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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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Coutinho CRM, Cardoso JF, Siqueira JAM, Machado RS, Chagas Júnior WDD, Tavares FN, Gabbay YB. Diversity of picornaviruses detected in diarrheal samples from children in Belém, Brazilian Amazon (1982-2019). J Med Virol 2023; 95:e28873. [PMID: 37349989 DOI: 10.1002/jmv.28873] [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: 01/10/2023] [Revised: 05/06/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
In this investigation, fecal specimens from children with diarrhea were collected from four community studies conducted between 1982 and 2019 in Belém, Brazilian Amazon. A total of 234 samples were tested by quantitative reverse transcription polymerase chain reaction (RT-qPCR) to detect infections by picornaviruses of the Enterovirus (EV), Parechovirus (HPeV), Cosavirus (HCoSV), Kobuvirus (Aichivirus - AiV) and Salivirus (SalV) genera. The positive samples were subjected to different amplification protocols of the VP1 region of the genome, such as nested PCR or snPCR, and were subsequently genotyped by sequencing VP1 and VP3 of the viral genome. Positivity was observed in 76.5% (179/234) of the samples tested using RT-qPCR for at least one virus, and co-infection was observed in 37.4% (67/179) of the cases. EV was detected in 50.8% (119/234), HPeV in 29.9% (70/234), HCoSV in 27.3% (64/234), and AiV/SalV in 2.1% (5/234) of the specimens tested by RT-qPCR. Using nested PCR and/or snPCR techniques, the positivity rates were 94.11% (112/119) for EV, 72.85% (51/70) for HPeV, and 20.31% (13/64) for HCoSV. It was not possible to amplify the samples that were positive for AiV/SalV. Sequencing revealed 67.2% (80/119) EV, 51.4% (36/70) HPeV, and 20.31% (13/64) HCoSV. Forty-five different types of EV were found among species A, B, and C; HCoSV identified five species, including a possible recombinant strain; all HPeV were identified as belonging to species A, in two samples a possible recombination involving three different strains was verified. This study demonstrated the high circulation and diversity of different types of picornaviruses in fecal samples, including those collected more than 30 years ago. This endorsed the evaluation of important points in the epidemiology of these viruses, such as the presence of co-infection and the possibility of knowing more about these agents, considering that some were recently described; therefore, their detection in older samples can provide more data about their ancestry.
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Affiliation(s)
| | - Jedson Ferreira Cardoso
- Laboratório de Bioinformática-BIOINFO, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Jones Anderson Monteiro Siqueira
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Raiana Scerni Machado
- Programa de Pós-graduação em Medicina Tropical, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - Wanderley Dias das Chagas Júnior
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Fernando Neto Tavares
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Yvone Benchimol Gabbay
- Laboratório de Vírus Gastroentéricos-LVG, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde e Ambiente-SVSA, Ministério da Saúde, Ananindeua, Pará, Brazil
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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: 1.7] [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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High Frequency of Salivirus in Pediatric Patients with Acute Gastroenteritis. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2021. [DOI: 10.52547/jommid.9.4.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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First Human Cosavirus Detection From Cerebrospinal Fluid in Hospitalized Children With Aseptic Meningitis and Encephalitis in Iran. Pediatr Infect Dis J 2021; 40:e459-e461. [PMID: 34870389 DOI: 10.1097/inf.0000000000003304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Human cosavirus (HCosV) is a newly recognized virus that seems to be partly related to nonpolio flaccid paralysis and acute gastroenteritis in pediatric patients. However, the relationship between HCosV and diseases in humans is unclear. To assess an investigation for the occurrence of HCosV among pediatric patients involved in meningitis and encephalitis, we implemented a real-time quantitative polymerase chain reaction assay for detection and quantification of HCosV in stool specimens. MATERIALS AND METHODS In this study, a total of 160 cerebrospinal fluid samples from September 2019 to October 2020 were collected from presenting pediatric patients with meningitis and encephalitis in a Karaj hospital, Iran. After viral RNA extraction, the real-time quantitative polymerase chain reaction was performed to amplify the 5'Un-Translated Region region of the HCosV genome and viral load was analyzed. RESULTS Of the 160 samples tested, the HCosV genomic RNA was detected in 2/160 (1.25%) of samples. The minimum viral load of HCosV was 3.5 × 103 copies/mL from 4 years male patient. The maximum viral load was determined to be 2.4 × 105 copies/mL in one sample obtained from 3.5 years female patient. CONCLUSIONS This is the first documentation of HCosV detection in cerebrospinal fluid samples that better demonstrates relation of HCosV with neurologic diseases including meningitis and encephalitis. Also, these results indicate that HCosV has been circulating among Iranian pediatric patients.
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do Socorro Fôro Ramos E, de Oliveira Ribeiro G, Villanova F, de Padua Milagres FA, Brustulin R, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, Luchs A, da Costa AC, Leal É. Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis. Viruses 2021; 13:2365. [PMID: 34960634 PMCID: PMC8704738 DOI: 10.3390/v13122365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 01/21/2023] Open
Abstract
Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.
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Affiliation(s)
- Endrya do Socorro Fôro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
| | - Geovani de Oliveira Ribeiro
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
| | - Flávio Augusto de Padua Milagres
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, Tocantins, Brazil
| | - Rafael Brustulin
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, Brazil;
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Virology Center, Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo 01246-000, São Paulo, Brazil;
| | - Antonio Charlys da Costa
- Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil;
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil; (E.d.S.F.R.); (G.d.O.R.); (F.V.)
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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: 0.2] [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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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: 3.8] [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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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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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: 1.0] [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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Near full length genome of a recombinant (E/D) cosavirus strain from a rural area in the central region of Brazil. Sci Rep 2018; 8:12304. [PMID: 30120342 PMCID: PMC6098101 DOI: 10.1038/s41598-018-30214-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022] Open
Abstract
In the present article we report the nearly full length genome of a Cosavirus strain (BRTO-83) isolated from a child with acute gastroenteritis, and who is an inhabitant of a rural area in the central region of Brazil. The sample was previously screened and negative for both: common enteric viruses (i.e. rotavirus and norovirus), bacteria, endoparasites and helminthes. Evolutionary analysis and phylogenetic inferences indicated that the Brazilian BRTO-83 Cosavirus strain was a recombinant virus highly related to the E/D recombinant NG385 strain (Genbank JN867757), which was isolated in Nigeria from an acute flaccid paralysis patient. This is the first report of a recombinant E/D Cosavirus strain detected in Brazil, and the second genome described worldwide. Further surveillance and molecular studies are required to fully understand the epidemiology, distribution and evolution of the Cosavirus.
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14
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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: 1.6] [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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15
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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: 1.1] [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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16
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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: 0.6] [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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