First Report of Potato Tuber Necrotic Ringspot Disease Caused by PVYNTN in Portugal

Specific differentiation of recombinant PVY(N:O) and PVY(NTN) isolates by multiplex RT-PCR

The recombinant isolates of tobacco veinal necrotic strain of Potato virus Y (PVYN) and potato tuber necrotic group (PVY(NTN)) contain segments of the PVYO and the PVY(N) genome. Three major recombinant junctions (RJ) are present in the genome of the recombinant PVY(NTN) at sites HC/Pro-P3, 6K2-NIa, and the C-terminal region of CP gene and one RJ at HC/Pro-P3 site in some recombinant PVYN isolates (termed PVY(N:O)). Protocols for specific differentiation of the recombinant PVY(NTN) and PVY(N:O) from the non-recombinant PVYN are described. Specific primer pairs were designed to target the three RJs so that sense and antisense primers completely matched the nucleotide sequences at either side of the RJ. In a uniplex reverse transcription-polymerase chain reaction (RT-PCR), the first primer pair amplified a fragment of 641bp from the recombinant PVY(NTN) and PVY(N:O). The second and third primer pairs exclusively amplified fragments of 448 and 290bp, respectively from the recombinant PVY(NTN). In a multiplex (triplex) RT-PCR, when all three primer pairs were used simultaneously, the three fragments (641, 448 and 290bp) were amplified exclusively from the recombinant PVY(NTN), while only one fragment (641bp) was amplified from the PVY(N:O) isolates, clearly differentiating the two recombinant isolates. No amplification was observed from the non-recombinant PVY, including PVYO and North American (NA)-PVY(N/NTN). For further improvement of the multiplex RT-PCR, effects of cDNA preparation using specific antisense primers, random primers or oligo(dT) plus random primers were investigated. The cDNA prepared by random primer plus oligo(dT) increased the overall band intensity.

Probable geographical grouping of PVY(N) and PVY(NTN) based on sequence variation in P1 and 5'-UTR of PVY genome and methods for differentiating North American PVY(NTN)

An increasing number of countries in recent years have reported the occurrence of potato tuber necrotic ringspot disease (PTNRD), caused by tobacco veinal necrosis strain of Potato virus Y (PVY(N)), belonging to the sub-group tuber necrosis (PVY(NTN)). Methods for the differentiation of PVY(NTN), based on primer sequences often detect isolates of European (EU) type but not the North American (NA) type. To resolve this problem, the nucleotide sequence of 5'-untranslated region (5'-UTR) and the P1 gene of 11 isolates of PVY(N) and PVY(NTN) from the European Union and North America was determined. Sequence comparison and phylogenetic analysis of 5'-UTR and P1 region indicated that PVY(N) isolates from the European Union and North America formed their own separate groups. Intra-group sequence identity for all except one was over 98%, as opposed to the inter-group identity of 90%. Additionally, the PVY(NTN) isolates from the European Union and North America clustered with their respective PVY(N) isolates. This indicates a possible evolution of PVY(NTN) isolates from the PVY(N) isolates of a geographical region. With this information of regional relationships of PVY(NTN) and PVY(N) isolates, two approaches were developed based on a competitive RT-PCR and a restriction pattern, for the differentiation of NA-PVY(NTN) from the local PVY(N) and from EU-PVY(NTN). Thus sequencing of the P1 gene and use of competitive RT-PCR approach could be applicable for determining the possible origin of new occurrences of PVY(NTN) from other geographical regions.