Sequence diversity studies of papaya ringspot virus isolates in South India reveal higher variability and recombination in the 5′-terminal gene sequences

Abstract

Papaya ringspot virus (PRSV) is one of the most devastating viruses which causes huge damage to papaya plantations across the globe. PRSV is a positive sense RNA virus encoding for a polyprotein that is processed into ten proteins. In this study for the first time we analyzed the variability for 15 PRSV isolates from a selected geographical region of a South Indian state Karnataka, which is under intensive papaya cultivation. Variability studies were done for two genes at the 5 0 end of the viral genome, namely P1 and helper component proteinase (Hc-Pro) and towards the 3 0 end, a 788 nt overlapping region of nuclear inclusion B (NIb, 692 nt) and of capsid protein (CP, 96 nt), referred as NIb-CP. Our studies indicate that the P1 is most variable region with a wider range of sequence identity, followed by Hc-Pro, while the 788 nt of NIb-CP was most conserved. P1 also showed maximum recombination events followed by Hc-Pro, whereas NIb-CP did not show any recombination. Further, the pattern and number of phylogenetic clusters was variable for each of the three genomic regions of PRSV isolates. Estimation of selection pressure for all the three PRSV genomic regions indicated negative and purifying selection.

Genetic variability and evolutionary dynamics of atypical Papaya ringspot virus infecting Papaya.

“…The highest recombination was detected towards the 5'region of the PRSV genome particularly including the first 1020 nt. The potential regions prone to recombination are 5'UTR and P1, thus playing a major role in PRSV genome dynamics as this information strengthen some preliminary findings 26 , followed by HC-Pro gene 39 and consistent with other potyviruses 40 as well. We conclude that PRSV from India (Meghalaya) (MF356497) acts as a major parent in this recent outbreak of recombination.…”

Genetic characterization of a mild isolate of papaya ringspot virus type-P (PRSV-P) and assessment of its cross-protection potential under greenhouse and field conditions

“…This clade shares a most recent ancestor with isolates from the USA (Hawaii and Texas), Mexico and France (Fig 2), supporting findings from other studies where a correlation between sequence diversity and geographic area was not apparent (11). No recombination events were predicted for any of the Ecuadorean or other American isolates, whereas the majority of recombinants were detected in Asian isolates, supporting previous results that place Asia as the origin center of PRSV (13,15,35). the DAG motif, in the CP of most potyviruses was shown to be hypervariable (37).…”

“…Studies based on the coat protein (CP) suggested that PRSV originated from southern Asia, as higher diversity levels were found among Indian and other Asian isolates compared to sequences from the rest of the world (11)(12)(13)(14). Further analyses using complete genomes of isolates from different geographical regions showed that recombination events, especially at the 5' end, and P1 gene, have played a pivotal role in the diversification of PRSV, supporting previous findings on the origin of the virus (14,15).…”

Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing

“…Recombination complicates phylogenetic analyses because various genome regions in a single individual may have different evolutionary histories. Accordingly, constructing phylogenies using different sections of SCMV and other potyviral genomes produces conflicting trees 35,36 . Recombination may also impede virus detection because increased genomic variation may lead to false negative results with common techniques such as PCR and antibody ELISA 11,37 .…”