Genotype turnover and global evolutionary dynamics of G gene duplication variants in human metapneumovirus: insights from prospective surveillance in Nantong, China, 2024–2025

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.