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Mbou-Boutambe C, Mombo IM, Rougeron V, Degrugillier F, Gauthier P, Makanga B, Ngoubangoye B, Leroy EM, Prugnolle F, Boundenga L. Investigation of caliciviruses and astroviruses in Gabonese rodents: A possible influence of national and international trade on the spread of enteric viruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105607. [PMID: 38806078 DOI: 10.1016/j.meegid.2024.105607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Caliciviruses (Caliciviridae) and astroviruses (Astroviridae) are among the leading cause of non-bacterial foodborne disease and gastroenteritis in human. These non-enveloped RNA viruses infect a wide range of vertebrate species including rodents. Rodents are among the most important hosts of infectious diseases globally and are responsible for over 80 zoonotic pathogens that affect humans. Therefore, screening pathogens in rodents will be is necessary to prevent cross-species transmission to prevent zoonotic outbreaks. In the present study, we screened caliciviruses and astroviruses in order to describe their diversity and whether they harbor strains that can infect humans. RNA was then extracted from intestine samples of 245 rodents and retrotranscribed in cDNA to screen caliciviruses and astroviruses by PCRs. All the samples tested negative for caliciviruses and while astroviruses were detected in 18 (7.3%) samples of Rattus rattus species. Phylogenetic analyses based on the RdRp gene showed that all the sequences belonged to Mamastrovirus genus in which they were genetically related to R. rattus related AstVs previously detected in Gabon or in Rattus spp. AstV from Kenya and Asia. These findings suggested that transportation such as land and railway, as well national and international trade, are likely to facilitate spread of AstVs by the dissemination of rodents.
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Affiliation(s)
- Clark Mbou-Boutambe
- Unité de Recherche en Écologie de la Santé (URES), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon; Ecole Doctorale Régionale d'Afrique Centrale en Infectiologie Tropicale (EDR), Franceville, BP 876, Gabon.
| | - Illich Manfred Mombo
- Unité Émergence des Maladies Virales, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon; Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier-IRD 224-CNRS 5290), Montpellier 34394, France
| | - Virginie Rougeron
- International Research Laboratory-REHABS, CNRS-Université Lyon 1-Nelson Mandela University, Nelson Mandela University George Campus, George 6531, South Africa
| | - Fanny Degrugillier
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier-IRD 224-CNRS 5290), Montpellier 34394, France
| | - Philippe Gauthier
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Boris Makanga
- Institut de Recherche en Écologie Tropicale (IRET/CENAREST), Libreville, BP 13354, Gabon
| | - Barthélemy Ngoubangoye
- Centre de Primatologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon
| | - Eric M Leroy
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier-IRD 224-CNRS 5290), Montpellier 34394, France
| | - Franck Prugnolle
- International Research Laboratory-REHABS, CNRS-Université Lyon 1-Nelson Mandela University, Nelson Mandela University George Campus, George 6531, South Africa
| | - Larson Boundenga
- Unité de Recherche en Écologie de la Santé (URES), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769, Gabon; Département d'Anthropologie, Université de Durham, South Road, Durham DH1 3LE, UK
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Kachooei A, Mirhoseinian M, Jalilvand S, Latifi T, Feizi M, Shahosseini Z, Arashkia A, Marashi SM, Shoja Z. Molecular characterization of human astrovirus infection in children under 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: co-infection with rotavirus. Virus Genes 2024:10.1007/s11262-024-02075-6. [PMID: 38744749 DOI: 10.1007/s11262-024-02075-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
Human astroviruses (HAstVs) are considered important causative pathogens of acute gastroenteritis (AGE) in children under 5 years of age worldwide, along with group A rotavirus (RVA), norovirus (NoV), and enteric adenovirus (EAdV). The present study was aimed to both detect HAstV and its co-infections and investigate genetic analysis of circulating HAstV and co-infected virus in hospitalized children under 5 years of age with AGE in Iran. Accordingly, a sum of 200 stool specimens were screened by PCR for HAstV during 2021-2022. The HAstV was found in 0.5% of 200 specimens (n = 1) while was co-infected with RVA. The genetic and phylogenetic analysis indicated HAstV1 genotype, which clustered with viruses from lineage 1b, which has not been previously reported in Iran. The detected RVA strain belonged to G1 lineage II/P[8]-lineage III, which has been reported previously in Iran as the most common strain. The further genetic analysis of RVA VP6 and NSP4 demonstrated an atypical genotype pattern G1P[8]-I1-E2, as a mono-reassortant of a Wa-like genogroup, which appeared to be reassorted with the NSP4 gene of E2 genotype of the G2P[4] DS-1 genogroup. Although the clinical outcomes of the AGE-causing viruses co-infection is not yet entirely clear, it seems that future studies will be helpful to merge clinical and epidemiological data of co-infecting viruses for a more accurate medical and clinical relevance in symptomatic children.
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Affiliation(s)
- Atefeh Kachooei
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahtab Mirhoseinian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Tayebeh Latifi
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Mahsa Feizi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Arash Arashkia
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran.
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
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Peña Rodríguez M, Fagan A, Sikaroodi M, Gillevet PM, Bajaj JS. Proton Pump Inhibitor Use and Complications of Cirrhosis Are Linked With Distinct Gut Microbial Bacteriophage and Eukaryotic Viral-Like Particle Signatures in Cirrhosis. Clin Transl Gastroenterol 2024; 15:e00659. [PMID: 37937851 PMCID: PMC10887442 DOI: 10.14309/ctg.0000000000000659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
INTRODUCTION Proton pump inhibitors (PPIs) modulate the progression of cirrhosis to hepatic encephalopathy (HE) and can affect the bacterial microbiome. However, the impact of PPI on the virome in cirrhosis using viral-like particle (VLP) analysis is unclear. METHODS We determined the VLP in the stool microbiome in patients with cirrhosis cross-sectionally (ascites, HE, and PPI use analyzed) who were followed up for 6-month hospitalizations and through 2 clinical trials of PPI withdrawal and initiation. RESULTS In a cross-sectional study, PPI users had greater ascites prevalence and 6-month hospitalizations, but VLP α diversity was similar. Among phages, PPI users had lower Autographviridae and higher Streptococcus phages and Herelleviridae than nonusers, whereas opposite trends were seen in ascites and HE. Trends of eukaryotic viruses (higher Adenoviridae and lower Virgaviridae/Smacoviridae) were similar for PPI, HE, and ascites. Twenty-one percent were hospitalized, mostly due to HE. α Diversity was similar in the hospitalized/nonhospitalized/not groups. Higher Gokushovirinae and lower crAssphages were related to hospitalizations such as HE-related cross-sectional VLP changes. As part of the clinical trial, PPIs were added and withdrawn in 2 different decompensated groups over 14 days. No changes in α diversity were observed. Withdrawal reduced crAssphages, and initiation reduced Gokushovirinae and Bacteroides phages. DISCUSSION In cirrhosis, PPI use has a gut microbial VLP phage signature that is different from that in HE and ascites, and VLP changes are linked with hospitalizations over 6 months, independent of clinical biomarkers. Eukaryotic viral patterns were consistent across PPI use, HE, and ascites, indicating a relationship with the progression of cirrhosis. PPIs alone showed modest VLP changes with withdrawal or initiation. Distinct phage and eukaryotic viral patterns are associated with the use of PPIs in cirrhosis.
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Affiliation(s)
| | - Andrew Fagan
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
| | | | | | - Jasmohan S. Bajaj
- Virginia Commonwealth University and Richmond VA Medical Center, Richmond, Virginia, USA
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Bhat S, Ansari MI, Kattoor JJ, Sircar S, Dar PS, Deol P, Vinodh Kumar OR, Thomas P, Ghosh S, El Zowalaty ME, Malik YS. Emerging porcine Enterovirus G infections, epidemiological, complete genome sequencing, evolutionary and risk factor analysis in India. Virology 2024; 590:109906. [PMID: 38096748 DOI: 10.1016/j.virol.2023.109906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 01/03/2024]
Abstract
The current study reports the in-depth analysis of the epidemiology, risk factors, and molecular characterization of a complete genome of Enterovirus G (EV-G) isolated from Indian pigs. We analysed several genes of EV-G isolates collected from various provinces in India, using phylogenetic analysis, recombination detection, SimPlot, and selection pressure analyses. Our analysis of 534 porcine faecal samples revealed that 11.61% (62/534) of the samples were positive for EV-G. While the G6 genotype was the most predominant, our findings showed that Indian EV-G strains also clustered with EV-G types G1, G6, G8, and G9. Furthermore, Indian EV-G strains exhibited the highest nucleotide similarity with Vietnamese (81.3%) and Chinese EV-G isolates (80.3%). Moreover, we identified a recombinant Indian EV-G strain with a putative origin from a Japanese isolate and South Korean EV-G isolate. In summary, our findings provide significant insights into the epidemiology, genetic diversity, and evolution of EV-G in India.
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Affiliation(s)
- Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
| | - Mohd Ikram Ansari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India; Department of Biosciences, Integral University Lucknow, India
| | - Jobin Jose Kattoor
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India; Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University, West Lafayette, IN 47907, USA
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India; Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Parvaiz Sikander Dar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
| | - Pallavi Deol
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India; Institute for Modeling Collaboration and Innovation and Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - O R Vinodh Kumar
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine,Basseterre P.O. 334, Saint Kitts and Nevis, West Indies
| | - Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women Campus, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates.
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India; College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141001, India.
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Roach MJ, Beecroft SJ, Mihindukulasuriya KA, Wang L, Paredes A, Cárdenas LAC, Henry-Cocks K, Lima LFO, Dinsdale EA, Edwards RA, Handley SA. Hecatomb: an integrated software platform for viral metagenomics. Gigascience 2024; 13:giae020. [PMID: 38832467 PMCID: PMC11148595 DOI: 10.1093/gigascience/giae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses. FINDINGS Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means "a great sacrifice." In this setting, Hecatomb is "sacrificing" false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome. CONCLUSION Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.
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Affiliation(s)
- Michael J Roach
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
- Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sarah J Beecroft
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Kathie A Mihindukulasuriya
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leran Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anne Paredes
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Luis Alberto Chica Cárdenas
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kara Henry-Cocks
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | | | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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Viviana B, Matias S, Daiana M, Rodney C, Matias V. Molecular Characterization of Gastroenteric Viruses in Wastewater from Cities in Uruguay. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:318-330. [PMID: 37872461 DOI: 10.1007/s12560-023-09567-y] [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: 06/23/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
Group A Rotavirus, Human Astrovirus, and Norovirus (RVA, HAstV, and NoV) are recognized as the major causative agents of acute gastroenteritis in children and adults worldwide. The aim of this study was to determine the prevalence and molecular epidemiology of RVA, HAstV, and NoV in wastewater from three cities in Uruguay. Thirty-six samples from Bella Unión, Salto, and Fray Bentos cities were analyzed using quantitative and qualitative PCR. RVA was the most frequently detected virus (50%), followed by HAstV (39%), NoV GII (36%), and NoV GI (25%). RVA strains were characterized as P[8] and G3 based on the VP4 and VP7 genes, respectively. Among NoV-positive samples, genotypes GI.2, GI.3, GI.5, GI.6, GI.7, GII.2, GII.6, and GII.4 were detected, and only one HAstV genotype (MLB1) was found. Our wastewater-based epidemiological approach provides a snapshot of the overall genetic diversity of these viruses in three cities of the Uruguay River basin during 2017-2018. These findings reinforce the importance of this environmental surveillance tool for monitoring epidemiological trends of enteric viruses circulating in the population, which can be used to guide public health intervention.
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Affiliation(s)
- Bortagaray Viviana
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Sede Salto, Universidad de la República, Salto, Uruguay
| | - Salvo Matias
- Department of Water, CENUR Litoral Norte, Sede Salto, Universidad de la República, Salto, Uruguay
| | - Mir Daiana
- Genomic and Bioinformatic Unit, Department of Biological Sciences, CENUR Litoral Norte, Sede Salto, Universidad de la República, Salto, Uruguay
| | - Colina Rodney
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Sede Salto, Universidad de la República, Salto, Uruguay
| | - Victoria Matias
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Sede Salto, Universidad de la República, Salto, Uruguay.
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Lu L, Zhong H, Xu M, Jia R, Liu P, Su L, Cao L, Zhu X, Xu J. Diversity of classic and novel human astrovirus in outpatient children with acute gastroenteritis in Shanghai, China. Front Microbiol 2023; 14:1265843. [PMID: 38029144 PMCID: PMC10679754 DOI: 10.3389/fmicb.2023.1265843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Human astrovirus (HAstV) is an important pathogen of acute gastroenteritis (AGE) in children. This study was aimed at investigating the diversity and epidemiology of classic and novel HAstV in outpatient children aged 0-16 years old with AGE in Shanghai. Methods From May 2020 to December 2022, a total of 1,482 stool samples were collected from children diagnosed as AGE from the Children's Hospital of Fudan University. HAstV was identified using pan-astrovirus consensus primers by Reverse transcription PCR. Results During the study period, 3.3% (49/1,482) of specimens were identified as HAstV, with a detection rate of 2.5% (37/1,482) for classic HAstV and 0.8% (12/1,482) for novel HAstV. Among the 12 novel HAstV strains, 11 (91.7%) belonged to the HAstV-MLB and 1 (8.3%) was HAstV-VA. Genotyping revealed six circulating genotypes. Strain HAstV-1 was predominant in the study population with a detection rate of 1.8% (26/1,482) followed by HAstV-MLB1 (0.7%, 10/1,482) and HAstV-4 (0.6%, 9/1,482). Of note, all the HAstV-4 strains detected in this study were close to one astrovirus strain isolated from Bactrian camels with 99.0-100.0% amino acid sequences identity. In this study, HAstV was detected in all age groups with the highest detection rate of HAstV-positive specimens observed in children older than 73 months (5.7%, 12/209). Discussion This study provided useful information and contributed to the molecular epidemiology of both classic and novel HAstV, which were simultaneously characterized and reported for the first time in Shanghai.
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Affiliation(s)
- Lijuan Lu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Ran Jia
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Xunhua Zhu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Jin Xu
- Department of Clinical Laboratory, National Children’s Medical Center, Children’s Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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Bub T, Hargest V, Tan S, Smith M, Vazquez-Pagan A, Flerlage T, Brigleb P, Meliopoulos V, Lindenbach B, Ramanathan HN, Cortez V, Crawford JC, Schultz-Cherry S. Astrovirus replication is dependent on induction of double-membrane vesicles through a PI3K-dependent, LC3-independent pathway. J Virol 2023; 97:e0102523. [PMID: 37668367 PMCID: PMC10537808 DOI: 10.1128/jvi.01025-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 09/06/2023] Open
Abstract
Human astrovirus is a positive-sense, single-stranded RNA virus. Astrovirus infection causes gastrointestinal symptoms and can lead to encephalitis in immunocompromised patients. Positive-strand RNA viruses typically utilize host intracellular membranes to form replication organelles, which are potential antiviral targets. Many of these replication organelles are double-membrane vesicles (DMVs). Here, we show that astrovirus infection leads to an increase in DMV formation through a replication-dependent mechanism that requires some early components of the autophagy machinery. Results indicate that the upstream class III phosphatidylinositol 3-kinase (PI3K) complex, but not LC3 conjugation machinery, is utilized in DMV formation. Both chemical and genetic inhibition of the PI3K complex lead to significant reduction in DMVs, as well as viral replication. Elucidating the role of autophagy machinery in DMV formation during astrovirus infection reveals a potential target for therapeutic intervention for immunocompromised patients. IMPORTANCE These studies provide critical new evidence that astrovirus replication requires formation of double-membrane vesicles, which utilize class III phosphatidylinositol 3-kinase (PI3K), but not LC3 conjugation autophagy machinery, for biogenesis. These results are consistent with replication mechanisms for other positive-sense RNA viruses suggesting that targeting PI3K could be a promising therapeutic option for not only astrovirus, but other positive-sense RNA virus infections.
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Affiliation(s)
- Theresa Bub
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Integrated Program of Biomedical Sciences, Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Virginia Hargest
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shaoyuan Tan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Maria Smith
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Ana Vazquez-Pagan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Tim Flerlage
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Pamela Brigleb
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Victoria Meliopoulos
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
- Department of Comparative Medicine, Yale University, New Haven, Connecticut, USA
| | - Harish N. Ramanathan
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, USA
- Department of Comparative Medicine, Yale University, New Haven, Connecticut, USA
| | - Valerie Cortez
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, California, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Bohou Kombila L, N’dilimabaka N, Garcia D, Rieu O, Engone Ondo JD, Ndong Mebaley T, Boundenga L, Fritz M, Lenguiya LH, Maganga GD, Leroy EM, Becquart P, Mombo IM. Molecular Identification of Enteric Viruses in Domestic Animals in Northeastern Gabon, Central Africa. Animals (Basel) 2023; 13:2512. [PMID: 37570320 PMCID: PMC10417819 DOI: 10.3390/ani13152512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Astroviruses (AstVs), enteroviruses (EVs), and caliciviruses (CaVs) infect several vertebrate taxa. Transmitted through the fecal-oral route, these enteric viruses are highly resistant and can survive in the environment, thereby increasing their zoonotic potential. Here, we screened for AstVs, EVs, and CaVs to investigate the role of domestic animals in the emergence of zoonoses, because they are situated at the human/wildlife interface, particularly in rural forested areas in Central Africa. Rectal swabs were obtained from 123 goats, 41 sheep, and 76 dogs in 10 villages located in northeastern Gabon. Extracted RNA reverse-transcribed into cDNA was used to detect AstVs, EVs, and CaVs by amplification of the RNA-dependent RNA polymerase (RdRp), or capsid protein (VP1) gene using PCR. A total of 23 samples tested positive, including 17 goats for AstVs, 2 goats, 2 sheep, 1 dog for EVs, and 1 dog for CaVs. Phylogenetic analyses revealed that AstV RdRp sequences clustered with sheep-, goat-, or bovine-related AstVs. In addition, one goat and two sheep VP1 sequences clustered with caprine/ovine-related Evs within the Enterovirus G species, and the CaV was a canine vesivirus. However, human-pathogenic Evs, EV-B80 and EV-C99, were detected in goats and dogs, raising questions on the maintenance of viruses able to infect humans.
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Affiliation(s)
- Linda Bohou Kombila
- Unité Émergence des Maladies Virales (UEMV), Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (L.B.K.); (N.N.); (T.N.M.); (G.D.M.)
| | - Nadine N’dilimabaka
- Unité Émergence des Maladies Virales (UEMV), Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (L.B.K.); (N.N.); (T.N.M.); (G.D.M.)
- Département de Biologie, Université des Sciences et Techniques de Masuku (USTM), Franceville BP 941, Gabon
| | - Déborah Garcia
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier—IRD 224–CNRS 5290), 34394 Montpellier, France; (D.G.); (O.R.); (M.F.); (E.M.L.); (P.B.)
| | - Océane Rieu
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier—IRD 224–CNRS 5290), 34394 Montpellier, France; (D.G.); (O.R.); (M.F.); (E.M.L.); (P.B.)
| | - Jéordy Dimitri Engone Ondo
- Unité des Infections Rétrovirales et Pathologies Associées (UIRPA), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon;
| | - Telstar Ndong Mebaley
- Unité Émergence des Maladies Virales (UEMV), Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (L.B.K.); (N.N.); (T.N.M.); (G.D.M.)
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier—IRD 224–CNRS 5290), 34394 Montpellier, France; (D.G.); (O.R.); (M.F.); (E.M.L.); (P.B.)
| | - Larson Boundenga
- Unité de Recherche en Écologie de la Santé (URES), Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon;
| | - Matthieu Fritz
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier—IRD 224–CNRS 5290), 34394 Montpellier, France; (D.G.); (O.R.); (M.F.); (E.M.L.); (P.B.)
| | | | - Gael Darren Maganga
- Unité Émergence des Maladies Virales (UEMV), Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (L.B.K.); (N.N.); (T.N.M.); (G.D.M.)
- Institut National Supérieur d’Agronomie et de Biotechnologies (INSAB), Université des Sciences et Techniques de Masuku (USTM), Franceville BP 913, Gabon
| | - Eric M. Leroy
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier—IRD 224–CNRS 5290), 34394 Montpellier, France; (D.G.); (O.R.); (M.F.); (E.M.L.); (P.B.)
| | - Pierre Becquart
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier—IRD 224–CNRS 5290), 34394 Montpellier, France; (D.G.); (O.R.); (M.F.); (E.M.L.); (P.B.)
| | - Illich Manfred Mombo
- Unité Émergence des Maladies Virales (UEMV), Département de Virologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville BP 769, Gabon; (L.B.K.); (N.N.); (T.N.M.); (G.D.M.)
- Institut de Recherche pour le Développement (IRD), Maladies Infectieuses et Vecteurs, Écologie, Génétique, Évolution et Contrôle (MIVEGEC) (Université de Montpellier—IRD 224–CNRS 5290), 34394 Montpellier, France; (D.G.); (O.R.); (M.F.); (E.M.L.); (P.B.)
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Ushijima H, Nishimura S, Shimizu-Onda Y, Thi Kim Pham N, Trinh QD, Okitsu S, Takano C, Kumthip K, Hoque SA, Komine-Aizawa S, Maneekarn N, Hayakawa S, Khamrin P. Outbreak of human astroviruses 1 and Melbourne 2 in acute gastroenteritis pediatric patients in Japan during the COVID-19 pandemic, 2021. J Infect Public Health 2023; 16:1301-1305. [PMID: 37336127 DOI: 10.1016/j.jiph.2023.05.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Human astrovirus (HAstV) infection is one of the leading causes of acute gastroenteritis in young children. The present study reports the outbreak of HAstV in children with acute gastroenteritis in Kyoto, Japan, during the COVID-19 pandemic, 2021. METHODS A total of 61 stool samples were collected from children with acute gastroenteritis who visited a pediatric outpatient clinic in Maizuru city, Kyoto, Japan from July to October, 2021. HAstV was screened by RT-PCR, and the genotypes were identified by nucleotide sequence analysis. RESULTS Of 61 cases of acute gastroenteritis, 20 were mono-infected with HAstV alone. In addition, mixed infection of HAstV and NoV, and HAstV and RVA were also detected in 15 and 1 cases, respectively. Of 36 HAstV strains detected in this outbreak, 29 and 7 were HAstV1 and MLB2 genotypes, respectively. All HAstV1 strains were closely related to the HAstV1 reported from Thailand and Japan in 2021 and all of them belonged to subgenotype HAstV1a. Among MLB2, they were most closely related to the MLB2 strains reported from China in 2016 and 2018. CONCLUSIONS After the kindergartens and schools were re-opened at the middle of 2021 in Japan, an outbreak of HAstV was reported. Control measures against the COVID-19 pandemics might affect the spread of diarrheal virus infection. Here we report the outbreak of HAstV1 and MLB2 in Kyoto, Japan, during COVID-19 pandemic in 2021.
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Affiliation(s)
- Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.
| | | | - Yuko Shimizu-Onda
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Quang Duy Trinh
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Sheikh Ariful Hoque
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Shihoko Komine-Aizawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan; Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand; Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
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Bub T, Hargest V, Tan S, Smith M, Vazquez-Pagan A, Flerlage T, Brigleb PH, Meliopoulos V, Lindenbach B, Cortez V, Crawford JC, Schultz-Cherry S. Astrovirus replication is dependent on induction of double membrane vesicles through a PI3K-dependent, LC3-independent pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536492. [PMID: 37090568 PMCID: PMC10120637 DOI: 10.1101/2023.04.11.536492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Human astrovirus is a positive sense, single stranded RNA virus. Astrovirus infection causes gastrointestinal symptoms and can lead to encephalitis in immunocompromised patients. Positive strand RNA viruses typically utilize host intracellular membranes to form replication organelles, which are potential antiviral targets. Many of these replication organelles are double membrane vesicles (DMVs). Here we show that astrovirus infection leads to an increase in DMV formation, and this process is replication-dependent. Our data suggest that astrovirus infection induces rearrangement of endoplasmic reticulum fragments, which may become the origin for DMV formation. Transcriptional data suggested that formation of DMVs during astrovirus infection requires some early components of the autophagy machinery. Results indicate that the upstream class III phosphatidylinositol 3-kinase (PI3K) complex, but not LC3 conjugation machinery, is utilized in DMV formation. Inhibition of the PI3K complex leads to significant reduction in viral replication and release from cells. Elucidating the role of autophagy machinery in DMV formation during astrovirus infection reveals a potential target for therapeutic intervention for immunocompromised patients. Importance These studies provide critical new evidence that astrovirus replication requires formation of double membrane vesicles, which utilize class III PI3K, but not LC3 conjugation autophagy machinery for biogenesis. These results are consistent with replication mechanisms for other positive sense RNA viruses. This suggests that targeting PI3K could be a promising therapeutic option for not only astrovirus, but other positive sense RNA virus infections.
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12
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Fu J, Yu F, Li H, Shen L, Tian Y, Jia L, Zhang D, Yang P, Wang Q, Gao Z. Acute gastroenteritis outbreaks caused by human astrovirus, 1978-2021: A systematic review. BIOSAFETY AND HEALTH 2023. [DOI: 10.1016/j.bsheal.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
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13
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High Burden of Co-Infection with Multiple Enteric Pathogens in Children Suffering with Diarrhoea from Rural and Peri-Urban Communities in South Africa. Pathogens 2023; 12:pathogens12020315. [PMID: 36839587 PMCID: PMC9959912 DOI: 10.3390/pathogens12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023] Open
Abstract
Infectious diarrhoea contributes to high morbidity and mortality in young children from sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and peri-urban communities in South Africa. A total of 275 diarrhoea stool specimens were collected between 2014 and 2016 from Hospitals and Primary Health Care clinics. The BioFire® FilmArray® Gastrointestinal panel was used to simultaneously detect 22 diarrhoea pathogens (viruses, bacteria, parasites) known to cause diarrhoea. A total of 82% (226/275) enteric pathogens were detected in the stool specimens. The two most detected bacterial, viral and parasitic pathogens each included: EAEC (42%), EPEC (32%), Adenovirus F40/41 (19%), Norovirus (15%), Giardia (8%) and Cryptosporidium (6%), respectively. Single enteric pathogen infections were recorded in 24% (65/275) specimens with EAEC, and Norovirus was found in 26% (17/65) and 14% (9/65) of the specimens, respectively. Multiple enteric pathogen combinations were recorded in 59% (161/275) of the stool specimens with 53% (85/161) containing two pathogens, 22% (35/161) containing three pathogens and 25% (41/161) containing four or more pathogens. The results from this study demonstrated the complex nature of pathogen co-infections in diarrhoeal episodes which could have an impact on treatment effectiveness.
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14
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Kumthip K, Khamrin P, Ushijima H, Maneekarn N. Detection of Six Different Human Enteric Viruses Contaminating Environmental Water in Chiang Mai, Thailand. Microbiol Spectr 2023; 11:e0351222. [PMID: 36533933 PMCID: PMC9927274 DOI: 10.1128/spectrum.03512-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
A 2-year surveillance study into enteric viruses contaminating environmental water samples was conducted in the city of Chang Mai, Thailand. The aim of the study was to investigate the prevalence of six different human enteric viruses, specifically, adenovirus (AdV), astrovirus (AstV), enteroviruses (EVs), human parechovirus (HPeV), rotavirus (RV), and saffold virus (SAFV), contaminating several types of environmental water using PCR and reverse transcription-PCR (RT-PCR) methods. All targeted viruses were detected with different levels of prevalence. The levels ranged from 0.8 to 4.8% (AdV, 0.8%; AstV, 4.8%; EV, 0.8%; HPeV, 3.2%; RV, 0.8%; SAFV, 3.2%). A wide variety of human enteric virus genotypes, including AdV-41, AstV-MLB1, coxsackievirus A, HPeV1, 5, and 6, RV G4[P8], and SAFV-2 and 3 were detected. The overall picture of the 13 human enteric viruses that were detected in environmental water in Chiang Mai, Thailand, is also summarized in this study. The data and the findings of this study will provide a better understanding of the viral dynamics in environmental water. The detection of these viruses in environmental water indicates there is the potential for human infection from this source. IMPORTANCE Human enteric viruses are a major cause of gastrointestinal illness, and these viruses can be introduced into environmental water through various routes. Viral contamination in water could play a significant role in human health. This study demonstrated the prevalence of six different enteric viruses, adenovirus, astrovirus, enteroviruses, human parechovirus, rotavirus, and saffold virus, contaminating environmental water. We also analyzed the overall prevalence of other enteric viruses that were in this area, and the findings revealed a wide diversity of the enteric viruses contaminating environmental water. The data provide a better understanding of the epidemiologic importance of viral contamination of the water and highlight the need for better management of wastewater disposal and effective environmental water treatment to prevent the human population from infection.
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Affiliation(s)
- Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence (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, Thailand
- Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Developmental Medical Sciences, The University of Tokyo, School of International Health, Graduate School of Medicine, Tokyo, Japan
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence (Emerging and Re-emerging Diarrheal Viruses), Chiang Mai University, Chiang Mai, Thailand
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Niendorf S, Mas Marques A, Bock CT, Jacobsen S. Diversity of human astroviruses in Germany 2018 and 2019. Virol J 2022; 19:221. [PMID: 36544187 PMCID: PMC9773458 DOI: 10.1186/s12985-022-01955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Aim of this study was to investigate the molecular diversity of human astroviruses (HAstV) in Germany. A follow-up study was performed with human stool samples collected in 2018-2019, which were genotyped retrospectively. A total of 2645 stool samples, collected between January 2018 and December 2019 from sporadic cases and outbreaks of acute gastroenteritis were analyzed. An algorithm of PCR systems was used to characterize human astrovirus. Human astroviruses were found in 40 samples (positive rate: 1.6%). During the study period, children aged 1-2 years (48%) were most affected by HAstV. Genotyping revealed a number of nine circulating genotypes representing four human Mamastrovirus species. Strain MLB1 was predominant in the study population with a detection rate of 25% followed by HAstV1 with a positive rate of 20%. The diversity of astrovirus genotypes seems to be rather stable in Germany in the last years. A clustering of regionally and/or temporally linked human astroviruses in Germany was not detectable.
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Affiliation(s)
- Sandra Niendorf
- grid.13652.330000 0001 0940 3744Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany ,grid.13652.330000 0001 0940 3744Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Andreas Mas Marques
- grid.13652.330000 0001 0940 3744Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany ,grid.13652.330000 0001 0940 3744Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Claus-Thomas Bock
- grid.13652.330000 0001 0940 3744Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | - Sonja Jacobsen
- grid.13652.330000 0001 0940 3744Unit Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany ,grid.13652.330000 0001 0940 3744Consultant Laboratory for Noroviruses, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
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Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol 2022; 55:101233. [PMID: 35690009 PMCID: PMC9575407 DOI: 10.1016/j.coviro.2022.101233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.
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Affiliation(s)
- Elizabeth A Kennedy
- Washington University School of Medicine, Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, St. Louis, MO 63110, USA
| | - Lori R Holtz
- Washington University School of Medicine, Department of Pediatrics, St. Louis, MO 63110, USA.
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Nolan LS, Baldridge MT. Advances in understanding interferon-mediated immune responses to enteric viruses in intestinal organoids. Front Immunol 2022; 13:943334. [PMID: 35935957 PMCID: PMC9354881 DOI: 10.3389/fimmu.2022.943334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Interferons (IFN) are antiviral cytokines with critical roles in regulating pathogens at epithelial barriers, but their capacity to restrict human enteric viruses has been incompletely characterized in part due to challenges in cultivating some viruses in vitro, particularly human norovirus. Accordingly, advancements in the development of antiviral therapies and vaccine strategies for enteric viral infections have been similarly constrained. Currently emerging is the use of human intestinal enteroids (HIEs) to investigate mechanisms of human enteric viral pathogenesis. HIEs provide a unique opportunity to investigate host-virus interactions using an in vitro system that recapitulates the cellular complexity of the in vivo gastrointestinal epithelium. This approach permits the exploration of intestinal epithelial cell interactions with enteric viruses as well as the innate immune responses mediated by IFNs and IFN-stimulated genes. Here, we describe recent findings related to the production, signaling, and function of IFNs in the response to enteric viral infections, which will ultimately help to reveal important aspects of pathogenesis and facilitate the future development of therapeutics and vaccines.
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Affiliation(s)
- Lila S. Nolan
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis Children’s Hospital, St. Louis, MO, United States
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Megan T. Baldridge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
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18
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Zhang F, Chase-Topping M, Guo CG, Woolhouse MEJ. Predictors of human-infective RNA virus discovery in the United States, China, and Africa, an ecological study. eLife 2022; 11:e72123. [PMID: 35666108 PMCID: PMC9278958 DOI: 10.7554/elife.72123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background The variation in the pathogen type as well as the spatial heterogeneity of predictors make the generality of any associations with pathogen discovery debatable. Our previous work confirmed that the association of a group of predictors differed across different types of RNA viruses, yet there have been no previous comparisons of the specific predictors for RNA virus discovery in different regions. The aim of the current study was to close the gap by investigating whether predictors of discovery rates within three regions-the United States, China, and Africa-differ from one another and from those at the global level. Methods Based on a comprehensive list of human-infective RNA viruses, we collated published data on first discovery of each species in each region. We used a Poisson boosted regression tree (BRT) model to examine the relationship between virus discovery and 33 predictors representing climate, socio-economics, land use, and biodiversity across each region separately. The discovery probability in three regions in 2010-2019 was mapped using the fitted models and historical predictors. Results The numbers of human-infective virus species discovered in the United States, China, and Africa up to 2019 were 95, 80, and 107 respectively, with China lagging behind the other two regions. In each region, discoveries were clustered in hotspots. BRT modelling suggested that in all three regions RNA virus discovery was better predicted by land use and socio-economic variables than climatic variables and biodiversity, although the relative importance of these predictors varied by region. Map of virus discovery probability in 2010-2019 indicated several new hotspots outside historical high-risk areas. Most new virus species since 2010 in each region (6/6 in the United States, 19/19 in China, 12/19 in Africa) were discovered in high-risk areas as predicted by our model. Conclusions The drivers of spatiotemporal variation in virus discovery rates vary in different regions of the world. Within regions virus discovery is driven mainly by land-use and socio-economic variables; climate and biodiversity variables are consistently less important predictors than at a global scale. Potential new discovery hotspots in 2010-2019 are identified. Results from the study could guide active surveillance for new human-infective viruses in local high-risk areas. Funding FFZ is funded by the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk/). MEJW has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 874735 (VEO) (https://www.veo-europe.eu/).
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
| | - Margo Chase-Topping
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUnited Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong KongHong KongChina
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Detection of Novel Human Astrovirus MLB1 by a Commercial Viral Gastroenteritis Multiplex Assay. Microbiol Spectr 2022; 10:e0046922. [PMID: 35604162 PMCID: PMC9241716 DOI: 10.1128/spectrum.00469-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Extensive genetic heterogeneity and molecular characteristics of emerging astroviruses causing fatal gout in goslings. Poult Sci 2022; 101:101888. [PMID: 35550999 PMCID: PMC9108738 DOI: 10.1016/j.psj.2022.101888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/22/2022] Open
Abstract
Since 2017, outbreaks of gosling astroviruses (GoAstV) causing the major symptoms related to gout in geese have posed a threat to China's poultry industry and caused huge economic losses. In this study, tissue samples from goslings with gout and urate deposition as the main symptoms were taken from 14 goose farms in different regions of China and screened for pathogen infection. The infection rate of GoAstV was 100%, whereas the infection rates of goose parvovirus, reovirus, Tembusu virus, and goose hemorrhagic polyomavirus were 2, 4, 0, and 0%, respectively. In total, 14 GoAstV strains were isolated and their complete genomes were sequenced. Based on the phylogenetic trees, the 14 isolated strains were classified as GoAstV (G-I) and were considered distant from strains belonging to GoAstV (G-II). The multiple sequence alignments indicated a tremendous amount of amino acid mutations in some parts of the encoding proteins of these strains; the main mutations were located in open reading frames (ORFs)—ORF1a and ORF2, such as M533V and F568S in ORF1a and A614T in ORF2. On the other hand, Further, 2 of the 14 GoAstV strains were possibly derived through inter-GoAstV-I recombination. Taken together, these findings indicate that GoAstVs are evolving in a more complex manner and have diverse transmission routes.
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21
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Hargest V, Bub T, Neale G, Schultz-Cherry S. Astrovirus-induced epithelial-mesenchymal transition via activated TGF-β increases viral replication. PLoS Pathog 2022; 18:e1009716. [PMID: 35452499 PMCID: PMC9067694 DOI: 10.1371/journal.ppat.1009716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 05/04/2022] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Human astroviruses (HAstV), positive sense single-stranded RNA viruses, are one of the leading causes of diarrhea worldwide. Despite their high prevalence, the cellular mechanisms of astrovirus pathogenesis remain ill-defined. Previous studies showed HAstV increased epithelial barrier permeability by causing a re-localization of the tight junction protein, occludin. In these studies, we demonstrate that HAstV replication induces epithelial-mesenchymal transition (EMT), by upregulating the transcription of EMT-related genes within 8 hours post-infection (hpi), followed by the loss of cell-cell contacts and disruption of polarity by 24 hpi. While multiple classical HAstV serotypes, including clinical isolates, induce EMT, the non-classical genotype HAstV-VA1 and two strains of reovirus are incapable of inducing EMT. Unlike the re-localization of tight junction proteins, HAstV-induced EMT requires productive replication and is dependent transforming growth factor-β (TGF-β) activity. Finally, inhibiting TGF-β signaling and EMT reduces viral replication, highlighting its importance in the viral life cycle. This finding puts classical strains of HAstV-1 in an exclusive group of non-oncogenic viruses triggering EMT.
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Affiliation(s)
- Virginia Hargest
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Theresa Bub
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Integrated Program of Biomedical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
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22
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Wei H, Khamrin P, Kumthip K, Yodmeeklin A, Maneekarn N. Emergence of Multiple Novel Inter-Genotype Recombinant Strains of Human Astroviruses Detected in Pediatric Patients With Acute Gastroenteritis in Thailand. Front Microbiol 2021; 12:789636. [PMID: 34966371 PMCID: PMC8710764 DOI: 10.3389/fmicb.2021.789636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022] Open
Abstract
Objective: Human astrovirus (HAstV) is recognized as an important cause of acute gastroenteritis in children. Recombination between different genotypes of HAstV can contribute to diversity and evolution of the virus. This study aimed to investigate the emergence of HAstV recombinant strains in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, spanning 2011–2020. Methods: A total of 92 archival HAstV strains collected from pediatric patients with acute gastroenteritis during 2011–2020 were further characterized to identify the recombinant strains. The ORF1b and ORF2 junction region of each strain was amplified and sequenced. The obtained sequences were analyzed in comparison with the reference sequences retrieved from GenBank database. Their genotypes were assigned using MEGA X software based on the partial ORF1b (RdRp) and ORF2 (capsid) regions, and the recombination breakpoints of recombinant strains were determined by SimPlot and RDP4 analyses. Results: Five inter-genotype recombinant strains with three recombination patterns of ORF1b/ORF2 of classic HAstV, HAstV8/HAstV1, HAstV8/HAstV3, and HAstV3/HAstV2, were detected. The recombination breakpoints of all strains were located at the 3′-end region of ORF1b close to the ORF1b/ORF2 junction. Conclusion: Several novel inter-genotype recombinant strains of classic HAstV genotypes were detected in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand, during the period of 10 years from 2011 to 2020.
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Affiliation(s)
- Hongyu Wei
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Department of Pathogenic Biology and Immunology, Youjiang Medical University for Nationalities, Baise, China
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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23
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Kim AH, Armah G, Dennis F, Wang L, Rodgers R, Droit L, Baldridge MT, Handley SA, Harris VC. Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants. Cell Host Microbe 2021; 30:110-123.e5. [PMID: 34932985 PMCID: PMC8763403 DOI: 10.1016/j.chom.2021.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/22/2021] [Accepted: 11/29/2021] [Indexed: 01/04/2023]
Abstract
Rotavirus vaccines (RVVs) have substantially diminished mortality from severe rotavirus (RV) gastroenteritis but are significantly less effective in low- and middle-income countries (LMICs), limiting their life-saving potential. The etiology of RVV’s diminished effectiveness remains incompletely understood, but the enteric microbiota has been implicated in modulating immunity to RVVs. Here, we analyze the enteric microbiota in a longitudinal cohort of 122 Ghanaian infants, evaluated over the course of 3 Rotarix vaccinations between 6 and 15 weeks of age, to assess whether bacterial and viral populations are distinct between non-seroconverted and seroconverted infants. We identify bacterial taxa including Streptococcus and a poorly classified taxon in Enterobacteriaceae as positively correlating with seroconversion. In contrast, both bacteriophage diversity and detection of Enterovirus B and multiple novel cosaviruses are negatively associated with RVV seroconversion. These findings suggest that virome-RVV interference is an underappreciated cause of poor vaccine performance in LMICs. Longitudinal analysis of microbiota of Ghanaian infants receiving rotavirus vaccine Streptococcus and Enterobacteriaceae taxa positively associate with RVV seroconversion Enterovirus B, Cosavirus A, and phage richness negatively associate with RVV serostatus
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24
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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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25
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Mihindukulasuriya KA, Mars RAT, Johnson AJ, Ward T, Priya S, Lekatz HR, Kalari KR, Droit L, Zheng T, Blekhman R, D'Amato M, Farrugia G, Knights D, Handley SA, Kashyap PC. Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome. Gastroenterology 2021; 161:1194-1207.e8. [PMID: 34245762 PMCID: PMC8463486 DOI: 10.1053/j.gastro.2021.06.077] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/21/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS. METHODS We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets. RESULTS We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses). CONCLUSIONS We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.
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Affiliation(s)
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Mauro D'Amato
- Gastrointestinal Genetics Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Dan Knights
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Medicine and Physiology, Mayo Clinic, Rochester, Minnesota.
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26
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Aggarwal S, Hassan E, Baldridge MT. Experimental Methods to Study the Pathogenesis of Human Enteric RNA Viruses. Viruses 2021; 13:975. [PMID: 34070283 PMCID: PMC8225081 DOI: 10.3390/v13060975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022] Open
Abstract
Every year, millions of children are infected with viruses that target the gastrointestinal tract, causing acute gastroenteritis and diarrheal illness. Indeed, approximately 700 million episodes of diarrhea occur in children under five annually, with RNA viruses norovirus, rotavirus, and astrovirus serving as major causative pathogens. Numerous methodological advancements in recent years, including the establishment of novel cultivation systems using enteroids as well as the development of murine and other animal models of infection, have helped provide insight into many features of viral pathogenesis. However, many aspects of enteric viral infections remain elusive, demanding further study. Here, we describe the different in vitro and in vivo tools available to explore different pathophysiological attributes of human enteric RNA viruses, highlighting their advantages and limitations depending upon the question being explored. In addition, we discuss key areas and opportunities that would benefit from further methodological progress.
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Affiliation(s)
- Somya Aggarwal
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
| | - Ebrahim Hassan
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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27
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KOBUVIRUS DETECTION IN THE CRITICALLY ENDANGERED PYGMY HOG ( PORCULA SALVANIA), INDIA. J Zoo Wildl Med 2021; 52:343-347. [PMID: 33827197 DOI: 10.1638/2019-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 11/21/2022] Open
Abstract
Pygmy hogs (Porcula salvania) are the smallest and rarest wild suid. It is categorized as a Critically Endangered species as per the Red List of the International Union for Conservation of Nature. This study reports the first detection of a single-stranded RNA virus species, Aichivirus C, belonging to the genus Kobuvirus (KobV) and the family Picornaviridae, in pygmy hogs. KobV species are identified as a cause of acute gastroenteritis among children in India. As of now, there exists no report on the detection of KobV in animals from India. We used a detection assay based on reverse transcription-polymerase chain reaction for KobV screening in pygmy hogs from a conservation center in India. The 3D polymerase gene-based molecular analysis revealed KobV presence in the Indian wild suid, pygmy hogs. Of the 15 samples tested, three were found positive for picornaviruses and were negative for rotavirus A, rotavirus C, astrovirus, picobirnavirus and caliciviruses. Nucleotide-based sequence analysis of the partial 3D polymerase gene revealed close identity with porcine KobV from the Czech Republic (JX232619, 90.6%-91.6%) and Hungary (NC_011829, 89.8%-91.6%), wherein one of the current study strains clustered with the Czech Republic JX232619 strain in the phylogenetic tree. Further investigation of the role of KobV in health and disease of pygmy hogs is warranted.
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28
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Huang D, Wang Z, Zhang F, Wang T, Zhang G, Sai L. Molecular and clinical epidemiological features of human astrovirus infections in children with acute gastroenteritis in Shandong province, China. J Med Virol 2021; 93:4883-4890. [PMID: 33811682 DOI: 10.1002/jmv.26995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 11/10/2022]
Abstract
Human astrovirus (HAstV) is one of the most common causative agents of acute gastroenteritis in children with an infection rate estimated to range from 2% to 9% worldwide. This study was aimed at investigating the molecular and clinical epidemiological features of human astrovirus infections in children under 5 years old with acute gastroenteritis in Shandong province, China from July 2017 to June 2018. In total, 376 fecal samples and the corresponding clinical information were collected and analyzed. HAstV infections were detected in all age groups with an overall positive rate of 8.51%. In addition to acute diarrhea, the main clinical manifestations were fever, abdominal pain, vomiting, and dehydration, in which fever was the most common complication. Infections could be seen throughout the year with a peak in the colder season. Four genotypes were detected in which HAstV-1 was the most prevalent genotype with a prevalence of 78.12%, followed by HAstV-5 (9.38%), MLB-1 (9.38%), and MLB-2 (3.12%). HAstV-1 strains were classified as lineage 1a, 1b, and 1d, in which lineage 1a strains were the most prevalent followed by lineage 1b and lineage 1d strains. All HAstV-5 strains were classified as lineage 5b and no other lineages were detected. The results showed that HAstV infection was an important cause of acute gastroenteritis among children under 5 years old in Shandong province. Given that their disease spectrum had been broadened, HAstVs should be paid more attention, not only as a causative agent of acute gastroenteritis but also as a potential pathogen of unexpected diseases.
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Affiliation(s)
- Deyu Huang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zheng Wang
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Fengjuan Zhang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ting Wang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guanyou Zhang
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Lintao Sai
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
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29
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Human Astroviruses: A Tale of Two Strains. Viruses 2021; 13:v13030376. [PMID: 33673521 PMCID: PMC7997325 DOI: 10.3390/v13030376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Since the 1970s, eight closely related serotypes of classical human astroviruses (HAstV) have been associated with gastrointestinal illness worldwide. In the late 2000s, three genetically unique human astrovirus clades, VA1-VA3, VA2-VA4, and MLB, were described. While the exact disease associated with these clades remains to be defined, VA1 has been associated with central nervous system infections. The discovery that VA1 could be grown in cell culture, supports exciting new studies aimed at understanding viral pathogenesis. Given the association of VA1 with often lethal CNS infections, we tested its susceptibility to the antimicrobial drug, nitazoxanide (NTZ), which we showed could inhibit classical HAstV infections. Our studies demonstrate that NTZ inhibited VA1 replication in Caco2 cells even when added at 12 h post-infection, which is later than in HAstV-1 infection. These data led us to further probe VA1 replication kinetics and cellular responses to infection in Caco-2 cells in comparison to the well-studied HAstV-1 strain. Overall, our studies highlight that VA1 replicates more slowly than HAstV-1 and elicits significantly different cellular responses, including the inability to disrupt cellular junctions and barrier permeability.
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30
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Shrestha SK, Shrestha J, Andreassen AK, Strand TA, Dudman S, Dembinski JL. Genetic Diversity of Astrovirus in Children From a Birth Cohort in Nepal. Front Microbiol 2021; 11:588707. [PMID: 33613461 PMCID: PMC7893100 DOI: 10.3389/fmicb.2020.588707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/21/2020] [Indexed: 11/27/2022] Open
Abstract
Objective: This study describes the types of Human astroviruses detected in stool samples collected from a birth cohort of children in Nepal. Methods: Using a commercial kit (ProSpecT), a total of 5,224 diarrheal and non-diarrheal stool samples were screened for Human astrovirus by ELISA. RT-PCR was performed on ELISA positive samples (2.8%) for further confirmation. The primary RT-PCR assay used targets the ORF2 region and detects human astrovirus type 1–8. Samples that were negative in this assay were further analyzed using primers that target the ORF1b region of human astrovirus which detect both classical type (HAstV 1–8) and novel types (MLB1–5, VA 1–5). PCR positive samples were analyzed by Sanger sequencing to determine the genotype. Results: A total of 148 available ELISA positive stool samples were analyzed by RT-PCR and further genotyped. RT-PCR analysis of these samples using the ORF2 and ORF1b assay revealed that 124 (84%) were positive for classical human types (HAstV 1–8). Seven different classical HAstV genotypes based on ORF2 and ORF1a were identified (HAstV 1- HAstV 8) with the greatest prevalence of HAstV 5 genotype (42.2%), followed by HAstV 1 (34.7%), HAstV 2 and HAstV 8 (7.4%), HAstV 4 (4.1%), HAstV 3 (3.3%), and HAstV 6 (0.8%). Non-classical types were not detected in our study. Conclusion: A high diversity of circulating Astrovirus strains were detected in young children, both with and without symptoms of gastroenteritis. HAstV 5 and HAstV 1 were the most common genotypes in young children in Nepal.
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Affiliation(s)
- Sanjaya Kumar Shrestha
- Center for International Health, University of Bergen, Bergen, Norway.,Walter Reed/Armed Forces Research Institute of Medical Sciences Research Unit Nepal, Kathmandu, Nepal
| | - Jasmin Shrestha
- Center for International Health, University of Bergen, Bergen, Norway.,Walter Reed/Armed Forces Research Institute of Medical Sciences Research Unit Nepal, Kathmandu, Nepal
| | | | - Tor A Strand
- Center for International Health, University of Bergen, Bergen, Norway.,Department of Research, Innlandet Hospital Trust, Lillehammer, Norway
| | - Susanne Dudman
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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31
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Zanella MC, Cordey S, Laubscher F, Docquier M, Vieille G, Van Delden C, Braunersreuther V, Ta MK, Lobrinus JA, Masouridi-Levrat S, Chalandon Y, Kaiser L, Vu DL. Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease. MICROBIOME 2021; 9:28. [PMID: 33487167 PMCID: PMC7831233 DOI: 10.1186/s40168-020-00953-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/06/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated pipeline and de novo analysis on pooled routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal, and unexpected viruses. RESULTS Median duration of intensive immunosuppression was 5.1 months (IQR 5.5). GvHD-related mortality rate was 36%. mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥ 3 distinct viruses were detected in 16/25 patients; Anelloviridae (24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7 patients with fatal outcomes, viral sequences not assessed by routine investigations were identified with mNGS and confirmed by RT-PCR. These cases included Usutu virus (1), rubella virus (1 vaccine strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1). CONCLUSIONS Clinically unrecognized viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid-refractory/dependent GvHD in consecutive samples. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations, or re-infection. Video abstract.
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Affiliation(s)
- M C Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland.
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland.
| | - S Cordey
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
- University of Geneva Medical School, Geneva, Switzerland
| | - F Laubscher
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
- University of Geneva Medical School, Geneva, Switzerland
| | - M Docquier
- iGE3 Genomics Platform, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - G Vieille
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
| | - C Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
- University of Geneva Medical School, Geneva, Switzerland
| | - V Braunersreuther
- Clinical Pathology Service, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - Mc Kee Ta
- Clinical Pathology Service, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - J A Lobrinus
- Clinical Pathology Service, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - S Masouridi-Levrat
- University of Geneva Medical School, Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Y Chalandon
- University of Geneva Medical School, Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - L Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
- University of Geneva Medical School, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva, Switzerland
| | - D L Vu
- Division of Infectious Diseases, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211, 14, Geneva, Switzerland
- University of Geneva Medical School, Geneva, Switzerland
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Nadan S, Taylor MB, Page NA. Circulation of classic and recombinant human astroviruses detected in South Africa: 2009 to 2014. J Clin Virol 2020; 135:104719. [PMID: 33388529 DOI: 10.1016/j.jcv.2020.104719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/13/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA). METHODS Astroviruses detected in stool specimens collected from hospitalised children were investigated retrospectively. Astroviruses were characterised using type-specific RT-PCR, partial nucleotide sequence analyses in ORF1 and ORF2 and whole genome sequencing. Different genotypes were compared with clinical features to investigate genotype-related associations. The Vesikari severity scale (VSS) was evaluated for scoring astrovirus diarrhoeal infections. RESULTS Of 405 astroviruses detected, 49.9 % (202/405) were characterised into 32 genotypes comprising 66.3 % (134/202) putative-recombinants and 33.7 % (68/202) classic strains. No trends by year of collection, age or site were observed. Whole genome analysis in eight strains revealed that genotypes assigned by partial nucleotide sequence analyses to five astroviruses were incorrect. Bivariate analyses showed there were no significant associations between genotypes and clinical symptoms or severity of infection. A comparison of Vesikari parameters with astrovirus-positive proxy values demonstrated that Vesikari scores for duration of diarrhoea and admission temperatures would result in a milder infection rating in astrovirus-positive cases. CONCLUSIONS Diverse genotypes co-circulated with putative-recombinants predominating. Astrovirus classification was complicated by the lack of a consistent characterisation system and reliable reference database. The VSS should be used cautiously to rate astrovirus diarrhoea. While surveillance in communities and out-patient clinics must be continued, screening for human astroviruses in alternate hosts is needed to determine the reservoir species.
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Affiliation(s)
- Sandrama Nadan
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa.
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa; National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa
| | - Nicola A Page
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa; Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa
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Jansen SA, Nijhuis W, Leavis HL, Riezebos-Brilman A, Lindemans CA, Schuurman R. Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics. Front Microbiol 2020; 11:560179. [PMID: 33281758 PMCID: PMC7705093 DOI: 10.3389/fmicb.2020.560179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Pediatric allogeneic hematopoietic stem cell transplantation (HSCT) patients often suffer from gastro-intestinal (GI) disease caused by viruses, Graft-versus-Host Disease (GVHD) or a combination of the two. Currently, the GI eukaryotic virome of HSCT recipients remains relatively understudied, which complicates the understanding of its role in GVHD pathogenicity. As decisions regarding immunosuppressive therapy in the treatment of virus infection or GVHD, respectively, can be completely contradicting, it is crucial to better understand the prevalence and relevance of viruses in the GI tract in the HSCT setting. A real time PCR panel for a set of specific viruses widely used to diagnose the most common causes of GI viral gastroenteritis is possibly insufficient to grasp the full extent of viruses present. Therefore, we applied the targeted sequence capture method ViroCap to residual fecal samples of 11 pediatric allogeneic HSCT recipients with GI symptoms and a suspicion of GVHD, to enrich for nucleic acids of viruses that are known to infect vertebrate hosts. After enrichment, NGS was applied to broadly detect viral sequences. Using ViroCap, we were able to detect viruses such as norovirus and adenovirus (ADV), that had been previously detected using clinical diagnostic PCR on the same sample. In addition, multiple, some of which clinically relevant viruses were detected, including ADV, human rhinovirus (HRV) and BK polyomavirus (BKV). Interestingly, in samples in which specific PCR testing for regular viral GI pathogens did not result in a diagnosis, the ViroCap pipeline led to the detection of viral sequences of human herpesvirus (HHV)-7, BKV, HRV, KI polyomavirus and astrovirus. The latter was an only recently described variant and showed extensive sequence mismatches with the applied real time PCR primers and would therefore not have been detected if tested. Our results indicate that target enrichment of viral nucleic acids through ViroCap leads to sensitive and broad possibly clinically relevant virus detection, including the detection of newer variants in clinical HSCT recipient samples. As such, ViroCap could be a useful detection tool clinically, but also in studying the associations between viral presence and GVHD.
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Affiliation(s)
- Suze A Jansen
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Wouter Nijhuis
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Caroline A Lindemans
- Division of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Stem Cell Transplantation, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Rob Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
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Mombo IM, Boundenga L, Suquet E, Ngoubangoye B, Maganga GD, Leroy EM, Charpentier MJ, Rougeron V. Natural infection of free-ranging mandrills (Mandrillus sphinx) by enteroviruses and astroviruses in southern Gabon. Microb Pathog 2020; 150:104659. [PMID: 33249166 DOI: 10.1016/j.micpath.2020.104659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 10/22/2022]
Abstract
Enteroviruses (Picornaviridae) and astroviruses (Astroviridae) cause various diseases in humans and animals, including in non-human primates (NHPs). Some enteroviruses and astroviruses detected in NHPs are genetically related to those infecting humans, indicating the occurrence of interspecies transmissions. In this study, we screened 200 fecal samples of 56 free-ranging mandrills (Mandrillus sphinx) by nested reverse transcription-PCR with primers targeting the VP1 and RdRp genes, to evaluate the diversity of enterovirus and astrovirus infection, respectively, and the associated zoonotic risk. Overall, ten samples from six mandrills were enterovirus-positive (5%), and three samples from three mandrills were astrovirus-positive (1.5%). This is the first evidence of astrovirus infection in mandrills. Phylogenetic analyses based on the VP1 sequences revealed that all ten enterovirus sequences were part of the species Enterovirus J, suggesting low zoonotic risk. Phylogenetic analysis of the three astrovirus sequences showed that they all belonged to the Mamastrovirus genus. Two astrovirus sequences were highly divergent from all human astrovirus sequences (63.4-73% nucleotide identity), while one sequence (AstV-5) suggested cross-species transmission from humans to mandrills. Additional studies are needed to better characterize the identified astroviruses and to confirm whether mandrills are host of astroviruses than can be transmitted to humans.
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Affiliation(s)
- Illich M Mombo
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon.
| | - Larson Boundenga
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Eloise Suquet
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Barthélémy Ngoubangoye
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Gaël D Maganga
- Centre International de Recherches Médicales de Franceville (CIRMF), BP769, Franceville, Gabon
| | - Eric M Leroy
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR5290, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université de Montpellier, 34394, Montpellier, France
| | - Marie J Charpentier
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR5554, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon (cc065), 34095, Montpellier, France
| | - Virginie Rougeron
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR5290, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université de Montpellier, 34394, Montpellier, France; Centre de Recherche en Ecologie et Evolution de la Santé (CREES), 34000, Montpellier, France
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Norovirus compared to other relevant etiologies of acute gastroenteritis among families from a semirural county in Chile. Int J Infect Dis 2020; 101:353-360. [PMID: 33059093 DOI: 10.1016/j.ijid.2020.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVE To determine the dynamics of norovirus disease, a major cause of acute gastroenteritis (AGE), compared to other relevant etiologies, among families living in a lower middle income area. STUDY DESIGN Families with three or more members and with one or more healthy children <24 months of age were followed for 1-2 years to detect any AGE. Stool samples were tested for viral and bacterial pathogens and a questionnaire was completed for those with norovirus or rotavirus AGE. RESULTS Between April and June 2016, 110 families were enrolled, with 103 of them completing ≥12 months of follow-up. A total of 159 family AGE episodes were detected, mostly affecting one individual (92%). At least one pathogen was detected in 56% (94/169) of samples, of which 75/94 (80%) were sole infections. Norovirus was most common (n=26), followed closely by enteropathogenic Escherichia coli (EPEC) (n=25), rotavirus (n=24), and astrovirus (n=23). The annual incidence of family AGE was 0.77, and 0.12 for norovirus. Most norovirus AGE occurred in children <4 years old (96%). Only 13/159 (8%) index AGE cases resulted in a secondary case, of which four were associated with norovirus. The majority of norovirus strains were GII (85%), with a mild predominance of GII.4 (9/26; 35%); most norovirus isolates (69%) were recombinants. CONCLUSIONS The family incidence of AGE in this lower middle income community was nearly one episode per year, mostly caused by viruses, specifically norovirus closely followed by rotavirus and astrovirus. Norovirus infections primarily affected children <4 years old and secondary cases were uncommon.
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Zhang W, Wang R, Liang J, Zhao N, Li G, Gao Q, Su S. Epidemiology, genetic diversity and evolution of canine astrovirus. Transbound Emerg Dis 2020; 67:2901-2910. [PMID: 32946195 DOI: 10.1111/tbed.13663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/30/2020] [Accepted: 05/30/2020] [Indexed: 01/19/2023]
Abstract
Astroviruses (AstVs) are major causative agents of gastroenteritis in children and have been reported in many species. Canine astrovirus (CaAstV), as an enteric pathogen, has been widely detected worldwide, but little is known about their genetic diversity and evolution, partly owing to a lack of genomic data. Here, we sequenced 12 nearly full-length CaAstV genomes to address the gap in knowledge. We found 14 (13.2%) and 7 (3.35%) CaAstV-positive samples from pet dogs with and without diarrhoea, respectively. Co-infections were with co-infection with Torque teno canis virus (TTCaV) reported for the first time. Phylogenetic analysis of the ORF2 gene revealed four major lineages. In particular, lineage 4 might have evolved from a recombinant virus from lineage 2 and lineage 3. The strains sequenced here clustered with lineages 2, 3 and 4 in contrast with other Chinese strains identified previously that clustered with lineages 2 and 4. Amino acid sequence alignment within lineage revealed intralineage amino acid diversity and that the type of epidemic strains within lineages changes over time. Three amino acids substitutions located in predicted B-cell epitopes, which might be involved escape of host immunity. Moreover, frequent inter-clade ORF2 gene recombinants were identified. The identification of individual recombination events and a recombinant lineage indicated that recombination plays a crucial role in CaAstV genetic evolution and diversity by generating divergent viruses. Moreover, phylogenetic analysis of ORF1b, the most conserved gene of astrovirus, revealed a close relationship between CaAstV and California sea lion astroviruses. Overall, we report detailed information on the genetic evolution and diversity of CaAstV, which indicates that CaAstV may pose challenges for diagnostics and future control strategies.
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Affiliation(s)
- Wenyan Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ruyi Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiawei Liang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Naiyu Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Gairu Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qi Gao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering 1. Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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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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Quintero-Ochoa G, Romero-Argüelles R, Aviles-Hernández A, Cejudo-Flores M, Calleja-García P, Domínguez-Gámez M, Cantú-Bernal S, Icedo-García R, Soñanez-Organis J, Rosas-Rodríguez J, Romo-Saenz C, Tamez-Guerra P, Flores-Mendoza L, González-Ochoa G. Viral agents of gastroenteritis and their correlation with clinical symptoms in rotavirus-vaccinated children. INFECTION GENETICS AND EVOLUTION 2019; 73:190-196. [DOI: 10.1016/j.meegid.2019.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/02/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
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Guo K, Li LL, Zhang Q, Yu JM, Ye Y. Diversified Variants of Astrovirus MLB2 in Patients Following Hematopoietic Stem Cell Transplantation and the Evolutionary Rates and Patterns of the Virus. Evol Bioinform Online 2019; 15:1176934319864922. [PMID: 31360058 PMCID: PMC6637835 DOI: 10.1177/1176934319864922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/03/2022] Open
Abstract
We assessed the quasispecies heterogeneity of a human astrovirus MLB2 (HAstV-MLB2-YJMGK) in immunocompromised patients following hematopoietic stem cell transplantation and performed genetic and evolutionary analyses of HAstV isolates circulating worldwide. The result showed that the virus had diversified variants and a strong positive selection in the patient, indicating that such patients may be a reservoir for astrovirus. The time to the most recent common ancestor of MLB2 and classic HAstVs was around 1800 years, and it has a decline in effective population size of HAstVs in the late 100 years.
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Affiliation(s)
- Ke Guo
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.,Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Li-Li Li
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Qing Zhang
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jie-Mei Yu
- Department of Diarrhea, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yan Ye
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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40
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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: 22] [Impact Index Per Article: 4.4] [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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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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Zhao W, Tao XL, Liu N, Lu HZ, Zheng CH, Li XY, Yu M, Li YG. Host protein CD63 promotes viral RNA replication by interacting with human astrovirus non-structural protein nsP1a/4. J Gen Virol 2019; 100:616-628. [DOI: 10.1099/jgv.0.001231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Wei Zhao
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
- 2Biological Anthropology institute, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
| | - Xiao Li Tao
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
| | - Nian Liu
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
- 2Biological Anthropology institute, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
| | - Heng Zhang Lu
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
| | - Chun Hong Zheng
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
| | - Xiang Yu Li
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
| | - Man Yu
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
| | - Yong Gang Li
- 1College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou 121200, Liaoning, PR China
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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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Zhao G, Droit L, Gilbert MH, Schiro FR, Didier PJ, Si X, Paredes A, Handley SA, Virgin HW, Bohm RP, Wang D. Virome biogeography in the lower gastrointestinal tract of rhesus macaques with chronic diarrhea. Virology 2019; 527:77-88. [PMID: 30468938 PMCID: PMC6333316 DOI: 10.1016/j.virol.2018.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 12/26/2022]
Abstract
The composition of gastrointestinal tract viromes has been associated with multiple diseases. Our understanding of virus communities in the GI tract is still very limited due to challenges in sampling from different GI sites. Here we defined the GI viromes of 15 rhesus macaques with chronic diarrhea. Luminal content samples from terminal ileum, proximal and distal colon were collected at necropsy while samples from the rectum were collected antemortem using a fecal loop. The composition of and ecological parameters associated with the terminal ileum virome were distinct from the colon and rectum samples; these differences were driven by bacteriophages rather than eukaryotic viruses. The six contigs that were most discriminative of the viromes were distantly related to bacteriophages from three different families. Our analysis provides support for using fecal loop sampling of the rectum as a proxy of the colonic virome in humans.
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Affiliation(s)
- Guoyan Zhao
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Lindsay Droit
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Margaret H Gilbert
- Divisions of Veterinary Medicine and Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - Faith R Schiro
- Divisions of Veterinary Medicine and Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - Peter J Didier
- Divisions of Veterinary Medicine and Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | | | - Anne Paredes
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott A Handley
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Herbert W Virgin
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rudolf P Bohm
- Divisions of Veterinary Medicine and Comparative Pathology, Tulane National Primate Research Center, Covington, LA, USA
| | - David Wang
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 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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Birch JM, Ullman K, Struve T, Agger JF, Hammer AS, Leijon M, Jensen HE. Investigation of the viral and bacterial microbiota in intestinal samples from mink (Neovison vison) with pre-weaning diarrhea syndrome using next generation sequencing. PLoS One 2018; 13:e0205890. [PMID: 30335814 PMCID: PMC6193705 DOI: 10.1371/journal.pone.0205890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 10/03/2018] [Indexed: 01/21/2023] Open
Abstract
Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2-3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing. In addition, we used deep sequencing to determine and compare the viral intestinal content in 31 healthy non-diarrheic and 30 diarrheic pooled samples (2-3 mink kits from the same litter per pool). The results showed high variations in composition of the bacterial species between the pools. Enterococci, staphylococci and streptococci dominated in both diarrheic and non-diarrheic pools. However, enterococci accounted for 70% of the reads in the diarrheic group compared to 50% in the non-diarrheic group and this increase was at the expense of staphylococci and streptococci which together accounted for 45% and 17% of the reads in the non-diarrheic and diarrheic group, respectively. Moreover, in the diarrheic pools there were more reads assigned to Clostridia, Escherichia-Shigella and Enterobacter compared to the non-diarrheic pools. The taxonomically categorized sequences from the virome showed that the most prevalent viruses in all pools were caliciviruses and mamastroviruses (almost exclusively type 10). However, the numbers of reads assigned to caliciviruses were almost 3 times higher in the diarrheic pools compared the non-diarrheic pools and Sapporo-like caliciviruses were more abundant than the Norwalk-like caliciviruses. The results from this study have contributed to the insight into the changes in the intestinal microbiota associated with the PWD syndrome of mink.
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Affiliation(s)
- Julie Melsted Birch
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Karin Ullman
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Tina Struve
- Kopenhagen Fur Diagnostics, Kopenhagen Fur, Glostrup, Denmark
| | - Jens Frederik Agger
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anne Sofie Hammer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mikael Leijon
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Henrik Elvang Jensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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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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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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50
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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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