Continuing rotavirus circulation in children and adults despite high coverage rotavirus vaccination in Finland

Molecular Evolution of GII.P31/GII.4_Sydney_2012 Norovirus over a Decade in a Clinic in Japan

Norovirus (NoV) genogroup II, polymerase type P31, capsid genotype 4, Sydney_2012 variant (GII.P31/GII.4_Sydney_2012) has been circulating at high levels for over a decade, raising the question of whether this strain is undergoing molecular alterations without demonstrating a substantial phylogenetic difference. Here, we applied next-generation sequencing to learn more about the genetic diversity of 14 GII.P31/GII.4_Sydney_2012 strains that caused epidemics in a specific region of Japan, with 12 from Kyoto and 2 from Shizuoka, between 2012 and 2022, with an emphasis on amino acid (aa) differences in all three ORFs. We found numerous notable aa alterations in antigenic locations in the capsid region (ORF2) as well as in other ORFs. In all three ORFs, earlier strains (2013-2016) remained phylogenetically distinct from later strains (2019-2022). This research is expected to shed light on the evolutionary properties of dominating GII.P31/GII.4_Sydney_2012 strains, which could provide useful information for viral diarrhea prevention and treatment.

The Emergence and Widespread Circulation of Enteric Viruses Throughout the COVID-19 Pandemic: A Wastewater-Based Evidence

Growing evidence shed light on the importance of wastewater-based epidemiology (WBE) during the pandemic, when the patients rarely visited the clinics despite the fact that the infections were still prevalent in the community as before. The abundance of infections in the community poses a constant threat of the emergence of new epidemic strains. Herein, we investigated enteric viruses in raw sewage water (SW) from Japan's Tohoku region and compared them to those from the Kansai region to better understand the circulating strains and their distribution across communities during the COVID-19 pandemic. Raw SW was collected between 2019 and 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major AGE viruses by RT-PCR. Sequence-based analyses were used to assess genotypes and evolutionary relationships. The most commonly detected enteric virus was rotavirus A (RVA) at 63.8%, followed by astrovirus (AstV) at 61.1%, norovirus (NoV) GII and adenovirus (AdV) at 33.3%, sapovirus (SV) at 25.0%, enterovirus (EV) at 19.4%, and NoV GI at 13.9%. The highest prevalence (46.0%) was found in the spring. Importantly, enteric viruses did not decline during the pandemic. Rather, several strains like NoV GII.2, DS-1-like human G3 (equine) RVA, MLB1 AstV, and different F41 HAdV emerged throughout the pandemic and spread widely over the Tohoku and Kansai regions. Tohoku's detection rate remained lower than that of the Kansai area (36 vs 58%). This study provides evidence for the emergence and spread of enteric viruses during the pandemic.

Genotype Diversity of Enteric Viruses in Wastewater Amid the COVID-19 Pandemic

Viruses remain the leading cause of acute gastroenteritis (AGE) worldwide. Recently, we reported the abundance of AGE viruses in raw sewage water (SW) during the COVID-19 pandemic, when viral AGE patients decreased dramatically in clinics. Since clinical samples were not reflecting the actual state, it remained important to determine the circulating strains in the SW for preparedness against impending outbreaks. Raw SW was collected from a sewage treatment plant in Japan from August 2018 to March 2022, concentrated by polyethylene-glycol-precipitation method, and investigated for major gastroenteritis viruses by RT-PCR. Genotypes and evolutionary relationships were evaluated through sequence-based analyses. Major AGE viruses like rotavirus A (RVA), norovirus (NoV) GI and GII, and astrovirus (AstV) increased sharply (10-20%) in SW during the COVID-19 pandemic, though some AGE viruses like sapovirus (SV), adenovirus (AdV), and enterovirus (EV) decreased slightly (3-10%). The prevalence remained top in the winter. Importantly, several strains, including G1 and G3 of RVA, GI.1 and GII.2 of NoV, GI.1 of SV, MLB1 of AstV, and F41 of AdV, either emerged or increased amid the pandemic, suggesting that the normal phenomenon of genotype changing remained active over this time. This study crucially presents the molecular characteristics of circulating AGE viruses, explaining the importance of SW investigation during the pandemic when a clinical investigation may not produce the complete scenario.

A Pooled Analysis of Sex Differences in Rotaviral Enteritis Incidence Rates in Three Countries Over Different Time Periods

Background: Sex differences in incidence rates (IRs) of infectious diseases could provide clues to the mechanisms of infection. The results of studies on sex differences in the incidence of rotaviral enteritis have been inconsistent.

Methods: We carried out a pooled analysis of sex differences in IRs for rotaviral enteritis in three countries for a period of 7–22 years. Male-to-female incidence rate ratios (IRRs) were computed by age group, country, and years of reporting. A meta-analytic methodology was used to combine IRRs. Metaregression was performed to evaluate the contribution of age group, country, and years of reporting to the IRR.

Results: Significantly higher IRs in males were found in the age groups 0–4, 5–9, and 10–14 years, with pooled IRRs (with 95% confidence intervals [CIs]) of 1.12 (1.09–1.14), 1.07 (1.05–1.09), and 1.13 (1.05–1.21), respectively. In adults, the sex differences were reversed with higher rates in females. The pooled male-to-female IRRs (with 95% CIs) were 0.66 (0.64–0.68), 0.78 (0.72–0.85), and 0.78 (0.72–0.84) for the age groups 15–44, 45–64, and 65+ years, respectively. Metaregression results demonstrated that age is responsible for much of the variation in IRRs.

Conclusions: The higher rotaviral enteritis IRs in males at a very early age suggest that sex-related factors unrelated to exposure may play a role. The higher IRs in adult females could result, at least partly, from behavioral and occupational factors.

A major decrease of viral acute gastroenteritis in hospitalized Finnish children as rotavirus returns as the most detected pathogen

INTRODUCTION

We assessed the prevalence and circulating genotypes of rotavirus, norovirus and sapovirus in children. The results were compared to previous surveillance studies from 2006-2008, 2009-2011 and 2012-2014 with similar methodology and setting, covering the start of universal vaccination with RotaTeq® in 2009.

METHODS

Stool samples were collected from children aged <16 years with acute gastroenteritis at Tampere University Hospital, Finland, from January 1^st, 2017 to December 31^st, 2018. The samples were analyzed using reverse transcription PCR and positive amplicons were sequenced.

RESULTS

A total of 178 stool samples were collected from 214 children. Rotavirus was detected in 56 (32 %), norovirus in 48 (27 %) and sapovirus in 11 (6.3 %) stool samples. Rotavirus G9P[8] and G12P[8] were the most detected genotypes in vaccinated and unvaccinated children. GII.4 comprised 96 % of the norovirus detections.

CONCLUSIONS

The prevalence of all-cause acute gastroenteritis in a hospital-setting has decreased by 51 % from 2012-2014, and by 88 % from 2006-2008. Rotavirus returns as the most common cause of viral acute gastroenteritis in children, but the prevalence remains at a low level. No considerable changes were seen in the genotyping results of norovirus and sapovirus.

Rotavirus gastroenteritis hospitalizations in provinces with different vaccination coverage rates in Spain, 2013-2018

BACKGROUND

Rotavirus (RV) vaccines are available in Spain since 2006 but are not included in the National Immunization Program. RV vaccination has reached an intermediate vaccination coverage rate (VCR) but with substantial differences between provinces. The aim of this study was to assess the ratio of RV gastroenteritis (RVGE) admissions to all-cause hospitalizations in children under 5 years of age in areas with different VCR.

METHODS

Observational, multicenter, cross-sectional, medical record-based study. All children admitted to the study hospitals with a RVGE confirmed diagnosis during a 5-year period were selected. The annual ratio of RVGE to the total number of all-cause hospitalizations in children < 5 years of age were calculated. The proportion of RVGE hospitalizations were compared in areas with low (< 30%), intermediate (31-59%) and high (> 60%) VCR.

RESULTS

From June 2013 to May 2018, data from 1731 RVGE hospitalizations (16.47% of which were nosocomial) were collected from the 12 study hospitals. RVGE hospital admissions accounted for 2.82% (95 CI 2.72-3.00) and 43.84% (95% CI 40.53-47.21) of all-cause and Acute Gastroenteritis (AGE) hospitalizations in children under 5 years of age, respectively. The likelihood of hospitalization due to RVGE was 56% (IC95%, 51-61%) and 27% (IC95%, 18-35%) lower in areas with high and intermediate VCR, respectively, compared to the low VCR areas.

CONCLUSIONS

RVGE hospitalization ratios are highly dependent on the RV VCR. Increasing VCR in areas with intermediate and low coverage rates would significantly reduce the severe burden of RVGE that requires hospital management in Spain. Clinical trial registration Not applicable.

The laboratory test procedure to confirm rotavirus vaccine infection in severe complex immunodeficiency patients

The rotavirus vaccine is a live vaccine, and there is a possibility of infection by the virus strain used in the vaccine. We investigated the process of determining whether an infection was caused by the vaccine strain in a severe complex immunodeficiency (SCID) patient with rotavirus infection. The patient was vaccinated with RotaTeq prior to being diagnosed with SCID. The testing process was conducted in the following order: confirming rotavirus infection, determining its genotype, and confirming the vaccine strain. Rotavirus infection was confirmed through enzyme immunoassay and VP6 gene detection. G1 and P[8] were identified by multiplex polymerase chain reaction for the genotype, and G3 was further identified using a single primer. By detecting the fingerprint gene (WC3) of RotaTeq, it was confirmed that the detected virus was the vaccine strain. Genotypes G1 and P[8] were identified, and the infection was suspected of having been caused by rotavirus G1P[8]. G1P[8] is the most commonly detected genotype worldwide and is not included in the recombinant strains used in vaccines. Therefore, the infection was confirmed to have been caused by the vaccine strain by analyzing the genetic relationship between VP4 and VP7. Rotavirus infection by the vaccine strain can be identified through genotyping and fingerprint gene detection. However, genetic linkage analysis will also help to identify vaccine strains.

The Long-Term Impact of Rotavirus Vaccines in Korea, 2008-2020; Emergence of G8P[8] Strain

This study evaluated the long-term impact of rotavirus vaccination on prevalence, seasonality, and genotype distribution in Gwangju, Korea for 13 seasons. Rotavirus was identified using ELISA and then sequenced for G and P genotypes by Reverse Transcription Polymerase Chain Reactions for diarrhoeagenic patient specimens from local hospitals between January 2008 and August2020. Of 26,902 fecal samples, 2919 samples (10.9%) were ELISA positive. The prevalence declined from 16.3% in pre-vaccine era to 5.4% in post-vaccine era. In the pre-vaccine period, G1P[8] was the most common genotype, followed by G2P[4], G3P[8], and G9P[8], etc. In the transitional period, the proportion of G2P[4] became the dominant genotype and G1P[8] was still commonly identified. In contrast, the novel genotype G8P[8] was predominant in the post-vaccine period. Meanwhile, G2P[4] and G8P[8] were major genotypes in both Rotarix and RotaTeq groups. The substantial decline of G1P[8] prevalence, reemergence of G1P[8], G3P[8], and G2P[4] rotavirus strains, and surge of the rare G8P[8] after vaccine introduction were interesting points to note. The continuous surveillance on the genotypes of RV will be needed to understand rotavirus epidemiology and their evolutionary patterns, as caution is required when interpreting temporal changes in RV genotype dynamic.

Lessons Learned from Long-Term Assessment of Rotavirus Vaccination in a High-Income Country: The Case of the Rotavirus Vaccine Belgium Impact Study (RotaBIS)

INTRODUCTION

The rotavirus (RV) vaccine Belgium Impact Study (RotaBIS) evaluated the vaccine effect on RV-related hospital care in children up to 5 years old over a period of 13 years. Different forces were identified that influence the reduction in hospital care. Our analysis aims to report on the current RotaBIS dataset and explore through model simulation whether, how, and when the results could have been improved.

METHODS

As performed in previous assessments, this analysis evaluated RV-related events per year, per age group, RV nosocomial infections, hospitalization duration, and herd effect. It subsequently identified results that were surprising or unexpected. To know whether those data could have been improved through specific interventions, we developed a model with the forces acting on the disease transmission and the vaccine effect on RV-related hospital care. Scenario analysis of the forces should explain the current findings and identify ways to optimize the results.

RESULTS

The RotaBIS data show that annual RV-related hospital cases (n = 1345 pre-vaccination) dropped by 70% (95% confidence interval [CI] 66-74%) by year 5 (n = 395) after vaccine introduction, and by 84% (95% CI 79-89%) by year 10 (n = 217). The herd effect during the first year was limited to 14% extra gain. During the last 5 years, small disease increases were seen biennially. The simulation model indicates that higher vaccine coverage of the major transmitters during the peak season of the first year of vaccination could have reduced RV-related hospital care by nearly 90% at 5 and 10 years after vaccine introduction owing to a higher herd effect. The smaller peaks observed in recent years would have been dramatically reduced.

CONCLUSION

The current RotaBIS data show a maintained reduction, around 76%, in RV hospitalization cases. Simulations show that these results could have been improved to an important extent with a more optimal initiation of the vaccination program.

TRIAL REGISTRATION

ClinicalTrials.gov identifier, NCT01563146 and NCT01563159.

Increasing detection of rotavirus G2P[4] strains in Nizhny Novgorod, Russia, between 2016 and 2019

Rotavirus infection is one of the leading causes of acute gastroenteritis in children in their first years of life. We studied the genotypic diversity of rotavirus A (RVA) strains in Nizhny Novgorod, Russia, during the period 2016-19. In total, 4714 samples of faeces from children admitted to the Nizhny Novgorod Hospital for Infectious Diseases with acute gastroenteritis were examined. The share of rotavirus-positive samples was 31.5% in 2016-17. It decreased to 21.6% in 2018-19. In Nizhny Novgorod, all six global types of RVA were detected (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]), as well as sporadic samples with genotypes G9P[4], G3P[9], G9P[9], G8P[8], G2P[8], G4P[4], G3P[9]. The fraction of strains with genotype G2P[4] gradually increased from 5.9% in 2016-17 to 39.1% in 2018-19. Simultaneously, the proportion of G9P[8] strains decreased from 63.2% to 27.7% in the same period. Phylogenetic analysis showed that rotaviruses with the G2P[4] genotype carried ubiquitous alleles of the VP7 and VP4 genes during the period of their prevalence: G2-IVa-1 and G2-IVa-3; P[4]-IVa and P[4]-IVb. As rotavirus vaccination is not widely used in the region because it is not included in the national vaccination calendar in Russia so far, the increase in the number of G2P[4] RVA is likely due to natural strain fluctuations.

Rotavirus disease and genotype diversity in older children and adults in Australia

Background

Rotavirus is a major cause of gastroenteritis in children <5 years of age. The disease burden in older children, adults, and the elderly is underappreciated. This study describes rotavirus disease and genotypic diversity in the Australian population comprising children ≥5 years of age and adults.

Methods

Rotavirus positive fecal samples were collected from laboratories Australia-wide participating in the Australian Rotavirus Surveillance Program between 2010 and 2018. Rotavirus samples were genotyped using a heminested multiplex reverse-transcription polymerase chain reaction. Notification data from the National Notifiable Diseases Surveillance System were also analyzed.

Results

Rotavirus disease was highest in children aged 5–9 years and adults ≥85 years. G2P[4] was the dominant genotype in the population ≥5 years of age. Genotype distribution fluctuated annually and genotypic diversity varied among different age groups. Geographical differences in genotype distribution were observed based on the rotavirus vaccine administered to infants <1 year of age.

Conclusions

This study revealed a substantial burden of rotavirus disease in the population ≥5 years of age, particularly in children 5–9 years and the elderly. This study highlights the continued need for rotavirus surveillance across the population, despite the implementation of efficacious vaccines.

Whole-genome sequence of a reassortant G9P[4] rotavirus A strain from two children in the Czech Republic

An unusual reassortant rotavirus A (RVA) strain was isolated during RVA surveillance in two previously hospitalized children in 2018. G/P typing revealed uncommon G9P[4] genotypes, so the strains were further characterized by Illumina next-generation sequencing. Whole-genome typing showed that the two strains had a DS-1-like backbone except for NSP2: G9-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2. The two strains shared 99.9-100% nucleotide sequence identity in all genes.