Iqbal Zafar, Alshoaibi Adil, Al Hashedi Sallah Ahmad, Sattar Muhammad Naeem, Ramadan Khaled Muhammad Amin
Central Laboratories, King Faisal University, Al-Ahsa, Saudi Arabia.
PLoS One. 2025 Jul 17;20(7):e0326349. doi: 10.1371/journal.pone.0326349. eCollection 2025.
Tomato leaf curl New Delhi virus (ToLCNDV), a swiftly spreading bipartite begomovirus infecting ~43 plant species across Asia, Africa, and Europe, poses a major agricultural threat. This study comprehensively investigated the genetic diversity and evolutionary dynamics of ToLCNDV using a large dataset of sequences from diverse geographic regions across Asia, Africa, and Europe. Phylogenetic analysis of DNA-A (TA) and DNA-B (TB) components revealed seven major clades for each component, demonstrating regional but not host-specific clustering. Notably, TA and TB exhibited distinct geographic segregation and genetic diversity, with cognate segments often clustering separately. Extensive recombination events were detected (44 in TA and 45 in TB), involving both intra- and interspecies events. While TA displayed higher overall genetic diversity indices, TB exhibited greater nucleotide diversity (π = 0.11%) compared to TA (π = 0.057%) and a slightly faster evolutionary rate (8.15 × 10‒04 substitutions/site/year vs. 7.25 × 10‒04 for TA). Demographic analysis indicated strong negative selection on both components (TA and TB) and their coding regions, albeit with varying intensity. India and Pakistan, known ToLCNDV hotspots, harbored the highest viral diversity and isolate numbers. This study highlights the complex interplay of genetic diversity, recombination, and selection in shaping ToLCNDV evolution, revealing distinct evolutionary trajectories for its genomic components and in different countries. These findings enhance understanding of ToLCNDV evolution and support informed control strategies.
番茄卷叶新德里病毒（ToLCNDV）是一种迅速传播的双分体菜豆金色花叶病毒，感染亚洲、非洲和欧洲的约43种植物，构成了重大的农业威胁。本研究使用来自亚洲、非洲和欧洲不同地理区域的大量序列数据集，全面调查了ToLCNDV的遗传多样性和进化动态。对DNA-A（TA）和DNA-B（TB）组分的系统发育分析显示，每个组分有七个主要分支，表明存在区域聚类而非宿主特异性聚类。值得注意的是，TA和TB表现出明显的地理隔离和遗传多样性，同源片段通常单独聚类。检测到广泛的重组事件（TA中有44个，TB中有45个），包括种内和种间事件。虽然TA显示出更高的总体遗传多样性指数，但与TA（π = 0.057%）相比，TB表现出更大的核苷酸多样性（π = 0.11%）和稍快的进化速率（8.15×10‒04替换/位点/年，而TA为7.25×10‒04）。群体分析表明，对两个组分（TA和TB）及其编码区都有强烈的负选择，尽管强度不同。印度和巴基斯坦是已知的ToLCNDV热点地区，拥有最高的病毒多样性和分离株数量。本研究强调了遗传多样性、重组和选择在塑造ToLCNDV进化中的复杂相互作用，揭示了其基因组组分在不同国家的不同进化轨迹。这些发现增进了对ToLCNDV进化的理解，并支持制定明智的控制策略。
