Xiaolei Ji, Zhenzhen Liu, Xiuli Cai, Ruyue Liang, Lu Chen, Xingpei Ji, Shiyao Chen, Yihua Sun, Chen Guo
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.
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.