastroenteritis. Limited data exist on the epidemiology and genetic diversity of HAstVs in Bangladesh. OBJECTIVE We describe the epidemiology of HAstV-associated diarrhea among hospitalized patients, including HAstV genotypes, clinical symptoms and co-infecting pathogens. STUDY DESIGN Stool samples were collected from an ongoing diarrhea etiology surveillance during 2010-2012. HAstV was detected using RT-PCR and positive samples were subsequently tested for other common viral and bacterial pathogens. Phylogenetic analysis was performed and genotyped HAstV sequences were compared with previously reported Bangladeshi HAstV strains. RESULTS Of 826 fecal specimens, HAstV was detected in 26 cases (3.1%) and the majority of these cases (92%) was observed in children under 3 years of age. For 6 out of the 26 cases (23%) no other co-infecting pathogens were observed, whereas for the 20 remaining cases (77%) a variety of other known enteric viral and bacterial pathogens were observed. Based on the overlap region between ORF1b (RdRp) and ORF2 (capsid), five different genotypes (HAstV-1, -2, -3, -5 and -6) were identified circulating during the study period, with HAstV-1 being the predominant type. Genetic analysis revealed that HAstV-1 strains detected in this study were distantly related (<90% similarity of the capsid protein on the nt level) with HAstV-1 strains previously reported from Bangladesh. CONCLUSION Our study provides an epidemiological overview and genetic diversity of HAstVs associated with acute diarrhea in Bangladesh.
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Pativada M, Bhattacharya R, Krishnan T. Novel human astrovirus strains showing multiple recombinations within highly conserved ORF1b detected from hospitalized acute watery diarrhea cases in Kolkata, India. INFECTION GENETICS AND EVOLUTION 2013; 20:284-91. [PMID: 24064378 DOI: 10.1016/j.meegid.2013.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/12/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
Abstract
Human astroviruses (HAstVs) associated with acute watery diarrhea among hospitalized infants, children and adults as sole or mixed infection, were earlier reported from Kolkata, India. Further, novel recombinations have been detected through sequencing of the highly conserved ORF1b (RdRp) region of seven human astrovirus strains in Kolkata, India. Primers were designed and the ORF1b region was amplified by RT-PCR and sequenced. To examine the evolutionary pressures influencing the evolution of human astroviruses we implemented evolutionary genetics analysis. Maximum recombination break points detected in Kolkata strain IDH1300 were 8 and a single break point location was detected at 1205nt position. Partition-wise phylogenetic analyses of the IDH1300 Kolkata strain did not show close homology to the reference strains. Further phylogenetic analyses of full length ORF1b region of the seven human astrovirus strains showed that they formed a close cluster with each other and displayed a separate lineage in comparison to reference human astrovirus strains worldwide. This study shows the emergence of novel recombinant human astrovirus strains in Kolkata, India, warranting stringent surveillance to monitor the genetic diversity of human astrovirus strains infecting different age groups.
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Affiliation(s)
- Madhusudhan Pativada
- Division of Virology, National Institute of Cholera and Enteric Diseases (NICED), P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata 700 010, West Bengal, India
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Emerging trends in the epidemiology of human astrovirus infection among infants, children and adults hospitalized with acute watery diarrhea in Kolkata, India. INFECTION GENETICS AND EVOLUTION 2012; 12:1685-93. [DOI: 10.1016/j.meegid.2012.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/19/2012] [Accepted: 07/31/2012] [Indexed: 11/17/2022]
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12
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Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Evidence of a recombinant wild-type human astrovirus strain from a Kenyan child with gastroenteritis. J Clin Microbiol 2010; 49:728-31. [PMID: 21106800 DOI: 10.1128/jcm.01093-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A human astrovirus (HAstV) strain from Kenya was characterized by nucleotide sequence analysis. Sequences from open reading frame 1a (ORF1a) clustered with genotype 6/7, those from ORF1b clustered with genotype 3, and those from ORF2 clustered with genotype 2. A recombination point in the ORF1b-ORF2 junction was identified, with a second possible recombination point within the ORF1a region.
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14
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Tayeb HT, Al-Ahdal MN, Cartear MJ, Al-Qahtani AA, Cruz DMD. Molecular epidemiology of human astrovirus infections in Saudi Arabia pediatric patients. J Med Virol 2010; 82:2038-42. [DOI: 10.1002/jmv.21897] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ulloa JC, Gutiérrez MF. Genomic analysis of two ORF2 segments of new porcine astrovirus isolates and their close relationship with human astroviruses. Can J Microbiol 2010; 56:569-77. [PMID: 20651856 DOI: 10.1139/w10-042] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Porcine astrovirus (PAstV) has been poorly studied and has been associated mainly with gastroenteritis. Computational analysis has revealed the close relationship of PAstV with astroviruses of humans (HAstV) and cats (FAstV). In this study, 105 and 171 stool specimens were collected from piglets and children under 5 years of age, respectively, in different Colombian regions during a 1-year period. The stool samples were examined for astroviruses by ELISA and RT-PCR; 23.8% and 4% were found to be positive for PAstV and HAstV, respectively. Additional sequence analysis with partial sequences obtained from ORF2 identified at least 2 probable groups of PAstVs and possible recombination events between porcine and human astroviruses. This study provides preliminary evidence of the high presence of PAstVs in pigs and proposes the existence of multiple PAstV types that are evolutionarily closely related to HAstVs.
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Affiliation(s)
- Juan Carlos Ulloa
- Department of Microbiology, Pontificia Universidad Javeriana, Bogotá, Colombia.
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16
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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] [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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17
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Hansman GS, Oka T, Li TC, Nishio O, Noda M, Takeda N. Detection of human enteric viruses in Japanese clams. J Food Prot 2008; 71:1689-95. [PMID: 18724766 DOI: 10.4315/0362-028x-71.8.1689] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A total of 57 clam packages that were collected from supermarkets and fish markets from 11 different sites in western Japan between 8 December 2005 and 6 September 2006 were examined for human enteric viruses (i.e., norovirus, Aichi virus, rotavirus, adenovirus, hepatitis A virus, and astrovirus), using PCR and reverse transcription PCR. Sixty-one percent of the packages were contaminated with one type of virus, 9% had two different types of viruses, 28% had three different types of viruses, and 9% had at least four different types of viruses. Thirty-one (54%) of 57 packages were contaminated with noroviruses. Norovirus genogroup I and genogroup II sequences were detected in 24 and 23 packages, respectively, and these sequences belonged to nine genogroup I and eight genogroup II genotypes. Aichi viruses were found in 19 (33%) of 57 packages, and these belonged to genogroup A. Rotaviruses (group A) were detected in 14 (42%) of 33 of packages and 9 of 14 rotavirus-positive packages contained two or more rotavirus genogroup types. Adenoviruses (Ad40 and Ad41) were detected in 17 (52%) of 33 packages. One of the 57 (2%) packages was positive with hepatitis A virus (subtype IA). Astrovirus was not detected in any of the packages. This is the first study to detect such a high level of contamination in Japanese clams. These results represent an important finding because the Japanese clams were considered suitable for human consumption. Further studies are needed to determine the health risks associated with eating these highly contaminated clams.
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Affiliation(s)
- Grant S Hansman
- Department of Virology II, National Institute of Infectious Diseases, Musashi-murayama, Tokyo 208-0011, Japan.
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18
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19
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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] [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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20
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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] [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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21
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Marshall JA, Bruggink LD, Sturge K, Subasinghe N, Tan A, Hogg GG. Molecular features of astrovirus associated with a gastroenteritis outbreak in an aged-care centre. Eur J Clin Microbiol Infect Dis 2007; 26:67-71. [PMID: 17203286 DOI: 10.1007/s10096-006-0250-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The study presented here was conducted in order to gain a better understanding of the role of astroviruses (AsVs) in outbreaks of gastroenteritis among the elderly. This report is the first to provide detailed information on the molecular characteristics of an AsV causing an outbreak in an aged-care centre and is the first to clearly establish that individuals infected in such an outbreak were, in fact, elderly. The outbreak under investigation took place in Victoria, Australia, in October 2005. Twelve individuals (mean age +/- standard deviation [SD] 85.5 +/- 12.3 years) became ill during the outbreak from a total population of 86 susceptible residents. The mean duration (+/-SD) of illness was 2.3 +/- 1.6 days; symptoms included diarrhoea, abdominal pain, nausea and headache. No bacterial pathogens were detected. AsV was identified in five faecal specimens using electron microscopy and reverse transcription-polymerase chain reaction methodologies; no other gastroenteritis virus was detected. Nucleotide sequence analysis indicated the AsV identified could be assigned to the 1d lineage of AsV serotype 1 and that the AsV was not a recombinant form. The findings, taken together with previous work, indicate the AsV serotype most commonly associated with gastroenteritis outbreaks among the elderly is serotype 1 AsV.
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Affiliation(s)
- J A Marshall
- Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia.
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22
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Nguyen TA, Hoang L, Pham LD, Hoang KT, Mizuguchi M, Okitsu S, Ushijima H. Identification of human astrovirus infections among children with acute gastroenteritis in the Southern Part of Vietnam during 2005–2006. J Med Virol 2007; 80:298-305. [DOI: 10.1002/jmv.21032] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Wu FT, Oka T, Katayama K, Wu HS, Donald Jiang DS, Miyamura T, Takeda N, Hansman GS. Genetic diversity of noroviruses in Taiwan between November 2004 and March 2005. Arch Virol 2006; 151:1319-27. [PMID: 16463123 DOI: 10.1007/s00705-005-0717-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Accepted: 12/20/2005] [Indexed: 11/24/2022]
Abstract
Noroviruses are a major health burden and are responsible for the majority of outbreaks of gastroenteritis in the world. Human noroviruses can be genetically divided into two main genogroups (GI and GII) and subdivided into many genotypes. In this study, stool specimens collected from 12 outbreaks of gastroenteritis in Taiwan were screened for viral agents between the 23rd of November 2004 and 9th of March 2005. Noroviruses were detected in all outbreaks. We detected six different norovirus genotypes: GI/11, GI/14, GII/3, GII/4, GII/6, and GII/18. Noroviruses belonging to GII/4 were dominant, 50 of 60 (83%) sequences, and were detected in 10 of 12 outbreaks. Furthermore, the norovirus GII/4 strains were detected throughout Taiwan, demonstrating their widespread distribution. We also found that three outbreaks had noroviruses from multiple genotypes. Our results have shown for the first time that noroviruses are an important cause of gastroenteritis in Taiwan.
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Affiliation(s)
- F-T Wu
- Center for Disease Control, Taipei, Taiwan
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24
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Gallimore CI, Taylor C, Gennery AR, Cant AJ, Galloway A, Lewis D, Gray JJ. Use of a heminested reverse transcriptase PCR assay for detection of astrovirus in environmental swabs from an outbreak of gastroenteritis in a pediatric primary immunodeficiency unit. J Clin Microbiol 2005; 43:3890-4. [PMID: 16081927 PMCID: PMC1234003 DOI: 10.1128/jcm.43.8.3890-3894.2005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An outbreak of astrovirus gastroenteritis occurred in the Primary Immunodeficiency Unit at Newcastle General Hospital in March 2004. Environmental swabbing of the unit was undertaken after the outbreak, with multiple sites swabbed pre- and postcleaning. Astroviruses were detected in four environmental swabs and from two patient fecal samples using heminested reverse transcriptase PCR. An astrovirus genotype 3 strain was identified in both environmental swabs and fecal specimens and was the strain identified as being responsible for the outbreak. Environmental transmission of the virus was thought to have occurred by contamination of a syringe pump outside the laminar-flow curtain of a patient who was admitted with astrovirus gastroenteritis. This was subsequently transmitted to a cubicle next door and to a television/games console in a parents' room in the ward. Environmental monitoring of surfaces/equipment, using PCR assays for gastroenteric viruses in hospital situations where infection can give rise to serious clinical complications, may have a role in controlling and monitoring cleaning and the subsequent prevention of nosocomial transmission of gastroenteritis.
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Affiliation(s)
- Chris I Gallimore
- Enteric Virus Unit, Virus Reference Department, Centre for Infections, Health Protection Agency, Colindale, London, NW9 5HT, United Kingdom.
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25
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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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26
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Hansman GS, Kuramitsu M, Kuroiwa C, Yoshida H, Katayama K, Takeda N, Ushijima H, Surenkhand G, Gantulga D. Viral gastroenteritis in Mongolian infants. Emerg Infect Dis 2005; 11:180-2. [PMID: 15714668 PMCID: PMC3294324 DOI: 10.3201/eid1101.040337] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Grant Stuart Hansman
- University of Tokyo, Tokyo, Japan
- National Institute of Infectious Diseases, Tokyo, Japan
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27
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Abstract
Astroviruses are positive-sense single-stranded RNA viruses. These viruses cause gastroenteritis in humans and in a variety of animal species, including turkey poults. Only human astroviruses are well characterized antigenically. In the current study, two turkey astrovirus isolates, TAstV1987 and TAstV2001, were antigenically compared using cross-neutralization tests in turkey embryos, as well as cross-reactivity of the two isolates by an enzyme-linked immunosorbent assay (ELISA). The antigenic relatedness values (R) were calculated using the Archetti and Horsfall formula. The R value based on the cross-neutralization tests was 0.56%, which indicates that TAstV1987 and TAstV2001 belong to different serotypes; the R value of the two viruses based on ELISA was 70.7%, which suggests these two viruses share common antigen(s).
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Affiliation(s)
- Y Tang
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, Ohio State University, 1680 Madison Avenue, Wooster, OH 44691, USA
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28
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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] [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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29
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Jakab F, Walter JE, Berke T, Matson DO, Mitchell DK, Szucs G. Molecular characterization and sequence analysis of human astroviruses circulating in Hungary. ACTA ACUST UNITED AC 2004; 39:97-102. [PMID: 14625092 DOI: 10.1016/s0928-8244(03)00236-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Human astroviruses (HAstVs) are major pathogens in viral gastroenteritis worldwide. Twenty-five HAstV strains were detected from stool specimens of children hospitalized for acute gastroenteritis in Budapest, Hungary, between 1995 and 1999. Sequence analysis was performed at the 3' end of the capsid gene to determine genotypic diversity of HAstVs circulating in Hungary. Five different genotypes of HAstVs were identified: HAstV-1 was predominant, followed by types 5, 8, 3 and 4. Two different subtypes of HAstV-1 were detected, but only one at a time in the community. This is the first report on the genetic diversity of HAstVs in Hungary and Central/Eastern Europe.
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Affiliation(s)
- Ferenc Jakab
- Center for Pediatric Research, Children's Hospital of The King's Daughters, Eastern Virginia Medical School, Norfolk, VA, USA
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30
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Yan H, Yagyu F, Okitsu S, Nishio O, Ushijima H. Detection of norovirus (GI, GII), Sapovirus and astrovirus in fecal samples using reverse transcription single-round multiplex PCR. J Virol Methods 2003; 114:37-44. [PMID: 14599677 DOI: 10.1016/j.jviromet.2003.08.009] [Citation(s) in RCA: 200] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A reverse transcription (RT) single-round multiplex polymerase chain reaction (smPCR) assay was developed to detect simultaneously Norovirus genogroup I and II, Sapovirus and astrovirus. A total of 377 diarrhea stool samples (screened for rotavirus- and adenorivus-negative) from four regions in Japan during July 2000 to June 2001 were examined by RT-smPCR. The positive rate was 16.4% (62 out of 377 stool samples). Norovirus, Sapovirus and astrovirus were detected in 42, 16, 4 of 60 positive samples, respectively. Coinfection was not found in these samples. Infections occurred mainly in November, December and January. The key elements of the RT-smPCR are (i) the cDNA synthesis with the Superscript RTII and random primer at 42 degrees C for 1 h, at 99 degrees C for 5 min, and (ii) single-round multiplex PCR by using Taq polymerase mixed together with a mixture of four different primer pairs (G1-SKF/G1-SKR for Norovirus genogroup I, COG2F/G2-SKR for Norovirus genogroup II, SLV5317/SLV5749 for Sapovirus, PreCAP1/82b for astrovirus). All of the four primer pairs amplify the capsid region of target viral genome, produce four size-specific amplicons of 330, 387, 434, 719 bp for Norovirus genogroup I and II, Sapovirus and astrovirus, respectively. This assay provides a more rapid and efficient way to detect these viruses from fecal samples in a single test, and also offers the potential for their molecular detection in food and environmental samples.
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Affiliation(s)
- Hainian Yan
- Department of Developmental Medical Sciences, Graduate School of Medicine, Institute of International Health, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Abstract
PURPOSE OF REVIEW Public health concerns related to enteric viral agents, such as astroviruses and caliciviruses, include their ability to cause sporadic diarrhea, large outbreaks of gastroenteritis, and hospitalizations or deaths resulting from vomiting, diarrhea, and dehydration. Improved surveillance and application of sensitive molecular assays has increased awareness of these enteric pathogens and reduced the 'diagnostic gap' or unknown causes of non-bacterial gastroenteritis. RECENT FINDINGS Molecular assays have been applied to further describe the epidemiology of human astroviruses from a variety of geographic areas. The burden of astrovirus infections compared with other enteric viral agents, including rotaviruses, caliciviruses, and enteric adenoviruses have been reported. New methods for detection of astroviruses such as reverse transcription-polymerase chain reaction and molecular typing methods have advanced the understanding of the epidemiology. Additional molecular studies have described the protein processing mechanisms of this single-stranded RNA virus. SUMMARY Astroviruses are increasingly recognized as significant gastrointestinal pathogens. The understanding of molecular epidemiology and molecular processing of the virus may lead to specific prevention strategies.
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Affiliation(s)
- Jolan E Walter
- Center for Pediatric Research, Children's Hospital of The King's Daughters and Eastern Virginia Medical School, Norfolk, Virginia 23510-1001, USA
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32
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Tatsumi M, Nakata S, Sakai Y, Honma S, Numata-Kinoshita K, Chiba S. Detection and differentiation of Norwalk virus by reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay. J Med Virol 2002; 68:285-90. [PMID: 12210421 DOI: 10.1002/jmv.10181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have developed a reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay (RT-PCR-ELISA), using genetic cluster-specific probes in a microtiter plate format, for the detection and differentiation of Norwalk virus (NV) in stool samples. The specificity of the RT-PCR-ELISA was confirmed by testing 76 stool specimens and 15 tissue culture fluids derived from growths of unrelated viruses. The sensitivity of the RT-PCR-ELISA was compared with conventional PCR and Southern hybridization by testing the four cDNA clones derived from the RNA-dependent RNA polymerase region of the NV68 (NV/GI) virus and viruses in the NV/GII/P1B, the NV/GII/P2A, and the NV/GII/P2B cluster. This assay was as sensitive as the conventional RT-PCR with Southern hybridization regardless of primer pairs and probes used in the experiments. However, the actual sensitivity of this method was higher when clinical stool samples were examined because this assay examines all the samples irrespective of the RT-PCR results. The RT-PCR-ELISA format is simple, time saving, and suitable for testing many samples. It should be reliable for large-scale epidemiological studies of NV.
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Affiliation(s)
- Masatoshi Tatsumi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
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33
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Wang QH, Kakizawa J, Wen LY, Shimizu M, Nishio O, Fang ZY, Ushijima H. Genetic analysis of the capsid region of astroviruses. J Med Virol 2001; 64:245-55. [PMID: 11424111 DOI: 10.1002/jmv.1043] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Eight serotypes of human astroviruses (HAstV-1 to HAstV-8) have been described. To date, the entire genomes of HAstV-1 and HAstV-2 as well as the ORF2 sequences of HAstV-1-6 and 8 have been reported. In this study, the ORF2 sequences of seventeen strains of HAstVs originating from different countries were determined, as well as the sequence ORF2 of one porcine astrovirus (PAstV) strain. Afterwards, comparison of the capsid protein precursors encoded by ORF2 of 46 strains of HAstVs, PAstV, and feline astrovirus (FAstV) was carried out. A phylogenetic tree showed eight genogroups of HAstVs that corresponded exactly to the serotypes. HAstV-3 and 7 were the most closely related, whereas HAstVs, FAstV, and PAstV segregated from each other. Compared to a PAstV, a FAstV is closer to HAstVs. Furthermore, the capsid protein precursors were divided into four regions (after amino acid residues 424, 688, and 776, respectively) based on sequence identity. Region I was the most conserved, and FAstV was very close in identity to HAstVs. Two amino acid motifs in region I were predicted to contain the common antigenic epitopes. Region II was relatively variable. Deletions and insertions were characteristic of region III, and region IV was relatively conserved. To our knowledge, this is the first comparative sequence analysis of the capsid protein precursors of eight serotypes of HAstVs as well as two animal astroviruses (FAstV and PAstV).
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Affiliation(s)
- Q H Wang
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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34
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35
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Abstract
Human astrovirus (HAstV) is a significant cause of acute diarrhea among children, resulting in outbreaks of diarrhea and occasionally in hospitalization. Improved detection methods for eight antigenic types of HAstV and studies assessing the frequency and severity of HAstV diarrhea have further defined the impact of HAstV infections in children. These studies have shown that HAstV infections are clinically milder (diarrhea, vomiting, fever) than rotavirus infections. However, frequent coinfection of HAstV with rotavirus and caliciviruses in childhood diarrhea complicates the epidemiology. Seroprevalence studies have provided evidence that the majority of children are infected by HAstV by 6 years of age. The route of transmission is probably fecal-oral from food or water sources. Recent and planned studies will help to define the epidemiology and in the future lead to prevention strategies, which could include vaccination.
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Affiliation(s)
- J E Walter
- Center for Pediatric Research, Eastern Virginia Medical School, Children's Hospital of The King's Daughters, Norfolk, USA
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36
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Sakamoto T, Negishi H, Wang QH, Akihara S, Kim B, Nishimura S, Kaneshi K, Nakaya S, Ueda Y, Sugita K, Motohiro T, Nishimura T, Ushijima H. Molecular epidemiology of astroviruses in Japan from 1995 to 1998 by reverse transcription-polymerase chain reaction with serotype-specific primers (1 to 8). J Med Virol 2000. [DOI: 10.1002/1096-9071(200007)61:3<326::aid-jmv7>3.0.co;2-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hachiya M, Matsui M, Sanogo M, Oseto M, Morooka K, Ushijima H. Genetic variation in the capsid region of human astrovirus serotype 4 isolated in Japan. Microbiol Immunol 1999; 43:1067-70. [PMID: 10609617 DOI: 10.1111/j.1348-0421.1999.tb01237.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The entire capsid regions of 12 serotype-4 astroviruses from Japan were sequenced and compared with those of other serotypes. Serotype-4 isolates were divided into two new subgroups. The intrasubgroup nucleic acid and deduced amino acid sequences were quite homologous (more than 93%), but slightly less so between subgroups (almost 85%). However, the serotype-4 sequences differed from those of serotypes 1, 2, 3, 5, 6, 7 and 8 (less than 50%). Determining whether these differences significantly alter the epidemiology and antigenicity will require further investigation.
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Affiliation(s)
- M Hachiya
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan
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