Cuong Ha

On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus

The potyvirus Papaya ringspot virus (PRSV) is found throughout the tropics and subtropics. Its P biotype is a devastating pathogen of papaya crops and its W biotype of cucurbits. PRSV-P is thought to arise by mutation from PRSV-W. However, the relative impact of mutation and movement on the structure of PRSV populations is not well characterized. To investigate this, we have determined the coat protein sequences of isolates of both biotypes of PRSV from Vietnam (50), Thailand (13), India (1) and the Philippines (1), and analysed them together with 28 PRSV sequences already published, so that we can better understand the molecular epidemiology and evolution of PRSV. In Thailand, variation was greater among PRSV-W isolates (mean nucleotide divergence 7.6%) than PRSV-P isolates (mean 2.6%), but in Vietnamese populations the P and W biotypes were more but similarly diverse. Phylogenetic analyses of PRSV also involving its closest known relative, Moroccan watermelon mosaic virus, indicate that PRSV may have originated in Asia, particularly in the Indian subcontinent, as PRSV populations there are most diverse and hence have probably been present longest. Our analyses show that mutation, together with local and long-distance movement, contributes to population variation, and also confirms an earlier conclusion that populations of the PRSV-P biotype have evolved on several occasions from PRSV-W populations.

Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses.

SummaryTwo pairs of degenerate primers were designed from sequences within the potyviral CI (CIFor/CIRev) and HC-Pro-coding regions (HPFo/HPRev), and these were shown to be highly specific to members of the genus Potyvirus. Using the CIFor and CIRev primers, three novel potyviruses infecting crop and weed species from Vietnam were detected, namely telosma mosaic virus (TelMV) infecting telosma (Telosma cordata, Asclepiadaceae), peace lily mosaic virus (PeLMV) infecting peace lily (Spathiphyllum patinii, Araceae) and wild tomato mosaic virus (WTMV) infecting wild tomato (Solanum torvum, Solanaceae). The fragments amplified by the two sets of primers enabled additional PCR and complete genomic sequencing of these viruses and a banana bract mosaic virus (BBrMV) isolate from the Philippines. All four viruses shared genomic features typical of potyviruses. Sequence comparisons and phylogenetic analyses indicated that WTMV was most closely related to chilli veinal mottle virus (ChiVMV) and pepper veinal mottle virus (PVMV), while PeLMV, TelMV and BBrMV were related to different extents to members of the bean common mosaic virus (BCMV) subgroup.

Characterisation of Rep-encoding components associated with banana bunchy top nanovirus in Vietnam

Summary. We have analysed the sequence variability of the banana bunchy top nanovirus (BBTV) DNA-1 sequence from 17 isolates collected throughout Vietnam, and showed that the level of DNA-1 sequence variation within Vietnam was approximately double that previously reported for Asian BBTV isolates. Furthermore, the sequences separated into two geographical subgroups that generally correlated to the northern or southern regions of Vietnam. We have also characterised an additional putative Rep-encoding component associated with some BBTV isolates from Vietnam. This component, which we have named BBTV-S3, shared 47%, 69%, 56% and 65% nucleotide sequence identity with the previously reported Rep-encoding components BBTV DNA-1, S1, S2 and Y1 respectively.

The complete nucleotide sequence of two distinct geminiviruses infecting cucurbits in Vietnam.

Summary. We have characterised two distinct geminiviruses that infect cucurbit cultivars in Vietnam. The genomes of both viruses consisted of two circular ssDNA components (DNA-A and DNA-B), with a genome arrangement and coding sequence typical of viruses in the Begomovirus genus in the family Geminiviridae. The sequence of DNA-A of one of the viruses was approximately 97% similar to Squash leaf curl virus-China (SLCV-Ch), for which a DNA-B has yet to be identified. We have named this virus Squash leaf curl virus-Vietnam (SLCV-Vn). The intergenic region of the SLCV-Vn DNA-B contained a 40 nt deletion between the putative AC1 TATA box and the stem loop. A second virus isolated from loofa in southern Vietnam was only 80% similar to SLCV-Vn over the complete DNA-A sequence, however the nucleotide sequence in the coat protein coding regions was 95% similar. We have named this virus Loofa yellow mosaic virus-Vietnam (LYMV-Vn). Other regions of the SLCV-Vn and LYMV-Vn genomes differed markedly, suggesting the coat protein coding region was recombinant. The DNA-B of both viruses were only 60% similar over the complete nucleotide sequence, although the encoded amino acid sequence of the BC1 gene was 90% identical.