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Mogotsi MT, Ogunbayo AE, Bester PA, O'Neill HG, Nyaga MM. Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics. Virus Res 2024; 346:199403. [PMID: 38776984 PMCID: PMC11169482 DOI: 10.1016/j.virusres.2024.199403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
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Affiliation(s)
- Milton Tshidiso Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Ayodeji Emmanuel Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Phillip Armand Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hester Gertruida O'Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
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Omatola CA, Ogunsakin RE, Onoja AB, Okolo MLO, Abraham-Oyiguh J, Mofolorunsho KC, Akoh PQ, Adejo OP, Idakwo J, Okeme TO, Muhammed D, Adaji DM, Samson SO, Aminu RF, Akor ME, Edegbo E, Adamu AM. Enteropathogenic viruses associated with acute gastroenteritis among African children under 5 years of age: A systematic review and meta-analysis. J Infect 2024; 88:106169. [PMID: 38697269 DOI: 10.1016/j.jinf.2024.106169] [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: 12/01/2023] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/04/2024]
Abstract
Gastroenteritis viruses are the leading etiologic agents of diarrhea in children worldwide. We present data from thirty-three (33) eligible studies published between 2003 and 2023 from African countries bearing the brunt of the virus-associated diarrheal mortality. Random effects meta-analysis with proportion, subgroups, and meta-regression analyses were employed. Overall, rotavirus with estimated pooled prevalence of 31.0 % (95 % CI 24.0-39.0) predominated in all primary care visits and hospitalizations, followed by norovirus, adenovirus, sapovirus, astrovirus, and aichivirus with pooled prevalence estimated at 15.0 % (95 % CI 12.0-20.0), 10 % (95 % CI 6-15), 4.0 % (95 % CI 2.0-6.0), 4 % (95 % CI 3-6), and 2.3 % (95 % CI 1-3), respectively. Predominant rotavirus genotype was G1P[8] (39 %), followed by G3P[8] (11.7 %), G9P[8] (8.7 %), and G2P[4] (7.1 %); although, unusual genotypes were also observed, including G3P[6] (2.7 %), G8P[6] (1.7 %), G1P[6] (1.5 %), G10P[8] (0.9 %), G8P[4] (0.5 %), and G4P[8] (0.4 %). The genogroup II norovirus predominated over the genogroup I-associated infections (84.6 %, 613/725 vs 14.9 %, 108/725), with the GII.4 (79.3 %) being the most prevalent circulating genotype. In conclusion, this review showed that rotavirus remains the leading driver of viral diarrhea requiring health care visits and hospitalization among under-five years children in Africa. Thus, improved rotavirus vaccination in the region and surveillance to determine the residual burden of rotavirus and the evolving trend of other enteric viruses are needed for effective control and management of cases.
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Affiliation(s)
| | - Ropo Ebenezer Ogunsakin
- School of Health Systems and Public Health, University of Pretoria, Faculty of Health Sciences, Pretoria, South Africa
| | | | | | - Joseph Abraham-Oyiguh
- Department of Microbiology, Kogi State University, Anyigba P.M.B. 1008, Kogi State, Nigeria
| | | | - Phoebe Queen Akoh
- Department of Microbiology, Kogi State University, Anyigba P.M.B. 1008, Kogi State, Nigeria
| | - Omebije Patience Adejo
- Department of Microbiology, Kogi State University, Anyigba P.M.B. 1008, Kogi State, Nigeria
| | - Joshua Idakwo
- Department of Animal and Environmental Biology, Kogi State University, Anyigba P.M.B. 1008, Kogi State, Nigeria
| | | | - Danjuma Muhammed
- Department of Biology, Epidemiology, and Public Health Unit, Universiti Putra Malaysia, Malaysia
| | - David Moses Adaji
- Department of Biotechnology Science and Engineering, University of Alabama, Huntsville, United States
| | | | - Ruth Foluke Aminu
- Department of Microbiology, Kogi State University, Anyigba P.M.B. 1008, Kogi State, Nigeria
| | - Monday Eneojo Akor
- Department of Microbiology, Kogi State University, Anyigba P.M.B. 1008, Kogi State, Nigeria
| | - Emmanuel Edegbo
- Department of Microbiology, Kogi State University, Anyigba P.M.B. 1008, Kogi State, Nigeria
| | - Andrew Musa Adamu
- Australian Institute of Tropical Health and Medicine, James Cook University, 4811 Queensland, Australia; College of Public Health, Medical and Veterinary Sciences, James Cook University, 4811 Queensland, Australia; Center for Tropical Biosecurity, James Cook University, 4811 Queensland, Australia.
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Li Y, Xue L, Gao J, Cai W, Zhang Z, Meng L, Miao S, Hong X, Xu M, Wu Q, Zhang J. A systematic review and meta-analysis indicates a substantial burden of human noroviruses in shellfish worldwide, with GII.4 and GII.2 being the predominant genotypes. Food Microbiol 2023; 109:104140. [DOI: 10.1016/j.fm.2022.104140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 10/14/2022]
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Pooled prevalence and genetic diversity of norovirus in Africa: a systematic review and meta-analysis. Virol J 2022; 19:115. [PMID: 35765033 PMCID: PMC9238157 DOI: 10.1186/s12985-022-01835-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Background Noroviruses are the leading cause of acute gastroenteritis in all age groups globally. The problem is magnified in developing countries including Africa. These viruses are highly prevalent with high genetic diversity and fast evolution rates. With this dynamicity, there are no recent review in the past five years in Africa. Therefore, this review and meta-analysis aimed to assess the prevalence and genetic diversity of noroviruses in Africa and tried to address the change in the prevalence and genetic diverisity the virus has been observed in Africa and in the world.
Methods Twenty-one studies for the pooled prevalence, and 11 out of the 21 studies for genetic characterization of norovirus were included. Studies conducted since 2006, among symptomatic cases of all age groups in Africa, conducted with any study design, used molecular diagnostic methods and reported since 2015, were included and considered for the main meta-analysis. PubMed, Cochrane Library, and Google Scholar were searched to obtain the studies. The quality the studies was assessed using the JBI assessment tool. Data from studies reporting both asymptomatic and symptomatic cases, that did not meet the inclusion criteria were reviewed and included as discussion points. Data was entered to excel and imported to STATA 2011 to compute the prevalence and genetic diversity. Heterogeneity was checked using I2 test statistics followed by subgroup and sensitivity analysis. Publication bias was assessed using a funnel plot and eggers test that was followed by trim and fill analysis. Result The pooled prevalence of norovirus was 20.2% (95% CI: 15.91, 24.4). The highest (36.3%) prevalence was reported in Ghana. Genogroup II noroviruses were dominant and reported as 89.5% (95% CI: 87.8, 96). The highest and lowest prevalence of this genogroup were reported in Ethiopia (98.3%), and in Burkina Faso (72.4%), respectively. Diversified genotypes had been identified with an overall prevalence of GII. 4 NoV (50.8%) which was followed by GII.6, GII.17, GI.3 and GII.2 with a pooled prevalence of 7.7, 5.1, 4.6, and 4.2%, respectively. Conclusion The overall pooled prevalence of norovirus was high in Africa with the dominance of genogroup II and GII.4 genotype. This prevalence is comparable with some reviews done in the same time frame around the world. However, in Africa, an in increasing trained of pooled prevalence had been reported through time. Likewise, a variable distribution of non-GII.4 norovirus genotypes were reported as compared to those studies done in the world of the same time frame, and those previous reviews done in Africa. Therefore, continuous surveillance is required in Africa to support future interventions and vaccine programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01835-w.
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Ekundayo TC, Igere BE, Oluwafemi YD, Iwu CD, Olaniyi OO. Human norovirus contamination in water sources: A systematic review and meta-analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118164. [PMID: 34534825 DOI: 10.1016/j.envpol.2021.118164] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/23/2021] [Accepted: 09/09/2021] [Indexed: 05/25/2023]
Abstract
The human norovirus (HNoV), on a global scale, is the prevailing cause of contagious viral gastroenteritis outbreaks, with more than 200 000 deaths annually. This study aimed at assessing specific prevalence of HNoV pollution in different water sources and their roles in the dissemination of HNoV, with a view to refocus water sources and sewage management options for policy making towards public health safety. In this regard, we conducted a systematic review and meta-analysis (SR/MA) of the prevalence of HNoV in water sources. We searched PubMed, Google Scholar, Scopus and Web of Science for studies on HNoV prevalence in water sources without temporal restriction, till January 30, 2021. We conducted a random-effects meta-analysis of the HNoV prevalence and stratified the study by water type, continent, gross national income (GNI) group and genogroup. Further, a mixed-effects meta-regression model was performed for sensitivity analysis. The literature search identified 61 studies on water source-based HNoV (WsHNoV) prevalence. The pooled WsHNoV prevalence was 31.7% (95%CI: 25.1-38.5) but varied according to water sources types; river water showing the highest estimate at 43.5% (95%CI: 33.9-53.4), followed by estuarine water (30.6%, 95%CI: 12.5-52.2), composite water (27.9%, 95%CI: 13.5-44.9), marine water (25.9%, 95%CI: 10.0-45.6), groundwater (19.7%, 95%CI: 9.4-32.3) and lake water (2.2%, 95%CI: 0-25.8). Further, the findings indicated the highest WsHNoV prevalence in Africa as 55.9% (95% CI: 28.2-81.9), followed by Asia (31.6%, 95% CI: 22.3-41.6), Europe (29.8%, 95% CI: 17.9-43.2), North America (27.7%, 95% CI: 11.2-47.6) and South America (27.1%, 95%CI: 0.09-49.4). The WsHNoV prevalence stratified by GNI group was 40.6% (95%CI: 27.9-53.9) in middle-income countries and 28.7% (95%CI: 21.7-36.1) in high-income countries respectively. The prevalence of GI, GII and GI & GII genogroup in natural water was 16.4% (95%CI: 12.0-21.3), 20.6% (95%CI: 15.7-25.8) and 12.8% (95%CI: 6.9-20.6) respectively. Evidently, prevalence of the HNoV genogroup in water sources mirrors the pattern of HNoV gastroenteritis and GII genogroup dominance worldwide. In conclusion, public health efforts against waterborne diseases should prioritize water resource/sewage management options and policies towards ardent water sources pollution prevention.
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Affiliation(s)
- Temitope C Ekundayo
- Department of Biological Sciences, University of Medical Sciences, Ondo City, Ondo State, Nigeria; Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa.
| | - Bright E Igere
- Department of Microbiology and Biotechnology, Western Delta University, Oghara, Delta State, Nigeria
| | - Yinka D Oluwafemi
- Department of Biological Sciences, University of Medical Sciences, Ondo City, Ondo State, Nigeria
| | - Chidozie D Iwu
- School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Oladipo O Olaniyi
- Department of Microbiology, Federal University of Technology Akure, Nigeria
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Lucero Y, Matson DO, Ashkenazi S, George S, O’Ryan M. Norovirus: Facts and Reflections from Past, Present, and Future. Viruses 2021; 13:v13122399. [PMID: 34960668 PMCID: PMC8707792 DOI: 10.3390/v13122399] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023] Open
Abstract
Human Norovirus is currently the main viral cause of acute gastroenteritis (AGEs) in most countries worldwide. Nearly 50 years after the discovery of the "Norwalk virus" by Kapikian and colleagues, the scientific and medical community continue to generate new knowledge on the full biological and disease spectrum of Norovirus infection. Nevertheless, several areas remain incompletely understood due to the serious constraints to effectively replicate and propagate the virus. Here, we present a narrated historic perspective and summarize our current knowledge, including insights and reflections on current points of interest for a broad medical community, including clinical and molecular epidemiology, viral-host-microbiota interactions, antivirals, and vaccine prototypes. We also include a reflection on the present and future impacts of the COVID-19 pandemic on Norovirus infection and disease.
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Affiliation(s)
- Yalda Lucero
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
- Hospital Dr. Roberto del Río Hospital, Department of Pediatrics and Pediatric Surgery (Northern Campus), Faculty of Medicine, Universidad de Chile, Santiago 8380418, Chile
- Clínica Alemana de Santiago, Faculty of Medicine, Universidad del Desarrollo-Clínica Alemana, Santiago 7650568, Chile
| | - David O. Matson
- Eastern Shore Health Department, Virginia Department of Public Health, Accomack County, VA 23301, USA;
| | - Shai Ashkenazi
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel;
- Department of Pediatrics A, Schneider Children’s Medical Center, Petach Tikva 49202, Israel
| | - Sergio George
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
| | - Miguel O’Ryan
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile; (Y.L.); (S.G.)
- Correspondence:
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Liao Y, Hong X, Wu A, Jiang Y, Liang Y, Gao J, Xue L, Kou X. Global prevalence of norovirus in cases of acute gastroenteritis from 1997 to 2021: An updated systematic review and meta-analysis. Microb Pathog 2021; 161:105259. [PMID: 34687838 DOI: 10.1016/j.micpath.2021.105259] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/10/2021] [Accepted: 10/15/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND The worldwide response towards the acute gastroenteritis epidemic was well known, but the absence of an updated systematic review of global norovirus epidemiology in cases of gastroenteritis existed. We aimed to conduct and update a systematic review and meta-analysis of studies assessing norovirus prevalence among gastroenteritis patients worldwide. METHODS Four databases (PubMed, EMBASE, Cochrane Library, and Web of Science) were searched for epidemiological papers from 2014 to 2021 which applied the PCR method to access the prevalence of norovirus in acute gastroenteritis patients more than a full year. Statistical analysis was conducted using R-4.0.0 software. RESULTS A total of 405 records with 842, 926 cases were included. The pooled prevalence of norovirus was 16% (95%CI 15, 17). Children under 5 years old were at a higher risk with norovirus. A higher prevalence was seen in South America (22%, 95% CI 18, 27), while other continents showed a similar result with the overall prevalence of norovirus. No association was found between national income level and norovirus prevalence. A gradient of decreasing prevalence was noticed from community (20%, 95% CI 16, 24) to outpatients (18%, 95% CI 16, 20) to hospital setting (included both in- and outpatients, 17%, 95% CI 16, 19) to inpatients (15%, 95% CI 13, 17). CONCLUSION Norovirus were associated with 16% acute gastroenteritis globally. To fully understand the prevalence of norovirus worldwide, the continual surveillance of norovirus epidemics was required.
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Affiliation(s)
- Yingyin Liao
- KingMed School of Laboratory Medicine of Guangzhou Medical University, Guangzhou, China
| | - Xiaojing Hong
- KingMed School of Laboratory Medicine of Guangzhou Medical University, Guangzhou, China
| | - Aiwu Wu
- KingMed School of Laboratory Medicine of Guangzhou Medical University, Guangzhou, China
| | - Yueting Jiang
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanhui Liang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, China
| | - Junshan Gao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, China.
| | - Xiaoxia Kou
- KingMed School of Laboratory Medicine of Guangzhou Medical University, Guangzhou, China.
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Liu P, Amin N, Miah R, Foster T, Raj S, Corpuz MJB, Rahman M, Willetts J, Moe CL. A method for correcting underestimation of enteric pathogen genome quantities in environmental samples. J Microbiol Methods 2021; 189:106320. [PMID: 34478762 DOI: 10.1016/j.mimet.2021.106320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Exposure to enteric pathogens in the environment poses a serious risk for infection and disease. The accurate detection and quantification of enteric pathogens in environmental samples is critical for understanding pathogen transport and fate and developing risk assessment models. In this study, we successfully applied TaqMan real-time PCR assays to quantitatively detect five human-specific pathogens (Shigella/EIEC, Salmonella Typhi, Vibrio cholera, Norovirus, and Giardia) in samples from open drains, canals, floodwater, septic tanks, and anaerobic baffled reactors (ABR) collected in Mirpur, Dhaka, Bangladesh from April to October 2019. Overall, the grab and sediment samples showed low inhibition but the ultrafiltration samples collected from open drain had significantly higher (P = 0.0049) degree of PCR inhibition (median Ct = 31.06) compared to the extraction controls (Ct = 28.54). We developed a two-step method to adjust underestimation of pathogen quantities due to PCR inhibition and non-optimum PCR efficiency. Compared to other sample types, ultrafiltration samples demonstrated a wide range of concentration increase (1.0%-182.5%) by pathogens after adjusting for PCR inhibition and non-optimum efficiencies. These quantitative qPCR assays are successful in quantifying multiple enteric pathogens in environmental samples, and the adjustment method would be useful for correcting underestimates of pathogen quantities due to partial PCR inhibition and non-optimum efficiency.
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Affiliation(s)
- Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
| | - Nuhu Amin
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh..
| | - Rana Miah
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh..
| | - Tim Foster
- Institute for Sustainable Futures, University of Technology Sydney, Australia..
| | - Suraja Raj
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
| | - Maria Julia Bianca Corpuz
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
| | - Mahbubur Rahman
- Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh..
| | - Juliet Willetts
- Institute for Sustainable Futures, University of Technology Sydney, Australia..
| | - Christine L Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA..
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Opere WM, John M, Ombori O. Molecular Detection of Human Enteric Adenoviruses in Water Samples Collected from Lake Victoria Waters Along Homa Bay Town, Homa Bay County, Kenya. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:32-43. [PMID: 33141920 DOI: 10.1007/s12560-020-09444-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Lake Victoria is the primary source of water for millions of people in the Sub-Saharan Africa region. In recent years, population development around the lake has resulted in compromised sanitation standards resulting in increased faecal pollution of the lake. Consequently, this condition has increased the chances of waterborne enteric viruses, such as adenoviruses' circulation in the community. Adenoviruses can affect health in both humans and animals by causing a myriad of diseases including the gastrointestinal infections. The study aimed to detect contamination of the lake water with pathogenic human adenoviruses along Homa Bay town, Homa Bay County, Kenya. To examine the presence of adenoviral genome, we collected a total of 216 (monthly n = 36) water samples from six different locations marked by high levels of anthropogenic activities along the shoreline. Molecular amplification technique using the nested PCR procedure was used to detect the genomes from the water samples. Human adenoviruses were detected in 11 samples (5.09%). Statistical analyses indicated a significant correlation between adenovirus presence and the approximate distance from pit latrines and sewage treatment works at the area. The findings indicate that faecal contamination of the lake waters originated from the point sources. The findings also suggest a possibility of elevated levels of faecal pollution in different surface waters within the lake basin. The findings indicate that some of the enteric viruses circulating in the local community are human adenovirus type 40, and 41. The data may provide a basis for recognizing the need to prioritize environmental monitoring for enteric virus contamination on an on-going basis.
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Affiliation(s)
- Wasonga Michael Opere
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya.
| | - Maingi John
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
| | - Omwoyo Ombori
- Department of Plant Sciences, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
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Ishaq AR, Manzoor M, Hussain A, Altaf J, Rehman SU, Javed Z, Afzal I, Noor A, Noor F. Prospect of microbial food borne diseases in Pakistan: a review. BRAZ J BIOL 2021; 81:940-953. [PMID: 33605364 DOI: 10.1590/1519-6984.232466] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 10/23/2020] [Indexed: 01/05/2023] Open
Abstract
Nowadays food borne illness is most common in people due to their epidemic nature. These diseases affect the human digestive system through bacteria, viruses and parasites. The agents of illness are transmitted in our body through various types of food items, water and uncooked. Pathogens show drastic changes in immunosuppressant people. This review gives general insights to harmful microbial life. Pakistan is a developed country and because of its improper food management, a lot of gastrointestinal problems are noted in many patients. Bacteria are most common agents to spread diarrhoea, villi infection, constipation and dysenteric disease in human and induce the rejection of organ transplant. Enhancement of their lifestyle, properly cooked food should be used and to overcome the outbreak of the diseases.
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Affiliation(s)
- A R Ishaq
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, China
| | - M Manzoor
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - A Hussain
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - J Altaf
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - S Ur Rehman
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Z Javed
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - I Afzal
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - A Noor
- Department of Zoology, Government College University Faisalabad, Faisalabad, Pakistan
| | - F Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
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Xu M, Lu F, Lyu C, Wu Q, Zhang J, Tian P, Xue L, Xu T, Wang D. Broad-range and effective detection of human noroviruses by colloidal gold immunochromatographic assay based on the shell domain of the major capsid protein. BMC Microbiol 2021; 21:22. [PMID: 33430771 PMCID: PMC7798207 DOI: 10.1186/s12866-020-02084-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Human noroviruses (HuNoVs) are a major cause of nonbacterial gastroenteritis in all age groups worldwide. HuNoVs can be detected in vitro using molecular assays such as RT-PCR and RT-qPCR. However, these molecular-based techniques require special equipment, unique reagents, experienced personnel, and extended time to obtain results. Besides, the diversity of viral genotypes is high. Therefore, methods that are rapid, broad-range and effective in the detection of HuNoVs are desiderated for screening the feces or vomit of infected people during outbreaks. RESULTS In this study, a colloidal-gold-based immunochromatographic assay (ICA) was developed for effective detection of HuNoVs in clinical samples. Monoclonal antibodies (MAbs) against the shell (S) domain in the major capsid protein of HuNoVs were used in the ICA. The limitations of detection for HuNoVs in clinical samples were 1.2 × 106 genomic copies per gram of stool sample (gc/g) and 4.4 × 105 gc/g for genogroup I and II (GI and GII) HuNoVs, respectively. A total of 122 clinical samples were tested for HuNoVs by ICA and compared against RT-qPCR. The relative sensitivity, specificity and agreement of ICA was 84.2% (95% CI: 83.6-84.8%), 100.0% (95% CI: 98.5-100.0%) and 87.7% (95% CI: 85.6-89.8%), respectively. No cross-reaction with other common enteric viruses or bacteria was observed. The ICA detected a broad range of genotypes, including GI.1, GI.3, GI.4, GI.6, GI.14, GII.2, GII.3, GII.4, GII.6, GII.13, and GII.17 HuNoVs. CONCLUSIONS This study demonstrates that ICA targeting the S domain of VP1 is a promising candidate for effectively identifying the different genotypes of HuNoVs in clinical samples with high sensitivity and specificity.
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Affiliation(s)
- Meng Xu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Feifeng Lu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chenang Lyu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Peng Tian
- Western Regional Research Center, Agricultural Research Service-United States Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, CA, 94706, USA.
| | - Liang Xue
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Ting Xu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Molecular Characterization of Norovirus Strains Isolated from Older Children and Adults in Impoverished Communities of Vhembe District, South Africa. Adv Virol 2020; 2020:8436951. [PMID: 32684935 PMCID: PMC7341391 DOI: 10.1155/2020/8436951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/09/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022] Open
Abstract
Background Human norovirus (NoV) is an etiological agent associated with acute gastroenteritis (AGE) in both children and adults worldwide. However, very few studies have been reported on the prevalence and genetic diversity of NoV strains in children older than 5 years of age and adults with little or inadequate water and sanitation conditions. Objectives The aim of this study was assessing the prevalence of the human norovirus in older children and adults suffering with diarrhoea from rural communities in the Vhembe district, Limpopo province. Methods Between August 2017 and October 2018, stool samples were collected from outpatients suffering from AGE and screened for NoV strains using the RIDA©GENE norovirus I and II real-time one-step RT-PCR. RNA extracts of NoV-positive samples were subjected to RT-PCR amplification and nucleotide sequencing to genotype the positive NoV strains. Results Out of 80 collected stool samples, 13 (16%) were tested positive for norovirus. Genogroup GII was identified in 6/13 (46%) samples and genogroup GI in 7/13 (54%) samples. The sequence analyses showed multiple genotypes including GII.Pg, GII.1, GII.2, GII.4, and GI.3. Phylogenetic analysis revealed the relatedness of NoV genotypes identified with other strains reported globally. Conclusion Continued systematic surveillance to evaluate norovirus association with diarrhoea is needed to assist with epidemiological surveillance and disease burden in people of all the age groups.
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El Moqri N, El Mellouli F, Hassou N, Benhafid M, Abouchoaib N, Etahiri S. Norovirus Detection at Oualidia Lagoon, a Moroccan Shellfish Harvesting Area, by Reverse Transcription PCR Analysis. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:268-273. [PMID: 30982112 DOI: 10.1007/s12560-019-09386-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 04/10/2019] [Indexed: 05/18/2023]
Abstract
Norovirus (NoV) is the leading cause of acute viral gastroenteritis outbreaks in the world. These outbreaks are frequently associated with bivalve shellfish consumption, particularly because these products are often eaten raw or only slightly cooked. In Morocco, regulations concerning the acceptable levels of enteric bacteria indicator organisms in these products have been put in place. However, these regulations do not take into account the risk of viral contamination, and many gastroenteritis outbreaks have been linked to the ingestion of bivalve shellfish from areas that comply with the current food safety criteria. The aim of this study was to investigate NoV presence in shellfish samples (n = 104) collected at four sites owcff Oualidia lagoon (Moroccan Atlantic coast) from November 2015 to February 2017. Samples were analysed using real-time RT-PCR in accordance with the ISO 15216-2 method. NoVs of the genogroup II were detected in 7% of samples that were all collected during the winter months. Moreover, 71% of NoV-positive samples were harvested at sites upstream of the lagoon. These results highlight the need of regularly monitoring viral contamination in bivalve shellfish to limit the risk of viral gastroenteritis outbreaks.
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Affiliation(s)
- N El Moqri
- Marine Biotechnology and Environment Laboratory, Faculty of Sciences, University Chouaib Doukkali, El Jadida, Morocco.
| | - F El Mellouli
- Casablanca Regional Research and Analysis Laboratory of National Office of Sanitary Safety and Food Products (ONSSA), Casablanca, Nouaceur, Morocco
| | - N Hassou
- Marine Biotechnology and Environment Laboratory, Faculty of Sciences, University Chouaib Doukkali, El Jadida, Morocco
| | - M Benhafid
- Virology Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - N Abouchoaib
- Casablanca Regional Research and Analysis Laboratory of National Office of Sanitary Safety and Food Products (ONSSA), Casablanca, Nouaceur, Morocco
| | - S Etahiri
- Marine Biotechnology and Environment Laboratory, Faculty of Sciences, University Chouaib Doukkali, El Jadida, Morocco
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van Zyl WB, A Zhou N, Wolfaardt M, Matsapola PN, Ngwana FB, Symonds EM, Fagnant-Sperati CS, Shirai JH, Kossik AL, Beck NK, Komen E, Mwangi B, Nyangao J, Boyle DS, Borus P, Taylor MB, Meschke JS. Detection of potentially pathogenic enteric viruses in environmental samples from Kenya using the bag-mediated filtration system. WATER SCIENCE & TECHNOLOGY, WATER SUPPLY 2019; 19:1668-1676. [PMID: 33584163 PMCID: PMC7797634 DOI: 10.2166/ws.2019.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/14/2019] [Indexed: 05/18/2023]
Abstract
Enteric virus environmental surveillance via a highly sensitive method is critical, as many enteric viruses have low infectious doses and can persist in the environment for extended periods. This study determined the potential of the novel bag-mediated filtration system (BMFS) to recover human enteric viruses and pepper mild mottle virus (PMMoV) from wastewater and wastewater-impacted surface waters, examined PMMoV use as a fecal contamination indicator in Kenya, and identified potential BMFS process controls. From April 2015 to April 2016, BMFS samples were collected from seven sites in Kenya (n = 59). Enteroviruses and PMMoV were detected in 100% of samples, and human adenovirus, human astrovirus, hepatitis A virus, norovirus GI, norovirus GII, sapovirus, and human rotavirus were detected in the majority of samples. The consistent detection of enteroviruses and PMMoV suggests that these viruses could be used as indicators in similarly fecally contaminated sites and BMFS process controls. As contamination of surface water sources remains a global issue, enteric virus environmental surveillance is necessary. This study demonstrates an effective way to sample large volumes of wastewater and wastewater-impacted surface waters for the detection of multiple enteric viruses simultaneously.
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Affiliation(s)
- Walda B van Zyl
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Nicolette A Zhou
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Marianne Wolfaardt
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Peter N Matsapola
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Fhatuwani B Ngwana
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
| | - Erin M Symonds
- College of Marine Science, University of South Florida, 830 1st St S, St Petersburg, FL 33701, USA
| | - Christine S Fagnant-Sperati
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Jeffry H Shirai
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Alexandra L Kossik
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Nicola K Beck
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
| | - Evans Komen
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - Benlick Mwangi
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - James Nyangao
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - David S Boyle
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA 98121, USA
| | - Peter Borus
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
| | - Maureen B Taylor
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
- College of Marine Science, University of South Florida, 830 1st St S, St Petersburg, FL 33701, USA
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA 98121, USA
| | - J Scott Meschke
- Department of Medical Virology, University of Pretoria, Faculty of Health Sciences, Private Bag X323, Arcadia 0007, South Africa
- (corresponding author) Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, Suite 100, Seattle, WA 98105, USA
- College of Marine Science, University of South Florida, 830 1st St S, St Petersburg, FL 33701, USA
- Centre for Viral Research, Kenya Medical Research Institute, Mbagathi Road, P.O. Box 54628, Nairobi 00200, Kenya
- PATH, 2201 Westlake Ave, Suite 200, Seattle, WA 98121, USA
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Mugyia AE, Ndze VN, Akoachere JFTK, Browne H, Boula A, Ndombo PK, Cannon JL, Vinjé J, Ndip LM. Molecular epidemiology of noroviruses in children under 5 years of age with acute gastroenteritis in Yaoundé, Cameroon. J Med Virol 2019; 91:738-743. [PMID: 30570784 DOI: 10.1002/jmv.25380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023]
Abstract
Norovirus is a common cause of acute gastroenteritis (AGE) among children in developing countries. Limited data on the prevalence and genetic variability of norovirus are available in Cameroon, where early childhood mortality due to AGE is common. We tested 902 fecal specimens from children younger than 5 years of age hospitalized with AGE between January 2010 and December 2013. Overall, 76 (8.4%) samples tested positive for norovirus, of which 83% (63/76) were among children below 12 months old. Most of the noroviruses detected were in children infected between July and December of each year. All norovirus-positive specimens were genotyped, with 80% (61/76) being GII.4 (three variants detected). Genotypes GI.2, GI.6, GII.1, GII.2, GII.3, GII.6, GII.16, GII.17, and GII.21 were also detected. Interestingly, GII.4 Sydney and GII.17 Kawasaki viruses were found as early as 2010, years before their emergence globally. This study suggests norovirus is a significant cause of moderate to severe gastroenteritis among young children in Cameroon. The results are important to highlight appropriate prevention and control strategies for reducing the burden of norovirus disease.
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Affiliation(s)
- Akongnwi E Mugyia
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
| | - Valentine N Ndze
- Department of Paediatrics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon.,Metabiota, Cameroon
| | | | - Hannah Browne
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Angeline Boula
- Deparment of Virology, Rotavirus National Reference Laboratory, Mother and Child Centre of the Chantal Biya Foundation, Yaoundé, Cameroon
| | - Paul Koki Ndombo
- Department of Paediatrics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon.,Deparment of Virology, Rotavirus National Reference Laboratory, Mother and Child Centre of the Chantal Biya Foundation, Yaoundé, Cameroon
| | | | - Jan Vinjé
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, Georgia
| | - Lucy M Ndip
- Department of Microbiology and Parasitology, Faculty of Science, University of Buea, Buea, Cameroon
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Prevalence of Human Sapovirus in Low and Middle Income Countries. Adv Virol 2018; 2018:5986549. [PMID: 30245718 PMCID: PMC6139206 DOI: 10.1155/2018/5986549] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/25/2018] [Indexed: 11/23/2022] Open
Abstract
Background Sapovirus (SV) infection is a public health concern which plays an important role in the burden of diarrhoeal diseases, causing acute gastroenteritis in people of all ages in both outbreaks and sporadic cases worldwide. Objective/Study Design The purpose of this report is to summarise the available data on the detection of human SV in low and middle income countries. A systematic search on PubMed and ScienceDirect database for SV studies published between 2004 and 2017 in low and middle income countries was done. Studies of SV in stool and water samples were part of the inclusion criteria. Results From 19 low and middle income countries, 45 published studies were identified. The prevalence rate for SV was 6.5%. A significant difference (P=0) in SV prevalent rate was observed between low income and middle income countries. Thirty-three (78.6%) of the studies reported on children and 8 (19%) studies reported on all age groups with diarrhoea. The majority (66.7%) of studies reported on hospitalised patients with acute gastroenteritis. Sapovirus GI was shown as the dominant genogroup, followed by SV-GII. Conclusion The detection of human SV in low and middle income countries is evident; however the reports on its prevalence are limited. There is therefore a need for systematic surveillance of the circulation of SV, and their role in diarrhoeal disease and outbreaks, especially in low and middle income countries.
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Mattison CP, Cardemil CV, Hall AJ. Progress on norovirus vaccine research: public health considerations and future directions. Expert Rev Vaccines 2018; 17:773-784. [PMID: 30092671 DOI: 10.1080/14760584.2018.1510327] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Noroviruses are the leading cause of foodborne illness worldwide, account for approximately one-fifth of acute gastroenteritis (AGE) cases globally, and cause a substantial economic burden. Candidate norovirus vaccines are in development, but there is currently no licensed vaccine. AREAS COVERED Noroviruses cause approximately 684 million cases and 212,000 deaths per year across all age groups, though burden estimates vary by study and region. Challenges to vaccine research include substantial and rapidly evolving genetic diversity, short-term and homotypic immunity to infection, and the absence of a single, well-established correlate of protection. Nonetheless, several norovirus vaccine candidates are currently in development, utilizing virus-like particles (VLPs), P particles, and recombinant adenoviruses. Of these, a bivalent GI.1/GII.4 VLP-based intramuscular vaccine (Phase IIb) and GI.1 oral vaccine (Phase I) are in clinical trials. EXPERT COMMENTARY A norovirus vaccine should target high-risk populations, including the young and the elderly, and protect them against the most common circulating norovirus strains. A norovirus vaccine would be a powerful tool in the prevention and control of norovirus while lessening the burden of AGE worldwide. However, more robust burden and cost estimates are needed to justify investments in and guide norovirus vaccine development.
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Affiliation(s)
- Claire P Mattison
- a Oak Ridge Institute for Science and Education , Oak Ridge , TN , USA.,b Division of Viral Diseases, Viral Gastroenteritis Branch , Centers for Disease Control and Prevention , Atlanta , USA
| | - Cristina V Cardemil
- b Division of Viral Diseases, Viral Gastroenteritis Branch , Centers for Disease Control and Prevention , Atlanta , USA
| | - Aron J Hall
- b Division of Viral Diseases, Viral Gastroenteritis Branch , Centers for Disease Control and Prevention , Atlanta , USA
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Thorne L, Nalwoga A, Mentzer AJ, de Rougemont A, Hosmillo M, Webb E, Nampiija M, Muhwezi A, Carstensen T, Gurdasani D, Hill AV, Sandhu MS, Elliott A, Goodfellow I. The First Norovirus Longitudinal Seroepidemiological Study From Sub-Saharan Africa Reveals High Seroprevalence of Diverse Genotypes Associated With Host Susceptibility Factors. J Infect Dis 2018; 218:716-725. [PMID: 29912471 PMCID: PMC6057498 DOI: 10.1093/infdis/jiy219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/17/2018] [Indexed: 11/14/2022] Open
Abstract
Background Human noroviruses (HuNoVs) are a prominent cause of gastroenteritis, yet fundamental questions remain regarding epidemiology, diversity, and immunity in sub-Saharan African children. We investigated HuNoV seroprevalence and genetic and sociodemographic risk factors in Ugandan children. Methods We randomly screened 797 participants of a longitudinal birth cohort (Entebbe, EMaBS) and 378 from a cross-sectional survey (rural Lake Victoria, LaVIISWA), for antibodies against HuNoV genotypes by ELISA. We used linear regression modeling to test for associations between HuNoV antibody levels and sociodemographic factors, and with the human susceptibility rs601338 FUT2 secretor SNP and histo-blood group antigens (A/B/O). Results Of EMaBS participants, 76.6% were seropositive by age 1, rising to 94.5% by age 2 years. Seroprevalence in 1 year olds of the rural LaVIISWA survey was even higher (95%). In the birth cohort, 99% of seropositive 2 year olds had responses to multiple HuNoV genotypes. We identified associations between secretor status and genogroup GII antibody levels (GII.4 P = 3.1 × 10-52), as well as ABO and GI (GI.2 P = 2.1 × 10-12). Conclusions HuNoVs are highly prevalent in Ugandan children, indicating a substantial burden of diarrhea-associated morbidity with recurrent infections. Public health interventions, including vaccination, and increased surveillance are urgently needed.
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Affiliation(s)
- Lucy Thorne
- Division of Virology, Department of Pathology, University of Cambridge, UK
- Division of Infection and Immunity, University College London, Medical Research Council Centre for Medical Molecular Virology, UK
| | - Angela Nalwoga
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
| | | | - Alexis de Rougemont
- Centre National de Référence des Virus Entériques, Laboratoire de Virologie-Sérologie, Centre Hospitalier Universitaire de Dijon, France
- L'Unité Mixte de Recherche Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté/AgroSup Dijon, France
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, UK
| | - Emily Webb
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, UK
| | - Margaret Nampiija
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
| | - Allan Muhwezi
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
| | | | | | - Adrian V Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK
- The Jenner Institute, University of Oxford, UK
| | - Manj S Sandhu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Alison Elliott
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, Entebbe, Uganda
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, UK
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, UK
- School of Public Health, University of Makeni, Sierra Leone
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Kreidieh K, Charide R, Dbaibo G, Melhem NM. The epidemiology of Norovirus in the Middle East and North Africa (MENA) region: a systematic review. Virol J 2017; 14:220. [PMID: 29126448 PMCID: PMC5681772 DOI: 10.1186/s12985-017-0877-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/27/2017] [Indexed: 12/14/2022] Open
Abstract
Norovirus (NoV) is considered the second leading cause of viral acute gastroenteritis (AGE). To our knowledge, there are no systematic reviews assessing the role of NoV in AGE in the Middle East and North Africa (MENA) region. Consequently, we conducted an extensive systematic literature review on articles studying NoV in the 24 countries of the MENA region during the past 15 years (2000-2015). The methods and reporting were set according to the 2015 PRISMA-P and based on the elements from the international prospective register of systematic reviews (PROSPERO). We retrieved 38 studies meeting our predefined inclusion criteria and were used to extract full data. Studies reporting on NoV were conducted in 15 out of the 24 countries of the region. The reported NoV infection rates in MENA countries ranged between 0.82% and 36.84%. The majority of studies were clinical observational studies assessing NoV rates mainly among children. Participants were recruited from in- and outpatient clinics. NoV infection was reported all year round with with peaks observed mainly during cold months. GII.4 was the predominant genotype detected in stool of participants as reported by 16 out of 25 studies (64%). Overall, there is an increasing recognition of NoV as an important causative agent of AGE across all age groups in the MENA region. Further studies are needed to assess the national and the regional burden of NoV among different age groups, its molecular diversity and seasonal variability.
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Affiliation(s)
- Khalil Kreidieh
- Medical Laboratory Sciences Program, Faculty of Health Sciences, American University of Beirut, P.O. Box 11-0236, Riad El Solh, Beirut, Lebanon
- Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Rana Charide
- Department of Epidemiology and Population Health, Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Ghassan Dbaibo
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Infectious Diseases, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nada M Melhem
- Medical Laboratory Sciences Program, Faculty of Health Sciences, American University of Beirut, P.O. Box 11-0236, Riad El Solh, Beirut, Lebanon.
- Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
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20
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Nguyen GT, Phan K, Teng I, Pu J, Watanabe T. A systematic review and meta-analysis of the prevalence of norovirus in cases of gastroenteritis in developing countries. Medicine (Baltimore) 2017; 96:e8139. [PMID: 28984764 PMCID: PMC5738000 DOI: 10.1097/md.0000000000008139] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND While norovirus (NoV) is well known as a leading causal pathogen for acute gastroenteritis in developed countries,structured data on prevalence in developing countries are not available thus far. This review aims to estimate the prevalence of NoV in cases of gastroenteritis in developing countries based on recently published reports. METHODS Relevant studies were identified by searching PubMed and Web of Science for the period January 1, 1990 through March 31, 2016. We included studies performed in developing countries with a study period of at least 12 months and which provided information on polymerase chain reaction (PCR)-confirmed NoV prevalence in patients diagnosed with acute gastroenteritis. A metaanalysis was conducted on NoV prevalence, focused on viral genogroups GI and GII, in cases of acute gastroenteritis. RESULTS Using evidence from 178 articles, the estimated NoV prevalence among 148,867 patients with acute gastroenteritis was 17% (95% confidence interval [CI]: 15-18%). The prevalence decreased from 18% (95% CI: 16-20%) for upper middle-income countries to 15% (13-18%) and 6% (3-10%) for lower middle- and low-income countries, respectively. There were no significant differences in NoV prevalence by age group (under 5 years, 5 years and over, and mixed ages) or severity of symptoms as defined by community, outpatient, or inpatient setting. The pooled prevalence of NoV GII (15%, 95% CI: 13-17%) was significantly higher than that of NoV GI (1%, 95% CI: 1-1%) in patients with acute gastroenteritis. CONCLUSION From the evidence considered in this review, the estimated prevalence of NoV in patients with acute gastroenteritis in developing countries was 17%. This estimate can be used to evaluate the burden of NoV-associated acute gastroenteritis in developing countries, which is currently unclear due to poor diagnosis and surveillance systems, and the estimation may enhance the development of human NoV vaccines.
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Affiliation(s)
- Gia Thanh Nguyen
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Department of Environmental and Occupational Health
- Institute for Community Health Research, College of Medicine and Pharmacy, Hue University, Hue city, Vietnam
| | - Kevin Phan
- Faculty of Medicine, University of Sydney
| | - Ian Teng
- Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Jian Pu
- Department of Food, Life and Environmental Sciences, Yamagata University, Tsuruoka, Yamagata, Japan
| | - Toru Watanabe
- Department of Food, Life and Environmental Sciences, Yamagata University, Tsuruoka, Yamagata, Japan
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21
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Kabue JP, Meader E, Hunter PR, Potgieter N. Genetic characterisation of Norovirus strains in outpatient children from rural communities of Vhembe district/South Africa, 2014-2015. J Clin Virol 2017; 94:100-106. [PMID: 28783578 DOI: 10.1016/j.jcv.2017.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/24/2017] [Accepted: 07/08/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Norovirus (NoV) is now the most common cause of both outbreaks and sporadic non-bacterial gastroenteritis worldwide. However, data supporting the role of NoV in diarrheal disease are limited in the African continent. OBJECTIVES This study investigates the distribution of NoV genotypes circulating in outpatient children from rural communities of Vhembe district/South Africa. STUDY DESIGN Stool specimens were collected from children under five years of age with diarrhea, and controls without diarrhea, between July 2014 and April 2015. NoV-positive samples, detected previously by Realtime PCR, were analysed using conventional RT-PCR targeting the partial capsid and polymerase genes. Nucleotide sequencing methods were performed to genotype the strains. RESULTS The sequence analyses demonstrated multiple NoV genotypes including GI.4 (13.8%), GI.5 (6.9%), GII.14 (6.9%), GII.4 (31%), GII.6 (3.4%), GII.P15 (3.4%), GII.P21 (3.4%) and GII.Pe (31%). The most prevalent NoV genotypes were GII.4 Sydney 2012 variants (n=7) among the capsid genotypes, GII.Pe (n=9) among the polymerase genotypes and GII.Pe/GII.4 Sydney 2012 (n=8) putative recombinants among the RdRp/Capsid genotypes. Two unassigned GII.4 variants were found. CONCLUSIONS The findings highlighted NoV genetic diversity and revealed continuous pandemic spread and predominance of GII.Pe/GII.4 Sydney 2012, indicative of increased NoV activity. An unusual RdRp genotype GII.P15 and two unassigned GII.4 variants were also identified from rural settings of the Vhembe district/South Africa. NoV surveillance is warranted to help to inform investigations into NoV evolution and disease burden, and to support on-going vaccine development programmes.
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Affiliation(s)
- Jean Pierre Kabue
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa.
| | - Emma Meader
- School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, UK
| | - Paul R Hunter
- School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, UK; Department of Environmental Health, Tshwane University of Technology, Pretoria, South Africa
| | - Natasha Potgieter
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa; Dean, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa
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22
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Zhou HL, Zhen SS, Wang JX, Zhang CJ, Qiu C, Wang SM, Jiang X, Wang XY. Burden of acute gastroenteritis caused by norovirus in China: A systematic review. J Infect 2017. [PMID: 28633888 DOI: 10.1016/j.jinf.2017.06.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND To understand the epidemiology and disease burden of norovirus (NoVs) gastroenteritis in China, a systematic review was conducted. METHODS Studies on acute gastroenteritis (AGE) caused by NoVs from mainland China, published before 2017 were searched. All retrieved articles were screened and reviewed by a standardized algorithm. NoVs detection rates as well as strain variations by ages, seasonal variations and geographic locations were analyzed using random-effects model. RESULTS A total of 225 articles were included in the final analysis. Similar detection rates at 21.0% and 19.8% were obtained from the North and the South, respectively. NoVs infection occurred year round, with a peak between October and January in the North and between August and November in the South. High detection rates (∼29%) of NoVs were found in adults and the elderly and in children aged 6-35 months (∼22%). The predominant strains were GII.4 (70.4%), followed by GII.3 (13.5%). CONCLUSION NoVs cause significant disease burden in China which warrants development of vaccines against NoVs, particularly for children and the elderly who are vulnerable to gastroenteritis diseases. To achieve a broad protection, continual monitoring NoV epidemics and strain variations for selection of proper vaccine strains is critical.
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Affiliation(s)
- Hong-Lu Zhou
- Key Laboratory Medical Molecular Virology, MoE/MoH, and the Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Shan-Shan Zhen
- Key Laboratory Medical Molecular Virology, MoE/MoH, and the Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China; Shanghai Minhang Center for Diseases Control and Prevention, Shanghai, 201101, People's Republic of China
| | - Jin-Xia Wang
- Key Laboratory Medical Molecular Virology, MoE/MoH, and the Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Can-Jing Zhang
- Key Laboratory Medical Molecular Virology, MoE/MoH, and the Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Chao Qiu
- Key Laboratory Medical Molecular Virology, MoE/MoH, and the Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China
| | - Song-Mei Wang
- Laboratory of Molecular Biology, Training Center of Medical Experiments, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xi Jiang
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Xuan-Yi Wang
- Key Laboratory Medical Molecular Virology, MoE/MoH, and the Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China; Research Center on Aging and Medicine, Fudan University, Shanghai, 200032, People's Republic of China.
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23
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Kabue JP, Meader E, Hunter PR, Potgieter N. Norovirus prevalence and estimated viral load in symptomatic and asymptomatic children from rural communities of Vhembe district, South Africa. J Clin Virol 2016; 84:12-18. [PMID: 27644014 PMCID: PMC5099155 DOI: 10.1016/j.jcv.2016.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 02/02/2023]
Abstract
NoV detection rates in cases and controls from children in Rural South Africa were not significantly different. Estimated GII viral load significantly higher in symptomatic than in asymptomatic children. First report on the difference between cases and controls with NoV in rural African population related to the viral load of NoV genogroups.
Background Human Norovirus (NoV) is recognized as a major etiological agent of sporadic acute gastroenteritis worldwide. Objectives This study describes the clinical features associated with Human NoV occurrence in children and determines the prevalence and estimated viral burden of NoV in symptomatic and asymptomatic children in rural South Africa. Study design Between July 2014 and April 2015, outpatient children under 5 years of age from rural communities of Vhembe district, South Africa, were enrolled for the study. A total of 303 stool specimens were collected from those with diarrhea (n = 253) and without (n = 50) diarrhea. NoVs were identified using real-time one-step RT-PCR. Results One hundred and four (41.1%) NoVs were detected (62[59.6%] GII, 16[15.4%] GI, and 26[25%] mixed GI/GII) in cases and 18 (36%) including 9(50%) GII, 2(11.1%) GI and 7(38.9%) mixed GI/GII in controls. NoV detection rates in symptomatic and asymptomatic children (OR = 1.24; 95% CI 0.66–2.33) were not significantly different. Comparison of the median CT values for NoV in symptomatic and asymptomatic children revealed significant statistical difference of estimated GII viral load from both groups, with a much higher viral burden in symptomatic children. Conclusions Though not proven predictive of diarrhea disease in this study, the high detection rate of NoV reflects the substantial exposure of children from rural communities to enteric pathogens possibly due to poor sanitation and hygiene practices. The results suggest that the difference between asymptomatic and symptomatic children with NoV may be at the level of the viral load of NoV genogroups involved.
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Affiliation(s)
- Jean Pierre Kabue
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, RSA, South Africa.
| | - Emma Meader
- School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, UK
| | - Paul R Hunter
- School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, UK; Department of Environmental Health, Tshwane University of Technology, Pretoria, RSA, South Africa
| | - Natasha Potgieter
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, RSA, South Africa; Dean, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, RSA, South Africa
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24
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Sisay Z, Djikeng A, Berhe N, Belay G, Gebreyes W, Abegaz WE, Njahira MN, Wang QH, Saif LJ. Prevalence and molecular characterization of human noroviruses and sapoviruses in Ethiopia. Arch Virol 2016; 161:2169-82. [PMID: 27193022 DOI: 10.1007/s00705-016-2887-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/03/2016] [Indexed: 01/02/2023]
Abstract
Viral gastroenteritis is a major public health problem worldwide. In Ethiopia, very limited studies have been done on the epidemiology of enteropathogenic viruses. The aim of this study was to detect and characterize noroviruses (NoVs) and sapoviruses (SaVs) from acute gastroenteritis patients of all ages. Fecal samples were collected from diarrheic patients (n = 213) in five different health centers in Addis Ababa during June-September 2013. The samples were screened for caliciviruses by reverse transcription polymerase chain reaction (RT-PCR) using universal and genogroup-specific primer pairs. Phylogenetic analyses were conducted using the sequences of the PCR products. Of the clinical samples, 25.3 % and 4.2 % were positive for NoV and SaV RNA, respectively. Among the norovirus positives, 22 were sequenced further, and diverse norovirus strains were identified: GI (n = 4), GII (n = 17) and GIV (n = 1). Most strains were GII (n = 17/22: 77.2 %), which were further divided into three different genotypes (GII.4, GII.12/GII.g recombinant-like and GII.17), with GII.17 being the dominant (7/17) strain detected. GI noroviruses, in particular GI.4 (n = 1), GI.5 (n = 2) and GI.8 (n = 1), were also detected and characterized. The GIV strain detected is the first from East Africa. The sapoviruses sequenced were also the first reported from Ethiopia. Collectively, this study showed the high burden and diversity of noroviruses and circulation of sapoviruses in diarrheic patients in Ethiopia. Continued surveillance to assess their association with diarrhea is needed to define their epidemiology, disease burden, and impact on public health.
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Affiliation(s)
- Zufan Sisay
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia. .,Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia.
| | - Appolinaire Djikeng
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O.Box 30709, Nairobi, 00100, Kenya
| | - Nega Berhe
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Gurja Belay
- Microbial, Cellular and Molecular Biology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Wondwossen Gebreyes
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Woldaregay Erku Abegaz
- Department of Microbiology and Immunology, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Moses N Njahira
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O.Box 30709, Nairobi, 00100, Kenya
| | - Q H Wang
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, 44691, USA
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research Development Center, The Ohio State University, Wooster, OH, 44691, USA.
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