Genomic insights into SARS-CoV-2 evolution in Yantai, China after the adjustment of the dynamic zero-COVID policy in 2023

Coronavirus Disease 2019 (COVID-19) cases surged after China adjusted the dynamic COVID-zero strategy at the end of 2022, posing significant public health challenges in Yantai. To monitor the evolutionary process and characterize variants circulating in Yantai in 2023, 613 nasopharyngeal swab samples from confirmed COVID-19 patients were sequenced, assigned to lineages, used for phylogenetic tree construction, and analyzed for spike protein mutations. The results showed that most of the sequences belonged to 10 lineages. Among these, 20.72% (127/613) were identified as BF.7.14, 21.04% (129/613) as EG, 14.03% (86/613) as HK, 12.40% (76/613) as DY, 8.32% (51/613) as XBB.1, 8.32% (51/613) as FL, 3.43% (21/613) as BA.5.2, 1.79% (11/613) as BN.1, 1.79% (11/613) as FY.3 and 0.65% (4/613) as DZ.1. A clear dominance shift was observed from BA.5-derived lineages in early 2023 to XBB-derived lineages in the latter half of the year, reflecting the nationwide replacement trend and the ongoing viral adaptation. The prevalent variants were consistent with the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants circulating in China at the same time. The spike protein of the prevalent variants shared 28 common mutations. In addition, several lineage-specific mutations were identified across different variants. Spike protein mutations gradually accumulated and augmented transmissibility and immune escape of variants. New variants with higher viral fitness appeared continuously and posed significant challenges to public health, so long-term genomic surveillance of SARS-CoV-2 is still necessary in the future. These findings provide an important scientific basis for optimizing public health policies, strengthening genomic surveillance systems, and improving preparedness for potential future epidemic waves.