Norovirus GII.P16/GII.2-Associated Gastroenteritis, China, 2016

Increasing Recombinant Strains Emerged in Norovirus Outbreaks in Jiangsu, China: 2015-2018

From January 2015 to December 2018, 213 norovirus outbreaks with 3,951 patients were reported in Jiangsu, China. Based on viral RdRp and VP1 genes, eight genotypes, GII.2[P16] (144, 67.6%), GII.3[P12] (21, 9.9%), GII.6[P7] (5, 2.3%), GII.14[P7] (4, 1.9%), GII.4 Sydney[P31] (3, 1.4%), GII.1[P33] (1, 0.5%), GII.2[P2] (3, 1.4%), and GII.17[P17] (16, 7.5%) were identified throughout the study period. These genotypes were further regrouped as GII.R (Recombinant) and GII.Non-R (Non-recombinant) strains. In this report we showed that GII.R strains were responsible for at least 178 (83.6%) of 213 norovirus-positive outbreaks with a peak in 2017 and 2018. Most norovirus outbreaks occurred in primary schools and 94 of 109 (86.2%) outbreaks in primary schools were caused by GII.R, while GII.Non-R and GII.NT (not typed) strains accounted for 6 (5.5%) and 9 (8.3%) norovirus outbreaks, respectively. The SimPlot analysis showed recombination breakpoints near the ORF1/2 junction for all six recombinant strains. The recombination breakpoints were detected at positions varying from nucleotides 5009 to 5111, localized in the ORF1 region for four strains (GII.2[P16], GII.3[P12], GII.6[P7], and GII.14[P7]) and in the ORF2 region for the other (GII.4 Sydney[P31] and GII.1[P33]). We identified four clusters, Cluster I through IV, in the GII.P7 RdRp gene by phylogenetic analysis and the GII.14[P7] variants reported here belonged to Cluster IV in the RdRp tree. The HBGA binding site of all known GII.14 strains remained conserved with several point mutations found in the predicted conformational epitopes. In conclusion, gastroenteritis outbreaks caused by noroviruses increased rapidly in the last years and these viruses were classified into eight genotypes. Emerging recombinant noroviral strains have become a major concern and challenge to public health.

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.

The epidemiology of norovirus gastroenteritis in China: disease burden and distribution of genotypes

With the improvements of sanitation and nationwide safe water supply the occurrence of bacterial diarrhea declined remarkably, while viruses became the leading causes of acute gastroenteritis (AGE). Of these viruses, noroviruses (NoVs) are responsible for a considerable burden of gastroenteritis, especially in children < 2 years and elderly ⩾ 65 years. NoVs circulating in the Chinese population are antigenically highly diverse with the genotype GII.4 being the dominant strain followed by GII.3. Given the widespread contamination in environmental sources, and highly infectious nature of NoVs, vaccination would be the desirable strategy for the control of NoV infections. However, a better understanding of acquired immunity after infection, and a reliable immunological surrogate marker are urgently needed, since two vaccine candidates based on virus-like particles (VLPs) are currently moving into clinical evaluations in China.

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.

Norovirus Activity and Genotypes in Sporadic Acute Diarrhea in Children in Shanghai During 2014-2018

BACKGROUND

Based on the impact public health of norovirus and the current progress in norovirus vaccine development, it is necessary to continuously monitor the epidemiology of norovirus infection, especially in children who are more susceptible to norovirus.

OBJECTIVES

To monitor the activity and genotypes of norovirus infection in sporadic diarrhea in Shanghainese children during 2014-2018.

STUDY DESIGN

Acute diarrheal cases were prospectively enrolled in the outpatient setting. Real-time reverse transcription-polymerase chain reaction was used for screening norovirus GI and GII genogroups. Dual norovirus genotypes were identified based on the partial capsid and polymerase gene sequences.

RESULTS

Of the 3422 children with diarrhea, 510 (14.9%) were positive for noroviruses with 13 (2.5%) strains being GI genogroup and 497 (97.5%) strains being GII genogroup. Five distinct capsid GII genotypes were identified, including GII.4-Sydney/2012 (71.8%), GII.3 (13.8%), GII.17 (7.8%), GII.2 (6.0%), GII.6 (0.3%) and GII.8 (0.3%). Seven polymerase GII genotypes were identified, including GII.Pe (77.0%), GII.P12 (11.0%), GII.P17 (9.0%), GII.P16 (2.1%), and GII.P7, GII.P8 and GII.P2 in each (0.3%). Eleven distinct polymerase/capsid genotypes were identified with GII.Pe/GII.4-Sydney/2012 (74.2%), GII.P12/GII.3 (11.7%) and GII.P17/GII.17 (7.7%) being common. GII.P17/GII.17 strains were detected since September 2014. Recombinant GII.P16/GII.2 strains were detected since December 2016.

CONCLUSIONS

Norovirus is a major pathogen causing diarrhea in Shanghainese children. GII.Pe/GII.4-Sydney/2012 strains remained the predominant genotype. The emergence of GII.P17/GII.17 and GII.P16/GII.2 strains in sporadic diarrhea was consistent with norovirus-associated outbreaks attributable to these 2 novel variants in China. Continuous monitoring norovirus genotypes circulating in pediatric population is needed for current vaccine development.

Molecular detection of enteric viruses in the stool samples of children without diarrhea in Bangladesh

A number of molecular epidemiological studies reported the detection of enteric viruses in asymptomatic children. The role of these viruses in an asymptomatic infection remains unclear. This study investigated the enteric viruses in the stool samples collected from children without diarrhea. Stool samples were collected during June to October 2016, from 227 children who lived in Matlab, Bangladesh. Seventeen enteric viruses, including rotavirus A, B, and C (RVA, RVB, and RVC), norovirus GI (NoV GI), norovirus GII (NoV GII), sapovirus (SaV), adenovirus (AdV), human astrovirus (HAstV), Aichivirus (AiV), human parechovirus (HPeV), enterovirus (EV), human bocavirus (HBoV), Saffold virus (SAFV), human cosavirus (HCoSV), bufavirus (BufV), salivirus (SalV), and rosavirus (RoV), were investigated by RT-PCR method. One hundred and eighty-two (80.2%; 182/227) samples were positive for some of these viruses, and 19.8% (45/227) were negative. Among the positive samples, 46.7% (85/182) were a single infection, and 53.3% (97/182) were coinfection with multiple viruses. The HCoSV was the most prevalent virus (41.4%), followed by EV (32.2%), NoV GII (25.6%), HPeV (8.8%), RVA (6.2%), AdV (5.7%), AiV (5.3%), SAFV (4.4%), and SaV (2.6%). Each of NoV GI, HAstV, HBoV, and BufV was detected at 0.4%. However, RVB, RVC, SalV, and RoV were not detected in this study. Phylogenetic analysis showed that diverse HCoSV species and genotypes were circulating in Bangladesh, and four strains of species A are proposed to be new genotypes. The data indicated that non-diarrheal Bangladeshi children were asymptomatically infected with wide varieties of enteric viruses.

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.

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.

Recalibration of the Grunow-Finke Assessment Tool to Improve Performance in Detecting Unnatural Epidemics

Successful identification of unnatural epidemics relies on a sensitive risk assessment tool designed for the differentiation between unnatural and natural epidemics. The Grunow-Finke tool (GFT), which has been the most widely used, however, has low sensitivity in such differentiation. We aimed to recalibrate the GFT and improve the performance in detection of unnatural epidemics. The comparator was the original GFT and its application in 11 historical outbreaks, including eight confirmed unnatural outbreaks and three natural outbreaks. Three steps were involved: (i) removing criteria, (ii) changing weighting factors, and (iii) adding and refining criteria. We created a series of alternative models to examine the changes on the parameter likelihood of unnatural outbreaks until we found a model that correctly identified all the unnatural outbreaks and natural ones. Finally, the recalibrated GFT was tested and validated with data from an unnatural and natural outbreak, respectively. A total of 238 models were tested. Through the removal of criteria, increasing or decreasing weighting factors of other criteria, adding a new criterion titled "special insights," and setting a new threshold for likelihood, we increased the sensitivity of the GFT from 38% to 100%, and retained the specificity at 100% in detecting unnatural epidemics. Using test data from an unnatural and a natural outbreak, the recalibrated GFT correctly classified their etiology. The recalibrated GFT could be integrated into routine outbreak investigation by public health institutions and agencies responsible for biosecurity.

An Outbreak of Gastroenteritis Associated with GII.17 Norovirus-Contaminated Secondary Water Supply System in Wuhan, China, 2017

A gastroenteritis outbreak occurred in a university in May, 2017, Wuhan, China. The epidemiological survey and pathogen analysis were conducted to identify the pathogen and control this outbreak. Feces or anal swabs from individuals, water, and swabs taken from tap surfaces of the secondary water supply system (SWSS) and foods were collected for the detection of viruses and pathogenic enteric bacteria by real-time RT-PCR and culture, respectively. Nucleotide sequences were determined by RT-PCR and direct sequencing. Genotyping, phylogenetic, and recombination analyses were conducted by a web-based genotyping tool, MEGA, and RDP4 programs, respectively. Of 144 individuals enrolled, 75 met the case definitions. The epidemic curve showed one peak of incidence suggesting the most probable spread of a single common source. In total, 33 specimens were collected before disinfection of the SWSS. Of these, norovirus was detected and identified as GII.P17-GII.17 with 100% nucleotide sequence identity among the strains detected in ten students (10/14), a maintenance worker (1/2) dealing with the SWSS, four water samples (4/8), and two swabs taken from tap surfaces (2/3). Pathogens including Vibrio cholerae, Salmonella, Shigella, Vibrio parahaemolyticus, Bacillus cereus, enteropathogenic Escherichia coli, rotavirus, astrovirus, and sapovirus were negative. The GII.17 strains in this outbreak clustered closely in the same branch of the phylogenetic tree, and slightly apart from the strains of other cities in China, neighboring countries and regions, European and American countries. This gastroenteritis outbreak was deduced to be attributed to GII.P17-GII.17 norovirus contamination of the SWSS.

Epidemiological, Molecular, and Clinical Features of Norovirus Infections among Pediatric Patients in Qatar

BACKGROUND

Norovirus (NoV) is recognized as the second most important etiological agent leading to acute gastroenteritis globally. In order to determine the burden and characteristics of NoV infections in children in Qatar, profiling of circulating genotypes and their correlation with demographics and clinical manifestations were evaluated.

METHODS

A total of 177 NoV-positive fecal samples were collected from children suffering from acute gastroenteritis (AGE) during two-year period between June 2016 and June 2018. The age of the subjects ranged between 3 months and 12 years (median of 15 months). Genotyping was performed by amplifying and sequencing parts of viral VP1 and RNA-dependent RNA polymerase (RdRp) regions. Phylogenetic analysis and evolutionary relationships were performed using MEGA7.0. Fisher's exact test was used to run statistical analysis for the clinical and demographical characteristics of circulating strains.

RESULTS

Overall, NoV infections were relatively higher in males than females with a ratio of 1.3:1 (p = 0.0073). Most of the NoV infections were reported in children between 1 and 3 years old (49.7%), followed by those <1 and >3 years of age (41.2% and 9.1%, respectively). NoV infections occurred throughout the year, with a noticeable increase in summer (36.6%) and drop in winter (25.4%). Nearly all (98.8%) NoV-infected children were positive for genogroup II (GII) compared to only two samples (1.2%) being positive for genogroup I (GI): GI.3 and GI.4. NoV genotype GII.4 (62.2%), GII.2 (15.8%), and GII.3 (13.5%) were predominant in our study. The detected strains shared >98% sequence homology with emerging recombinant strain of GII.P16-GII.4/RUS/Novosibirsk/2017 (MG892929), GII.P16-GII.4 Sydney/2012 (KY887601), GII.4 Sydney/2012, recombinant GII.P4 New Orleans /2009/GII.4 Sydney 2012 (MG585810.1), and the emerging strain GII.P16-GII.2 CHN/2017 (MH321823). Severe clinical illness (vesikari score >10) was reported in children infected with genotypes sharing homology with the above emerging strains. While GII.4 was reported in all age groups, NoV GII.3 infections were higher in children <1 year of age. Both genogroups (GII.4 and GII.3) in addition to GII.2 reported higher incidence in Qatari subjects compared to other nationalities (p = 0.034).

CONCLUSION

This is the first report about NoV molecular epidemiology in Qatar. The most detected NoV strain was genogroup GII, which is the dominant genotype in the Middle East region. Further, we report GII.4, GII.2, and GII.3 as the most predominant NoV genotypes in our study. Moreover, disease severity scores were higher among children genotyped with genogroup GI (GI.4) and genogroup GII (GII.4, GII.2, GII.3, GII.6, and GII.7).

Epidemiology of Norovirus Outbreaks Reported to the Public Health Emergency Event Surveillance System, China, 2014⁻2017

We conducted a retrospective analysis of norovirus outbreaks reported to the National Public Health Emergency Event Surveillance System (PHEESS) in China from January 1, 2014 to December 31, 2017. We reviewed all acute gastroenteritis outbreaks (n = 692) submitted to PHEESS to identify the frequency, seasonality, geographic distribution, setting, and transmission mode of outbreaks due to norovirus. A total of 616 norovirus outbreaks resulting in 30,848 cases were reported. Among these outbreaks, 571 (93%) occurred in school settings including 239 (39%) in primary schools, 136 (22%) in childcare facilities, and 121 (20%) in secondary schools. The majority of outbreaks (63%) were due to person-to-person transmission, followed by multiple modes of transmission (11%), foodborne (5%) and waterborne (3%) transmission. These findings highlight the importance of improving hand hygiene and environmental disinfection in high-risk settings. Developing a standard and quantitative outbreak reporting structure could improve the usefulness of PHEESS for monitoring norovirus outbreaks.

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.

Surveillance of norovirus contamination in commercial fresh/frozen berries from Heilongjiang Province, China, using a TaqMan real-time RT-PCR assay

Norovirus (NoV), a major food-borne virus, causes non-bacterial acute gastroenteritis in humans. Berries are generally harvested from low-growing bushes by hand and are minimally processed before being sold to consumers. Therefore, the consumption of berries has been linked to numerous food-borne gastroenteritis outbreaks caused by NoV in many countries. We performed a survey of NoV contamination in commercial fresh/frozen berry fruits collected from 2016 to 2017 in the Heilongjiang Province, the main berry-producing area in China, using a TaqMan-based real-time reverse transcription-PCR assay. Among 900 frozen and 900 fresh domestic retail berry samples, the prevalence of NoV was 9% (81/900) and 12.11% (109/900), including 35.80% (29/81) and 29.36% (32/109) of genotype GI alone, 54.32% (44/81) and 60.55% (66/109) of GII alone, and 9.88% (8/81) and 10.09% (11/109) of both GI and GII, respectively. No NoV was detected among the 677 frozen berry samples for export. Thus, the occurrence of NoV contamination was significantly higher in domestic berries than in exported berries and higher in fresh berries than in frozen berries. This study highlights the need for further risk surveillance for NoV contamination in berries produced in the Heilongjiang Province and recommends region-extended monitoring of retail berries for NoV.

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.

Distribution of norovirus and sapovirus genotypes with emergence of NoV GII.P16/GII.2 recombinant strains in Chiang Mai, Thailand

Norovirus (NoV) and sapovirus (SaV) are recognized as the causative agents of acute gastroenteritis, and NoV is one of the leading pathogens reported worldwide. This study reports on the distribution of NoV and SaV genotypes in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand, from January 2015 to February 2017. From a total of 843 stool samples, 170 (20.2%) and 16 (1.9%) were identified as having NoV and SaV infections, respectively. Two samples (0.2%) were positive for both NoV and SaV. Of these, NoV GII.4 (57.2%) was the dominant genotype, followed by GII.2, GII.3, GII.17, GII.6, GII.7, GII.13, GII.14, GII.15, GII.21, GI.6, and GI.5. Among the NoV GII.4 variants, Sydney 2012 was the dominant variant during the period 2015-2016, while the other variants detected in this study were Asia 2003 and New Orleans 2009. Interestingly, an increase of NoV GII.2 was observed in 2016 and 2017. Characterization of partial RNA-dependent RNA polymerase and VP1 nucleotide sequences of GII.2 strains revealed that more than half of the GII.2 strains circulating in 2016 and 2017 were recombinant strains of GII.P16/GII.2. For SaV, the majority of strains belonged to GI.1 (55.6%) and GI.2 (33.3%), while GII.5 accounted for 11.1%. In conclusion, this study demonstrates the diversity of NoV and SaV, and the emergence of NoV GII.P16/GII.2 recombinant strains in 2016 and 2017 in Chiang Mai, Thailand.

Age, primary symptoms, and genotype characteristics of norovirus outbreaks in Shanghai schools in 2017

Sixty norovirus outbreaks that occurred in Pudong District, Shanghai in 2017 and affected 959 people were summarised. Of the outbreaks, 29 (48.3%), 27 (45.0%), and 4 (6.7%) occurred in kindergartens, primary schools, and middle schools, respectively. Although the total number of outbreaks peaked in March (13/60, 21.7%), outbreaks in kindergartens and primary schools peaked in April (6/29, 20.7%) and March (8/27, 29.6%), respectively. Primary schools had the highest median number of cases per outbreak (19) and the highest proportion of cases (54.6%). The male-to-female case ratio differed among school classifications, with the highest male case ratio (69.2%) occurring in middle schools. Primary symptoms also differed across the school classifications. Molecular virology analysis showed that a single viral strain caused each outbreak at each school. In turn, 50.6, 28.8, and 20.6% of cases were infected by GII.4, GII.2, and GII.17, respectively. Vomiting was seen in 98.2, 97.3, and 88.6% of the subjects infected with noroviruses GII.17, GII.4, and GII.2, respectively, and nausea in 73.6, 43.9, and 39.0%. In conclusion, noroviruses mainly affect primary school and kindergarten students. GII.4, GII.2, and GII.17 are the main epidemic strains in the local area, and the primary symptoms differed by age and genotype.

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.

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.

Molecular epidemiology and spatiotemporal dynamics of norovirus associated with sporadic acute gastroenteritis during 2013-2017, Zhoushan Islands, China

A total of 1 590 fecal swabs and stool samples from sporadic acute gastroenteritis patients of all ages were collected from January 2013 to March 2018 in the Zhoushan Islands, China, with 99 (6.23%) samples subsequently identified as human norovirus (HuNoV) positive. Phylogenetic analysis of partial RdRp and VP1 gene regions identified 10 genotypes of the GII genogroup and 3 genotypes of the GI genogroup. The predominant genotype was GII.P17-GII.17 (42.86%, 33/77), followed by GII.Pe-GII.4_Sydney 2012 (24.68%, 19/77) and GII.P16-GII.2 (12.96%, 10/77). However, the prevailing genotype in the Zhoushan Islands has shifted on three separate occasions. The GII.Pe-GII.4_Sydney_2012 strain was dominant in 2013-2014, the GII.P17-17 strain was dominant in 2015-2016, and the GII.P16-GII.2 strain was dominant in 2017. Divergence analysis showed that the re-emerging GII.P16-GII.2 strains clustered with the Japanese 2010-2012 GII.P16-GII.2 strains, and the time of the most recent common ancestor was estimated to have occurred in 2012 to 2013. The evolutionary rates of the RdRp gene region of the GII.P16 genotype and the VP1 gene region of the GII.2 genotype were 2.64 × 10(-3) (95% HPD interval, 2.17-3.08 × 10(-3)) and 3.36 × 10(-3) (95% HPD interval, 2.66-4.04 × 10(-3)) substitutions/site/year, respectively. The migration pattern of the HuNoV GII.2 genotype in China demonstrated that the re-emerging GII.P16-GII.2 strains were first introduced into Hong Kong from Japan, and then spread from Hong Kong to other coastal areas. Our results also showed that the GII.P16-GII.2 strains in the Zhoushan Islands were likely introduced from Jiangsu Province, China, in 2016.

An acute gastroenteritis outbreak associated with person-to-person transmission in a primary school in Shanghai: first report of a GI.5 norovirus outbreak in China

Background

GII noroviruses are a common cause of acute gastroenteritis (AGE) outbreaks in institutional settings globally. However, AGE outbreaks caused by GI norovirus, especially the GI.5 genotype, are relatively uncommon.

Methods

In February 2017, an AGE outbreak occurred in a primary school in Shanghai, China. An outbreak investigation was undertaken, and fecal specimens, rectal swabs, and environmental swabs were collected. Pathogen detection was performed and the positive specimens were characterized by gene sequencing.

Results

The descriptive epidemiological analysis suggested that this outbreak, involving 19 cases in two classes (designated classes A and B), was a small-scale propagated epidemic and person-to-person transmission was the most plausible transmission mode. The outbreak comprised two peaks, with 15 cases occurring in class A during the main peak and four cases occurring in class B in the subsequent minor peak. The primary attack rate was 38% and the secondary attack rate was 10%. Univariable logistic regression indicated that contacting a suspect case was a risk factor for norovirus infection, with an unadjusted OR of 5.6 (95% CI: 1.6–20.1). Six fecal specimens were positive for GI norovirus, with a single genotype, GI.5 norovirus, being involved, as characterized by genotyping. This outbreak was the first reported outbreak of GI.5 norovirus in China.

Conclusions

This study implies that GI.5 norovirus is a potential agent of outbreaks spread by person-to-person transmission in institutional settings. The investigation highlights the importance of sensitive surveillance, timely isolation of individuals who are ill, adequate hand hygiene, and proper environmental disinfection for prevention and control of AGE outbreaks caused by norovirus.

Increased Detection of Emergent Recombinant Norovirus GII.P16-GII.2 Strains in Young Adults, Hong Kong, China, 2016-2017

A new recombinant norovirus GII.P16-GII.2 outnumbered pandemic GII.4 as the predominant GII genotype in the winter of 2016-2017 in Hong Kong, China. Half of hospitalized case-patients were older children and adults, including 13 young adults. This emergent norovirus targets a wider age population compared with circulating pandemic GII.4 strains.

Gastroenteritis outbreak at a health function caused by an emerging recombinant strain of Norovirus GII.P16/GII.4 Sydney 2012, Australia

An emerging recombinant norovirus GII.P16/GII.4 Sydney 2012 strain caused a gastroenteritis outbreak amongst attendees at a large health function in regional New South Wales, Australia. This was the third outbreak caused by the recombinant GII.P16/GII.4 Sydney 2012 strain in this region in 2017, which appears to be emerging as a common strain in the Hunter New England region.

Emerging recombinant noroviruses identified by clinical and waste water screening

Norovirus is estimated to cause 677 million annual cases of gastroenteritis worldwide, resulting in 210,000 deaths. As viral gastroenteritis is generally self-limiting, clinical samples for epidemiological studies only partially represent circulating noroviruses in the population and is biased towards severe symptomatic cases. As infected individuals from both symptomatic and asymptomatic cases shed viruses into the sewerage system at a high concentration, waste water samples are useful for the molecular epidemiological analysis of norovirus genotypes at a population level. Using Illumina MiSeq and Sanger sequencing, we surveyed circulating norovirus within Australia and New Zealand, from July 2014 to December 2016. Importantly, norovirus genomic diversity during 2016 was compared between clinical and waste water samples to identify potential pandemic variants, novel recombinant viruses and the timing of their emergence. Although the GII.4 Sydney 2012 variant was prominent in 2014 and 2015, its prevalence significantly decreased in both clinical and waste water samples over 2016. This was concomitant with the emergence of multiple norovirus strains, including two GII.4 Sydney 2012 recombinant viruses, GII.P4 New Orleans 2009/GII.4 Sydney 2012 and GII.P16/GII.4 Sydney 2012, along with three other emerging strains GII.17, GII.P12/GII.3 and GII.P16/GII.2. This is unusual, as a single GII.4 pandemic variant is generally responsible for 65–80% of all human norovirus infections at any one time and predominates until it is replaced by a new pandemic variant. In sumary, this study demonstrates the combined use of clinical and wastewater samples provides a more complete picture of norovirus circulating within the population.

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.

Emergence of multiple norovirus strains in Thailand, 2015-2017

Norovirus is a major cause of non-bacterial acute gastroenteritis worldwide. Infection can be sporadic or result in widespread outbreaks. The surveillance of norovirus samples (n = 1591) obtained from patients with diarrhea in Thailand from January 2015 to February 2017 suggested that the predominance of norovirus GII.4 often seen in sporadic infection had been superseded by the emergence of GII.17. More recently, a sharp increase in acute gastroenteritis associated with norovirus GII·P16-GII.2 recombinant strain was observed at the end of 2016. Thus, previously rare norovirus strains and their recombinant derivatives may be more frequently responsible for future outbreaks.

Molecular epidemiology of genogroup II norovirus infections in acute gastroenteritis patients during 2014-2016 in Pudong New Area, Shanghai, China

BACKGROUND

Norovirus (NoV), a member of the Caliciviridae, is now recognized as the leading cause of acute gastroenteritis (AGE) worldwide. Globally, the GII.4 Sydney_2012 variant has predominated in NoV-related AGE since 2012, although the novel variant GII.17 has also been reported as responsible for gastroenteritis outbreaks in East Asia since 2014. This study aimed to disclose the recent genotype patterns of NoV genogroup II (GII) presenting in AGE patients in Pudong New Area of Shanghai through a laboratory-based syndromic surveillance system. The study further aimed to delineate the predominant strains circulating in the population.

METHODS

Pudong New Area is located in eastern Shanghai and covers 20.89% of the Shanghai population. The laboratory-based syndromic surveillance system is composed of 12 sentinel hospitals among the 68 general hospitals in this area. AGE patients who sought medical care were sampled following an AGE surveillance protocol. Stool samples were collected from participating patients, and a standardized questionnaire was given to each patient by trained nurses to gain information on the disease profiles and demographics of the patients. Real-time reverse transcription polymerase chain reaction (qRT-PCR) was used to screen the GI nd GII NoV and RT-PCR was used to amplify NoV GII partial capsid protein open reading frame 2 (ORF2). NoV Genotyping Tool (version 1.0, RIVM, MA Bilthoven, Netherlands) was used for genotyping, and a phylogenetic analysis was conducted by MEGA 7.0.

RESULTS

During 2014-2016, among the 2069 virus-infected AGE cases, 65.88% were caused by NoV. NoV-AGE occurred most frequently in the periods from October to March. The patients with more severe diarrheal symptoms and vomiting were more likely to be infected by NoV. The main genotypes were GII.17 (44.69%) and GII.4 (39.26%), which dominated the NoV-AGE epidemics jointly or in turn, whereas a slight increase in GII.2 was observed beginning in May 2016. The GII.17 strains tended to cluster more with the Hu/JP/2014/GII.P17_GII.17/Kawasaki323 variants, representing novel prevalent strains. Among the GII.4 strains, the GII.4 Sydney_2012 variant was still the predominant strain.

CONCLUSIONS

NoV GII has become the main cause of virus-infected AGE in Pudong New Area, Shanghai. The predominant genotypes of NoV GII were GII.17 and GII.4. Comprehensive laboratory-based surveillance is important for clinical diagnosis and treatment. Identification of emerging new genotypes is also crucial for the prevention and control of NoV-infected AGE.

Complete Genome Sequence of a Novel Recombinant GII.P16-GII.1 Norovirus Associated with a Gastroenteritis Outbreak in Shandong Province, China, in 2017

We report here the complete genome sequence of a novel recombinant GII.P16-GII.1 norovirus identified from eight fecal samples collected during an acute gastroenteritis outbreak in Jinan, Shandong Province, China, in 2017. The virus had nucleotide identities of 99% and 91% in the ORF1 and ORF2 genes of related strains, respectively.

Characterization of a Norovirus-specific monoclonal antibody that exhibits wide spectrum binding activities

Noroviruses (NoVs) are increasingly recognized as the leading cause of acute non-bacterial gastroenteritis worldwide. To screen for NoV-specific monoclonal antibodies (mAbs) with wide spectrum binding activities that could be used for the development of NoV-related detection reagents, we immunized mice with a combination of virus like particles (VLPs) derived from eight different genotypes (two from genogroup I and six from genogroup II), of which two (GI.7 and GII.2) were newly produced VLPs. Indirect enzyme-linked immunosorbent assay (ELISA) confirmed that two mAbs (8D8 and 10B11) bound to all eight major capsid proteins (VP1) with varied binding abilities. Epitope mapping using short peptides covering the N-terminal half of GII.3 VP1 indicated that the binding site of mAb 8D8 was located between amino acid 31 and 60. Multiple amino acid sequence alignment of VP1 suggested that this site harbors conservative sequences across all genogroups. Indirect and sandwich ELISA indicated that mAb 8D8 was unable bind intact VLPs. In summary, we successfully produced GI.7 and GII.2 VLPs using recombinant baculovirus expression system and a cross-reactive mAb by immunizing mice with eight different VLPs that might be useful in the studying and detecting NoVs.

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.

Characterization of Antigenic Relatedness between GII.4 and GII.17 Noroviruses by Use of Serum Samples from Norovirus-Infected Patients

A novel GII.17 norovirus variant caused major gastroenteritis epidemics in China in 2014 to 2016. To explore the host immune factors in selection of the emergence of this new variant, we characterized its antigenic relatedness with the GII.4 noroviruses that have dominated in China for decades. Through an enzyme-linked immunosorbent assay (ELISA) and a histo-blood group antigen (HBGA) blocking assay using sera from GII.4 and the GII.17 variant-infected patients, respectively, we observed limited cross-immune reactivity by the ELISA but little reactivity by the HBGA blocking assay between GII.4 norovirus and the new GII.17 variant. Our data suggest that, among other possible factors, GII.4-specific herd immunity had little role in the emergence of the new GII.17 variant. Thus, GII.17 may be an important active antigenic type or immunotype that needs to be considered for future vaccine strategies against human noroviruses.

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.