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Kane Y, Tendu A, Li R, Chen Y, Mastriani E, Lan J, Catherine Hughes A, Berthet N, Wong G. Viral diversity in wild and urban rodents of Yunnan Province, China. Emerg Microbes Infect 2024; 13:2290842. [PMID: 38047395 PMCID: PMC10829829 DOI: 10.1080/22221751.2023.2290842] [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: 07/30/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Rodents represent over 40% of known mammal species and are found in various terrestrial habitats. They are significant reservoirs for zoonotic viruses, including harmful pathogens such as arenaviruses and hantaviruses, yet knowledge of their hosts and distributions is limited. Therefore, characterizing the virome profile in these animals is invaluable for outbreak preparedness, especially in potential hotspots of mammal diversity. This study included 681 organs from 124 rodents and one Chinese tree shrew collected from Yunnan Province, China, during 2020-2021. Metagenomic analysis revealed unique features of mammalian viruses in rodent organs across habitats with varying human disturbances. R. tanezumi in locations with high anthropogenic disturbance exhibited the highest mammal viral diversity, with spleen and lung samples showing the highest diversities for these viruses at the organ level. Mammal viral diversity for both commensal and non-commensal rats was identified to positively correlate with landscape disturbance. Some virus families were associated with particular organs or host species, suggesting tropism for these pathogens. Notably, known and novel viral species that are likely to infect humans were identified. R. tanezumi was identified as a reservoir and carrier for various zoonotic viruses, including porcine bocavirus, hantavirus, cardiovirus, and lyssavirus. These findings highlight the influence of rodent community composition and anthropogenic activities on diverse virome profiles, with R. tanezumi as an important reservoir for zoonotic viruses.
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Affiliation(s)
- Yakhouba Kane
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Alexander Tendu
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Ruiya Li
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yanhua Chen
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, People’s Republic of China
| | - Emilio Mastriani
- Centre for Microbes, Development, and Health, and Unit of Discovery and Molecular Characterization of Pathogens, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Jiaming Lan
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Alice Catherine Hughes
- Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, People’s Republic of China
- School of Biological Sciences, University of Hong Kong, Hong Kong SAR, People’s Republic of China
| | - Nicolas Berthet
- Centre for Microbes, Development, and Health, and Unit of Discovery and Molecular Characterization of Pathogens, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- Institut Pasteur, Unité Environnement et Risque Infectieux, Cellule d’Intervention Biologique d’Urgence, Paris, France
- Institut Pasteur, Université Paris-cite, Unité Epidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Gary Wong
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, People’s Republic of China
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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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Okuwa T, Himeda T, Utani K, Higuchi M. Generation of a recombinant Saffold Virus expressing UnaG as a marker for the visualization of viral infection. Virol J 2023; 20:175. [PMID: 37550694 PMCID: PMC10408109 DOI: 10.1186/s12985-023-02142-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/26/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Saffold virus (SAFV), which belongs to the genus Cardiovirus of the family Picornaviridae, is associated with acute respiratory or gastrointestinal illnesses in children; it is also suspected to cause severe diseases, such as acute flaccid paralysis and aseptic meningitis. However, the understanding of the mechanism of its pathogenicity is still limited due to the many unknowns about its lifecycle; for example, the cellular receptor for its infection remains to be determined. A system to monitor SAFV infection in vitro and in vivo is required in order to accelerate research on SAFV. RESULTS We generated a recombinant SAFV expressing green fluorescent protein (GFP) or UnaG, a novel fluorescent protein derived from Japanese eel. HeLa cells infected by either GFP or UnaG-expressing SAFV showed a bright green fluorescent signal, enabling convenient monitoring of SAFV infection. However, the expression of GFP but not UnaG was quickly lost during virus passaging due to the difference in genetic stability in the SAFV virus genome; the UnaG gene was stably maintained in the virus genome after at least five passages. CONCLUSIONS SAFV infection of cultured cells can easily be monitored using UnaG-expressing SAFV, which is superior to GFP in terms of genetic stability in the virus genome. This virus could be a useful tool for SAFV research, such as comparing the susceptibility of various cells to SAFV infection and evaluating the effects of antivirals on SAFV infection in high-throughput screening.
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Affiliation(s)
- Takako Okuwa
- Department of Microbiology, Kanazawa Medical University School of Medicine, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Toshiki Himeda
- Department of Microbiology, Kanazawa Medical University School of Medicine, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Koichi Utani
- Department of Microbiology, Kanazawa Medical University School of Medicine, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan
| | - Masaya Higuchi
- Department of Microbiology, Kanazawa Medical University School of Medicine, 1-1 Daigaku, Uchinada, Ishikawa, 920-0293, Japan.
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Razizadeh MH, Khatami A, Zarei M. Global Status of Bufavirus, Cosavirus, and Saffold Virus in Gastroenteritis: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2022; 8:775698. [PMID: 35096871 PMCID: PMC8792846 DOI: 10.3389/fmed.2021.775698] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/29/2021] [Indexed: 01/20/2023] Open
Abstract
Background: Bufavirus (BuV), Human Cosavirus (HCoSV), and Saffold (SAFV) virus are three newly discovered viruses and have been suggested as possible causes of gastroenteritis (GE) in some studies. The aim of the present study was to estimate the overall prevalence of viruses and their association with GE. Methods: A comprehensive systematic search was conducted in Scopus, Web of Science, PubMed, and Google scholar between 2007 and 2021 to find studies on the prevalence of BuV, HCoSV, and SAFV viruses. Result: Meta-analysis of the 46 included studies showed the low prevalence of BuV (1.%, 95% CI 0.6-1.5%), HCoSV (0.8%, 95% CI 0.4-1.5%), and SAFV (1.9%, 95% CI 1.1-3.1%) worldwide. Also, no significant association between these viruses and GE was observed. BuV was isolated from patients with GE in Africa, while SAFV was more common in Europe. BuV1 and BuV2 have the same prevalence between the three identified genotypes of BuV. HCoSV-C was the most prevalent genotype of HCoSV, and SAFV2 was the commonest genotype of SAFV. All of these viruses were more prevalent in children older than 5 years of age. Conclusion: This was the first meta-analysis on the prevalence and association of BuV, HCoSV, and SAFV with GE. While no significant association was found between infection with these viruses and GE, we suggest more studies, especially with case-control design and from different geographical regions in order to enhance our knowledge of these viruses.
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Affiliation(s)
| | - Alireza Khatami
- Faculty of Medicine, Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Zarei
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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Chong YM, Chan YF, Jamaluddin MFH, Hasan MS, Pang YK, Ponnampalavanar S, Syed Omar SF, Voon KGL, Sam IC. Detection of respiratory viruses in adults with suspected COVID-19 in Kuala Lumpur, Malaysia. J Clin Virol 2021; 145:105000. [PMID: 34739838 PMCID: PMC8526124 DOI: 10.1016/j.jcv.2021.105000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/05/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022]
Abstract
Background Reports of co-circulation of respiratory viruses during the COVID-19 pandemic and co-infections with SARS-CoV-2 vary. However, limited information is available from developing countries. Objectives We aimed to investigate the incidence of respiratory viruses in adult patients with suspected COVID-19 in Kuala Lumpur, Malaysia. Study Design We collected 198 respiratory samples from adult patients hospitalized with suspected COVID-19 in a single teaching hospital in Kuala Lumpur in February-May 2020 and tested combined oro-nasopharyngeal swabs with the NxTAG Respiratory Pathogen Panel (Luminex) and Allplex RV Essential (Seegene) assays. Forty-five negative samples further underwent viral metagenomics analysis. Results Of the 198 samples, 74 (37.4%) had respiratory pathogens, including 56 (28.3%) with SARS-CoV-2 and 18 (9.1%) positive for other respiratory pathogens. There were five (2.5%) SARS-CoV-2 co-infections, all with rhinovirus/enterovirus. Three samples (6.7%; 3/45) had viruses identified by metagenomics, including one case of enterovirus D68 and one of Saffold virus genotype 6 in a patient requiring ICU care. Most of the COVID-19 patients (91.1%; 51/56) had mild symptoms but 5.4% (3/56) died. Conclusion During the early COVID-19 period, common respiratory viruses other than SARS-CoV-2 only accounted for 9.1% of hospitalization cases with ARI and co-infections with SARS-CoV-2 were rare. Continued surveillance is important to understand the impact of COVID-19 and its associated public health control measures on circulation of other respiratory viruses. Metagenomics can identify unexpected or rare pathogens, such as Saffold virus, which is rarely described in adults.
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Affiliation(s)
- Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - M Shahnaz Hasan
- Department of Anaesthesiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | | | | | - Kenny Gah Leong Voon
- Division of Pathology, International Medical University, 57000 Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Medical Microbiology, University of Malaya Medical Centre, 59100 Kuala Lumpur, Malaysia.
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Vandesande H, Edman K, Rondahl E, Falkeborn T, Serrander L, Lindberg AM. Saffold virus infection in elderly people with acute gastroenteritis in Sweden. J Med Virol 2021; 93:3980-3984. [PMID: 32827319 DOI: 10.1002/jmv.26452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/20/2020] [Indexed: 12/24/2022]
Abstract
Viral gastroenteritis is a major source of morbidity and mortality, predominantly caused by so-called NOROAD viruses (norovirus, rotavirus, and adenovirus). In approximately onethird of all cases, however, the exact etiology is unknown. The in 2007 discovered human cardiovirus Saffold virus (SAFV) may prove to be a plausible candidate to explain this diagnostic gap. This virus, a member of the Picornaviridae family which is closely related to the murine viruses Theiler's murine encephalomyelitis virus and Theravirus, is a widespread pathogen and causes infection early in life. Screening of 238 fecal or vomitus samples obtained from NOROAD-negative, elderly patients with acute gastroenteritis at the University Hospital of Linköping showed that SAFV is present in low abundance (4.6%). Phylogenetic analysis of the VP1 gene revealed a Swedish isolate belonging to the highly common and in Europe widespread SAFV-3 genotype. This genotype is also related to previously reported Asian strains. This study describes the first molecular typing of a Swedish SAFV isolate and is the first report to document the circulation of SAFV among elderly people. The pathogenicity of SAFV is, as of yet, still under debate; further studies are necessary to determine its role in the development of disease.
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Affiliation(s)
- Helena Vandesande
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Kjell Edman
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
| | - Elin Rondahl
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tina Falkeborn
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Lena Serrander
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
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Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Viruses 2020; 12:v12050502. [PMID: 32370153 PMCID: PMC7290774 DOI: 10.3390/v12050502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 01/10/2023] Open
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a lethal zoonotic pathogen circulating in the Arabian Peninsula since 2012. There is no vaccine for MERS and anti-viral treatment is generally not applicable. We investigated the evolution of the MERS-CoV spike gene sequences and changes in viral loads over time from patients in Saudi Arabia from 2105-2017. All the MERS-CoV strains belonged to lineage 5, and showed high sequence homology (99.9%) to 2017 strains. Recombination analysis showed a potential recombination event in study strains from patients in Saudi Arabia. The spike gene showed eight amino acid substitutions, especially between the A1 and B5 lineage, and contained positively selected codon 1020. We also determined that the viral loads were significantly (p < 0.001) higher in fatal cases, and virus shedding was prolonged in some fatal cases beyond 21 days. The viral concentration peaked during the first week of illness, and the lower respiratory specimens had higher levels of MERS-CoV RNA. The presence of the diversifying selection and the topologies with the structural mapping of residues under purifying selection suggested that codon 1020 might have a role in the evolution of spike gene during the divergence of different lineages. This study will im-prove our understanding of the evolution of MERS-CoV, and also highlights the need for enhanced surveillance in humans and dromedaries. The presence of amino acid changes at the N-terminal domain and structural mapping of residues under positive selection at heptad repeat 1 provides better insight into the adaptive evolution of the spike gene and might have a potential role in virus-host tropism and pathogenesis.
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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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Bonanno Ferraro G, Mancini P, Veneri C, Iaconelli M, Suffredini E, Brandtner D, La Rosa G. Evidence of Saffold virus circulation in Italy provided through environmental surveillance. Lett Appl Microbiol 2019; 70:102-108. [PMID: 31742735 DOI: 10.1111/lam.13249] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022]
Abstract
Saffold virus (SAFV) is an emerging human cardiovirus associated with respiratory and gastrointestinal infection, and, more recently, to symptoms related to the endocrine, cardiovascular, and neurological systems. Information about SAFV circulation in Italy is scarce. In order to provide insights into the epidemiology of SAFV in Italy, 141 raw sewage samples collected throughout Italy were tested using broad-range nested RT-PCR primers targeting the 5'-NC region. Seven samples (5·0%) were confirmed as SAFV in samples collected in North, Centre and Southern Italy. Typing was attempted through amplification of the VP1 coding region, using both published and newly designed primers, and one sample was characterized as SAFV-2. SIGNIFICANCE AND IMPACT OF THE STUDY: Prevalence, genetic diversity and geographic distribution of SAFV in Italy is currently unknown. This study represents the first detection of SAFV in sewage samples in Italy, suggesting that it is circulating in the population despite lack of clinical reporting. Whether the virus is associated with asymptomatic cases or with undetected gastroenteritis or respiratory illness is unknown. Further studies are needed to investigate on the occurrence and persistence of SAFV in water environments and its waterborne transmission potential.
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Affiliation(s)
- G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
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The Saffold Virus-Penang 2B and 3C Proteins, but not the L Protein, Induce Apoptosis in HEp-2 and Vero Cells. Virol Sin 2019; 34:262-269. [PMID: 31016480 DOI: 10.1007/s12250-019-00116-1] [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: 10/02/2018] [Accepted: 02/22/2019] [Indexed: 10/27/2022] Open
Abstract
Our previous work has shown that Saffold virus (SAFV) induced several rodent and primate cell lines to undergo apoptosis (Xu et al. in Emerg Microb Infect 3:1-8, 2014), but the essential viral proteins of SAFV involved in apoptotic activity lack study. In this study, we individually transfected the viral proteins of SAFV into HEp-2 and Vero cells to assess their ability to induce apoptosis, and found that the 2B and 3C proteins are proapoptotic. Further investigation indicated the transmembrane domain of the 2B protein is essential for the apoptotic activity and tetramer formation of the 2B protein. Our research provides clues for the possible mechanisms of apoptosis induced by SAFV in different cell lines. It also opens up new directions to study viral proteins (the 2B, 3C protein), and sets the stage for future exploration of any possible link between SAFV, inclusive of its related uncultivable genotypes, and multiple sclerosis.
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11
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Yinda CK, Vanhulle E, Conceição-Neto N, Beller L, Deboutte W, Shi C, Ghogomu SM, Maes P, Van Ranst M, Matthijnssens J. Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses. mSphere 2019; 4:e00585-18. [PMID: 30674646 PMCID: PMC6344602 DOI: 10.1128/msphere.00585-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/17/2018] [Indexed: 12/11/2022] Open
Abstract
Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably.IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world's virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.
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Affiliation(s)
- Claude Kwe Yinda
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Emiel Vanhulle
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Nádia Conceição-Neto
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Leen Beller
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ward Deboutte
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Chenyan Shi
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, Biotechnology Unit, Molecular and Cell Biology Laboratory, University of Buea, Buea, Cameroon
| | - Piet Maes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
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Recombination Located over 2A-2B Junction Ribosome Frameshifting Region of Saffold Cardiovirus. Viruses 2018; 10:v10100520. [PMID: 30249971 PMCID: PMC6213509 DOI: 10.3390/v10100520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/26/2018] [Accepted: 09/04/2018] [Indexed: 01/15/2023] Open
Abstract
Here we report the nearly full-length genome of a recombinant Saffold virus strain (SAFV-BR-193) isolated from a child with acute gastroenteritis. Evolutionary analysis performed using all available near-full length Saffold picornavirus genomes showed that the breakpoint found in the Brazilian strain (SAFV-BR-193) is indeed a recombination hotspot. Notably, this hotspot is located just one nucleotide after the ribosomal frameshift GGUUUUU motif in the SAFV genome. Empirical studies will be necessary to determine if this motif also affects the binding affinity of RNA-dependent RNA-polymerase (RdRp) and therefore increases the changes of RdRp swap between molecules during the synthesis of viral genomes.
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13
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Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds. Sci Rep 2018; 8:8686. [PMID: 29875375 PMCID: PMC5989203 DOI: 10.1038/s41598-018-26851-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 01/19/2023] Open
Abstract
We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples. We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the "ribosomal activity microbiome"; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.
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Itagaki T, Aoki Y, Matoba Y, Tanaka S, Ikeda T, Matsuzaki Y, Mizuta K. Detection of Saffold viruses from children with acute respiratory infections in Yamagata, Japan, between 2008 and 2015. J Med Virol 2017; 90:34-40. [PMID: 28851118 DOI: 10.1002/jmv.24928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 07/28/2017] [Indexed: 12/14/2022]
Abstract
Although Saffold virus (SAFV) was reported as a novel human cardiovirus in 2007, no causative association between SAFV and clinical disease has been proven and the longitudinal epidemiology of SAFVs is not available. To establish the relationship between SAFVs and acute respiratory infections (ARIs) and to clarify the longitudinal epidemiology of SAFVs, 7258 nasopharyngeal specimens were collected from children with ARIs in Yamagata, Japan between 2008 and 2015. The specimens were inoculated on a microplate including six cell lines as part of routine surveillance, and molecular screening was performed for SAFVs using a reverse transcription (RT)-PCR method. Throughout the study period, 95 (1.3%) SAFV genotype 2 (SAFV2), and 28 (0.4%) SAFV3 were detected, mainly between September and November. There were two outbreaks of SAFV2 in 2009 and 2013, and one outbreak of SAFV3 in 2012 and the positive rates during these outbreaks were 12.1% (53/439), 11% (35/319), and 4.4% (20/453), respectively. Sixty-three SAFV2 and 28 SAFV3 strains were detected as a single virus from children with ARIs such as pharyngitis, herpangina, and tonsillitis. These results suggested that SAFV2 and SAFV3 are possible causative agents of ARIs among children and their infections occur mainly in the autumn season in Japan.
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Affiliation(s)
| | - Yoko Aoki
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Yohei Matoba
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Shizuka Tanaka
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Tatsuya Ikeda
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
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15
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Prevalence of human cosavirus and saffold virus with an emergence of saffold virus genotype 6 in patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, 2014–2016. INFECTION GENETICS AND EVOLUTION 2017; 53:1-6. [DOI: 10.1016/j.meegid.2017.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/02/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
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16
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Analysis of Aichi virus and Saffold virus association with pediatric acute gastroenteritis. J Clin Virol 2016; 87:37-42. [PMID: 27992789 DOI: 10.1016/j.jcv.2016.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/28/2022]
Abstract
BACKGROUND Aichi virus (AiV) and Saffold virus (SAFV) have been reported in children with acute gastroenteritis and respiratory disease worldwide; however, their causative role in acute gastroenteritis remains ambiguous. OBJECTIVES To assess the clinical association of AiV and SAFV with acute gastroenteritis in the pediatric population. STUDY DESIGN A case-control study involving 461 paired stool samples from pediatric cases with diarrhea and healthy controls was conducted in China. Quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) was used to screen AiV and SAFV. RESULTS In the 461 paired samples, AiV and SAFV were more prevalent among asymptomatic children than children with acute gastroenteritis (0.87% vs. 0.43% and 2.8% vs. 1.5%, respectively), with no significant differences between groups (p=0.142 and p=0.478, respectively). Cox regression model analysis revealed no correlation between AiV (odds ratio, OR=2.24; 95% confidence interval, CI, 0.76-6.54) or SAFV infection (OR=1.36; 95% CI, 0.86-2.15) and diarrhea. High viral loads were found in both AiV- and SAFV-positive groups, with no significant difference in viral load between the groups (p=0.507 and p=0.677, respectively). No other known enteric pathogens were found in the AiV-positive samples but common in SAFV-positive cases. Phylogenetic analysis revealed that all 6 AiV subjects clustered with genotype B. All 7 SAFV-positive cases and 8 of 13 SAFV-positive controls were genotyped successfully; the genotypes identified included SAFV-1, SAFV-2 SAFV-3, and SAFV-6. CONCLUSION Our study revealed no association of these viruses in acute gastroenteritis in children. These viruses may have the ability to replicate in humans; however, the infections are usually asymptomatic.
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17
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Intracerebral Inoculation of Mouse-Passaged Saffold Virus Type 3 Affects Cerebellar Development in Neonatal Mice. J Virol 2016; 90:10007-10021. [PMID: 27581974 DOI: 10.1128/jvi.00864-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/22/2016] [Indexed: 01/04/2023] Open
Abstract
Saffold virus (SAFV), a human cardiovirus, is occasionally detected in infants with neurological disorders, including meningitis and cerebellitis. We recently reported that SAFV type 3 isolates infect cerebellar glial cells, but not large neurons, in mice. However, the impact of this infection remained unclear. Here, we determined the neuropathogenesis of SAFV type 3 in the cerebella of neonatal ddY mice by using SAFV passaged in the cerebella of neonatal BALB/c mice. The virus titer in the cerebellum increased following the inoculation of each of five passaged strains. The fifth passaged strain harbored amino acid substitutions in the VP2 (H160R and Q239R) and VP3 (K62M) capsid proteins. Molecular modeling of the capsid proteins suggested that the VP2-H160R and VP3-K62M mutations alter the structural dynamics of the receptor binding surface via the formation of a novel hydrophobic interaction between the VP2 puff B and VP3 knob regions. Compared with the original strain, the passaged strain showed altered growth characteristics in human-derived astroglial cell lines and greater replication in the brains of neonatal mice. In addition, the passaged strain was more neurovirulent than the original strain, while both strains infected astroglial and neural progenitor cells in the mouse brain. Intracerebral inoculation of either the original or the passaged strain affected brain Purkinje cell dendrites, and a high titer of the passaged strain induced cerebellar hypoplasia in neonatal mice. Thus, infection by mouse-passaged SAFV affected cerebellar development in neonatal mice. This animal model contributes to the understanding of the neuropathogenicity of SAFV infections in infants. IMPORTANCE Saffold virus (SAFV) is a candidate neuropathogenic agent in infants and children, but the neuropathogenicity of the virus has not been fully elucidated. Recently, we evaluated the pathogenicity of two clinical SAFV isolates in mice. Similar to other neurotropic picornaviruses, these isolates showed mild infectivity of glial and neural progenitor cells, but not of large neurons, in the cerebellum. However, the outcome of this viral infection in the cerebellum has not been clarified. Here, we examined the tropism of SAFV in the cerebellum. We obtained an in vivo-passaged strain from the cerebella of neonatal mice and examined its genome and its neurovirulence in the neonatal mouse brain. The passaged virus showed high infectivity and neurovirulence in the brain, especially the cerebellum, and affected cerebellar development. This unique neonatal mouse model will be helpful for elucidating the neuropathogenesis of SAFV infections occurring early in life.
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18
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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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19
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Sorgeloos F, Lardinois C, Jacobs S, van Kuppeveld FJM, Kaspers B, Michiels T. Neurotropism of Saffold virus in a mouse model. J Gen Virol 2016; 97:1350-1355. [PMID: 26959376 DOI: 10.1099/jgv.0.000452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Saffold virus (SAFV) is a highly seroprevalent human Cardiovirus discovered recently. No clear association between SAFV infection and human disease has been established. Rare infection cases, however, correlated with neurological symptoms. To gain insight into the pathogenesis potential of the virus, we performed experimental mouse infection with SAFV strains of genotypes 2 and 3 (SAFV-2 and SAFV-3). After intraperitoneal infection, both strains exhibited a typical Cardiovirus tropism. Viral load was most prominent in the pancreas. Heart, spleen, brain and spinal cord were also infected. In IFN-receptor 1 deficient (IFNAR-KO) mice, SAFV-3 caused a severe encephalitis. The virus was detected by immunohistochemistry in many parts of the brain and spinal cord, both in neurons and astrocytes, but astrocyte infection was more extensive. In vitro, SAFV-3 also infected astrocytes better than neurons in mixed primary cultures. Astrocytes were, however, very efficiently protected by IFN-α/β treatment.
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Affiliation(s)
- Frédéric Sorgeloos
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, UK
| | - Cécile Lardinois
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74 Avenue Hippocrate, Brussels B-1200, Belgium
| | - Sophie Jacobs
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74 Avenue Hippocrate, Brussels B-1200, Belgium
| | - Frank J M van Kuppeveld
- Moleculaire Virologie, Universiteit Utrecht, Yalelaan 1 Kamer W.512, 3584 CL Utrecht, The Netherlands
| | - Bernd Kaspers
- Institut für Tierphysiologie, Veterinärstr 13, 80539 München, Germany
| | - Thomas Michiels
- de Duve Institute, Université Catholique de Louvain, VIRO B1.74.07, 74 Avenue Hippocrate, Brussels B-1200, Belgium
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20
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Kotani O, Naeem A, Suzuki T, Iwata-Yoshikawa N, Sato Y, Nakajima N, Hosomi T, Tsukagoshi H, Kozawa K, Hasegawa H, Taguchi F, Shimizu H, Nagata N. Neuropathogenicity of Two Saffold Virus Type 3 Isolates in Mouse Models. PLoS One 2016; 11:e0148184. [PMID: 26828718 PMCID: PMC4734772 DOI: 10.1371/journal.pone.0148184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/14/2016] [Indexed: 12/11/2022] Open
Abstract
Objective Saffold virus (SAFV), a picornavirus, is occasionally detected in children with acute flaccid paralysis, meningitis, and cerebellitis; however, the neuropathogenicity of SAFV remains undetermined. Methods The virulence of two clinical isolates of SAFV type 3 (SAFV-3) obtained from a patient with aseptic meningitis (AM strain) and acute upper respiratory inflammation (UR strain) was analyzed in neonatal and young mice utilizing virological, pathological, and immunological methods. Results The polyproteins of the strains differed in eight amino acids. Both clinical isolates were infective, exhibited neurotropism, and were mildly neurovirulent in neonatal ddY mice. Both strains pathologically infected neural progenitor cells and glial cells, but not large neurons, with the UR strain also infecting epithelial cells. UR infection resulted in longer inflammation in the brain and spinal cord because of demyelination, while the AM strain showed more infectivity in the cerebellum in neonatal ddY mice. Additionally, young BALB/c mice seroconverted following mucosal inoculation with the UR, but not the AM, strain. Conclusions Both SAFV-3 isolates had neurotropism and mild neurovirulence but showed different cell tropisms in both neonatal and young mouse models. This animal model has the potential to recapitulate the potential neuropathogenicity of SAFV-3.
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Affiliation(s)
- Osamu Kotani
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Virology and Viral Infections, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Asif Naeem
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriko Nakajima
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takushi Hosomi
- The Public Health Institute of Kochi Prefecture, Kochi, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Gunma, Japan
| | - Hideki Hasegawa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fumihiro Taguchi
- Department of Virology and Viral Infections, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail:
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21
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Leguia M, Loyola S, Rios J, Juarez D, Guevara C, Silva M, Prieto K, Wiley M, Kasper MR, Palacios G, Bausch DG. Full Genomic Characterization of a Saffold Virus Isolated in Peru. Pathogens 2015; 4:816-25. [PMID: 26610576 PMCID: PMC4693166 DOI: 10.3390/pathogens4040816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/17/2015] [Indexed: 11/16/2022] Open
Abstract
While studying respiratory infections of unknown etiology we detected Saffold virus in an oropharyngeal swab collected from a two-year-old female suffering from diarrhea and respiratory illness. The full viral genome recovered by deep sequencing showed 98% identity to a previously described Saffold strain isolated in Japan. Phylogenetic analysis confirmed the Peruvian Saffold strain belongs to genotype 3 and is most closely related to strains that have circulated in Asia. This is the first documented case report of Saffold virus in Peru and the only complete genomic characterization of a Saffold-3 isolate from the Americas.
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Affiliation(s)
- Mariana Leguia
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Steev Loyola
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Jane Rios
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Diana Juarez
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | | | - Maria Silva
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | - Michael Wiley
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | | | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases (USAMRIID), Frederick, MD 21702, USA.
| | - Daniel G Bausch
- Naval Medical Research Unit No. 6 (NAMRU-6), Callao 2, Peru.
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Tapia G, Bøås H, de Muinck EJ, Cinek O, Stene LC, Torjesen PA, Rasmussen T, Rønningen KS. Saffold Virus, a Human Cardiovirus, and Risk of Persistent Islet Autoantibodies in the Longitudinal Birth Cohort Study MIDIA. PLoS One 2015; 10:e0136849. [PMID: 26317929 PMCID: PMC4552579 DOI: 10.1371/journal.pone.0136849] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/10/2015] [Indexed: 01/27/2023] Open
Abstract
The aim of this study was to describe the frequency and distribution of Saffold virus in longitudinal stool samples from children, and test for association with development of persistent autoantibodies predictive of type 1 diabetes. A cohort of Norwegian children carrying the HLA genotype associated with highest risk of type 1 diabetes (“DR4-DQ8/DR3-DQ2”) was followed with monthly stool samples from 3 to 35 months of age. Blood samples were tested for autoantibodies to insulin, glutamic acid decarboxylase65 and Islet Antigen-2. 2077 stool samples from 27 children with ≥2 repeatedly positive islet autoantibodies (cases), and 53 matched controls were analysed for Saffold virus genomic RNA by semi-quantitative real-time reverse transcriptase PCR. Saffold virus was found in 53 of 2077 (2.6%) samples, with similar proportions between cases (2.5%) and controls (2.6%). The probability of being infected by 3 years of age was 28% (95% CI 0.18–0.40). Viral quantities ranged from <1 to almost 105 copies/μl. Estimated odds ratio between islet autoimmunity and infection episodes prior to seroconversion was 1.98 (95% CI: 0.57–6.91, p = 0.29). Saffold virus had no statistically significant association with islet autoimmunity.
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Affiliation(s)
- German Tapia
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon Bøås
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
- * E-mail:
| | - Eric J. de Muinck
- Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ondrej Cinek
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lars C. Stene
- Department of Chronic Diseases, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Peter A. Torjesen
- Hormone Laboratory, Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Trond Rasmussen
- Department of IT and e-health, Division of Institute Resources, Norwegian Institute of Public Health, Oslo, Norway
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23
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Linsuwanon P, Poovorawan Y, Li L, Deng X, Vongpunsawad S, Delwart E. The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses. PLoS One 2015; 10:e0135573. [PMID: 26288145 PMCID: PMC4545796 DOI: 10.1371/journal.pone.0135573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 07/24/2015] [Indexed: 01/21/2023] Open
Abstract
Hand, foot, and mouth disease (HFMD) affects infant and young children. A viral metagenomic approach was used to identify the eukaryotic viruses in fecal samples from 29 Thai children with clinical diagnosis of HFMD collected during the 2012 outbreak. These children had previously tested negative by PCR for enterovirus 71 and coxsackievirus A16 and A6. Deep sequencing revealed nine virus families: Picornaviridae, Astroviridae, Parvoviridae, Caliciviridae, Paramyxoviridae, Adenoviridae, Reoviridae, Picobirnaviridae, and Polyomaviridae. The highest number of viral sequences belonged to human rhinovirus C, astrovirus-MLB2, and coxsackievirus A21. Our study provides an overview of virus community and highlights a broad diversity of viruses found in feces from children with HFMD.
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Affiliation(s)
- Piyada Linsuwanon
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
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24
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Aoki Y, Matoba Y, Tanaka S, Yahagi K, Hirokawa C, Tamura T, Itagaki T, Matsuzaki Y, Mizuta K. Isolation of Saffold Virus Type 2 from Children with Acute Respiratory Infections by Using the RD-18S-Niigata Cell Line. Jpn J Infect Dis 2015; 68:438-41. [DOI: 10.7883/yoken.jjid.2015.093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Yoko Aoki
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Yohei Matoba
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Shizuka Tanaka
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Kazue Yahagi
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
| | - Chika Hirokawa
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Science
| | - Tsutomu Tamura
- Department of Virology, Niigata Prefectural Institute of Public Health and Environmental Science
| | | | - Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine
| | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health
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DA virus mutant H101 has altered CNS pathogenesis and causes immunosuppression. J Neuroimmunol 2014; 277:118-26. [PMID: 25468274 DOI: 10.1016/j.jneuroim.2014.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/21/2022]
Abstract
Viruses use various mechanisms to evade clearance by the host. Investigating how a few changes in the genome of a non-lethal virus can lead to altered disease, from survivable to immunosuppression/death, would provide valuable information into viral pathogenesis. The Daniels strain of Theiler's murine encephalomyelitis virus causes an asymptomatic infection or acute encephalitis followed by viral clearance. A mutant, H101, carries several alterations in the viral genome. H101 infection causes profound immunosuppression and death. Thus, a virus that is normally cleared by its natural host can become lethal due to just a few changes in the viral genome.
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