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Lin X, Xu M, Zhao Y, Ji F, Liu Y, Wang S, Chen M, Zhang W, Tao Z, Xu A. Environmental Surveillance of Human Astroviruses in Jinan City of China, 2020-2021. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:50-57. [PMID: 38212480 DOI: 10.1007/s12560-023-09576-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Human astroviruses (HAstVs) are a significant etiological agent of acute gastroenteritis in children. In order to investigate the circulation of HAstVs during the COVID-19 pandemic, a 2-year environmental surveillance was conducted in Jinan between 2020 and 2021. A total of 24 sewage samples were collected and concentrated. Real-time PCR indicated a positive rate of 83.3%, 79.2% (19/24), and 62.5% for classic, MLB, and VA types of HAstV in sewage samples, respectively, with genomic copies ranging from 6.4 × 103 to 3.7 × 107, 3.2 × 104 to 2.2 × 106, and 1.2 × 104 to 1.6 × 107 l-1. Next-generation sequencing (NGS) analysis on complete ORF2 amplicons from each sewage concentrate revealed the presence of 11 HAstV types, including HAstV-1, -2, -4, -5, MLB1, and VA1 to VA6, as well as non-human animal astroviruses. The most abundant HAstV types were HAstV-1, -4, and -5, which accounted for 70.3%, 12.6%, and 9.1% of total HAstV reads, respectively. Phylogenetic analysis revealed that the sequences obtained in this study were segregated into multiple transmission lineages, yet exhibited less genetic divergence among themselves than with foreign strains. These findings provide insight into the genotype diversity and genetic characterization of HAstVs during the COVID-19 pandemic, and highlight the effectiveness of utilizing NGS approaches to investigate sewage HAstVs.
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Affiliation(s)
- Xiaojuan Lin
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Mingyi Xu
- Shandong Academy of Occupational Health and Occupational Medicine, Jinan, 250062, China
| | - Yun Zhao
- School of Public Health, Shandong University Cheeloo College of Medicine, Jinan, China
| | - Feng Ji
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Yao Liu
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Suting Wang
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Meng Chen
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Wenqiang Zhang
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Zexin Tao
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China.
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, Jinan, 250014, China.
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David EDS, Fonseca EDC, de Carvalho JFN, Marinho RDSS, Duro RLS, Komninakis SV, Souto RNP. Metagenomics applied to the detection of diarrhea viruses in humans: Systematic Review. Acta Trop 2022; 227:106287. [PMID: 34929178 DOI: 10.1016/j.actatropica.2021.106287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
Abstract
To analyze the application of the metagenomics method in the identification of viral infectious agents that lead to diarrhea outbreaks. This study is a systematic review, which looked for publications on the following platforms: PubMed, Scientific Electronic Library Online (SciELO), LILACS and CAPES periodicals, conducted according to the PRISMA methodology, investigating in the literary composition studies related to metagenomics applied in the identification of viral infectious agents, which lead to diarrhea in humans. 1198 publications were identified. Of these, after analyzes and exclusions at different stages, 18 studies remained, which directly corresponded to the theme. Diarrhea was presented as a universal health concern. Despite the emergence of vaccines, cases of diarrhea remain persistent in poor populations. In this context, metagenomics emerges as a primary tool in detecting enteric viruses and identifying new viruses, revolutionizing health diagnoses, knowledge of viral diversity, and health surveillance, contributing to the correct etiology of infectious agents that would never be identified by conventional methods. The 18 articles studied point to advances in research in viral metagenomics of diarrheal samples, contributing to the discernment of diarrhea outbreaks, and properly associating with their etiological agents, they are presented in an innovative way for studies on the understanding of viral diversity.
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Janowski AB, Owen MC, Dudley H, López T, Espinosa R, Elvin-Lewis M, Colichon A, Arias CF, Burbelo PD, Wang D. High Seropositivity Rate of Neutralizing Antibodies to Astrovirus VA1 in Human Populations. mSphere 2021; 6:e0048421. [PMID: 34468168 PMCID: PMC8550256 DOI: 10.1128/msphere.00484-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/17/2021] [Indexed: 02/04/2023] Open
Abstract
Astroviruses are common pathogens of the human gastrointestinal tract, but they have been recently identified from cases of fatal meningoencephalitis. Astrovirus VA1 is the most frequently detected astrovirus genotype from cases of human encephalitis, but the prevalence of neutralizing antibodies to VA1 in human sera is unknown. We developed a focus reduction neutralization assay (FRNT) for VA1 and measured the seroprevalence of neutralizing antibodies from two cohorts of adult and pediatric serum samples: (i) an age-stratified cohort from St. Louis, MO, collected from 2007 to 2008 and (ii) a cohort from the Peruvian Amazonian River Basin collected in the late 1990s. In the St. Louis cohort, the lowest seropositivity rate was in children 1 year of age (6.9%), rising to 63.3% by ages 9 to 12, and 76.3% of adults ≥20 years were positive. The Peruvian Amazon cohort showed similar seropositivity rates across all ages, with individuals under age 20 having a rate of 75%, while 78.2% of adults ≥20 years were seropositive. In addition, we also identified the presence neutralizing antibodies to VA1 from commercial lots of intravenous immunoglobulin (IVIG). Our results demonstrate that a majority of humans are exposed to VA1 by adulthood, with the majority of infections occurring between 2 and 9 years of age. In addition, our results indicate that VA1 has been circulating in two geographically and socioeconomically divergent study cohorts over the past 20 years. Nonetheless, a significant proportion of the human population lacks neutralizing immunity and remains at risk for acute infection. IMPORTANCE Astroviruses are human pathogens with emerging disease associations, including the recent recognition of their capacity to cause meningoencephalitis. Astrovirus VA1 is the most commonly identified astrovirus genotype from cases of human encephalitis, but it is unknown what percentage of the human population has neutralizing antibodies to VA1. We found that 76.3 to 78.2% of adult humans ≥20 years of age in two geographically and socioeconomically distinct cohorts are seropositive for VA1, with the majority of infections occurring between 2 and 9 years of age. These results demonstrate that VA1 has been circulating in human populations over the past 2 decades and that most humans develop neutralizing antibodies against this virus by adulthood. However, a subset of humans lack evidence of neutralizing antibodies and are at risk for diseases caused by VA1, including encephalitis.
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Affiliation(s)
- Andrew B. Janowski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Macee C. Owen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Holly Dudley
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rafaela Espinosa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Alejandro Colichon
- Department of Immunology, Peruvian University Cayetano Heredia, Lima, Peru
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Peter D. Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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Arowolo KO, Ayolabi CI, Adeleye IA, Lapinski B, Santos JS, Raboni SM. Molecular epidemiology of astrovirus in children with gastroenteritis in southwestern Nigeria. Arch Virol 2020; 165:2461-2469. [PMID: 32770482 PMCID: PMC7414288 DOI: 10.1007/s00705-020-04741-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022]
Abstract
Human astrovirus (HAstV) is recognized as one of the major causative agents of acute gastroenteritis in children worldwide. Data on the genetic diversity of HAstV in Nigeria are limited. The aim of this study was to determine the prevalence and molecular epidemiology of classical HAstV in children under 5 years of age with acute gastroenteritis in Ogun State, Nigeria. Fecal samples (331) as well as socio-demographic and clinical data were collected across the three senatorial districts of the state from February 2015 to April 2017. One hundred seventy-five samples were randomly selected and analyzed for the presence of HAstV using RT-PCR. PCR amplicons from positive samples were sequenced, and phylogenetic analysis was done to determine genotypes and lineages. The overall prevalence rate was 19.4% (34), with the highest occurrence observed in 2015 (41.4%). Viral coinfections were detected in 13 cases (38.2%). HAstV infection occurred throughout the year and in all age groups, mainly in the age group of 0-12 months. There was significant association between prevalence rate and collection year; however, no association was observed with gender, age, symptoms or risk factors. HAstV-5 was the predominant genotype (76.5%) circulating throughout the study period, followed by HAstV-1 (23.5%), which circulated only in the first 2 years of the study. Phylogenetic analysis showed that all HAstV-5 strains detected belonged to the 5a lineage, while HAstV-1 strains were grouped into lineage 1b. This study, to the best of our knowledge, is the first comprehensive report on molecular characterization of classical HAstV among children with gastroenteritis in the country, and this will serve as baseline information for implementing appropriate infection control practices.
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Affiliation(s)
- K O Arowolo
- Department of Microbiology, University of Lagos, Lagos, Nigeria
- Virology Laboratory, Infectious Diseases Division, Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Department of Biological Sciences, Lagos State Polytechnic, Ikorodu, Lagos, Nigeria
| | - C I Ayolabi
- Department of Microbiology, University of Lagos, Lagos, Nigeria
| | - I A Adeleye
- Department of Microbiology, University of Lagos, Lagos, Nigeria
| | - B Lapinski
- Virology Laboratory, Infectious Diseases Division, Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - J S Santos
- Virology Laboratory, Infectious Diseases Division, Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Sonia M Raboni
- Virology Laboratory, Infectious Diseases Division, Hospital de Clinicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.
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Vu DL, Sabrià A, Aregall N, Michl K, Sabrià J, Rodriguez Garrido V, Goterris L, Bosch A, Pintó RM, Guix S. A Spanish case-control study in <5 year-old children reveals the lack of association between MLB and VA astrovirus and diarrhea. Sci Rep 2020; 10:1760. [PMID: 32020041 PMCID: PMC7000717 DOI: 10.1038/s41598-020-58691-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023] Open
Abstract
Novel human astroviruses (HAstV) were discovered 10 years ago and have been associated with fatal cases of central nervous system infections. Their role in gastroenteritis is controversial, as they have been identified in symptomatic and asymptomatic subjects. The aim of the study was to investigate novel HAstV in a gastroenteritis case-control study including a pediatric population in Spain over a one-year period. We included stool samples from patients with gastroenteritis and negative results for viruses screened by routine diagnostics, and stool samples of control subjects who sought for a routine medical consultation. All samples were screened by real-time RT-PCR assays for novel HAstV. An additional screening for rotavirus, norovirus GI, GII, sapovirus, classic HAstV and adenovirus was also performed for the control group. Overall, 23/363 stool samples from case patients (6.3%) and 8/199 stool samples from control patients (4%) were positive for ≥1 novel HAstV. MLB1 was predominant (64.5% of positives). Seasonality was observed for the case group (p = 0.015), but not the control group (p = 0.95). No difference was observed in the prevalence of novel HAstV between the case and control groups (OR 1.78, 95% CI 0.68–5.45; p = 0.30). Nevertheless, MLB genome copy numbers/ml of fecal suspension was significantly higher in the control group than in the case group (p = 0.008). In our study, we identified a lack of association between novel HAstV and gastroenteritis in the studied population, which could indicate a potential role of reservoir for children, especially given the higher viral load observed in the asymptomatic group for some of them.
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Affiliation(s)
- Diem-Lan Vu
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain. .,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain. .,Department of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | - Aurora Sabrià
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Nuria Aregall
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Kristina Michl
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Jaume Sabrià
- Primary Health Care Center El Serral, Generalitat de Catalunya, Sant Vicenç dels Horts, Spain
| | | | - Lidia Goterris
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Rosa Maria Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain. .,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain.
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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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Novel Human Astroviruses: Prevalence and Association with Common Enteric Viruses in Undiagnosed Gastroenteritis Cases in Spain. Viruses 2019; 11:v11070585. [PMID: 31252663 PMCID: PMC6669616 DOI: 10.3390/v11070585] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
A remarkable percentage of acute gastroenteritis cases remain etiologically undiagnosed. The aim of the study was to determine the prevalence of common and emerging enteric viruses, such as novel human astroviruses, among undiagnosed samples from children with acute gastroenteritis. Epidemiological studies for novel human astroviruses are still scarce. Stool samples collected over two consecutive winter seasons (2016–2017) from children with gastroenteritis in Spain, which were negative for bacteria, rotavirus, and adenovirus by routine diagnostics were screened by real-time RT-PCR assays for the presence of classical and novel astrovirus, rotavirus, norovirus GI and GII, sapovirus, and adenovirus. Overall, 220/384 stool samples (57.3%) were positive for at least one virus. Co-infections were identified in 21% of cases. Among a total of 315 viruses identified, adenovirus was the most prevalent (n = 103), followed by rotavirus (n = 51), sapovirus (n = 50), classical astrovirus (n = 43), novel astroviruses (n = 42), and norovirus (n = 26). Novel astroviruses were present in 13.3% of virus-positive cases. Most novel astroviruses were found in children <2-year-old (30/39 children, 77%, p = 0.01) and were found in co-infection (66%). Only classical astroviruses demonstrated significant differences in the Cq values during mono-infections compared to co-infections. In conclusion, common enteric viruses may be frequently found in children with undiagnosed gastroenteritis, indicating the need to implement more sensitive diagnostic methods. Novel astroviruses circulate in the community and could be the cause of gastroenteritis among young children.
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Human Astrovirus MLB Replication In Vitro: Persistence in Extraintestinal Cell Lines. J Virol 2019; 93:JVI.00557-19. [PMID: 31019055 DOI: 10.1128/jvi.00557-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
MLB astroviruses were identified 10 years ago in feces from children with gastroenteritis of unknown etiology and have been unexpectedly detected in severe cases of meningitis/encephalitis, febrile illness of unknown etiology, and respiratory syndromes. The aim of this study was to establish a cell culture system supporting MLB astrovirus replication. We used two clinical strains to infect several cell lines, an MLB1 strain from a gastroenteritis case, and an MLB2 strain associated with a neurologic infection. Efforts to propagate the viruses in the Caco-2 cell line were unsuccessful. In contrast, we identified two human nonintestinal cell lines, Huh-7 and A549, permissive for both genotypes. After serial passages in the Huh-7.5 cell line, the adapted strains were able to establish persistent infections in the Huh-7.5, Huh-7AI, and A549 cell lines, with high viral loads (up to 10 log10 genome copies/ml) detected by quantitative reverse transcription-PCR (RT-qPCR) in the culture supernatant. Immunofluorescence assays demonstrated infection in about 10% of cells in persistently infected cultures. Electron microscopy revealed particles of 32 to 33 nm in diameter after negative staining of cell supernatants and capsid arrays in ultrathin sections with a particularly high production in Huh-7.5 cells. Interferon (IFN) expression by infected cells and effect of exogenous IFN varied depending on the type of infection and the cell line. The availability of a cell culture system to propagate MLB astroviruses represents a key step to better understand their replicative cycle, as well as a source of viruses to conduct a wide variety of basic virologic studies.IMPORTANCE MLB astroviruses are emerging viruses infecting humans. More studies are required to determine their exact epidemiology, but several reports have already identified them as the cause of unexpected clinical diseases, including severe neurologic diseases. Our study provides the first description of a cell culture system for the propagation of MLB astroviruses, enabling the study of their replicative cycle. Moreover, we demonstrated the unknown capacity of MLB astrovirus to establish persistent infections in cell culture. Whether these persistent infections are also established in vivo remains unknown, but the clinical consequences would be of high interest if persistence was confirmed in vivo Finally, our analysis of IFN expression provides some trails to understand the mechanism by which MLB astroviruses can cause persistent infections in the assayed cultures.
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Tao Z, Wang H, Zhang W, Xu A. Novel astrovirus types circulating in Shandong Province (Eastern China) during 2016: A clinical and environmental surveillance. J Clin Virol 2019; 116:69-73. [PMID: 31125792 DOI: 10.1016/j.jcv.2019.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/29/2019] [Accepted: 05/11/2019] [Indexed: 01/31/2023]
Abstract
BACKGROUND In recent years, several novel astroviruses have been discovered by molecular assays. Their prevalence in many parts of the world remains unclear. OBJECTIVES To investigate the existence and genetic diversity of novel astroviruses in China. STUDY DESIGN Stool specimens were collected from patients suffering gastroenteritis from two hospitals in Jinan city in 2016, and were screened for novel astroviruses by real-time RT-PCR assay. Positive samples were subject of ORF2-amplification by conventional RT-PCR and Sanger sequencing. In addition, 1 liter of sewage sample was collected monthly in 2016 and concentrated via the membrane adsorption/elution method. Partial ORF2 amplification, cloning and Sanger sequencing were conducted, and phylogenetic analysis was performed for genotyping all the obtained sequences. RESULTS 18 of 635 specimens (2.8%) were positive for novel astrovirus detection by real-time RT-PCR assay and were further genotyped by Sanger sequencing as 13 MLB1, 4 MLB2, and 1 VA3. 100% (12/12) of sewage samples were positive for novel astroviruses by conventional RT-PCR. After cloning and sequencing, six known novel astroviruses (MLB1, MLB2, VA1, VA2, VA3, and VA5) were identified. VA2, MLB1, and VA1 were the most common subtypes being detected in 100.0% (12/12), 91.7% (11/12), and 91.7% (11/12) of the samples, respectively. Eighteen sequences that could not be classified into any known subtypes were found. CONCLUSIONS These results demonstrate the wide circulation and high diversity of novel astroviruses in Jinan, Shandong Province, China, and underline the significance of environmental surveillance combined with population-based surveillance for understanding the molecular epidemiology of enteric viruses.
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Affiliation(s)
- Zexin Tao
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, People's Republic of China
| | - Haiyan Wang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, People's Republic of China
| | - Wenqiang Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, People's Republic of China
| | - Aiqiang Xu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, People's Republic of China; School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, People's Republic of China.
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Wohlgemuth N, Honce R, Schultz-Cherry S. Astrovirus evolution and emergence. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 69:30-37. [PMID: 30639546 PMCID: PMC7106029 DOI: 10.1016/j.meegid.2019.01.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/19/2022]
Abstract
Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown. Recombination events can lead to drastic evolutionary changes and contribute to cross-species transmission events. This work reviews the current state of research on astrovirus evolution and emergence, especially as it relates to cross-species transmission and recombination of astroviruses.
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Affiliation(s)
- Nicholas Wohlgemuth
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38105, United States
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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Janowski AB, Wang D. Infection and Propagation of Astrovirus VA1 in Cell Culture. CURRENT PROTOCOLS IN MICROBIOLOGY 2019; 52:e73. [PMID: 30444308 PMCID: PMC6340763 DOI: 10.1002/cpmc.73] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Astrovirus VA1/HMO-C (VA1) is the representative genotype of mamastrovirus 9, a species of the single-stranded, positive-sense RNA viral family, Astroviridae. Astroviruses have been traditionally considered pathogens of the gastrointestinal tract but they have been recently associated with neurological diseases in humans, cattle, mink, sheep, and pigs. VA1 is the astrovirus genotype most commonly identified from human cases of meningoencephalitis and has been recently propagated in cell culture. VA1 can now be used as a model system to study pathogenesis of the neurological diseases associated with astrovirus infection. In this article, we describe two fundamental assays to quantify replication and propagation of VA1, a quantitative reverse transcription-PCR (qRT-PCR) to measure viral RNA and a 50% tissue culture infectious dose (TCID50 ) assay to measure infectious viral particles. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Andrew B Janowski
- Washington University School of Medicine, Campus Box 8230, 660 S. Euclid Ave, St. Louis, MO 63110 USA., Phone: 314-286-1124, Fax: 314-362-1232,
| | - David Wang
- Washington University School of Medicine, Campus Box 8230, 660 S. Euclid Ave, St. Louis, MO 63110 USA., Phone: 314-286-1124, Fax: 314-362-1232,
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12
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Nadan S, Taylor MB, Groome MJ, Cohen C, Madhi SA, Page NA. Epidemiology of human astroviruses among children younger than 5 years: Prospective hospital-based sentinel surveillance in South Africa, 2009-2014. J Med Virol 2018; 91:225-234. [PMID: 30192398 DOI: 10.1002/jmv.25308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/02/2018] [Accepted: 09/02/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND The epidemiology of human astroviruses (HAstVs) in hospitalised patients less than 5 years of age from selected sites in South Africa was investigated. Diarrheagenic stool specimens collected from April 2009 to May 2014 were screened retrospectively for selected viruses, bacteria and parasites. METHOD Patient data were analysed to identify epidemiologic factors most frequently detected with HAstV infections. The following case-comparisons were investigated; HAstV-positive and HAstV-negative children, human immunodeficiency virus (HIV)-infected and HIV-uninfected (HAstV-positive) children and HIV-exposed and unexposed (HAstV-positive HIV-uninfected) children. RESULTS Astrovirus was identified in 7.0% (234/3340) of cases and most frequently in ages 7 to 12 months (9.2%; 90/975) compared with 5.8% to 6.6% in other 6-month age groups. No seasonal trends were observed. More HAstVs were detected in children from homes that used outdoor water sources (7.6%) compared to indoor sources [5.7%; adjusted odds ratio (aOR), 1.5; 95% CI, 1.1-2.1; P = 0.009]. Astroviruses were detected in 8.4% (67/799) of HIV-uninfected patients that were exposed to HIV compared with 5.9% (74/1257) of HIV-unexposed patients ( P = 0.032). CONCLUSION Astroviruses were most prevalent in children aged 7 to 12 months and were detected throughout the study period. The study was limited as only hospitalised patients were investigated and no comparisons were made to diarrhoea-free control groups. Future HAstV surveillance should include community-based studies and children presenting at outpatient facilities.
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Affiliation(s)
- Sandrama Nadan
- Centre for Enteric Diseases, Virology Division, National Institute for Communicable Disease, Sandringham, South Africa.,Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
| | - Michelle J Groome
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, Epidemiology Division, National Institute for Communicable Disease, Sandringham, South Africa
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicola A Page
- Centre for Enteric Diseases, Virology Division, National Institute for Communicable Disease, Sandringham, South Africa.,Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
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Reuter G, Pankovics P, Boros Á. Nonsuppurative (Aseptic) Meningoencephalomyelitis Associated with Neurovirulent Astrovirus Infections in Humans and Animals. Clin Microbiol Rev 2018; 31:e00040-18. [PMID: 30158300 PMCID: PMC6148189 DOI: 10.1128/cmr.00040-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Astroviruses are thought to be enteric pathogens. Since 2010, a certain group of astroviruses has increasingly been recognized, using up-to-date random amplification and high-throughput next-generation sequencing (NGS) methods, as potential neurovirulent (Ni) pathogens of severe central nervous system (CNS) infections, causing encephalitis, meningoencephalitis, and meningoencephalomyelitis. To date, neurovirulent astrovirus cases or epidemics have been reported for humans and domesticated mammals, including mink, bovines, ovines, and swine. This comprehensive review summarizes the virology, epidemiology, pathology, diagnosis, therapy, and future perspective related to neurovirulent astroviruses in humans and mammals, based on a total of 30 relevant articles available in PubMed (searched by use of the terms "astrovirus/encephalitis" and "astrovirus/meningitis" on 2 March 2018). A paradigm shift should be considered based on the increasing knowledge of the causality-effect association between neurotropic astroviruses and CNS infection, and attention should be drawn to the role of astroviruses in unknown CNS diseases.
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Affiliation(s)
- Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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14
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PCR assays for detection of human astroviruses: In silico evaluation and design, and in vitro application to samples collected from patients in the Netherlands. J Clin Virol 2018; 108:83-89. [PMID: 30266005 DOI: 10.1016/j.jcv.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/30/2018] [Accepted: 09/11/2018] [Indexed: 11/21/2022]
Abstract
BACKGROUND Human astroviruses (HAstV) comprise three phylogenetically compact and non-adjacent groups of species including classical HAstV (HAstV-C) and the novel ones (HAstV-VA/HMO and HAstV-MLB). Of these, HAstV-C is known to be responsible for gastroenteritis while the novel HAstV are associated with cases of neurological disorders. Accurate detection of all known variants by (real-time) PCR is challenging because of the high intra- and intergroup genetic divergence of HAstV. OBJECTIVES To evaluate published HAstV PCR assays in silico, design de novo real-time PCR assays that can detect and discriminate three groups of HAstV, and apply those to patient samples to analyse the prevalence of HAstV in stool and cerebrospinal fluid (CSF) specimens. STUDY DESIGN In silico evaluation of published PCR assays and design of real-time PCR assays for detection of different subsets of HAstV was conducted within a common computational framework that used all astrovirus full genome sequences from GenBank. The newly designed real-time PCR assays were evaluated in vitro and applied to faecal samples (collected in January-May 2016) and cerebrospinal fluid specimens (2010-2016) from patients in the Netherlands. RESULTS Quantitative in silico evaluation of published PCRs is provided. The newly designed real-time PCR assays can reliably assign all available HAstV genome sequences to one of the three phylogenetic groups in silico, and differentiate among HAstV-specific controls in vitro. A total of 556 samples were tested using these PCR assays. Fourteen fecal samples (2.5%) tested positive for HAstV, 3 of which could be identified as the novel HAstV-MLB variants. No novel HAstV were found in CSF specimens. CONCLUSION Newly designed real-time PCR assays with improved detection of all known HAstV allowed the first-time identification of novel astroviruses from stool samples in the Netherlands.
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Kumthip K, Khamrin P, Ushijima H, Maneekarn N. Molecular epidemiology of classic, MLB and VA astroviruses isolated from <5 year-old children with gastroenteritis in Thailand, 2011-2016. INFECTION GENETICS AND EVOLUTION 2018; 65:373-379. [PMID: 30153477 DOI: 10.1016/j.meegid.2018.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 08/23/2018] [Indexed: 12/23/2022]
Abstract
This study aimed to investigate the molecular epidemiology and genetic diversity of astrovirus circulating in pediatric patients with acute gastroenteritis in Thailand. A total of 2034 fecal specimens collected between 2011 and 2016 from children hospitalized with acute gastroenteritis were analyzed for astrovirus infection using RT-PCR and nucleotide sequencing techniques. Overall, 54 samples were positive for astrovirus (2.6%). About half of the virus-positive samples (57.4%) were co-infection cases, mainly with rotavirus or norovirus. Genotyping revealed that three major clades, classic human astrovirus (HAstV) and newly emerging MLB and VA astroviruses co-circulated in the study population. At least seven different genotypes were identified and HAstV1 was the most predominant genotype detected (50%), followed by MLB1 (16.7%), HAstV4 (11.1%), HAstV5 and HAstV8 (7.4% each), MLB2 and VA2 (3.7% each). This study provided a useful information and contributed to molecular epidemiology of astroviruses including the novel MLB and VA astoviruses have been characterized and reported for the first time in Thailand.
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Affiliation(s)
- Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, 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
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
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16
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Boujon CL, Koch MC, Seuberlich T. The Expanding Field of Mammalian Astroviruses: Opportunities and Challenges in Clinical Virology. Adv Virus Res 2017; 99:109-137. [PMID: 29029723 DOI: 10.1016/bs.aivir.2017.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Astroviruses are best known as being one of the leading causes of diarrhea in infants and were first described in this context in 1975. In its first years, astrovirus research was mainly restricted to electron microscopy and serology studies. The ability to culture some of these viruses in vitro allowed a first consequent step forward, especially at the molecular level. Since the emergence of more powerful genetic methods, though, the face of this research field has dramatically changed and evolved. From the exponential number of discoveries of new astrovirus strains in the most varied of animal species to their association with atypical diseases, these viruses revealed a lot of surprises, and many more are probably still waiting to be uncovered. This chapter summarizes the most important knowledge about astroviruses and discusses the implication of the latest findings in this area of research.
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17
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Propagation of Astrovirus VA1, a Neurotropic Human Astrovirus, in Cell Culture. J Virol 2017; 91:JVI.00740-17. [PMID: 28701405 DOI: 10.1128/jvi.00740-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/21/2017] [Indexed: 01/11/2023] Open
Abstract
Astrovirus VA1/HMO-C (VA1; mamastrovirus 9) is a recently discovered astrovirus genotype that is divergent from the classic human astroviruses (mamastrovirus 1). The gastrointestinal tract is presumed to be the primary site of infection and pathogenicity for astroviruses. However, VA1 has been independently detected in brain tissue of five cases of human encephalitis. Studies of the pathogenicity of VA1 are currently impossible because there are no reported cell culture systems or in vivo models that support VA1 infection. Here, we describe successful propagation of VA1 in multiple human cell lines. The initial inoculum, a filtered clinical stool sample from the index gastroenteritis case cluster that led to the discovery of VA1, was first passaged in Vero cells. Serial blind passage in Caco-2 cells yielded increasing copies of VA1 RNA, and multistep growth curves demonstrated a >100-fold increase in VA1 RNA 72 h after inoculation. The full-length genomic and subgenomic RNA strands were detected by Northern blotting, and crystalline lattices of viral particles of ∼26-nm diameter were observed by electron microscopy in infected Caco-2 cells. Unlike other human astrovirus cell culture systems, which require addition of exogenous trypsin for continued propagation, VA1 could be propagated equally well with or without the addition of trypsin. Furthermore, VA1 was sensitive to the type I interferon (IFN-I) response, as VA1 RNA levels were reduced by pretreatment of Caco-2 cells with IFN-β1a. The ability to propagate VA1 in cell culture will facilitate studies of the neurotropism and neuropathogenesis of VA1.IMPORTANCE Astroviruses are an emerging cause of central nervous system infections in mammals, and astrovirus VA1/HMO-C is the most prevalent astrovirus in cases of human encephalitis. This virus has not been previously propagated, preventing elucidation of the biology of this virus. We describe the first cell culture system for VA1, a key step necessary for the study of its ability to cause disease.
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18
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Melamed R, Storch GA, Holtz LR, Klein EJ, Herrin B, Tarr PI, Denno DM. Case-Control Assessment of the Roles of Noroviruses, Human Bocaviruses 2, 3, and 4, and Novel Polyomaviruses and Astroviruses in Acute Childhood Diarrhea. J Pediatric Infect Dis Soc 2017; 6:e49-e54. [PMID: 28186546 PMCID: PMC6251662 DOI: 10.1093/jpids/piw083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/08/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The etiology of acute childhood diarrhea often eludes identification. We used a case-control study-stool archive to determine if nucleic acid tests for established and newly identified viruses diminish our previously published 32% rate of microbiologically unexplained episodes. METHODS Using polymerase chain reaction, we sought to detect noroviruses GI and GII, classic and novel astroviruses, and human bocaviruses (HBoVs) 2, 3, and 4 among 178 case and 178 matched control stool samples and St. Louis and Malawi polyomaviruses among a subset of 98 case and control stool samples. We calculated adjusted odds ratios and 95% confidence intervals using conditional logistic regression. RESULTS Noroviruses were more common in cases (GI, 2.2%; GII, 16.9%) than in controls (GI, 0%; GII, 4.5%) (adjusted odds ratio, 5.2 [95% confidence interval, 2.5-11.3]). Astroviruses and HBoVs 2, 3, and 4 were overrepresented among the cases, although this difference was not statistically significant. Malawi polyomavirus was not associated with case status, and St. Louis polyomavirus was identified in only 1 subject (a control). When identified in cases, HBoVs 2, 3, and 4 were frequently (77%) found in conjunction with a bona fide diarrheagenic pathogen. Thirty-five (20%) case and 3 (2%) control stool samples contained more than 1 organism of interest. Overall, a bona fide or plausible pathogen was identified in 79% of the case stool samples. Preceding antibiotic use was more common among cases (adjusted odds ratio, 4.5 [95% confidence interval, 2.3-8.5]). CONCLUSION Noroviruses were found to cause one-third of the diarrhea cases that previously had no identified etiology. Future work should attempt to ascertain etiologic agents in the approximately one-fifth of cases without a plausible microbial cause, understand the significance of multiple agents in stools, and guide interpretation of nonculture diagnostics.
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Affiliation(s)
- Rimma Melamed
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Lori R Holtz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Eileen J Klein
- Departments of Pediatrics,Department of Pediatrics, Seattle Children’s Hospital, Seattle, Washington
| | - Brittany Herrin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Donna M Denno
- Departments of Pediatrics,Global Health, University of Washington School of Medicine, Seattle, Washington,Department of Pediatrics, Seattle Children’s Hospital, Seattle, Washington,Correspondence: D. M. Denno, MD, MPH, Division of General Pediatrics, University of Washington, Box 354920, 6200 NE 74th St., Suite 110, Seattle, WA 98118 ()
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19
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Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea. J Virol 2017; 91:JVI.00952-17. [PMID: 28659484 DOI: 10.1128/jvi.00952-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.
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20
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Lewandowska DW, Zagordi O, Geissberger FD, Kufner V, Schmutz S, Böni J, Metzner KJ, Trkola A, Huber M. Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. MICROBIOME 2017; 5:94. [PMID: 28789678 PMCID: PMC5549297 DOI: 10.1186/s40168-017-0317-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. RESULTS In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. CONCLUSIONS The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karin J Metzner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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21
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Donato C, Vijaykrishna D. The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses. Viruses 2017; 9:v9050102. [PMID: 28489047 PMCID: PMC5454415 DOI: 10.3390/v9050102] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 01/23/2023] Open
Abstract
Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.
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Affiliation(s)
- Celeste Donato
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
| | - Dhanasekaran Vijaykrishna
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia.
- Duke-NUS Medical School, Singapore 169857, Singapore.
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22
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Ao YY, Yu JM, Li LL, Cao JY, Deng HY, Xin YY, Liu MM, Lin L, Lu S, Xu JG, Duan ZJ. Diverse novel astroviruses identified in wild Himalayan marmots. J Gen Virol 2017; 98:612-623. [PMID: 28100306 DOI: 10.1099/jgv.0.000709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
With advances in viral surveillance and next-generation sequencing, highly diverse novel astroviruses (AstVs) and different animal hosts had been discovered in recent years. However, the existence of AstVs in marmots had yet to be shown. Here, we identified two highly divergent strains of AstVs (tentatively named Qinghai Himalayanmarmot AstVs, HHMAstV1 and HHMAstV2), by viral metagenomic analysis in liver tissues isolated from wild Marmota himalayana in China. Overall, 12 of 99 (12.1 %) M. himalayana faecal samples were positive for the presence of genetically diverse AstVs, while only HHMAstV1 and HHMAstV2 were identified in 300 liver samples. The complete genomic sequences of HHMAstV1 and HHMAstV2 were 6681 and 6610 nt in length, respectively, with the typical genomic organization of AstVs. Analysis of the complete ORF 2 sequence showed that these novel AstVs are most closely related to the rabbit AstV, mamastrovirus 23 (with 31.0 and 48.0 % shared amino acid identity, respectively). Phylogenetic analysis of the amino acid sequences of ORF1a, ORF1b and ORF2 indicated that HHMAstV1 and HHMAstV2 form two distinct clusters among the mamastroviruses, and may share a common ancestor with the rabbit-specific mamastrovirus 23. These results suggest that HHMAstV1 and HHMAstV2 are two novel species of the genus Mamastrovirus in the Astroviridae. The remarkable diversity of these novel AstVs will contribute to a greater understanding of the evolution and ecology of AstVs, although additional studies will be needed to understand the clinical significance of these novel AstVs in marmots, as well as in humans.
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Affiliation(s)
- Yuan-Yun Ao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, PR China
| | - Jie-Mei Yu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, PR China
| | - Li-Li Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, PR China
| | - Jing-Yuan Cao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, PR China
| | - Hong-Yan Deng
- Medical College of Qingdao University, Qingdao 266021, Shandong, PR China
| | - Yun-Yun Xin
- The First Affiliated Hospital of Hunan Normal University, Changsha 410000, Hunan, PR China
| | - Meng-Meng Liu
- Medical College of Qingdao University, Qingdao 266021, Shandong, PR China
| | - Lin Lin
- Shandong Center for Disease Control and Prevention, Jinan 250014, Shandong, PR China
| | - Shan Lu
- National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Jian-Guo Xu
- National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Zhao-Jun Duan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, PR China
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23
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Vu DL, Bosch A, Pintó RM, Guix S. Epidemiology of Classic and Novel Human Astrovirus: Gastroenteritis and Beyond. Viruses 2017; 9:v9020033. [PMID: 28218712 PMCID: PMC5332952 DOI: 10.3390/v9020033] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/20/2022] Open
Abstract
Since they were identified in 1975, human astroviruses have been considered one of the most important agents of viral acute gastroenteritis in children. However, highly divergent astroviruses infecting humans have been recently discovered and associated with extra-intestinal infections. The report of cases of fatal meningitis and encephalitis, especially in immunocompromised individuals, has broadened their disease spectrum. Although zoonotic transmission among animal and human astroviruses has not been clearly recognized, the genetic similarity between some human and animal viruses makes it likely to occur. This review provides an update on the epidemiology of both classic and novel human astroviruses, and a comprehensive view on confirmed or potential association between astrovirus and human disease.
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Affiliation(s)
- Diem-Lan Vu
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
| | - Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona 08028, Spain.
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Santa Coloma de Gramenet 08921, Spain.
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Abstract
Foodborne viral illness, resulting from the consumption of contaminated food or water containing pathogenic viruses, remains a major public health problem globally with substantial economic impact. Major challenges regarding recognizing, detecting, characterizing, and effectively responding to foodborne viral threats to health exist. Adequate health crisis management is largely dependent on early detection of potential public health threats, which is hampered by changing trends in disease outbreaks, from localized clusters of disease in confined populations to dispersed outbreaks with excellent opportunity for further transmission. In addition, no precise and consistent global baseline syndrome and diagnostic surveillance information exists. An integrated multidisciplinary approach with a combination of sustained pathogen syndrome and diagnostic surveillance, genomics-based, and standardized global analytical networks gathering clinical, epidemiological and genetic data alike would be required to understand the dynamics of foodborne viral infection and to mitigate potential effects of future threats. A huge global effort in virus syndrome and diagnostic surveillance may be justified in the light of global health impact in general, and timely with the development of new metagenomics tools that hold the promise of not only identifying viral pathogens, but possibly the complete microbiome in a single assay.
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Pérot P, Lecuit M, Eloit M. Astrovirus Diagnostics. Viruses 2017; 9:v9010010. [PMID: 28085120 PMCID: PMC5294979 DOI: 10.3390/v9010010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 01/25/2023] Open
Abstract
Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes.
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Affiliation(s)
- Philippe Pérot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Institut Pasteur, Centre d'innovation et de Recherche Technologique (Citech), 75015 Paris, France.
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Paris Descartes University, Sorbonne Paris Cité, 75005, Paris, France.
- Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, 75015 Paris, France.
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Laboratory of Pathogen Discovery, 75015 Paris, France.
- Ecole Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France.
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26
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Narrowing of the Diagnostic Gap of Acute Gastroenteritis in Children 0-6 Years of Age Using a Combination of Classical and Molecular Techniques, Delivers Challenges in Syndromic Approach Diagnostics. Pediatr Infect Dis J 2016; 35:e262-70. [PMID: 27276177 PMCID: PMC4987234 DOI: 10.1097/inf.0000000000001208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Twenty-five percent to 50% of acute gastroenteritis (AGE) cases remain etiologically undiagnosed. Our main aim was to determine the most appropriate list of enteric pathogens to be included in the daily diagnostics scheme of AGE, ensuring the lowest possible diagnostic gap. METHODS Two hundred ninety seven children ≤6 years of age, admitted to hospital in Slovenia, October 2011 to October 2012, with AGE, and 88 ≤6 years old healthy children were included in the study. A broad spectrum of enteric pathogens was targeted with molecular methods, including 8 viruses, 6 bacteria and 2 parasites. RESULTS At least one enteric pathogen was detected in 91.2% of cases with AGE and 27.3% of controls. Viruses were the most prevalent (82.5% and 15.9%), followed by bacteria (27.3% and 10.2%) and parasites (3.0% and 1.1%) in cases and controls, respectively. A high proportion (41.8%) of mixed infections was observed in the cases. For cases with undetermined etiology (8.8%), stool samples were analyzed with next generation sequencing, and a potential viral pathogen was detected in 17 additional samples (5.8%). CONCLUSIONS Our study suggests that tests for rotaviruses, noroviruses genogroup II, adenoviruses 40/41, astroviruses, Campylobacter spp. and Salmonella sp. should be included in the initial diagnostic algorithm, which revealed the etiology in 83.5% of children tested. The use of molecular methods in diagnostics of gastroenteritis is preferable because of their high sensitivity, specificity, fast performance and the possibility of establishing the concentration of the target. The latter may be valuable for assessing the clinical significance of the detected enteric, particularly viral pathogens.
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Vu DL, Cordey S, Brito F, Kaiser L. Novel human astroviruses: Novel human diseases? J Clin Virol 2016; 82:56-63. [PMID: 27434149 DOI: 10.1016/j.jcv.2016.07.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/28/2016] [Accepted: 07/10/2016] [Indexed: 10/21/2022]
Abstract
Astroviruses are small, non-enveloped, single-stranded positive RNA viruses that belong to the Astroviridae family. While classical human astroviruses (HAstV) are a well-recognized cause of acute non-bacterial diarrhea among young children worldwide, novel astroviruses, named HAstV-MLB and HAstV-VA/HMO, have been identified recently in humans by molecular assays. They are phylogenetically more related to animal astroviruses than to classical human astroviruses, thus suggesting cross-species transmission. Serological studies demonstrated a surprisingly high seroprevalence in certain populations and highlighted a high infection rate in the early years of life. Although their pathogenic role has not yet been clearly determined, novel astrovirus RNA sequences have been identified in different biological specimens of symptomatic patients, including the feces, plasma, cerebrospinal fluid, and brain biopsies. Thus, there is evidence that they could contribute not only to digestive tract infection, but also to unexpected clinical syndromes, notably encephalitis and meningitis. Severe infections affect mainly immunocompromised patients. These findings indicate that novel astroviruses should be considered in the differential diagnosis of immunocompromised patients with meningitis or encephalitis of unknown origin.
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Affiliation(s)
- Diem-Lan Vu
- Laboratory of Virology, Division of Laboratory Medicine and Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland.
| | - Samuel Cordey
- Laboratory of Virology, Division of Laboratory Medicine and Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland.
| | - Francisco Brito
- Swiss Institute of Bioinformatics, University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland.
| | - Laurent Kaiser
- Laboratory of Virology, Division of Laboratory Medicine and Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland.
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Schneeberger PHH, Becker SL, Pothier JF, Duffy B, N'Goran EK, Beuret C, Frey JE, Utzinger J. Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study. INFECTION GENETICS AND EVOLUTION 2015; 40:389-397. [PMID: 26391184 DOI: 10.1016/j.meegid.2015.08.044] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/17/2015] [Accepted: 08/31/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND The intestinal microbiome is a complex community and its role in influencing human health is poorly understood. While conventional microbiology commonly attributes digestive disorders to a single microorganism, a metagenomic approach can detect multiple pathogens simultaneously and might elucidate the role of microbial communities in the pathogenesis of intestinal diseases. We present a proof-of-concept that a shotgun metagenomic approach provides useful information on the diverse composition of intestinal pathogens and antimicrobial resistance profiles in human stool samples. METHODS In October 2012, we obtained stool specimens from patients with persistent diarrhea in south Côte d'Ivoire. Four stool samples were purposefully selected and subjected to microscopy, multiplex polymerase chain reaction (PCR), and a metagenomic approach. For the latter, we employed the National Center for Biotechnology Information nucleotide database and screened for 36 pathogenic organisms (bacteria, helminths, intestinal protozoa, and viruses) that may cause digestive disorders. We further characterized the bacterial population and the prevailing resistance patterns by comparing our metagenomic datasets with a genome-specific marker database and with a comprehensive antibiotic resistance database. RESULTS In the four patients, the metagenomic approach identified between eight and 11 pathogen classes that potentially cause digestive disorders. For bacterial pathogens, the diagnostic agreement between multiplex PCR and metagenomics was high; yet, metagenomics diagnosed several bacteria not detected by multiplex PCR. In contrast, some of the helminth and intestinal protozoa infections detected by microscopy were missed by metagenomics. The antimicrobial resistance analysis revealed the presence of genes conferring resistance to several commonly used antibiotics. CONCLUSIONS A metagenomic approach provides detailed information on the presence and diversity of pathogenic organisms in human stool samples. Metagenomic studies allow for in-depth molecular characterization such as the antimicrobial resistance status, which may be useful to develop setting-specific treatment algorithms. While metagenomic approaches remain challenging, the benefits of gaining new insights into intestinal microbial communities call for a broader application in epidemiologic studies. TRIAL REGISTRATION ISRCTN86951400.
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Affiliation(s)
- Pierre H H Schneeberger
- Department of Diagnostics and Risk Assessment Plant Protection, Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland; Department of Virology, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Sören L Becker
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland; Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany.
| | - Joël F Pothier
- Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland.
| | - Brion Duffy
- Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland.
| | - Eliézer K N'Goran
- Unité de Formation et de Recherche Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire; Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire.
| | - Christian Beuret
- Department of Virology, Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland.
| | - Jürg E Frey
- Department of Diagnostics and Risk Assessment Plant Protection, Agroscope, Institute for Plant Production Sciences IPS, Wädenswil, Switzerland.
| | - Jürg Utzinger
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
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Lizasoain A, Tort L, García M, Gómez M, Leite J, Miagostovich M, Cristina J, Colina R, Victoria M. Environmental assessment reveals the presence of MLB-1 human astrovirus in Uruguay. J Appl Microbiol 2015; 119:859-67. [DOI: 10.1111/jam.12856] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/12/2015] [Accepted: 05/14/2015] [Indexed: 11/28/2022]
Affiliation(s)
- A. Lizasoain
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - L.F.L. Tort
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - M. García
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - M.M. Gómez
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Oswaldo Cruz Foundation; Rio de Janeiro Brazil
| | - J.P.G. Leite
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Oswaldo Cruz Foundation; Rio de Janeiro Brazil
| | - M.P. Miagostovich
- Laboratory of Comparative and Environmental Virology; Oswaldo Cruz Institute; Oswaldo Cruz Foundation; Rio de Janeiro Brazil
| | - J. Cristina
- Laboratory of Molecular Virology; Nuclear Investigation Center; School of Sciences; Universidad de la República; Montevideo Uruguay
| | - R. Colina
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
| | - M. Victoria
- Laboratory of Molecular Virology; Department of Biological Sciences; Regional Norte, CENUR Noroeste; Universidad de la República; Salto Uruguay
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Arnold F, Hober D, Chaussade H, Dumarest M, Sané F, Nowakowsjki M, Rigaud E, Bellalou J, Desailloud R, Coursaget P, Eloit M. Antibodies to VP1 of swine pasivirus in humans without evidence of transmission from a pig source. J Clin Virol 2015. [PMID: 26209375 DOI: 10.1016/j.jcv.2015.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND Swine pasivirus (SPaV1) is a recently described enteric virus close to human parechoviruses and highly prevalent in pigs. Antibodies to Escherichia coli-expressed VP1 of SpaV1 have been found in a majority of humans in China. OBJECTIVES The objectives were to estimate the antibody prevalence in a European country, to test if exposure to the virus was linked to pig products and if this exposure was a risk factor for the development of diabetes type 1. STUDY DESIGN An ELISA test was developed and used to screen 842 healthy subjects with known exposure to pig products, 39 patients with diabetes type 1 and 20 controls. RESULTS We identified a high seroprevalence (15.6%) reacting to VP1 of SPaV1 among healthy human subjects. Analysis of risk factors argues against cross-species transmission from pigs as the source of infection. Data also indicate that the presence of SPaV1 VP1-binding antibodies is not associated with diabetes type 1 in humans. CONCLUSION Our results suggest that the seroreactivity frequently found in humans against SpaV1 is due to cross-reactivity with related antigen, perhaps a picornavirus, and that SpaV1 is not a zoonotic virus.
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Affiliation(s)
- Francoise Arnold
- Université François Rabelais, Tours, France; UMR INRA 1282, Tours, France
| | - Didier Hober
- Université Lille 2 Faculté de Médecine, CHRU Lille Laboratoire de Virologie EA3610, Loos-lez-Lille, 59120, France
| | - Hélène Chaussade
- University Hospital, Infectious Diseases Department, Tours, France
| | - Marine Dumarest
- Institut Pasteur, Laboratory of Pathogen Discovery, Biology of Infection Unit, Inserm U1117, 28 rue du Docteur Roux, F-75724 Paris, France
| | - Famara Sané
- Université Lille 2 Faculté de Médecine, CHRU Lille Laboratoire de Virologie EA3610, Loos-lez-Lille, 59120, France
| | - Mireille Nowakowsjki
- Institut Pasteur, Plate-forme de Production de Protéines Recombinantes, Département de Biologie Structurale et Chimie, 25 rue du Docteur Roux, 75015 Paris, France
| | - Emma Rigaud
- Mutualité Sociale Agricole, Bagnolet, France
| | - Jacques Bellalou
- Institut Pasteur, Plate-forme de Production de Protéines Recombinantes, Département de Biologie Structurale et Chimie, 25 rue du Docteur Roux, 75015 Paris, France
| | | | | | - Marc Eloit
- Institut Pasteur, Laboratory of Pathogen Discovery, Biology of Infection Unit, Inserm U1117, 28 rue du Docteur Roux, F-75724 Paris, France; PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France.
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31
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Meyer CT, Bauer IK, Antonio M, Adeyemi M, Saha D, Oundo JO, Ochieng JB, Omore R, Stine OC, Wang D, Holtz LR. Prevalence of classic, MLB-clade and VA-clade Astroviruses in Kenya and The Gambia. Virol J 2015; 12:78. [PMID: 25975198 PMCID: PMC4465002 DOI: 10.1186/s12985-015-0299-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infectious diarrhea leads to significant mortality in children, with 40 % of these deaths occurring in Africa. Classic human astroviruses are a well-established etiology of diarrhea. In recent years, seven novel astroviruses have been discovered (MLB1, MLB2, MLB3, VA1/HMO-C, VA2/HMO-B, VA3/HMO-A, VA4); however, there have been few studies on their prevalence or potential association with diarrhea. METHODS To investigate the prevalence and diversity of these classic and recently described astroviruses in a pediatric population, a case-control study was performed. Nine hundred and forty nine stools were previously collected from cases of moderate-to-severe diarrhea and matched controls of patients less than 5 years of age in Kenya and The Gambia. RT-PCR screening was performed using pan-astrovirus primers. RESULTS Astroviruses were present in 9.9 % of all stool samples. MLB3 was the most common astrovirus with a prevalence of 2.6 %. Two subtypes of MLB3 were detected that varied based on location in Africa. In this case-control study, Astrovirus MLB1 was associated with diarrhea in Kenya, whereas Astrovirus MLB3 was associated with the control state in The Gambia. Classic human astrovirus was not associated with diarrhea in this study. Unexpectedly, astroviruses with high similarity to Canine Astrovirus and Avian Nephritis Virus 1 and 2 were also found in one case of diarrhea and two control stools respectively. CONCLUSIONS Astroviruses including novel MLB- and VA-clade members are commonly found in pediatric stools in Kenya and The Gambia. The most recently discovered astrovirus, MLB3, was the most prevalent and was found more commonly in control stools in The Gambia, while astrovirus MLB1 was associated with diarrhea in Kenya. Furthermore, a distinct subtype of MLB3 was noted, as well as 3 unanticipated avian or canine astroviruses in the human stool samples. As a result of a broadly reactive PCR screen for astroviruses, new insight was gained regarding the epidemiology of astroviruses in Africa, where a large proportion of diarrheal morbidity and mortality occur.
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Affiliation(s)
| | - Irma K Bauer
- Washington University School of Medicine, Saint Louis, MO, USA.
| | | | | | - Debasish Saha
- Medical Research Council Unit, Banjul, The Gambia. .,Center for International Health, Department of Preventive and Social Medicine, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
| | - Joseph O Oundo
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya.
| | - John B Ochieng
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya.
| | - Richard Omore
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya.
| | - O Colin Stine
- University of Maryland School of Medicine, Baltimore, MD, USA.
| | - David Wang
- Washington University School of Medicine, Saint Louis, MO, USA.
| | - Lori R Holtz
- Washington University School of Medicine, Saint Louis, MO, USA.
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