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.

Sapovirus is increasingly recognized as an important cause of acute gastroenteritis (AGE) worldwide; however, studies of sapovirus prevalence, genetic diversity, and strain-specific clinical implications have been scarce. To fill this knowledge gap, we used reverse transcription–real-time PCR and sequencing of the partial major capsid protein VP1 gene to analyze stool specimens and rectal swabs obtained from 3,347 children with AGE and 1,355 asymptomatic controls (all <18 years old) collected between December 2014 and August 2018 in Alberta, Canada.

It is important to understand the diagnostic accuracy of multiplex panels such as the Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) as they are increasingly employed for routine diagnostics worldwide. Recent evaluations in our laboratory identified lower detection rates of norovirus genogroup II (NoV GII) using GPP compared to our laboratory-developed RT-qPCR, Gastroenteritis Virus Panel (GVP). To characterize the cases of discordant NoV GII results between GPP and GVP and determine the sensitivity of the two assays for specific NoV GII genotypes. We genotyped discordant NoV GII strains identified in stool samples or rectal swabs collected prospectively from a cohort of children with acute gastroenteritis between December 2014 and July 2016. The sensitivities of GVP and GPP for NoV GII were compared by analyses of GVP threshold cycle (Ct) and ten-fold serial dilutions of positive samples of various NoV GII genotypes. All discordant samples (63/607) were NoV GII positive by GVP but negative by GPP. Twenty-two were successfully genotyped, fourteen of which were NoV GII genotype 2 (GII.2). The median Ct value of concordant positives was lower than that of discordant results (19.8 vs. 33.7; P<0.0001). GVP was 10 and at least 10,000-fold more sensitive than GPP in detecting NoV GII.3 and GII.2, respectively, but has similar sensitivity for NoV GII.4. Discordant GII.2 variant differed genetically from concordant GII.2 variants. GPP has lower sensitivity to detect NoV GII.2 than GVP and its use may lead to undetected cases clinically, and an underestimation of NoV disease burden at the population level.

Rotavirus molecular surveillance remains important in the postvaccine era to monitor the changes in transmission patterns, identify vaccine‐induced antigenic changes and discover potentially pathogenic vaccine‐related strains. The Canadian province of Alberta introduced rotavirus vaccination into its provincial vaccination schedule in June 2015. To evaluate the impact of this program on stool rotavirus positivity rate, strain diversity, and seasonal trends, we analyzed a prospective cohort of children with acute gastroenteritis recruited between December 2014 and August 2018. We identified dynamic changes in rotavirus positivity and genotype trends during pre‐ and post‐rotavirus vaccine introduction periods. Genotypes G9P[8], G1P[8], G2P[4], and G12P[8] predominated consecutively each season with overall lower rotavirus incidence rates in 2016 and 2017. The demographic and clinical features of rotavirus gastroenteritis were comparable among wild‐type rotaviruses; however, children with G12P[8] infections were older (p < 0.001). Continued efforts to monitor changes in the molecular epidemiology of rotavirus using whole genome sequence characterization are needed to further understand the impact of the selection pressure of vaccination on rotavirus evolution.