Complete Genomic Sequence Analysis of Sweet Potato Virus 2 Isolates from the Shandong and Jiangsu Provinces in China

Sweet potatoes are significant cash crops, however, their yield and quality are greatly compromised by viral diseases. In this study, the complete genomic sequences of two Sweet Potato Virus 2 (SPV2) isolates from infected sweet potato leaves in the Shandong (designated as SPV2-SDYT, GenBank No. PQ855660.1) and Jiangsu (designated as SPV2-JSXZ, GenBank No. PQ855661.1) provinces in China were obtained using 5′ RACE and RT-PCR amplification. Consistency, phylogeny, codon usage bias, recombination, and selection pressure analyses were conducted using the SPV2-SDYT and SPV2-JSXZ genome sequences. The complete genome sequences of SPV2-SDYT and SPV2-JSXZ were 10561 nucleotides (nt) in length, with respective nucleotide and amino acid identities of 99.25% and 99.12%, respectively. Both isolates were closely related to the SPV2 isolate from China (SPV2-LN). In both SPV2-SDYT and SPV2-JSXZ, the identity of the P1 protein was the highest, whereas that of the P3 protein was the lowest. There were 26 codons with relatively synonymous codon usage (RSCU) values greater than 1 in SPV2-SDYT and 27 codons with RSCU values greater than 1 in SPV2-JSXZ. High-frequency codons in their genomes were predominantly found to end with A/U. Recombination analysis revealed no major recombination sites in either SPV2-SDYT or SPV2-JSXZ. Further selection pressure analysis showed that the non-synonymous substitution rate/synonymous substitution rate (dN/dS) value of all 10 SPV2 proteins was less than 1. This is the first report on the evolutionary relationships of the 17 known SPV2 isolates. Our findings lay the molecular groundwork for preventing and controlling SPV2 infection in root-tuber crops. These findings also contribute to our understanding of the spread and evolution of SPV2, its pathogenic mechanisms, and the development of antiviral strategies against it.