Long-term dynamics of Norovirus transmission in Japan, 2005-2019

Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance

Nucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of their genetic diversity. Here, we calculated the variability of nucleotides within the genomes of 10 human viral species in silico and found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay's target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.IMPORTANCENucleic acid-based assays, such as polymerase chain reaction (PCR), that amplify and detect organism-specific genome sequences are employed widely as a standard method for infectious disease surveillance. However, challenges arise for virus surveillance because of the rapid evolution and genetic variation of viruses. The study analyzed clinical and wastewater samples using multiple PCR assays and found significant performance variation among the PCR assays for genetically diverse norovirus surveillance. This finding suggests that some PCR assays may miss detecting certain virus strains, leading to a compromise in detection sensitivity. To address this issue, we propose a metric called the probability of detection, which can be simply calculated in silico using a code developed in this study, to evaluate nucleic acid-based assays for genetically diverse virus surveillance. This new approach can help improve the sensitivity and accuracy of virus detection, which is crucial for effective infectious disease surveillance and control.

Genotypic diversity and recombination of norovirus GI.6[P11] associated acute gastroenteritis outbreaks in Beijing, China, from 2016 to 2019

Norovirus (NoV) is the leading pathogen responsible for global acute gastroenteritis (AGE) outbreaks and sporadic cases. NoV evolves through gene mutation and recombination, leading to the emergence of new strains capable of causing global epidemics. This study aimed to learn the epidemiological characteristics of 39 GI.6[P11] NoV outbreaks in Beijing, China, from 2016 to 2019 and to analyze the genetic diversity and phylogenetic process of GI.6[P11] strains. The Bayesian phylogenetic analysis of partial VP1 and RNA-dependent RNA polymerase (RdRp) genes showed that GI.6[P11] strains were clustered into four subclades. Eleven whole genome sequences were obtained through the amplicon sequencing with 16 pairs of newly designed primers. The phylogenetic trees based on the whole genome and ORF1, 2, and 3 showed that the clustering of the 11 strains was consistent with that of partial VP1 and RdRp genes. The Bayesian inference revealed that the most recent ancestor (TMRCA) for the four subclades of the phylogenetic tree based on the whole genome sequences was 2012.42, 2014.81, 2011.74, and 2015.53, respectively. The recombination sites of GI.6[P11] strains in Beijing were located near the ORF1/2 junction. The histo-blood group antigens (HBGA) binding sites of GI.6[P11] strains in Beijing were conserved and there were some unique amino acid mutations in non-structural proteins in the ORF1 region.

Global prevalence of asymptomatic norovirus infection in outbreaks: a systematic review and meta-analysis

BACKGROUND

Although many studies on asymptomatic norovirus infection in outbreaks have been conducted globally, structured data (important for emergency management of outbreaks) on the prevalence of this epidemic are still not available. This study assessed the global prevalence of asymptomatic norovirus infection in outbreaks.

METHODS

We identified publications on asymptomatic infections from norovirus outbreaks by searching the PubMed, Embase, Cochrane Library, Medline, and Web of Science databases and screening references from the articles reviewed. Prevalence of asymptomatic norovirus infection in outbreaks was employed as the primary summary data. The random-effects model of the meta-analysis was fitted to generate estimates of the prevalence in the overall and subgroup populations.

RESULTS

In total, 44 articles with a sample size of 8,115 asymptomatic individuals were included. The estimated pooled prevalence of asymptomatic norovirus infection in outbreaks was 21.8% (95%CI, 17.4-27.3). The asymptomatic prevalence of norovirus GII (20.1%) was similar to that of GI (19.8%); however, the proportion prevalence of asymptomatic individuals involved in the former (33.36%) was significantly higher than that of in the latter (0.92%) and the former (93.18%) was reported much more frequently than the latter (15.91%) in the included articles. These studies had significant heterogeneity (I2 = 92%, τ2 = 0.4021, P < 0.01). However, the source of heterogeneity could not be identified even after subgroup analysis of 10 possible influencing factors (geographical area, outbreak settings, outbreak seasons, sample types, norovirus genotypes, transmission routes, subjects' occupations, subjects' age, per capita national income, and clear case definition). Meta-regression analysis of these 10 factors demonstrated that the geographical area could be partly responsible for this heterogeneity (P = 0.012).

CONCLUSIONS

The overall pooled asymptomatic prevalence of norovirus in outbreaks was high, with genome II dominating. Asymptomatic individuals may play an important role in norovirus outbreaks. This knowledge could help in developing control strategies and public health policies for norovirus outbreaks.

Current assumptions for quantitative microbial risk assessment (QMRA) of Norovirus contamination of drinking water catchments due to recreational activities: an update

Contamination of drinking water from Norovirus (NoV) and other waterborne viruses is a major public health concern globally. Increasingly, quantitative microbial risk assessment (QMRA) is being used to assess the various risks from waterborne pathogens and evaluate control strategies. As urban populations grow and expand, there is increasing demand for recreational activities in drinking water catchments. QMRA relies on context-specific data to map out the pathways by which viruses can enter water and be transferred to drinking water consumers and identify risk factors and appropriate controls. This review examines the current evidence base and assumptions for QMRA analysis of NoV and other waterborne viral pathogens and recommends numerical values based on the most recent evidence to better understand the health risks associated with recreators in Australian drinking water sources; these are broadly applicable to all drinking water sources where recreational access is allowed. Key issues include the lack of an agreed upon data and dose-response models for human infectious NoV genotypes, faecal shedding by bathers, the extent of NoV infectivity and aggregation, resistance (secretor status) to NoV and the extent of secondary transmission.