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Mogotsi MT, Ogunbayo AE, Bester PA, O'Neill HG, Nyaga MM. Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics. Virus Res 2024; 346:199403. [PMID: 38776984 PMCID: PMC11169482 DOI: 10.1016/j.virusres.2024.199403] [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: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
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Affiliation(s)
- Milton Tshidiso Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Ayodeji Emmanuel Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Phillip Armand Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hester Gertruida O'Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
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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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3
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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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David EDS, Fonseca EDC, de Carvalho JFN, Marinho RDSS, Duro RLS, Komninakis SV, Souto RNP. Metagenomics applied to the detection of diarrhea viruses in humans: Systematic Review. Acta Trop 2022; 227:106287. [PMID: 34929178 DOI: 10.1016/j.actatropica.2021.106287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
Abstract
To analyze the application of the metagenomics method in the identification of viral infectious agents that lead to diarrhea outbreaks. This study is a systematic review, which looked for publications on the following platforms: PubMed, Scientific Electronic Library Online (SciELO), LILACS and CAPES periodicals, conducted according to the PRISMA methodology, investigating in the literary composition studies related to metagenomics applied in the identification of viral infectious agents, which lead to diarrhea in humans. 1198 publications were identified. Of these, after analyzes and exclusions at different stages, 18 studies remained, which directly corresponded to the theme. Diarrhea was presented as a universal health concern. Despite the emergence of vaccines, cases of diarrhea remain persistent in poor populations. In this context, metagenomics emerges as a primary tool in detecting enteric viruses and identifying new viruses, revolutionizing health diagnoses, knowledge of viral diversity, and health surveillance, contributing to the correct etiology of infectious agents that would never be identified by conventional methods. The 18 articles studied point to advances in research in viral metagenomics of diarrheal samples, contributing to the discernment of diarrhea outbreaks, and properly associating with their etiological agents, they are presented in an innovative way for studies on the understanding of viral diversity.
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Vizzi E, Fernández R, Angulo LA, Blanco R, Pérez C. HUMAN COSAVIRUS INFECTION IN HIV SUBJECTS WITH DIARRHOEA: PERSISTENT DETECTION ASSOCIATED WITH FATAL OUTCOME. J Clin Virol 2021; 139:104825. [PMID: 33940330 DOI: 10.1016/j.jcv.2021.104825] [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: 12/09/2020] [Revised: 03/18/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Human cosavirus (HCoSV) is a new member of the Picornaviridae family, geographically widespread among humans. It has been suggested as a causative agent of acute gastroenteritis, but its pathogenicity is not currently certain. In HIV-infected subjects, diarrhoea is one of the most frequent gastrointestinal manifestations, whose aetiology remains often unexplained. OBJECTIVES To identify the cause of viral diarrhoea among HIV infected patients by molecular assays. STUDY DESIGN A total of 143 stool samples from HIV subjects with and without diarrhoea, were screened for conventional enteric viruses (rotavirus, adenovirus, norovirus and astrovirus) by molecular assays. The presence of HCoSV genome was investigated by nested RT-PCR for the 5'UTR region. Positive samples were further characterized by sequencing and phylogenetic analysis. RESULTS Enteric viruses were more frequently found in diarrhoea cases (9/82) than controls (0/61) (p=0.007). HCoSV was detected in five (3.5%) of the subjects affected by diarrhoea. Phylogenetic analysis revealed the predominance of the HCoSV species D. One patient suffered a persistent cosavirus infection with a same strain and after eight months he had a fatal outcome. No other pathogens could be detected. CONCLUSIONS The results suggest a role of non-conventional enteric viruses, as HCoSV, as a potential opportunistic agent causing persistent infection and deterioration of the clinical conditions in HIV-infected patients. Screening procedures and monitoring including such viruses would be helpful in the clinical management of such patients.
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Affiliation(s)
- Esmeralda Vizzi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC). Carretera Panamericana Km 11, Caracas 1020-A, Edo. Miranda, Venezuela.
| | - Rixio Fernández
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC). Carretera Panamericana Km 11, Caracas 1020-A, Edo. Miranda, Venezuela
| | - Luis A Angulo
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC). Carretera Panamericana Km 11, Caracas 1020-A, Edo. Miranda, Venezuela; Present address: Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán. Departamento de Infectología. Laboratorio Virología Molecular. Mexico, D.F., Mexico
| | - Ruth Blanco
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC). Carretera Panamericana Km 11, Caracas 1020-A, Edo. Miranda, Venezuela; Present address: Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC. Carretera Panamericana Km 11, Caracas 1020-A, Edo. Miranda, Venezuela
| | - Carlos Pérez
- Servicio de Infectología. Hospital General del Oeste "Dr. José Gregorio Hernández". Catia, Sector Los Magallanes de Catia. Caracas, Venezuela
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6
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Daprà V, Galliano I, Montanari P, Zaniol E, Calvi C, Alliaudi C, Bergallo M. Bufavirus, Cosavirus, and Salivirus in Diarrheal Italian Infants. Intervirology 2021; 64:165-168. [PMID: 33784689 DOI: 10.1159/000514384] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 01/13/2021] [Indexed: 11/19/2022] Open
Abstract
Three newly discovered viruses have been recently described in diarrheal patients: Cosavirus (CosV) and Salivirus (SalV), 2 picornaviruses, and bufavirus (BuV), a parvovirus. The detection rate and the role of these viruses remain to be established in acute gastroenteritis (AGE) in diarrheal Italian infants. From November 2016 to November 2017, stool samples were collected from 160 children <5 years old suffering from AGE and attending the Children's Hospital in Turin, Italy. During the study period, 1 (0.5%) sample was positive for 1 of the 3 investigated viruses: 0 (0%) CosV, 1 (0.5%) SalV, and 0 (0%) BuV, whereas 42 (26.0%) children were infected with rotavirus and 2 (1%) with adenovirus. No mixed infections involving the 3 viruses were found. Although these viruses are suspected to be responsible for AGE in children, our data showed that this association was uncertain. Therefore, further studies with large cohorts of healthy and diarrheal children will be needed to evaluate their clinical role in AGE.
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Affiliation(s)
- Valentina Daprà
- Department of Public Health and Pediatric Sciences, Pediatrics Laboratory, University of Turin, Medical School, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Pediatrics Laboratory, University of Turin, Medical School, Turin, Italy.,Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Pediatrics Laboratory, University of Turin, Medical School, Turin, Italy.,Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Elena Zaniol
- Department of Public Health and Pediatric Sciences, Pediatrics Laboratory, University of Turin, Medical School, Turin, Italy.,Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, Pediatrics Laboratory, University of Turin, Medical School, Turin, Italy.,Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Carla Alliaudi
- Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Pediatrics Laboratory, University of Turin, Medical School, Turin, Italy.,Department of Pediatrics, Infectious Diseases Unit, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
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7
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Schneider J, Engler M, Hofmann J, Selinka HC, Jones TC, Drosten C, Diedrich S, Corman VM, Böttcher S. Molecular detection of cosaviruses in a patient with acute flaccid paralysis and in sewage samples in Germany. Virus Res 2021; 297:198285. [PMID: 33548413 DOI: 10.1016/j.virusres.2020.198285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/02/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
Cosaviruses (CoSV) were first identified in stool samples collected from non-polio acute flaccid paralysis (AFP) cases and their healthy contacts in Pakistan in 2003. The clinical importance of CoSV remains unclear as data on epidemiology are scarce and no routine diagnostic testing is done. In this study, we characterized human CoSV (HCoSV) in a child with non-polio AFP and in sewage samples collected in Berlin, Germany. Using unbiased high-throughput sequencing and specific PCR, we characterized a HCoSV-D in stool samples of a three-year-old child hospitalized in Germany with non-polio AFP and travel history to Pakistan. The shedding pattern and absence of other relevant pathogens suggests that HCoSV-D may have been involved in the genesis of AFP. The HCoSV-RNA concentration was high, with 2.57 × 106 copies per mL fecal/suspension, decreasing in follow-up samples. To investigate the possibility of local circulation of HCoSV, we screened Berlin sewage samples collected between 2013 and 2018. Molecular testing of sewage samples has shown the presence of CoSV in several parts of the world, but until now not in Germany. Of our sewage samples, 54.3 % were positive for CoSV, with up to three viral species identified in samples. Phylogenetically, the German sequences clustered intermixed with sequences obtained globally. Together, these findings emphasize the need for further clinical, epidemiological, environmental, pathogenicity and phylogenetic studies of HCoSV.
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Affiliation(s)
- J Schneider
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - M Engler
- Department of Paediatrics, Sana Klinikum Offenbach GmbH, Starkenburgring 66, 63069, Offenbach am Main, Germany
| | - J Hofmann
- Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - H C Selinka
- German Environment Agency, Microbiological Risks, Corrensplatz 1, 14195, Berlin, Germany
| | - T C Jones
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - C Drosten
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany
| | - S Diedrich
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany
| | - V M Corman
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany.
| | - S Böttcher
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany.
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Lobo PS, Cardoso JF, Barata RR, Lemos PS, Guerra SFS, Soares LS, Nunes MRT, Mascarenhas JDP. Near-complete genome of cosavirus A from a child hospitalized with acute gastroenteritis, Brazil. INFECTION GENETICS AND EVOLUTION 2020; 85:104555. [PMID: 32931954 DOI: 10.1016/j.meegid.2020.104555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/06/2020] [Accepted: 09/09/2020] [Indexed: 11/25/2022]
Abstract
Acute gastroenteritis (AG) is responsible for 525,000 deaths worldwide in children under-5-years and is caused by the Human Cosavirus (HCoSV; family Picornaviridae, Genus Cosavirus). Although its health importance, a significant percentage of diarrhea cases (≈ 40 %) still of unknown etiology. In Brazil, few studies have reported HCoSV-A sequences analyzing partial 5' UTR. This study characterized the first near-complete genome of a Cosavirus A (strain AM326) from a child hospitalized with AG in Amazonas state, Northern Brazil. High throughput sequencing (HTS) was performed using the HiSeq™ 2500 platform (Illumina) in one fecal specimen collected from the Surveillance of Rotavirus Network of the Evandro Chagas Institute collected in 2017. Sequence reads were assembled by the De Novo approach using three distinct algorithmic (IDBA-UD, Spades, and MegaHit). The final contig was recovered from the HCoSV-AM326 sample revealing 7,735 nt in length (SRA number SRR12535029; GenBank MT023104) and the genetic characterization, as well as phylogenetic analysis demonstrated a new variant strain from Brazil, highlighting the association of HCoSV-A as a possible causative agent of AG. This finding demonstrates the importance of the metagenomic approach to elucidate cases of diarrhea without a defined etiology, as well as providing a better understanding about the virus genetics, evolution and epidemiology.
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Affiliation(s)
- Patrícia S Lobo
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Jedson F Cardoso
- Postgraduate Program in Virology, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Rafael R Barata
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Poliana S Lemos
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Sylvia F S Guerra
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Luana S Soares
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Márcio R T Nunes
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil
| | - Joana D P Mascarenhas
- Evandro Chagas Institute, Health Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Pará, Brazil.
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Rezig D, Lamari A, Touzi H, Meddeb Z, Triki H. Typing of Human Cosaviruses by sequencing of full VP1: Update on global genetic diversity and identification of possible new genotypes circulating in Tunisia, North Africa. INFECTION GENETICS AND EVOLUTION 2019; 78:104115. [PMID: 31715246 DOI: 10.1016/j.meegid.2019.104115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 10/25/2022]
Abstract
Human Cosaviruses (HCoSVs) are relatively newly characterized picornaviruses; they have been described in non-polio acute flaccid paralysis, diarrheal patients, and healthy individuals. Previous studies showed HCoSV circulation in Tunisia and only six genotypes circulating in the country were reported. In the present study, we sequenced 27 complete VP1 genomic region from HCoSV isolates in human feces from healthy individuals and patients with acute flaccid paralysis in Tunisia. Most of the Tunisian sequences belong to species A (78%, 21 out of 27). Three sequences belong to species B, two to species E and one sequence to species D. The Tunisian sequences belonged to genotype A6, A7, A8, A10, A1, A17 and E2. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we also identified 4 new HCoSV genotypes named A25, B2, B3 and D6. Our study updates the genetic classification of HCoSVs, proposes new genotypes within species A, B and D and contributes to a better knowledge of the HCoSV circulation throughout the world.
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Affiliation(s)
- Dorra Rezig
- University of Tunis El Manar, Pasteur Institute of Tunis, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, 13 Place Pasteur, 1002- Le Belvédère BP74, Tunis, Tunisia.
| | - Asma Lamari
- University of Tunis El Manar, Pasteur Institute of Tunis, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, 13 Place Pasteur, 1002- Le Belvédère BP74, Tunis, Tunisia; University of Tunis El Manar, Faculty of Sciences, BP94 Cité Rommana, 1068 Tunis, Tunisia
| | - Henda Touzi
- University of Tunis El Manar, Pasteur Institute of Tunis, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, 13 Place Pasteur, 1002- Le Belvédère BP74, Tunis, Tunisia
| | - Zina Meddeb
- University of Tunis El Manar, Pasteur Institute of Tunis, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, 13 Place Pasteur, 1002- Le Belvédère BP74, Tunis, Tunisia
| | - Henda Triki
- University of Tunis El Manar, Pasteur Institute of Tunis, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, 13 Place Pasteur, 1002- Le Belvédère BP74, Tunis, Tunisia
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10
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Okitsu S, Khamrin P, Takanashi S, Thongprachum A, Hoque SA, Takeuchi H, Khan MA, Hasan SMT, Iwata T, Shimizu H, Jimba M, Hayakawa S, Maneekarn N, Ushijima H. Molecular detection of enteric viruses in the stool samples of children without diarrhea in Bangladesh. INFECTION GENETICS AND EVOLUTION 2019; 77:104055. [PMID: 31629889 DOI: 10.1016/j.meegid.2019.104055] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/25/2019] [Accepted: 09/29/2019] [Indexed: 12/14/2022]
Abstract
A number of molecular epidemiological studies reported the detection of enteric viruses in asymptomatic children. The role of these viruses in an asymptomatic infection remains unclear. This study investigated the enteric viruses in the stool samples collected from children without diarrhea. Stool samples were collected during June to October 2016, from 227 children who lived in Matlab, Bangladesh. Seventeen enteric viruses, including rotavirus A, B, and C (RVA, RVB, and RVC), norovirus GI (NoV GI), norovirus GII (NoV GII), sapovirus (SaV), adenovirus (AdV), human astrovirus (HAstV), Aichivirus (AiV), human parechovirus (HPeV), enterovirus (EV), human bocavirus (HBoV), Saffold virus (SAFV), human cosavirus (HCoSV), bufavirus (BufV), salivirus (SalV), and rosavirus (RoV), were investigated by RT-PCR method. One hundred and eighty-two (80.2%; 182/227) samples were positive for some of these viruses, and 19.8% (45/227) were negative. Among the positive samples, 46.7% (85/182) were a single infection, and 53.3% (97/182) were coinfection with multiple viruses. The HCoSV was the most prevalent virus (41.4%), followed by EV (32.2%), NoV GII (25.6%), HPeV (8.8%), RVA (6.2%), AdV (5.7%), AiV (5.3%), SAFV (4.4%), and SaV (2.6%). Each of NoV GI, HAstV, HBoV, and BufV was detected at 0.4%. However, RVB, RVC, SalV, and RoV were not detected in this study. Phylogenetic analysis showed that diverse HCoSV species and genotypes were circulating in Bangladesh, and four strains of species A are proposed to be new genotypes. The data indicated that non-diarrheal Bangladeshi children were asymptomatically infected with wide varieties of enteric viruses.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Japan; Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan.
| | - 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
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan
| | | | - Sheikh Ariful Hoque
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Haruko Takeuchi
- Department of Community and Global Health, Graduate School of Medicine, The University of Tokyo, Japan
| | - Md Alfazal Khan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - S M Tafsir Hasan
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Japan
| | - Masamine Jimba
- Department of Community and Global Health, Graduate School of Medicine, The University of Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 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
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Japan; Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Japan
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11
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Lamari A, Triki H, Driss N, Touzi H, Meddeb Z, Ben Yahia A, Barbouche MR, Rezig D. Iterative Excretion of Human Cosaviruses from Different Genotypes Associated with Combined Immunodeficiency Disorder. Intervirology 2019; 61:247-254. [PMID: 30726837 DOI: 10.1159/000495182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Human cosaviruses (HCoSVs) are newly discovered enteric viruses in the Picornaviridae family. They have been described in non-polio acute flaccid paralysis, diarrheal patients, and healthy individuals. They remain rarely documented in immunodeficient patients. OBJECTIVES This study reports iterative excretion of HCoSVs in a patient with major histocompatibility complex (MHC) class II combined immunodeficiency, a relatively common primary immunodeficiency in consanguineous settings. METHODS A total of 35 samples were collected from a patient followed for oral polio vaccine strains detection in stool samples during a 57-month period. Detection of HCoSVs in stools was performed by nested RT-PCR in the 5' noncoding region. The genotype identification and screening for recombinant strains was performed by sequencing in the VP1 and 3D genomic regions followed by phylogenetic analysis. RESULTS The patient was infected with HCoSVs twice at a 3-year interval. The excreted viruses belonged to 2 different genotypes with 2 probable recombinant viruses. During HCoSV infections, the patient was also excreting Sabin-related polioviruses. CONCLUSIONS This study describes excretion kinetics and genetic characteristics of HCoSVs in a patient with combined immunodeficiency due to MHC class II expression defect. The patient did not have concomitant symptoms related to the HCoSV infection.
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Affiliation(s)
- Asma Lamari
- Faculty of Sciences, University of Tunis El Manar, Tunis, Tunisia.,WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nadia Driss
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ahlem Ben Yahia
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mohamed-Ridha Barbouche
- Laboratory of Immunology, Pasteur Institute of Tunis and Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - Dorra Rezig
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia,
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12
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Bonanno Ferraro G, Mancini P, Divizia M, Suffredini E, Della Libera S, Iaconelli M, La Rosa G. Occurrence and Genetic Diversity of Human Cosavirus in Sewage in Italy. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:386-390. [PMID: 30167976 DOI: 10.1007/s12560-018-9356-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 08/27/2018] [Indexed: 06/08/2023]
Abstract
Human Cosavirus (HCoSV) is a newly discovered virus whose role in human enteric diseases is still unknown. In Italy, the prevalence and genetic diversity of HCoSV are unexplored. One hundred forty-one raw sewage samples collected throughout Italy were screened for HCoSV by RT-nested PCR. HCoSV was detected in 25.5% of samples. Species A, C, and D, and a potentially new species were detected. Our results show a significant circulation and heterogeneity of HCoSV in Italy.
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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
| | - M Divizia
- Department Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - S Della Libera
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and 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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13
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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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14
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Yu JM, Ao YY, Li LL, Duan ZJ. Identification of a novel cosavirus species in faeces of children and its relationship with acute gastroenteritis in China. Clin Microbiol Infect 2017; 23:550-554. [DOI: 10.1016/j.cmi.2017.02.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/08/2017] [Accepted: 02/14/2017] [Indexed: 11/26/2022]
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15
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Yang Y, Ju A, Xu X, Cao X, Tao Y. A novel type of cosavirus from children with nonpolio acute flaccid paralysis. Virol J 2016; 13:169. [PMID: 27729038 PMCID: PMC5059993 DOI: 10.1186/s12985-016-0630-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/03/2016] [Indexed: 11/10/2022] Open
Abstract
Human cosavirus (HCoSV) is a genus recently identified in the family Picornaviridae, which contains important pathogens to human health. Here, a novel type of HCoSV strain, cosavirus-zj-1 (GenBank no. KX545380), was identified in the fecal sample of a child with nonpolio acute flaccid paralysis (AFP) in China. Phylogenetic and sequence analyses suggested that this virus strain belonged to a new genotype in HCoSV B species. Our data show that surveillance of HCoSV is necessary for detecting viral agents in children with AFP, despite being the low detection rate.
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Affiliation(s)
- Yan Yang
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China.
| | - Aiping Ju
- Department of Clinical Laboratory, Women and Children's Hospital of Huadu District, Guangzhou, Guangdong, 510800, China
| | - Xiaofen Xu
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China
| | - Xinyu Cao
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China
| | - Ying Tao
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China
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16
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Ayouni S, Estienney M, Hammami S, Neji Guediche M, Pothier P, Aouni M, Belliot G, de Rougemont A. Cosavirus, Salivirus and Bufavirus in Diarrheal Tunisian Infants. PLoS One 2016; 11:e0162255. [PMID: 27631733 PMCID: PMC5025138 DOI: 10.1371/journal.pone.0162255] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/21/2016] [Indexed: 11/17/2022] Open
Abstract
Three newly discovered viruses have been recently described in diarrheal patients: Cosavirus (CosV) and Salivirus (SalV), two picornaviruses, and Bufavirus (BuV), a parvovirus. The detection rate and the role of these viruses remain to be established in acute gastroenteritis (AGE) in diarrheal Tunisian infants. From October 2010 through March 2012, stool samples were collected from 203 children <5 years-old suffering from AGE and attending the Children's Hospital in Monastir, Tunisia. All samples were screened for CosV, SalV and BuV as well as for norovirus (NoV) and group A rotavirus (RVA) by molecular biology. Positive samples for the three screened viruses were also tested for astrovirus, sapovirus, adenovirus, and Aichi virus, then genotyped when technically feasible. During the study period, 11 (5.4%) samples were positive for one of the three investigated viruses: 2 (1.0%) CosV-A10, 7 (3.5%) SalV-A1 and 2 (1.0%) BuV-1, whereas 71 (35.0%) children were infected with NoV and 50 (24.6%) with RVA. No mixed infections involving the three viruses were found, but multiple infections with up to 4 classic enteric viruses were found in all cases. Although these viruses are suspected to be responsible for AGE in children, our data showed that this association was uncertain since all infected children also presented infections with several enteric viruses, suggesting here potential water-borne transmission. Therefore, further studies with large cohorts of healthy and diarrheal children will be needed to evaluate their clinical role in AGE.
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Affiliation(s)
- Siwar Ayouni
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,Faculté de Pharmacie, Université de Monastir, Monastir, Tunisie
| | - Marie Estienney
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France
| | - Sabeur Hammami
- Service de Pédiatrie, Hôpital Universitaire Fattouma-Bourguiba, Monastir, Tunisie.,Faculté de Médicine, Université de Monastir, Monastir, Tunisie
| | - Mohamed Neji Guediche
- Service de Pédiatrie, Hôpital Universitaire Fattouma-Bourguiba, Monastir, Tunisie.,Faculté de Médicine, Université de Monastir, Monastir, Tunisie
| | - Pierre Pothier
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
| | - Mahjoub Aouni
- Faculté de Pharmacie, Université de Monastir, Monastir, Tunisie
| | - Gael Belliot
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
| | - Alexis de Rougemont
- Centre National de Référence des virus entériques, Laboratoire de virologie-sérologie, Pôle Technique de Biologie, CHU de Dijon, Dijon, France.,UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, Dijon, France
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17
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Oude Munnink BB, van der Hoek L. Viruses Causing Gastroenteritis: The Known, The New and Those Beyond. Viruses 2016; 8:E42. [PMID: 26867198 PMCID: PMC4776197 DOI: 10.3390/v8020042] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/15/2016] [Accepted: 01/23/2016] [Indexed: 02/07/2023] Open
Abstract
The list of recently discovered gastrointestinal viruses is expanding rapidly. Whether these agents are actually involved in a disease such as diarrhea is the essential question, yet difficult to answer. In this review a summary of all viruses found in diarrhea is presented, together with the current knowledge about their connection to disease.
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Affiliation(s)
- Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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18
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19
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Okitsu S, Khamrin P, Hanaoka N, Thongprachum A, Takanashi S, Fujimoto T, Mizuguchi M, Shimizu H, Hayakawa S, Maneekarn N, Ushijima H. Cosavirus (family Picornaviridae) in pigs in Thailand and Japan. Arch Virol 2015; 161:159-63. [PMID: 26467926 DOI: 10.1007/s00705-015-2637-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/04/2015] [Indexed: 11/24/2022]
Abstract
Cosavirus is a recently established genus in the family Picornaviridae. The present study investigated the prevalence and genetic diversity of cosaviruses in stool samples collected from piglets and pigs with and without diarrhea in Thailand and Japan. It was observed that the cosavirus-positive rate in Thailand was higher than in Japan (55.4 % vs. 18.9 %). Phylogenetic analysis of a portion of the 5' untranslated region showed that porcine cosavirus strains clustered together in the same branch with members of the species Cosavirus A. These strains showed 97.0 to 100 % nucleotide sequence identity to each other. The virus concentration of cosavirus was very low compared with that detected in a infant with diarrhea. These results demonstrated that cosaviruses were circulating in the swine populations of both countries during the study term; however, it remains unclear whether the virus causes diarrhea in piglets and pigs.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchi-kamicho, Itabashi, Tokyo, 173-8610, Japan. .,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Nozomu Hanaoka
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aksara Thongprachum
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsuguto Fujimoto
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masashi Mizuguchi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Shimizu
- Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchi-kamicho, Itabashi, Tokyo, 173-8610, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1, Oyaguchi-kamicho, Itabashi, Tokyo, 173-8610, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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20
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Rezig D, Ben Farhat E, Touzi H, Meddeb Z, Ben Salah A, Triki H. Prevalence of human cosaviruses in Tunisia, North Africa. J Med Virol 2015; 87:940-3. [PMID: 25649285 DOI: 10.1002/jmv.24076] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2014] [Indexed: 12/22/2022]
Abstract
A new picornavirus, named human Cosavirus (HCoSV) was isolated recently from stools of children with acute flaccid paralysis (AFP) and healthy children in Pakistan and Afghanistan. Since then, it was also isolated from patients from other countries. Five species are presently identified forming a new genus in the Picornaviridae family. This study reports the detection of HCoSV in stool specimens collected as part of the National Poliovirus surveillance Program in Tunisia, between 2011 and 2012, from patients with AFP and healthy individuals among their contacts. One hundred and ninety four stool samples were investigated by RT-PCR in the 5' non-coding region of the genome. A total of 64 specimens (33%) tested positive for HCoSV. HCoSV positive specimens were found in 36 cases with neurological syndromes and 28 of their healthy contacts. The highest rate of HCoSV infection (62.5%) occurred in children younger than 6 years of age. The sampling date of stool specimens suggested that HCoSV infection occurred regularly over time. Also, the sampling origin of stool specimen showed that HCoSV infection was detected in almost all the governorates of Tunisia from the North to the South of the country. This study is the first report of HCoSV prevalence in the North African region. It contributes to a better knowledge on the geographic distribution and the epidemiology of these viruses.
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Affiliation(s)
- Dorra Rezig
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles, Institut Pasteur de Tunis, Tunis-Belvédère, Tunisia
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21
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Rezig D, Touzi H, Meddeb Z, Triki H. Cytopathic effect of Human cosavirus (HCoSV) on primary cell cultures of human embryonic lung MRC5. J Virol Methods 2014; 207:12-5. [DOI: 10.1016/j.jviromet.2014.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 04/07/2014] [Accepted: 06/06/2014] [Indexed: 11/30/2022]
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22
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Detection and molecular characterization of human cosavirus in a pediatric patient with acute gastroenteritis, Japan. INFECTION GENETICS AND EVOLUTION 2014; 28:125-9. [PMID: 25251675 DOI: 10.1016/j.meegid.2014.09.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/13/2014] [Accepted: 09/15/2014] [Indexed: 12/17/2022]
Abstract
Human cosavirus (HCoSV) is a genus recently identified in the family Picornaviridae, which includes important pathogens in human health. The pathogenicity of HCoSV remains unclear. This study reports that an HCoSV strain, 10928/2012/JPN, was identified and collected from the stool sample of a child with acute gastroenteritis in Japan, with the detection rate of 0.16%. The patient was not co-infected with other common diarrhea-causal viruses, suggesting HCoSV as a causal pathogen in this pediatric patient. Phylogenetic and sequence analyses exhibited that the virus strain was classified as a new genotype in HCoSV A species, and this study is first to detect HCoSV in a clinical specimen collected in Japan. These results showed that surveillance of HCoSV is important for detecting viral agents in children with diarrhea, despite being the low detection rate.
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23
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Detection and genetic characterization of cosavirus in a pediatric patient with diarrhea. Arch Virol 2014; 159:2485-9. [DOI: 10.1007/s00705-014-2091-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/13/2014] [Indexed: 10/25/2022]
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24
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Campanini G, Rovida F, Meloni F, Cascina A, Ciccocioppo R, Piralla A, Baldanti F. Persistent human cosavirus infection in lung transplant recipient, Italy. Emerg Infect Dis 2014; 19:1667-9. [PMID: 24047954 PMCID: PMC3810744 DOI: 10.3201/eid1910.130352] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Human cosavirus is a novel picornavirus recently identified in feces from children in southern Asia. We report infection with human cosavirus in a patient in the Mediterranean area. The patient was an adult double lung transplant recipient who had chronic diarrhea associated with persistent infection with human cosavirus.
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25
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Haramoto E, Otagiri M. Occurrence of Human Cosavirus in Wastewater and River Water in Japan. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:62-66. [PMID: 23943064 DOI: 10.1007/s12560-013-9120-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 07/29/2013] [Indexed: 06/02/2023]
Abstract
Human cosavirus was detected using reverse transcription-quantitative polymerase chain reaction in 71 % of raw sewage and 29 % each of secondary-treated sewage and river water samples in the Kofu Basin, Japan. The highest concentration was 2.80 × 10(6) copies/l. Nucleotide sequence analysis revealed multiple genotypes of the virus in wastewater.
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Affiliation(s)
- Eiji Haramoto
- International Research Center for River Basin Environment, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan.
| | - Mikie Otagiri
- International Research Center for River Basin Environment, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan
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26
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Popgeorgiev N, Temmam S, Raoult D, Desnues C. Describing the silent human virome with an emphasis on giant viruses. Intervirology 2013; 56:395-412. [PMID: 24157886 DOI: 10.1159/000354561] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions. Despite these studies, the description of the presumably healthy viral flora, i.e. the normal human virome, is still in its infancy regarding viral composition and dynamics. This review summarizes our current knowledge of the human virome under non-pathological conditions.
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Affiliation(s)
- Nikolay Popgeorgiev
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France
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Maan HS, Chowdhary R, Shakya AK, Dhole TN. Genetic diversity of cosaviruses in nonpolio acute flaccid paralysis cases of undefined etiology, Northern India, 2010–2011. J Clin Virol 2013; 58:183-7. [DOI: 10.1016/j.jcv.2013.04.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/20/2013] [Accepted: 04/27/2013] [Indexed: 11/26/2022]
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Xie G, Yu J, Duan Z. New strategy for virus discovery: viruses identified in human feces in the last decade. SCIENCE CHINA-LIFE SCIENCES 2013; 56:688-96. [PMID: 23917840 PMCID: PMC7089042 DOI: 10.1007/s11427-013-4516-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/16/2013] [Indexed: 02/08/2023]
Abstract
Emerging and re-emerging viruses continue to surface all over the world. Some of these viruses have the potential for rapid and global spread with high morbidity and mortality, such as the SARS coronavirus outbreak. It is extremely urgent and important to identify a novel virus near-instantaneously to develop an active preventive and/or control strategy. As a culture-independent approach, viral metagenomics has been widely used to investigate highly divergent and completely new viruses in humans, animals, and even environmental samples in the past decade. A new model of Koch’s postulates, named the metagenomic Koch’s postulates, has provided guidance for the study of the pathogenicity of novel viruses. This review explains the viral metagenomics strategy for virus discovery and describes viruses discovered in human feces in the past 10 years using this approach. This review also addresses issues related to the metagenomic Koch’s postulates and the challenges for virus discovery in the future.
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Affiliation(s)
- GuangCheng Xie
- National Institute of Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Tapparel C, Siegrist F, Petty TJ, Kaiser L. Picornavirus and enterovirus diversity with associated human diseases. INFECTION GENETICS AND EVOLUTION 2012. [PMID: 23201849 DOI: 10.1016/j.meegid.2012.10.016] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Members of the Picornaviridae family are non-enveloped, positive-stranded RNA viruses with a 30nm icosahedral capsid. This virus family exhibits a considerable amount of genetic variability driven both by mutation and recombination. Recently, three previously unknown human picornaviruses, namely the human Saffold cardiovirus, cosavirus and salivirus, have been identified in stools or respiratory samples from subjects presenting symptoms ranging from gastroenteritis to acute flaccid paralysis. However, these viruses were also frequently detected in asymptomatic subjects and their clinical relevance remains to be elucidated. The Enterovirus genus is a prototype example of the Picornaviridae heterogeneity at both genetic and phenotypic levels. This genus is divided into 10 species, seven of which contain human viruses, including three Rhinovirus species. Both human rhino- and enteroviruses are also characterized by high levels of genetic variability, as exemplified by the existence of over 250 different serotypes and the recent discovery of new enterovirus genotypes and the Rhinovirus C species. Despite their common genomic features, rhinoviruses are restricted to the respiratory tract, whereas the vast majority of enteroviruses infect the gastrointestinal tract and can spread to other organs, such as the heart or the central nervous system. Understanding the genetic determinants of such phenotypic diversity is an important challenge and a field for future investigation. Better characterization of these ubiquitous human pathogens may help to develop vaccines or antiviral treatments and to monitor the emergence of new strains.
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Affiliation(s)
- Caroline Tapparel
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
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Stöcker A, Souza BFDCD, Ribeiro TCM, Netto EM, Araujo LO, Corrêa JI, Almeida PS, de Mattos AP, Ribeiro HDC, Pedral-Sampaio DB, Drosten C, Drexler JF. Cosavirus infection in persons with and without gastroenteritis, Brazil. Emerg Infect Dis 2012; 18:656-9. [PMID: 22469070 PMCID: PMC3309695 DOI: 10.3201/eid1804.111415] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
To determine possible cosavirus association with clinical disease, we used real-time reverse transcription PCR to test children and HIV-positive adults in Brazil with and without gastroenteritis. Thirteen (3.6%) of 359 children with gastroenteritis tested positive, as did 69 (33.8%) of 204 controls. Low prevalence, frequent viral co-infections, and low fecal cosavirus RNA concentrations argue against human pathogenicity.
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Abstract
During a study of the fecal microbiomes from two healthy piglets using high-throughput sequencing (HTS), we identified a viral genome containing an open reading frame encoding a predicted polyprotein of 2,133 amino acids. This novel viral genome displayed the typical organization of picornaviruses, containing three structural proteins (VP0, VP3, and VP1), followed by seven nonstructural proteins (2A, 2B, 2C, 3A, 3B, 3C(pro), and 3D(pol)). Given its particular relationship with Parechovirus, we propose to name it "Pasivirus" for Parecho sister clade virus, with "Swine pasivirus 1" (SPaV1) as the type species. Fecal samples collected at an industrial farm from healthy sows and piglets from the same herd (25 and 75, respectively) with ages ranging from 4 to 28 weeks were analyzed for the presence of SPaV1 by one-step reverse transcription (RT)-PCR targeting a 3D region of 151 bp. SPaV1 was detected in fecal samples from 51/75 healthy piglets (68% of the animals) and in none of the 25 fecal samples from healthy sows, indicating that SPaV1 circulates through enteric infection of healthy piglets. We propose that SPaV1 represents the first member of a novel Picornaviridae genus related to parechoviruses.
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Kapusinszky B, Phan TG, Kapoor A, Delwart E. Genetic diversity of the genus Cosavirus in the family Picornaviridae: a new species, recombination, and 26 new genotypes. PLoS One 2012; 7:e36685. [PMID: 22615791 PMCID: PMC3353919 DOI: 10.1371/journal.pone.0036685] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/11/2012] [Indexed: 11/24/2022] Open
Abstract
The proposed viral genus human Cosavirus (HCoSV) consists of diverse picornaviruses found at high prevalence in the feces of children from developing countries. We sequenced four near-full length genomes and 45 partial VP1 region from HCoSV in human feces from healthy children and children with acute flaccid paralysis in Pakistan, Nigeria and Tunisia and from healthy and diarrhetic adults in Nepal. Genetic analyses of the near-full length genomes revealed presence of a new candidate cosavirus species provisionally labelled as species F (HCoSV-F). A HCoSV genome showed evidence of recombination between species D and E viruses at the P1/P2 junction indicating that these viruses may be reclassified as a single highly diverse species. Based on genetic distance criteria for assigning genotypes corresponding to neutralization serotypes in enteroviruses we identified 26 new HCoSV genotypes belonging to species A, D, and E. The detection of a large number of HCoSV genotypes based on still limited geographic sampling indicates that the phenotypic effects of cosaviruses on infected subjects are likely to be as highly diverse as those of human enteroviruses.
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Affiliation(s)
- Beatrix Kapusinszky
- 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
- Department of Viral Diagnostics, National Center for Epidemiology, Budapest, Hungary
| | - Tung G. Phan
- 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
| | - Amit Kapoor
- Center for Infection and Immunity, Columbia University, New York, United States of America
| | - 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
- * E-mail:
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33
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Detection and molecular characterization of cosavirus in adults with diarrhea, Thailand. Virus Genes 2011; 44:244-6. [DOI: 10.1007/s11262-011-0700-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
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