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Objective To characterize the whole-genome features and evolutionary variation patterns of severe acute respiratory syndrome coronavirus 2 circulating in Jining City during 2024–2025. Methods Whole-genome sequencing was performed on clinical specimens collected from SARS-CoV-2–infected cases in Jining City during 2024–2025 using next-generation sequencing technology. Phylogenetic and mutation analyses were conducted using standard bioinformatics tools. Results A total of 429 complete SARS-CoV-2 genome sequences were obtained between January 2024 and December 2025, including 240 sequences in 2024 and 189 sequences in 2025. In 2024, circulating strains showed a sequential replacement from the XBB.1.9 lineage to the BA.2.86 lineage and subsequently to the XDV.1 lineage. All sequences obtained in 2025 belonged to the XDV.1 lineage and its sublineages. Whole-genome nucleotide similarity between the 429 sequences and the Wuhan-Hu-1 reference strain ranged from 99.64 to 99.81%, with the lowest nucleotide similarity observed in the ORF6 and spike genes. Amino acid mutation analysis revealed that the spike proteins of the XBB.1.9, BA.2.86, and XDV.1 lineages harbored an average of 42.67, 53.61, and 55.15 amino acid mutation, respectively. The XDV.1 lineage and its sublineages showed the greatest number of spike protein amino acid substitutions. In addition, ORF8 G8 stop and ORF8 Q18 stop mutations were identified, and frameshift mutations in ORF8 were detected in 10 sequences. Conclusion Different Omicron lineages circulated alternately in Jining City during 2024–2025, with XDV.1 and its sublineages becoming the predominant circulating strains in 2025. These findings highlight the critical importance of continuous genomic surveillance for real-time monitoring of viral evolution, and provide key data to support the timely adjustment of vaccines and public health strategies in response to emerging variants. Continuous whole-genome sequencing and analysis of SARS-CoV-2 are essential for timely monitoring of viral evolution and provide a theoretical basis for effective prevention and control strategies.
Yang et al. (2026) studied this question.