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Hogben E, Khamrin P, Kumthip K, Yodmeeklin A, Maneekarn N. Distribution and molecular characterization of saffold virus and human cosavirus in children admitted to hospitals with acute gastroenteritis in Thailand, 2017-2022. J Med Virol 2023; 95:e29159. [PMID: 37805831 DOI: 10.1002/jmv.29159] [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: 05/26/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023]
Abstract
Saffold virus (SAFV) and human cosavirus (HCoSV) are emerging viruses of the Picornaviridae family. They have been shown to associate with gastrointestinal infection and more recently these viruses have also been demonstrated to associate with other clinical infections such as the respiratory tract, cardiovascular system, and the cerebral ventricular system. In this study, 2459 stool specimens collected from pediatric patients admitted to hospitals with acute gastroenteritis from January 2017 to December 2022, were screened for SAFV and HCoSV utilizing reverse transcription-polymerase chain reaction. Positive samples were then characterized into genotypes via nucleotide sequencing and bioinformatic analysis. Of the 2459 samples, 21 and 39 were positive for SAFV (0.9%) and HCoSV (1.6%), respectively. Three genotypes of SAFV were identified-SAFV-1 (38%), SAFV-2 (24%), and SAFV-3 (38%). Two genetic groups of HCoSV were identified-HCoSV-C (97%) and HCoSV-A (3%), demonstrating a large increase of HCoSV-C as compared to those reported previously from the same geographical region in Thailand. This study provides the prevalence of SAFV and HCoSV genotypes in Chiang Mai, Thailand during a period of 6 years from 2017 to 2022.
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Affiliation(s)
- Emily Hogben
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - 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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Aminipour M, Ghaderi M, Harzandi N. First Occurrence of Saffold Virus in Sewage and River Water Samples in Karaj, Iran. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:75-80. [PMID: 31729639 DOI: 10.1007/s12560-019-09415-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
Saffold virus as a newly discovered virus, which seems to be related to acute gastroenteritis as with other enteric viruses and to human airway diseases in children belongs to Cardiovirus genus in picornaviridae family with 11 genotypes. Saffold virus initially was detected in America from infant stool sample. Saffold virus has also been detected in environmental water samples. Until now, two reports have demonstrated that sewage water sources are contaminated with Saffold viruses. Molecular detection of Saffold virus mostly depended on reverse transcription PCR methods and RT-qPCR, which had targeted 5'UTR region of the viral genome. The present study aims to evaluate the molecular detection and quantity of Saffold virus in sewage water and river water specimens by RT-qPCR assay in Karaj, Iran. Fifty samples collected from environmental waters containing treated and untreated sewage water and river water samples were included in this study. After viral RNA extraction, the Real-time PCR was developed to amplify the 5'UTR sequence of Saffold virus genome and viral load was assessed. Out of the 50 samples tested (consisting 28 river water samples and 22 sewage water samples), the Saffold virus genomic RNA was identified in 10/28 (35.7%) of river water samples and in 4/12 (33.3%) of treated and 4/10 (40%) of untreated sewage samples. The maximum viral load was 6.8 × 106 copies/l in untreated sewage water sample in December, and the lower viral load was 1.2 × 106 copies/l related to treated sewage water taken in October. Our results for the first time indicate that Saffold virus has apparently been circulating among Iranian peoples. Also, the viral prevalence of Saffold virus in each of the three sets of tested samples was within moderate to high in range.
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Affiliation(s)
- Mona Aminipour
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Mostafa Ghaderi
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran.
| | - Naser Harzandi
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
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Tan SZK, Tan MZY, Prabakaran M. Saffold virus, an emerging human cardiovirus. Rev Med Virol 2016; 27. [PMID: 27723176 PMCID: PMC7169152 DOI: 10.1002/rmv.1908] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 01/16/2023]
Abstract
Saffold virus (SAFV) is an emerging human cardiovirus that has been shown to be ubiquitous. Initial studies of SAFV focused on respiratory and gastrointestinal infection; however, it has also recently been associated with diverse clinical symptoms including the endocrine, cardiovascular, and neurological systems. Given the systemic nature of SAFV, and its high prevalence, understanding its pathogenicity and clinical impact is of utmost importance. This comprehensive review highlights and discusses recent developments in epidemiology, human pathogenicity, animal, and molecular studies related to SAFV. It also provides detailed insights into the neuropathogenicity of SAFV. We argue that human studies have been confounded by coinfections and therefore require support from robust molecular and animal research. Thereby, we aim to provide foresight into further research to better understand this emerging virus.
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Affiliation(s)
- Shawn Zheng Kai Tan
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore, Republic of Singapore
| | - Mark Zheng Yi Tan
- Critical Care Unit, Central Manchester Foundation NHS Trust, Manchester, UK
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore, Republic of Singapore
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Brañas P, García M, Prieto C, Folgueira L. Saffold virus respiratory infection in children and immunocompromised patients in Spain. J Infect 2014; 70:679-80. [PMID: 25459664 DOI: 10.1016/j.jinf.2014.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/11/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Patricia Brañas
- Department of Clinical Microbiology, University Hospital 12 de Octubre, Avda. Córdoba s/n, 28041 Madrid, Spain.
| | - Monica García
- Department of Clinical Microbiology, University Hospital 12 de Octubre, Avda. Córdoba s/n, 28041 Madrid, Spain
| | - Columbiana Prieto
- Department of Clinical Microbiology, University Hospital 12 de Octubre, Avda. Córdoba s/n, 28041 Madrid, Spain
| | - Lola Folgueira
- Department of Clinical Microbiology, University Hospital 12 de Octubre, Avda. Córdoba s/n, 28041 Madrid, Spain
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Naeem A, Hosomi T, Nishimura Y, Alam MM, Oka T, Zaidi SSZ, Shimizu H. Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan. J Gen Virol 2014; 95:1945-1957. [PMID: 24899154 DOI: 10.1099/vir.0.066498-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human cardioviruses or Saffold viruses (SAFVs) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of 11 SAFV genotypes from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases using reverse transcriptase-PCR targeting the 5' untranslated region (UTR). Further characterization based on complete VP1 analysis revealed 71 SAFVs belonging to 11 genotypes, including three previously unidentified genotypes. SAFV showed high genetic diversity and recombination based on phylogenetic, pairwise distance distributions and recombination mapping analyses performed herein. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFVs. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23 and 10 % divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of the species Theilovirus, such as Thera virus and Theiler's murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41-56 % aa pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV.
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Affiliation(s)
- Asif Naeem
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takushi Hosomi
- The Meat Inspection Center of Kochi Prefecture, Kochi, Japan
| | - Yorihiro Nishimura
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
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Lambert SB, Ware RS, Cook AL, Maguire FA, Whiley DM, Bialasiewicz S, Mackay IM, Wang D, Sloots TP, Nissen MD, Grimwood K. Observational Research in Childhood Infectious Diseases (ORChID): a dynamic birth cohort study. BMJ Open 2012; 2:bmjopen-2012-002134. [PMID: 23117571 PMCID: PMC3547315 DOI: 10.1136/bmjopen-2012-002134] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Even in developed economies infectious diseases remain the most common cause of illness in early childhood. Our current understanding of the epidemiology of these infections is limited by reliance on data from decades ago performed using low-sensitivity laboratory methods, and recent studies reporting severe, hospital-managed disease. METHODS AND ANALYSIS The Observational Research in Childhood Infectious Diseases (ORChID) study is an ongoing study enrolling a dynamic birth cohort to document the community-based epidemiology of viral respiratory and gastrointestinal infections in early childhood. Women are recruited antenatally, and their healthy newborn is followed for the first 2 years of life. Parents keep a daily symptom diary for the study child, collect a weekly anterior nose swab and dirty nappy swab and complete a burden diary when a child meets pre-defined illness criteria. Specimens will be tested for a wide range of viruses by real-time PCR assays. Primary analyses involves calculating incidence rates for acute respiratory illness (ARI) and acute gastroenteritis (AGE) for the cohort by age and seasonality. Control material from children when they are without symptoms will allow us to determine what proportion of ARIs and AGE can be attributed to specific pathogens. Secondary analyses will assess the incidence and shedding duration of specific respiratory and gastrointestinal pathogens. ETHICS AND DISSEMINATION This study is approved by The Human Research Ethics Committees of the Children's Health Queensland Hospital and Health Service, the Royal Brisbane and Women's Hospital and The University of Queensland. TRIAL REGISTRATION clinicaltrials.gov NCT01304914.
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Affiliation(s)
- Stephen Bernard Lambert
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
- Queensland Health Immunisation Program, Communicable Diseases Branch, Queensland Health, Brisbane, Queensland, Australia
| | - Robert S Ware
- School of Population Health and the Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne L Cook
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Frances A Maguire
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
| | - David M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Seweryn Bialasiewicz
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Ian M Mackay
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University, School of Medicine, St. Louis, Missouri, USA
| | - Theo P Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
- Microbiology Division, Pathology Queensland Central Laboratory, Queensland Health, Brisbane, Queensland, Australia
| | - Michael D Nissen
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
- Microbiology Division, Pathology Queensland Central Laboratory, Queensland Health, Brisbane, Queensland, Australia
| | - Keith Grimwood
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland and the Royal Children's Hospital, Brisbane, Queensland, Australia
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