Genetic variation and evolutionary forces shaping Cucumber vein yellowing virus populations: risk of emergence of virulent isolates in Europe

Abstract

The genetic variation and evolutionary mechanisms shaping Cucumber vein yellowing virus (CVYV) populations were investigated by analysis of nucleotide sequences coding for P1b, P1b/P3 and coat proteins (CP) from isolates collected in different countries. The complete genome sequence of isolate ISM from Israel was also determined and compared to those of isolates Jor from Jordan and ALM32 from Spain. This isolate had overall nucleotide identities of 94·23 and 94·96% with ALM32 and Jor, respectively. Nucleotide variation among isolates was not homogeneously distributed, with the 5′ half of the genome being more variable than the 3′ half. A Bayesian phylogenetic tree of the CP showed that CVYV isolates clustered into two main clades: isolates from the Middle East region (Lebanon, Israel and Jordan) clustered in both clades whereas the isolate from Tunisia clustered in clade I and the European isolates clustered as a homogeneous phylogroup in Clade II. A similar topology was observed for P1b but with incongruences with respect to the CP, suggesting genetic exchange among virus isolates, which were confirmed with recombination algorithms. The low genetic diversity within the European phylogroup with respect to the other isolates, neutralist tests and genetic differentiation analyses suggest that the Middle East region is the cradle of CVYV and that a unique virus introduction event occurred in Europe, where the virus spread rapidly. Taken together, these findings indicate a risk of emergence of virulent CVYV isolates in Europe either through migration from the Middle East or by genetic changes of the European isolates.

Evidence for long‐term prevalence of cucumber vein yellowing virus in Sudan and genetic variation of the virus in Sudan and the Mediterranean Basin

“…Although the centre of origin of CVYV remains to be determined, particularly through deeper insights into its prevalence and phylogeography throughout Africa, it could be located in eastern Africa, a centre of diversification for melon and watermelon (Romay et al , ). However, as previously described, the direct origin of the currently emerging European isolates obviously lies in the Middle East/North African populations (Velasco et al , ) rather than sub‐Saharan ones. Analysis of 11 full‐length CVYV sequences indicated the presence of recombination events in Mediterranean populations, and possibly among Sudanese populations.…”

“…Analysis of 11 full‐length CVYV sequences indicated the presence of recombination events in Mediterranean populations, and possibly among Sudanese populations. Phylogenetic discrepancies suggestive of recombination have been previously observed between the P1a, P3 and CP coding regions of Jordanian isolates (Velasco et al , ). In this work, recombination signals were detected in several isolates for which complete sequences were available, suggesting a rather high frequency of recombinants in Mediterranean CVYV populations, and possibly also in Sudanese ones.…”

“…Previous studies on CVYV molecular variability suggested that the virus originated in the Middle East and spread throughout the Mediterranean Basin that constitutes its present geographic range (Velasco et al , ). The present study has shown that CVYV was present in Sudan since at least 1992, and that Sudanese isolates are highly divergent molecularly from the Mediterranean Basin isolates.…”

“…The partial CVYV sequences obtained were compared with the sequences currently available from Europe and the Middle East (Yakoubi et al, 2007;Velasco et al, 2016). The best substitution model was determined with MEGA 6.0 (Tamura et al, 2013).…”

“…Genetic diversity (P i ) of CVYV and gene Plant Pathology (2019) 68, 1268-1275 flow, measured as F ST between Sudanese and other isolates, were calculated with DNASP (Rozas et al, 2003). Genetic differentiation was estimated with DNASP using three permutation-based statistical tests (Hudson, 2000) as in Velasco et al (2016).…”