Clinical characteristics and genetic diversity of noroviruses in adults with acute gastroenteritis in Beijing, China in 2008-2009

Identification of a recombinant GII.13[P21] norovirus strain: molecular dynamic simulations indicate that gene mutations shifted its spectrum of binding to host receptor glycans

Human norovirus is a pervasive pathogen that causes global outbreaks of viral gastroenteritis. Previous studies have suggested that histo-blood group antigens (HBGAs) can interact with human norovirus, facilitating its entry of host cells and significantly affecting its evolution. In this study, the complete genome sequence of recombinant GII.13[P21] norovirus from fecal samples was analyzed. Molecular dynamics simulations of GII.13 norovirus P proteins from 1978 to 2019 showed changes in their capacity to bind to HBGAs. Initially, GII.13 proteins bound A or B/H-type HBGAs, but subsequent mutations resulted in a loss of this binding capacity, favoring binding to the HBGA type I precursor (Lewis c) over A or B/H and Lewis antigens.

Quantitative RT-PCR detection of human noroviruses and hepatitis A virus in fresh produce and surface water used for irrigation in the Mansoura and Giza regions, Egypt

Surface water used as an irrigation source can be a significant source of viral contamination of fresh produce. Enteric viruses such as hepatitis A virus (HAV) and human norovirus genogroup I (HNoV GI) and genogroup II (HNoV GII) can be transmitted to human via fresh produce when irrigated with contaminated water or when prepared by infected food handlers. In the current study, we investigated the presence of HAV, HNoV GI and GII in fresh produce and surface water used in cultivation of this produce using real-time PCR. Samples were collected from six different points in the Mansoura and Giza regions, Egypt. Our analysis showed that at least one virus was found in 41.6% (30/72) of surface water samples and 27% (13/48) of fresh produce samples. HAV (23/72) with a mean viral concentration = 4 × 10⁶ genome copies/litre (GC/L) was the most frequently identified virus in surface water samples, followed by human norovirus genogroup II (HNoV GII) (15/72, with a mean concentration = 1.2 × 10⁶ GC/L, and human noroviruses genogroup I (HNoV GI) (12/72, with a mean concentration = 1.4 × 10⁴ GC/L). Additionally, HAV (10/48) with a mean concentration = 5.2 × 10⁵ genome copies/gram (GC/g) was also the most frequently detected virus in the fresh produce samples, followed by HNoV GII (8/48, with a mean concentration = 1.7 × 10⁴ GC/g); meanwhile, HNoV GI (6/48) was less detected virus with a mean concentration = 3 × 10³ GC/g. This work suggests a wide prevalence of human enteric viruses in surface waters and fresh produce, which is of concern when the fresh produce is eaten raw. Thus, additional monitoring for viral pathogens in irrigation water and food is needed to increase the awareness of this issue to rise the control measures to reduce illness from contaminated food.

Environmental and Adaptive Changes Necessitate a Paradigm Shift for Indicators of Fecal Contamination

Changes in the occurrence, distribution, and seasonal variation of waterborne pathogens due to global climate change may increase the risk of human exposure to these microorganisms, thus heightening the need for more reliable surveillance systems. Routine monitoring of drinking water supplies and recreational waters is performed using fecal indicator microorganisms, such as Escherichia coli , Enterococcus spp., and coliphages. However, the presence and numbers of these indicators, especially E. coli and Enterococcus spp., do not correlate well with those of other pathogens, especially enteric viruses, which are a major cause of waterborne outbreaks associated with contaminated water and food, and recreational use of lakes, ponds, rivers, and estuarine waters. For that reason, there is a growing need for a surveillance system that can detect and quantify viral pathogens directly in water sources to reduce transmission of pathogens associated with fecal transmission. In this review, we present an updated overview of relevant waterborne enteric viruses that we believe should be more commonly screened to better evaluate water quality and to determine the safety of water use and reuse and of epidemiological data on viral outbreaks. We also discuss current methodologies that are available to detect and quantify these viruses in water resources. Finally, we highlight challenges associated with virus monitoring. The information presented in this review is intended to aid in the assessment of human health risks due to contact with water sources, especially since current environmental and adaptive changes may be creating the need for a paradigm shift for indicators of fecal contamination.

Quantitative PCR Detection of Enteric Viruses in Wastewater and Environmental Water Sources by the Lisbon Municipality: A Case Study

Current regulations and legislation require critical revision to determine safety for alternative water sources and water reuse as part of the solution to global water crisis. In order to fulfill those demands, Lisbon municipality decided to start water reuse as part of a sustainable hydric resources management, and there was a need to confirm safety and safeguard for public health for its use in this context. For this purpose, a study was designed that included a total of 88 samples collected from drinking, superficial, underground water, and wastewater at three different treatment stages. Quantitative Polimerase Chain Reaction (PCR) detection (qPCR) of enteric viruses Norovirus (NoV) genogroups I (GI) and II (GII) and Hepatitis A (HepA) was performed, and also FIB (E. coli, enterococci and fecal coliforms) concentrations were assessed. HepA virus was only detected in one untreated influent sample, whereas NoV GI/ NoV GI were detected in untreated wastewater (100/100%), secondary treated effluent (47/73%), and tertiary treated effluent (33/20%). Our study proposes that NoV GI and GII should be further studied to provide the support that they may be suitable indicators for water quality monitoring targeting wastewater treatment efficiency, regardless of the level of treatment.

Detection of Sapoviruses in two biological lines of Tunisian hospital wastewater treatment

The efficiency of rotating biodisks and natural oxidizing lagoon procedures is investigated at a Tunisian semi-industrial pilot plant, El Menzeh I, where the wastewater is mainly provided by three different neighbouring hospital clinics. Throughout 2011, 102 wastewater samples were collected from the two mentioned wastewater treatment procedures. Results showed that the Sapovirus (SaV) frequency was approximately 29.4% using the real-time reverse transcription polymerase chain reaction (RT-PCR) technique, and about 16.6% using the conventional RT-PCR. Also, the SaV genogroups and genotypes were identified and genotyping revealed that all of the four Tunisian SaV strains obtained belonged to the two genogroups GIV.1 and GGI.3. In addition, two new genotypes, D and C, were detected. A moderate decrease in the SaV frequencies was observed at the exit of the two treatment processes and the SaV removal rate was around 90% in the natural oxidizing lagoons and 94% in the rotating biodisks procedure showing the temperate sensitivity of these viruses to the implemented biological wastewater. Therefore, an urgent disinfection process should be implemented downstream of the two biological treatment procedures for safe release of treated effluent in the different natural environments. Abbreviations: NoV: Noroviruses; SaV: Sapoviruses; EC: Electrical Conductivity; COD: Chemical Oxygen Demand; BOD5: Biological Oxygen Demand; SS: Suspended Solids; NH4-N: Ammonium Nitrogen; P-PO4: Ortho-Phosphate; AlCl3: aluminum chloride.

Prevalence of noroviruses in children hospitalized for acute gastroenteritis in Hohhot, China, 2012-2017

BACKGROUND

Noroviruses (NVs) are an important cause of acute gastroenteritis (AGE) worldwide. There are limited data on the prevalence and molecular characterization of NVs in children in Hohhot, China.

METHODS

Between January 2012 and December 2017, 1863 stool samples were collected at Maternal and Child Health Hospital in Hohhot. All samples were screened for NVs by real-time reverse transcription polymerase chain reaction (real-time RT-PCR).

RESULTS

NVs were detected in 24.15% of these inpatient cases, ranging from 12.78 to 32.92% in different years. NV was detected throughout the year, with a peak in winter. Based on sequence analysis of the partial VP1 gene, the 306 identified NV strains were divided into six genotypes: GII.3 (71.24%), GII.4 (23.53%), and GII.2, GII.5, GII.6, and GII.13 (total 5.23%). Based on further sequence analysis of the RNA-dependent RNA polymerase (RdRp), GII.P12/GII.3, GII.Pe/GII.4, and GII.P4/GII.4 were identified as predominant genotypes, accounting for 92.6% of genotyped strains. The median age of the children with NV infection was 8.0 (range 0-59) months. However, children infected with GII.3 were younger (median 7.0 months) than GII.4-positive patients (median 10.0 months).

CONCLUSION

NV contributed greatly to AGE among hospitalized children in Hohhot in China. Continuous surveillance is important for understanding the local prevalence and characterization of NV.

Household transmission of acute gastroenteritis during the winter season in Japan

Objectives

Acute gastroenteritis, including illness caused by norovirus, is sometimes transmissible among susceptible persons who experience close contact, including those within a household, and it disturbs social activities of patients and their family. However, epidemiological assessment of the transmissibility and its heterogeneity has not been conducted. The present study aimed to quantify the frequency of household transmission that was likely caused by norovirus, and characterize its determinants.

Methods

A household survey was conducted, analyzing the history of suspected norovirus infection from January to March, 2017. Noro-like illness was clinically defined as a patient with either: (i) diarrhea or vomiting multiple times a day; or (ii) diarrhea or vomiting persisting for 2 or more days.

Results

Among 380 households, 132 households (34.7%) were eligible for epidemiological analysis, with an estimated secondary attack risk of 13.8% (38/276). Age-specific secondary attack risk was highest among index case patients aged 0 to 14 years (25.8%). The prevalence of vomiting in this age group was higher than in other age groups, with an odds ratio of household transmission estimated at 4.3.

Conclusions

Age-dependent heterogeneity was successfully identified, offering critical insights into future considerations for norovirus control at various social settings.

Norovirus Infection in Older Adults: Epidemiology, Risk Factors, and Opportunities for Prevention and Control

Norovirus is the leading cause of acute gastroenteritis. In older adults, it is responsible for an estimated 3.7 million illnesses; 320,000 outpatient visits; 69,000 emergency department visits; 39,000 hospitalizations; and 960 deaths annually in the United States. Older adults are particularly at risk for severe outcomes, including prolonged symptoms and death. Long-term care facilities and hospitals are the most common settings for norovirus outbreaks in developed countries. Diagnostic platforms are expanding. Several norovirus vaccines in clinical trials have the potential to reap benefits. This review summarizes current knowledge on norovirus infection in older adults.

Cloning, sequencing and characterization of the genome of a recombinant norovirus of the rare genotype GII.P7/GII.6 in China

The genome sequence of a rare recombinant norovirus (NoV) genotype obtained from clinical samples in China was determined using one-step reverse transcription PCR. It was identified as the GII.P7/GII.6 genotype using both phylogenetic and SimPlot analyses. A high degree of variability was observed in the P2 subdomain, especially in the B-loop structure. The recombination breakpoints of all available GII.P7/GII.6 strains were mapped to two different positions within the RdRp region, both of which were at least 40 nt upstream of the overlap of ORF1 and 2. The GII.P7/GII.6 genotype appears to have been circulating in Asia for at least 10 years.

Case-control study of diarrheal disease etiology in individuals over 5 years in southwest China

Background

Acute diarrhea is one of the major public health problems worldwide. Most of studies on acute diarrhea have been made on infants aged below 5 years and few efforts have been made to identify the etiological agents of acute diarrhea in people over five, especially in China.

Methods

271 diarrhea cases and 149 healthy controls over 5 years were recruited from four participating hospitals between June 2014 and July 2015. Each stool specimen was collected to detect a series of enteric pathogens, involving five viruses (Rotavirus group A, RVA; Norovirus, NoV; Sapovirus, SaV; Astrovirus, As; and Adenovirus, Ad), seven bacteria (diarrheagenic Escherichia coli, DEC; non-typhoidal Salmonella, NTS; Shigella spp.; Vibrio cholera; Vibrio parahaemolyticus; Aeromonas spp.; and Plesiomonas spp.) and three protozoa (Cryptosporidium spp., Giardia lamblia, G. lamblia, and Blastocystis hominis, B. hominis). Standard microbiological and molecular methods were applied to detect these pathogens. Data was analyzed using Chi square, Fisher-exact tests and logistic regressions.

Results

The prevalence of at least one enteric pathogen was detected in 29.2% (79/271) acute diarrhea cases and in 12.1% (18/149) in healthy controls (p < 0.0001). Enteric viral infections (14.4%) were the most common in patients suffering from acute diarrhea, followed by bacteria (13.7%) and intestinal protozoa (4.8%). DEC (12.5%) was the most common causative agent in diarrhea cases, followed by NoV GII (10.0%), RVA (7.4%) and B. hominis (4.8%). The prevalence of co-infection was statistically higher (p = 0.0059) in the case group (7.7%) than in the healthy control (1.3%). RVA–NoV GII (3.0%) was the most common co-infection in symptomatic cases.

Conclusions

DEC was the most predominant pathogen in diarrhea cases, but it was largely overlooked because the lack of laboratory capacities. Because of the high prevalence of co-infections, it is recommended the urgent development of alternative laboratory methods to assess polymicrobial infections. Such methodological improvements will result in a better prevention and treatment strategies to control diarrhea illness in China.

Electronic supplementary material

The online version of this article (doi:10.1186/s13099-016-0141-1) contains supplementary material, which is available to authorized users.

Emergence of human caliciviruses among diarrhea cases in southwest China

BACKGROUND

Acute diarrhea is one of the most serious problems in global public health that causes considerable morbidity and mortality worldwide. Human caliciviruses (HuCV) including norovirus (NoV, genogroup GI and GII) and sapovirus (SaV), is a leading cause of acute sporadic diarrhea in individuals across all age groups. However, few studies had been conducted clarifying the characteristics of HuCV in diarrhea cases across all age groups in China. Our study was aimed at assessing the HuCV-related diarrhea burden and NoV genotypes distribution in southwest China.

METHODS

The study was conducted in four hospitals in Kunming city, Yunnan province, from June 2014 to July 2015. Stool specimens were collected from 1,121 diarrhea cases and 319 healthy controls in outpatient departments. Reverse transcription polymerase chain reaction (RT-PCR) was used to detect NoV (GI, GII) and SaV. Sequencing was applied to confirm the three viral infections and phylogenetic analysis was performed to determine their genotypes. A structured questionnaire was used to record the demographic information and clinical symptoms of subjects.

RESULTS

HuCV was detected at an 11.0 % infection rate in 1,121 diarrhea cases and at 3.4 % rate in 319 non-diarrhea subjects (p < 0.0001, OR = 3.5, 95 % CI 1.8-6.5). The prevalence of the NoV genogroup GII and genotype GII.4 in diarrhea cases was significantly higher than that found in healthy controls (p < 0.0001, p = 0.018, respectively). NoV GII (n = 118, 10.5 %) was the most common HuCV subtype in diarrhea cases, followed by SaV (n = 3, 0.3 %) and NoV GI (n = 2, 0.2 %). Of 118 NoV GII strains isolated from diarrhea patients. GII.4 (n = 55, 46.6 %) was the predominant strain, followed by GII.3 (n = 28, 23.7 %), GII.12 (n = 25, 21.2 %), GII.17 (n = 8, 6.8 %), and GII.5 (n = 2, 1.7 %). Of the 55 GII.4 strains, the GII.4 Sydney 2012 variant had absolutely predominant prevalence (n = 52, 94.5 %), followed by the NoV GII.4-2006b variant (n = 3, 5.5 %). The GII.4 Orleans 2009 variant was not found in diarrhea cases of the study.

CONCLUSIONS

NoV GII was the major genogroup and GII.4 was the most predominant strain detected in diarrhea patients. The GII.17 is an emergent variant in sporadic diarrhea and might become the predominant strain in diarrhea cases in the near future. Rapid, accurate detection kits need to be developed to help us find and treat NoV-associated diarrhea in clinical settings in a timely manner.

A decade of norovirus disease risk among older adults in upper-middle and high income countries: a systematic review

BACKGROUND

Noroviruses (NoVs) are the most common cause of acute gastroenteritis (AGE) causing both sporadic and outbreak-associated illness. Norovirus (NoV) infections occur across all ages but certain sub-groups are considered at increased risk due to heightened transmission and/or symptom severity. Older adults are potentially at high risk of NoV-associated illness due to frequent outbreaks in long-term care facilities (LTCFs) and severe health outcomes following infection. Elucidation of NoV risk among older adults will support prevention, treatment and control efforts.

METHODS

We conducted a systematic literature review to summarize the published risk estimates of NoV-associated illness, hospitalization and death among individuals aged 65 years and older. A structured search using defined NoV and gastroenteritis (GE) terms was performed in the PubMed and EMBASE databases of human studies published between January 1, 2003 and May 16, 2013.

RESULTS

We identified 39 studies from high income (HI) and upper-middle income (UMI) countries. Thirty-six percent of publications provided risk estimates based on laboratory-confirmed or epidemiologically-linked population-based surveillance data using molecular diagnostic methods. Over the study period, estimated annual NoV rates and extrapolated number of cases among older adults in HI and UMI countries were: 29-120/10,000 or 1.2-4.8 million NoV-associated illnesses; 18-54/10,000 or 723,000-2.2 million NoV-associated outpatient visits; 1-19/10,000 or 40,00-763,000 NoV-associated inpatient visits; 0.04-0.32/10,000 or 2000-13,000 NoV-associated deaths. NoV was responsible for approximately 10-20 % of GE hospitalizations and 10-15 % of all-cause GE deaths among older adults. Older adults experienced a heightened risk of nosocomial infections. Those in LTCFs experience frequent NoV outbreaks and the range in attack rates was 3-45 %, case hospitalization rates 0.5-6 % and case fatality rates 0.3-1.6 %.

CONCLUSIONS

Older adults are at increased risk of severe NoV-associated health outcomes. NoV-associated hospitalization rates were higher, more severe, resulted in longer stays and incurred greater costs than for younger patients. NoV-associated mortality rates were approximately 200 % higher among individuals 65 years and older compared to <5 years. The burden of NoV among older adults is expected to rise along with societal aging and increased need for institutionalized care. NoV prevention in older adults, including potential vaccination, may significantly impact risk of severe illness.

Clinical characteristics and molecular epidemiology of noroviruses in outpatient children with acute gastroenteritis in Huzhou of China

BACKGROUND

Noroviruses (NoVs) are considered major causative pathogens associated with the morbidity and mortality of young children with acute gastroenteritis. However, few studies have examined NoVs causing acute diarrhea among outpatient children worldwide. This study was conducted to investigate the clinical features and molecular epidemiology of NoVs in outpatient children with acute gastroenteritis in Huzhou, China, between April 2013 and April 2014.

METHODS

Stool specimens from 1346 outpatient children enrolled (under 5 years of age) with acute gastroenteritis were examined for NoVs by multiplex RT-PCR, and sequences of the partial capsids of NoVs were analyzed phylogenetically, while the relevant clinical data were analyzed statistically.

RESULTS

Of 1346 specimens, 383 (28.5%, 383/1346) were positive for NoVs. The proportion of GII genotypes (26.9%) was significantly higher than that of GI genotypes (1.6%). The GII.4 genotype was the most prevalent of GII genotypes and was clustered into GII.4/Sydney (37.8%) and GII.4/2006b (62.2%), whereas GI strains were clustered into GI.1. Additionally, the younger children (12 to <24 months of age) were more susceptible to NoVs than children in other age groups, and the highest percentage of NoV infections occurred in April 2013. The diarrheal frequency (times/d) and WBC counts of the infected outpatient group with NoVs were significantly higher than were those of the uninfected outpatient group.

CONCLUSION

NoVs were confirmed to be the major viral agents responsible for acute gastroenteritis in outpatient children in Huzhou, China, and GII.4/Sydney and GII.4/2006b variants were identified as the predominant strains in this study.

Prevalence and genetic diversity of noroviruses in adults with acute gastroenteritis in Huzhou, China, 2013-2014

Norovirus (NoV) infection is the most common cause of nonbacterial acute gastroenteritis, which affects both adults and children. However, the molecular epidemiology of NoV in adults with acute gastroenteritis in China has not been investigated extensively. In this study, we investigated the occurrence of NoV infections and analyzed the genetic diversity of NoV in adults with acute gastroenteritis in Huzhou, China. A total of 796 fecal samples were collected from outpatients (≥16 years of age) between March 2013 and February 2014. Real-time RT-PCR was performed to detect NoV genogroups I (GI) and II (GII). For genotyping, the capsid and RNA-dependent RNA polymerase (RdRp) genes were partially amplified and sequenced for phylogenetic analysis. NoVs were detected in 26.51 % (211/796) of the specimens, with GII being predominant, representing 96.20 % of the NoV infections. At least nine genotypes were identified among GI and GII specimens, including GI.P2/GI.2, GI.P3/GI.3, GI.P4/GI.4, GII.Pe/GII.4 Sydney_2012, GII.P12/GII.3, GII.P7/GII.6, GII.P16/GII.13, GII.Pe, and GII.Pg (RdRp only). This is the first report of a GII.P16/GII.13 recombinant virus in adults in China. GII.Pe/GII.4 Sydney_2012 was the most prevalent genotype and the only GII.4 variant identified during the study period. Our findings suggested that NoV was a common causative agent of acute gastroenteritis in adults in Huzhou, China. During the study period, the NoVs circulating in adults in Huzhou were predominantly GII.4 Sydney_2012 variants and GII NoV recombinants.

Acute gastroenteritis outbreak caused by a GII.6 norovirus

AIM: To report an acute gastroenteritis outbreak caused by a genogroup 2 genotype 6 (GII.6) strain norovirus in Shanghai, China.

METHODS: Noroviruses are responsible for approximately half of all reported gastroenteritis outbreaks in many countries. Genogroup 2 genotype 4 strains are the most prevalent. Rare outbreaks caused by GII.6 strains have been reported. An acute gastroenteritis outbreak occurred in an elementary school in Shanghai in December of 2013. Field and molecular epidemiologic investigations were conducted.

RESULTS: The outbreak was limited to one class in an elementary school located in southwest Shanghai. The age of the students ranged from 9 to 10 years. The first case emerged on December 10, 2013, and the last case emerged on December 14, 2013. The cases peaked on December 11, 2013, with 21 new cases. Of 45 students in the class, 32 were affected. The main symptom was gastroenteritis, and 15.6% (5/32) of the cases exhibited a fever. A field epidemiologic investigation showed the pathogen may have been transmitted to the elementary school from employees in a delicatessen via the first case student, who had eaten food from the delicatessen one day before the gastroenteritis episodes began. A molecular epidemiologic investigation identified the cause of the gastroenteritis as norovirus strain GII.6; the viral sequence of the student cases showed 100% homology with that of the shop employees. Genetic relatedness analyses showed that the new viral strain is closely related to previously reported GII.6 sequences, especially to a strain reported in Japan.

CONCLUSION: This is the first report to show that norovirus strain GII.6 can cause a gastroenteritis outbreak. Thus, the prevalence of GII.6 noroviruses requires attention.

Epidemiology of norovirus infections among diarrhea outpatients in a diarrhea surveillance system in Shanghai, China: a cross-sectional study

Background

Norovirus is an important cause of gastroenteritis both in children and adults. In China, few studies have been conducted on adult populations. This study aimed to determine the contribution of norovirus to gastroenteritis, characterize the features of norovirus infections, compare them with other pathogens, and test the effectiveness of the surveillance system.

Methods

A citywide surveillance network on diarrhea patients was established. Samples were collected with intervals from both children and adults among diarrhea outpatients in hospitals and tested for viruses using rRT-PCR and for bacteria in CDCs. Patient information was acquired through interviews and recorded into a dedicated online system. The Pearsonχ² test, multivariate logistic regression models and discriminant models were fitted into its comparisons with the non-norovirus group and other pathogens.

Results

Norovirus was detected in 22.91% of sampled diarrhea patients. The seasonal distribution of norovirus infections was different from non-norovirus patients (p < 0.001), with a half-year peak. Higher proportions of males (p = 0.001, OR = 1.303, 95% CI = 1.110-1.529), local citizens (p < 0.001) and officials/clerks (p = 0.001, OR = 1.348, 95% CI = 1.124-1.618) were affected with norovirus when compared with non-norovirus patients. Diarrhea patients affected with norovirus featured nausea (p < 0.001, OR = 1.418, 95% CI = 1.176-1.709) and vomiting (p < 0.001, OR = 1.969, 95% CI = 1.618-2.398), while fewer manifested fever (p = 0.046, OR = 0.758, 95% CI = 0.577-0.996) and abdominal pain (p = 0.018, OR = 0.815, 95% CI = 0.689-0.965). Children were more vulnerable to rotavirus (p = 0.008, OR = 1.637, 95% CI = 1.136-2.358) and bacteria (p = 0.027, OR = 1.511, 95% CI = 1.053-2.169) than norovirus. There was a seasonal difference between the GI and GII genotypes (p < 0.001). Officials or clerks were more easily affected with GI than GII (p = 0.006, OR = 1.888, 95% CI = 1.205-2.958).

Conclusions

This study was based on a citywide hospital-sentinel surveillance system with multiple enteric pathogens included. Norovirus was recognized as the most prevalent enteric pathogen in Shanghai. The seasonal peak was from October to April. Males had a higher prevalence than females. Local citizens and officials/clerks were more vulnerable to norovirus than other pathogens. Compared with rotavirus and bacteria, children were less frequently affected by norovirus. Nausea and vomiting were typical of norovirus, whereas fever and abdominal pain were uncommon symptoms of this pathogen. GI and GII infections were centered in different seasons. Officials and clerks were more easily affected by GI than GII.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-015-0922-z) contains supplementary material, which is available to authorized users.

Norovirus GII.17 Predominates in Selected Surface Water Sources in Kenya

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.