Mumps virus (MuV) genotype G is widely represented among circulating strains, but the evolutionary patterns of the hemagglutinin–neuraminidase (HN) gene remain incompletely understood. In this study, we analyzed publicly available full-length genotype G HN sequences using phylogenetic, phylodynamic, codon-based selection, and structure-guided epitope prediction approaches. The genotype G HN sequences were categorized into Clade 1, an operationally defined Diverse group, and Clade 2. Clade 1, which was composed mainly of Japanese strains, showed a relatively structured pattern over time. In contrast, Clade 2 showed more recent diversification and an overall increase in relative genetic diversity, although this phylodynamic pattern was sensitive to sampling structure. The Diverse group was phylogenetically heterogeneous, and its Bayesian skyline estimates were not used for biological interpretation because repeated analyses showed unstable posterior behavior. Root-to-tip regression supported temporal structure in the complete dataset, with the strongest signal in Clade 2. Bayesian molecular dating estimated the time to the most recent common ancestor of the sampled genotype G HN sequences at approximately 1932, and the mean evolutionary rate was 4.925 × 10−4 substitutions/site/year. Although the HN protein is a major surface antigen and a target of neutralizing antibodies, codon-based analyses showed no robust evidence of positive selection using multiple methods. Instead, many codon sites were inferred to be under purifying selection, suggesting that genotype G HN evolution is largely constrained by the need to maintain protein function. Predicted B-cell epitope regions were broadly similar among representative genotype G strains. Overall, these findings indicate that genotype G HN lineages have followed distinct evolutionary patterns, while the HN gene remains mainly shaped by purifying selection. These findings may help improve our understanding of MuV genotype G HN gene evolution and support future molecular surveillance.
Shiga toxin (Stx)-producing Escherichia coli (STEC) is a major cause of serious gastrointestinal illness, including diarrhoea, haemorrhagic colitis and life-threatening haemolytic-uraemic syndrome. Although O157:H7 STEC strains are the most prevalent, the incidence of STEC infections caused by several other serotypes has recently increased. O103:H2 STEC is one of these major non-O157 STEC strains, but systematic whole-genome sequence (WGS) analyses have not yet been conducted. To gain a global phylogenetic overview of O103:H2 STEC based on WGSs, we analysed 2,701 WGSs of O103:H2 strains, including 193 sequenced in this study. Sequence type (ST)-based classification divided the O103:H2 strains into three distinct E. coli lineages. As the virulence marker genes of typical STECs (stx, eae and ehxA) were found only in the major O103:H2 lineage (n=2,658) comprising ST17 and its single- and double-locus variants, we performed a global phylogenetic analysis of the major lineage. This analysis revealed that this lineage was divided into five clades (C1-C5) and that C1 was the ancestral clade, C2 and C3 emerged from C1 and C4 and C5 emerged from C3. While stx2 genes were sporadically distributed in limited STEC O103:H2 strains, stx1a, eae and ehxA were highly conserved throughout the entire STEC O103:H2 lineage. However, through a detailed comparison of seven closed genomes of STEC strains, covering the five clades and including four obtained in this study, we found marked variation in the genetic elements encoding the virulence genes (Stx1a phage, the locus of enterocyte effacement (LEE) and the virulence plasmid), such as rearrangement in the LEE accessory region, a shift in the integration sites of the Stx1a phage due to the replacement of the integrase gene-containing genomic segments, the replacement of the virulence plasmid and the gain and loss of virulence-related genes in the virulence plasmid. Overall, this study highlights the current global population structure of O103:H2 strains and provides evolutionary insights into the variation in virulence determinants within STEC O103:H2, which is relatively understudied among the major STEC lineages.
Vaporized free chlorine, primarily present as hypochlorous acid (HOCl), is increasingly used for indoor microbial control; however, virus-dependent susceptibility and its molecular determinants remain unclear. We evaluated virucidal effects under controlled indoor conditions (0-9 ppb) against echovirus 30 (E30), influenza A/H1N1, and human adenovirus type 3 (HAdV3). Infectious titers were quantified by TCID50 assays. Computational fluid dynamics (CFD) simulations and gas-sensor measurements assessed spatial dispersion, and structural analyses examined oxidation-sensitive amino acid residues. Significant reductions in infectivity were observed for E30 (99.0%, p = 0.00727) and influenza A/H1N1 (99.9%, p = 0.000597), whereas no significant reduction was detected for HAdV3 (p = 0.142). Analyses including all data points without outlier exclusion confirmed the robustness of these findings. CFD indicated uniform dispersion, although spatial heterogeneity within the indoor environment cannot be excluded. These findings suggest that viral susceptibility to vaporized HOCl is associated with residue-level composition and structural context; however, this relationship should be interpreted as correlative rather than causal. Moreover, integration of molecular and structural analyses provides a plausible mechanistic framework, although direct biochemical validation remains necessary. Structural analyses showed lower proportions of oxidation-sensitive residues in adenoviral proteins compared with influenza A hemagglutinin (OR = 0.34-0.40, adjusted p < 0.001) and the E30 VP1 intermediate. Residues were clustered in surface-exposed functional domains in susceptible viruses.
In this study, we investigated the long-term evolutionary dynamics of human norovirus GII.17[P17] using the RNA-dependent RNA polymerase (RdRp) region and the VP1 capsid gene, integrating phylogenetics, time-scaled inference, phylodynamics, and structure-based analyses. Maximum-likelihood phylogenies of both genomic regions consistently resolved four major clades (Clades 1-4). VP1 patristic-distance distributions indicated higher within-clade diversity in the phylogenetically basal Clades 1 and 3, whereas Clades 2 and 4 showed lower diversity, consistent with recent demographic expansion. Similarity-plot analysis identified pronounced variability in the VP1 P2 domain, while the S and P1 domains remained comparatively conserved, supporting P2 as the primary hotspot of diversification. Bayesian time-scaled analyses estimated the most recent common ancestor around 1993 (VP1) and 2000 (RdRp) and revealed two major lineages (Clade 1/2 and Clade 3/4), with the split between Clades 3 and 4 occurring around 2016-2017. Bayesian skyline plots showed a marked increase in effective population size after 2013, and substitution-rate estimates indicated faster evolution in VP1 than in RdRp, with higher VP1 rates in the Clade 3/4 lineage than in Clade 1/2. Capsid dimer modeling further mapped high-confidence conformational B-cell epitopes and positively selected residues predominantly to the distal surface of P2, with broadly conserved spatial patterns across clades. Compared with the Clade 1 reference (Kawasaki323), Clade 2 accumulated numerous P2 substitutions, whereas Clades 3 and 4 retained fewer changes and remained closer to Clade 1 at the amino-acid level. Together, these results suggest lineage turnover within GII.17[P17] driven by constrained diversification at the P2 surface, potentially contributing to the recent predominance of the Clade 3/4 lineage.
Human rhinovirus (HRV) commonly causes mild respiratory illness but may occasionally result in severe disease requiring hospitalization. Herein, we report a respiratory outbreak at a residential hospital for individuals with severe motor and intellectual disabilities (SMID) where HRV was detected. The facility housed 47 residents, 31 of whom developed symptoms. Further, 20 symptomatic patients were tested, and HRV-C was detected in 15 of them using RT-PCR. The nucleotide identity of the detected strains was 100%, and based on phylogenetic analysis, the strain was identified as the HRV-C56 type. No other pathogens were detected. Although the specific mode of transmission remains unclear, the patients had been residing at the facility for an extended period of time with limited mobility. Therefore, healthcare workers or visitors may have been the source of infection. In this outbreak, HRV-C disseminated rapidly among the residents, resulting in the spread of infections to healthcare workers and affecting healthcare. It is imperative for medical institutions, particularly long-term care facilities, to establish systems for the early detection and management of respiratory infections.
