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Badjo AOR, Niendorf S, Jacobsen S, Zongo A, Mas Marques A, Vietor AC, Kabore NF, Poda A, Some SA, Ouattara A, Ouangraoua S, Schubert G, Eckmanns T, Leendertz FH, Belarbi E, Ouedraogo AS. Genetic diversity of enteric viruses responsible of gastroenteritis in urban and rural Burkina Faso. PLoS Negl Trop Dis 2024; 18:e0012228. [PMID: 38976836 PMCID: PMC11230633 DOI: 10.1371/journal.pntd.0012228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/20/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Viral gastrointestinal infections remain a major public health concern in developing countries. In Burkina Faso, there are very limited updated data on the circulating viruses and their genetic diversity. OBJECTIVES This study investigates the detection rates and characteristics of rotavirus A (RVA), norovirus (NoV), sapovirus (SaV) and human astrovirus (HAstV) in patients of all ages with acute gastrointestinal infection in urban and rural areas. STUDY DESIGN & METHODS From 2018 to 2021, stool samples from 1,295 patients with acute gastroenteritis were collected and screened for RVA, NoV, SaV and HAstV. Genotyping and phylogenetic analyses were performed on a subset of samples. RESULTS At least one virus was detected in 34.1% of samples. NoV and SaV were predominant with detection rates of respectively 10.5 and 8.8%. We identified rare genotypes of NoV GII, RVA and HAstV, recombinant HAstV strains and a potential zoonotic RVA transmission event. CONCLUSIONS We give an up-to-date epidemiological picture of enteric viruses in Burkina Faso, showing a decrease in prevalence but a high diversity of circulating strains. However, viral gastroenteritis remains a public health burden, particularly in pediatric settings. Our data advocate for the implementation of routine viral surveillance and updated management algorithms for diarrheal disease.
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Affiliation(s)
- Ange Oho Roseline Badjo
- Laboratory of Emerging and Re-emerging Pathogens, Nazi Boni University, Bobo Dioulasso, Burkina Faso
| | | | | | | | | | | | | | - Armel Poda
- Laboratory of Emerging and Re-emerging Pathogens, Nazi Boni University, Bobo Dioulasso, Burkina Faso
- Centre MURAZ, Bobo-Dioulasso, Burkina Faso
- Department of Infectious Diseases, University Hospital Souro Sanou, Bobo-Dioulasso, Burkina Faso
| | | | - Aminata Ouattara
- Laboratory of Emerging and Re-emerging Pathogens, Nazi Boni University, Bobo Dioulasso, Burkina Faso
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | | | | | | | | | - Abdoul-Salam Ouedraogo
- Laboratory of Emerging and Re-emerging Pathogens, Nazi Boni University, Bobo Dioulasso, Burkina Faso
- Centre MURAZ, Bobo-Dioulasso, Burkina Faso
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
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Olaimat AN, Taybeh AO, Al-Nabulsi A, Al-Holy M, Hatmal MM, Alzyoud J, Aolymat I, Abughoush MH, Shahbaz H, Alzyoud A, Osaili T, Ayyash M, Coombs KM, Holley R. Common and Potential Emerging Foodborne Viruses: A Comprehensive Review. Life (Basel) 2024; 14:190. [PMID: 38398699 PMCID: PMC10890126 DOI: 10.3390/life14020190] [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: 12/13/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Human viruses and viruses from animals can cause illnesses in humans after the consumption of contaminated food or water. Contamination may occur during preparation by infected food handlers, during food production because of unsuitably controlled working conditions, or following the consumption of animal-based foods contaminated by a zoonotic virus. This review discussed the recent information available on the general and clinical characteristics of viruses, viral foodborne outbreaks and control strategies to prevent the viral contamination of food products and water. Viruses are responsible for the greatest number of illnesses from outbreaks caused by food, and risk assessment experts regard them as a high food safety priority. This concern is well founded, since a significant increase in viral foodborne outbreaks has occurred over the past 20 years. Norovirus, hepatitis A and E viruses, rotavirus, astrovirus, adenovirus, and sapovirus are the major common viruses associated with water or foodborne illness outbreaks. It is also suspected that many human viruses including Aichi virus, Nipah virus, tick-borne encephalitis virus, H5N1 avian influenza viruses, and coronaviruses (SARS-CoV-1, SARS-CoV-2 and MERS-CoV) also have the potential to be transmitted via food products. It is evident that the adoption of strict hygienic food processing measures from farm to table is required to prevent viruses from contaminating our food.
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Affiliation(s)
- Amin N. Olaimat
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (M.A.-H.); (M.H.A.)
| | - Asma’ O. Taybeh
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan; (A.O.T.); (A.A.-N.); (T.O.)
| | - Anas Al-Nabulsi
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan; (A.O.T.); (A.A.-N.); (T.O.)
| | - Murad Al-Holy
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (M.A.-H.); (M.H.A.)
| | - Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Jihad Alzyoud
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (J.A.); (I.A.)
| | - Iman Aolymat
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (J.A.); (I.A.)
| | - Mahmoud H. Abughoush
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan; (M.A.-H.); (M.H.A.)
- Science of Nutrition and Dietetics Program, College of Pharmacy, Al Ain University, Abu Dhabi P.O. Box 64141, United Arab Emirates
| | - Hafiz Shahbaz
- Department of Food Science and Human Nutrition, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan;
| | - Anas Alzyoud
- Faculty of Medicine, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Tareq Osaili
- Department of Nutrition and Food Technology, Faculty of Agriculture, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan; (A.O.T.); (A.A.-N.); (T.O.)
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Mutamed Ayyash
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, P.O. Box 15551, Al Ain 53000, United Arab Emirates;
| | - Kevin M. Coombs
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| | - Richard Holley
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
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Su L, Mao H, Sun Y, Yan H, Ge Q, Gong L, Zhang Y. The analysis of the genotype of Sapovirus outbreaks in Zhejiang Province. Virol J 2023; 20:268. [PMID: 37974193 PMCID: PMC10655437 DOI: 10.1186/s12985-023-02202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Sapovirus (SaV) infection is increasing globally. Concurrently, several SaV-outbreaks were observed in children of Zhejiang province, China, in recent years, In this study, the genotypes of Sapovirus from seven outbreaks in the Zhejiang province were analysed. METHODS A total of 105 faecal samples were collected from children aged between 4 and 17 years from the Zhejiang Provincial Center for Disease Control and Prevention between October 2021 and February 2023. Genotypes were processed using reverse transcription polymerase chain reaction and Sanger sequencing, while next-generation sequencing was used to generate a complete viral genome. Deduced amino acid sequences were analysed to detect VP1 gene mutations. RESULTS In total, 60 SaV-positive patients were detected at a 57.14% (60/105) positivity rate. Positive rates in the seven outbreaks were: 22.22% (2/9), 15.00% (3/20), 93.10% (27/29), 84.21% (16/19), 28.57% (2/7), 53.33% (8/15) and 33.33% (2/6), respectively. Four genotypes were identified in the seven outbreaks, of which, GI.1 accounted for 14.29% (1/7), GI.2 accounted for 14.29% (1/7), GI.6 and GII.5 accounted for 14.29% (1/7), and GI.6 accounted for 57.14% (4/7). All patients were children and outbreaks predominantly occurred in primary schools and during cold seasons. Additionally, the complete sequence from the GI.6 outbreak strain showed high homology (identity: 99.99%) with few common substitutions (Y300S, N302S and L8M) in VP1 protein. CONCLUSIONS SaV genotype diversity was observed in the seven outbreaks, with GI.6 being the main SaV genotype in Zhejiang province. It demonstrated high homology and may provide a platform for SaV prevention and control measures.
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Affiliation(s)
- Lingxuan Su
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Haiyan Mao
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Yi Sun
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Hao Yan
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Qiong Ge
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China
| | - Liming Gong
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China.
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, 3399 Binsheng Road, Hangzhou, 310051, China.
- Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Provincial, 3399 Binsheng Road, Hangzhou, 310051, China.
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Jiao Y, Han T, Qi X, Gao Y, Zhao J, Zhang Y, Li B, Zhang Z, Du J, Sun L. Genotypes Diversity of Acute Gastroenteritis Outbreaks Caused by Human Sapovirus - Beijing Municipality, China, 2015-2021. China CDC Wkly 2023; 5:625-631. [PMID: 37520444 PMCID: PMC10372411 DOI: 10.46234/ccdcw2023.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/05/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Human sapovirus (HuSaV) is an enteric virus responsible for sporadic cases and outbreaks of acute gastroenteritis (AGE) globally. A seven-year active surveillance study was conducted to investigate the molecular epidemiology of HuSaVs associated with AGE outbreaks in Chaoyang District of Beijing Municipality, China from January 2015 to December 2021. Methods Fecal and anal swab samples were obtained from patients experiencing AGE outbreaks. HuSaVs were identified through reverse transcription polymerase chain reaction (RT-PCR), and partial viral protein 1 (VP1) sequences (approximately 434 base pairs) were utilized for genotyping, single nucleotide polymorphism (SNP) analysis, and phylogenetic examination. Results HuSaVs were identified in 71 AGE outbreaks, demonstrating a detection rate of 10.5%, second only to norovirus. The primary demographic affected by HuSaV were children under the age of 5 in kindergarten settings. Infection rates tended to peak during two distinct periods: May to June and September to December. Upon genotyping, seven distinct genotypes emerged. GII.3 was the most prevalent, accounting for 54.9% of cases, followed by GI.1 (12.7%), GI.2 (9.9%), GII.5 (7.0%), GI.5 (2.8%), GI.6 (1.4%), GII.1 (1.4%), and untyped cases (9.9%). A phylogenetic analysis of GII.3 identified three distinct groups, with 15 notable SNPs observed. Conclusions This study offers a comprehensive analysis of the persistent prevalence of HuSaV outbreaks in Chaoyang District, Beijing Municipality, China. Over time, the diversity of HuSaV subtypes has shifted, and it is now recognized as the second leading viral agent responsible for AGE outbreaks. This highlights the importance of ongoing surveillance in the future.
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Affiliation(s)
- Yang Jiao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Taoli Han
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Xiao Qi
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Yan Gao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Jianhong Zhao
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Yue Zhang
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Beibei Li
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Zheng Zhang
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Jialiang Du
- National Institutes for Food and Drug Control, Beijing, China
| | - Lingli Sun
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
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High Burden of Co-Infection with Multiple Enteric Pathogens in Children Suffering with Diarrhoea from Rural and Peri-Urban Communities in South Africa. Pathogens 2023; 12:pathogens12020315. [PMID: 36839587 PMCID: PMC9959912 DOI: 10.3390/pathogens12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023] Open
Abstract
Infectious diarrhoea contributes to high morbidity and mortality in young children from sub-Saharan Africa. The aim of this study was to assess the prevalence of single and multiple diarrhoeal-causing pathogen combinations in children suffering from diarrhoea from rural and peri-urban communities in South Africa. A total of 275 diarrhoea stool specimens were collected between 2014 and 2016 from Hospitals and Primary Health Care clinics. The BioFire® FilmArray® Gastrointestinal panel was used to simultaneously detect 22 diarrhoea pathogens (viruses, bacteria, parasites) known to cause diarrhoea. A total of 82% (226/275) enteric pathogens were detected in the stool specimens. The two most detected bacterial, viral and parasitic pathogens each included: EAEC (42%), EPEC (32%), Adenovirus F40/41 (19%), Norovirus (15%), Giardia (8%) and Cryptosporidium (6%), respectively. Single enteric pathogen infections were recorded in 24% (65/275) specimens with EAEC, and Norovirus was found in 26% (17/65) and 14% (9/65) of the specimens, respectively. Multiple enteric pathogen combinations were recorded in 59% (161/275) of the stool specimens with 53% (85/161) containing two pathogens, 22% (35/161) containing three pathogens and 25% (41/161) containing four or more pathogens. The results from this study demonstrated the complex nature of pathogen co-infections in diarrhoeal episodes which could have an impact on treatment effectiveness.
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Matamoros DJP, Worsfold CS, Campos RC, Acuña HMB, Chacón EC, Sánchez CFJ. Molecular characterization of norovirus and sapovirus detected in animals and humans in Costa Rica: Zoo-anthropozoonotic potential of human norovirus GII.4. Open Vet J 2023; 13:74-89. [PMID: 36777439 PMCID: PMC9897497 DOI: 10.5455/ovj.2023.v13.i1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Background Noroviruses (NoV) and sapoviruses (SaV) are major causes of acute viral gastroenteritis in humans worldwide, as well as gastrointestinal infections in animals. However, it has not been determined whether these viruses are zoonotic pathogens. Aim In this study, we investigated the presence of NoV and SaV in stool samples from dogs, pigs, cows, and humans to determine some aspects of the molecular epidemiology and the genetic relationship of several strains present in these species. Methods Polymerase chain reaction and sequencing of NoV and SaV strains present in stool samples from humans and dogs with diarrhea, pigs, and cattle with and without diarrhea were carried out during fragmented periods from 2002 to 2012. Results Of all samples analyzed, 11.6% (123/1,061) of the samples were positive for NoV and 0.88% (9/1,023) were positive for SaV. The phylogenetic analysis confirmed 16 human strains of NoV (HuNoV) belonging to HuNoV G?/GII.P2 (1), GII.4/GII.P4 (5), G?/GII.P4 (9), and GII.6/GII.P6 (1) and allowed us to verify and assign three strains of human SaV to genotypes GI.2 (1) and GII.5 (2). In dogs, eight strains of NoV [HuNoV G?/GII.P4 (4) and canine G?/GVI.P1 (4)] and two strains of canine SaV were determined. In pigs, six strains were assigned to HuNoV G?/GII.P4 and four strains to porcine SaV were assigned to genogroup GIII (2), GVIII (1), and GXI (1). In bovines, five strains were characterized as HuNoV G?/GII.P4. Conclusions This study showed that NoV and SaV prototype strains have been present in humans and dogs in Costa Rica. Additionally, it revealed that the zoonotic potential of SaV is very limited, while the zoonotic implications for HuNoV GII.4 are stronger due to the simultaneous circulation of strains related to HuNoV GII.4 in four species, which suggests a zoo-anthropozoonosis.
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Affiliation(s)
- Derling José Pichardo Matamoros
- Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica,Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Corresponding Author: Derling José Pichardo Matamoros. Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica.
| | | | - Rocío Cortés Campos
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
| | - Hilda María Bolaños Acuña
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Elena Campos Chacón
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Carlos Francisco Jiménez Sánchez
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
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Colito DA, Dorta-Guerra R, Da Costa Lima HS, Pina C, Gonçalves D, Valladares B, Foronda P. Epidemiological investigations of diarrhea in children in Praia city, Cape Verde. Front Microbiol 2022; 13:1059431. [PMID: 36619987 PMCID: PMC9814011 DOI: 10.3389/fmicb.2022.1059431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Diarrheal disease is a major cause of infant mortality and morbidity in Africa and results primarily from contaminated food and water sources, but its prevalence predictors in Cape Verde are not completely known. For this reason, this study aimed to identify the etiological agents of diarrhea in Cape Verdean children and assess its associated risk factors. Methods A survey questionnaire was used, and a total of 105 stool samples from children with diarrhea aged 0-12 years at the Central Hospital of Praia (Santiago, Cape Verde) were analyzed. The analyses were carried out using Biofire FilmArray Gastrointestinal Panels. Possible risk factors for these pathogens were analyzed using logistic regression, chi-square tests, or Fisher's exact test. Results Among the bacteria, enteroaggregative Escherichia coli (45.71%; 95% CI: 36.71-56.70), enteropathogenic E. coli (40%; 95% CI: 30.56-50.02), Shigella/enteroinvasive E. coli (29.52%; 95% CI: 21.02-39.22), E. coli enterotoxigenic (12.38%; 95% CI: 6.76-20.24), Campylobacter sp. (10.48%; 95% CI: 5.35-1.97), Vibrio sp. (4.76%; 95% CI: 1.56-10.76), Clostridioides difficile (3.81%; 95% CI: 1.05-9.47), Vibrio cholerae (2.86%; 0.59-8.12), Shiga-like toxin-producing E. coli (2.86%; 0.59-8.12) and Salmonella sp. (0.95%; 0.02-5.19) were identified; four viruses, Rotavirus A (28.57%; 95% CI: 20.18-38.21), Sapovirus I. II. IV and V (11.43%; 95% CI: 6.05-19.11), Norovirus GI.GII (6.67%; 95% CI: 2.72-13.25) and Adenovirus F 40.41 (6.67%; 95% CI: 2.72-13.25) were also observed. All the pathogens detected in this study were found in coinfections. Significant associations with risk factors were found; specifically, having a bathroom at home reduced the risk of Campylobacter sp., having animals at home increased the risk of Shigella/EIEC infection, and drinking bottled water reduced the risk of Sapovirus infection. Discussion From the findings of this study, it can be concluded that, in Cape Verde, there is a high prevalence and diversity of pathogens among children. Our results could help to establish an adequate diagnosis and effective treatments for diarrheal disease.
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Affiliation(s)
| | - Roberto Dorta-Guerra
- Departamento de Matemáticas, Estadística e IO, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Carine Pina
- Faculty of Science and Technology, University of Cape Verde, Palmarejo, Cape Verde
| | - Deisy Gonçalves
- Faculty of Science and Technology, University of Cape Verde, Palmarejo, Cape Verde
| | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Pilar Foronda
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, San Cristóbal de La Laguna, Spain,*Correspondence: Pilar Foronda,
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Elbashir I, Aldoos NF, Mathew S, Al Thani AA, Emara MM, Yassine HM. Molecular epidemiology, genetic diversity, and vaccine availability of viral acute gastroenteritis in the middle East and North Africa (MENA) region. J Infect Public Health 2022; 15:1193-1211. [PMID: 36240530 DOI: 10.1016/j.jiph.2022.09.001] [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: 05/15/2022] [Revised: 08/26/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
Acute gastroenteritis is the cause of considerable mortality and morbidity worldwide, particularly among children under five years in underdeveloped countries. Most acute gastroenteritis (AGE) cases are attributed to viral etiologies, including rotavirus, norovirus, adenovirus, astrovirus, and sapovirus. This paper aimed to determine the prevalence rate of different viral etiologies of AGE in the Middle East and North Africa (MENA) region. Moreover, this paper explored rotavirus phylogenetic relatedness, compared VP7 and VP4 antigenic regions of rotavirus with vaccine strains, and explored the availability of vaccines in the MENA region. The literature search identified 160 studies from 18 countries from 1980 to 2019. The overall prevalence of rotavirus, norovirus, adenovirus, astrovirus, and sapovirus were 29.8 %, 13.9 %, 6.3 %, 3.5 %, and 3.2 % of tested samples, respectively. The most common rotavirus genotype combinations in the MENA region were G1P[8], G9P[9], and G2P[4], whereas GII.4 was the predominant norovirus genotype all of which were reported in almost all the studies with genotyping data. The comparison of VP7 and VP4 between circulating rotavirus in the MENA region and vaccine strains has revealed discrete divergent regions, including the neutralizing epitopes. Rotavirus vaccine was introduced to most of the countries of the MENA region; however, only a few studies have assessed the effectiveness of vaccine introduction. This paper provides a comprehensive update on the prevalence of the different viral agents of AGE in the MENA region.
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Affiliation(s)
- Israa Elbashir
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Noor F Aldoos
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar.
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
| | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar; Department of Biomedical Sciences, College of Health Science-QU Health, Qatar University, Doha 2713, Qatar
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar.
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, 2713 Doha, Qatar.
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Partial Analysis of the Capsid Protein (VP1) of Human Sapovirus Isolated from Children with Diarrhoea in Rural Communities of South Africa. Adv Virol 2022; 2022:9928378. [PMID: 35693126 PMCID: PMC9184228 DOI: 10.1155/2022/9928378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
Background Viral diarrhoea is a concern in acute gastroenteritis cases among children younger than 5 years of age. Sapovirus has been noted as an emerging causative agent of acute gastroenteritis worldwide. Objective/Study Design. The aim of this study was to characterize human sapoviruses targeting the VP1 (NVR and N-terminal) region. Twenty-five samples were randomly selected from 40 sapovirus-positive samples previously detected and analyzed for the VP1 region using the One-Step RT-PCR assay. The PCR products were subjected to Sanger sequencing analysis. Results The polyprotein segment (NVR and N-terminal) was successfully amplified from 10/25 samples. Sapovirus GI.1 was the most predominant strain (6/10; 60%), followed by SV-GII.1 (2/10; 20%) and 10% of each GI.3 and GII.3. Conclusion Through the partial analysis of the VP1 region, this study provides more data to add on the human sapovirus genetic characterization of circulating strains in South Africa, with the proposition of further analysis of sapovirus VP1 fragments for the viral structure and function.
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Hoque SA, Nishimura K, Thongprachum A, Khamrin P, Thi Kim Pham N, Islam MT, Khandoker N, Okitsu S, Onda-Shimizu Y, Dey SK, Maneekarn N, Kobayashi T, Hayakawa S, Ushijima H. An Increasing Trend of Human Sapovirus Infection in Japan, 2009 to 2019: An Emerging Public Health Concern. J Infect Public Health 2022; 15:315-320. [DOI: 10.1016/j.jiph.2022.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
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Zaki MES, Shrief R, Hassan RH. Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020. F1000Res 2021; 10:123. [PMID: 34900224 PMCID: PMC8630562 DOI: 10.12688/f1000research.29991.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Sapovirus has emerged as a viral cause of acute gastroenteritis. However, there is limited data on sapovirus in Egypt. . The present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis <5 years in Mansoura, Egypt from January 2019 to February 2020 by reverse transcriptase-polymerase chain reaction (RT-PCR). Methods: The cross-sectional study enrolled a 100 children <5 years who presented with acute gastroenteritis at an outpatient clinic in Mansoura, Egypt between January 2019 and February 2020. Clinical data, demographic data and a stool sample was collected from each child. Stools were screened by microscopy for parasites and culture methods for bacteria and excluded from the study if positive for either. Specimens were also screened for rotavirus by enzyme immune assays (EIA) and sapovirus by reverse transcription PCR. Results: The most frequently detected virus was rotavirus by ELISA 25% (25/100). RT-PCR detected sapovirus in 7% (7/100) of the stool samples. The children with sapovirus were all from rural regions and presented mainly during the winter season in Egypt 42.9% (3/7). The main presenting symptoms were fever 71.4% (5/7) and vomiting 57.1% (4/7). None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in five samples (5/7) , 71.4%, P=0.01. Conclusion: The present study highlights the emergence of sapovirus as a frequent pathogen associated with acute gastroenteritis in children. There is a need for a national survey program for the study of sapovirus among other pathogens associated with acute gastroenteritis for better management of such infection.
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Affiliation(s)
- Maysaa El Sayed Zaki
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Raghdaa Shrief
- Medical Microbioogy and Immunology Department, Faculty of Medicine, Damietta University, New Damietta, 34511, Egypt
| | - Rasha H Hassan
- Pediatrics Department, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
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Razizadeh MH, Khatami A, Zarei M. Global molecular prevalence and genotype distribution of Sapovirus in children with gastrointestinal complications: A systematic review and meta-analysis. Rev Med Virol 2021; 32:e2302. [PMID: 34626019 DOI: 10.1002/rmv.2302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/11/2023]
Abstract
Sapovirus (SaV) is an emerging cause of children gastrointestinal complications such as acute gastroenteritis (AGE). The aim of the present systematic review and meta-analysis was to estimate the global prevalence of the SaV in children and association of infection with SaVs and AGE in children based on case-control studies. Four international databases (PubMed, Scopus, Web of Sciences and Google Scholar) were used to retrieve English-language studies published between January 2000 and December 2020. Comprehensive Meta-Analysis software was applied to estimate the overall prevalence, publication bias and heterogeneity index. The pooled prevalence of SaV infection among children with gastroenteritis was 3.4% [95% confidence interval (CI): 2.9%-3.9%] based on a random-effects meta-analysis. Genogroup I was the dominant genogroup of SaV in children with gastroenteritis [2.2% (95% CI: 1.6%-3.0%)], association analysis showed that SaV was associated with gastroenteritis [OR: 1.843 (95% CI: 1.27-2.66)]. Given the significant prevalence of the virus in children, it is necessary to pay more attention to this situation. Therefore, preventive health measures in children should be a priority.
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Affiliation(s)
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Zarei
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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Rahman R, Rahman S, Afrad MMH, Talha M, Islam D, Uddin KMM, Ahmed S, Afrad MH, Faruque ASG, Hossian ME, Rahman M. Epidemiology and genetic characterization of human sapovirus among hospitalized acute diarrhea patients in Bangladesh, 2012-2015. J Med Virol 2021; 93:6220-6228. [PMID: 34081341 DOI: 10.1002/jmv.27125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/09/2022]
Abstract
Human sapovirus, which causes acute gastroenteritis, is not well studied and poorly understood. This study aims to investigate the contribution of sapovirus in diarrhea, their clinical association, and genotypic diversity. Fecal specimens (n = 871) were randomly selected from diarrheal patients who attended International Centre for Diarrhoeal Disease Research, Bangladesh hospital in Dhaka, Bangladesh during January 2012-December 2015 and tested for the presence of sapovirus RNA using real-time polymerase chain reaction. Sapovirus RNA was identified in 2.3% (n = 20) of the samples. Seventy-five percent of the sapovirus positive cases were coinfected with other pathogens, such as rotavirus, norovirus, enterotoxigenic Escherichia coli, adenovirus, Shigella spp., and Vibrio cholerae. A vast genetic diversity was observed among sapovirus with at least seven common genotypes (GI.1, GI.2, GI.7, GII.1, GII.4, GII.6, and GIV), and a new genotype GII.NA1. Some of the GI.1 strains detected were similar to GI.4 in the polymerase region sequence and were confirmed as recombinant strains. Our findings suggest that the overall contribution of sapovirus in hospitalized diarrheal illness is low but highlight enormous genetic diversity.
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Affiliation(s)
- Rajibur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Sezanur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Md M H Afrad
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Muhammad Talha
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Deen Islam
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - K M Main Uddin
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mokibul H Afrad
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Abu S G Faruque
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mohammad E Hossian
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, Infectious Diseases Division (IDD), International Centre for Diarrhoeal Disease Research (ICDDR), Bangladesh, Dhaka, Bangladesh
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Cilli A, Luchs A, Morillo SG, Carmona RDCC, Dos Santos FCP, Maeda AY, Primo D, Pacheco GT, Souza EV, Medeiros RS, Timenetsky MDCST. Surveillance and molecular characterization of human sapovirus in patients with acute gastroenteritis in Brazil, 2010 to 2017. J Clin Virol 2021; 140:104844. [PMID: 33971579 DOI: 10.1016/j.jcv.2021.104844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/06/2021] [Accepted: 04/17/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Human sapoviruses (HuSaV) are associated with acute gastroenteritis (AGE), causing sporadic cases and outbreaks in patients worldwide. In Brazil, however, there are few reports describing the prevalence of HuSaV in patients with AGE. OBJECTIVE Describing the diversity of HuSaV in Brazil by detecting and molecularly characterizing HuSaV among patients with AGE during an 8-year period (2010-2017). STUDY DESIGN A total of 3974 stool samples, testing negative for rotavirus (RVA), norovirus (NoV) and human adenovirus (HAdV), were selected and screened for the presence of HuSaV. Nested RT-PCR were performed for a partial region of VP1, sequenced and genetic analyzed for genotyping the positive samples. RESULTS In the current study, the HuSaV prevalence was determined to be 3.7% (149/3974). A higher prevalence, 5.7% (118/2074), was observed in children under 2 years of age. During the surveillance period, 13 outbreaks were detected: 12 outbreaks in children under 3 years old and one outbreak in adults. Among the 149 HuSaV positive cases, 106 samples (71%) were successfully sequenced. The most prevalent genotype found was GI.1 (44.3%), followed by GI.2 (21.7%), GI.3 (3.8%), GI.6 (2.8%), GII.1 (5.7%), GII.2 (8.5%), GII.3 (2.8%), GII.4 (2.8%), GII.5 (5.7%) and GIV.1 (1.9%). Two GIV.1 strains characterized in this study are, to date, the only strains of this genotype reported in Brazil. CONCLUSIONS The present study elucidated the circulation of HuSaV in Brazil and highlight that HuSaV has not assumed an epidemiological importance in the country after the introduction of the RVA vaccine.
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Affiliation(s)
- Audrey Cilli
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil.
| | - Adriana Luchs
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Simone G Morillo
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | | | | | - Adriana Y Maeda
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Dieli Primo
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Gabriela T Pacheco
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Ellen V Souza
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Roberta S Medeiros
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
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Manouana GP, Nguema-Moure PA, Mbong Ngwese M, Bock CT, Kremsner PG, Borrmann S, Eibach D, Mordmüller B, Velavan TP, Niendorf S, Adegnika AA. Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon. Viruses 2021; 13:545. [PMID: 33805214 PMCID: PMC8064335 DOI: 10.3390/v13040545] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022] Open
Abstract
Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.
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Affiliation(s)
- Gédéon Prince Manouana
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP 242, Gabon
| | - Paul Alvyn Nguema-Moure
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
| | - Mirabeau Mbong Ngwese
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
| | - C.-Thomas Bock
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
- Division of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Peter G. Kremsner
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP 242, Gabon
- German Center for Infection Research (DZIF), 72074 Tübingen, Germany
| | - Steffen Borrmann
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP 242, Gabon
- German Center for Infection Research (DZIF), 72074 Tübingen, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany;
| | - Benjamin Mordmüller
- Department of Medical Microbiology, Radboudumc, 6524 GA Nijmegen, The Netherlands;
| | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 100000, Vietnam
- Faculty of Medicine, Duy Tan University, Da Nang 550000, Vietnam
| | - Sandra Niendorf
- Division of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Ayola Akim Adegnika
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, 72074 Tübingen, Germany; (G.P.M.); (P.A.N.-M.); (M.M.N.); (C.-T.B.); (P.G.K.); (S.B.); (T.P.V.); (A.A.A.)
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné BP 242, Gabon
- German Center for Infection Research (DZIF), 72074 Tübingen, Germany
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Magwalivha M, Ngandu JPK, Traore AN, Potgieter N. Prevalence and Genetic Characterisation of Human Sapovirus from Children with Diarrhoea in the Rural Areas of Vhembe District, South Africa, 2017-2020. Viruses 2021; 13:393. [PMID: 33804579 PMCID: PMC8000493 DOI: 10.3390/v13030393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/29/2022] Open
Abstract
Diarrhoeal disease is considered an important cause of morbidity and mortality in developing areas, and a large contributor to the burden of disease in children younger than five years of age. This study investigated the prevalence and genogroups of human sapovirus (SV) in children ≤5 years of age in rural communities of Vhembe district, South Africa. Between 2017 and 2020, a total of 284 stool samples were collected from children suffering with diarrhoea (n = 228) and from children without diarrhoea (n = 56). RNA extraction using Boom extraction method, and screening for SV using real-time PCR were done in the lab. Positive samples were subjected to conventional RT-PCR targeting the capsid fragment. Positive sample isolates were genotyped using Sanger sequencing. Overall SV were detected in 14.1% (40/284) of the stool samples (16.7% (38/228) of diarrhoeal and 3.6% (2/56) of non-diarrhoeal samples). Significant correlation between SV positive cases and water sources was noted. Genogroup-I was identified as the most prevalent strain comprising 81.3% (13/16), followed by SV-GII 12.5% (2/16) and SV-GIV 6.2% (1/16). This study provides valuable data on prevalence of SV amongst outpatients in rural and underdeveloped communities, and highlights the necessity for further monitoring of SV circulating strains as potential emerging strains.
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Affiliation(s)
- Mpho Magwalivha
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou 0950, South Africa; (J.-P.K.N.); (A.N.T.); (N.P.)
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Sakagami A, Ueki Y, Dapat C, Saito M, Oshitani H. Genetic analysis of sapoviruses detected in outbreaks and sporadic cases of acute gastroenteritis in Miyagi Prefecture, Japan. J Clin Virol 2020; 132:104648. [PMID: 33038625 DOI: 10.1016/j.jcv.2020.104648] [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: 04/17/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Human sapovirus (SaV) causes sporadic and endemic acute gastroenteritis worldwide. However, little is known about the relationship between the mode of transmission and genetic characteristics of SaV. OBJECTIVE To investigate the molecular characteristics of SaV-associated acute gastroenteritis among sporadic cases, foodborne, and nonfoodborne outbreaks. STUDY DESIGN We performed a systematic review of publications and genetic analysis of SaV in fecal specimens from 98 outpatients with acute gastroenteritis, 32 stool samples from 8 foodborne outbreaks, and 63 stool samples from 23 nonfoodborne outbreaks in Miyagi Prefecture, Japan from 1993 and between 2004 and 2020. Reverse transcription polymerase chain reaction (RT-PCR) was employed for the detection of SaV, and the partial capsid gene was sequenced for genotyping and phylogenetic analysis. RESULTS The overall detection rate of SaV in sporadic cases, foodborne, and nonfoodborne outbreaks was 5.8, 1.7, and 4.3%, respectively. Genotypic analysis revealed GI.1 to be the predominant genotype in sporadic cases (31.5%) and nonfoodborne outbreaks (52.1%), whereas it was not detected in foodborne outbreaks. Some outbreaks occurred following sporadic cases with the same genotype. CONCLUSIONS The distribution of SaV genotypes was different between foodborne outbreaks and other settings. The effective SaV infection control may differ depending on the genomic characteristics.
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Affiliation(s)
- Akie Sakagami
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, 4-7-2 Saiwai-cho, Miyagino-ku, Sendai, Miyagi 983-0836, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, 4-7-2 Saiwai-cho, Miyagino-ku, Sendai, Miyagi 983-0836, Japan
| | - Clyde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
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Molecular detection and characterisation of sapoviruses and noroviruses in outpatient children with diarrhoea in Northwest Ethiopia. Epidemiol Infect 2020; 147:e218. [PMID: 31364546 PMCID: PMC6625200 DOI: 10.1017/s0950268819001031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Childhood morbidity and mortality of diarrhoeal diseases are high, particularly in low-income countries and noroviruses and sapoviruses are among the most frequent causes worldwide. Their epidemiology and diversity remain not well studied in many African countries. To assess the positivity rate and the diversity of sapoviruses and noroviruses in Northwest Ethiopia, during November 2015 and April 2016, a total of 450 faecal samples were collected from outpatient children aged <5 years who presented with diarrhoea. Samples were screened for noroviruses and sapoviruses by real-time RT-PCR. Partial VP1 genes were sequenced, genotyped and phylogenetically analysed. Norovirus and sapovirus stool positivity rate was 13.3% and 10.0%, respectively. Noroviruses included GII.4 (35%), GII.6 (20%), GII.17 (13.3%), GII.10 (10%), GII.2 (6.7%), GII.16 (5%), GII.7 (3.3%), GII.9, GII.13, GII.20 and GI.3 (1.7% each) strains. For sapoviruses, GI.1, GII.1 (20.0% each), GII.6 (13.3%), GI.2 (8.9%), GII.2 (11.1%), GV.1 (8.9%), GIV.1 (6.7%), GI.3 and GII.4 (2.2% each) genotypes were detected. This study demonstrates a high genetic diversity of noroviruses and sapoviruses in Northwest Ethiopia. The positivity rate in stool samples from young children with diarrhoea was high for both caliciviruses. Continued monitoring is recommended to identify trends in genetic diversity and seasonal variations.
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Li W, Dong S, Xu J, Zhou X, Han J, Xie Z, Gong Q, Peng H, Zhou C, Lin M. Viral metagenomics reveals sapoviruses of different genogroups in stool samples from children with acute gastroenteritis in Jiangsu, China. Arch Virol 2020; 165:955-958. [PMID: 32048042 PMCID: PMC7131977 DOI: 10.1007/s00705-020-04549-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/13/2020] [Indexed: 11/26/2022]
Abstract
Sapoviruses (SAVs), including several genogroups (GI to GV), are one of the causes of acute gastroenteritis (AGE). In this study, viral metagenomics revealed the presence of sapoviruses of different genogroups in stool from children with AGE. Eight different complete SAV genomes were determined, of which five belonged to GI and the other three belonged to GII, GIV and GV, respectively. Although they were highly similar to published sequences, the GIV and GV were the first complete genome sequences of these SAVs found in China. In a prevalence investigation, 19% of subjects with AGE were positive for SAVs, while none of the control group was positive.
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Affiliation(s)
- Wang Li
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Surong Dong
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Juan Xu
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Xiaobin Zhou
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Junling Han
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Zhaqing Xie
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Qin Gong
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Hailin Peng
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China.
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China.
| | - Mei Lin
- Taizhou People's Hospital, 366 Taihu Road, Taizhou, 225300, Jiangsu, China.
- The Fifth Affiliated Hospital of Nantong University, Taizhou, 225300, Jiangsu, China.
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20
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Kumthip K, Khamrin P, Ushijima H, Chen L, Li S, Maneekarn N. Genetic recombination and diversity of sapovirus in pediatric patients with acute gastroenteritis in Thailand, 2010-2018. PeerJ 2020; 8:e8520. [PMID: 32071820 PMCID: PMC7007980 DOI: 10.7717/peerj.8520] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
Background Human sapovirus (SaV) is an etiologic agent of acute gastroenteritis (AGE) in all age groups worldwide. Genetic recombination of SaV has been reported from many countries. So far, none of SaV recombinant strain has been reported from Thailand. This study examined the genetic recombination and genotype diversity of SaV in children hospitalized with AGE in Chiang Mai, Thailand. Methods Stool samples were collected from children suffering from diarrhea who admitted to the hospitals in Chiang Mai, Thailand between 2010 and 2018. SaV was detected by RT-PCR and the polymerase and capsid gene sequences were analysed. Results From a total of 3,057 samples tested, 50 (1.6%) were positive for SaV. Among positive samples, SaV genotype GI.1 was the most predominant genotype (40%; 20/50), followed by GII.1 and GII.5 (each of 16%; 8/50), GI.2 (14%; 7/50), GIV.1 (4%; 2/50), and GI.5 (2%; 1/50). In addition, 4 SaV recombinant strains of GII.1/GII.4 were identified in this study (8%; 4/50). Conclusions The data revealed the genetic diversity of SaV circulating in children with AGE in Chiang Mai, Thailand during 2010 to 2018 and the intragenogroup SaV recombinant strains were reported for the first time in Thailand.
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Affiliation(s)
- Kattareeya Kumthip
- Department of Microbiology, Chiang Mai University, Faculty of Medicine, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Department of Microbiology, Chiang Mai University, Faculty of Medicine, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Limin Chen
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Shilin Li
- Institute of blood transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Niwat Maneekarn
- Department of Microbiology, Chiang Mai University, Faculty of Medicine, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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21
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Mann P, Pietsch C, Liebert UG. Genetic Diversity of Sapoviruses among Inpatients in Germany, 2008-2018. Viruses 2019; 11:v11080726. [PMID: 31394867 PMCID: PMC6723979 DOI: 10.3390/v11080726] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/28/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022] Open
Abstract
Sapovirus enteric disease affects people of all ages across the globe, in both sporadic cases and outbreak settings. Sapovirus is seldom assessed in Germany and its epidemiology in the country is essentially unknown. Thus, sapovirus occurrence and genetic diversity were studied by real-time reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of major viral structural protein (VP1) gene in two different sets of stool samples: (1) a selection of 342 diarrheal stools collected from inpatient children during 2008−2009, and (2) 5555 stool samples collected during 2010–2018 from inpatients of all age groups with gastrointestinal complaints. Results showed year-round circulation of sapoviruses, with peaks during cooler months. In total, 30 samples (8.8%) of the first and 112 samples of the second set of samples (2.0%) were sapovirus positive. Capsid gene sequencing was successful in 134/142 samples (94.4%) and showed circulation of all known human pathogenic genogroups. Genotype GI.1 predominated (31.8%), followed by GII.1 (16.7%), GII.3 (14.5%), GI.2 (13.8%) and GV.1 (12.3%). Additionally, minor circulation of GI.3, GI.6, GII.2, GII.4, GII.6 and GIV.1 was shown. Consequently, sapovirus diagnostics need broadly reactive RT-PCR protocols and should particularly be considered in infants and young children. Further studies from other sampling sites are essential to extend our knowledge on sapovirus epidemiology in Germany.
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Affiliation(s)
- Pia Mann
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany.
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
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22
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Desselberger U. Caliciviridae Other Than Noroviruses. Viruses 2019; 11:v11030286. [PMID: 30901945 PMCID: PMC6466229 DOI: 10.3390/v11030286] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
Besides noroviruses, the Caliciviridae family comprises four other accepted genera: Sapovirus, Lagovirus, Vesivirus, and Nebovirus. There are six new genera proposed: Recovirus, Valovirus, Bavovirus, Nacovirus, Minovirus, and Salovirus. All Caliciviridae have closely related genome structures, but are genetically and antigenically highly diverse and infect a wide range of mammalian host species including humans. Recombination in nature is not infrequent for most of the Caliciviridae, contributing to their diversity. Sapovirus infections cause diarrhoea in pigs, humans and other mammalian hosts. Lagovirus infections cause systemic haemorrhagic disease in rabbits and hares, and vesivirus infections lead to lung disease in cats, vesicular disease in swine, and exanthema and diseases of the reproductive system in large sea mammals. Neboviruses are an enteric pathogen of cattle, differing from bovine norovirus. At present, only a few selected caliciviruses can be propagated in cell culture (permanent cell lines or enteroids), and for most of the cultivatable caliciviruses helper virus-free, plasmid only-based reverse genetics systems have been established. The replication cycles of the caliciviruses are similar as far as they have been explored: viruses interact with a multitude of cell surface attachment factors (glycans) and co-receptors (proteins) for adsorption and penetration, use cellular membranes for the formation of replication complexes and have developed mechanisms to circumvent innate immune responses. Vaccines have been developed against lagoviruses and vesiviruses, and are under development against human noroviruses.
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Affiliation(s)
- Ulrich Desselberger
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
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