Development of RT-PCR degenerate primers to overcome the high genetic diversity of grapevine virus T.

Development of RT-PCR degenerate primers to overcome the high genetic diversity of grapevine virus T.
J Virol Methods. 2020 May 15;:113883
Authors: Diaz-Lara A, Golino D, Preece JE, Al Rwahnih M
Abstract
Grapevine virus T (GVT) is a new member of the genus Foveavirus and has been reported to infect grapevines in several European countries. In 2018, GVT was detected for the first time in California in a domestic selection of wine grape, cv. Lambrusca di Alessandria, via high-throughput sequencing (HTS). To further investigate the presence of GVT in other grapevine plants, a two-step reverse transcription (RT)-PCR assay involving degenerate primers was developed. In order to cover the high genetic diversity of GVT, the sequences of available isolates were aligned to identify a conserved region in the coat protein gene that was a suitable target for the assay. The results of the RT-PCR assay showed that GVT was present in three additional grapevine selections among 416 plants integrating the Foundation Plant Services introduction pipeline; all were later confirmed by HTS. A complete and three near-complete genomes of the four GVT isolates were characterized and found to be divergent, sharing an overall 81% pairwise identity in their nucleotide sequences. This suggested that the new RT-PCR assay was effective in detecting a broad range of GVT variants. The RT-PCR detection method developed in this study would be useful for routine virus ...

Source: Journal of Virological Methods - May 14, 2020 Category: Virology Authors: Diaz-Lara A, Golino D, Preece JE, Al Rwahnih M Tags: J Virol Methods Source Type: research