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Moreni G, van Eijk H, Koen G, Johannesson N, Calitz C, Benschop K, Cremer J, Pajkrt D, Sridhar A, Wolthers K. Non-Polio Enterovirus C Replicate in Both Airway and Intestine Organotypic Cultures. Viruses 2023; 15:1823. [PMID: 37766230 PMCID: PMC10537321 DOI: 10.3390/v15091823] [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: 08/10/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Non-polio enteroviruses (EV) belonging to species C, which are highly prevalent in Africa, mainly among children, are poorly characterized, and their pathogenesis is mostly unknown as they are difficult to culture. In this study, human airway and intestinal organotypic models were used to investigate tissue and cellular tropism of three EV-C genotypes, EV-C99, CVA-13, and CVA-20. Clinical isolates were obtained within the two passages of culture on Caco2 cells, and all three viruses were replicated in both the human airway and intestinal organotypic cultures. We did not observe differences in viral replication between fetal and adult tissue that could potentially explain the preferential infection of infants by EV-C genotypes. Infection of the airway and the intestinal cultures indicates that they both can serve as entry sites for non-polio EV-C. Ciliated airway cells and enterocytes are the target of infection for all three viruses, as well as enteroendocrine cells for EV-C99.
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Affiliation(s)
- Giulia Moreni
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Hetty van Eijk
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
| | - Gerrit Koen
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
| | - Nina Johannesson
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Carlemi Calitz
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Kimberley Benschop
- National Institute for Public Health and Environment, RIVM, 3721 MA Bilthoven, The Netherlands; (K.B.); (J.C.)
| | - Jeroen Cremer
- National Institute for Public Health and Environment, RIVM, 3721 MA Bilthoven, The Netherlands; (K.B.); (J.C.)
| | - Dasja Pajkrt
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Adithya Sridhar
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
- OrganoVIR Labs, Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Katja Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location AMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (H.v.E.); (G.K.); (N.J.); (C.C.); (A.S.); (K.W.)
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Faleye TO, Skidmore P, Elyaderani A, Adhikari S, Kaiser N, Smith A, Yanez A, Perleberg T, Driver EM, Halden RU, Varsani A, Scotch M. Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.09.25.22280344. [PMID: 36203558 PMCID: PMC9536034 DOI: 10.1101/2022.09.25.22280344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.
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Affiliation(s)
- Temitope O.C. Faleye
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peter Skidmore
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Amir Elyaderani
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Sangeet Adhikari
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
| | - Nicole Kaiser
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Abriana Smith
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
| | - Allan Yanez
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Tyler Perleberg
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Erin M. Driver
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Rolf U. Halden
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, 85287, USA
- OneWaterOneHealth, Nonprofit Project of the Arizona State University Foundation, Tempe, AZ, USA
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- College of Health Solutions, Arizona State University, Tempe, AZ, USA
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National Surveillance of Acute Flaccid Paralysis Cases in Senegal during 2017 Uncovers the Circulation of Enterovirus Species A, B and C. Microorganisms 2022; 10:microorganisms10071296. [PMID: 35889015 PMCID: PMC9319795 DOI: 10.3390/microorganisms10071296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Abstract
Polioviruses have been eliminated in many countries; however, the number of acute flaccid paralysis cases has not decreased. Non-polio enteroviruses are passively monitored as part of the polio surveillance program. Previous studies have shown that some enteroviruses do not grow in conventional cell lines used for the isolation of poliovirus according to the WHO guidelines. In order to evaluate the presence of enteroviruses, real-time RT-PCR was performed on Human Rhabdomyosarcoma (RD)-positive and RD-negative stool samples. A total of 310 stool samples, collected from children under the age of 15 years with acute flaccid paralysis in Senegal in 2017, were screened using cell culture and real-time RT-PCR methods. The selected isolates were further characterized using Sanger sequencing and a phylogenetic tree was inferred based on VP1 sequences. Out of the 310 stool samples tested, 89 were positive in real-time RT-PCR. A total of 40 partial VP1 sequences were obtained and the classification analysis showed that 3 (13%), 19 (82.6%), and 1 (4.4%) sequences from 23 RD-positive non-polio enterovirus isolates and 3 (17.6%), 7 (41.1%), and 7 (41.1%) sequences from 17 RD-negative stool samples belonged to the species EV-A, B, and C, respectively. Interestingly, the EV-B sequences from RD-negative stool samples were grouped into three separate phylogenetic clusters. Our data exhibited also a high prevalence of the EV-C species in RD-negative stool samples. An active country-wide surveillance program of non-polio enteroviruses based on direct RT-PCR coupled with sequencing could be important not only for the rapid identification of the involved emergence or re-emergence enteroviruses, but also for the assessment of AFP’s severity associated with non-polio enteroviruses detected in Senegal.
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Abstract
Laboratory surveillance for poliovirus (PV) relies on virus isolation by cell culture to identify PV in stool specimens from acute flaccid paralysis (AFP) cases. Although this method successfully identifies PV, it is time-consuming and necessitates the additional biorisk of growing live virus in an increasingly polio-free world. To reduce the risk of culturing PV, the Global Polio Laboratory Network (GPLN) must switch to culture-independent diagnostic methods with sensitivity at least equivalent to that of cell culture procedures. Five commercial nucleic acid extraction kits and one enrichment method were tested for PV extraction efficiency. RNA yield was measured using real-time reverse transcription (RT)-PCR. Based on greater RNA yield, compared with the other kits, the Quick-RNA viral kit was selected for further testing and was optimized using an RNA extraction procedure for stool suspensions. RNA extraction was retrospectively tested with 182 stool samples that had previously tested positive for PVs, in parallel with the standard GPLN virus isolation algorithm. After virus isolation or RNA extraction, real-time RT-PCR assays were performed. RNA extraction was significantly more sensitive than virus isolation (McNemar’s test, P < 0.001). Thereafter, the RNA extraction method was tested in parallel for 202 prospective samples; RNA extraction and virus isolation were not significantly different from each other (McNemar’s test, P = 0.13). Direct RNA extraction was noninferior to current cell culture methods for detecting PV in stool samples. Our results show that direct RNA extraction can make downstream manipulation safer and can reduce the risk of accidental posteradication viral release. The method is amenable to implementation in a wide variety of polio laboratories. IMPORTANCE Successfully identifying poliovirus from acute flaccid paralysis (AFP) cases is a vital role of the Global Polio Laboratory Network to achieve the goals of the Global Polio Eradication Initiative. Currently, laboratory surveillance relies on virus isolation by cell culture to test for PV present in stool samples. Although this method can identify polioviruses, laboratories must switch to culture-independent methods to reduce the risk associated with growing live viruses in a soon-to-be polio-free world. By implementing this streamlined method, in combination with real-time RT-PCR, laboratories can quickly screen for and type polioviruses of programmatic importance to support the final stages of global polio eradication.
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Lizasoain A, Mir D, Victoria M, Barrios ME, Blanco-Fernández MD, Rodríguez-Osorio N, Nates S, Cisterna D, Mbayed VA, Colina R. Human Enterovirus Diversity by Next-Generation Sequencing Analysis in Urban Sewage Samples From Buenos Aires Metropolitan Area, Argentina: A Retrospective Study. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:259-269. [PMID: 33675515 DOI: 10.1007/s12560-021-09468-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Human Enteroviruses (hEVs) are responsible for a wide variety of human diseases. During hEVs infection, virions are excreted in human feces and the fecal-oral route is the primary pathway for person-to-person transmission. Sewage surveillance could help in monitoring hEVs circulation and describing their diversity in a specific population. In this study, sewage samples collected in Buenos Aires Metropolitan Area (Argentina) were retrospectively studied through an amplicon-deep sequencing approach and phylogenetic analyses to characterize hEVs spread. We identified 17 different hEVs types belonging to A, B, and C species. To the best of our knowledge, this is the first report in Buenos Aires for 7 identified hEV-C types. Phylogenetic analyses suggest several introductions of coxsackievirus B4, echovirus 1, and echovirus 9 in the country, along with the national spread reached by some variants. Besides, well-supported monophyletic groups of Argentine, Uruguayan, and Brazilian strains unveiled regional circulation patterns for some variants. These results extend our knowledge about hEVs circulation in Buenos Aires and might exhort authorities to implement more active sewage surveillance in the region.
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Affiliation(s)
- A Lizasoain
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional del Litoral Norte. Universidad de La República, 1350 Gral. Rivera St. Salto, 50000, Salto, Uruguay
| | - D Mir
- Unidad de Genómica y Bioinformática. Departamento de Ciencias Biológicas, Centro Universitario Regional del Litoral Norte. Universidad de La República, Salto, Uruguay
| | - M Victoria
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional del Litoral Norte. Universidad de La República, 1350 Gral. Rivera St. Salto, 50000, Salto, Uruguay
| | - M E Barrios
- Cátedra de Virología, Instituto de Investigaciones en Bacteriología y Virología Molecular. Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - M D Blanco-Fernández
- Cátedra de Virología, Instituto de Investigaciones en Bacteriología y Virología Molecular. Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - N Rodríguez-Osorio
- Unidad de Genómica y Bioinformática. Departamento de Ciencias Biológicas, Centro Universitario Regional del Litoral Norte. Universidad de La República, Salto, Uruguay
| | - S Nates
- Laboratorio de Gastroenteritis Virales y Sarampión. Instituto de Virología Dr. J. M. Vanella. Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - D Cisterna
- Servicio de Neurovirosis, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas. Administración Nacional de Laboratorios e Institutos de Salud Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - V A Mbayed
- Cátedra de Virología, Instituto de Investigaciones en Bacteriología y Virología Molecular. Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - R Colina
- Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional del Litoral Norte. Universidad de La República, 1350 Gral. Rivera St. Salto, 50000, Salto, Uruguay.
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Faleye TOC, George UE, Klapsa D, Majumdar M, Oragwa AO, Adewumi MO, Martin J, Adeniji JA. Isolation and Genomic Characterization of Echovirus 11 from faeces of a Non-Human Primate in Nigeria. ECOHEALTH 2020; 17:461-468. [PMID: 33993387 DOI: 10.1007/s10393-021-01515-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 11/23/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
We recently investigated the presence of enteroviruses (EVs) in non-human primates (NHPs) in Northern Nigeria and documented the presence of EV-A76 of South-East Asian ancestry in an NHP. In this study, we go further to ask if we could also find EVs in NHPs indigenous to the forested South-south Nigeria. Fresh faecal samples were collected from the floor of 10 cages housing NHPs in Cross River Nigeria, re-suspended in PBS and subjected to RNA extraction, cDNA synthesis, PanEnt 5'-UTR and PanEnt VP1 PCR assays. None of the samples was positive for the PanEnt VP1 assay, but one sample was positive for PanEnt 5'-UTR PCR. This sample was subsequently inoculated into RD cell line, produced CPE and the isolate analysed by PCR assays, next-generation whole genome sequencing and passage in four different cell lines showing replication in two of them. Analysis of the complete genome of the isolate identified it as an Echovirus 11 (E11) and revealed a recombinant genomic structure. Phylogenetic analysis showed that the E11 NHP strain was related to human clinical isolates suggesting a zoonotic behaviour. We describe the first isolation and complete genome characterization of an E11 obtained from an NHP in Nigeria having zoonotic potential.
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Affiliation(s)
- T O C Faleye
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
- Centre for Human Virology and Genomics, Department of Microbiology, Nigerian Institute for Medical Research, Lagos, Nigeria
| | - U E George
- Department of Biological Sciences, Redeemer's University, Ede, Nigeria
| | - D Klapsa
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - M Majumdar
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - A O Oragwa
- Department of Veterinary Microbiology and Pathology, Faculty of Veterinary Medicine, University of Jos, Jos, Nigeria
| | - M O Adewumi
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.
| | - J Martin
- Division of Virology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - J A Adeniji
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- WHO National Polio Laboratory, University of Ibadan, Ibadan, Nigeria
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Alidjinou EK, Dorsi Di Meglio M, Biron A, Jeannoel M, Schuffenecker I, Gourinat AC. Enterovirus and Parechovirus Coinfection in a Sudden Unexpected Infant Death. Pediatrics 2020; 146:peds.2019-3686. [PMID: 32817397 DOI: 10.1542/peds.2019-3686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2020] [Indexed: 11/24/2022] Open
Abstract
Viruses are suspected to play a role in the multifactorial pathogenesis of sudden infant death. We described a sudden and unexpected death in a 5-month-old boy, with detection of both enterovirus and parechovirus RNA in the blood. This is the first report of a dual viraemia of enterovirus and parechovirus and its potential association with a sudden unexpected infant death. Extensive sampling and testing especially using molecular methods currently available is needed to better understanding the "hypothetical" link between viral infections and sudden infant death.
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Affiliation(s)
- Enagnon Kazali Alidjinou
- Microbiology Laboratory, Centre Hospitalier Territorial de Nouvelle-Calédonie, Dumbea, New Caledonia; .,Laboratoire de Virologie ULR 3610, Université Lille, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Marine Dorsi Di Meglio
- Service de Néonatologie, Centre Hospitalier Territorial de Nouvelle-Calédonie, Dumbea, New Caledonia; and
| | - Antoine Biron
- Microbiology Laboratory, Centre Hospitalier Territorial de Nouvelle-Calédonie, Dumbea, New Caledonia
| | - Marion Jeannoel
- Laboratoire de Virologie, Centre National de Référence Entérovirus et Parechovirus, Centre Hospitalier Universitaire de Lyon, Lyon, France
| | - Isabelle Schuffenecker
- Laboratoire de Virologie, Centre National de Référence Entérovirus et Parechovirus, Centre Hospitalier Universitaire de Lyon, Lyon, France
| | - Ann-Claire Gourinat
- Microbiology Laboratory, Centre Hospitalier Territorial de Nouvelle-Calédonie, Dumbea, New Caledonia
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Di Cristanziano V, Weimer K, Böttcher S, Sarfo FS, Dompreh A, Cesar LG, Knops E, Heger E, Wirtz M, Kaiser R, Norman B, Phillips RO, Feldt T, Eberhardt KA. Molecular Characterization and Clinical Description of Non-Polio Enteroviruses Detected in Stool Samples from HIV-Positive and HIV-Negative Adults in Ghana. Viruses 2020; 12:v12020221. [PMID: 32079128 PMCID: PMC7077198 DOI: 10.3390/v12020221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/31/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
In the post-polio eradication era, increasing attention is given to non-polio enteroviruses. Most of the data about enteroviruses in sub-Saharan Africa are related to acute flaccid paralysis surveillance and target the pediatric population. This study aimed to investigate the presence of enterovirus in PLHIV (people living with HIV) and HIV-negative individuals in Ghana. Stool samples from HIV-positive individuals (n = 250) and healthy blood donors (n = 102) attending the Komfo Anokye Teaching Hospital in Kumasi, Ghana, were screened by real-time PCR for enterovirus. Molecular typing of the VP1 region was performed. Enterovirus-positive samples were tested for norovirus, adenovirus, rotavirus, sapovirus, and cosaviruses. Twenty-six out of 250 HIV-positive subjects (10.4%) and 14 out of 102 HIV-negative individuals (13.7%) were detected enterovirus-positive, not showing a significant different infection rate between the two groups. HIV-negative individuals were infected with Enterovirus C strains only. HIV-positive participants were detected positive for species Enterovirus A, Enterovirus B, and Enterovirus C. Co-infections with other viral enteric pathogens were almost exclusively detected among HIV-positive participants. Overall, the present study provides the first data about enteroviruses within HIV-positive and HIV-negative adults living in Ghana.
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Affiliation(s)
- Veronica Di Cristanziano
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Kristina Weimer
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Sindy Böttcher
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
| | - Fred Stephen Sarfo
- Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana;
| | | | | | - Elena Knops
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Eva Heger
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Maike Wirtz
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany; (V.D.C.); (K.W.); (E.K.); (E.H.); (M.W.); (R.K.)
| | - Betty Norman
- Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana;
| | - Richard Odame Phillips
- Kwame Nkrumah University of Science and Technology, Kumasi 00233, Ghana; (F.S.S.); (B.N.); (R.O.P.)
- Komfo Anokye Teaching Hospital, Kumasi 00233, Ghana;
- Kumasi Center for Collaborative Research in Tropical Medicine, Kumasi 00233, Ghana
| | - Torsten Feldt
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, 40225 Düsseldorf, Germany;
| | - Kirsten Alexandra Eberhardt
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany
- Correspondence: ; Tel.: +49-40-428-180
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Detection and Characterization of Human Enteroviruses, Human Cosaviruses, and a New Human Parechovirus Type in Healthy Individuals in Osun State, Nigeria, 2016/2017. Viruses 2019; 11:v11111037. [PMID: 31703317 PMCID: PMC6893832 DOI: 10.3390/v11111037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022] Open
Abstract
Human enteroviruses and human parechoviruses are associated with a broad range of diseases and even severe and fatal conditions. For human cosaviruses, the etiological role is yet unknown. Little is known about the circulation of non-polio enteroviruses, human parechoviruses, and human cosaviruses in Nigeria. A total of 113 stool samples were collected from healthy individuals in Osun State between February 2016 and May 2017. RT-PCR assays targeting the 5' non-coding region (5' -NCR) were used to screen for human enteroviruses, human parechoviruses, and human cosaviruses. For human enteroviruses, species-specific RT-PCR assays targeting the VP1 regions were used for molecular typing. Inoculation was carried out on RD-A, CaCo-2, HEp-2C, and L20B cell lines to compare molecular and virological assays. Ten samples tested positive for enterovirus RNA with 11 strains detected, including CV-A13 (n = 3), E-18 (n = 2), CV-A20 (n = 1), CV-A24 (n = 1), EV-C99 (n = 1), and EV-C116 (n = 2). Three samples tested positive for human parechovirus RNA, and full genome sequencing on two samples allowed assignment to a new Parechovirus A type (HPeV-19). Thirty-three samples tested positive for cosavirus with assignment to species Cosavirus D and Cosavirus A based on the 5'-NCR region. Screening of stool samples collected from healthy individuals in Nigeria in 2016 and 2017 revealed a high diversity of circulating human enteroviruses, human parechoviruses, and human cosaviruses. Molecular assays for genotyping showed substantial benefits compared with those of cell-culture assays.
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Complete Genome Sequence of a Human Enterovirus C99 Strain Isolated from a Healthy Child in Yunnan, China, in 2013. Microbiol Resour Announc 2019; 8:8/16/e01489-18. [PMID: 31000560 PMCID: PMC6473154 DOI: 10.1128/mra.01489-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of a human enterovirus C99 strain isolated from a healthy child in Yunnan, China, in 2013 was determined. The isolate belonged to genotype C, according to phylogenetic and homogeneity analyses. The complete genome sequence of a human enterovirus C99 strain isolated from a healthy child in Yunnan, China, in 2013 was determined. The isolate belonged to genotype C, according to phylogenetic and homogeneity analyses.
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Adewumi OM, Faleye TOC, Okeowo CO, Oladapo AM, Oyathelemhi J, Olaniyi OA, Isola OC, Adeniji JA. Identification of previously untypable RD cell line isolates and detection of EV-A71 genotype C1 in a child with AFP in Nigeria. Pathog Glob Health 2018; 112:421-427. [PMID: 30474520 DOI: 10.1080/20477724.2018.1548117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We previously attempted to identify 96 nonpolio enteroviruses (EVs) recovered in RD cell culture from children <15 years with acute flaccid paralysis in Nigeria. We succeeded in identifying 69 of the isolates. Here, we describe an attempt to identify the remaining 27 isolates. Twenty-six (the 27th isolate was exhausted) isolates/samples that could not be typed previously were further analyzed. All were subjected to RNA extraction, cDNA synthesis, enterovirus 5'-UTR-VP2 PCR assay and a modified VP1 snPCR assay. Both the 5'-UTR-VP2 and VP1 amplicons were sequenced, isolates identified and subjected to phylogenetic analysis.Twenty of the 26 samples analyzed were identified. Altogether, 23 (three samples had co-infection) EV strains were recovered. These belong to 11 EV (one EVA, nine EVB and one EVC) types which were EVA71 genotype C1 (1 strain), CVB3 (7 strains), CVB5 (1 strain), E5 (2 strain), E11 (3 strains), E13 (2 strain), E19 (1 strain), E20 (1 strain), E24 (2 strains), EVB75 (1 strain) and EVC99 (2 strains). Of the 11 EV types, the 5'-UTR-VP2 assay identified seven while the VP1 assay identified 10. Both assays simultaneously detected 7 of the 11 EV types identified in this study with 100% congruence. We successfully identified 20 of 26 samples that were previously untypable. We also provided evidence that suggests a clade of EVA71 genotype C1 might have been circulating in sub-Saharan Africa since 2008. Finally, we showed that the 5'-UTR -VP2 assay might be as valuable as the VP1 assay in EV identification.
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Affiliation(s)
| | - Temitope Oluwasegun Cephas Faleye
- a Department of Virology , College of Medicine, University of Ibadan , Ibadan , Nigeria.,b Department of Microbiology, Faculty of Science , Ekiti State University , Ado-Ekiti , Nigeria
| | - Christopher Olaoluwa Okeowo
- c Department of Science Laboratory Technology, Faculty of Science , Ekiti State University , Ado-Ekiti , Nigeria
| | - Akintunde Michael Oladapo
- c Department of Science Laboratory Technology, Faculty of Science , Ekiti State University , Ado-Ekiti , Nigeria
| | - Joyce Oyathelemhi
- c Department of Science Laboratory Technology, Faculty of Science , Ekiti State University , Ado-Ekiti , Nigeria
| | - Olawumi A Olaniyi
- c Department of Science Laboratory Technology, Faculty of Science , Ekiti State University , Ado-Ekiti , Nigeria
| | - Oluwatoyosi Catherine Isola
- c Department of Science Laboratory Technology, Faculty of Science , Ekiti State University , Ado-Ekiti , Nigeria
| | - Johnson Adekunle Adeniji
- a Department of Virology , College of Medicine, University of Ibadan , Ibadan , Nigeria.,d WHO National Polio Laboratory , University of Ibadan , Ibadan , Nigeria
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Donbraye E, Olasunkanmi OI, Opabode BA, Ishola TR, Faleye TOC, Adewumi OM, Adeniji JA. Abundance of enterovirus C in RD-L20B cell culture-negative stool samples from acute flaccid paralysis cases in Nigeria is geographically defined. J Med Microbiol 2018; 67:854-865. [PMID: 29708482 DOI: 10.1099/jmm.0.000737] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PURPOSE We recently showed that enteroviruses (EVs) andenterovirus species C (EV-C) in particular were abundant in faecal samples from children who had been diagnosed with acute flaccid paralysis (AFP) in Nigeria but declared to be EV-free by the RD-L20B cell culture-based algorithm. In this study, we investigated whether this observed preponderance of EVs (and EV-Cs) in such samples varies by geographical region. METHODOLOGY One hundred and eight samples (i.e. 54 paired stool suspensions from 54 AFP cases) that had previously been confirmed to be negative for EVs by the WHO-recommended RD-L20B cell culture-based algorithm were analysed. The 108 samples were made into 54 pools (27 each from North-West and South-South Nigeria). All were subjected to RNA extraction, cDNA synthesis and the WHO-recommended semi-nested PCR assay and its modifications. All of the amplicons were sequenced, and the enteroviruses identified, using the enterovirus genotyping tool and phylogenetic analysis. RESULTS EVs were detected in 16 (29.63 %) of the 54 samples that were screened and successfully identified in 14 (25.93 %). Of these, 10 were from North-West and 4 were from South-South Nigeria. One (7.14 %), 2 (14.29 %) and 11 (78.57 %) of the strains detected were EV-A, EV-B and EV-C, respectively. The 10 strains from North-West Nigeria included 7 EV types, namely CV-A10, E29, CV-A13, CV-A17, CV-A19, CV-A24 and EV-C99. The four EV types recovered from South-South Nigeria were E31, CV-A1, EV-C99 and EV-C116. CONCLUSION The results of this study showed that the presence of EVs and consequently EV-Cs in AFP samples declared to be EV-free by the RD-L20B cell culture-based algorithm varies by geographical region in Nigeria.
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Affiliation(s)
- Emmanuel Donbraye
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | | | - Babatunde Ayoola Opabode
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Temitayo Rachael Ishola
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Temitope Oluwasegun Cephas Faleye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti, State, Nigeria
| | - Olubusuyi Moses Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Johnson Adekunle Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- WHO National Polio Laboratory, University of Ibadan, Ibadan, Oyo State, Nigeria
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Faleye TOC, Adewumi MO, Ozegbe NP, Ogunsakin OE, Ariyo G, Adeshina FW, Ogunga OS, Oluwadare SD, Adeniji JA. Extending the utility of the WHO recommended assay for direct detection of enteroviruses from clinical specimen for resolving poliovirus co-infection. BMC Res Notes 2018; 11:47. [PMID: 29347972 PMCID: PMC5774100 DOI: 10.1186/s13104-018-3155-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/09/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES In a polio-free world there might be reduced funding for poliovirus surveillance. There is therefore the need to ensure that enterovirologist globally, especially those outside the global polio laboratory network, can participate in poliovirus surveillance without neglecting their enterovirus type of interest. To accomplish this, assays are needed that allow such active participation. RESULTS In this study we describes a sensitive and specific utility extension of the recently recommended WHO RT-snPCR assay that enables independent detection of the three poliovirus types especially in cases of co-infection. More importantly, it piggy-backs on the first round PCR product of the WHO recommended assay and consequently ensures that enterovirologists interested in nonpolio enteroviruses can continue their investigations, and contribute significantly and specifically to poliovirus surveillance, by using the excess of their first round PCR product.
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Affiliation(s)
- Temitope Oluwasegun Cephas Faleye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State Nigeria
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Ekiti State Nigeria
| | - Moses Olubusuyi Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State Nigeria
| | - Naomi Princess Ozegbe
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Ekiti State Nigeria
| | | | - Grace Ariyo
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Ekiti State Nigeria
| | - Faith Wuraola Adeshina
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Ekiti State Nigeria
| | - Oluwaseun Sarah Ogunga
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Ekiti State Nigeria
| | | | - Johnson Adekunle Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State Nigeria
- WHO National Polio Laboratory, University of Ibadan, Ibadan, Oyo State Nigeria
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Comparison of Algorithms for the Detection of Enteroviruses in Stool Specimens from Children Diagnosed with Acute Flaccid Paralysis. J Pathog 2017; 2017:9256056. [PMID: 29445548 PMCID: PMC5763071 DOI: 10.1155/2017/9256056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/10/2017] [Indexed: 12/04/2022] Open
Abstract
This study was designed to compare both the cell culture dependent and independent enterovirus detection algorithms recommended by the WHO and assess how either might impact our perception of the diversity of enterovirus types present in a sample. Sixteen paired samples (16 isolates from RD cell culture and their corresponding stool suspension, i.e., 32 samples) from AFP cases in Nigeria were analyzed in this study. All the samples were subjected to RNA extraction, cDNA synthesis, the WHO recommended RT-snPCR, and its modification. Amplicons were sequenced and strains identified. Enterovirus diversity was the same between the isolates and fecal suspension for the control and five of the samples. It was, however, different for the remaining 10 (62.5%) samples. Nine (CV-B4, E6, E7, E13, E14, E19, E29, EV-B75, and EV-B77) and five (CV-A1, CV-A11, CV-A13, EV-C99, and PV2) EV-B and EV-C types, respectively, were detected. Particularly, E19 and EV-B75 were only recovered from the isolates while E14, EV-B77, CV-A11, and CV-A13 were only recovered from fecal suspension. Both the cell culture dependent and independent protocols bias our perception of the diversity of enterovirus types present in a sample. Hence, effort should be directed at harmonizing both for increased sensitivity.
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Faleye TOC, Adewumi MO, Japhet MO, David OM, Oluyege AO, Adeniji JA, Famurewa O. Non-polio enteroviruses in faeces of children diagnosed with acute flaccid paralysis in Nigeria. Virol J 2017; 14:175. [PMID: 28899411 PMCID: PMC5596853 DOI: 10.1186/s12985-017-0846-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 09/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background The need to investigate the contribution of non-polio enteroviruses to acute flaccid paralysis (AFP) cannot be over emphasized as we move towards a poliovirus free world. Hence, we aim to identify non-polio enteroviruses recovered from the faeces of children diagnosed with AFP in Nigeria. Methods Ninety-six isolates, (95 unidentified and one previously confirmed Sabin poliovirus 3) recovered on RD cell culture from the stool of children <15 years old diagnosed with AFP in 2014 were analyzed. All isolates were subjected to RNA extraction, cDNA synthesis and three different PCR reactions (one panenterovirus 5′-UTR and two different VP1 amplification assays). VP1 amplicons were then sequenced and isolates identified. Results 92.71% (89/96) of the isolates were detected by at least one of the three assays as an enterovirus. Precisely, 79.17% (76/96), 6.25% (6/96), 7.30% (7/96) and 7.30% (7/96) of the isolates were positive for both, positive and negative, negative and positive, as well as negative for both the 5′-UTR and VP1 assays, respectively. In this study, sixty-nine (69) of the 83 VP1 amplicons sequenced were identified as 27 different enterovirus types. The most commonly detected were CV-B3 (10 isolates) and EV-B75 (5 isolates). Specifically, one, twenty-four and two of the enterovirus types identified in this study belong to EV-A, EV-B and EV-C respectively. Conclusions This study reports the circulating strains of 27 non-polio enterovirus types in Nigerian children with AFP in 2014 and Nigerian strains of CV-B2, CV-B4, E17, EV-B80, EV-B73, EV-B97, EV-B93, EV-C99 and EV-A120 were reported for the first time. Furthermore, it shows that being positive for the 5′-UTR assay should not be the basis for subjecting isolates to the VP1 assays.
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Affiliation(s)
- T O C Faleye
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - M O Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - M O Japhet
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria. .,Department of Microbiology, Faculty of Science, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria.
| | - O M David
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria
| | - A O Oluyege
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria
| | - J A Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria.,WHO, National Polio Laboratory, Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - O Famurewa
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado-Ekiti, Ekiti State, Nigeria.,Microbiology Unit, Department of Biological Sciences, Kings University, P.M.B. 555, Odeomu, Osogbo, Osun State, Nigeria
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