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Cao M, Yuan F, Ma X, Ma J, Ma X, Chen H, Zhang W, Zhao J, Kuai W. Surveillance of human Group A rotavirus in Ningxia, China (2015-2021): Emergence and prevalence of G9P[8]-E2 and G3P[8]-E2 genotypes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105469. [PMID: 37331499 DOI: 10.1016/j.meegid.2023.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND Group A rotaviruses (RVA) are the primary pathogens of acute gastroenteritis. Currently, two live attenuated RVA vaccines, LLR and RotaTeq, have been introduced into mainland China but are not included in the national immunization program. Because of the unknown genetic evolution of group A rotavirus in an all-age population in Ningxia, China, we monitored the epidemiological characteristics and circulating genotypes of RVA as a reference for developing vaccine strategies. METHODS We conducted seven years of consecutive surveillance of RVA based on stool samples from patients with acute gastroenteritis in sentinel hospitals in Ningxia, China, from 2015 to 2021. Reverse transcription quantitative polymerase chain reaction(RT-qPCR) was used to detect RVA in stool samples. Genotyping and phylogenetic analysis of VP7, VP4 and NSP4 genes were performed by reverse transcription-polymerase chain reaction(RT-PCR) and nucleotide sequence determination. RESULTS RVA was detected in 16.58% (1436/8662) of 8662 stool samples. The positive rates were 7.17% (201/2805) and 21.09% (1235/5857) in adults and children, respectively. The most affected age group was infants and children aged 12-23 months, with a positive rate of 29.53% (p < 0.05). A significant winter/spring seasonality was observed. 23.29% positive rate in 2020 was the highest in 7 years (p < 0.05). The region with the highest positive rate in the adult group was Yinchuan, and the children's group was Guyuan. A total of 9 genotype combinations were found to be distributed in Ningxia. The dominant genotype combinations in this region gradually changed from G9P[8]-E1, G3P[8]-E1, G1P[8]-E1 to G9P[8]-E1, G9P[8]-E2, and G3P[8]-E2 during these seven years. Rare strains (e.g., G9P[4]-E1, G3P[9]-E3 and G1P[8]-E2) were occasionally detected during the study. CONCLUSIONS During the study period, changes in the significant RVA circulating genotype combinations and the emergence of reassortment strains were observed, particularly the emergence and prevalence of G9P[8]-E2, G3P[8]-E2 reassortants in the region. These results indicate the importance of continuous monitoring of the molecular evolution and recombination characteristics of RVA, and should not be limited to G/P genotyping but should consider multi-gene fragment co-analysis and whole genome sequencing.
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Affiliation(s)
- Min Cao
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Fang Yuan
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xueping Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Jiangtao Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Xuemin Ma
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Hui Chen
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wei Zhang
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Jianhua Zhao
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China
| | - Wenhe Kuai
- Ningxia Center for Disease Control and Prevention, NO. 528 Shengli South Road, Yingchuan 750004, Ningxia Province, China.
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Maina MM, Faneye AO, Motayo BO, Nseabasi-Maina N, Adeniji AJ. Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine. J Int Med Res 2022; 50:3000605221121956. [PMID: 36138570 PMCID: PMC9511342 DOI: 10.1177/03000605221121956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objective This cross-sectional study investigated the circulating strains of rotavirus and screened for noravirus in Ibadan, Nigeria as the country introduces the rotavirus vaccine into its national immunization program. Methods Sixty-five stool samples were collected from children younger than 5 years with clinically diagnosed diarrhea and screened for the presence of rotavirus and norovirus using RT-PCR. Rotavirus-positive samples were further analyzed to determine the G and P genotypes using semi-nested multiplex PCR. Results The rates of rotavirus and norovirus positivity were 30.8% and 10.8%, respectively, whereas the rate of rotavirus and norovirus mixed infection was 4.6%. G1 was the predominant VP7 genotype, followed by G2, G9, and G1G2G9, whereas the predominant VP4 genotype was P[4], followed by P[6], P[8], and P[9]. The mixed P types P[4]P[8] and P[4]P[6] were also detected. G1P[4] was the most common VP4 and VP7 combination, followed by G2P[4], G1[P6], G1P[8], G2P[6], G2P[9], G9P[6], G2G9P[4], G2P[4]P[6], G1P[4]P[8], G2G9P[8], G1G2G9P[8], and G1[non-typable] P[non-typable], which were detected in at least 5% of the samples. Four samples had a combination of non-typable G and P types. Conclusions It is essential to monitor the circulation of virus strains prior to and during the implementation of the immunization program.
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Affiliation(s)
- Meshach Maunta Maina
- Department of Veterinary Microbiology, University of Maiduguri, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Nigeria
| | | | | | | | - Adekunle Johnson Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Nigeria.,WHO National Poliovirus laboratory, Department of Virology, University of Ibadan, Nigeria
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Motayo BO, Faneye AO, Adeniji JA. VP7, VP4, and NSP4 genes of species a rotaviruses isolated from sewage in Nigeria, 2014/2015: partial sequence characterization and biophysical analysis of NSP4 (enterotoxin). Virus Genes 2022; 58:180-187. [PMID: 35303217 DOI: 10.1007/s11262-022-01895-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
Abstract
Species A rotavirus are an important cause of childhood gastroenteritis, and the main contributor to its pathogenicity is the enterotoxin (NSP4) protein. Some biophysical properties of partial NSP4 genes of RVAs isolated from sewage in Nigeria during 2014/2015 were investigated. Samples were typed by RT-PCR and Sanger sequencing of partial VP4, VP7 and NSP4 genes. Phylogeny identified lineages within genotypes, predicted glycosylation sites; hydrophobicity profiles and amino acid alignments were employed to determine some biophysical properties of the NSP4 protein. The VP7 sequences of our isolates were the most diversified, the majority of the isolates carried NSP4 genes of the E1 genotype. Genotype specific variations both in hydrophobicity and potential glycosylation were identified, mutations were highest within the H3 hydrophobic domain and VP4 binding domain. The study of RVA NSP4 genes from non-clinical samples revealed that there were structural consistencies with those of reference genes.
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Affiliation(s)
- Babatunde O Motayo
- Department of Medical Microbiology, Federal Medical Center, Abeokuta, Nigeria.
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Olalemi AO, Akinwumi IM. Microbial health risks associated with rotavirus and enteric bacteria in River Ala in Akure, Nigeria. J Appl Microbiol 2022; 132:3995-4006. [PMID: 35179285 DOI: 10.1111/jam.15497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/19/2022] [Accepted: 02/13/2022] [Indexed: 11/28/2022]
Abstract
AIM This study was carried out to determine the microbial health risks associated with a surface water commonly used for bathing, drinking, domestic and irrigational activities in Akure, Nigeria. METHODS AND RESULTS Water samples were collected from the river from March to June, 2018. The load of enteric bacteria, somatic coliphages and rotavirus in the water samples were determined using culture-based methods and molecular technique. The physicochemical characteristics of the water samples were determined using standard methods. The risks of rotavirus, Salmonella and Shigella infections resulting from ingestion of the water from the river were estimated using dose-response model. Redundancy analysis revealed that the levels of E. coli and Salmonella were highly associated with salinity and turbidity. The risks of infection associated with rotavirus (3.3 × 10-3 ) was higher than those associated with Salmonella (1.3 × 10-4 ) and Shigella (1.3 × 10-3 ), and were all above the WHO acceptable risk limit (10-4 ). CONCLUSION Accidental or intentional ingestion of water from the river may pose potential risks of gastrointestinal illness to humans. SIGNIFICANCE AND IMPACT OF STUDY Quantitative microbial risk assessment is essential in establishing adequate water management practices that must be strictly followed in order to protect human health.
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Affiliation(s)
- A O Olalemi
- Department of Microbiology, Federal University of Technology, Ondo, Nigeria
| | - I M Akinwumi
- Department of Microbiology, Federal University of Technology, Ondo, Nigeria
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Manjate F, João ED, Chirinda P, Garrine M, Vubil D, Nobela N, Kotloff K, Nataro JP, Nhampossa T, Acácio S, Tate JE, Parashar U, Mwenda JM, Alonso PL, Nyaga M, Cunha C, Mandomando I. Molecular Epidemiology of Rotavirus Strains in Symptomatic and Asymptomatic Children in Manhiça District, Southern Mozambique 2008-2019. Viruses 2022; 14:v14010134. [PMID: 35062336 PMCID: PMC8781303 DOI: 10.3390/v14010134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 12/22/2022] Open
Abstract
Group A rotaviruses remain the leading cause of diarrhoea in children aged <5 years. Mozambique introduced rotavirus vaccine (Rotarix®) in September 2015. We report rotavirus genotypes circulating among symptomatic and asymptomatic children in Manhiça District, Mozambique, pre- and post-vaccine introduction. Stool was collected from enrolled children and screened for rotavirus by enzyme-immuno-sorbent assay. Positive specimens were genotyped for VP7 (G genotypes) and VP4 (P genotypes) by the conventional reverse transcriptase polymerase chain reaction. The combination G12P[8] was more frequently observed in pre-vaccine than in post-vaccine introduction, in moderate to severe diarrhoea (34%, 61/177 vs. 0, p < 0.0001) and controls (23%, 26/113 vs. 0, p = 0.0013) and mixed genotypes (36%, 24/67 vs. 7% 4/58, p = 0.0003) in less severe diarrhoea. We observed changes in post-vaccine compared to pre-vaccine introduction, where G3P[4] and G3P[8] were prevalent in moderate to severe diarrhoea (10%, 5/49 vs. 0, p = 0.0002; and 14%, 7/49 vs. 1%, 1/177, p < 0.0001; respectively), and in less severe diarrhoea (21%, 12/58 vs. 0, p = 0.003; and 24%, 14/58 vs. 0, p < 0.0001; respectively). Our surveillance demonstrated the circulation of similar genotypes contemporaneously among cases and controls, as well as switching from pre- to post-vaccine introduction. Continuous surveillance is needed to evaluate the dynamics of the changes in genotypes following vaccine introduction.
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Affiliation(s)
- Filomena Manjate
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal;
- Correspondence: (F.M.); (I.M.)
| | - Eva D. João
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
| | - Percina Chirinda
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
| | - Marcelino Garrine
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal;
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
| | - Nélio Nobela
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
| | - Karen Kotloff
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA;
| | - James P. Nataro
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA;
| | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene 1120, Mozambique
| | - Sozinho Acácio
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene 1120, Mozambique
| | - Jacqueline E. Tate
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (J.E.T.); (U.P.)
| | - Umesh Parashar
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (J.E.T.); (U.P.)
| | - Jason M. Mwenda
- African Rotavirus Surveillance Network, Immunization, Vaccines and Development Program, World Health Organization, Regional Office for Africa, Brazzaville P.O. Box 2465, Congo;
| | - Pedro L. Alonso
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
- ISGlobal, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
- Global Malaria Program, World Health Organization, 1211 Geneva, Switzerland
| | - Martin Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa;
| | - Celso Cunha
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal;
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça, Maputo 1929, Mozambique; (E.D.J.); (P.C.); (M.G.); (D.V.); (N.N.); (T.N.); (S.A.); (P.L.A.)
- Instituto Nacional de Saúde, Ministério da Saúde, Marracuene 1120, Mozambique
- Correspondence: (F.M.); (I.M.)
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Adeyemi OO, Alabi AS, Adeyemi OA, Talabi OT, Abidakun OM, Joel IY, Stonehouse NJ. Acute gastroenteritis and the usage pattern of antibiotics and traditional herbal medications for its management in a Nigerian community. PLoS One 2021; 16:e0257837. [PMID: 34607333 PMCID: PMC8490005 DOI: 10.1371/journal.pone.0257837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/12/2021] [Indexed: 11/23/2022] Open
Abstract
Acute gastroenteritis (AGE) is the highest cause of mortality worldwide in children under the age of 5 years, with the highest mortalities occurring in low-to-middle income countries. Treatment can involve use of unregulated herbal medication and antibiotics. A cross sectional study was carried out to investigate the use of antibiotics and traditional herbal medications in the management of AGE among Yòrùbá-speaking communities in Kwara State, Nigeria. Our findings suggest habitual use of antibiotics (54.6%) and herbal medication (42.5%) in the management of AGE with high levels of self-prescription of antibiotics (21.7%) and herbal medications (36.2%) within the community. Ethanolic extracts of selected herbal plants reported (i.e. Aristolochia ringens, Azadirachta indica, Chromolaena odorata, Etanda Africana, Ficus capensis, Ficus vogelii, Mangifera indica, Momordica charantia, Ocimum gratisimum, Senna alata, Sorghum bicolor and Vernonia amygdalina) were investigated for antibacterial properties, using bacteria known to be causative agents of AGE. Our findings showed that, with exception of Ficus vogelii, which enhanced bacterial growth, the plant extracts reported all showed some antibacterial activity. We further discuss our findings within a regulatory context, with the aim to guide the use of traditional and herbal medication in low-to medium income countries (LMICs) and reduce the potential risks associated with the development of antimicrobial resistance.
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Affiliation(s)
- Oluwapelumi Olufemi Adeyemi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Garstang Building, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (OOA); (NJS)
| | - Ade Stephen Alabi
- Department of Anatomy, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | | | - Olaoluwa Temitope Talabi
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Idi-Araba, Lagos, Nigeria
| | | | | | - Nicola J. Stonehouse
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, Garstang Building, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail: (OOA); (NJS)
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Makinde OM, Ayeni KI, Sulyok M, Krska R, Adeleke RA, Ezekiel CN. Microbiological safety of ready‐to‐eat foods in low‐ and middle‐income countries: A comprehensive 10‐year (2009 to 2018) review. Compr Rev Food Sci Food Saf 2020; 19:703-732. [DOI: 10.1111/1541-4337.12533] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/01/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Michael Sulyok
- Department of Agrobiotechnology (IFA–Tulln)Institute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU) Tulln Austria
| | - Rudolf Krska
- Department of Agrobiotechnology (IFA–Tulln)Institute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU) Tulln Austria
- Institute for Global Food Security, School of Biological SciencesQueen's University Belfast Belfast United Kingdom
| | - Rasheed A. Adeleke
- Department of MicrobiologyNorth‐West University Potchefstroom South Africa
| | - Chibundu N. Ezekiel
- Department of MicrobiologyBabcock University Ilishan Remo Nigeria
- Department of Agrobiotechnology (IFA–Tulln)Institute of Bioanalytics and Agro‐Metabolomics, University of Natural Resources and Life Sciences Vienna (BOKU) Tulln Austria
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Motayo BO, Oluwasemowo OO, Olusola BA, Opayele AV, Faneye AO. Phylogeography and evolutionary analysis of African Rotavirus a genotype G12 reveals district genetic diversification within lineage III. Heliyon 2019; 5:e02680. [PMID: 31687512 PMCID: PMC6820252 DOI: 10.1016/j.heliyon.2019.e02680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/30/2019] [Accepted: 10/14/2019] [Indexed: 12/11/2022] Open
Abstract
Group A rotavirus (RVA) genotype G12 has spread globally and has become one of the most prevalent genotypes of rotavirus in Africa. To understand the drivers for its genetic diversity and rapid spread we investigated the Bayesian phylogeography, viral evolution and population demography of Rotavirus G12 in Africa. We downloaded and aligned VP7 gene sequences of Rotavirus genotype G12, from thirteen African countries (n = 96). Phylogenetic analysis, Evolutionary analysis and Bayesian Phylogeography was carried out, using MEGA Vs 6, BEAST, and SPREAD3. Phylogenetic analysis revealed that all the African sequences fell into lineage III diversifying into two major clades. The evolutionary rate of the African rotavirus G12 sequences was 1.678×10-3, (95% HPD, 1.201×10-3 - 2.198×10-3) substitutions/site/year, with TMRC of 16.8 years. The Maximum clade credibility (MCC) tree clustered into three lineages (II, III, IV), African strains fell within lineage III, and diversified into three clusters. Phylogeography suggested that South Africa seemed to be the epicentre of dispersal of the genotype. The demographic history of the G12 viruses revealed a steady increase between the years1998-2007, followed by a sharp decrease in effective population size between the years 2008-2011. We have shown the potential for genetic diversification of Rotavirus genotype G12 in Africa. We recommend the adoption of Molecular surveillance across Africa to further control spread and diversification of Rotavirus.
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Affiliation(s)
- Babatunde Olanrewaju Motayo
- Department of Virology, College of Medicine, University of Ibadan, Nigeria.,Department of Medical Microbiology, Federal Medical Center, Abeokuta, Nigeria
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