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Genetic variability and population structure of Grapevine leafroll-associated virus 3 isolates

¹ Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi and Istituto di Virologia Vegetale del CNR, Sezione di Bari, via Amendola 165/A, 70126 Bari, Italy
² Istituto Agronomico Mediterraneo, Valenzano, Bari, Italy

Correspondence
Pasquale Saldarelli
csvvps04{at}area.ba.cnr.it

The genetic variability and population structure of a collection of 45 Grapevine leafroll-associated virus 3 (GLRaV-3) isolates were studied by single-stranded conformation polymorphism (SSCP) and sequence analysis of the RNA-dependent RNA polymerase (RdRp), heat-shock protein 70 homologue (HSP-70) and coat protein (CP) genes. The distribution of SSCP profiles was not correlated with the geographical origin of the isolates, indicating that GLRaV-3 is a single, undifferentiated population. The majority of the isolates showed an SSCP profile and a population structure that were composed of a single predominant variant. However, 10 % of the isolates for the RdRp and HSP-70 genes and 15 % for the CP gene were composed of a combination of two or more variants. Estimation of genetic diversity and phylogenetic analysis disclosed the possible existence of vines with mixed infections by diverging sequence variants, showing, in some cases, possible recombination events. Furthermore, differences in the genetic diversity and constraints existing in the three regions analysed indicated a higher variability in the CP gene. The epidemiological and biological implications of this finding are discussed.

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are AJ748510–AJ748536 and AJ606338–AJ606356.

Details of the GLRaV-3 isolates used are available as supplementary material in JGV Online.

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