BACKGROUND:Airway mucus plugs on chest computed tomography (CT) are increasingly recognized for their impact and potential as treatable traits. However, radiation exposure warrants reasonable patient selection. OBJECTIVE:To develop and externally validate a practical clinical score to predict CT-detected mucus plug presence in 2 asthma cohorts and to evaluate its association with clinical outcomes. METHODS:This multicenter retrospective analysis used clinical and CT data from adult patients with stable asthma. The primary outcome was mucus plug presence on CT. We identified independent predictors using multivariable logistic regression, derived a practical scoring system in the exploratory cohort, and validated it in an independent cohort. RESULTS:The prevalence of mucus plugs was 50.8% (218 of 429) in the exploratory cohort and 76.5% (143 of 187) in the validation cohort. Age (A; maximum 2 points), body mass index (B; maximum 2 points), blood eosinophil count (E; maximum 2 points), fractional exhaled nitric oxide (N; maximum 1 point), and percent-predicted FEV1 (F; maximum 2 points) were independently associated with the presence of mucus plugs. The derived score (ABENF score; maximum 9 points) showed good discrimination in both cohorts (cohort 1: area under the receiver-operating characteristic curve, 0.781, 95% CI, 0.742-0.820; cohort 2: area under the receiver-operating characteristic curve, 0.836, 95% CI, 0.783-0.889). The high-score group (ABENF score ≥4) had a shorter time to first exacerbation (P = .046) and higher sputum eosinophil percentage (P < .001) in the validation cohort. CONCLUSIONS:The ABENF score could be a practical tool to estimate mucus plug presence, potentially supporting more selective CT use.

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.

Bioinformatics has transformed modern virology by linking genomic variation to epidemiology, protein structure, and public health action. This review integrates core analytical frameworks-sequence alignment and genome annotation; maximum-likelihood and Bayesian phylogenetic/phylodynamic inference; codon-based selection and recombination analyses; and AI-assisted structural prediction combined with deep mutational scanning (DMS)-to convert viral sequences into mechanistic and predictive insight. We emphasize how global surveillance ecosystems (GISRS, GISAID, and Nextstrain) and sustained regional programs reveal genotype turnover, antigenic drift, and seasonality in RSV, HPIV, norovirus, and SARS-CoV-2, enabling near real-time lineage tracking and vaccine-strain deliberation. Mapping positively selected residues and recombination breakpoints onto three-dimensional protein structures clarifies immune escape in key surface glycoproteins (e.g., RSV F/G, HPIV HN/F, norovirus VP1) and strengthens genotype-phenotype interpretation. Comparative reinfection patterns-lifelong immunity in measles versus recurrent RSV/HPIV infections-illustrate how evolutionary rate and antigenic constraint shape population immunity and control strategies. Despite major advances, progress remains constrained by geographic sampling bias, incomplete metadata, uneven computational capacity, and uncertainties in molecular clocks, recombination inference, and machine-learning predictions. The field is now moving toward predictive virology, integrating AI-enabled structural modeling, mutational fitness landscapes, and clinical-immunological metadata within real-time analytical platforms to anticipate immune-escape trajectories. Prioritizing pediatric respiratory pathogens alongside influenza and coronaviruses, and reinforcing equitable data-sharing and governance, will be essential for globally inclusive, forward-looking viral surveillance and intervention.

A 65-year-old man, who had undergone laryngectomy two years earlier, was incidentally found to have nodular shadows and ground-glass opacity (GGO) in both lower lobes, identified nine months ago, which gradually progressed. He was diagnosed with lipoid pneumonia based on a transbronchial lung biopsy. The daily application of Vaseline to the tracheostomy site was considered the cause of exogenous lipoid pneumonia. Although GGO improved after the discontinuation of Vaseline use, it persisted 2 years later. This case is notable for its unusually short onset interval of 1.5 years and the longest reported follow-up of Vaseline-induced lipoid pneumonia after laryngectomy.

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.

Human norovirus (HuNoV) is a major cause of acute viral gastroenteritis. Although it can be replicated in vitro using human intestinal enteroids (HIEs), generating high-titer viral laboratory stocks remains challenging due to low infection and passage efficiencies. Interferon response and chemokine signaling may be key host pathways that restrict efficient HuNoV replication. Here, we evaluated the effect of their inhibitors, ruxolitinib-a Janus kinase (JAK) 1/JAK2 inhibitor-and TAK-779-a C-X-C motif chemokine receptor 3 (CXCR3)/C-C motif chemokine receptor (CCR) 5/CCR2 antagonist-on HuNoV replication in wild-type jejunal HIEs. TAK-779 increased GII.17 HuNoV replication by 2.3- and 6.0-fold at 48 and 96 h postinfection (hpi), respectively, compared with the DMSO-treated control. In contrast, ruxolitinib alone did not affect viral replication. Notably, simultaneous treatment with these compounds further enhanced GII.17 replication by 6.0- and 10.7-fold at 48 and 96 hpi, respectively, which enabled serial passaging. These findings imply that the simultaneous suppression of these pathways potentially benefits GII.17 HuNoV replication.

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 metapneumovirus genotype B (HMPV-B) is an important respiratory pathogen, requiring detailed elucidation of the evolutionary and antigenic features of its fusion (F) gene. Using 500 sequences collected between 1982 and 2024, we investigated the molecular evolution, phylodynamics, and structural epitope landscape of the HMPV-B F gene. Time-scaled phylogeny dated the divergence of sublineages B1 and B2 to around 1937, and Bayesian Skyline Plot analysis showed that these sublineages exhibited distinct demographic trajectories over time. The F gene evolved at a rate of 1.01 × 10−3 substitutions/site/year; however, amino acid variation remained limited, consistent with pervasive purifying selection, with 39% of codons under strong negative selection and little consensus evidence for positive selection. Conformational B-cell epitope prediction demonstrated a high degree of conservation across neutralizing antibody binding regions (sites Ø and I–V), and amino acid substitutions occurring within these sites were not predicted to substantially alter epitope architecture. Together, these findings indicate that the HMPV-B F gene evolves under strong evolutionary constraint while maintaining stable antigenic features, supporting the potential for antibody-based strategies that target neutralizing antibody binding regions of the F protein.

Asthma-like features, defined as a high blood eosinophil count (BEC), atopy, and bronchodilator reversibility, characterize patients with chronic obstructive pulmonary disease (COPD) under optimal treatment. However, whether these features contribute to the phenotype of mucus plugging has not been elucidated. In this study, we aimed to examine the functional and clinical outcomes related to mucus plugging in patients with and without asthma-like features. Mucus plug score was assessed using inspiratory computed tomography (CT) scans in participants from the Hokkaido COPD cohort study who underwent CT examinations using the same protocol, were categorized based on asthma-like features, and completed the St. George’s Respiratory Questionnaire (SGRQ). To evaluate the association between mucus plug score and pulmonary function indices, multivariate analyses were performed to examine the relationships between the mucus plug score and percent predicted forced expiratory volume in 1 s (

Rationale: Idiopathic pleuroparenchymal fibroelastosis (iPPFE) is a rare type of idiopathic interstitial pneumonias characterized by upper lobe predominant subpleural fibrosis. Although there are cases with a good prognosis, as the disease progresses, most cases suffer from complications such as pneumothorax, cachexia, and respiratory failure. However, previous reports were limited to a small number of facilities, the overall prevalence and characteristics of iPPFE in Japan remain unclear. We conducted a prospective cohort study of iPPFE from multi-center in Japan. Methods: Our iPPFE registry consisted of 216 cases from 36 facilities in Japan. Clinical findings, laboratory data, respiratory function tests, image findings, and the prognosis were collected. Results: 53.7% were male. The median age at disease onset was 67 (IQR 59-72) years, and BMI was 17.6 (15.8-19.7) at the time of entry. %FVC at enrollment was low at 68.3 (53.0-91.9). KL-6 was within normal range at 396 (292-572) U/L, while SP-D was high at 185 (122-294) ng/mL. The flat chest ratio was 0.56 (0.52-0.61). The survival rate 2 years after enrollment was 76.9%. Conclusions: Our cohort included 216 patients with iPPFE, and we conducted a 2-year survival analysis.

Human norovirus (HuNoV) is a major causative agent of foodborne illness and causes acute viral gastroenteritis. This study aimed to compare the virucidal efficacies of alcohol-based disinfectants against HuNoV and its surrogates for murine norovirus and feline calicivirus using a cell culture infectivity assay. Additionally, the study evaluated the validity of estimating virucidal efficacy on HuNoV from the results of virucidal efficacy on the surrogate virus. All disinfectants decreased the titer of each virus by >3 log10 and >4 log10 for an exposure duration of 30 s against murine norovirus and feline calicivirus, respectively. However, acidic alcohol-based disinfectants completely inactivated the HuNoV GII.17 strain for 30 or 60 s, whereas an alkaline alcohol-based disinfectant did not inactivate HuNoV GII.17 for 60 s. This finding indicates that the pH of alcohol disinfectants affects their virucidal effects against HuNoV, and acidity has a higher virucidal efficacy against HuNoV than alkalinity. Disinfectants showing virucidal efficacy against surrogates were not effective against HuNoV. Few studies have used cell culture infectivity assays to test the inactivating effects of hand sanitizers on HuNoV and its surrogates. Our study provides useful information for the development of disinfectants that are effective against HuNoV.

Norovirus norwalkense in humans (HuNoV) is a major cause of acute gastroenteritis, primarily consisting of genogroups GI and GII. Each genogroup is made of genotypes with distinct antigenicity, which is derived mainly from variations in P2 subdomain of viral protein 1 (VP1). Given that multiple genotypes circulate with varying prevalence, predicting dominant genotypes in a particular season could aid in vaccine development. Here, models for forecasting dominant genotypes were evaluated by analyzing observed genotype frequencies in Japan and amino acid sequences of P2 subdomain. Genotypes GI.1-GI.7 in GI, and GII.2-GII.4, GII.6, GII.7, GII.14, and GII.17 in GII were considered as potential candidates. In contrast to the null model, which assumes that genotype proportions are unchanged from the previous season, the fitness model, which takes into account genotypespecific proliferation efficiency and recombination, demonstrated better performance. The fitness model was improved when herd immunity was assumed to be triggered not only by identical amino acids but also by different amino acids with similar physicochemical properties in P2 subdomain across different strains. Moreover, it was suggested that herd immunity may persist for around a decade in GI and GII.

Oz virus (OZV), an emerging negative-sense single-stranded RNA virus classified under the family Orthomyxoviridae and genus Thogotovirus, was first isolated from Amblyomma testudinarium ticks in Ehime Prefecture, Japan, in 2013. Moreover, a single fatal case in an elderly individual, suspected to be associated with OZV infection, was reported in Ibaraki Prefecture in 2023. Given these circumstances, this study was conducted to investigate the molecular epidemiology and seroepidemiology of OZV in Ibaraki Prefecture, Japan. From April to November 2023, a total of 2430 ticks were collected at 19 sites. The OZV RNA was detected in one A. testudinarium nymph. Additionally, among 934 wild boar serum samples collected between 2019 and 2023, one sample tested positive for OZV RNA. Neutralizing antibody assays revealed that 243 samples (26.0%) obtained from wild boars were seropositive, indicating widespread exposure among wild boars. Antibody prevalence and titers were highest in the central–western mountainous region, suggesting an active transmission hotspot. Sequence analysis of the OZV viral RNA detected from one tick sample and one wild boar serum revealed that a 212 bp fragment of segment 4 and a 261 bp fragment of segment 5 were 100% identical to a human-derived strain isolated in the same prefecture, suggesting the circulation of a single viral lineage within the local environment. These findings represent the first report demonstrating the circulation of OZV in the natural environment in Ibaraki Prefecture, implicating A. testudinarium as the principal vector and wild boars as a potential source of OZV infection These results suggest that OZV should be considered a potential emerging zoonotic pathogen. Further seroepidemiological studies among residents are warranted to assess the risk of human infection in the region.

To better understand the phylogenomics of the hemagglutinin-neuraminidase (HN) gene and HN protein in human parainfluenza virus type 4 (HPIV4), we performed phylogenomic analyses using various bioinformatics methods. The main bioinformatics analyses included a time-scaled phylogeny, genetic distance assessments, and three-dimensional (3D) structure mapping of the HN protein with conformational epitope and selective pressure analyses. The time-scaled phylogenetic tree indicated that the most recent common ancestor of the HN gene emerged approximately 100 years ago. Additionally, the tree revealed two distinct clusters corresponding to HPIV4a and HPIV4b. The divergence times for the most recent common ancestors of the HN gene in HPIV4a and HPIV4b strains were estimated to be around 1993 and 1986, respectively. The evolutionary rates of the gene varied significantly between clusters, ranging from approximately 1.2 × 10−3 to 8.7 × 10−4 substitutions per site per year. Genetic distances within each cluster were relatively short (less than 0.04). Phylodynamic analyses demonstrated an increase in the genome population size around the year 2000. Structural analyses revealed that the active sites of the HN protein were located at the protein’s head. Furthermore, the most conformational epitopes were located in adjacent active sites of the protein. These results suggested that reinfection may be unlikely to occur in the case of most HPIV4. Together, the HN gene and protein of HPIV4 strains isolated in Japan have undergone unique evolutionary changes. In addition, antibodies targeting the conformational epitopes of the HPIV4 HN protein may contribute to protection against the virus.

Post-acute sequelae of SARS-CoV-2 infection (PASC), commonly known as “Long COVID”, represents a significant clinical challenge characterized by persistent symptoms following acute COVID-19 infection. We conducted a comprehensive retrospective cohort study to identify serum autoantibody biomarkers associated with PASC. Initial screening using a protein bead array comprising approximately 20,000 human proteins identified several candidate PASC-associated autoantibodies. Subsequent validation by enzyme-linked immunosorbent assay (ELISA) in an expanded cohort—consisting of PASC patients, non-PASC COVID-19 convalescents, and pre-pandemic healthy controls—revealed two promising biomarkers: autoantibodies targeting PITX2 and FBXO2. PITX2 autoantibodies demonstrated high accuracy in distinguishing PASC patients from both non-PASC convalescents (area under the curve [AUC] = 0.891) and healthy controls (AUC = 0.866), while FBXO2 autoantibodies showed moderate accuracy (AUC = 0.762 and 0.786, respectively). Notably, the levels of these autoantibodies were associated with several PASC symptoms, including fever, dyspnea, palpitations, loss of appetite, and brain fog. The identification of PITX2 and FBXO2 autoantibodies as biomarkers not only enhances our understanding of PASC pathophysiology but also provides promising candidates for further investigation.

HIV-2 viral protein X (Vpx) plays a pivotal role in antagonizing the host restriction factors, including SAMHD1 and components of the HUSH complex, to facilitate viral replication. However, the regulatory mechanisms controlling Vpx stability remain unclear. In this study, we identify the von Hippel-Lindau (VHL) tumor suppressor as a novel E3 ubiquitin ligase that specifically targets Vpx for proteasomal degradation. Mechanistically, we demonstrate that VHL-mediated degradation depends on the oxygen-dependent hydroxylation of Vpx at proline residue 41 (Pro41), a modification catalyzed by prolyl hydroxylase domain-containing protein 3 (PHD3). Using an integrated approach combining crosslinking mass spectrometry and molecular modeling analyses, we elucidate the structural architecture of the PHD3-Vpx complex, revealing the spatial orientation of the catalytic domain of PHD3 required for Pro41 hydroxylation. Furthermore, we establish the physiological significance of this pathway in human macrophages, where pharmacological inhibition or genetic ablation of VHL or PHD3 enhances HIV-2 infection by facilitating Vpx-mediated SAMHD1 degradation. Collectively, our findings unveil a previously unrecognized oxygen-sensitive regulatory mechanism influencing HIV-2 infection and suggest novel therapeutic strategies targeting Vpx stability through modulation of its prolyl hydroxylation status.

Review Reinfection Mechanisms of Various Viruses and Their Societal Implications Ryusuke Kimura 1,2,†, Yuriko Hayashi 3,†, Yuka Sato-Fujimoto 4, Kei Miyakawa 5, Kazuya Shirato 6, Koo Nagasawa 7, Fuminori Mizukoshi 6, Takeshi Tsugawa 8, Akihide Ryo 4 and Hirokazu Kimura 2,3,* 1 Department of Bacteriology, Graduate School of Medicine, Gunma University, Maebashi-shi 371-8511, Gunma, Japan 2 Advanced Medical Science Research Center, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan 3 Department of Health Science, Graduate School of Health Sciences, Gunma Paz University, Takasaki-shi 370-0006, Gunma, Japan 4 Faculty of Healthcare, Tokyo Healthcare University, Setagaya-ku 141-8648, Tokyo, Japan 5 Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Musashimurayama-shi 208-011, Tokyo, Japan 6 Department of Virology III, Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Tokyo, Japan 7 Department of Pediatrics, Chiba University Hospital, Chiba-shi 260-8670, Chiba, Japan 8 Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo-shi 060-8543, Hokkaido, Japan * Correspondence: h-kimura@paz.ac.jp † These authors contributed equally to this work. Received: 27 December 2024; Revised: 22 January 2025; Accepted: 24 February 2025; Published: 26 February 2025 Abstract: Viral infections involve numerous pathogens, some of which allow reinfection while others, such as measles virus, provide lifelong immunity. The differences in reinfection mechanisms can be attributed to variations in viral antigenicity and host immune responses. Measles virus exhibits highly conserved hemagglutinin (HA) proteins, where neutralizing antibody-binding regions overlap with host receptor-binding sites, resulting in effective immune protection against reinfection. In contrast, influenza viruses undergo rapid antigenic evolution driven by immune selection pressures, leading to immune escape variants that facilitate annual reinfections. SARS-CoV-2, similarly, shows frequent mutations in its spike protein receptor-binding domain (RBD), contributing to reinfection despite prior immunity from vaccination or infection. Respiratory syncytial virus (RSV) and human respirovirus type 3 (HRV3) are monoserotype viruses capable of lifelong reinfections. Structural analyses indicate that their conformational epitopes do not align with neutralizing antibody-binding sites, undermining the effectiveness of immune responses. To better understand these mechanisms highlights the interplay between viral evolution and host defenses, providing essential insights for developing targeted vaccines and therapeutic strategies to combat respiratory virus reinfections. Moreover, understanding of the reinfection mechanisms regarding various virus infections may significantly influence public health policies, emphasizing the need for effective vaccination strategies, risk communication, and consideration of cultural factors to address challenges in vaccine adoption, health behaviors, and societal stigma.