Genotype turnover and global evolutionary dynamics of G gene duplication variants in human metapneumovirus: insights from prospective surveillance in Nantong, China, 2024–2025
Aug 2026· Frontiers in Microbiology· Vol 17· 0 citations· 48 references
Medicine
TL;DR
The global dominance of 111nt_dup is better explained by lineage-specific molecular selection than neutral drift, and a model in which predicted glycosylation-driven optimization of the G protein mucin-like domain may enhance fitness, with implications for hMPV vaccine strain surveillance is suggested.
Abstract
Background Human metapneumovirus (hMPV) is a leading cause of acute respiratory infections worldwide, yet whole-genome surveillance data remain scarce in eastern China. The evolutionary dynamics of G gene duplication variants and their molecular drivers are poorly characterized. Methods From 2024 to 2025, we conducted prospective hMPV surveillance in Nantong, Jiangsu Province, screening 1,602 respiratory specimens by multiplex qPCR. Complete whole-genome sequences were obtained from 26 of 27 positive strains via probe-capture next-generation sequencing, and integrated with 574 global reference genomes. G gene duplication variants (111nt_dup/180nt_dup) were characterized, O-glycosylation sites predicted (NetOGlyc 4.0), and Bayesian phylodynamic analysis (BEAST v1.10.4) performed on the 111nt_dup lineage. Results The overall detection rate was 1.7% (27/1,602), with the highest burden in children aged 0–5 years (3.6%) and peak circulation in winter and spring. Phylogenetic analysis revealed a sharp genotype shift among the sequenced strains—from A2.2.2 in 2024 to B2 in 2025 (12/12 vs. 0/14; p < 0.001, Fisher’s exact test)—concordant with contemporaneous observations in Shanghai and Beijing. Globally, 111nt_dup prevalence rose from <10% before 2015 to >90% by 2025 (Cochran-Armitage trend test, p = 6.86 × 10−7), whereas 180nt_dup disappeared after 2021. The 111nt_dup lineage displayed near-complete fixation of serine at G protein position 90 (S90, 98.9% vs. 0% in 180nt_dup; p < 0.001). S90 frequency and 111nt_dup prevalence rose in tight synchrony (Pearson’s r > 0.95). Bayesian Skyline analysis showed a pandemic-associated population bottleneck (2020–2021) followed by rapid recovery to pre-pandemic levels by late 2022. Conclusion The global dominance of 111nt_dup is better explained by lineage-specific molecular selection than neutral drift. Co-occurrence of the 111nt_dup with the predicted S90 O-glycosylation site suggests a model in which predicted glycosylation-driven optimization of the G protein mucin-like domain may enhance fitness, with implications for hMPV vaccine strain surveillance.
Newcastle disease virus (NDV) remains one of the most economically important avian pathogens worldwide, causing recurrent outbreaks in poultry despite decades of vaccination and disease control efforts. Since the first reported outbreak of NDV a hundred years ago, numerous molecular epidemiological studies have been conducted globally across diverse geographic and production settings. Following a century of NDV circulation and evolution, the present study aimed to compile all publicly available NDV sequence data and perform a comprehensive global analysis of the genetic diversity, phylogenetic relationship, and global spatiotemporal distribution of NDV over a 100-year timescale. All publicly available NDV complete genome and full-length fusion (F) gene sequences were retrieved from GenBank up to February 2026. Following rigorous quality control, phylogenetic analyses were performed based on complete genomes and F gene datasets. Phylogenetic analysis identified two genotypes within Class I and 20 genotypes within Class II NDVs, with extensive diversification at the sub-genotype level. Genotype XIII exhibited the greatest sub-genotypic diversity, while genotype VII represented the most globally disseminated genotype, reported across 36 countries. Chronological assessment based on the earliest available reports indicated an increasing number of recognized genotypes from the 1930s to recently described sub-genotypes such as XIII.2.3 and XXII.2.2. Regional diversity analysis revealed the highest genotype diversity in Western Africa, Eastern Asia, and Southern Asia. Comparative residue analysis demonstrated substantial genotype-specific variation within critical functional domains of the fusion protein, including cleavage sites, neutralizing epitopes, and heptad repeat regions. Overall, this study provides the first comprehensive 100-year global overview of NDV evolution and phylogeography. The findings highlight continuous viral diversification, broad geographic dissemination of multiple genotypes, and ongoing molecular variation, emphasizing the need for sustained genomic surveillance and periodic evaluation of vaccine compatibility with emerging NDV genotypes.
Aziz ul-Rahman, M. Shabbir, M. Munir· Virus Research· 0 citations
Since NADC30-like PRRSV-2 was first detected in Henan Province in 2012, it has continued to spread and has become one of the predominant PRRSV-2 groups in mainland China. However, the long-term spatiotemporal dynamics, interprovincial transmission patterns, transmission drivers and recombination associated evolutionary features of sublineage L1C (L1C; NADC30-like) remain incompletely resolved. Here, we analysed 9541 quality-controlled lineage 1 ORF5 sequences from 12 countries, including ORF5 sequences from 62 laboratory-derived complete genomes assigned to L1C. Globally, 3787 sequences were classified as L1C. Among the 1648 lineage 1 sequences from China, 1362 were assigned to L1C, accounting for 82.65% of Chinese lineage 1 sequences. Phylodynamic analysis dated the global common ancestor of L1C to around 2002 and suggested that strains circulating in mainland China were likely introduced from US-related strains around 2008. Before the African swine fever (ASF) outbreak, inferred interprovincial transmission links were concentrated in a limited number of key provinces. During the early ASF period, observable links decreased, but they subsequently recovered and expanded across more provinces. Transmission-driver analysis suggested that pig inventory and pig output were associated with stronger inferred interprovincial L1C transmission links, whereas geographic distance was associated with a spatial-decay effect. Whole-genome recombination analysis revealed extensive recombination signals in L1C genomes involving other PRRSV-2 lineages. Among inter-lineage associations, L8E (HP-PRRSV/JXA1-like) was the most frequently implicated background, followed by L5 and L3. These findings provide systematic evidence for the persistent prevalence, regional transmission and recombination-driven evolution of L1C in mainland China, and support molecular surveillance, regional risk warning and optimization of PRRSV-2 control strategies.
Ji-Yu Zhang, Wei-Sheng Wu, Zixuan Wang et al.· Viruses· 0 citations
ABSTRACT Subtype H9N2 of the avian influenza virus (AIV) poses a growing threat to the poultry industry and public health. However, since 2014, there has been no systematic study of its genetic evolution, genotype, spatial dynamics, and pathogenicity in China. Therefore, we performed a large-scale sequence analysis of the genome of Chinese H9N2 viruses from 2014 to 2025 using public databases and laboratory isolates. We identified 52 different genotypes in 1,591 H9N2 viruses, including 4 previously recognized genotypes (G6, G57, G58, and G68) and 48 newly defined genotypes (G118–G163) in this study. G57 and G118 were the main epidemic genotypes in China from 2014 to 2025. Bayesian phylogeographic analysis showed that there were 12 obvious migration paths for the spread of H9N2 AIVs in China from 2017 to 2022. In particular, the South China region was the main transmission centre. H9N2 AIV continues to circulate in chickens and ducks in China and spreads to other hosts. The H9N2 AIVs with the G57 and G118 genotypes could effectively replicate in MDCK, CEF, A549, and HBE cells with titres of 0.97–8.5 lgTCID50/mL. The G57 and G118 genotypes H9N2 viruses preferentially bound to α-2,6-linked sialic acid glycopolymers (human receptors), and effectively replicate in multiple organs of mice and chickens and cause pathological changes in the lungs. Thus, it is necessary to strengthen the monitoring and prevention of H9N2 AIVs in China.
Zifeng Pang, Peiting Zhong, Cuishan Mai et al.· Emerging Microbes and Infect...· 0 citations
The 2022–2023 outbreak of highly pathogenic avian influenza (HPAI) H5N1 in Chile caused extensive mortality in wild birds, domestic poultry, and marine mammals, highlighting the rapid transboundary spread of this emerging pathogen in South America. However, the evolutionary and ecological processes shaping viral dissemination within Chile have remained insufficiently characterized. Here, we integrated whole‐genome sequencing, Bayesian phylogeographic analyses, and ecological modeling to reconstruct introduction routes, diversification patterns, and environmental drivers of H5N1 circulation in Chile. All analyzed genomes belonged to clade 2.3.4.4b, genotype B3.2. Phylogenetic analyses revealed multiple Chilean subclusters, including a lineage characterized by PB2 F323L and D740N substitutions and a single virus carrying the previously mammalian‐associated PB2 D701N mutation. Phylogeographic inference identified strongly supported viral movements across South America, with Argentina acting as a major regional connector. Key diffusion pathways linked Peru to Chile and revealed extensive connectivity among Argentina, Chile, Brazil, Uruguay, and the Falkland Islands, delineating three interacting transboundary transfer systems along the Pacific Coast, the Southern Cone, and the Southwest Atlantic. Within Chile, viral population structure reflected ecological segregation. Northern lineages were predominantly associated with coastal and raptor species, whereas southern lineages were mainly linked to freshwater birds. Ecological modeling showed that H5N1 detection probability in wild birds increased with temperature and relative humidity and decreased with human population density, with freshwater species exhibiting the highest infection probability. Together, these results demonstrate how integrating genomic and ecological data provides an integrated framework for risk‐based surveillance and early warning, enabling the identification of high‐risk host groups, environments, and transboundary corridors critical for anticipating and mitigating the regional spread of emerging avian influenza viruses.
Franco Vega-Macaya, Constanza Díaz-Gavidia, Fernanda Sánchez-Rodríguez et al.· Transboundary and Emerging D...· 0 citations
The identification of a novel A2–B3 recombinant lineage provides evidence of ongoing viral evolution through recombination, a mechanism that may alter transmissibility, virulence, or immune responses, and underscores the importance of whole-genome surveillance for accurate viral characterization.
A. Fall, C. Morris, O. Elgazayerly et al.· Microbiology spectrum· 0 citations
BACKGROUND
Human metapneumovirus (hMPV) is a globally recognized cause of influenza-like illness (ILI), especially among children, but data from Northeast India are limited. This study analyzed epidemiological and molecular features of hMPV detected in Dibrugarh, Assam, over a decade-long surveillance period.
METHODS
Between May 2014 and November 2025, 3,597 ILI patients were screened for hMPV at a tertiary hospital in Dibrugarh, Assam. Clinical samples (nasopharyngeal/throat swabs) were tested using multiplex respiratory panels and TaqMan-based real-time RT-PCR. Partial sequencing of the G gene was performed by Sanger sequencing, followed by phylogenetic and glycosylation analyses using MEGA 11, NetNGlyc, and NetOGlyc tools. Statistical analysis was done using SPSS v26.
RESULTS
Overall, hMPV prevalence was 3.1% (112/3597), significantly higher among children aged <5 years than older individuals (3.9% vs. 1.3%; p = 0.003). hMPV activity exhibited marked winter seasonality, with significantly higher positivity during the colder months (5.6% vs. 0.8%; p < 0.001). Phylogenetic analysis demonstrated the circulation of A2.2.1 (A2b1), A2.2.2 (A2b2), and B2 lineages in Assam. The two 2025 A2.2.2 strains harbored the characteristic 111-nucleotide G-gene duplication, while comparative glycosylation analysis revealed lineage-specific variation in predicted N- and O-linked glycosylation profiles.
CONCLUSION
hMPV remains an important cause of pediatric influenza-like illness in Northeast India, with marked winter seasonality. The detection of A2.2.1, A2.2.2, and B2 lineages, including A2.2.2 strains with the characteristic 111-nucleotide G-gene duplication, underscores the importance of continued molecular surveillance.
B. Borkakoty, N. Bali, Aniruddha Jakharia et al.· Indian Journal of Medical Mi...· 0 citations
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