Global Genetic Diversity of ZYMV Coat Protein Isolates in Cucurbits: Comparative Sequence Analysis and Phylogenetic Insights for Diagnostic Applications

Abstract

Zucchini yellow mosaic virus (ZYMV), a member of the Potyvirus genus, poses a major threat to cucurbit crops worldwide. This study aimed to provide a comprehensive comparative analysis of ZYMV isolates collected from six global regions-Africa, Asia, Europe, North America, South America, and Oceania-using the Egyptian reference strain ZYMV ASSM-2025 (LC866761.1 for nucleotide, BFZ76578.1 for protein) as a benchmark. Partial nucleotide and amino acid sequences of the polyprotein and coat protein genes were aligned to assess genetic diversity, sequence identity, and regional variation. Results showed substantial sequence conservation across most isolates, with nucleotide identity ranging from 85.10 % to 98.71 %. African and European isolates displayed the highest levels of nucleotide similarity to the reference strain, while Oceania (particularly Australia) exhibited the greatest divergence. At the protein level, conservation was even more pronounced, with polyprotein and coat protein identities frequently exceeding 95 % and, in several cases, reaching 100 %. This indicates strong functional constraints on viral proteins that are essential for replication, movement, and host interactions. Despite this conservation, notable regional variations were observed; particularly in the coat protein gene, which may reflect adaptation to local hosts, environmental pressures, or vector dynamics. These differences were especially evident in recent North American and Australian isolates. Such divergence highlights the potential for ongoing viral evolution and underscores the importance of continuous surveillance. The findings of this study offer valuable insights for developing accurate diagnostic tools, effective resistance breeding programs, and region-specific management strategies to control the spread and impact of ZYMV in diverse agro-ecosystems.