Genetic and Epidemiologic Trends of Norovirus Outbreaks in the United States from 2013 to 2016 Demonstrated Emergence of Novel GII.4 Recombinant Viruses

Molecular epidemiology of norovirus outbreaks in Argentina, 2013-2018

Noroviruses are a leading cause of endemic and epidemic acute gastroenteritis in all age groups. However, in Latin America, there are limited and updated data regarding circulating genotypes. The aim of this study was to assess the prevalence and genetic diversity of norovirus outbreaks in Argentina from 2013 to 2018. Stool samples from 29 acute gastroenteritis (AGE) outbreaks were available for viral testing. Norovirus was detected in samples from 18 (62.1%) outbreaks (2 GI and 16 GII). Both GI outbreaks were typed as GI.6[P11] whereas 10 different GII genotypes were detected, in which GII.4 viruses were the most frequently detected (29.4%, associated with GII.P31 and GII.P16) followed by GII.1[P33] and GII.6[P7] (17.6% each). Like GII.4 viruses, GII.2 viruses were also detected in association with different polymerases (GII.P2 and GII.P16). Our findings underscore the importance of dual RNA-dependent RNA polymerase-VP1 typing since recombinant strains with new polymerase sequences emerge frequently suggesting a possible role in improved fitness of these viruses. This study represents the most recent multi-year assessment of the molecular epidemiology of norovirus strains associated with AGE outbreaks in Argentina. Molecular surveillance of norovirus has to be considered to monitor possible changes in dominant genotypes which may assist to inform the formulation of future vaccines.

Human Norovirus Infection in Dogs, Thailand

In July 2018, recombinant norovirus GII.Pe-GII.4 Sydney was detected in dogs who had diarrhea in a kennel and in children living on the same premises in Thailand. Whole-genome sequencing and phylogenetic analysis of 4 noroviruses from Thailand showed that the canine norovirus was closely related to human norovirus GII.Pe-GII.4 Sydney, suggesting human-to-canine transmission.

Molecular Evolution of the Protease Region in Norovirus Genogroup II

Noroviruses are a major cause of viral epidemic gastroenteritis in humans worldwide. The protease (Pro) encoded in open reading frame 1 (ORF1) is an essential enzyme for proteolysis of the viral polyprotein. Although there are some reports regarding the evolutionary analysis of norovirus GII-encoding genes, there are few reports focused on the Pro region. We analyzed the molecular evolution of the Pro region of norovirus GII using bioinformatics approaches. A time-scaled phylogenetic tree of the Pro region constructed using a Bayesian Markov chain Monte Carlo method indicated that the common ancestor of GII diverged from GIV around 1680 CE [95% highest posterior density (HPD), 1607-1749]. The GII Pro region emerged around 1752 CE (95%HPD, 1707-1794), forming three further lineages. The evolutionary rate of GII Pro region was estimated at more than 10-3 substitutions/site/year. The distribution of the phylogenetic distances of each genotype differed, and showed genetic diversity. Mapping of the negative selection and substitution sites of the Pro structure showed that the substitution sites in the Pro protein were mostly produced under neutral selection in positions structurally adjacent to the active sites for proteolysis, whereas negative selection was observed in residues distant from the active sites. The phylodynamics of GII.P4, GII.P7, GII.P16, GII.P21, and GII.P31 indicated that their effective population sizes increased during the period from 2005 to 2016 and the increase in population size was almost consistent with the collection year of these genotypes. These results suggest that the Pro region of the norovirus GII evolved rapidly, but under no positive selection, with a high genetic divergence, similar to that of the RNA-dependent RNA polymerase (RdRp) region and the VP1 region of noroviruses.

The Norovirus Epidemiologic Triad: Predictors of Severe Outcomes in US Norovirus Outbreaks, 2009-2016

BACKGROUND

Noroviruses are the leading cause of acute gastroenteritis outbreaks worldwide. Clarifying the viral, host, and environmental factors (epidemiologic triad) associated with severe outcomes can help target public health interventions.

METHODS

Acute norovirus outbreaks reported to the National Outbreak Reporting System (NORS) in 2009-2016 were linked to laboratory-confirmed norovirus outbreaks reported to CaliciNet. Outbreaks were analyzed for differences in genotype (GII.4 vs non-GII.4), hospitalization, and mortality rates by timing, setting, transmission mode, demographics, clinical symptoms, and health outcomes.

RESULTS

A total of 3747 norovirus outbreaks were matched from NORS and CaliciNet. Multivariable models showed that GII.4 outbreaks (n = 2353) were associated with healthcare settings (odds ratio [OR], 3.94 [95% confidence interval {CI}, 2.99-5.23]), winter months (November-April; 1.55 [95% CI, 1.24-1.93]), and older age of cases (≥50% aged ≥75 years; 1.37 [95% CI, 1.04-1.79]). Severe outcomes were more likely among GII.4 outbreaks (hospitalization rate ratio [RR], 1.54 [95% CI, 1.23-1.96]; mortality RR, 2.77 [95% CI, 1.04-5.78]). Outbreaks in healthcare settings were also associated with higher hospitalization (RR, 3.22 [95% CI, 2.34-4.44]) and mortality rates (RR, 5.65 [95% CI, 1.92-18.70]).

CONCLUSIONS

Severe outcomes more frequently occurred in norovirus outbreaks caused by GII.4 and those in healthcare settings. These results should help guide preventive interventions for targeted populations, including vaccine development.

Minimally Invasive Saliva Testing to Monitor Norovirus Infection in Community Settings

Background

Norovirus is a leading cause of acute gastroenteritis worldwide. Routine norovirus diagnosis requires stool collection. The goal of this study was to develop and validate a noninvasive method to diagnose norovirus to complement stool diagnostics and to facilitate studies on transmission.

Methods

A multiplex immunoassay to measure salivary immunoglobulin G (IgG) responses to 5 common norovirus genotypes (GI.1, GII.2, GII.4, GII.6, and GII.17) was developed. The assay was validated using acute and convalescent saliva samples collected from Peruvian children <5 years of age with polymerase chain reaction (PCR)–diagnosed norovirus infections (n = 175) and controls (n = 32). The assay sensitivity and specificity were calculated to determine infection status based on fold rise of salivary norovirus genotype-specific IgG using norovirus genotype from stool as reference.

Results

The salivary assay detected recent norovirus infections and correctly assigned the infecting genotype. Sensitivity was 71% and specificity was 96% across the evaluated genotypes compared to PCR-diagnosed norovirus infection.

Conclusions

This saliva-based assay will be a useful tool to monitor norovirus transmission in high-risk settings such as daycare centers or hospitals. Cross-reactivity is limited between the tested genotypes, which represent the most commonly circulating genotypes.

Emergence of a Novel Recombinant Norovirus GII.P16-GII.12 Strain Causing Gastroenteritis, Alberta, Canada

We identified a novel recombinant GII.P16-GII.12 norovirus associated with epidemic and endemic gastroenteritis during March 1, 2018–February 12, 2019, in Alberta, Canada. GII.12 viruses have not been detected in Alberta since 2000. Comparing the full genome of this strain to previously published sequences revealed this virus to be a novel recombinant strain.

Emergence of norovirus strains: A tale of two genes

Noroviruses are a very diverse group of viruses that infect different mammalian species. In humans, norovirus is a major cause of acute gastroenteritis. Multiple norovirus infections can occur in a lifetime as the result of limited duration of acquired immunity and cross-protection among different strains. A combination of advances in sequencing methods and improvements on surveillance has provided new insights into norovirus diversification and emergence. The generation of diverse norovirus strains has been associated with (1) point mutations on two different genes: ORF1, encoding the non-structural proteins, and ORF2, encoding the major capsid protein (VP1); and (2) recombination events that create chimeric viruses. While both mechanisms are exploited by all norovirus strains, individual genotypes utilize each mechanism differently to emerge and persist in the human population. GII.4 noroviruses (the most prevalent genotype in humans) present an accumulation of amino acid mutations on VP1 resulting in the chronological emergence of new variants. In contrast, non-GII.4 noroviruses present co-circulation of different variants over long periods with limited changes on their VP1. Notably, genetic diversity of non-GII.4 noroviruses is mostly related to the high number of recombinant strains detected in humans. While it is difficult to determine the precise mechanism of emergence of epidemic noroviruses, observations point to multiple factors that include host-virus interactions and changes on two regions of the genome (ORF1 and ORF2). Larger datasets of viral genomes are needed to facilitate comparison of epidemic strains and those circulating at low levels in the population. This will provide a better understanding of the mechanism of norovirus emergence and persistence.

Nucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants

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 3^rd 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.

Viral Etiology of Acute Gastroenteritis in <2-Year-Old US Children in the Post-Rotavirus Vaccine Era

BACKGROUND

The rotavirus disease burden has declined substantially since rotavirus vaccine was introduced in the United States in 2006. The aim of this study was to determine the viral etiology of acute gastroenteritis (AGE) in US children aged <2 years.

METHODS

The New Vaccine Surveillance Network (NVSN) of geographically diverse US sites conducts active pediatric population-based surveillance in hospitals and emergency departments. Stool samples were collected from children aged <2 years with symptoms of AGE (n = 330) and age-matched healthy controls (HCs) (n = 272) between January and December 2012. Samples were tested by real-time reverse-transcriptase polymerase chain reaction assays {adenovirus (type 40 and 41), norovirus, parechovirus A, enterovirus, sapovirus, and astrovirus} and an enzyme immunoassay (rotavirus). All samples that tested positive were genotyped.

RESULTS

Detection rates of pathogens in children with AGE versus those of HCs were, respectively, 23.0% versus 6.6% for norovirus (P < .01), 23.0% versus 16.0% for adenovirus (P = .08), 11.0% versus 16.0% for parechovirus A (P = .09), 11.0% versus 9.0% for enterovirus (P = .34), 7.0% versus 3.0% for sapovirus (P = .07), 3.0% versus 0.3% for astrovirus (P = .01), and 3.0% versus 0.4% for rotavirus (P = .01). A high prevalence of adenovirus was detected at 1 surveillance site (49.0% for children with AGE and 43.0% for HCs). Norovirus GII.4 New Orleans was the most frequently detected (33.0%) norovirus genotype. Codetection of >1 virus was more common in children with AGE (16.0%) than in HCs (10.0%) (P = .03).

CONCLUSIONS

Norovirus, astrovirus, sapovirus, and rotavirus were detected significantly more in children with AGE than in HCs, and norovirus was the leading AGE-causing pathogen in US children aged <2 years during the year 2012.

Sera Antibody Repertoire Analyses Reveal Mechanisms of Broad and Pandemic Strain Neutralizing Responses after Human Norovirus Vaccination

Rapidly evolving RNA viruses, such as the GII.4 strain of human norovirus (HuNoV), and their vaccines elicit complex serological responses associated with previous exposure. Specific correlates of protection, moreover, remain poorly understood. Here, we report the GII.4-serological antibody repertoire—pre- and post-vaccination—and select several antibody clonotypes for epitope and structural analysis. The humoral response was dominated by GII.4-specific antibodies that blocked ancestral strains or by antibodies that bound to divergent genotypes and did not block viral-entry-ligand interactions. However, one antibody, A1431, showed broad blockade toward tested GII.4 strains and neutralized the pandemic GII.P16-GII.4 Sydney strain. Structural mapping revealed conserved epitopes, which were occluded on the virion or partially exposed, allowing for broad blockade with neutralizing activity. Overall, our results provide high-resolution molecular information on humoral immune responses after HuNoV vaccination and demonstrate that infection-derived and vaccine-elicited antibodies can exhibit broad blockade and neutralization against this prevalent human pathogen.

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Serum vaccine response is dominated by a small number of abundant antibody clonotypes

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Vaccine-boosted antibodies predominantly target conserved norovirus epitopes

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Identified cross-genogroup and strain-specific epitopes

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Discovered a pandemic-genotype neutralizing antibody recognizing a conserved epitope

Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013-2017

Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013-2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10-3 and ~2.3 × 10-3 substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years.

Epidemiological analysis of norovirus infectious diarrhea outbreaks in Chongqing, China, from 2011 to 2016

OBJECTIVE

We investigated the epidemiological characteristics of norovirus infection from 2011 to 2016 in Chongqing, China, in order to provide evidence for strategies on epidemic prevention and control.

METHODS

We collected data on norovirus infectious diarrhea epidemics in 38 districts and counties, and analyzed the information using descriptive epidemiological methods.

RESULTS

In 2011, the first case of norovirus infectious diarrhea in Chongqing was reported. From 2011 to 2015, 38 districts and counties in Chongqing reported a total of 4 epidemics. In 2016, however, the city reported 117 outbreaks. From 2011 to 2016, there were 1637 cases of norovirus infection but no deaths. In 2016, most outbreaks occurred over a 5-month period with a clear peak in December and higher incidence in major urban areas than smaller communities (83.61% vs. 16.39%). Of these 1637 cases, 99.18% occurred in urban schools and nurseries, and 80% were transmitted person-to-person. Infection by genogroup II genotype 2 (GII.2) viruses accounted for 98.71% of cases. Leukocytes were increased in 67.81% of patients, neutrophils in 65%, and lymphocytes in 50%. Medical treatment was sought by 70% of patients or guardians but only 3.66% of cases were hospitalized. The most frequent misdiagnosis was "suspected food poisoning".

CONCLUSION

The frequency of norovirus infectious diarrhea epidemics increased over 20-fold from 2011 to 2016 in Chongqing, China. These epidemics occurred predominantly in urban schools and nurseries. However, epidemics showed little spread to outlying districts and counties, so prevention and control pressures were relatively high.

SUGGESTIONS

Healthcare professionals and institutions should strengthen health education for groups at high-risk of norovirus infection, such as school children, and increase norovirus testing capacity to further improve emergency investigation. Prevention and control knowledge should be disseminated to the general public to reduce transmission risk and total disease burden. Finally, governments and health administrative departments should invest special funds to prevent and control norovirus epidemics.

Population Genomics of GII.4 Noroviruses Reveal Complex Diversification and New Antigenic Sites Involved in the Emergence of Pandemic Strains

Noroviruses are an important cause of viral gastroenteritis around the world. An obstacle delaying the development of norovirus vaccines is inadequate understanding of the role of norovirus diversity in immunity. Using a population genomics approach, we identified new residues on the viral capsid protein (VP1) from GII.4 noroviruses, the predominant genotype, that appear to be involved in the emergence and antigenic topology of GII.4 variants. Careful monitoring of the substitutions in those residues involved in the diversification and emergence of new viruses could help in the early detection of future novel variants with pandemic potential. Therefore, this novel information on the antigenic diversification could facilitate GII.4 norovirus vaccine design.

GII.4 noroviruses are a major cause of acute gastroenteritis. Their dominance has been partially explained by the continuous emergence of antigenically distinct variants. To gain insights into the mechanisms of viral emergence and population dynamics of GII.4 noroviruses, we performed large-scale genomics, structural, and mutational analyses of the viral capsid protein (VP1). GII.4 noroviruses exhibited a periodic replacement of predominant variants with accumulation of amino acid substitutions. Genomic analyses revealed (i) a large proportion (87%) of conserved residues; (ii) variable residues that map on the previously determined antigenic sites; and (iii) variable residues that map outside the antigenic sites. Residues in the third pattern category formed motifs on the surface of VP1, which suggested extensions of previously predicted and new uncharacterized antigenic sites. The role of two motifs (C and G) in the antigenic makeup of the GII.4 capsid protein was confirmed with monoclonal antibodies and carbohydrate blocking assays. Amino acid profiles from antigenic sites (A, C, D, E, and G) correlated with the circulation patterns of GII.4 variants, with three of them (A, C, and G) containing residues (352, 357, 368, and 378) linked with the diversifying selective pressure on the emergence of new GII.4 variants. Notably, the emergence of each variant was followed by stochastic diversification with minimal changes that did not progress toward the next variant. This report provides a methodological framework for antigenic characterization of viruses and expands our understanding of the dynamics of GII.4 noroviruses and could facilitate the design of cross-reactive vaccines.

Application of the susceptible-infected-recovered deterministic model in a GII.P17 emergent norovirus strain outbreak in Romania in 2015

Purpose

This study shows the epidemiological profile of the first gastroenteritis outbreak of GII.P17 in the Romanian territory. An outbreak with such large amplitude in a European territory was previously undocumented.

Patients and methods

Using a cross-sectional design, with the susceptible-infected-recovered (SIR) deterministic compartmental model for a fixed population, and the cluster method for establishing the high-incidence zones, we carried out our investigation by means of questionnaires containing personal data, affected collectivities, disease onset and duration, symptoms displayed, medical assistance provided, previous antibiotic intake where applicable, food consumption and water sources, and sanitation conditions. The confirmation of cases was done based on the typical norovirus gastroenteritis symptomatology and using three laboratory confirmations (by molecular diagnosis) for GII.P17-GII.17 genotype noroviruses from three patients.

Results

A gastroenteritis outbreak occurred in October-November 2015, affecting 328 people in Arad, a county in Western Romania, covering 44 neighbouring localities with a total population of 35,440 people. The study detected an inter-human transmission of the infection, with an intrafamilial risk of disease of 2.26 (95% CI 1.76 to 2.90) compared with the community transmission (in school collectivity). The basic reproduction number Ro dropped from 1.26 to 0.18 during weeks 43:44, after controlling the transmission by decontamination and isolation.

Conclusion

SIR made it possible to highlight the expansion of the emerging norovirus strain infection from community to family collectivities. This study provides practical solutions to limit disease cases, even in the absence of etiology, and shows the importance of sometimes underestimated traditional control methods.

The resurgence of the norovirus GII.4 variant associated with sporadic gastroenteritis in the post-GII.17 period in South China, 2015 to 2017

Background

Human norovirus is regarded as the leading cause of nonbacterial acute diarrhea in developing and developed countries. Among all genotypes, GII.4 has been the predominant genotype, but in East Asia, it was replaced by the GII.17 in 2014/2015. However, after the prevalence of new GII.17 variant in South China, a sharply increase in the number of norovirus infections associated with sporadic acute diarrhea was detected. In this study, we would investigate the prevalence and genetic diversity of noroviruses in the sporadic acute gastroenteritis cases in the post-GII.17 period in South China.

Methods

Norovirus was screened from 217 patients with sporadic acute gastroenteritis from August 2015 to October 2017 by reverse transcription-polymerase chain reaction. Then, two regions including the partial RNA polymerase and the capsid gene of positive samples were amplified and sequenced. Phylogenetic analyses were performed to determine norovirus genotypes. Complete VP1 sequences of GII.4 strains detected in this study were also amplified and subjected into evolutionary tracing analyses.

Results

A total of 43 (19.82%) norovirus samples were confirmed from 217 stool specimens, and it was found that GII.4 resurged as the new predominant variant, accounting for 76.74% (33/43) of positive samples. Only one local strain GZ2015-L550 was clustered with the contemporary GII.P16/GII.4–2012 recombinant variant, and other 32 local strains belonged to the clade with the GII.Pe/GII.4–2012 variant. Other genotypes including GII.17 (n = 4), GII.3 (n = 4), GII.8 (n = 1) and GI. 6 (n = 1) were also detected. Furthermore, all GII.4 strains were phylogenetic analyzed based on their capsid P2 subdomains. Combined with other reported 754 strains, the GII.4–2012 variant could be divided into two clades. Most GII.4 strains collected in 2016 and 2017 in this study (7/8) formed a new cluster A in Clade II with additional 103 contemporaneous strains. In addition, evolutionary tracing of the capsid P2 subdomain of this variant was also analyzed, and one specific amino acid substitutions (N373) was identified for Cluster A.

Conclusion

In summary, this study confirmed a norovirus infection peak in the post-GII.17 period in South China, which was caused by the resurgence of the GII.4 variant.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4331-6) contains supplementary material, which is available to authorized users.

Analysis of GII.P7 and GII.6 noroviruses circulating in Italy during 2011-2016 reveals a replacement of lineages and complex recombination history

Noroviruses are important human enteric pathogens and monitoring their genetic diversity is important for epidemiological surveillance, vaccine development, and understanding of RNA viruses evolution. Epidemiological investigations have revealed that genogroup II, genotype 6 noroviruses (GII.6) are common agents of gastroenteritis. Upon sequencing of the ORF2 (encoding the viral capsid), GII.6 viruses have been distinguished into three variants. Sentinel hospital-based surveillance in Italy revealed that GII.6 noroviruses were the second most common capsid genotype in 2015, mostly in association with a GII.P7 ORF1 (encoding the viral polymerase). Upon molecular characterization of the ORF1 and ORF2, the GII.P7_GII.6 epidemic viruses circulating in 2014-2015 (variant GII.6b) were different from those that circulated sporadically in 2011-2013 (variant GII.6a). Analysis of the ORF1 (GII.P7) and ORF2 (GII.6) sequences available in the databases unveiled marked genetic diversity and peculiarities in the phylogenetic segregation patterns, suggesting multiple recombination events. Phylogenetic analyses suggest that recent GII.P7_GII.6b viruses were circulating as early as 2008, and formed a genetically homogenous group that emerged globally.

Genotypic prevalence of norovirus GII in gastroenteritis outpatients in Shanghai from 2016 to 2018

BACKGROUND

With the help of an existing citywide comprehensive surveillance on gastroenteritis outpatients, although norovirus genogroup II (NoV GII) was tested routinely, its genotypes were never investigated systematically on a municipal level. This study aimed to understand the prevalence, major genotypes and evolutional trends of NoV GII in Shanghai during the period of 2016-2018, and to provide molecular bases for early warning for any potential NoV outbreaks.

METHODS

27 sentinel hospitals from all 16 districts were recruited by stratified probability proportional to size (PPS) method in Shanghai comprehensive diarrhea surveillance programme. Stool samples were collected and screened for NoV GII by real-time reverse transcription polymerase chain reaction (qRT-PCR). For samples that were positive in qRT-PCR, conventional RT-PCR was performed to amplify the ORF1-ORF2 junction of NoV GII gene. Generated sequences were typed by RIVM online genotyping tool, and then strains of interest were analyzed phylogenetically using MEGA 6.0.

RESULTS

A total of 7883 stool samples were collected from diarrhea outpatients, among which 6474 were from adults and 1409 were from children. 13.66% (1077 cases) were screened positive in qRT-PCR for NoV GII, from which 71.96% (775 cases) were sequenced successfully. The top three genotypes were GII.Pe/GII.4 (37%), GII.P17/GII.17 (26%) and GII.P16/GII.2 (17%). While GII.Pe/GII.4 detection rate decreased significantly over the 3 years (from 48.4 to 20.9%); GII.P16/GII.2 appeared for the first time in October 2016 and rose rapidly to 27.0% in 2017, but fell back to 23.4% in 2018. Meanwhile there was a significant increase for both GII.P12/GII.3 and GII.P7/GII.6 recombinant genotypes detected in adult population in 2018. Phylogenic analysis revealed the existence of multiple gene clusters within both of these recombinant genotypes.

CONCLUSION

Unlike the alternating circulation of GII.4 and non-GII.4 NoV observed in 2016 or 2017, the genotype profile of NoV GII in 2018 was characterized by the co-prevalence of multiple recombinant genotypes. A recent increase in detection rate in less reported recombinant genotypes such as GII.P12/GII.3 and GII.P7/GII.6 among adult population calls for a continuing close monitoring on NoV GII genotypes in case of potential local outbreaks.

Lessons learned from a prolonged norovirus GII.P16-GII.4 Sydney 2012 variant outbreak in a long-term care facility in Portugal, 2017

OBJECTIVE

To investigate an outbreak of acute gastroenteritis caused by norovirus (NoV) in a long-term care facility (LTCF) in Portugal to describe and estimate its extent, and we implemented control measures.

DESIGN

Outbreak investigation.

METHODS

Probable cases were residents or staff members in the LTCF with at least 1 of the following symptoms: (1) diarrhea, (2) vomiting, (3) nausea, and/or (4) abdominal pain between October 31 and December 8, 2017. Confirmed cases were probable cases with positive NoV infection detected by real-time polymerase chain reaction (RT-PCR) and the same genotype in stool specimens.

RESULTS

The outbreak was caused by NoV GII.P16-GII.4 Sydney 2012 variant and affected 146 people. The highest illness rates were observed in residents (97 of 335, 29%) and nurses (16 of 83, 19%). All 11 resident wards were affected. Data on cases and their working or living areas suggest that movement between wards facilitated the transmission of NoV, likely from person to person.

CONCLUSIONS

The delay in the identification of the causative agent, a lack of restrictions of resident and staff movement between wards, and ineffective initial deep-cleaning procedures resulted an outbreak that continued for >1 month. The outbreak ended only after implementation of strict control measures. Recommendations for controlling future NoV outbreaks in LTCFs include emphasizing the need to control resident's movements and to restrict visitors, timely and effective environmental cleaning and disinfection, leave of absence for ill staff, and encouraging effective hand hygiene.

Human noroviruses: recent advances in a 50-year history

PURPOSE OF REVIEW

Noroviruses are a major cause of gastroenteritis. This review summarizes new information on noroviruses that may lead to the development of improved measures for limiting their human health impact.

RECENT FINDINGS

GII.4 strains remain the most common human noroviruses causing disease, although GII.2 and GII.17 strains have recently emerged as dominant strains in some populations. Histo-blood group antigen (HBGA) expression on the gut mucosa drives susceptibility to different norovirus strains. Antibodies that block virus binding to these glycans correlate with protection from infection and illness. Immunocompromised patients are significantly impacted by norovirus infection, and the increasing availability of molecular diagnostics has improved infection recognition. Human noroviruses can be propagated in human intestinal enteroid cultures containing enterocytes that are a significant primary target for initiating infection. Strain-specific requirements for replication exist with bile being essential for some strains. Several vaccine candidates are progressing through preclinical and clinical development and studies of potential antiviral interventions are underway.

SUMMARY

Norovirus epidemiology is complex and requires continued surveillance to track the emergence of new strains and recombinants, especially with the continued progress in vaccine development. Humans are the best model to study disease pathogenesis and prevention. New in-vitro cultivation methods should lead to better approaches for understanding virus-host interactions and ultimately to improved strategies for mitigation of human norovirus-associated disease.

Higher Viral Load of Emerging Norovirus GII.P16-GII.2 than Pandemic GII.4 and Epidemic GII.17, Hong Kong, China

We compared viral load of emerging recombinant norovirus GII.P16-GII.2 with those for pandemic GII.Pe-GII.4 and epidemic GII.P17-GII.17 genotypes among inpatients in Hong Kong. Viral load of GII.P16-GII.2 was higher than those for other genotypes in different age groups. GII.P16-GII.2 is as replication competent as the pandemic genotype, explaining its high transmissibility and widespread circulation.

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.

Emerging Novel GII.P16 Noroviruses Associated with Multiple Capsid Genotypes

Noroviruses evolve by antigenic drift and recombination, which occurs most frequently at the junction between the non-structural and structural protein coding genomic regions. In 2015, a novel GII.P16-GII.4 Sydney recombinant strain emerged, replacing the predominance of GII.Pe-GII.4 Sydney among US outbreaks. Distinct from GII.P16 polymerases detected since 2010, this novel GII.P16 was subsequently detected among GII.1, GII.2, GII.3, GII.10 and GII.12 viruses, prompting an investigation on the unique characteristics of these viruses. Norovirus positive samples (n = 1807) were dual-typed, of which a subset (n = 124) was sequenced to yield near-complete genomes. CaliciNet and National Outbreak Reporting System (NORS) records were matched to link outbreak characteristics and case outcomes to molecular data and GenBank was mined for contextualization. Recombination with the novel GII.P16 polymerase extended GII.4 Sydney predominance and increased the number of GII.2 outbreaks in the US. Introduction of the novel GII.P16 noroviruses occurred without unique amino acid changes in VP1, more severe case outcomes, or differences in affected population. However, unique changes were found among NS1/2, NS4 and VP2 proteins, which have immune antagonistic functions, and the RdRp. Multiple polymerase-capsid combinations were detected among GII viruses including 11 involving GII.P16. Molecular surveillance of protein sequences from norovirus genomes can inform the functional importance of amino acid changes in emerging recombinant viruses and aid in vaccine and antiviral formulation.

Variation of human norovirus GII genotypes detected in Ibaraki, Japan, during 2012-2018

Background

Human norovirus (HuNoV) is the major cause of viral acute gastroenteritis for all age groups in various countries. HuNoV GII in particular accounted for the majority of norovirus outbreaks, among which GII.4 caused repeated outbreaks for a long time. Besides GII.4, other norovirus genotypes, GII.2, GII.6, and GII.17, have also been prevalent in various contexts in recent years, but few detailed epidemiological studies of them have been performed and are poorly understood. We thus conducted an epidemiological analysis of HuNoV GII in Ibaraki Prefecture, Japan, by performing surveillance in the six seasons from September 2012 to August 2018.

Results

HuNoV GI occurred almost sporadically for all genotypes; however, each genotype of GII exhibited its typical epidemiological characteristics. Although the number of outbreaks of GII.4 decreased season by season, it reemerged in 2017/2018 season. The timing of the epidemic peak in terms of number of cases for GII.17 differed from that for the other genotypes. The patients age with GII.2 and GII.6 were younger and outbreak of GII.17 occurred frequently as food poisoning. Namely, the primarily infected outbreak group differed for each genotype of HuNoV GII. Moreover, the viral load of patients differed according to the genotype.

Conclusions

Various HuNoV genotypes including GII.2, GII.4, GII.6, and GII.17 were shown to be associated with various types of outbreak sites (at childcare and educational facilities, involving cases of food poisoning, and at elderly nursing homes) in this study. These genotypes emerged in recent years, and their prevalence patterns differed from each other. Moreover, differences in outbreak sites and viral load of patients among the genotypes were identified.

High genetic diversity of noroviruses in children from a community-based study in Rio de Janeiro, Brazil, 2014-2018

We report on the occurrence and diversity of noroviruses in children (younger than 5 years old of age) from a low-income urban area in Rio de Janeiro, Brazil. Sixty-one stool specimens collected from children between 1 and 4 years old with acute diarrhoeic episodes (ADE) and non-ADE were investigated. RT-qPCR and sequencing of PCR products after conventional RT-PCR analysis were performed. Noroviruses were detected in 29 (47.5%) samples: 21 (46.7%) from cases with ADE and 8 (50%) from non-ADE cases. Molecular characterization showed 10 different genotypes circulating in this community between November 2014 and April 2018.

Human Norovirus Replication in Human Intestinal Enteroids as Model to Evaluate Virus Inactivation

Human noroviruses are a leading cause of epidemic and endemic acute gastroenteritis worldwide and a leading cause of foodborne illness in the United States. Recently, human intestinal enteroids (HIEs) derived from human small intestinal tissue have been shown to support human norovirus replication. We implemented the HIE system in our laboratory and tested the effect of chlorine and alcohols on human norovirus infectivity. Successful replication was observed for 6 norovirus GII genotypes and was dependent on viral load and genotype of the inoculum. GII.4 viruses had higher replication levels than other genotypes. Regardless of concentration or exposure time, alcohols slightly reduced, but did not completely inactivate, human norovirus. In contrast, complete inactivation of the 3 GII.4 viruses occurred at concentrations as low as 50 ppm of chlorine. Taken together, our data confirm the successful replication of human noroviruses in HIEs and their utility as tools to study norovirus inactivation strategies.

Prevalence and genetic diversity of viral gastroenteritis viruses in children younger than 5 years of age in Guatemala, 2014-2015

BACKGROUND

Acute diarrhea is an important cause of morbidity and mortality in children and is associated with approximately 500,000 deaths/year globally. Rotavirus and norovirus are leading causes of acute diarrhea accounting for more than half of this burden.

OBJECTIVE/STUDY DESIGN

To determine the prevalence and genotype distribution of acute diarrhea caused by rotavirus, norovirus, sapovirus and astrovirus among children <5 years of age at two departments in Guatemala from January 2014 to December 2015, we tested 471 stool specimens (202 samples from hospitalized children and 269 samples from children in ambulatory clinics) by real-time reverse transcription-PCR and genotyped positive samples.

RESULTS

Rotavirus was detected in 20.4%, norovirus in 18.5%, sapovirus in 7% and astrovirus in 4.2% of the samples. Co-infection of rotavirus and norovirus was found in 2.6% of the samples. Most norovirus (87.4%) and rotavirus (81.3%) infections were detected in children in the 6-12 months age group. The proportion of patients with rotavirus (34%) and norovirus (23%) was higher in hospitalized patients compared to ambulatory patients, whereas the prevalence of sapovirus and astrovirus was similar in both settings. Of the 40 genotyped norovirus strains, 62.5% were GII.4 and 15% GII.3. Sapovirus genotypes included GI.1 (15.4%), GII.2 (15.4%), GII.5 (38.5%) and GIV.1 (30.8%).

CONCLUSIONS

Our data demonstrate that in 2014-2015, gastroenteritis viruses account for 50% of acute diarrhea in children younger than 5 years of age in Guatemala, highlighting the importance of continuous surveillance to guide impact of the current rotavirus vaccine and formulation of future norovirus vaccines.

Active Surveillance for Norovirus in a US Veterans Affairs Patient Population, Houston, Texas, 2015-2016

Background

Norovirus is a leading cause of acute gastroenteritis (AGE); however, few data exist on endemic norovirus disease burden among adults. Candidate norovirus vaccines are currently in development for all ages, and robust estimates of norovirus incidence among adults are needed to provide baseline data.

Methods

We conducted active surveillance for AGE among inpatients at a Veterans Affairs (VA) hospital in Houston, Texas. Patients with AGE (≥3 loose stools, ≥2 vomiting episodes, or ≥1 episode of both loose stool and vomiting, within 24 hours) within 10 days of enrollment and non-AGE control patients were enrolled. Demographic data and clinical characteristics were collected. Stool samples were tested using the FilmArray gastrointestinal panel; virus-positives were confirmed by real-time reverse transcription polymerase chain reaction and genotyped by sequencing.

Results

From November 2, 2015 through November 30, 2016, 147 case patients and 19 control patients were enrolled and provided a stool specimen. Among case patients, 139 (95%) were male and 70 (48%) were aged ≥65 years. Norovirus was the leading viral pathogen detected (in 16 of 20 virus-positive case patients) and accounted for 11% of all AGE cases. No viral pathogens were detected among control patients. Incidence of norovirus-associated hospitalization was 20.3 cases/100 000 person-years and was similar among those aged <65 and ≥65 years.

Conclusions

This active surveillance platform employed screening and enrollment of hospitalized VA patients meeting a standardized AGE case definition, as well as non-AGE control patients. Data from this study highlight the burden of norovirus in a VA inpatient population and will be useful in policy considerations of a norovirus vaccine.

Cell Cycle Arrest is a Conserved Function of Norovirus VPg Proteins

Murine norovirus (MNV) viral protein genome-linked (VPg) manipulates the cell cycle to induce a G0/G1 arrest and gain a beneficial replication environment. All viruses of the norovirus genus encode a VPg protein; however, it is unknown if the G0/G1 arrest induced by MNV VPg is conserved in other members of the genus. RNA transcripts encoding a representative viral VPg from five norovirus genogroups were transfected into RAW-Blue murine macrophages, and the percentage of cells in each phase of the cell cycle was determined. A G0/G1 cell cycle arrest was observed for all norovirus VPg proteins tested, and in the wider Caliciviridae family the arrest was also conserved in rabbit hemorrhagic disease virus (RHDV) VPg and human sapovirus (HuSV) VPg. Truncation of MNV VPg shows that the first 62 amino acids are sufficient for a cell cycle arrest, and alignment of VPg sequences revealed a conserved motif in the N-terminal region of VPg. Analysis of VPg constructs with single N-terminal region point mutations, or exchange of N-terminal regions between VPg proteins, confirmed the importance of the N-terminal region for cell cycle arrest. These results provide evidence that G0/G1 cell cycle arrest is a conserved function of norovirus VPg proteins that involves the N-terminal region of these proteins.

Changes in norovirus genotype diversity in gastroenteritis outbreaks in Alberta, Canada: 2012-2018

Background

The emergence of norovirus genotype GII.4 variants has been associated with gastroenteritis pandemics worldwide, prompting molecular surveillance for early detection of novel strains. In this study, we aimed to analyze the outbreak activity of norovirus and characterize the norovirus strains circulating in Alberta between July 2012 and February 2018.

Methods

Stool samples from gastroenteritis outbreaks in Alberta were tested for norovirus at the Provincial Laboratory for Public Health using a multiplex real time-RT PCR assay. The ORF1 and ORF2-genotypes of norovirus positive samples were assigned based on phylogenetic analyses of partial polymerase and capsid sequences, respectively.

Results

A total of 530 norovirus outbreaks were identified. During July 2012 and June 2017 there was a gradual decrease in the annual number of GII.4 outbreaks, however, outbreak numbers increased from June 2017–February 2018. Four novel strains emerged: GII.17 Kawasaki in July 2014–June 2015, GII.P16/GII.4 Sydney in July 2015–June 2016, GII.P16/GII.2 and GII.P4 New Orleans/GII.4 Sydney in July 2016–June 2017. GII.Pe/GII.4 Sydney was the single predominant strain responsible for the majority (over 50%) of all norovirus outbreaks up to June 2015. Between June 2017 and February 2018, GII.P16/GII.4 Sydney was the leading strain causing 63% of all norovirus outbreaks.

Conclusions

GII.4 stands as the predominant capsid genotype causing a large majority of the norovirus outbreaks in early 2018. An increase in genotype diversity was observed in the last years, characterized by a high circulation of non-GII.4 strains and GII.4 recombinants.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-3792-y) contains supplementary material, which is available to authorized users.

Viral gastroenteritis among children of 0-5 years in Nigeria: Characterization of the first Nigerian aichivirus, recombinant noroviruses and detection of a zoonotic astrovirus

BACKGROUND

Viruses are the leading cause of acute gastroenteritis in children worldwide. Understanding of the occurrence and genetic diversity of these viruses can help to prevent infections.

OBJECTIVES

The present study describes the presence, genetic diversity and possible recombination of five enteric viruses in children with gastroenteritis in Southwestern Nigeria.

STUDY DESIGN

From August 2012 to December 2013, stool samples and sociodemographic data of 103 diarrheic children <5 years were collected to detect and characterize rotavirus A, norovirus, human astrovirus, aichivirus and sapovirus using PCR techniques followed by sequencing and phylogenetic analyses.

RESULTS

At least one virus was identified in 58.3% (60/103) of the stool samples. Rotavirus, norovirus and astrovirus were detected in 39.8% (41/103), 10.7% (11/103), and 6.8% (7/103) respectively. Notably, aichivirus was detected for the first time in Nigeria (1/103; 0.97%). Sapovirus was not detected in the study. Co-infections with rotavirus were observed in eight samples either with norovirus or astrovirus or aichivirus. Phylogenetic analyses of different genome regions of norovirus positive samples provided indication for recombinant norovirus strains. A novel astrovirus strain closely related to canine astrovirus was identified and further characterized for the first time.

CONCLUSIONS

Viruses are the common cause of acute gastroenteritis in Nigerian infants with rotavirus as most frequently detected pathogen. New norovirus recombinants and a not yet detected zoonotic astrovirus were circulating in Southwestern Nigeria, providing new information about emerging and unusual strains of viruses causing diarrhea.

Detection of norovirus epidemic genotypes in raw sewage using next generation sequencing

Noroviruses are a leading cause of epidemic and pandemic acute gastroenteritis (AGE) worldwide, and contaminated food and water are important routes for its transmission. Raw sewage has been used for viral surveillance to monitor the emergence of new norovirus strains with the potential to cause epidemics. In this study, we investigated norovirus occurrence and norovirus RNA levels in 156 samples collected from May 2013 to May 2014, across three different stages (52 samples each) of a wastewater treatment plant (WWTP) in Rio de Janeiro, Brazil. We also explored norovirus GII diversity in raw sewage samples by next-sequencing generation (NGS). In addition, we examined norovirus prevalence and molecular epidemiology from acute gastroenteritis cases. Using RT-qPCR, norovirus GI and GII was detected in 38.5% and 96.1% of raw sewage samples, 40.4% and 96.1% of primary effluent samples and 1.9% and 5.8% of final effluent samples, respectively. Norovirus RNA levels varied from 4 to 6.2 log₁₀ genome copies per litre (gc L^-1) for GI and from 4.4 to 7.3 log₁₀ gc L^-1 for GII. Using MiSeq NGS, we identified 13 norovirus genotypes over the one-year period, with six dominant capsid genotypes, including GII.4, GII.17, GII.5, GII.2, GII.3 and GII.1. GII.4 noroviruses were the most prevalent in wastewater samples (68.5%), and a similar trend was observed in AGE cases (71%). The emergent GII.17 was the second most prevalent genotype (14.3%) identified in the raw sewage samples, however, it was not detected in clinical cases. Due to the high burden of norovirus outbreaks and the lack of vaccine and antiviral drugs, it is essential to understand the genotypic diversity of norovirus at the population level. Complementary data obtained from both clinical and environmental (sewage) samples proved to be an effective strategy to monitor the circulation and emergence of norovirus epidemic genotypes.

Sentinel hospital-based surveillance for norovirus infection in children with gastroenteritis between 2015 and 2016 in Italy

Noroviruses are one of the leading causes of gastro-enteric diseases worldwide in all age groups. Novel epidemic noroviruses with GII.P16 polymerase and GII.2 or GII.4 capsid type have emerged worldwide in late 2015 and in 2016. We performed a molecular epidemiological study of the noroviruses circulating in Italy to investigate the emergence of new norovirus strains. Sentinel hospital-based surveillance, in three different Italian regions, revealed increased prevalence of norovirus infection in children (<15 years) in 2016 (14.4% versus 9.8% in 2015) and the emergence of GII.P16 strains in late 2016, which accounted for 23.0% of norovirus infections. The majority of the strains with a GII.P16 polymerase showed a GII.2 capsid genotype (79.5%). Also, a marked circulation of strains with a GII.17 capsid (14.0%) was observed, chiefly in early 2016. The emergence and global spread of non-GII.4 noroviruses pose challenges for the development of vaccine strategies.

Recombinant noroviruses detected in Mid-West region of Brazil in two different periods 2009-2011 and 2014-2015: Atypical breakpoints of recombination and detection of distinct GII.P7-GII.6 lineages

Noroviruses are an important cause of acute gastroenteritis. The high incidence of norovirus is a reflection of its great genomic and antigenic variability resultant of evolutionary mechanisms, such as recombination. Herein, the main objective of this study was to characterize partially two regions of norovirus genome (RdRp and VP1) from fecal samples, collected in two different time periods (2009-2011 and 2014-2015) in the Mid-West region of Brazil. Twenty samples were sequenced and characterized (GI.P5-GI.5, GII.P16-GII.3, GI.P7-GI.7, GII.Pe-GII.4 and GII.P7-GII.6). Sequences of GII.Pe-GII.4 genotype were also characterized as Sydney 2012 variant. Genotypes GII.P7-GII.6, GII.P16-GII.3 and GII.Pe-GII.4 (16/20-80%) were identified as norovirus recombinants by phylogeny and bioinformatic analyzes. The GII.P7-GII.6 (62.5%) and GII.Pe-GII.4 (25%) genotypes had recombination point's upstream ORF1/2 overlapping region, whereas GII.P16-GII.3 (12.5%) genotype had the recombination point in the overlapping region. Furthermore, the GII.P7-GII.6, from samples collected in 2009-2011 had different recombinant points than the GII.P7-GII.6 from samples obtained in 2014-2015, forming two different clusters in the phylogenetic analysis. Our study brings information on the circulation of recombinant norovirus genotypes in Mid-West of Brazil, including recombinants with atypical recombination breakpoints, and provides evidence for the circulation of different lineages of the same recombinant genotype.

Country-wide surveillance of norovirus outbreaks in the Portuguese Army, 2015-2017

INTRODUCTION

Gastrointestinal infections are among the most common foodborne and waterborne diseases in military populations, with direct implications in operational efficiency and force readiness. Through the surveillance system of reportable acute gastrointestinal illness in the Portuguese Army, four norovirus outbreaks were identified between October 2015 and October 2017 in mainland Portugal and the Azores archipelago. The present study documents the epidemiological, clinical and laboratory investigations of these norovirus outbreaks.

METHODS

Cases were investigated and epidemiological questionnaires were distributed to all soldiers in each military setting where the outbreaks occurred. Stool samples from soldiers with acute gastroenteritis illness were collected and screened for common enteropathogenic agents. Food and water samples served on the settings were also collected for microbiological investigation. Norovirus-positive samples were further characterised by sequence analysis using a public automated genotyping tool.

RESULTS

The four outbreaks affected a total of 99 soldiers among the 618 stationed on base units and in a military exercise. A total of 27 soldiers provided a stool sample, of which 20 were positive for norovirus by real-time PCR. Phylogenetic analysis showed that the noroviruses involved were all genogroup II, namely GII.17, GII.Pe-GII.4 Sydney 2012, GII.P2-GII.2 and GII.P16-GII.2. Of note, 30 soldiers had to receive treatment at the military hospital due to severity of symptoms.

CONCLUSION

In this short, two-year surveillance period, a total of four norovirus gastroenteritis outbreaks were detected in the Portuguese Army which caused a considerable morbidity, showing once again the impact of norovirus on Army effectiveness and force readiness.

Key characteristics of foods with an elevated risk for viral enteropathogen contamination

Viral enteropathogens are one of the leading causative agents of foodborne illnesses in both the United States and the European Union. While human noroviruses and hepatitis A virus cause the vast majority of outbreaks and illnesses, there are handful of human enteric viruses that contribute to sporadic outbreaks worldwide including astrovirus, sapovirus, rotavirus, enterovirus and Aichi virus. In addition, hepatitis E virus is increasingly being recognized as an emerging zoonotic threat within the food supply. This review aims to briefly describe the primary human enteric viruses of concern with respect to foodborne transmission. Next, we focus on the contamination and persistence of these viruses within three high-risk food commodities-leafy greens, soft red fruits and bivalve mollusks. As opposed to detailing the specific routes by which these foods can be contaminated with enteric viruses, we have chosen to focus on their persistence and specific interactions within the food itself. Therefore, the processes of attachment and internalization of the viruses in foods have been emphasized. Looking forward, the implications of these specific interactions of human enteric viruses with leafy greens, soft red fruits and bivalve mollusks are briefly considered within the context of future prevention and control strategies.

Epidemiologic and Genotypic Distribution of Noroviruses Among Children With Acute Diarrhea and Healthy Controls in a Low-income Rural Setting

Background

Noroviruses are the most common cause of epidemic and endemic acute gastroenteritis (AGE) worldwide. The burden of norovirus disease in low-income settings is poorly understood.

Methods

We tested stool samples from children less than 5 years of age with diarrhea who were admitted in a rural hospital in Bangladesh from 2010–2012 and from matched, healthy controls from the same catchment area.

Results

Norovirus was detected in 109 (18%) of 613 children with diarrhea and in 30 (15%) of 206 healthy controls. Most (n = 118; 85%) norovirus infections belonged to genogroup II (GII). Of these, GII.4 viruses were identified in 36 (33%) of the cases and in 6 (21%) of the controls. Other major genotypes included GII.3 (13%), GII.6 (11%), and GII.13 (11%) in the cases and GII.6 (17%) and GII.2 (14%) in the controls. The greatest risk of severe norovirus disease (Vesikari score ≥11) was associated with GII.4 infections. GII.4 viruses were the predominant genotype detected during the winter (55%) and rainy season (23%), while GII.3 (19%) and GII.13 (19%) viruses were the most prevalent genotypes during the summer. Vomiting was significantly associated with GII.4 infections, while longer durations of diarrhea were associated with GI.3 infections.

Conclusions

Future studies are needed to understand the high rates of virus shedding in children without AGE symptoms.

Recombinant GII.P16/GII.4 Sydney 2012 Was the Dominant Norovirus Identified in Australia and New Zealand in 2017

For the past two decades, norovirus pandemic variants have emerged every 3–5 years, and dominate until they are replaced by alternate strains. However, this scenario changed in 2016 with the co-circulation of six prevalent viruses, three of which possessed the pandemic GII.4 Sydney 2012 capsid. An increased number of institutional gastroenteritis outbreaks were reported within the Oceania region in mid-2017. This study identified emerging noroviruses circulating in Australia and New Zealand in 2017 to assess the changing dynamics of the virus infection. RT-PCR-based methods, next generation sequencing, and phylogenetic analyses were used to genotype noroviruses from both clinical and wastewater samples. Antigenic changes were observed between the capsid of pandemic Sydney 2012 variant and the two new Sydney recombinant viruses. The combination of these antigenic changes and the acquisition of a new ORF1 through recombination could both facilitate their ongoing persistence in the population. Overall, an increased prevalence of GII.P16/GII.4 Sydney 2012 viruses was observed in 2017, replacing the GII.P16/GII.2 recombinant that dominated in the region at the end of 2016. This shift in strain dominance was also observed in wastewater samples, demonstrating the reliability of wastewater as a molecular surveillance tool.

Performance evaluation of a newly developed molecular assay for the accurate diagnosis of gastroenteritis associated with norovirus of genogroup II

The performance of a newly proposed fully automated cassette-based sample-to-results solution for norovirus (NoV) detection, InGenius Norovirus ELITe MGB®, was evaluated. A total of 120 selected archival stool samples from children hospitalized for acute gastroenteritis were used to compare the results to a reference real-time RT-PCR. The InGenius NoV assay showed optimal diagnostic accuracy (sensitivity, 100%; specificity, 95.7%) and was able to correctly detect the entire wide panel of epidemiologically relevant genotypes tested. These preliminary results suggest that the InGenius NoV assay can be recommended as a valuable method for accurate diagnosis of NoV GII infection in epidemic and sporadic gastroenteritis.

Mechanisms and consequences of positive-strand RNA virus recombination

Genetic recombination in positive-strand RNA viruses is a significant evolutionary mechanism that drives the creation of viral diversity by the formation of novel chimaeric genomes. The process and its consequences, for example the generation of viruses with novel phenotypes, has historically been studied by analysis of the end products. More recently, with an appreciation that there are both replicative and non-replicative mechanisms at work, and with new approaches and techniques to analyse intermediate products, the viral and cellular factors that influence the process are becoming understood. The major influence on replicative recombination is the fidelity of viral polymerase, although RNA structures and sequences may also have an impact. In replicative recombination the viral polymerase is necessary and sufficient, although roles for other viral or cellular proteins may exist. In contrast, non-replicative recombination appears to be mediated solely by cellular components. Despite these insights, the relative importance of replicative and non-replicative mechanisms is not clear. Using single-stranded positive-sense RNA viruses as exemplars, we review the current state of understanding of the processes and consequences of recombination.