Phylogeographic Structure and Molecular Evolution of Squash Leaf Curl China Virus

Squash leaf curl China virus (SLCCNV) is an important geminivirus that infects cucurbit crops and is widely distributed across Asia. To elucidate its population structure and molecular evolution, 101 DNA-A and 67 DNA-B strain sequences of SLCCNV that were publicly available from 2001 to 2024 were analyzed. The strains clustered into three major geographic clades, including South Asia, the Malay Archipelago, and Mainland Southeast Asia. Recombination analysis revealed breakpoints mainly concentrated in the AC2 and BC1 regions. Signals of positive selection were indicated for AC4 and AC5 by selection pressure analysis. Significant genetic differentiation among SLCCNV populations from different geographic origins, but frequent gene flow was observed between among populations from South Asia, the Malay Archipelago, and Mainland Southeast Asia. In addition, AC5 and AV2 exhibited high variability at both the nucleotide and amino acid levels, while AC1, AC2, and AC3 were relatively conserved. Collectively, the evolutionary dynamics of SLCCNV are shaped by geographic isolation, recombination events, and differential selection pressures. This study provides important insights into the molecular evolution of SLCCNV and offers valuable guidance for region-specific surveillance, quarantine strategies, and the deployment of durable resistance against emerging viral variants.