Epidemiological characteristics and genetic evolution of rhinovirus in Jining City, 2024–2025
TL;DR
Rinovirus species RV-A was the predominant rhinovirus species circulating in Jining City during 2024–2025, with high genotypic diversity, and rhinoviruses in this region exhibit ongoing evolution in the VP1 region.
Abstract
Objective To investigate the epidemiological characteristics and genetic evolution of rhinovirus (RV) among patients with influenza-like illness (ILI) in Jining City, Shandong Province, from 2024 to 2025, and to provide scientific evidence for the formulation of regional respiratory virus prevention and control strategies. Methods A total of 2,724 throat swab specimens were collected from ILI cases at Jining First People’s Hospital between 2024 and 2025. Ten respiratory viruses were screened using real-time reverse transcription-quantitative PCR. Of 101 RV-positive specimens, 30 with lower cycle threshold (Ct) values were subjected to whole-genome targeted enrichment sequencing. Molecular typing was performed based on VP1 region nucleotide sequences. A maximum likelihood (ML) phylogenetic tree was constructed, and genetic distances and key amino acid substitution sites were analyzed. Results Among the 2,724 specimens, influenza virus had the highest detection rate (14.98%), followed by SARS-CoV-2 (7.05%), with rhinovirus ranking third (3.71%, 101/2,724). The RV-positive rate in 2025 (5.53%) was significantly higher than in 2024 (1.95%; χ2 = 23.55, P < 0.001). An unusually high RV positivity rate (23.53%) was observed in November 2025. The 30 sequenced strains were classified into RV-A (73.33%, 17 genotypes), RV-B (10.00%, 3 genotypes), and RV-C (16.67%, 3 genotypes), with RV-A as the predominant species and genotypes exhibiting high diversity. Phylogenetic analysis revealed co-circulation of multiple species and genotypes, with 2025 strains distributed across a broader range of the phylogenetic tree. The nucleotide similarity between the VP1 regions of the 30 strains and their respective reference strains ranged from 86.08% to 95.37%, and amino acid similarity from 91.58% to 99.65%, with 1–24 amino acid substitution sites per strain. Conclusion RV-A was the predominant rhinovirus species circulating in Jining City during 2024–2025, with high genotypic diversity. The detection rate in 2025 increased significantly compared with 2024, accompanied by an autumn epidemic peak. Rhinoviruses in this region exhibit ongoing evolution in the VP1 region. Enhanced molecular surveillance is warranted to dynamically monitor epidemiological and evolutionary trends.