1
|
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.
Collapse
|
2
|
Lu MC, Lin SC, Hsu YH, Chen SY. Epidemiology, Clinical Features, and Unusual Complications of Norovirus Infection in Taiwan: What We Know after Rotavirus Vaccines. Pathogens 2022; 11:pathogens11040451. [PMID: 35456126 PMCID: PMC9026459 DOI: 10.3390/pathogens11040451] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 02/01/2023] Open
Abstract
Noroviruses (NoVs) are one of the emerging and rapidly spreading groups of pathogens threatening human health. A reduction in sporadic NoV infections was noted following the start of the COVID-19 pandemic, but the return of NoV gastroenteritis during the COVID-19 pandemic has been noted recently. Research in recent years has shown that different virus strains are associated with different clinical characteristics; moreover, there is a paucity of research into extraintestinal or unusual complications that may be associated with NoV. The genomic diversity of circulating NoVs is also complex and may vary significantly. Therefore, this short narrative review focuses on sharing the Taiwan experience of NoV infection including epidemiology, clinical features, and complications following suboptimal rotavirus immunization in Taiwan (after October 2006). We also highlight the unusual complications associated with NoV infections and the impacts of NoV infection during the COVID-19 pandemic in the literature for possible future research directions. To conclude, further research is needed to quantify the burden of NoV across the spectrum of disease severity in Taiwan. The evidence of the connection between NoV and the unusual complications is still lacking.
Collapse
Affiliation(s)
- Meng-Che Lu
- Division of Allergy, Asthma and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (M.-C.L.); (S.-C.L.)
| | - Sheng-Chieh Lin
- Division of Allergy, Asthma and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (M.-C.L.); (S.-C.L.)
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei city 11031, Taiwan
| | - Yi-Hsiang Hsu
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA;
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shih-Yen Chen
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei city 11031, Taiwan
- Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Correspondence:
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Fang Y, Dong Z, Liu Y, Wang W, Hou M, Wu J, Wang L, Zhao Y. Molecular epidemiology and genetic diversity of norovirus among hospitalized children with acute gastroenteritis in Tianjin, China, 2018-2020. BMC Infect Dis 2021; 21:682. [PMID: 34261441 PMCID: PMC8277986 DOI: 10.1186/s12879-021-06375-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Background Norovirus (NoV) is a major cause of viral acute gastroenteritis (AGE) in children worldwide. Epidemiological analysis with respect to the virus strains is limited in China. This study aimed to investigate the prevalence, patterns, and molecular characteristics of NoV infection among children with AGE in China. Methods A total 4848 stool samples were collected from children who were admitted with AGE in Tianjin Children’s Hospital from August 2018 to July 2020. NoV was preliminarily detected using real-time reverse transcription polymerase chain reaction (RT-PCR). Partial sequences of the RNA-dependent RNA polymerase (RdRp) and capsid genes of positive samples were amplified by conventional RT-PCR and then sequenced. The NoV genotype was determined by online Norovirus Typing Tool Version 2.0, and phylogenetic analysis was conducted using MEGA 6.0. Results The prevalence of NoV was 26.4% (1280/4848). NoV was detected in all age groups, with the 7–12 months group having the highest detection rate (655/2014, 32.5%). NoV was detected during most part of the year with higher frequency in winter than other seasons. Based on the genetic analysis of RdRp, GII. Pe was the most predominant genotype detected at 70.7% (381/539) followed by GII.P12 at 25.4% (137/539). GII.4 was the most predominant capsid genotype detected at 65.3% (338/518) followed by GII.3 at 26.8% (139/518). Based on the genetic analysis of RdRp and capsid sequences, the strains were clustered into 10 RdRp–capsid genotypes: GII.Pe-GII.4 Sydney 2012 (65.5%), GII.P12-GII.3 (27.2%), GII.P16-GII.2 (1.8%), GII.P12-GII.2 (0.2%), GII.P17-GII.17 (1.1%), GII.Pe-GII.3 (1.8%), GII.Pe-GII.2 (1.1%), GII.Pe-GII.1 (0.4%), GII.16-GII.4 Sydney 2012 (0.7%), and GII.P7-GII.6 (0.2%). The predominant NoV genotypes changed from GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 between August 2018 and July 2019 to GII.Pe-GII.4 Sydney 2012 and GII.P16-GII.2 between August 2019 and July 2020. The patients with GII.Pe-GII.4 Sydney 2012 genotype were more likely to suffer from vomiting symptom than those with GII.P12-GII.3. Conclusions NoV is an important pathogen responsible for viral AGE among children in China. GII.Pe-GII.4 Sydney 2012 and GII.P12-GII.3 were major recombinant genotypes. Knowledge of circulating genotypes and seasonal trends is of great importance for disease prevention and surveillance.
Collapse
Affiliation(s)
- Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Zhaoying Dong
- Department of Neurology, Tianjin Union Medical Centre, No. 190 Jieyuan Road, Hongqiao District, Tianjin, 300121, China
| | - Yan Liu
- Clinical Pediatric College of Tianjin Medical University, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Wei Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Yu Zhao
- Department of Digestion, Tianjin Children's Hospital (Children's Hospital of Tianjin University), No.238 Longyan Road, Beichen District, Tianjin, 300134, China.
| |
Collapse
|
5
|
Elmahdy EM, Shaheen MNF, Rizk NM, Saad-Hussein A. Quantitative Detection of Human Adenovirus and Human Rotavirus Group A in Wastewater and El-Rahawy Drainage Canal Influencing River Nile in the North of Giza, Egypt. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:218-225. [PMID: 32388732 DOI: 10.1007/s12560-020-09429-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
Environmental monitoring is critical in a developing country like Egypt where there is an insufficient framework for recording and tracking outbreaks. In this study, the prevalence of human adenovirus (HAdV), rotavirus group A (RVA) was determined in urban sewage, activated sludge, drainage water, drainage sediment, Nile water, and Nile sediment, using quantitative polymerase chain reaction (qPCR) analysis. HAdV was detected in 50% of urban sewage with viral concentrations ranging from 103 to 107 genome copies/liter (GC/L), 33% of activated sludge with viral concentrations ranging from 103 to 107 GC/kilogram (GC/kg), 95% of drainage water with viral concentrations ranging from 103 to 107 GC/L, 75% of drainage sediment with viral concentrations ranging from 103 to 107 GC/L, 50% of Nile water with viral concentrations ranging from 103 to 107 GC/L, and 45% of Nile sediment with viral concentrations ranging from 103 to 107 GC/kg. RVA was detected in 50% of urban sewage with viral concentrations ranging from 103 to 107 GC/L, 75% of activated sludge with viral concentrations ranging from 103 to 107 GC/L, 58% of drainage water with viral concentrations ranging from 103 to 107 GC/L, 50% of drainage sediment with viral concentrations ranging from 103 to 107 GC/L, and 45% of Nile water with viral concentrations ranging from 103 to 107 GC/kg. In conclusion, Abu-Rawash WWTP acts as a source of HAdV and RVA, releasing them into El-Rahawy drain then to the River Nile Rosetta branch.
Collapse
Affiliation(s)
- Elmahdy M Elmahdy
- Environmental Virology Laboratory, Department of Water Pollution Research, Environmental Research Division, National Research Centre, Dokki, Giza, 12622, Egypt.
| | - Mohamed N F Shaheen
- Environmental Virology Laboratory, Department of Water Pollution Research, Environmental Research Division, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Neveen M Rizk
- Environmental Virology Laboratory, Department of Water Pollution Research, Environmental Research Division, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Amal Saad-Hussein
- Environmental & Occupational Medicine Department, National Research Center, Cairo, Egypt
| |
Collapse
|
6
|
Potgieter N, Karambwe S, Mudau LS, Barnard T, Traore A. Human Enteric Pathogens in Eight Rivers Used as Rural Household Drinking Water Sources in the Northern Region of South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E2079. [PMID: 32245071 PMCID: PMC7142607 DOI: 10.3390/ijerph17062079] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/28/2020] [Accepted: 03/09/2020] [Indexed: 11/16/2022]
Abstract
People living in rural areas still rely on the use of environmental water that is contaminated by human and animal activities. This study assessed the occurrence of human enteric pathogens in rivers that are used by rural communities Vhembe District of South Africa as a source of drinking water covering two seasons (winter and summer) over a one-year period. Water quality was assessed using physico characteristics and indicator organisms (total coliforms, E. coli, Clostridium perfringens). Pathogens tested included bacteria (Pathogenic E. coli, Salmonella-, Shigella- and Vibrio spp.), protozoa (Cryptosporidium- and Giardia spp.), and enteric viruses (Rota-, Noro-, Entero-, and Adenoviruses) while using published molecular protocols. The results showed that the indicator bacteria counts exceeded South African drinking water quality guideline limits and pathogenic E. coli was detected in the samples. No Shigella spp. were isolated, while Vibrio spp. and Salmonella spp. were present; parasites were detected in four rivers and Enteric viruses were predominantly detected in the winter season. The results indicated the poor condition of water and the potential health risks to consumers highlighting the need for implementing river catchment management strategies for continued sustainability in these rivers.
Collapse
Affiliation(s)
- Natasha Potgieter
- Microbiology Department, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; (S.K.); (A.T.)
- Dean, School of Mathematical and Natural Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa
| | - Simbarashe Karambwe
- Microbiology Department, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; (S.K.); (A.T.)
| | - Lutendo Sylvia Mudau
- Department of Environmental Health, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa;
| | - Tobias Barnard
- Water & Health Research Center, University of Johannesburg, PO Box 524, 2006 Auckland Park, Johannesburg 2094, South Africa;
| | - Afsatou Traore
- Microbiology Department, University of Venda, Private Bag X5050, Thohoyandou 0950, South Africa; (S.K.); (A.T.)
| |
Collapse
|
7
|
Chukwu MO, Abia ALK, Ubomba-Jaswa E, Dewar JB, Obi C. Mixed Aetiology of Diarrhoea in Infants Attending Clinics in the North-West Province of South Africa: Potential for Sub-Optimal Treatment. Pathogens 2020; 9:E198. [PMID: 32155961 PMCID: PMC7157715 DOI: 10.3390/pathogens9030198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/28/2019] [Accepted: 12/01/2019] [Indexed: 11/17/2022] Open
Abstract
Routine diagnostic methods for the aetiologic agents of diarrhoea in most developing countries are usually not sensitive enough, leading to under-diagnosis. Thus, this study investigated possible mixed diarrhoeal aetiology by using cultures and real-time polymerase chain reactions (PCR) in children younger than four years old in the Northwest Province, South Africa. In total, 505 stool samples were collected from symptomatic and asymptomatic children who were attending three clinics and the Brits hospital in Madibeng District, between September 2016 and December 2017. Rotavirus, norovirus, Campylobacter, Arcobacter, and diarrhoeagenic Escherichia coli (DEC) were targeted. Campylobacter spp. (24.6%), Arcobacter (15.8%) and DEC (19.6%) were detected using PCR; only Campylobacter spp. (29.7%) and DEC (26.9%) were detected through the culture. Campylobacter jejuni (36%), Campylobacter coli (28%), Campylobacter upsalensis (12%), and Arcobacter butzleri (15.8%) were the only spp. of Campylobacter and Arcobacter identified. The eaeA gene (31.4%) of enteropathogenic E. coli/enterohaemorrhagic E. coli (EPEC/EHEC) was the most prevalent DEC virulence gene (VG) identified. Rotavirus and norovirus were detected at 23.4% and 20%, respectively. Mixed viral aetiology (7.3%) and the co-infection of A. butzleri and Campylobacter (49%) were recorded. A mixed bacterial-viral aetiology was observed in 0.6% of the specimens. Sensitive diagnostic procedures like PCR should be considered to provide the best treatment to children experiencing diarrhoea.
Collapse
Affiliation(s)
- Martina O. Chukwu
- Department of Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Corner Christiaan De wet and Pioneer Avenue, Florida Park, Roodepoort 1724, Gauteng, South Africa;
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
| | - Eunice Ubomba-Jaswa
- Department of Biotechnology, University of Johannesburg, 37 Nind Street, Doornfontein 2094, Gauteng, South Africa;
- Water Research Commission, Lynnwood Bridge Office Park, Bloukrans Building, 4 Daventry Street, Lynnwood Manor, Pretoria 0081, South Africa
| | - John Barr Dewar
- Department of Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Corner Christiaan De wet and Pioneer Avenue, Florida Park, Roodepoort 1724, Gauteng, South Africa;
| | - C.L. Obi
- School of Science and Technology, Sefako Makgatho Health Science University, Ga-Rankuwa 0208, South Africa;
| |
Collapse
|
8
|
Dan W, Jin Y, Tang Z, Li Y, Yao H. Nucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants. J Biomol Struct Dyn 2019; 38:4764-4773. [PMID: 31684837 DOI: 10.1080/07391102.2019.1689171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Norovirus GII.4 variants, a genotype in genogroup II belonging to the genus Norovirus, is a single-strand positive sense RNA containing three open reading frames (ORF1, ORF2 and ORF3) and is the most important pathogen causing nonbacterial gastroenteritis outbreaks. By using bioinformatic softwares such as Codon W, SPSS and so on, a total of 292 strains of the viruses isolated from 1974 to 2016 were analyzed for nucleotide composition and synonymous codon usage in each ORF. The result shows that it is enriched for A over the other bases in nucleotide composition, G behind the other bases in the 3rd site of all synonymous codons in the three ORFs. The patterns of nucleotide composition and codon bias of ORF2 are similar to those of ORF3 and different from those of ORF1. There are generally UpA motif and CpG motif in the codons with the lowest proportion. Correspondence analysis indicates that the codon usage may be changing over a certain time period for ORF1 in 2006 and 2012, ORF2 in 2012, and ORF3 in 2013. ENC (effective number of codons) plot and other analyses indicate that both natural selection and mutational pressure play partly roles in the ORFs, but natural selection is more important for ORF2 and ORF3. Besides, we also found all optimal codons in the ORFs. The study provides a basic understanding of the mechanism for norovirus GII.4 codon usage bias. AbbreviationsORFOpen Reading FrameENCEffective Number of CodonsCOAcorrespondence analysisRSCURelative Synonymous Codon UsageCAICodon Adaptation IndexCBICodon Bias IndexFopfrequency of optimal codonsL_symnumber of synonymous codonsL_aalength amino acidsGRAVYgrand average of hydropathicityAromaaromaticityCommunicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Wei Dan
- College of Life Science, Sichuan Agriculture University, Ya'an, Sichuan, China
| | - Yan Jin
- College of Life Science, Sichuan Agriculture University, Ya'an, Sichuan, China
| | - Zizhong Tang
- College of Life Science, Sichuan Agriculture University, Ya'an, Sichuan, China
| | - Yongmin Li
- College of Life Science, Sichuan Agriculture University, Ya'an, Sichuan, China
| | - Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, Sichuan, China
| |
Collapse
|
9
|
Nadan S, Taylor MB, Groome MJ, Cohen C, Madhi SA, Page NA. Epidemiology of human astroviruses among children younger than 5 years: Prospective hospital-based sentinel surveillance in South Africa, 2009-2014. J Med Virol 2018; 91:225-234. [PMID: 30192398 DOI: 10.1002/jmv.25308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/02/2018] [Accepted: 09/02/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND The epidemiology of human astroviruses (HAstVs) in hospitalised patients less than 5 years of age from selected sites in South Africa was investigated. Diarrheagenic stool specimens collected from April 2009 to May 2014 were screened retrospectively for selected viruses, bacteria and parasites. METHOD Patient data were analysed to identify epidemiologic factors most frequently detected with HAstV infections. The following case-comparisons were investigated; HAstV-positive and HAstV-negative children, human immunodeficiency virus (HIV)-infected and HIV-uninfected (HAstV-positive) children and HIV-exposed and unexposed (HAstV-positive HIV-uninfected) children. RESULTS Astrovirus was identified in 7.0% (234/3340) of cases and most frequently in ages 7 to 12 months (9.2%; 90/975) compared with 5.8% to 6.6% in other 6-month age groups. No seasonal trends were observed. More HAstVs were detected in children from homes that used outdoor water sources (7.6%) compared to indoor sources [5.7%; adjusted odds ratio (aOR), 1.5; 95% CI, 1.1-2.1; P = 0.009]. Astroviruses were detected in 8.4% (67/799) of HIV-uninfected patients that were exposed to HIV compared with 5.9% (74/1257) of HIV-unexposed patients ( P = 0.032). CONCLUSION Astroviruses were most prevalent in children aged 7 to 12 months and were detected throughout the study period. The study was limited as only hospitalised patients were investigated and no comparisons were made to diarrhoea-free control groups. Future HAstV surveillance should include community-based studies and children presenting at outpatient facilities.
Collapse
Affiliation(s)
- Sandrama Nadan
- Centre for Enteric Diseases, Virology Division, National Institute for Communicable Disease, Sandringham, South Africa.,Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
| | - Michelle J Groome
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, Epidemiology Division, National Institute for Communicable Disease, Sandringham, South Africa
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicola A Page
- Centre for Enteric Diseases, Virology Division, National Institute for Communicable Disease, Sandringham, South Africa.,Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, South Africa
| |
Collapse
|
10
|
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.
Collapse
|
11
|
Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
Collapse
|
12
|
Makhaola K, Moyo S, Lechiile K, Goldfarb DM, Kebaabetswe LP. Genetic and epidemiological analysis of norovirus from children with gastroenteritis in Botswana, 2013-2015. BMC Infect Dis 2018; 18:246. [PMID: 29848303 PMCID: PMC5975618 DOI: 10.1186/s12879-018-3157-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/21/2018] [Indexed: 12/16/2022] Open
Abstract
Background Norovirus is a leading cause of viral gastroenteritis worldwide with a peak of disease seen in children. The epidemiological analysis regarding the virus strains in Africa is limited. The first report of norovirus in Botswana was in 2010 and currently, the prevalence and circulating genotypes of norovirus are unknown, as the country has no systems to report the norovirus cases. This study investigated the prevalence, patterns and molecular characteristics of norovirus infections among children ≤5 years of age admitted with acute gastroenteritis at four hospitals in Botswana. Methods A total of 484 faecal samples were collected from children who were admitted with acute gastroenteritis during the rotavirus vaccine impact survey between July 2013 and December 2015. Norovirus was detected using real-time RT-PCR. Positive samples were genotyped using conventional RT-PCR followed by partial sequencing of the capsid and RdRp genes. Norovirus strains were determined by nucleotide sequence analysis using the online Norovirus Genotyping Tool Version 1.0, and confirmed using maximum likelihood tree construction as implemented in MEGA 6.0. Results The prevalence of norovirus was 9.3% (95% CI 6.7–11.9). The genotype diversity was dominated by the GII.4 strain at 69.7%. This was followed by GII.2, GII.12 each at 9.1%, GI.9 at 6.6% and GII.6, GII.10 each at 3.0%. The most common combined RdRp/Capsid genotype was the GII.Pe/GII.4 Sydney 2012. Norovirus was detected during most part of the year; however, there was a preponderance of cases in the wet season (December to March). Conclusion The study showed a possible decline of norovirus infections in the last 10 years since the first report. An upward trend seen between 2013 and 2015 may be attributable to the success of rotavirus vaccine introductions in 2012. Knowledge of circulating genotypes, seasonal trends and overall prevalence is critical for prevention programming and possible future vaccine design implications. Electronic supplementary material The online version of this article (10.1186/s12879-018-3157-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kgomotso Makhaola
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag, 16, Palapye, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Harvard T.H Chan School of Public Health, Boston, MA, USA
| | | | - David M Goldfarb
- Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Pathology, University of British Columbia, Vancouver, Canada
| | - Lemme P Kebaabetswe
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag, 16, Palapye, Botswana.
| |
Collapse
|
13
|
Petrignani M, Verhoef L, de Graaf M, Richardus JH, Koopmans M. Chronic sequelae and severe complications of norovirus infection: A systematic review of literature. J Clin Virol 2018; 105:1-10. [PMID: 29804008 DOI: 10.1016/j.jcv.2018.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 11/17/2022]
Abstract
Norovirus causes an estimated 18% of all cases of acute gastroenteritis worldwide and is found to be associated with mortality. To create a first overview of severe complications and chronic sequelae of norovirus infections, a systematic review of literature was performed. Of 3928 individual hits, 176 publications remained for data extraction. Study periods varied between 1974 and 2017, though strongly skewed towards the last decade (n = 122, 70%). Countries of studies were worldwide, though Africa, and Carribean, Central and South America were underrepresented. Strong evidence was found for chronic diarrhea in immunocompromised patients, affecting 9%-100% of investigated cohorts. The duration of chronic diarrhea varied from four weeks up to nine years, leading to either wasting, weight loss or failure to thrive in a third of the reported cases (224). Other complications with significant evidence were necrotizing enterocolitis (NEC) in preterm infants associated with norovirus infection (8 papers), and benign infantile convulsions with gastroenteritis (BICG; 19 papers). Studies on norovirus infection and inflammatory bowel disease (IBD) mostly concluded against this association (5 of 7). The remaining papers mentioned a large variety of possible sequelae or complications. Based on the available literature, chronic norovirus diarrhea is the major sequela of norovirus infection in primary immune deficient, oncologic and transplant patients. Norovirus infection - like other gastrointestinal pathogens - can cause a range of sequelae and complications, and should be considered in the differential diagnosis of these manifestations.
Collapse
Affiliation(s)
- Mariska Petrignani
- Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands.
| | - Linda Verhoef
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan Hendrik Richardus
- Public Health Department, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| |
Collapse
|
14
|
Mabasa VV, Meno KD, Taylor MB, Mans J. Environmental Surveillance for Noroviruses in Selected South African Wastewaters 2015-2016: Emergence of the Novel GII.17. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:16-28. [PMID: 28779481 DOI: 10.1007/s12560-017-9316-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/29/2017] [Indexed: 06/07/2023]
Abstract
Norovirus (NoV) GII.4 is the predominant genotype associated with gastroenteritis pandemics and new strains emerge every 2-3 years. Between 2008 and 2011, environmental studies in South Africa (SA) reported NoVs in 63% of the sewage-polluted river water samples. The aim of this study was to assess whether wastewater samples could be used for routine surveillance of NoVs, including GII.4 variants. From April 2015 to March 2016, raw sewage and effluent water samples were collected monthly from five wastewater treatment plants in SA. A total of 108 samples were screened for NoV GI and GII using real-time RT-qPCR. Overall 72.2% (78/108) of samples tested positive for NoVs with 4.6% (5/108) GI, 31.5% (34/108) GII and 36.1% (39/108) GI + GII strains being detected. Norovirus concentrations ranged from 1.02 × 102 to 3.41 × 106 genome copies/litre for GI and 5.00 × 103 to 1.31 × 106 genome copies/litre for GII. Sixteen NoV genotypes (GI.2, GI.3, GI.4, GI.5, GI.6, GII.2, GII.3, GII.4, GII.7, GII.9, GII.10, GII.14, GII.16, GII.17, GII.20, and GII.21) were identified. Norovirus GII.2 and GII.17 co-dominated and the majority of GII.17 strains clustered with the novel Kawasaki 2014 variant. Sewage surveillance facilitated detection of Kawasaki 2014 in SA, which to date has not been detected with surveillance in children with gastroenteritis <5 years of age. Combined surveillance in the clinical setting and environment appears to be a valuable strategy to monitor emergence of NoV strains in countries that lack NoV outbreak surveillance.
Collapse
Affiliation(s)
- V V Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa
| | - K D Meno
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa
| | - M B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Private Bag X323, Pretoria, 0007, South Africa.
| |
Collapse
|
15
|
Van Abel N, Mans J, Taylor MB. Quantitative microbial risk assessment to estimate the health risk from exposure to noroviruses in polluted surface water in South Africa. JOURNAL OF WATER AND HEALTH 2017; 15:908-922. [PMID: 29215355 DOI: 10.2166/wh.2017.305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This study assessed the risks posed by noroviruses (NoVs) in surface water used for drinking, domestic, and recreational purposes in South Africa (SA), using a quantitative microbial risk assessment (QMRA) methodology that took a probabilistic approach coupling an exposure assessment with four dose-response models to account for uncertainty. Water samples from three rivers were found to be contaminated with NoV GI (80-1,900 gc/L) and GII (420-9,760 gc/L) leading to risk estimates that were lower for GI than GII. The volume of water consumed and the probabilities of infection were lower for domestic (2.91 × 10-8 to 5.19 × 10-1) than drinking water exposures (1.04 × 10-5 to 7.24 × 10-1). The annual probabilities of illness varied depending on the type of recreational water exposure with boating (3.91 × 10-6 to 5.43 × 10-1) and swimming (6.20 × 10-6 to 6.42 × 10-1) being slightly greater than playing next to/in the river (5.30 × 10-7 to 5.48 × 10-1). The QMRA was sensitive to the choice of dose-response model. The risk of NoV infection or illness from contaminated surface water is extremely high in SA, especially for lower socioeconomic individuals, but is similar to reported risks from limited international studies.
Collapse
Affiliation(s)
- Nicole Van Abel
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, 0007 Arcadia, Pretoria, South Africa E-mail:
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, 0007 Arcadia, Pretoria, South Africa E-mail:
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, 0007 Arcadia, Pretoria, South Africa E-mail:
| |
Collapse
|
16
|
Wi SW, Lee SJ, Kang EK, Cho SM. Ileal Perforation with Norovirus Gastroenteritis in a 3-Month-Old Infant. Pediatr Gastroenterol Hepatol Nutr 2017; 20:130-133. [PMID: 28730138 PMCID: PMC5517380 DOI: 10.5223/pghn.2017.20.2.130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/27/2016] [Accepted: 07/26/2016] [Indexed: 11/14/2022] Open
Abstract
Noroviruses have been recognized as the leading cause of epidemic and sporadic gastroenteritis since the advent of molecular diagnostic technique. They have been documented in 5-31% of pediatric patients hospitalized with gastroenteritis. Although norovirus gastroenteritis is typically mild and self-limited, it causes severe, but sometimes fatal, conditions in the vulnerable population such as immunocompromised patients, young children, and the elderly. Bowel perforation due to norovirus infection is rare. We report a case of small bowel perforation with norovirus gastroenteritis in the infant with Down syndrome during the hospitalization with pneumonia. Severe dehydration may cause bowel ischemia and could have triggered bowel perforation in this case. Physicians should be alert to the potential surgical complications followed by severe acute diarrhea, especially in high risk groups.
Collapse
Affiliation(s)
- Seol Woo Wi
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, Korea
| | - Su Jin Lee
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, Korea
| | - Eun Kyeong Kang
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, Korea
| | - Sung Min Cho
- Department of Pediatrics, Dongguk University Ilsan Hospital, Goyang, Korea
| |
Collapse
|
17
|
Norovirus epidemiology in South African children <5 years hospitalised for diarrhoeal illness between 2009 and 2013. Epidemiol Infect 2017; 145:1942-1952. [PMID: 28393756 DOI: 10.1017/s0950268817000668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Public health interest in norovirus (NoV) has increased in recent years following improved diagnostics, global burden estimates and the development of NoV vaccine candidates. This study aimed to describe the detection rate, clinical characteristics and environmental features associated with NoV detection in hospitalized children <5 years with diarrhoea in South Africa (SA). Between 2009 and 2013, prospective diarrhoeal surveillance was conducted at four sites in SA. Stool specimens were collected and screened for NoVs and other enteric pathogens using molecular and serological assays. Epidemiological and clinical data were compared in patients with or without detection of NoV. The study detected NoV in 15% (452/3103) of hospitalized children <5 years with diarrhoea with the majority of disease in children <2 years (92%; 417/452). NoV-positive children were more likely to present with diarrhoea and vomiting (odds ratio (OR) 1·3; 95% confidence interval (CI) 1·1-1·7; P = 0·011) with none-to-mild dehydration (adjusted OR 0·5; 95% CI 0·3-0·7) compared with NoV-negative children. Amongst children testing NoV positive, HIV-infected children were more likely to have prolonged hospitalization and increased mortality compared with HIV-uninfected children. Continued surveillance will be important to consider the epidemic trends and estimate the burden and risk of NoV infection in SA.
Collapse
|
18
|
Norovirus infections in young children in Lusaka Province, Zambia: clinical characteristics and molecular epidemiology. BMC Infect Dis 2017; 17:92. [PMID: 28114885 PMCID: PMC5260028 DOI: 10.1186/s12879-017-2206-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/16/2017] [Indexed: 12/12/2022] Open
Abstract
Background The burden, clinical features, and molecular epidemiology of norovirus infection in young children in southern Africa are not well defined. Methods Using data from a health facility-based surveillance study of children <5 years in Lusaka Province, Zambia presenting with diarrhea, we assessed the burden of norovirus infection. A convenience sample of 454 stool specimens was tested for norovirus using reverse-transcriptase polymerase chain reaction (RT-PCR). RT-PCR positive samples underwent additional nucleotide sequencing for genogroup and genotype identification. Clinical features and severity of diarrheal illnesses were compared between norovirus-positive and -negative subjects using Chi-squared and t-tests. Results Norovirus was detected in 52/454 (11.5%) specimens tested. Abdominal pain, fever, and vomiting were the most common presenting features in norovirus-associated illnesses. However, there were no significant differences in the clinical features of norovirus-positive compared to norovirus-negative illnesses. Of 43 isolates that were available for sequencing, 31 (72.1%) were genogroup II (GII) and 12 (27.9%) were genogroup I (GI). The distribution of genotypes was diverse. Conclusions Noroviruses were detected in approximately 10% of young children with diarrhea in the Lusaka Province of Zambia, with GII representing the majority of infections. These findings support the role of norovirus in symptomatic diarrhea disease in Africa. Further studies are needed to confirm these observations and to evaluate prevention strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2206-2) contains supplementary material, which is available to authorized users.
Collapse
|
19
|
Botha J, Taylor M, Mans J. Comparative analysis of South African norovirus GII.4 strains identifies minor recombinant variants. INFECTION GENETICS AND EVOLUTION 2017; 47:26-34. [DOI: 10.1016/j.meegid.2016.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/28/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022]
|
20
|
Adefisoye MA, Nwodo UU, Green E, Okoh AI. Quantitative PCR Detection and Characterisation of Human Adenovirus, Rotavirus and Hepatitis A Virus in Discharged Effluents of Two Wastewater Treatment Facilities in the Eastern Cape, South Africa. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:262-274. [PMID: 27236707 PMCID: PMC5093187 DOI: 10.1007/s12560-016-9246-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/18/2016] [Indexed: 05/18/2023]
Abstract
The occurrence of enteric viruses in reclaimed wastewater, their removal by efficient treatment processes and the public health hazards associated with their release into the environments are of great significance in environmental microbiology. In this study, TaqMan-based real-time polymerase chain reaction (qPCR) was used to assess the prevalence of human adenovirus (HAdV), rotavirus (RV) and hepatitis A virus (HAV) in the final effluents of two wastewater treatment plants in the Eastern Cape Province, South Africa, over a twelve-month sampling period. The correlation between the concentrations of viruses in the effluents samples and faecal coliform (FC) densities were assessed as to validate the use of FC as microbiological indicator in water quality assessment. HAdV was detected in 62.5 % (30/48) of the samples with concentrations ranging between 8.4 × 101 and 1.0 × 105 genome copies/L while HAV and RV were only detected at concentrations below the set detection limits. FCs densities ranged from 1 to 2.7 × 104 CFU/100 ml. Adenovirus species HAdV-B (serotype 2) and HAdV-F (serotype 41) were detected in 86.7 % (26/30) and 6.7 % (2/30) of the HAdV-positive samples, respectively. No consistent seasonal trend was observed in HAdV concentrations, however, increased concentrations of HAdV were generally observed in the winter months. Also, there was no correlation between the occurrence of HAdV and FC at both the treatment plants. The persistent occurrence of HAdV in the discharged treated effluents points to the potential public health risk through the release of HAdV into the receiving watersheds, and the possibility of their transmission to human population.
Collapse
Affiliation(s)
- Martins Ajibade Adefisoye
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, 5700, South Africa.
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa.
| | - Uchechukwu U Nwodo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, 5700, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa
| | - Ezekiel Green
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa
| | - Anthony Ifeanyin Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, 5700, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa
| |
Collapse
|
21
|
He Y, Jin M, Chen K, Zhang H, Yang H, Zhuo F, Zhao D, Zeng H, Yao X, Zhang Z, Chen L, Zhou Y, Duan ZJ. Gastroenteritis Outbreaks Associated with the Emergence of the New GII.4 Sydney Norovirus Variant during the Epidemic of 2012/13 in Shenzhen City, China. PLoS One 2016; 11:e0165880. [PMID: 27829005 PMCID: PMC5102426 DOI: 10.1371/journal.pone.0165880] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 10/19/2016] [Indexed: 12/19/2022] Open
Abstract
Noroviruses (NoVs) are the leading cause of gastroenteritis outbreaks in humans worldwide. Since late 2012, a new GII.4 variant Sydney 2012 has caused a significant increase in NoV epidemics in several countries. From November of 2012 to January of 2013, three gastroenteritis outbreaks occurred in two social welfare homes (Outbreaks A and B) and a factory (Outbreak C) in Shenzhen city of China. Feces and swabs were collected for laboratory tests for causative agents. While no bacterial pathogen was identified, all three outbreaks were caused by NoVs with detection rates of 26.2% (16/61) at Outbreak A, 35.2% (38/108) at Outbreak B), and 59.3% (16/27) at Outbreaks C. For Outbreak B, 25 of the 29 symptomatic individuals (86.2%) and 13 of the 79 asymptomatic individuals (16.5%) were found NoV-positive. For Outbreak C, an asymptomatic food handler was NoV-positive. All thirteen NoV sequences from the three outbreaks were classified into genogroup II and genotype 4 (GII.4), which we identified to be the GII.4 Sydney 2012 variant. The genome of two isolates from Outbreaks A and B were recombinant with the opening reading frame (ORF) 1 of GII.4 Osaka 2007 and ORF2 and 3 of the GII.4 New Orleans. Our study indicated that the GII.4 Sydney 2012 variant emerged and caused the outbreaks in China.
Collapse
Affiliation(s)
- Yaqing He
- Southern Medical University, Guangzhou, Guangdong, China
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Miao Jin
- Key Laboratory of Medical Virology and Viral Diseases; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Kena Chen
- Key Laboratory of Medical Virology and Viral Diseases; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Hailong Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Hong Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Fei Zhuo
- Shenzhen Luohu Center for Disease Control and Prevention, Shenzhen, China
| | - Dejian Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Huatang Zeng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiangjie Yao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Zhen Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Long Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yuanping Zhou
- Southern Medical University, Guangzhou, Guangdong, China
- * E-mail: (ZJD); (YPZ)
| | - Zhao-jun Duan
- Key Laboratory of Medical Virology and Viral Diseases; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
- * E-mail: (ZJD); (YPZ)
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Abstract
Norovirus (NoV) is recognised as a leading cause of gastroenteritis worldwide across all age groups. The prevalence and diversity of NoVs in many African countries is still unknown, although early sero-prevalence studies indicated widespread early infection. Reports on NoVs in Africa vary widely in terms of study duration, population groups and size, inclusion of asymptomatic controls, as well as genotyping information. This review provides an estimate of NoV prevalence and distribution of genotypes of NoVs in Africa. Inclusion criteria for the review were study duration of at least 6 months, population size of >50 and diagnosis by RT-PCR. As regions used for genotyping varied, or genotyping was not always performed, this was not considered as an inclusion criteria. A literature search containing the terms norovirus+Africa yielded 74 publications. Of these 19 studies from 14 out of the 54 countries in Africa met the inclusion criteria. Data from studies not meeting the inclusion criteria, based on sample size or short duration, were included as discussion points. The majority of studies published focused on children, under five years of age, hospitalised with acute gastroenteritis. The mean overall prevalence was 13.5% (range 0.8–25.5%) in children with gastroenteritis and 9.7% (range 7–31%) in asymptomatic controls, where tested. NoV GII.4 was the predominant genotype identified in most of the studies that presented genotyping data. Other prevalent genotypes detected included GII.3 and GII.6. In conclusion, NoV is a common pathogen in children with diarrhoea in Africa, with considerable carriage in asymptomatic children. There is however, a paucity of data on NoV infection in adults.
Collapse
Affiliation(s)
- Janet Mans
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- * E-mail:
| | - George E. Armah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - A. Duncan Steele
- MRC Diarrhoeal Pathogens Research Unit, University of Limpopo, Pretoria, South Africa
| | - Maureen B. Taylor
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
24
|
Rahman M, Rahman R, Nahar S, Hossain S, Ahmed S, Golam Faruque AS, Azim T. Norovirus diarrhea in Bangladesh, 2010-2014: prevalence, clinical features, and genotypes. J Med Virol 2016; 88:1742-50. [PMID: 27003679 DOI: 10.1002/jmv.24530] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2016] [Indexed: 01/22/2023]
Abstract
Norovirus infections in diarrhea patients attending an urban and a rural hospital in Bangladesh were investigated. A total of 953 fecal specimens from both children and adults collected during 2010-2014 were tested for the presence of norovirus using real time PCR. One fourth (25%) of the specimens were positive for norovirus RNA which was identified both in children and adults. Norovirus was associated with short duration of diarrhea, high abdominal pain, and more moderate to severe dehydration when compared with rotavirus infections. Norovirus GII (69%) was the most prevalent genogroup followed by GI (18%), mixed GI/GII/GIV (11%), and GIV (2%). Among GII genogroup, GII.4 (42%) was the most prevalent genotype followed by GII.3 (21%), GII.6 (7%), GII.7 (6%), and GII.21 (6%). GII.4 and GII.3 strains were frequently identified (82% and 75%, respectively) in children <2 years of age and less commonly (16% and 15%) in adults more than 18 years of age. The present study reinforces the importance of norovirus-associated hospitalizations both in children and adults. The dynamic molecular epidemiology of norovirus requires routine strain surveillance to identify changes in prevailing strains. J. Med. Virol. 88:1742-1750, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Rajibur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Shakhaowat Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Tasnim Azim
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| |
Collapse
|
25
|
Page N, Groome MJ, Murray T, Nadan S, Netshikweta R, Keddy KH, Poonsamy B, Moyes J, Walaza S, Kahn K, Kuonza L, Taylor MB, Madhi SA, Cohen C. Sapovirus prevalence in children less than five years of age hospitalised for diarrhoeal disease in South Africa, 2009-2013. J Clin Virol 2016; 78:82-8. [PMID: 27002709 DOI: 10.1016/j.jcv.2016.03.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/08/2016] [Accepted: 03/12/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND Although sapovirus (SaV) has been detected in 2.2-12.7% of gastroenteritis cases globally, there are limited data on SaV epidemiology. OBJECTIVES Describe the epidemiology, clinical characteristics and factors associated with SaV gastroenteritis in hospitalised children <5 years of age in South Africa. STUDY DESIGN Between 2009 and 2013 during prospective diarrhoeal surveillance, stool specimens were collected from four sites and screened for SaVs and associated enteric pathogens using ELISA, microscopy, conventional and real-time PCR. Epidemiological and clinical data were compared in patients with or without SaV. Odds ratios were assessed by bivariate and stepwise multivariable logistic regression analysis. RESULTS Sapoviruses were detected in 7.7% (238/3103) of children admitted to hospital and 11.4% (9/79) of deaths. Sapovirus was detected more commonly in children 19-24 months compared to<6months (aOR=2.3; p=0.018) and in males (aOR=2.0; p=0.001). Additional factors associated with SaV detection included residing with≥7 inhabitants compared to ≤3 (aOR=2.2; p=0.011) and concomitant norovirus infections (aOR=3.0; p=0.003). HIV-infected children with SaV were more likely to have bloody stools (aOR=16.8; p<0.001), low birth weight (<2.5kg; aOR=5.8; p=0.007) and live in environments without flush toilets (aOR=8.1; p=0.003) compared to HIV-uninfected children. CONCLUSIONS Sapoviruses, which are perceived to cause mild diarrhoea, were detected in hospitalised children and diarrhoeal deaths in South Africa. Determinants increasing the odds of SaV included overcrowding and concomitant infections while HIV-infected children with SaV displayed bloody stools, low birth weight and reduced access to proper sanitation. Mitigation strategies against SaV infections include improved sanitation.
Collapse
Affiliation(s)
- Nicola Page
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa; School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa; Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
| | - Michelle J Groome
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of Witwatersrand, Johannesburg, South Africa
| | - Tanya Murray
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Sandrama Nadan
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa; Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Rembuluwani Netshikweta
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa; Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Karen H Keddy
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa; Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Bhavani Poonsamy
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa
| | - Jocelyn Moyes
- School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Sibongile Walaza
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Lazarus Kuonza
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa; School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Shabir A Madhi
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Private Bag x4, Sandringham, 2131, South Africa
| |
Collapse
|
26
|
Murray TY, Nadan S, Page NA, Taylor MB. Diverse sapovirus genotypes identified in children hospitalised with gastroenteritis in selected regions of South Africa. J Clin Virol 2016; 76:24-9. [PMID: 26803285 DOI: 10.1016/j.jcv.2016.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 12/15/2015] [Accepted: 01/05/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Sapoviruses (SaVs) are recognised as causative agents of gastroenteritis worldwide. However, data on the genetic diversity of this virus in Africa are lacking, particularly in the form of current long-term studies. OBJECTIVE To determine the genetic diversity of SaVs in children hospitalised with gastroenteritis in South Africa (SA). STUDY DESIGN From April 2009 to December 2013, SaVs were characterised from stool specimens from children hospitalised with gastroenteritis in four provinces of SA. RESULTS Fourteen different SaV genotypes were identified from the 221 strains that were characterised. Genogroup (G) IV predominated overall and was detected in 24% (53/221) of specimens. The other identified genotypes included six belonging to GI (GI.1-GI.3, GI.5, GI.6, and GI.7) and seven belonging to GII (GII.1-GII.7). CONCLUSION This study has provided the first comprehensive data on the genetic diversity of SaVs in a clinical setting in SA, contributing to the global knowledge of this virus.
Collapse
Affiliation(s)
- Tanya Y Murray
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007 Pretoria, South Africa.
| | - Sandrama Nadan
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007 Pretoria, South Africa; Centre for Enteric Diseases, National Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131 Johannesburg, South Africa.
| | - Nicola A Page
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131 Johannesburg, South Africa.
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007 Pretoria, South Africa.
| |
Collapse
|
27
|
Munjita SM. Current Status of Norovirus Infections in Children in Sub-Saharan Africa. J Trop Med 2015; 2015:309648. [PMID: 26649055 PMCID: PMC4663330 DOI: 10.1155/2015/309648] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/22/2015] [Indexed: 01/16/2023] Open
Abstract
Noroviruses are a leading cause of acute sporadic gastroenteritis worldwide. In Sub-Saharan Africa, information regarding norovirus infections in children is scarce. A systematic review of studies performed between 1993 and June 2015 was conducted to establish the genotypic distribution and prevalence of norovirus infections in children (≤17) in Sub-Saharan Africa. Analysis of data from 19 studies involving 8,399 samples from children with symptomatic and nonsymptomatic gastroenteritis revealed prevalence of 12.6% (range 4.6% to 32.4%). The prevalence of norovirus infections was higher in symptomatic children (14.2%) than asymptomatic children (9.2%). Genogroup II (GII) was the most prevalent genogroup accounting for 76.4% of all the reported norovirus infections. The rest of the infections were GI (21.7%) and GI/GII (1.9%). The most common genotypes were GII.4 (65.2%), GI.7 (33.3%), and GI.3 (21.3%). These statistics were calculated from studies carried out in 12 out of 48 Sub-Saharan African countries. Therefore, more studies involving several countries are required to determine fully the epidemiology of noroviruses and their contribution to childhood diarrhoea in Sub-Saharan Africa.
Collapse
Affiliation(s)
- Samuel Munalula Munjita
- Department of Biomedical Sciences, School of Medicine, University of Zambia, 15101 Lusaka, Zambia
| |
Collapse
|
28
|
Bischel HN, Özel Duygan BD, Strande L, McArdell CS, Udert KM, Kohn T. Pathogens and pharmaceuticals in source-separated urine in eThekwini, South Africa. WATER RESEARCH 2015; 85:57-65. [PMID: 26302215 DOI: 10.1016/j.watres.2015.08.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/06/2015] [Accepted: 08/11/2015] [Indexed: 05/12/2023]
Abstract
In eThekwini, South Africa, the production of agricultural fertilizers from human urine collected from urine-diverting dry toilets is being evaluated at a municipality scale as a way to help finance a decentralized, dry sanitation system. The present study aimed to assess a range of human and environmental health hazards in source-separated urine, which was presumed to be contaminated with feces, by evaluating the presence of human pathogens, pharmaceuticals, and an antibiotic resistance gene. Composite urine samples from households enrolled in a urine collection trial were obtained from urine storage tanks installed in three regions of eThekwini. Polymerase chain reaction (PCR) assays targeted 9 viral and 10 bacterial human pathogens transmitted by the fecal-oral route. The most frequently detected viral pathogens were JC polyomavirus, rotavirus, and human adenovirus in 100%, 34% and 31% of samples, respectively. Aeromonas spp. and Shigella spp. were frequently detected gram negative bacteria, in 94% and 61% of samples, respectively. The gram positive bacterium, Clostridium perfringens, which is known to survive for extended times in urine, was found in 72% of samples. A screening of 41 trace organic compounds in the urine facilitated selection of 12 priority pharmaceuticals for further evaluation. The antibiotics sulfamethoxazole and trimethoprim, which are frequently prescribed as prophylaxis for HIV-positive patients, were detected in 95% and 85% of samples, reaching maximum concentrations of 6800 μg/L and 1280 μg/L, respectively. The antiretroviral drug emtricitabine was also detected in 40% of urine samples. A sulfonamide antibiotic resistance gene (sul1) was detected in 100% of urine samples. By coupling analysis of pathogens and pharmaceuticals in geographically dispersed samples in eThekwini, this study reveals a range of human and environmental health hazards in urine intended for fertilizer production. Collection of urine offers the benefit of sequestering contaminants from environmental release and allows for targeted treatment of potential health hazards prior to agricultural application. The efficacy of pathogen and pharmaceutical inactivation, transformation or removal during urine nutrient recovery processes is thus briefly reviewed.
Collapse
Affiliation(s)
- Heather N Bischel
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| | - Birge D Özel Duygan
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Linda Strande
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Christa S McArdell
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Kai M Udert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
29
|
Kabue JP, Meader E, Hunter PR, Potgieter N. Human Norovirus prevalence in Africa: a review of studies from 1990 to 2013. Trop Med Int Health 2015; 21:2-17. [PMID: 26436862 DOI: 10.1111/tmi.12617] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVES To assess the contribution of Human Norovirus to diarrhoeal diseases in Africa. METHODS We conducted a systematic review of the PubMed and EMBASE databases for published articles of Human Norovirus in Africa between 1990 and 2013. Data were extracted from selected studies and analysed. RESULTS A total of 208 eligible studies were identified, of which 55 (from 19 countries) met the inclusion criteria. Many cases were of sporadic gastroenteritis (70.9%) in children (82%), 65.4% of which were seen in an outpatient setting. Over half (59.4%) of the affected children were under 5 years of age. The pooled prevalence rate of Human NoV was 11% (95% CI 8-14%), and the meta-analysis indicated significant heterogeneity between the studies. However, the conditional negative binomial regression could not clearly find the factors affecting the Human NoV prevalence rates reported. A close relationship was found between Human Norovirus strains from environmental and clinical samples. CONCLUSION Unreported sporadic gastroenteritis cases of Human Norovirus are common in Africa. Most are community-associated infections. Possible environmental transmission routes have been documented. Combined environmental and clinical studies are required for targeted actions to control transmission of Human Norovirus in Africa. Systematic surveillance of Human Norovirus is needed to measure the burden of Norovirus-induced gastroenteritis in Africa and support any requirements for vaccine development.
Collapse
Affiliation(s)
- Jean Pierre Kabue
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, RSA
| | - 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
| | - Natasha Potgieter
- Department of Microbiology, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, RSA
| |
Collapse
|
30
|
Norovirus diversity in children with gastroenteritis in South Africa from 2009 to 2013: GII.4 variants and recombinant strains predominate. Epidemiol Infect 2015; 144:907-16. [PMID: 26374265 DOI: 10.1017/s0950268815002150] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
From 2009 to 2013 the diversity of noroviruses (NoVs) in children (⩽5 years) hospitalized with gastroenteritis in South Africa was investigated. NoVs were genotyped based on nucleotide sequence analyses of partial RNA-dependent RNA polymerase (RdRp) and capsid genes. Seventeen RdRp genotypes (GI.P2, GI.P3, GI.P6, GI.P7, GI.P not assigned (NA), GI.Pb, GI.Pf, GII.P2, GII.P4, GII.P7, GII.P13, GII.P16, GII.P21, GII.Pc, GII.Pe, GII.Pg, GII.PNA) and 20 capsid genotypes (GI.1, GI.2, GI.3, GI.5, GI.6, GI.7, GI.NA, GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.10, GII.12, GII.13, GII.14, GII.16, GII.17, GII.21) were identified. The combined RdRp/capsid genotype was determined for 275 GII strains. Fifteen confirmed recombinant NoV strains circulated during the study period. NoV GII.P4/GII.4 (47%) and GII.Pe/GII.4 (18%) predominated, followed by GII.PNA/GII.3 (10%) and GII.P21/GII.3 (7%). Other prevalent strains included GII.Pg/GII.12 (6%) and GII.Pg/GII.1 (3%). Two novel recombinants, GII.Pg/GII.2 and GII.Pg/GII.10 were identified. In 2013 the replacement of GII.4 New Orleans 2009 and GII.P21/GII.3, which predominated during the early part of the study, with GII.4 Sydney 2012 and GII.PNA/GII.3 was observed. This study presents the most comprehensive recent data on NoV diversity in Africa.
Collapse
|
31
|
Pringle K, Lopman B, Vega E, Vinje J, Parashar UD, Hall AJ. Noroviruses: epidemiology, immunity and prospects for prevention. Future Microbiol 2015; 10:53-67. [PMID: 25598337 DOI: 10.2217/fmb.14.102] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In recent years, noroviruses have become recognized as an important cause of both sporadic and epidemic acute gastroenteritis (AGE), largely due to the improved availability of broadly reactive real-time RT-PCR (TaqMan-based RT-PCR) assays. While there is substantial diversity among noroviruses, one specific genotype, GII.4, is the most common etiology in sporadic and epidemic AGE. Outbreaks of norovirus AGE most commonly occur in healthcare facilities and restaurants and result in significant morbidity and mortality and substantial healthcare costs. Norovirus vaccine development is progressing, and Phase I and II human trials have shown proof-of-principle that norovirus vaccines can reduce illness and infection.
Collapse
Affiliation(s)
- Kimberly Pringle
- Division of Viral Diseases, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, 1600 Clifton Road, Mailstop A-34, Atlanta, GA, 30333, USA
| | | | | | | | | | | |
Collapse
|
32
|
Osborne CM, Montano AC, Robinson CC, Schultz-Cherry S, Dominguez SR. Viral gastroenteritis in children in Colorado 2006-2009. J Med Virol 2015; 87:931-9. [PMID: 25776578 PMCID: PMC7166904 DOI: 10.1002/jmv.24022] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2014] [Indexed: 02/04/2023]
Abstract
Acute gastroenteritis accounts for a significant burden of medically attended illness in children under the age of five. For this study, four multiplex reverse transcription PCR assays were used to determine the incidence of adenovirus, astrovirus, coronavirus, norovirus GI and GII, rotavirus, and sapovirus in stool samples submitted for viral electron microscopy (EM) to the Children's Hospital Colorado. Of 1105 stool samples available, viral RNA/DNA was detected in 247 (26.2%) of 941 pediatric samples (median age = 2.97 years, 54% male) with 28 (3.0%) positive for more than one virus. Adenovirus, astrovirus, norovirus GI, norovirus GII, rotavirus, and sapovirus were detected in 95 (10.0%), 33 (3.5%), 8 (0.9%), 90 (9.6%), 49 (5.2%), and 2 (0.2%) of the pediatric samples, respectively. No coronaviruses were identified. Sequencing of norovirus positive samples indicated an outbreak of norovirus strain GII.4 in 2006 with evidence of numerous circulating strains. Multiple samples from the same immunocompromised patients demonstrated symptomatic shedding of norovirus for up to 32 weeks and astrovirus for 12 weeks. RT-PCR detected 99 of 111 (89%) adenovirus-positive samples versus 12 (11%) by EM, and 186 of 192 (97%) sapovirus/astrovirus/norovirus-positive samples versus 21 (11%) by EM. Noroviruses and adenoviruses are common causes of gastroenteritis in children. Immunocompromised patients can be infected with multiple viruses and shed viruses in their stools for prolonged periods. This data support the superiority of RT-PCR compared to EM for diagnosis of viral gastroenteritis.
Collapse
|
33
|
Lekana-Douki SE, Kombila-Koumavor C, Nkoghe D, Drosten C, Drexler JF, Leroy EM. Molecular epidemiology of enteric viruses and genotyping of rotavirus A, adenovirus and astrovirus among children under 5 years old in Gabon. Int J Infect Dis 2015; 34:90-5. [PMID: 25796432 DOI: 10.1016/j.ijid.2015.03.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES This study aimed to determine the prevalence of enteric viruses causing gastroenteritis, and the circulating stains, in Gabonese children under five years old who visited health centers between March 2010 and June 2011. METHODS Stool specimens were collected and sent for analysis to CIRMF (Centre International de Recherches Médicales de Franceville). Stools were screened for six enteric viruses (rotavirus, adenovirus, norovirus I and II, sapovirus, human astrovirus) by means of a multiplex real-time reverse transcription polymerase chain reaction, and Rotavirus A, Adenovirus and Astrovirus were genotyped. RESULTS Among the 317 specimens analyzed, 193 (60.9%) were positive for at least one enteric virus. Rotavirus A (RVA) (27.1%) was the most frequently detected virus, followed by human Adenovirus (HAdV) (19.6%), Norovirus II (NoVs-II) (13.9%), Norovirus I (NoVs-I) (9.1%), Sapovirus (SaV) (9.5%) and human Astrovirus (HAstV) (6.3%). One-third of the 193 positive samples contained more than one virus. The most common Rotavirus A genotype was G6P[6]. Various HAdV serotypes were found. HAstV-1 was identified. CONCLUSIONS These findings improve our knowledge of circulating enteric viruses in Gabon. The emergence of unusual G6P[6] strain of rotavirus A, predominant, suggested a particular epidemiological surveillance of circulating rotavirus strains during the introduction of vaccination in Gabon.
Collapse
Affiliation(s)
| | | | - Dieudonné Nkoghe
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; Ministère de la Santé Publique, BP 5978 Libreville, Gabon.
| | | | | | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, BP 769 Franceville, Gabon; UMR (IRD 224 /CNRS 5290 / UM1-UM2), Institut de Recherche pour le Développement, Montpellier, France.
| |
Collapse
|
34
|
Molecular epidemiology of noroviruses detected in Nepalese children with acute diarrhea between 2005 and 2011: Increase and predominance of minor genotype GII.13. INFECTION GENETICS AND EVOLUTION 2015; 30:27-36. [DOI: 10.1016/j.meegid.2014.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/24/2014] [Accepted: 12/02/2014] [Indexed: 12/17/2022]
|
35
|
Tan D, Deng L, Wang M, Li X, Ma Y, Liu W. High prevalence and genetic diversity of noroviruses among children with sporadic acute gastroenteritis in Nanning City, China, 2010-2011. J Med Virol 2014; 87:498-503. [DOI: 10.1002/jmv.24103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Dongmei Tan
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control; Nanning; Guangxi China
| | - Lili Deng
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control; Nanning; Guangxi China
| | - Mingliu Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control; Nanning; Guangxi China
| | - Xiugui Li
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control; Nanning; Guangxi China
| | - Yuyan Ma
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control; Nanning; Guangxi China
| | - Wei Liu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control; Nanning; Guangxi China
| |
Collapse
|
36
|
Kiulia NM, Mans J, Mwenda JM, Taylor MB. Norovirus GII.17 Predominates in Selected Surface Water Sources in Kenya. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:221-31. [PMID: 25059212 DOI: 10.1007/s12560-014-9160-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/07/2014] [Indexed: 05/21/2023]
Abstract
In this study, the prevalence and genotypes of noroviruses (NoVs) in selected water sources from rural, urban and refugee settings in Kenya were investigated. Ten litres each of river, household and borehole water was collected in rural (Mboone River), urban (Nairobi and Mutoine River) and refugee (Dadaab refugee camp) settings. NoVs were recovered from the water samples by a glass wool adsorption-elution technique and/or PEG/NaCl precipitation. Nucleic acid was extracted using the automated MagNA Pure platform. NoVs were detected with singleplex real-time reverse transcription-polymerase chain reaction assays and characterised by nucleotide sequence analysis. NoVs were detected in 63% (25/40) of the selected water samples comprising GII (42.5%), GI (2.5%) and mixed GI/GII (17.5%) positive samples. The prevalence of NoVs in the Mutoine River (urban area) was higher than in the Mboone River (rural area) (P = 0.0013). Noroviruses GI.1, GI.3, GI.9, GII.4, GII.6, GII.12, GII.16 and GII.17 were identified, with GII.17 accounting for 76% (16/21) of the typed strains. The NoV GII.17 predominance differs to other studies in Africa and further surveillance of NoVs in clinical and environmental settings is required to clarify/elucidate this observation. As information regarding NoVs in Kenyan water sources is limited this report provides valuable new data on NoV genotypes circulating in environmental water sources and the surrounding communities in Kenya.
Collapse
Affiliation(s)
- N M Kiulia
- Enteric Viruses Research Group, Institute of Primate Research, P.O Box 24481, Karen, Nairobi, 00502, Kenya.
- Department of Medical Virology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.
| | - J Mans
- Department of Medical Virology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - J M Mwenda
- Enteric Viruses Research Group, Institute of Primate Research, P.O Box 24481, Karen, Nairobi, 00502, Kenya
| | - M B Taylor
- Department of Medical Virology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| |
Collapse
|
37
|
Mans J, Murray TY, Taylor MB. Novel norovirus recombinants detected in South Africa. Virol J 2014; 11:168. [PMID: 25228444 PMCID: PMC4181420 DOI: 10.1186/1743-422x-11-168] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/12/2014] [Indexed: 12/26/2022] Open
Abstract
Background Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and diversity was investigated in South Africa (SA). Results Between 2010 and 2013, eleven types of NoV recombinants were identified in SA. Amplification of the polymerase/capsid region spanning the ORF1/2 junction and phylogenetic analysis confirmed each of the recombinant types. SimPlot and maximum x2 analysis indicated that all recombinants had a breakpoint in the region of the ORF1/2 junction (P < 0.05). The majority (9/11) were intergenotype recombinants, but two intragenotype GII.4 recombinants were characterised. Three combinations represent novel recombinants namely GII.P not assigned (NA)/GII.3, GII.P4 New Orleans 2009/GII.4 NA and GII.P16/GII.17. Several widely reported recombinants were identified and included GII.P21/GII.2, GII.P21/GII.3, GII.Pe/GII.4 Sydney 2012, and GII.Pg/GII.12. Other recombinants that were identified were GII.Pg/GII.1, GII.Pe/GII.4 Osaka 2007, GII.P4 New Orleans 2009/GII.4 Sydney 2012, GII.P7/GII.6. To date these recombinant types all have a reportedly restricted geographic distribution. This is the first report of the GII.P4 New Orleans 2009/GII.4 Sydney 2012 recombinant in Africa. Conclusions Over the past four years, remarkably diverse NoV recombinants have been circulating in SA. Pandemic strains such as the GII.Pe/GII.4 Sydney 2012 recombinant co-circulated with novel and emerging recombinant strains. Combined polymerase- and capsid-based NoV genotyping is essential to determine the true diversity and global prevalence of these viruses.
Collapse
Affiliation(s)
- Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| | | | | |
Collapse
|
38
|
Genetic diversity of norovirus in hospitalised diarrhoeic children and asymptomatic controls in Dar es Salaam, Tanzania. INFECTION GENETICS AND EVOLUTION 2014; 26:340-7. [DOI: 10.1016/j.meegid.2014.06.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 01/26/2023]
|
39
|
Chigor VN, Sibanda T, Okoh AI. Assessment of the risks for human health of adenoviruses, hepatitis A virus, rotaviruses and enteroviruses in the Buffalo River and three source water dams in the Eastern Cape. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:87-98. [PMID: 24676673 DOI: 10.1007/s12560-014-9138-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 03/12/2014] [Indexed: 05/03/2023]
Abstract
Buffalo River is an important water resource in the Eastern Cape Province of South Africa. The potential risks of infection constituted by exposure to human enteric viruses in the Buffalo River and three source water dams along its course were assessed using mean values and static quantitative microbial risk assessment (QMRA). The daily risks of infection determined by the exponential model [for human adenovirus (HAdV) and enterovirus (EnV)] and the beta-Poisson model (for hepatitis A virus (HAV) and rotavirus (RoV)) varied with sites and exposure scenario. The estimated daily risks of infection values at the sites where the respective viruses were detected, ranged from 7.31 × 10(-3) to 1 (for HAdV), 4.23 × 10(-2) to 6.54 × 10(-1) (RoV), 2.32 × 10(-4) to 1.73 × 10(-1) (HAV) and 1.32 × 10(-4) to 5.70 × 10(-2) (EnV). The yearly risks of infection in individuals exposed to the river/dam water via drinking, recreational, domestic or irrigational activities were unacceptably high, exceeding the acceptable risk of 0.01% (10(-4) infection/person/year), and the guideline value used as by several nations for drinking water. The risks of illness and death from infection ranged from 6.58 × 10(-5) to 5.0 × 10(-1) and 6.58 × 10(-9) to 5.0 × 10(-5), respectively. The threats here are heightened by the high mortality rates for HAV, and its endemicity in South Africa. Therefore, we conclude that the Buffalo River and its source water dams are a public health hazard. The QMRA presented here is the first of its kinds in the Eastern Cape Province and provides the building block for a quantitatively oriented local guideline for water quality management in the Province.
Collapse
Affiliation(s)
- Vincent N Chigor
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, 5700, South Africa,
| | | | | |
Collapse
|
40
|
Trainor E, Lopman B, Iturriza-Gomara M, Dove W, Ngwira B, Nakagomi O, Nakagomi T, Parashar U, Cunliffe N. Detection and molecular characterisation of noroviruses in hospitalised children in Malawi, 1997-2007. J Med Virol 2014; 85:1299-306. [PMID: 23918547 DOI: 10.1002/jmv.23589] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2013] [Indexed: 11/10/2022]
Abstract
Despite the increasing recognition of noroviruses as major pathogens associated with community-acquired diarrhoea in children, there are few studies from Africa. Long-term surveillance studies of rotavirus gastroenteritis in Malawian children have provided an opportunity to undertake a study of the importance and epidemiological features of norovirus infection in this population. Faecal specimens were collected from children <5 years of age admitted to hospital with acute diarrhoea, as well as from a comparison group of diarrhoea-free children, in Blantyre, Malawi between 1997 and 2007. Norovirus was detected using real-time PCR and strains genotyped by nucleotide sequence analysis. Norovirus was detected in 220/1,941 (11.3%) faecal specimens, comprising genogroup GI (1.8%), GII (9.4%) and mixed GI/GII (0.1%). The median age of children with norovirus was 6 months (range, 0-48 months). Norovirus was detected throughout the year, with peaks at the end of the rainy season (March) and towards the end of the dry season (August-November). Norovirus GII.4 was the most commonly detected genotype accounting for 70% of strains characterised, followed by GII.2 (6%), GII.6 (4%) and GII.12 (4%). Sub typing of GII.4 noroviruses demonstrated local circulation of strains prior to their subsequent detection in association with global epidemics of gastroenteritis. The prevalence of norovirus in children without diarrhoea was similar to the level in cases. This largest study to date of norovirus infection in African children indicates the potential role of paediatric surveillance in predicting the emergence of norovirus strains with global epidemic potential.
Collapse
Affiliation(s)
- Eamonn Trainor
- Department of Clinical Infection, Microbiology & Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Mans J, van Zyl WB, Taylor MB, Page NA, Sobsey MD, Barnard TG, Potgieter N. Applicability of Bio-wipes for the collection of human faecal specimens for detection and characterisation of enteric viruses. Trop Med Int Health 2013; 19:293-300. [DOI: 10.1111/tmi.12251] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- J. Mans
- Department of Medical Virology; University of Pretoria; Pretoria South Africa
| | - W. B. van Zyl
- Department of Medical Virology; University of Pretoria; Pretoria South Africa
| | - M. B. Taylor
- Department of Medical Virology; University of Pretoria; Pretoria South Africa
- National Health Laboratory Service; Tswhane Academic Division; Pretoria South Africa
| | - N. A. Page
- Virology Division, Center for Enteric Diseases; National Institute for Communicable Diseases; Johannesburg South Africa
| | - M. D. Sobsey
- Department of Environmental Sciences and Engineering; University of North Carolina; Chapel Hill NC USA
| | - T. G. Barnard
- Water and Health Research Centre; University of Johannesburg; Doornfontein South Africa
| | - N. Potgieter
- Department of Microbiology; University of Venda; Thohoyandou South Africa
| |
Collapse
|
42
|
Abstract
BACKGROUND The study aimed to investigate the molecular epidemiology of severe viral gastroenteritis (AGE) in children in Taiwan after the implementation of the rotavirus vaccine in the private sector. METHODS Fecal samples from hospitalized children with severe AGE from April 2004 to March 2011 were examined by reverse transcription-polymerase chain reaction or polymerase chain reaction to identify enteric viral pathogens. The study period was divided to prevaccine (before September 2006) and postvaccine (after October 2006) periods. The prevalence of enteric viruses between the 2 periods was analyzed. The disease burdens of rotavirus- and norovirus-associated diseases were assessed according to vaccine implementation status and were adjusted for age. RESULTS A total of 755 stool samples were collected from hospitalized patients with AGE; enteric viruses were identified in 586 patients (77.6%), including 44 with concomitant bacterial infection. Viral enteric infection by rotavirus, norovirus, astrovirus, sapovirus, enteric adenovirus, multiple viruses and bacterial coinfections were found in 216 (28.6%), 128 (17.0%), 24 (3.2%), 6 (0.8%), 69 (9.1 %), 99 (13.1%) and 44 (5.8%) patients, respectively. A significant increase of norovirus infection was found in the postvaccine period (P < 0.001); on the other hand, rotavirus infection in infants has been reduced substainally (P = 0.056) and the annual peak of rotavirus infection has gradually become less prominent, with a significant decline of coinfection of rotavirus with other pathogens. CONCLUSIONS Suboptimal use of rotavirus vaccines in the private sector caused a slow but modest impact on severe rotavirus AGE, whereas norovirus infection became more common.
Collapse
|
43
|
Huynen P, Mauroy A, Martin C, Savadogo LGB, Boreux R, Thiry E, Melin P, De Mol P. Molecular epidemiology of norovirus infections in symptomatic and asymptomatic children from Bobo Dioulasso, Burkina Faso. J Clin Virol 2013; 58:515-21. [DOI: 10.1016/j.jcv.2013.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 08/07/2013] [Accepted: 08/16/2013] [Indexed: 10/26/2022]
|
44
|
Mans J, Murray TY, Kiulia NM, Mwenda JM, Musoke RN, Taylor MB. Human caliciviruses detected in HIV-seropositive children in Kenya. J Med Virol 2013; 86:75-81. [PMID: 24123054 DOI: 10.1002/jmv.23784] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 12/15/2022]
Abstract
The human caliciviruses (HuCVs) are important causes of gastroenteritis worldwide. Norovirus (NoV) and sapovirus (SaV) have been detected in HIV-seropositive children but the genetic diversity of HuCVs circulating in these individuals is largely unknown. In this study the prevalence and genotype diversity of HuCVs circulating in Kenyan HIV-positive children, with or without diarrhea, from the year 1999 to 2000 was investigated. The overall prevalence of HuCVs was 19% with NoV predominating at 17% (18/105) and SaV present in 5.7% (6/105) of specimens. Human CVs were detected in both symptomatic (24%) and asymptomatic (16%) children. Co-infections with other enteric viruses were detected in 21.6% of children with diarrhea but only in 4.4% of children without diarrhea. Remarkable genetic diversity was observed with 12 genotypes (7 NoV, 5 SaV) being identified in 20 HuCV-infected children. NoV genogroup II (GII) strains predominated with GII.2 and GII.4 each representing 27% of the NoV-positive strains. The GII.4 strain was most closely related to the nonepidemic GII.4 Kaiso 2003 variant. Other NoV genotypes detected were GI.3, GII.6, GII.12, GII.14, and GII.17. Five different SaV genotypes (GI.2, GI.6, GII.1, GII.2, and GII.4) were characterized from six specimens. Diarrheal symptoms were not associated with any specific HuCV genotype. Overall the HuCV genotype distribution detected in this study reflects those in other studies worldwide. The strains detected are closely related to genotypes that have circulated on several continents since the year 2000.
Collapse
Affiliation(s)
- Janet Mans
- Department of Medical Virology, University of Pretoria, Arcadia, Pretoria, South Africa
| | | | | | | | | | | |
Collapse
|
45
|
Marques Mendanha de Oliveira D, Souza M, Souza Fiaccadori F, César Pereira Santos H, das Dôres de Paula Cardoso D. Monitoring of Calicivirus among day-care children: evidence of asymptomatic viral excretion and first report of GI.7 Norovirus and GI.3 Sapovirus in Brazil. J Med Virol 2013; 86:1569-75. [PMID: 24123103 DOI: 10.1002/jmv.23791] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 12/16/2022]
Abstract
Caliciviruses (Norovirus and Sapovirus) are important causes of acute gastroenteritis, with Norovirus (NoV) considered the leading cause of epidemic non-bacterial acute gastroenteritis; however, molecular and epidemiological data of the circulating Calicivirus (CV) strains among day-care children are still considered scarce. The role of asymptomatic CV excretion on viral transmission also remains poorly understood. The aim of the present study was to monitor the occurrence of NoV and Sapovirus (SaV) in a day-care center and to describe the molecular epidemiology of the circulating strains. Genomic sequencing and phylogenetic analysis of the capsid region were carried out in CV positive samples obtained from children younger than 5 years, with or without diarrhea, between October 2009 and October 2011. A total of 539 fecal samples were screened for CV. Forty-three (8%) were positive for NoV and 25 (4.6%) for SaV. Surprisingly, positivity rates for CV were significant in asymptomatic children, and virus circulation was detected in every month of the study. Great genomic diversity of CV was observed, and the circulating NoV strains were: GII.6, GII.2, GII.1, GI.7, GII.4, and GI.1. The SaV genotypes GI.1 and GI.3 were also detected. Five CV outbreaks caused by distinct viral strains were documented. This study provides an insight on the genetic diversity of CV in a day-care in Central West Brazil, highlighting the probable role of asymptomatic viral excretion and the significance of semi-closed settings in the dissemination of these agents.
Collapse
|
46
|
Tsai CN, Lin CY, Lin CW, Shih KC, Chiu CH, Chen SY. Clinical relevance and genotypes of circulating noroviruses in northern Taiwan, 2006-2011. J Med Virol 2013; 86:335-46. [DOI: 10.1002/jmv.23728] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Chi-Neu Tsai
- Graduate Institute of Clinical Medical Sciences; Chang Gung University; Kweishan Taoyuan Taiwan
| | - Chun-Yuan Lin
- Department of Computer Science and Information Engineering; Chang Gung University; Kweishan Taoyuan Taiwan
| | - Che-Wei Lin
- Graduate Institute of Clinical Medical Sciences; Chang Gung University; Kweishan Taoyuan Taiwan
| | - Kuei-Chung Shih
- Department of Computer Science; National Tsing Hua University; Hsinchu Taiwan
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases; Chang Gung Children's Hospital, Kweishan; Taoyuan Taiwan
- Molecular Infectious Disease Research Center; Chang Gung Memorial Hospital, Kweishan; Taoyuan Taiwan
| | - Shih-Yen Chen
- Division of Pediatric Gastroenterology; Chang Gung Children's Hospital; Kweishan Taoyuan Taiwan
| |
Collapse
|
47
|
Nordgren J, Nitiema LW, Ouermi D, Simpore J, Svensson L. Host genetic factors affect susceptibility to norovirus infections in Burkina Faso. PLoS One 2013; 8:e69557. [PMID: 23894502 PMCID: PMC3716642 DOI: 10.1371/journal.pone.0069557] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/10/2013] [Indexed: 12/03/2022] Open
Abstract
Norovirus (NoV) constitutes the second most common viral pathogen causing pediatric diarrhea after rotavirus. In Africa, diarrhea is a major health problem in children, and yet few studies have been performed regarding NoV. The association of histo-blood group antigens (HBGA) and susceptibility to NoV infection is well established in Caucasian populations with non-secretors being resistant to many common NoV strains. No study regarding HBGA and NoV susceptibility has yet been performed in Africa. We collected 309 stool and 208 saliva samples from diarrheal children in Ouagadougou, Burkina Faso; May 2009 to March 2010. NoV was detected using real-time PCR, and genotyped by sequencing. Saliva samples were ABO, Lewis and secretor phenotyped using in house ELISA assays. NoV was detected in 12% (n = 37) of the samples. The genotype diversity was unusually large; overall the 37 positive samples belonged to 14 genotypes. Only children <2 years of age were NoV positive and the GII.4 NoVs were more frequent in the late dry season (Jan-May). NoV infections were observed less in children with the secretor-negative phenotype or blood group A (OR 0.18; p = 0.012 and OR 0.31; p = 0.054; respectively), with two non-secretors infected with genotypes GII.7 and GII.4 respectively. Lewis-negative (Lea−b−) children, representing 32% of the study population, were susceptible to GII, but were not infected with any NoV GI. GII.4 strains preferentially infected children with blood group B whereas secretor-positive children with blood group O were infected with the largest variety of genotypes. This is the first study identifying host genetic factors associated with susceptibility to NoV in an African population, and suggests that while the non-secretor phenotype provides protection; the Lewis b antigen is not necessary for GII infection.
Collapse
Affiliation(s)
- Johan Nordgren
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | | | | | | | | |
Collapse
|
48
|
Abstract
Norovirus (NoV) is the leading cause of viral gastroenteritis globally. Since 1996, NoV variants of a single genetic lineage, GII.4, have been associated with at least six pandemics of acute gastroenteritis and caused between 62 and 80% of all NoV outbreaks. The emergence of these novel GII.4 variants has been attributed to rapid evolution and antigenic variation in response to herd immunity; however, the contribution of recombination as a mechanism facilitating emergence is increasingly evident. In this study, we sought to examine the role that intragenotype recombination has played in the emergence of GII.4 variants. Using a genome-wide approach including 25 complete genome sequences generated as part of this study, 11 breakpoints were identified within the NoV GII.4 lineage. The breakpoints were located at three recombination hot spots: near the open reading frame 1/2 (ORF1/2) and ORF2/3 overlaps, as well as within ORF2, which encodes the viral capsid, at the junction of the shell and protruding domains. Importantly, we show that recombination contributed to the emergence of the recent pandemic GII.4 variant, New Orleans 2009, and a newly identified GII.4 variant, termed Sydney 2012. Reconstructing the evolutionary history of the GII.4 lineage reveals the widespread impact of both inter- and intragenotype recombination on the emergence of many GII.4 variants. Lastly, this study highlights the many challenges in the identification of true recombination events and proposes that guidelines be applied for identifying NoV recombinants.
Collapse
|
49
|
Murray TY, Mans J, Taylor MB. Human calicivirus diversity in wastewater in South Africa. J Appl Microbiol 2013; 114:1843-53. [PMID: 23414393 DOI: 10.1111/jam.12167] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/11/2013] [Accepted: 02/11/2013] [Indexed: 01/19/2023]
Abstract
AIM To investigate the diversity of human caliciviruses (HuCVs) in wastewater from small- to medium-sized communities in five provinces of South Africa (SA). METHODS AND RESULTS Wastewater samples (51) were screened for norovirus (NoV) GI, GII, GIV and sapovirus (SaV) using real-time reverse transcription (RT)-PCR. Partial capsid nucleotide sequences were analysed for genotyping. At least one HuCV was detected in 42 samples (82%) with NoV GI being detected in 15 (29%), NoV GII in 32 (63%) and SaV in 37 (73%) samples. NoV GIV was not detected. Five NoV GI genotypes (GI.1, GI.3, GI.4, GI.8 and GI.unassigned), eight NoV GII genotypes (GII.2, GII.3, GII.4, GII.6, GII.7, GII.12, GII.13 and GII.17) and six SaV genotypes (GI.2, GI.3, GI.6, GI.7, GII.1 and GII.2) were characterized. CONCLUSIONS Many NoV and SaV genotypes were detected in wastewater, demonstrating a high genetic diversity of HuCVs in the surrounding communities. Caliciviruses were characterized from several provinces in SA, indicating widespread occurrence in the country. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides valuable new data on CVs circulating in SA, including the first data on SaV strains from wastewater in Africa. Environmental surveillance is especially important in countries like SA where outbreak reporting systems or routine HuCV surveillance is lacking.
Collapse
Affiliation(s)
- T Y Murray
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Arcadia, Pretoria, South Africa.
| | | | | |
Collapse
|
50
|
Hoa Tran TN, Trainor E, Nakagomi T, Cunliffe NA, Nakagomi O. Molecular epidemiology of noroviruses associated with acute sporadic gastroenteritis in children: global distribution of genogroups, genotypes and GII.4 variants. J Clin Virol 2012; 56:185-93. [PMID: 23218993 DOI: 10.1016/j.jcv.2012.11.011] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 11/07/2012] [Accepted: 11/13/2012] [Indexed: 12/22/2022]
Abstract
Noroviruses are a leading cause of epidemic and sporadic acute gastroenteritis worldwide. The development of sensitive molecular diagnostic techniques has revolutionized our understanding of norovirus epidemiology over the past two decades, but norovirus strain types associated with sporadic gastroenteritis remain poorly described. Therefore, we conducted a systematic review of studies performed after 2000 to clarify the genotypic distribution of noroviruses in children (≤18 years of age) with sporadic acute gastroenteritis. Genogroup GII norovirus was the most prevalent, accounting for 96% of all sporadic infections. GII.4 was the most prevalent genotype, accounting for 70% of the capsid genotypes and 60% of the polymerase genotypes, followed by the capsid genotype GII.3 (16%) and the polymerase genotype GII.b (14%). The most common ORF1/ORF2 inter-genotype recombinants were GII.b, GII.12, and GII.4 polymerase genotypes combined with the capsid genotype GII.3, accounting for 19% of all genotyped strains. The distribution of GII.4 variants over the last decade was dominated by successive circulation of GII.4/2002, GII.4/2004, GII.4/2006b, and GII.4/2008 with GII.4/2006b continuing to date. Genotypes GII.4 and GII.3 have predominated in children during the past decade; this is most notable in the global emergence of GII.4 variant noroviruses. As the burden of rotavirus disease decreases following the introduction of childhood immunization programs, the relative importance of norovirus in the etiology of acute childhood gastroenteritis will likely increase. In order for a successful norovirus vaccine to be developed, it should provide immunity against strains with capsid genotypes GII.4 and GII.3.
Collapse
Affiliation(s)
- T N Hoa Tran
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, The Global Center of Excellence, Nagasaki University, Nagasaki, Japan
| | | | | | | | | |
Collapse
|