Molecular Diversity of Human Respiratory Syncytial Virus before and during the COVID-19 Pandemic in Two Neighboring Japanese Cities

Genotypic Characterization of Human Respiratory Syncytial Viruses Detected in Mexico Between 2021 and 2024

Human respiratory syncytial virus (HRSV) is a leading cause of severe respiratory infections among children, older adults, and immunocompromised individuals. The COVID-19 pandemic and the non-pharmacological interventions to mitigate it resulted in significant changes in HRSV epidemiology and seasonality patterns. Worldwide, there was a considerable reduction in the number of HRSV infections during that period, and the impact of those changes on genotype distribution is still not fully understood. In this work, we analyzed the genotypic characteristics of HRSV strains detected between 2021 and 2024 in Mexico with the aim of identifying changes in circulating lineages. HRSV positive samples collected in five states in Mexico were used. The complete viral attachment glycoprotein gene was sequenced, and phylogenetic inference was performed using datasets including all sequences available at GenBank and GISAID until 30 June 2024. We obtained 114 HRSV sequences (63.2% HRSV-A and 36.8% HRSV-B); 19 were from the 2021-2022 season, 53 from 2022-2023, and 42 from 2023-2024. All HRSV-A sequences clustered with sequences from other countries within A.D lineages, including A.D.1, A.D.3, A.D.5.1, and A.D.5.2 lineages. All HRSV-B sequences clustered in the B.D.E.1 lineage with sequences collected between 2020 and 2024. In conclusion, the characterization of HRSV viruses circulating in Mexico during and after the SARS-CoV-2 pandemic and comparison to all available sequences reported to date corroborates that, on a global scale, HRSV-A viruses of several A.D lineages circulate simultaneously, while HRSV-B viruses are restricted to the B.D.E.1 lineage.

Optimization of a 6-plex Crystal Digital PCR® assay and its application to simultaneous surveillance of enteric and respiratory viruses in wastewater

Multiplex digital PCR (dPCR) approaches are commonly employed in wastewater-based epidemiology (WBE) studies. However, optimizing the dPCR workflow is a critical step to ensure its reliability and accuracy before application. In this study, a 6-plex Crystal Digital PCR® (cdPCR) workflow was optimized for the simultaneous detection of six epidemiologically important pathogens, including three enteric viruses, noroviruses of genogroups I and II (NoV-GI and GII) and enteroviruses (EnV), and three respiratory viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), influenza A virus (InfA), and respiratory syncytial virus B (RSVB), in wastewater. Four cDNA input ratios (20 %-70 %) and two extraction kits were evaluated for optimization, with 30 % cDNA input and the AllPrep PowerViral DNA/RNA Kit (Qiagen) exhibiting optimal performance. The optimized 6-plex cdPCR assay was applied to a year-long wastewater surveillance study in Japan (n = 52), revealing distinct trends and prevalence ratios for enteric and respiratory viruses. NoV-GII was detected in 96 % of the samples with the highest mean concentration (6.1 ± 0.6 log10 copies/L), while SARS-CoV-2 and InfA were detected in 60 % and 50 % of the samples, respectively, which reflected the circulation of these pathogens within the community. Notably, RSVB was detected less frequently (25 %), in line with the fewer cases of RSVB reported during the study period. The wastewater concentrations of EnV and InfA showed significant positive correlations with hand foot and mouth disease and herpangina and influenza cases, respectively. However, no positive correlations were observed for RSV and COVID-19, possibly due to the testing of RSVB while RSVA was more prevalent and also due to cluster outbreaks. These findings demonstrated the utility of the 6-plex cdPCR assay in detecting pathogens and provided insights into community disease trends, representing an advancement in WBE.

Molecular Epidemiology of Respiratory Syncytial Virus during 2019-2022 and Surviving Genotypes after the COVID-19 Pandemic in Japan

To evaluate the changes in respiratory syncytial virus (RSV) collected between 2019 and 2022, we analyzed RSV-A and RSV-B strains from various prefectures in Japan before and after the COVID-19 pandemic. RT-PCR-positive samples collected from children with rapid test positivity at outpatient clinics in 11 prefectures in Japan were sequenced for the ectodomain of the G gene to determine the genotype. Time-aware phylogeographic analyses were performed using the second hypervariable region (HVR) of the G gene from 2012 to 2022. Of 967 samples, 739 (76.4%) were found to be RSV-positive using RT-PCR. RSV peaked in September 2019 but was not detected in 2020, except in Okinawa. Nationwide epidemics occurred with peaks in July 2021 and 2022. The genotype remained the same, ON1 for RSV-A and BA9 for RSV-B during 2019-2022. Phylogeographic analysis of HVR revealed that at least seven clusters of RSV-A had circulated previously but decreased to two clusters after the pandemic, whereas RSV-B had a single monophyletic cluster over the 10 years. Both RSV-A and RSV-B were transferred from Okinawa into other prefectures after the pandemic. The RSV epidemic was suppressed due to pandemic restrictions; however, pre-pandemic genotypes spread nationwide after the pandemic.