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Tokarz R, Hyams JS, Mack DR, Boyle B, Griffiths AM, LeLeiko NS, Sauer CG, Shah S, Markowitz J, Baker SS, Rosh J, Baldassano RN, Kugathasan S, Walters T, Tagliafierro T, Sameroff S, Lee B, Che X, Oleynik A, Denson LA, Lipkin WI. Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis. Inflamm Bowel Dis 2019; 25:1656-1662. [PMID: 31112614 PMCID: PMC7108593 DOI: 10.1093/ibd/izz099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Viral infections have been suggested as possible triggers for the onset of ulcerative colitis (UC). METHODS We employed VirCapSeq-Vert, a high-throughput sequencing virus capture platform, to examine the stool virome of children with newly diagnosed moderate to severe UC. We surveyed fecal samples collected at presentation, after symptom remission, and from a control group diagnosed with irritable bowel syndrome. RESULTS Seventy subjects with UC (mean age 13 years, 45 had moderate symptoms, 25 had severe, 69 of 70 had a Mayo endoscopy subscore 2/3) were studied. We detected a wide range of animal viruses that were taxonomically classified into 12 viral families. A virus was present in 50% of fecal samples collected at presentation, 41% of samples collected after remission, and 40% of samples in our control group. The most frequently identified viruses were diet-based gyroviruses. The UC cohort had a significantly higher prevalence of anelloviruses compared with the control cohort. However, we did not identify a single virus that can be implicated in the onset of UC and did not find an association between UC disease severity and viral presence. CONCLUSION Presence of virus in stool was not associated with the onset of pediatric UC.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA,Address correspondence to: Rafal Tokarz, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, New York, NY 10032, USA. E-mail:
| | | | - David R Mack
- Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | - Sapana Shah
- Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - James Markowitz
- Cohen Children’s Medical Center of New York, New Hyde Park, NY, USA
| | - Susan S Baker
- Women & Children’s Hospital of Buffalo WCHOB, Buffalo, NY, USA
| | - Joel Rosh
- Goryeb Children’s Hospital, Atlantic Health, Morristown, NJ, USA
| | | | | | | | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Bohyun Lee
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | | | - W Ian Lipkin
- Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
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Japhet MO, Famurewa O, Adesina OA, Opaleye OO, Wang B, Höhne M, Bock CT, Mas Marques A, Niendorf S. Viral gastroenteritis among children of 0-5 years in Nigeria: Characterization of the first Nigerian aichivirus, recombinant noroviruses and detection of a zoonotic astrovirus. J Clin Virol 2018; 111:4-11. [PMID: 30580015 DOI: 10.1016/j.jcv.2018.12.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/14/2018] [Accepted: 12/16/2018] [Indexed: 11/18/2022]
Abstract
BACKGROUND Viruses are the leading cause of acute gastroenteritis in children worldwide. Understanding of the occurrence and genetic diversity of these viruses can help to prevent infections. OBJECTIVES The present study describes the presence, genetic diversity and possible recombination of five enteric viruses in children with gastroenteritis in Southwestern Nigeria. STUDY DESIGN From August 2012 to December 2013, stool samples and sociodemographic data of 103 diarrheic children <5 years were collected to detect and characterize rotavirus A, norovirus, human astrovirus, aichivirus and sapovirus using PCR techniques followed by sequencing and phylogenetic analyses. RESULTS At least one virus was identified in 58.3% (60/103) of the stool samples. Rotavirus, norovirus and astrovirus were detected in 39.8% (41/103), 10.7% (11/103), and 6.8% (7/103) respectively. Notably, aichivirus was detected for the first time in Nigeria (1/103; 0.97%). Sapovirus was not detected in the study. Co-infections with rotavirus were observed in eight samples either with norovirus or astrovirus or aichivirus. Phylogenetic analyses of different genome regions of norovirus positive samples provided indication for recombinant norovirus strains. A novel astrovirus strain closely related to canine astrovirus was identified and further characterized for the first time. CONCLUSIONS Viruses are the common cause of acute gastroenteritis in Nigerian infants with rotavirus as most frequently detected pathogen. New norovirus recombinants and a not yet detected zoonotic astrovirus were circulating in Southwestern Nigeria, providing new information about emerging and unusual strains of viruses causing diarrhea.
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Affiliation(s)
- M O Japhet
- Department of Microbiology, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria; Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria; Department of Infectious Diseases, Unit of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | - O Famurewa
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria; Department of Biological Sciences, Microbiology Unit, Kings University, Odeomu, Osun State, Nigeria
| | - O A Adesina
- Department of Microbiology, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - O O Opaleye
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University, Osogbo, Osun state, Nigeria
| | - B Wang
- Department of Infectious Diseases, Unit of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | - M Höhne
- Department of Infectious Diseases, Unit of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | - C T Bock
- Department of Infectious Diseases, Unit of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin, Germany; Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Andreas Mas Marques
- Department of Infectious Diseases, Unit of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | - S Niendorf
- Department of Infectious Diseases, Unit of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin, Germany.
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Bergallo M, Galliano I, Montanari P, Rassu M, Daprà V. Aichivirus in Children with Diarrhea in Northern Italy. Intervirology 2018; 60:196-200. [PMID: 29502122 DOI: 10.1159/000487051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/22/2018] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE Since its discovery, Aichivirus (AiV) A has been detected, with an incidence of 0.9-4.1%, primarily when studying outbreaks of diarrhea in children or young adults. In this paper, we report the first detection of AiV in Piedmont, Italy, in pediatric patients. METHODS A total of 159 fecal specimens (from 96 males and 63 females) previously screened for rotaviruses, adenoviruses, noroviruses, human parechoviruses, saliviruses, and sapoviruses were collected from infants and children with acute gastroenteritis. RESULTS The most commonly detected virus was norovirus GII (33.80%), fol lowed by rotavirus (21.30%), astrovirus (18.87%), boca virus (13.92%), sapovirus (10.90%), parechovirus (8%), norovirus GI (6.70%), adenovirus (1%), and salivirus (0.52%). Real-time polymerase chain reaction detected AiV A in 1 (0.62%) case subjects. AiV A was detected in monoinfection only in January. CONCLUSIONS Our results indicate that AiV may be associated with a limited number of diarrhea cases in pediatric patients.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy.,SC Pediatric U Regina Margherita Hospital, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy.,SC Pediatric U Regina Margherita Hospital, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy.,SC Pediatric U Regina Margherita Hospital, Turin, Italy
| | - Marco Rassu
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy
| | - Valentina Daprà
- Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy
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Epidemiology and genetic diversity of human parechoviruses circulating among children hospitalised with acute gastroenteritis in Pune, Western India: a 5-years study. Epidemiol Infect 2017; 146:11-18. [DOI: 10.1017/s095026881700262x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
SUMMARYHuman parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n= 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006–December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5′UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and ‘RGD absent’ HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.
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Oyinloye SO, Aminu M, Ella EE, Jatau ED. The prevalence and predisposing factors of norovirus and astrovirus infection among diarrheic children in north east, Nigeria. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/jphe2016.0840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Kitajima M, Gerba CP. Aichi virus 1: environmental occurrence and behavior. Pathogens 2015; 4:256-68. [PMID: 25996404 PMCID: PMC4493473 DOI: 10.3390/pathogens4020256] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 11/30/2022] Open
Abstract
Aichi virus 1 (AiV-1), belonging to the genus Kobuvirus in the family Picornaviridae, has been proposed as a causative agent of human gastroenteritis potentially transmitted by fecal-oral routes through contaminated food or water. AiV-1 is globally distributed and has been detected in various types of environmental samples, such as sewage, river water, groundwater, and shellfish. Recent environmental studies revealed that this virus could be detected in higher frequency and greater abundance than other human enteric viruses. These findings suggest that AiV-1 could potentially be an appropriate indicator of viral contamination in the environment because of its high prevalence in water environments as well as structural and genetic similarity with some of the other important enteric viruses. Further studies on the occurrence and fate of AiV-1 in environments, even in combination with clinical studies of many regions, are needed for a better understanding of their epidemiology, temporal and geographical distribution, environmental stability, and potential health risks to humans.
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Affiliation(s)
- Masaaki Kitajima
- Department of Soil, Water and Environmental Science, The University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA.
| | - Charles P Gerba
- Department of Soil, Water and Environmental Science, The University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA.
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Yip CCY, Lo KL, Que TL, Lee RA, Chan KH, Yuen KY, Woo PCY, Lau SKP. Epidemiology of human parechovirus, Aichi virus and salivirus in fecal samples from hospitalized children with gastroenteritis in Hong Kong. Virol J 2014; 11:182. [PMID: 25326707 PMCID: PMC4283143 DOI: 10.1186/1743-422x-11-182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Emerging human picornaviruses, including human parechovirus (HPeV), Aichi virus (AiV) and salivirus (SalV) were found to be associated with gastroenteritis, but their roles in enteric infections are not fully understood. In addition, no report on the circulation of these viruses in Hong Kong is available. The objective of this study was to investigate the prevalence and genetic diversity of HPeV, AiV and SalV in fecal samples from hospitalized children with gastroenteritis in Hong Kong. METHODS Fecal samples from hospitalized children with gastroenteritis were subject to detection of HPeV, AiV and SalV by RT-PCR using consensus primers targeted to their 5'UTRs. Positive samples were subject to capsid and/or 3CD region analysis for genotype determination. The epidemiology of HPeV, AiV and SalV infections was analyzed. RESULTS Among 1,708 fecal samples subjected to RT-PCR using primers targeted to 5'UTR of HPeV, AiV and SalV, viruses were detected in 55 samples, with 50 positive for HPeV only, 3 positive for AiV only, 1 positive for both HPeV and AiV, and 1 positive for both HPeV and SalV. Phylogenetic analysis of the partial VP1 gene of the 33 HPeV strains revealed the presence of genotypes of HPeV- 1, 3, 4, 5, 7, 10, among which HPeV-1 was the predominant genotype circulating in our population. The peak activity of HPeV infection was in fall. Of the 3 children with AiV infection, the 3 AiV strains were found to belong to genotype A based on the phylogenetic analysis of their partial VP1 and 3CD regions. The genotype of a SalV strain detected in this study could not be determined. Co-detection of different pathogens was observed in 24 samples (43.6%) of 55 fecal samples positive for HPeV, AiV and SalV. CONCLUSIONS HPeV, AiV and SalV were detected in fecal samples of hospitalized children with gastroenteritis in Hong Kong, with the former having the highest prevalence. HPeV-1 was the predominant genotype among HPeVs, while genotype A was the predominant genotype among AiVs in this study.
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Affiliation(s)
| | | | | | | | | | | | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, Hong Kong.
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Noroviruses associated with outbreaks of acute gastroenteritis in the State of Rio Grande do Sul, Brazil, 2004-2011. J Clin Virol 2014; 61:345-52. [PMID: 25223919 DOI: 10.1016/j.jcv.2014.08.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/19/2014] [Accepted: 08/26/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND Acute gastroenteritis norovirus (NoV) in a country of continental dimensions like Brazil has resulted in under-reporting of the number of outbreaks, as well as the genotypes associated. OBJECTIVES To demonstrate the role of NoV in outbreaks occurring in the State of Rio Grande do Sul, Southern Brazil, we determined its prevalence, as well as the genotypes associated, and evaluated clinical and epidemiological aspects. STUDY DESIGN NoV investigation was carried out in rotavirus group A negative stool samples from 2265 patients from 741 outbreaks that occurred in the State of Rio Grande do Sul, Brazil, during a period of eight years (2004-2011). NoV detection and nucleotide sequencing for genotype characterization was carried by using sets of primers targeting a conservative Rd-Rp polymerase genome region and the viral capsid gene, respectively. RESULTS NoVs were detected in 817 stool samples (36.1%) and associated with 327 outbreaks (44.1%). NoV GII.2, GII.3, GII.4, GII.6, GII.12, GII.13, GII.14, GII.15, GII.17, GII.21; and GI.1 and GI.3 were characterized. GII.4 was the most frequently detected (72.3%), with five variants identified (Asia_2003, Hunter_2004, Yerseke_2006a, Den_Haag_2006b, New Orleans_2009). This study describes the first detection of GI.1 and GII.13 and GII.15 in Brazil and demonstrates NoV winter-spring seasonality in this region of the country. CONCLUSIONS NoVs were responsible for almost 50% of outbreaks, with about 70% of them resulting from genotype GII.4 and its variants. The seasonality observed could help health authorities to establish a system of active surveillance in order to reduce NoV impact especially in congregate settings.
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Lodder WJ, Rutjes SA, Takumi K, de Roda Husman AM. Aichi virus in sewage and surface water, the Netherlands. Emerg Infect Dis 2014; 19:1222-30. [PMID: 23876456 PMCID: PMC3739534 DOI: 10.3201/eid1908.130312] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Detection of Aichi virus in humans was initially reported in Japan in 1989. To establish a timeline for the prevalence of Aichi virus infection among humans in the Netherlands, we conducted molecular analysis of archival water samples from 1987–2000 and 2009–2012. Aichi virus RNA was detected in 100% (8/8) of sewage samples and 100% (7/7) of surface water samples collected during 1987–2000 and 100% (8/8) of sewage samples and 71% (5/7) of surface water samples collected during 2009–2012. Several genotype A and B Aichi virus lineages were observed over the 25-year period studied, but the time course of viral genetic diversity showed recent expansion of the genotype B population over genotype A. Our results show that Aichi virus has been circulating among the human population in the Netherlands since before its initial detection in humans was reported and that genotype B now predominates in this country.
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Affiliation(s)
- Willemijn J Lodder
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and theEnvironment, PO Box 1, NL-3720 BA Bilthoven, the Netherlands.
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Han TH, Park SH, Hwang ES, Reuter G, Chung JY. Detection of Aichi virus in South Korea. Arch Virol 2014; 159:1835-9. [PMID: 24510169 DOI: 10.1007/s00705-014-2006-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 01/24/2014] [Indexed: 10/25/2022]
Abstract
Aichi virus (AiV) is considered to be a possible etiologic agent of acute gastroenteritis (GE). We analyzed 1,568 stool samples collected by the Seoul Metropolitan Health Research Center from patients with GE during outbreaks in Seoul, together with 378 archived common-enteric-virus-negative stool samples from children with GE hospitalized at a tertiary hospital in Seoul. AiV was detected in 1.7 % (27/1,568) of the first group but not found in the second group (0 %, 0/378). Genotypes A and B of AiV were both detected in this study. This is the first study confirming the circulation of AiV in Korea.
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Affiliation(s)
- Tae-Hee Han
- Department of Diagnostic Laboratory Medicine, Sanggyepaik Hospital, Inje University College of Medicine, Seoul, South Korea
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Control of Foodborne Viruses at Retail. RETAIL FOOD SAFETY 2014. [PMCID: PMC7122658 DOI: 10.1007/978-1-4939-1550-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kitajima M, Hata A, Yamashita T, Haramoto E, Minagawa H, Katayama H. Development of a reverse transcription-quantitative PCR system for detection and genotyping of aichi viruses in clinical and environmental samples. Appl Environ Microbiol 2013; 79:3952-8. [PMID: 23603673 PMCID: PMC3697579 DOI: 10.1128/aem.00820-13] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/14/2013] [Indexed: 11/20/2022] Open
Abstract
Aichi viruses (AiVs) have been proposed as a causative agent of human gastroenteritis potentially transmitted by fecal-oral routes through contaminated food or water. In the present study, we developed a TaqMan minor groove binder (MGB)-based reverse transcription-quantitative PCR (RT-qPCR) system that is able to quantify AiVs and differentiate between genotypes A and B. This system consists of two assays, an AiV universal assay utilizing a universal primer pair and a universal probe and a duplex genotype-specific assay utilizing the same primer pair and two genotype-specific probes. The primers and probes were designed based on multiple alignments of the 21 available AiV genome sequences containing the capsid gene. Using a 10-fold dilution of plasmid DNA containing the target sequences, it was confirmed that both assays allow detection and quantification of AiVs with a quantitative range of 1.0 × 10(1) to 1.0 × 10(7) copies/reaction, and the genotype-specific assay reacts specifically to each genotype. To validate the newly developed assays, 30 clinical stool specimens were subsequently examined with the assays, and the AiV RNA loads were determined to be 1.4 × 10(4) to 6.6 × 10(9) copies/g stool. We also examined 12 influent and 12 effluent wastewater samples collected monthly for a 1-year period to validate the applicability of the assays for detection of AiVs in environmental samples. The AiV RNA concentrations in influent and effluent wastewater were determined to be up to 2.2 × 10(7) and 1.8 × 10(4) copies/liter, respectively. Our RT-qPCR system is useful for routine diagnosis of AiVs in clinical stool specimens and environmental samples.
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Affiliation(s)
- Masaaki Kitajima
- Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, USA.
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Chhabra P, Payne DC, Szilagyi PG, Edwards KM, Staat MA, Shirley SH, Wikswo M, Nix WA, Lu X, Parashar UD, Vinjé J. Etiology of viral gastroenteritis in children <5 years of age in the United States, 2008-2009. J Infect Dis 2013; 208:790-800. [PMID: 23757337 DOI: 10.1093/infdis/jit254] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Although rotavirus and norovirus cause nearly 40% of severe endemic acute gastroenteritis (AGE) in children <5 years of age in the United States, there are limited data on the etiologic role of other enteric viruses in this age group. METHODS We conducted active population-based surveillance in children presenting with AGE to hospitals, emergency departments, and primary care clinics in 3 US counties. Stool specimens from these children and from age-matched healthy controls collected between October 2008 and September 2009 were tested for enteric adenovirus, astrovirus, sapovirus, parechovirus, bocavirus, and aichivirus. Typing was performed by sequencing and phylogenetic analysis. RESULTS Adenovirus, astrovirus, sapovirus, parechovirus, bocavirus, and aichivirus were detected in the stool specimens of 11.8%, 4.9%, 5.4%, 4.8%, 1.4%, and 0.2% of patients with AGE and 1.8%, 3.0%, 4.2%, 4.4%, 2.4%, and 0% of healthy controls, respectively. Adenovirus (type 41), astrovirus (types 1, 2, 3, 4, and 8), sapovirus (genogroups I and II), parechovirus (types 1, 3, 4, and 5), and bocavirus (types 1, 2, and 3) were found cocirculating. CONCLUSIONS Adenovirus, astrovirus, and sapovirus infections were detected in 22.1% of the specimens from children <5 years of age who had medical visits for AGE and tested negative for rotavirus and norovirus. No causal role for parechovirus and bocavirus was found.
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Affiliation(s)
- Preeti Chhabra
- Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Han X, Zhang W, Xue Y, Shao S. Sequence analysis reveals mosaic genome of Aichi virus. Virol J 2011; 8:390. [PMID: 21819561 PMCID: PMC3168422 DOI: 10.1186/1743-422x-8-390] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 08/05/2011] [Indexed: 01/08/2023] Open
Abstract
Aichi virus is a positive-sense and single-stranded RNA virus, which demonstrated to be related to diarrhea of Children. In the present study, phylogenetic and recombination analysis based on the Aichi virus complete genomes available in GenBank reveal a mosaic genome sequence [GenBank: FJ890523], of which the nt 261-852 region (the nt position was based on the aligned sequence file) shows close relationship with AB010145/Japan with 97.9% sequence identity, while the other genomic regions show close relationship with AY747174/German with 90.1% sequence identity. Our results will provide valuable hints for future research on Aichi virus diversity. Aichi virus is a member of the Kobuvirus genus of the Picornaviridae family [1,2] and belongs to a positive-sense and single-stranded RNA virus. Its presence in fecal specimens of children suffering from diarrhea has been demonstrated in several Asian countries [3-6], in Brazil and German [7], in France [8] and in Tunisia [9]. Some reports showed the high level of seroprevalence in adults [7,10], suggesting the widespread exposure to Aichi virus during childhood. The genome of Aichi virus contains 8,280 nucleotides and a poly(A) tail. The single large open reading frame (nt 713-8014 according to the strain AB010145) encodes a polyprotein of 2,432 amino acids that is cleaved into the typical picornavirus structural proteins VP0, VP3, VP1, and nonstructural proteins 2A, 2B, 2C, 3A, 3B, 3C and 3D [2,11]. Based on the phylogenetic analysis of 519-bp sequences at the 3C-3D (3CD) junction, Aichi viruses can be divided into two genotypes A and B with approximately 90% sequence homology [12]. Although only six complete genomes of Aichi virus were deposited in GenBank at present, mosaic genomes can be found in strains from different countries.
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Affiliation(s)
- Xiaohong Han
- School of Medical Science and Laboratory Medicine, Jiangsu University, Zhenjiang, PR China
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