Increase of GII.2 norovirus infections during the 2009-2010 season in Osaka City, Japan

Concurrent Circulation of Viral Agents in Pediatric Patients Presenting with Respiratory Illness and Diarrheal Symptoms in Metropolitan Region of São Paulo, Brazil, 2021

Pneumonia and diarrhea are the leading causes of death in children under 5 globally, worsened by viral infections. This study investigates viral agents in children ≤ 3 years with respiratory illness and diarrhea in Metropolitan Region of São Paulo, Brazil, during spring 2021. Twenty paired samples (oropharyngeal swab and feces) were tested using in-house qPCR for HBoV and HAdV, RT-qPCR for RVA, EV, PeV-A, and NoV, and a commercial RT-qPCR kit for SARS-CoV-2, Flu A/B, and RSV. HAstV was detected with conventional nested (RT)-PCR. Positive samples were sequenced for molecular characterization and phylogenetic analysis. Seven viruses were identified: HBoV, NoV, HAdV, PeV-A, EV, RSV, and Flu A. HBoV and NoV were detected in 75% of cases, with co-infection in 65% of patients, indicating their involvement in the gastro-respiratory illness. Genotyping of HBoV (HBoV-1), NoV (GII.4_Sydney[P16], GII.2[P16], and GII.4_Sydney[P31]), EV (Coxsackievirus A6), HAdV (species C, type 6), and PeV-A (genotype 1) showed local virus diversity. Phylogenetic analysis indicated no ongoing community outbreak, with distinct clusters observed. The findings highlight the overlap of respiratory and enteric diseases, revealing local viral diversity and high exposure to enteric viruses. This underscores the challenges in differential diagnosis and the need for syndromic surveillance.

Complete genome sequence of a rare recombinant GII.5[P16] norovirus found in Russian Siberia

Noroviruses (family Caliciviridae) are common causes of acute gastroenteritis worldwide. Multiple polymerase/capsid combinations have been identified among members of norovirus genogroup GII, at least 10 of which contain GII.P16 polymerase. During hospital-based surveillance (2003-2013) in Russia, we identified eight noroviruses with GII.P16 polymerase - five GII.3[P16], two GII.16[P16], and one GII.5[P16]. This is the first report of the nearly complete genome sequence of a rare recombinant GII.5[P.16] norovirus, which was found in the feces of a child in 2010. Phylogenetic analysis revealed that ORF1 and ORF2/3 of the strain GII.5[P.16]/RUS/Novosibirsk/Nsk-N490/2010 formed separate branches in clusters GII.P16 and GII.5, respectively.

Epidemiological Features of Human Norovirus Genotypes before and after COVID-19 Countermeasures in Osaka, Japan

We investigated the molecular epidemiology of human norovirus (HuNoV) in all age groups using samples from April 2019 to March 2023, before and after the COVID-19 countermeasures were implemented. GII.2[P16] and GII.4[P31], the prevalent strains in Japan before COVID-19 countermeasures, remained prevalent during the COVID-19 pandemic, except from April to November 2020; in 2021, the prevalence of GII.2[P16] increased among children. Furthermore, there was an increase in the prevalence of GII.4[P16] after December 2022. Phylogenetic analysis of GII.P31 RdRp showed that some strains detected in 2022 belonged to a different cluster of other strains obtained during the present study period, suggesting that HuNoV strains will evolve differently even if they have the same type of RdRp. An analysis of the amino acid sequence of VP1 showed that some antigenic sites of GII.4[P16] were different from those of GII.4[P31]. The present study showed high infectivity of HuNoV despite the COVID-19 countermeasures and revealed changes in the prevalent genotypes and mutations of each genotype. In the future, we will investigate whether GII.4[P16] becomes more prevalent, providing new insights by comparing the new data with those analyzed in the present study.

Predominance of Recombinant Norovirus Strains in Greece, 2016-2018

GII.4 noroviruses have caused the overwhelming majority of norovirus-related gastroenteritis cases during the past two decades. However, a trend towards the emergence of new genotypes and novel GII.4 variants provided the impetus to explore further the changing patterns in norovirus epidemiology during the present study. Genotyping of 60 norovirus strains detected during a period of 33 months (January 2016-October 2018) was performed on the basis of the capsid VP1-coding ORF2 gene sequence. All norovirus strains detected were classified into seven genotypes, six of which belonged to genogroup GII. GII.2 was the dominant genotype till February 2017, whereas GII.4 prevailed thereafter. Most of the GII.4 strains were of the Sydney_2012 variant, whereas five strains could not be classified. Further recombination analysis at the ORF1/ORF2 gene junction revealed that 23 out of 24 strains were recombinant, thereby showcasing the significant role of genetic recombination in norovirus evolution and epidemiology. Continuous genomic surveillance and molecular characterization are essential for tracking norovirus evolution, which could contribute to the elucidation of new aspects of virus-host interactions that potentially affect host morbidity and epidemiology.

Biological Specimen Banking as a Time Capsule to Explore the Temporal Dynamics of Norovirus Epidemiology

Norovirus is recognised as a major cause of epidemic and sporadic acute gastroenteritis (AGE) in all age groups. Information on the genetic diversity of the noroviruses circulating in the 1980s and 1990s, before the development and adoption of dedicated molecular assays, is limited compared with the last decades. Between 1986 and 2020, uninterrupted viral surveillance was conducted in symptomatic children hospitalized with AGE in Palermo, Italy, providing a unique time capsule for exploring the epidemiological and evolutionary dynamics of enteric viruses. A total of 8433 stool samples were tested using real-time RT-PCR. All samples were stored at -20 or -80 °C until processing. In this 35-year long time span, noroviruses of genogroup II (GII) were detected in 15.6% of AGE requiring hospitalization, whilst GI noroviruses were detected in 1.4% of AGE. Overall, the predominant norovirus capsid (Cap) genotype was GII.4 (60.8%), followed by GII.3 (13.3%) and GII.2 (12.4%). Temporal replacement of the GII.4 Cap variants associated with different polymerase (Pol) types were observed over the study period. The chronology of emergence and circulation of the different GII.4 variants were consistent with data available in the literature. Also, for GII.3 and GII.2 NoVs, the circulation of different lineages/strains, differing in either the Cap or Pol genes or in both, was observed. This long-term study revealed the ability of noroviruses to continuously and rapidly modify their genomic makeup and highlights the importance of surveillance activities in vaccine design.

Changing predominance of norovirus strains in children with acute gastroenteritis in Shanghai, 2018-2021

Norovirus (NoV) is a major pathogen that causes acute gastroenteritis (AGE) in people of all ages, especially in children. In this study, we investigated the molecular epidemiological characteristics of NoV in children with AGE in Shanghai from 2018 to 2021. The overall detection rate of NoV was 11.9% (181/1545), with annual detection rates of 9.4% (36/381), 13.6% (29/213), 5.8% (13/226) and 14.2% (103/725), respectively. Of note, the prevalence of NoV in 2020 was significantly lower than that in 2018-2019 (10.9%, 65/594) (P ​= ​0.023) and 2021 (14.2%, 103/725) (P ​= ​0.000). The 181 NoV strains identified in this study were classified into the GI group (1.1%, 2/181), GII group (98.3%, 178/181) and GIX group (0.6%, 1/181) according to the VP1 gene. The most common NoV VP1 genotype was GII.4 Sydney_2012 (63.5%, 115/181), followed by GII.3 (19.9%, 36/181) and GII.2 (9.4%, 17/181). For P genotypes, 174 strains were sequenced successfully according to the RdRp gene, and the predominant genotype was GII.P16 (44.8%, 78/174), followed by GII.P31 (25.9%, 45/174) and GII.P12 (21.3%, 37/174). Among the 174 cases, GII.4 Sydney_2012[P16] (36.8%, 64/174) was the dominant genotype, followed by GII.4 Sydney_2012[P31] (25.3%, 44/174), GII.3[P12] (20.1%, 35/174) and GII.2[P16] (8.0%, 14/174). In particular, the dominant genotypes in Shanghai changed from GII.4 Sydney_2012[P31] in 2018-2019 to GII.4 Sydney_2012[P16] in 2020-2021. This is the first report to describe the epidemiological changes in NoV infection before and during the COVID-19 pandemic in Shanghai. These data highlight the importance of continuous surveillance for NoV in children with AGE in Shanghai.

Clinical and virological characteristics of viral shedding in children with norovirus gastroenteritis

BACKGROUND

The correlation between the clinical manifestations and fecal viral load of norovirus (NoV) infection remains unknown.

METHODS

We established a SYBR® Green-based real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) method to quantify NoV and then sequenced its genomes from the feces of patients admitted at the Chang Gung Memorial Hospital from 2017 to 2018.

RESULTS

NoV GII.4 Sydney (n = 21, 36.2%) and GII.P16-GII.2 (n = 19, 32.8%), the two predominant genotypes found among 58 isolates, were closely related to the Taiwan variant 2012a cluster in the VP1 region and genotypes of China strain. An increase in viral load could be observed on Day 3 following the onset of NoV infection. The viral load then declined rapidly from days 10-15 but remained high for >1 month in a severe combined immunodeficiency patient. Significantly longer shedding was found in patients with fever (p = 0.03) or infected by the GII.4 Sydney strain (p < 0.01).

CONCLUSION

The qRT-PCR-mediated method proposed in this work could quantify the viral load in patients with NoV infection. Significant viral shedding over a period of 2 weeks in children with acute gastroenteritis and >1 month in an immunodeficient patient was observed. Significantly longer shedding could be correlated with infection by the GII.4 Sydney strain and febrile patients.

Evolutionary Analyses of Emerging GII.2[P16] and GII.4 Sydney [P16] Noroviruses

GII.2[P16] and GII.4 Sydney [P16] are currently the two predominant norovirus genotypes. This study sought to clarify their evolutionary patterns by analyzing the major capsid VP1 and RNA-dependent RNA polymerase (RdRp) genes. Sequence diversities were analyzed at both nucleotide and amino acid levels. Selective pressures were evaluated with the Hyphy package in different models. Phylogenetic trees were constructed by the maximum likelihood method from full VP1 sequences, and evolutionary rates were estimated by the Bayesian Markov Chain Monte Carlo approach. The results showed that (1) several groups of tightly linked mutations between the RdRp and VP1 genes were detected in the GII.2[P16] and GII.4[P16] noroviruses, and most of these mutations were synonymous, which may lead to a better viral fitness to the host; (2) although the pattern of having new GII.4 variants every 2–4 years has been broken, both the pre- and the post-2015 Sydney VP1 had comparable evolutionary rates to previously epidemic GII.4 variants, and half of the major antigenic sites on GII.4 Sydney had residue substitutions and several caused obvious changes in the carbohydrate-binding surface that may potentially alter the property of the virus; and (3) GII.4 Sydney variants during 2018–21 showed geographical specificity in East Asia, South Asia, and North America; the antigenic sites of GII.2 are strictly conserved, but the GII.2 VP1 chronologically evolved into nine different sublineages over time, with sublineage IX being the most prevalent one since 2018. This study suggested that both VP1 and RdRp of the GII.2[P16] and GII.4 Sydney [P16] noroviruses exhibited different evolutionary directions. GII.4[P16] is likely to generate potential novel epidemic variants by accumulating mutations in the P2 domain, similar to previously epidemic GII.4 variants, while GII.2[P16] has conserved predicted antigenicity and may evolve by changing the properties of nonstructural proteins, such as polymerase replicational fidelity and efficiency. This study expands the understanding of the evolutionary dynamics of GII.2[P16] and GII.4[P16] noroviruses and may predict the emergence of new variants.

Epidemiology and evolution of Norovirus in China

Norovirus (NoV) has been recognized as a leading cause of gastroenteritis worldwide. This review estimates the prevalence and genotype distribution of NoV in China to provide a sound reference for vaccine development. Studies were searched up to October 2020 from CNKI database and inclusion criteria were study duration of at least one calendar year and population size of >100. The mean overall NoV prevalence in individuals with sporadic diarrhea/gastroenteritis was 16.68% (20796/124649, 95% CI 16.63-16.72), and the detection rate of NoV was the highest among children. Non-GII.4 strains have replaced GII.4 as the predominant caused multiple outbreaks since 2014. Especially the recombinant GII.P16-GII.2 increased sharply, and virologic data show that the polymerase GII.P16 rather than VP1 triggers pandemic. Due to genetic diversity and rapid evolution, predominant genotypes might change unexpectedly, which has become major obstacle for the development of effective NoV vaccines.

Prevalence and Evolution of Noroviruses between 1966 and 2019, Implications for Vaccine Design

Noroviruses (NoVs), a group of single-stranded RNA viruses causing epidemic acute gastroenteritis in humans, are highly diverse, consisting of multiple genogroups with >30 genotypes. Their continual evolutions make NoV vaccine design and development difficult. Here, we report a study of NoV sequences obtained from a population-based diarrhea surveillance in Zhengding County of Hebei Province spanning from 2001 to 2019 and those available in the GenBank database from 1966 to 2019. NoV genotypes and/or variants that may evade immunity were screened and identified based on primary and conformational structures for vaccine design. We selected 366, 301, 139, 74 and 495 complete VP1-coding nucleotide sequences representing the predominant genotypes of GII.4, GII.2, GII.3, GII.6 and GII.17, respectively. A total of 16 distinct GII.4 variants were identified, showing a typical linear evolutionary pattern of variant replacement, while only 1–4 variants of the other genotypes were found to co-circulate over the 40–50-year period without typical variant replacement. The vaccine strain GII.4c is close to variant Sydney_2012 (0.053) in their primary structure, but they are distinct at epitopes A and E in conformations. Our data suggested GII.4 variant Sydney_2012, GII.2 variant A, a GII.3 strain, GII.6 variants B and C and GII.17 variant D are primary candidate strains for NoV vaccine development.

Recombinant GII.P16 genotype challenges RT-PCR-based typing in region A of norovirus genome

OBJECTIVES

In latest years GII.4[P16] and GII.2[P16] noroviruses have become predominant in some temporal/geographical settings. In parallel with the emergence of the GII.P16 polymerase type, norovirus surveillance activity in Italy experienced increasing difficulties in generating sequence data on the RNA polymerase genomic region A, using the widely adopted JV12A/JV13B primer set. Two sets of modified primers (Deg1 and Deg2) were tested in order to improve amplification and typing of the polymerase gene.

METHODS

Amplification and typing performance of region A primers was assessed in RT-PCR on 452 GII norovirus positive samples obtained from 2194 stool samples collected in 2016-2019 from children hospitalized with acute gastroenteritis.

RESULTS

The use of Deg1 increased the rate of samples types in region A from 49.5% to 81.4% and from 21.9% to 69.7% in 2016 and 2017, respectively. The rate of Deg1 typed samples remained high in 2018 (90.1%), but sharply decreased to 11.8% in 2019. The second primers set, Deg2, was able to increase to 64.9% the rate of 2019 samples typed in region A, while typing efficiently 73.2%, 69%, and 86.4% of samples collected in 2016, 2017 and 2018, respectively.

CONCLUSIONS

The plasticity of norovirus genomes requires continuous updates of the primers used for strain characterization.

Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil

From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GII.6[P7] (14%, 7/50), GII.17[P17] (6%, 3/50), GII.1[P33] (6%, 3/50), GII.3[P16] (4%, 2/50), GII.2[P16] (2%, 1/50), GII.2[P2] (2%, 1/50), and GII.4_New Orleans[P4] (2%, 1/50). Distinct GII.6[P7] variants were recognized, indicating the presence of different co-circulating strains. Elucidating norovirus genetic diversity will improve our understanding of their potential health burden, in particular for the GII.4_Sydney[P31] variant.

Differences in Illness Severity among Circulating Norovirus Genotypes in a Large Pediatric Cohort with Acute Gastroenteritis

Norovirus is a major pathogen identified in children with acute gastroenteritis (AGE), little is known about the strain's diversity and their clinical severity. Stool and/or rectal swabs were collected from children ≤18 years of age recruited at emergency departments (ED), and a provincial nursing advice phone line due to AGE symptoms in the province of Alberta, Canada between December 2014 and August 2018. Specimens were tested using a reverse transcription real time PCR and genotyped by Sanger sequencing. The Modified Vesikari Scale score (MVS) was used to evaluate the disease severity. The objectives are to identify the Genogroup and Genotype distribution and to compare illness severity between the GI and GII genogroups and to complete further analyses comparing the GII genotypes identified. GII.4 was the genotype most commonly identified. Children with GII.4 had higher MVS scores (12.0 (10.0, 14.0; p = 0.002)) and more prolonged diarrheal (5 days (3.0, 7.8)) and vomiting (3.2 days (1.7, 5.3; p < 0.001)) durations compared to other non GII.4 strains. The predominant strain varied by year with GII.4 Sydney[P31] predominant in 2014/15, GII.4 Sydney[P16] in 2015/16 and 2017/18, and GII.3[P12] in 2016/17. Genogroup II norovirus strains predominated in children with AGE with variance between years; clinical severity associated with different strains varied with episodes being most severe among GII.4 infected children.

Bile Facilitates Human Norovirus Interactions with Diverse Histoblood Group Antigens, Compensating for Capsid Microvariation Observed in 2016-2017 GII.2 Strains

Human norovirus (HuNoV) is the leading cause of global infectious acute gastroenteritis, causing ~20% of reported diarrheal episodes. Typically, GII.4 strains cause 50-70% of yearly outbreaks, and pandemic waves of disease approximately every 2-7 years due to rapid evolution. Importantly, GII.4 dominance is occasionally challenged by the sudden emergence of other GII strains, most recently by GII.2 strains which peaked in 2016-2017, dramatically increasing from 1% to 20% of total HuNoV outbreaks. To determine if viral capsid evolution may account for the sudden rise in GII.2 outbreaks, Virus Like Particles (VLPs) of two 2016-2017 GII.2 strains were compared by antigenic and histo blood group antigen (HBGA) binding profiles to the prototypic 1976 GII.2 Snow Mountain Virus (SMV) strain. Despite >50 years of GII.2 strain persistence in human populations, limited sequence diversity and antigenic differences were identified between strains. However, capsid microvariation did affect HBGA binding patterns, with contemporary strains demonstrating decreased avidity for type A saliva. Furthermore, bile salts increased GII.2 VLP avidity for HBGAs, but did not alter antigenicity. These data indicate that large changes in antigenicity or receptor binding are unlikely to explain GII.2 emergence, in contrast to the pandemic GII.4 strains, and indicate that host factors such as waning or remodeling of serum or mucosal immunity likely contributed to the surge in GII.2 prevalence.

Characterization of the complete genome sequence of the recombinant norovirus GII.P16/GII.4_Sydney_2012 revealed in Russia

Noroviruses (the Caliciviridae family) are a common cause of acute gastroenteritis in all age groups. These small non-envelope viruses with a single-stranded (+)RNA genome are characterized by high genetic variability. Continuous changes in the genetic diversity of co-circulating noroviruses and the emergence of new recombinant variants are observed worldwide. Recently, new recombinant noroviruses with a novel GII.P16 polymerase associated with different capsid proteins VP1 were reported. As a part of the surveillance study of sporadic cases of acute gastroenteritis in Novosibirsk, a total of 46 clinical samples from children with diarrhea were screened in 2016. Norovirus was detected in six samples from hospitalized children by RT-PCR. The identified noroviruses were classified as recombinant variants GII.P21/GII.3, GII. Pe/GII.4_Sydney_2012, and GII.P16/GII.4_Sydney_2012 by sequencing of the ORF1/ORF2 junction. In Novosibirsk, the first appearance of the new recombinant genotype GII.P16/ GII.4_Sydney_2012 was recorded in spring 2016. Before this study, only four complete genome sequences of the Russian GII.P16/GII.3 norovirus strains were available in the GenBank database. In this work, the complete genome sequence of the Russian strain Hu/GII.P16-GII.4/RUS/Novosibirsk/NS16-C38/2016 (GenBank KY210980) was determined. A comparison of the nucleotide and the deduced amino acid sequences showed a high homology of the Russian strain with GII.P16/GII.4_Sydney_2012 strains from other parts of the world. A comparative analysis showed that several unique substitutions occurred in the GII.P16 polymerase, N-terminal p48 protein, and minor capsid protein VP2 genes, while no unique changes in the capsid VP1 gene were observed. A functional significance of these changes suggests that a wide distribution of the strains with the novel GII.P16 polymerase may be associated both with several amino acid substitutions in the polymerase active center and with the insertion of glutamic acid or glycine in an N-terminal p48 protein that blocks the secretory immunity of intestinal epithelial cells. Further monitoring of genotypes will allow determining the distribution of norovirus recombinants with the polymerase GII.P16 in Russia.

GII.17 norovirus infections in outbreaks of acute nonbacterial gastroenteritis in Osaka City, Japan during two decades

Norovirus (NoV) is a major cause of viral gastroenteritis, and GII.4 has been the predominant genotype worldwide since the mid-1990s. During the 2014 to 2015 winter, a rare genotype, NoV GII.17, emerged and became prevalent mainly in East Asia. Over the past two decades, NoV molecular surveillance in Osaka City, Japan, has revealed that NoV GII.17 was detected for the first time in February 2001 and that NoV GII.17-associated outbreaks remarkably increased during the 2014 to 2015 season, with higher incidence recorded in January to March 2015. Genetic analysis indicated that 28 GII.17 outbreak strains were closely related to the novel GII.P17-GII.17 variants represented by the Kawasaki308/2015/JP strain, similar to that in other regions. Statistical analysis showed that NoV GII.17 infections were more common in adults than GII.3 and GII.4 infections, suggesting that the affected adults most likely did not have antibodies against NoV GII.17 and the novel GII.17 variant had recently appeared. Regarding transmission, food was one of the most important factors involved in the spread of NoV GII.17 among adults; 61% of GII.17 outbreaks were foodborne, with oysters being the most common vehicle. Interplay between pathogens, hosts, and environmental factors was considered to be important in the 2014 to 2015 NoV GII.17 epidemic.

Specific Interactions between Human Norovirus and Environmental Matrices: Effects on the Virus Ecology

Human norovirus is the major cause of non-bacterial epidemic gastroenteritis. Human norovirus binds to environmental solids via specific and non-specific interactions, and several specific receptors for human norovirus have been reported. Among them, histo-blood group antigens (HBGA) are the most studied specific receptor. Studies have identified the presence of HBGA-like substances in the extracellular polymeric substances (EPS) and lipopolysaccharides (LPS) of human enteric bacteria present in aquatic environments, gastrointestinal cells, gills, and palps of shellfish, and cell walls, leaves, and veins of lettuce. These HBGA-like substances also interact with human norovirus in a genotype-dependent manner. Specific interactions between human norovirus and environmental matrices can affect norovirus removal, infectivity, inactivation, persistence, and circulation. This review summarizes the current knowledge and future directions related to the specific interactions between human norovirus and HBGA-like substances in environmental matrices and their possible effects on the fate and circulation of human norovirus.

Genome characterization and temporal evolution analysis of a non-epidemic norovirus variant GII.8

Noroviruses are the primary cause of non-bacterial acute gastroenteritis worldwide, and GII.8 belongs to a non-epidemic genotype with a limited understanding currently. In this study, we assembled the first GII.8 norovirus genome from China and clarified the temporal evolutionary process of this non-epidemic variant. Using the "4+1+1" application strategy with newly designed primer sets, the genome of one GII.8 strain GZ2017-L601 from China was firstly sequenced that comprised 7476 nucleotides. The homology of the new genome and the previous only GII.8 genome reached 93.8% identity at the nucleotide level, but only 10, 6, 7 amino acid mutations occurred in three ORFs. When compared the new strain with other GII reference strains, p22 and P2 were calculated as the variable encoding regions, and NTPase, VPg, 3CL, RdRp and S were shown as the conserved ones. We then reconstructed the evolutionary process of the GII.8 genotype using other available sequences in GenBank. Based on the partial N/C region, all GII.8 strains could be subdivided chronologically into four clusters, which spans 1967-1994, 1997-2005, 2003-2009, and 2007-2017, respectively. Moreover, differences of capsid P proteins between GII.8 strains and the epidemic GII.4 strain VA387 were also compared. There existed 147/310 distinct amino acid sites in the alignment, including two insertion and three deletion mutations. Distribution of antigen epitopes of two GII.8 variants was comparable, but the numbers of antigenic sites of GII.8 strains were less than that of VA387. In summary, the first GII.8 genome from China was assembled and extensively characterized, and a time-order evolutionary process of this genotype was identified with a static pattern of antigenic variations.

Should we pay attention to recombinant norovirus strain GII.P7/GII.6?

BACKGROUND

Recombinant norovirus strain GII.P7/GII.6 has been circulating in Asia and around the world for at least 20 years, but has been responsible for relatively few outbreaks.

METHODS

We used statistical analyses, real-time reverse transcription - PCR, and genome sequence analyses to investigate an outbreak of gastroenteritis, identifying the pathogen, the risk factors associated with the outbreak, and the molecular features of GII.P7/GII.6 strains.

RESULTS

An outbreak of gastroenteritis was reported at a school involving 12 students and lasting 6 days, from September 13 to September 18, 2017. Epidemiological studies suggested that norovirus was transmitted from person to person and not via contaminated food or drinking water in this outbreak. Using a sequence analysis of the junction region between open reading frames 1 and 2, the pathogen was identified as a recombinant norovirus (strain GII.P7/GII.6). The full-length genome of the outbreak strain shared 86%-97% identity with those of other GII.P7/GII.6 strains. Phylogenetic trees were constructed from partial open reading frame 1 (ORF1) and ORF2 sequences from the outbreak strain and GII.P7/GII.6 norovirus sequences available in GenBank. On the ORF1 tree, the partial sequences of ORF1 were grouped into cluster A (with GII.6), cluster B (with GII.7), and a separate cluster (C), based on the GII.6 and GII.7 reference strains. The ORF2 tree showed all GII.P7/GII.6 strains formed a cluster together with GII.6 strains. Amino-acid substitutions and insertions/deletions were common in the capsid protein, especially in it's P2 and P1 domains. The outbreak was controlled within several days using appropriate measures.

CONCLUSIONS

Because it may play a prominent role in future outbreaks, recombinant norovirus strain GII.P7/GII.6 should be monitored with routine surveillance.

Emergence of norovirus GII.P16-GII.2 strains in patients with acute gastroenteritis in Huzhou, China, 2016-2017

Background

In late 2016, an uncommon recombinant NoV genotype called GII.P16-GII.2 caused a sharp increase in outbreaks of acute gastroenteritis in different countries of Asia and Europe, including China. However, we did not observe a drastic increase in sporadic norovirus cases in the winter of 2016 in Huzhou. Therefore, we investigate the prevalence and genetic diversity of NoVs in the sporadic acute gastroenteritis (AGE) cases from January 2016 to December 2017 in Huzhou City, Zhejiang, China.

Methods

From January 2016 to December 2017, a total of 1001 specimens collected from patients with AGE were screened for NoV by real-time RT-PCR. Partial sequences of the RNA-dependent RNA polymerase (RdRp) and capsid gene of the positive samples were amplified by RT-PCR and sequenced. Genotypes of NoV were confirmed by online NoV typing tool and phylogenetic analysis. Complete VP1 sequences of GII.P16-GII.2 strains detected in this study were further obtained and subjected into sequence analysis.

Results

In total, 204 (20.4%) specimens were identified as NoV-positive. GII genogroup accounted for most of the NoV-infected cases (98.0%, 200/204). NoV infection was found in all age groups tested (< 5, 5–15, 16–20, 21–30, 31–40, 41–50, 51–60, and >60 years), with the 5–15 year age group having the highest detection rate (17/49, 34.7%). Higher activity of NoV infection could be seen in winter-spring season. The predominant NoV genotypes have changed from GII.Pe-GII.4 Sydney2012 and GII.P17-GII.17 in 2016 to GII.P16-GII.2, GII.Pe-GII.4 Sydney2012 and GII.P17-GII.17 in 2017. Phylogenetic analyses revealed that 2016–2017 GII.P16-GII.2 strains were most closely related to Japan 2010–2012 cluster in VP1 region and no common mutations were found in the amino acids of the HBGA-binding sites and the predicted epitopes.

Conclusions

We report the emergence of GII.P16-GII.2 strains and characterize the molecular epidemiological patterns NoV infection between January 2016 and December 2017 in Huzhou. The predominant genotypes of NoV during our study period are diverse. VP1 amino acid sequences of 2016–2017 GII.P16-GII.2 strains remain static after one year of circulation.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3259-6) contains supplementary material, which is available to authorized users.

Waterborne Norovirus outbreak at a seaside resort likely originating from municipal water distribution system failure

In May 2016 a Norovirus (NoV) gastroenteritis outbreak involved a high school class visiting a seaside resort near Taormina (Mascali, Sicily). Twenty-four students and a teacher were affected and 17 of them showed symptoms on the second day of the journey, while the others got ill within the following 2 days. Symptoms included vomiting, diarrhoea and fever, and 12 students required hospitalisation. Stool samples tested positive for NoV genome by Real-Time polymerase chain reaction assay in all 25 symptomatic subjects. The GII.P2/GII.2 NoV genotype was linked to the outbreak by ORF1/ORF2 sequence analysis. The epidemiological features of the outbreak were consistent with food/waterborne followed by person-to-person and/or vomit transmission. Food consumed at a shared lunch on the first day of the trip was associated to illness and drinking un-bottled tap water was also considered as a risk factor. The analysis of water samples revealed the presence of bacterial indicators of faecal contamination in the water used in the resort as well as in other areas of the municipal water network, linking the NoV gastroenteritis outbreak to tap water pollution from sewage leakage. From a single water sample, an amplicon whose sequence corresponded to the capsid genotype recovered from patients could be obtained.

Temporal evolutionary analysis of re-emerging recombinant GII.P16_GII.2 norovirus with acute gastroenteritis in patients from Hubei Province of China, 2017

Norovirus (NoV) is a major pathogenic agent of human acute viral gastroenteritis that occurs worldwide. In March 2017, a series of acute NoV-associated gastroenteritis outbreaks occurred in Hubei Province in central China. Here, we sought to better understand the main genotypes and potential evolutionary advantages of circulating NoV strains underlying these outbreaks. During the outbreak, 111 fecal swabs and stool samples were collected from outpatients with acute NoV-associated gastroenteritis in Hubei Province. RNA was extracted from the samples and used as a template for real-time RT-PCR. Sequencing of a portion of the capsid gene and the ORF1/ORF2 overlap was used to assess DNA sequence homology, phylogeny, and recombination using pairwise alignments, MEGA, and Simplot, respectively. Bayesian evolutionary inference analysis was performed using the BEAST software platform to assess the genetic relationships, evolution rate, and evolutionary history of norovirus. GII NoV was determined to be the major pathogen of the acute gastroenteritis outbreaks in Hubei Province, with a 57.7% positive rate. Homology and phylogenic analysis of a portion of the capsid region for GII NoV isolates collected during outbreaks in Hubei showed that the isolates had a very high sequence identity and belonged to GII.2 genotype. Phylogenetic analysis of recombination using the ORF1/ORF2 overlap region revealed a recombinant strain, GII.P16_GII.2, in samples isolated from Hubei Province. The partial polymerase region and capsid gene of the recombinant strain had very high identity (98.7-98.8%) with the NoV strains isolated in Germany in 2016. The evolutionary rate of VP1 gene of GII.2 was distinctly higher than that of the partial polymerase region of GII.16. A phylogenetic tree generated using MCMC showed that the recombinant NoV GII.16_GII.2 was significantly divergent from other GII.16_GII.2 strains observed in China and Japan. Continued circulation of this GII.16_GII.2 recombinant could overtake the predominant GII.4 NoV strain with geographic expansion. Further analysis of the evolutionary dynamics of norovirus is necessary to develop more effective prevention and control strategies.

Outbreaks of acute gastroenteritis associated with a re-emerging GII.P16-GII.2 norovirus in the spring of 2017 in Jiangsu, China

A total of 64 acute gastroenteritis outbreaks with 2,953 patients starting in December of 2016 and occurring mostly in the late spring of 2017 were reported in Jiangsu, China. A recombinant GII.P16-GII.2 norovirus variant was associated with 47 outbreaks (73.4%) for the gastroenteritis epidemic, predominantly occurring in February and March of 2017. Sequence analysis of the RNA-dependent RNA polymerase (RdRp) and capsid protein of the viral isolates from these outbreaks confirmed that this GII.P16-GII.2 strain was the GII.P16-GII.2 variant with the intergenotypic recombination, identified in Taiwan, Hong Kong, and other cities in China in 2016. This GII.P16-GII.2 recombinant variant appeared to a re-emerging strain, firstly identified in 2011-2012 from Japan and USA but might be independently originated from other GII.P16-GII.2 variants for sporadic and outbreaks of gastroenteritis in Japan and China before 2016. Further identification of unique amino acid mutations in both VP1 and RdRp of NoV strain as shown in this report may provide insight in explaining its structural and antigenic changes, potentially critical for the variant recombinant to gain its predominance in causing regional and worldwide epidemics.

Detection and molecular characterization of the novel recombinant norovirus GII.P16-GII.4 Sydney in southeastern Brazil in 2016

Noroviruses are the leading cause of acute gastroenteritis (AGE) in all age groups worldwide. Despite the high genetic diversity of noroviruses, most AGE outbreaks are caused by a single norovirus genotype: GII.4. Since 1995, several different variants of norovirus GII.4 have been associated with pandemics, with each variant circulating for 3 to 8 years. The Sydney_2012 variant was first reported in Australia and then in other countries. A new variant, GII.P16-GII.4, was recently described in Japan and South Korea and then in the USA, France, Germany and England. In our study, 190 faecal specimens were collected from children admitted to a paediatric hospital and a public health facility during a surveillance study of sporadic cases of AGE conducted between January 2015 and July 2016. The norovirus was detected by RT-qPCR in 51 samples (26.8%), and in 37 of them (72.5%), the ORF1-2 junction was successfully sequenced. The new recombinant GII.P16-GII.4 Sydney was revealed for the first time in Brazil in 2016 and predominated among other strains (9 GII.Pe-GII.4, 3 GII.P17-GII.17, 1 GII.Pg-GII.1, 1 GII.P16-GII.3 and 1 GII.PNA-GII.4). The epidemiological significance of this new recombinant is still unknown, but continuous surveillance studies may evaluate its impact on the population, its potential to replace the first recombinant GII.Pe-GII.4 Sydney 2012 variant, and the emergence of new recombinant forms of GII.P16.

Recombinant GII.P16-GII.2 Norovirus, Taiwan, 2016

In Taiwan, acute gastroenteritis outbreaks caused by a new norovirus genotype GII.2 increased sharply toward the end of 2016. Unlike previous outbreaks, which often involved restaurants, GII.2 outbreaks mainly occurred in schools. Phylogenetic analysis indicates that these noroviruses are recombinant GII.P16-GII.2 strains.

Phylogenetic Analyses Suggest that Factors Other Than the Capsid Protein Play a Role in the Epidemic Potential of GII.2 Norovirus

Norovirus is the leading cause of acute gastroenteritis worldwide. For over two decades, a single genotype (GII.4) has been responsible for most norovirus-associated cases. However, during the winter of 2014 to 2015, the GII.4 strains were displaced by a rarely detected genotype (GII.17) in several countries of the Asian continent. Moreover, during the winter of 2016 to 2017, the GII.2 strain reemerged as predominant in different countries worldwide. This reemerging GII.2 strain is a recombinant virus that presents a GII.P16 polymerase genotype. In this study, we investigated the evolutionary dynamics of GII.2 to determine the mechanism of this sudden emergence in the human population. The phylogenetic analyses indicated strong linear evolution of the VP1-encoding sequence, albeit with minor changes in the amino acid sequence over time. Without major genetic differences among the strains, a clustering based on the polymerase genotype was observed in the tree. This association did not affect the substitution rate of the VP1. Phylogenetic analyses of the polymerase region showed that reemerging GII.P16-GII.2 strains diverged into a new cluster, with a small number of amino acid substitutions detected on the surface of the associated polymerase. Thus, besides recombination or antigenic shift, point mutations in nonstructural proteins could also lead to novel properties with epidemic potential in different norovirus genotypes. IMPORTANCE Noroviruses are a major cause of gastroenteritis worldwide. Currently, there is no vaccine or specific antiviral available to treat norovirus disease. Multiple norovirus strains infect humans, but a single genotype (GII.4) has been regarded as the most important cause of viral gastroenteritis outbreaks worldwide. Its persistence and predominance have been explained by the continuous replacement of variants that present new antigenic properties on their capsid protein, thus evading the herd immunity acquired to the previous variants. Over the last three seasons, minor genotypes have displaced the GII.4 viruses as the predominant strains. One of these genotypes, GII.2, reemerged as predominant during 2016 to 2017. Here we show that factors such as minor changes in the polymerase may have driven the reemergence of GII.2 during the last season. A better understanding of norovirus diversity is important for the development of effective treatments against noroviruses.

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

Noroviruses are the most frequent cause of epidemic acute gastroenteritis in the United States. Between September 2013 and August 2016, 2,715 genotyped norovirus outbreaks were submitted to CaliciNet. GII.4 Sydney viruses caused 58% of the outbreaks during these years. A GII.4 Sydney virus with a novel GII.P16 polymerase emerged in November 2015, causing 60% of all GII.4 outbreaks in the 2015-2016 season. Several genotypes detected were associated with more than one polymerase type, including GI.3, GII.2, GII.3, GII.4 Sydney, GII.13, and GII.17, four of which harbored GII.P16 polymerases. GII.P16 polymerase sequences associated with GII.2 and GII.4 Sydney viruses were nearly identical, suggesting common ancestry. Other common genotypes, each causing 5 to 17% of outbreaks in a season, included GI.3, GI.5, GII.2, GII.3, GII.6, GII.13, and GII.17 Kawasaki 308. Acquisition of alternative RNA polymerases by recombination is an important mechanism for norovirus evolution and a phenomenon that was shown to occur more frequently than previously recognized in the United States. Continued molecular surveillance of noroviruses, including typing of both polymerase and capsid genes, is important for monitoring emerging strains in our continued efforts to reduce the overall burden of norovirus disease.

Molecular characterization of new emerging GII.17 norovirus strains from South China

Noroviruses are still the primary cause of non-bacterial acute gastroenteritis worldwide. Recently, a novel GII.17 norovirus variant emerged and caused an infection peak in the cold season of 2014/2015 in some Asian countries, including China. In this study, in order to understand the evolutionary advantage of the novel variant, complete genomic sequences of GII.17 NoV strains from South China were comprehensively analyzed. Pairwise alignments of new GII.17 genomes with representative sequences of each GII genotype were performed. Inconsistent homology was observed between different protein-encoding regions, of which VPg (NS5) and P2 were found to be the most conserved and variable ones, respectively. The differences between new sequences and other reported GII.17 genomes were also compared, and 84 mismatched nucleotides were found, resulting in 15 amino acid changes. Then, all capsid sequences of different GII.17 NoV variants were collected for multiple alignments, and a total of 87 spots were identified during their evolution process. Homology modeling of capsid proteins of four GII.17 variants was carried out based on comparison with GII.4 VA387 strain, and structural differences were mainly embodied in five extended loops. Furthermore, positions of potential conformational epitope regions of new GII.17 variants were found more similar or adjacent to those of GII.4 rather than those of the former GII.17 variants. In summary, nine GII.17 strains from South China were extensively characterized based on their complete genomes, and a different distribution pattern of epitope residues was predicted on the new GII.17 variant capsid from that of the former ones.

Epidemics of GI.2 sapovirus in gastroenteritis outbreaks during 2012-2013 in Osaka City, Japan

Sapovirus (SaV) is a causative agent of gastroenteritis in humans in both sporadic cases and outbreaks. During the period from January 2005 to August 2014, SaV was detected in 30 (5.9%) of 510 gastroenteritis outbreaks in Osaka City, Japan using real-time RT-PCR. Seasonal distribution of SaV-associated outbreaks revealed an increase during the 2011-2012 season and the highest frequency of outbreaks during the 2012-2013 season. Genotyping analysis based on the capsid region demonstrated that the most common genotype was GI.2 (36.7%), in which the strains were closely related. The comparison of complete capsid gene sequences with 18 GI.2 strains (7 strains in this study and 11 from GenBank) between 1990 and 2013 showed that GI.2 strains were classified into at least three genetic clusters (1990-2000, 2004-2007, and 2008-2013) with chronologically unique amino acid residues and accumulation of mutations in the predicted P domain, suggesting the one of the causes of emergence and spread of GI.2 strains. This study will also be helpful for understanding the evolutionary mechanism of the SaV genome.

Epidemiology of gastroenteritis viruses in Japan: Prevalence, seasonality, and outbreak

Acute gastroenteritis has been recognized as one of the most common diseases in humans and continues to be a major public health problem worldwide. Several groups of viruses have been reported as the causative agents of acute gastroenteritis, including rotavirus, norovirus, sapovirus, human astrovirus, adenovirus, and an increasing number of others which have been reported more recently. The epidemiology, prevalence, seasonality, and outbreaks of these viruses have been reviewed in a number of studies conducted in Japan over three decades. Rotavirus and norovirus were the two most common viruses detected almost equally in children under 5 years of age who were suffering from acute gastroenteritis. Like many other countries, the main rotavirus strains circulating in pediatric patients in Japan are G1P[8], G2P[4], G3P[8], and G9P[8]. Norovirus GII.4 was involved in most outbreaks in Japan and found to be associated with the emergence of new variants Sydney_2012. The classic human astrovirus, MLB, and VA clades astroviruses were also commonly found in pediatric patients with acute diarrhea. The sapovirus and adenovirus have been identified as the minor viral causative agents for acute gastroenteritis in Japan.

Norovirus genotype diversity in community-based sporadic gastroenteritis incidents: a five-year study

Although norovirus is a known cause of sporadic gastroenteritis, the incidence and genotypes of norovirus associated with sporadic community-based gastroenteritis are poorly understood. The current study examined this issue by using material from alleged food poisoning incidents in the state of Victoria, Australia, for the period 2008-2012. Norovirus was identified, by either ORF (open reading frame) 1 or ORF 2 RT-PCR methodology, in 159 of 379 (42.0%) sporadic gastroenteritis incidents, thereby showing that norovirus was an important cause of sporadic gastroenteritis. The number of sporadic norovirus incidents did not vary significantly from year to year, indicating that the pool of circulating norovirus remained constant. Norovirus ORF 1 genotypes identified included GI.1, GI.2, GI.3, GI.4, GI.b, GI.d, GII.2, GII.4 (including variants 2006a, 2006b, 2007, and 2009), GII.16, GII.22, GII.b, GII.e, and GII.g. Norovirus ORF 2 genotypes identified included GI.1, GI.2, GI.3, GI.4, GI.6, GII.2, GII.3, GII.4 (variants 2006b, 2009, 2009-like, 2012, and "unknown"), GII.6, GII.7, GII.9, GII.12, and GII.13. Five ORF 1/ORF 2 norovirus recombinant forms were confirmed: GII.b/GII.3, GII.e/GII.4 (2012), GII.e/GII.4 (unknown), GII.g/GII.12 and GII.16/GII.2. Although the incidence of ORF 2 GI.3 was significantly higher in children than in adults, this was not the case for other major ORF 2 genotypes (GII.2, GII.4, and GII.6) which occurred equally in all age groups. The findings demonstrate the importance and diverse nature of norovirus in sporadic community-based gastroenteritis incidents and indicate that the development of successful vaccine strategies may be difficult.

Genome characterization of a GII.6 norovirus strain identified in China

Noroviruses (NoVs) are the primary cause of non-bacterial acute gastroenteritis worldwide. Most NoV infections are caused by GII.4, but GII.6 is also an important genotype with a long-term persistence in human populations. In this study, the complete genome sequence of a NoV strain GZ2010-L96 isolated in China was identified and analyzed phylogenetically. The viral genome comprised 7550 nucleotides, and its phylogenetic analysis revealed that the strain belonged to GII.6 genotype. All reported GII.6 NoV capsid protein sequences were also collected for comparative analysis, and GZ2010-L96 was clustered into GII.6-b with other 8 strains. Meanwhile, it was found that 53 spots on viral capsid showed subcluster specificity according to multiple alignments. Moreover, homologous modeling of GZ2010-L96 based on comparison with GII.4 VA387 strain showed a different antigen distribution pattern. In summary, the genome of the GII.6 strain GZ2010-L96 detected in China was extensively characterized, and phylogenetic analyses of GII.6 NoVs based on the capsid proteins may reveal a different evolution process from the predominant genotype GII.4.

Evolutionary phylodynamics of Korean noroviruses reveals a novel GII.2/GII.10 recombination event

Viral gastroenteritis is the most common causal agent of public health problems worldwide. Noroviruses cause nonbacterial acute gastroenteritis in humans of all ages. In this study, we investigated the occurrence of norovirus infection in children with acute gastroenteritis admitted to university hospitals in South Korea. We also analyzed the genetic diversity of the viruses and identified novel recombination events among the identified viral strains. Of 502 children with acute gastroenteritis admitted to our three hospitals between January 2011 and March 2012, genotyping of human noroviruses was performed in 171 (34%) norovirus-positive samples. Of these samples, 170 (99.5%) were in genogroup II (GII), while only one (0.5%) was in genogroup I (GI). The most common GII strain was the GII.4-2006b variant (n = 96, 56.5%), followed by GII.6 (n = 23, 13.5%), GII.12 (n = 22, 12.9%), GII.3 (n = 20, 11.8%), GII.2 (n = 6, 3.5%), GII.b (n = 2, 1.2%), and GII.10 (n = 1, 0.6%). Potential recombination events (polymerase/capsid) were detected in 39 GII strains (22.9%), and the most frequent genotypes were GII.4/GII.12 (n = 12, 30.8%), GII.4/GII.6 (n = 12, 30.8%), GII.4/GII.3 (n = 8, 20.5%), GII.b/GII.3 (n = 3, 7.7%), GII.16/GII.2 (n = 2, 5.1%), GII.4/GII.2 (n = 1, 2.6%), and GII.2/GII.10 (n = 1, 2.6%). For the first time, a novel GII.2/GII.10 recombination was detected; we also identified the GII.16/GII.2 strain for the first time in South Korea. Our data provided important insights into new recombination events, which may prove valuable for predicting the emergence of circulating norovirus strains with global epidemic potential.

Genetic susceptibility to norovirus GII.3 and GII.4 infections in Chinese pediatric diarrheal disease

BACKGROUND

Noroviruses (NoVs) are a leading cause of viral diarrhea in young children. Secretor status has been confirmed to be linked with Norwalk virus (NoV GI.1) infection but there is limited information about whether secretor genotypes are associated with pediatric NoV epidemic strains in vivo.

METHODS

In this study, fecal specimens and serum samples were collected from 124 hospitalized children with acute diarrhea in Xi'an, China. TaqMan real-time reverse transcription polymerase chain reaction was used to detect NoVs in fecal samples, and NoV-positive samples were further verified using conventional reverse transcription polymerase chain reaction and sequenced. DNA was extracted from sera and TaqMan single-nucleotide polymorphism genotyping assay was applied to determine the FUT2 A385T polymorphism.

RESULTS

Only NoV GII.3 and GII.4 genotypes were found in NoV-positive samples, and NoVs were detected in 25% (15/60), 40.5% (17/42) and 9.1% (2/22) of children with homozygous secretor genotype (Se 385 Se 385), heterozygous secretor genotype (Se 385 se 385) and homozygous weak secretor genotype (se 385 se 385), respectively. Children with secretor genotypes Se 385 Se 385 and Se 385 se 385 were significantly (P < 0.05) more susceptible to combined NoV GII.3 and GII.4 infections than children with weak secretor genotype se 385 se 385.

CONCLUSIONS

These findings indicate that secretor positivity is significantly associated with GII.3 and GII.4 infections in Chinese pediatric diarrheal disease and the weak secretor phenotype does not completely protect children from GII.3 and GII.4 infections.

Novel norovirus recombinants detected in South Africa

Background

Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and diversity was investigated in South Africa (SA).

Results

Between 2010 and 2013, eleven types of NoV recombinants were identified in SA. Amplification of the polymerase/capsid region spanning the ORF1/2 junction and phylogenetic analysis confirmed each of the recombinant types. SimPlot and maximum x² analysis indicated that all recombinants had a breakpoint in the region of the ORF1/2 junction (P < 0.05). The majority (9/11) were intergenotype recombinants, but two intragenotype GII.4 recombinants were characterised. Three combinations represent novel recombinants namely GII.P not assigned (NA)/GII.3, GII.P4 New Orleans 2009/GII.4 NA and GII.P16/GII.17. Several widely reported recombinants were identified and included GII.P21/GII.2, GII.P21/GII.3, GII.Pe/GII.4 Sydney 2012, and GII.Pg/GII.12. Other recombinants that were identified were GII.Pg/GII.1, GII.Pe/GII.4 Osaka 2007, GII.P4 New Orleans 2009/GII.4 Sydney 2012, GII.P7/GII.6. To date these recombinant types all have a reportedly restricted geographic distribution. This is the first report of the GII.P4 New Orleans 2009/GII.4 Sydney 2012 recombinant in Africa.

Conclusions

Over the past four years, remarkably diverse NoV recombinants have been circulating in SA. Pandemic strains such as the GII.Pe/GII.4 Sydney 2012 recombinant co-circulated with novel and emerging recombinant strains. Combined polymerase- and capsid-based NoV genotyping is essential to determine the true diversity and global prevalence of these viruses.

Pediatric norovirus infection

Noroviruses (NoVs) are among the most frequent causes of acute pediatric gastroenteritis. Although the disease is often self-limiting and recovery is the rule, it constitutes an important health problem because of its highly contagious nature and the high rate of morbidity. NoVs are responsible for 47-96 % of outbreaks of acute pediatric gastroenteritis, and 5-36 % of sporadic cases. NoV-induced gastroenteritis is a frequent cause of hospitalization, and severe and sometimes fatal cases have been reported in immunocompromised children. The increasing recognition of NoVs as the cause of pediatric disease and the limited success in preventing outbreaks have led to consideration of vaccines. However, while awaiting the development of a vaccine, there is an urgent need for more epidemiological data concerning childhood NoV infection, including the impact of NoVs on different age groups, the possible etiological role of NoVs in infections other than gastroenteritis, and the socioeconomic impact of NoVs on households.

Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009 to 2013

Noroviruses are the leading cause of epidemic acute gastroenteritis in the United States. From September 2009 through August 2013, 3,960 norovirus outbreaks were reported to CaliciNet. Of the 2,895 outbreaks with a known transmission route, person-to-person and food-borne transmissions were reported for 2,425 (83.7%) and 465 (16.1%) of the outbreaks, respectively. A total of 2,475 outbreaks (62.5%) occurred in long-term care facilities (LTCF), 389 (9.8%) in restaurants, and 227 (5.7%) in schools. A total of 435 outbreaks (11%) were typed as genogroup I (GI) and 3,525 (89%) as GII noroviruses. GII.4 viruses caused 2,853 (72%) of all outbreaks, of which 94% typed as either GII.4 New Orleans or GII.4 Sydney. In addition, three non-GII.4 viruses, i.e., GII.12, GII.1, and GI.6, caused 528 (13%) of all outbreaks. Several non-GII.4 genotypes (GI.3, GI.6, GI.7, GII.3, GII.6, and GII.12) were significantly more associated with food-borne transmission (odds ratio, 1.9 to 7.1; P < 0.05). Patients in LTCF and people ≥65 years of age were at higher risk for GII.4 infections than those in other settings and with other genotypes (P < 0.05). Phylogeographic analysis identified three major dispersions from two geographic locations that were responsible for the GI.6 outbreaks from 2011 to 2013. In conclusion, our data demonstrate the cyclic emergence of new (non-GII.4) norovirus strains, and several genotypes are more often associated with food-borne outbreaks. These surveillance data can be used to improve viral food-borne surveillance and to help guide studies to develop and evaluate targeted prevention methods such as norovirus vaccines, antivirals, and environmental decontamination methods.

Novel intergenotype human norovirus recombinant GII.16/GII.3 in Bangladesh

Noroviruses (NoVs) are one of the major etiological agents of acute gastroenteritis in all age groups. In this study, we identified an intergenotype NoV recombinant strain in the fecal specimens of two male infants with acute diarrhea in Bangladesh. Phylogenetic analysis showed that the identified strains were recombinant NoV strains with a GII.3 capsid and a GII.16 polymerase gene. The recombination breakpoint was located in the ORF1/ORF2 overlap region. To the best of our knowledge this is the first report of a NoV recombinant GII.16/GII.3 strain worldwide.

Genetic analysis and homology modeling of capsid protein of norovirus GII.14

In this study, a more detailed genetic characterization of the VP1 capsid protein of uncommon norovirus (NoV) GII.14 strains reported previously in Japan and China was performed using sequence analyses and homology modeling technique. The result of genetic comparison with the M7 prototype strain of GII.14 revealed that 10 amino acid mutations were observed at the same positions across the P2 and P1-2 subdomains in both Japanese and Chinese strains. By the homology modeling of the P domain, 7 out of these 10 mutations were predicted to be located on the surface-exposed P2 and P1-2 subdomains. All GII.14 strains had an altered RGD-like motif (RGT → KGT). While the Chinese strains contained 5 random amino acid changes in the S domain and the P2 subdomain, these changes were not detected in the Japanese strains. In addition, the histo-blood group antigen (HBGA)-binding interfaces remain identical to those of the previously determined GII.4 structure (VA387), suggesting the conservation of HBGA binding profile within the GII genogroup. Taken together, this report provides supportive structural data that antigenic drifts that occurred mostly in the P2 and P1-2 subdomains might be sufficient to generate new mutants, thus permitting the GII.14 virus to escape the host pre-existing immunity. These results also suggest the need for comparing the evolutionary profiles and structural models of rare NoV genotypes to an insight into NoV evolution.