Molecular diversity of Papaya ringspot virus in India: genetic recombination and mutations between the isolates from different hosts and geo-climatic locations are role players in virus evolution

  • Y. B. BasavarajEmail author
  • Ashwini Kumar
  • Rakesh Kumar Jain
  • Pushpendra Kumar
  • B. Parameswari
  • Jai Prakash
Research Article


Among 10 proteins encoded by Papaya ringspot virus (PRSV), only coat protein (CP) has been studied extensively from mainly the papaya-originated isolates i.e. PRSV-P. In this study, besides CP, the helper component proteinase (HC-pro) and nuclear inclusion protein-a (NIa-pro) coding regions from 19 PRSV-P and -W isolates originating from different geo-climatic locations and hosts were analyzed. Unlike CP, both HC-pro and NIa-pro did not reveal the variability in their length. HC-pro and NIa-pro sequences revealed less than 10% deduced amino acid (daa) diversity worldwide, the CP was found highly variable (up to 20% daa diversity). Highest variability in CP sequence was noticed among the cucurbit-originating PRSV-P Indian isolates, especially from Warm semi-arid climate, which was attributed to a large number of aa insertions/deletions. However, papaya-originating PRSV-P isolates from the Oceanic climate were less variable (up to 5% daa diversity). In NIa-pro, besides already known host/pathotype-specific switching of aa Lys/Asp27, switching of Lys27 → Arg27 and Asp27 → Glu27 was identified within P and W pathotypes. Additionally, a novel aa switching from Ser/Met134 → Thr134 between P and W pathotypes respectively was identified. The phylogeny of PRSV isolates was largely based on the geo-climatic locations and hosts. Through recombination detection analysis, three recombinant isolates were detected based on both NIa-pro and CP sequences, which possessed cucurbit-originated PRSV (either -P or -W) isolates as one of their parents (either major or minor.) Patterns of codon usage among the three protein coding sequences generated further revealed that the CP gene is under maximum selection pressure (with six sites) followed by NIa-pro gene (with one site). This investigation shows that the genetic recombination between the isolates originating from different hosts and geo-climatic locations as well as mutations are the significant mechanisms playing their role in generating diverse populations of PRSV.


Papaya ringspot virus Pathotypes Hosts Geo-climatic location Recombination Natural selection pressure 



Authors are highly grateful to Indian Council of Agricultural Research and Indian Agricultural Research Institute, New Delhi, Government of India (IARI Fellowship for Ph.D.) for providing research opportunity and financial support. The critical scientific discussions with Dr. Sunil Chauhan, DJ college of Dental Science and research, Modinagar, Uttar Pradesh (India) and Dr. S.P Singh, CSIR-National Physical Laboratory, New Delhi (India) are gratefully acknowledged.

Supplementary material

42360_2019_157_MOESM1_ESM.pptx (2.9 mb)
SUPPLEMENTARY FIGURE 1. Symptoms of PRSV-P isolates on papaya [(a) mottling; (b) mosaic; (c) vein banding; (d) leaf blistering and distortion; (e) vein clearing; and (f) filiformy/shoe stringing and leaf distortion)] and PRSV-W isolates only on pumpkin (Cucurbita moschata) [(g) mottling; (h) mosaic; (i) leaf blistering & green islands; (j) vein banding; (k) filiformy & blistering; and (l) leaf distortion/deformation) under glasshouse conditions after sap inoculation (PPTX 2942 kb)
42360_2019_157_MOESM2_ESM.pptx (316 kb)
SUPPLEMENTARY FIGURE 2. Multiple alignment of deduced amino acid sequences showing (a) unique amino acid switching at 27th position known to impart host specificity, as well as at 134th positions, a newly identified position of amino acid switching in nuclear inclusion protein-a (NIa-pro); and (b) the amino acid sequences imparting maximum variability in the coat protein (CP) of Papaya ringspot virus isolates (PPTX 316 kb)
42360_2019_157_MOESM3_ESM.docx (24 kb)
SUPPLEMENTARY TABLE 1. Details of the primer sets used for PCR amplification and the amplicon sizes of three different genomic regions of PRSV isolates. SUPPLEMENTARY TABLE 2. Sequence homology among Papaya ring spot virus (PRSV) isolates originating from India in relation to those from rest of the world based on (a) helper component proteinase (HC-pro), (b) NIa-pro and (c) CP coding sequences. This table represents pairwise percent sequence identities at nucleotide and Amino acid levels. SUPPLEMENTARY TABLE 3. Sequence homology among Papaya ring spot virus (PRSV) isolates originating from different geo-ecological regions (a novel approach) based on (a) helper component proteinase (HC-pro), (b) NIa-pro and (c) CP coding sequences. This table represents pairwise percent sequence identities at nucleotide and Amino acid levels (DOCX 23 kb)


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Copyright information

© Indian Phytopathological Society 2019

Authors and Affiliations

  1. 1.Plant Virology Unit, Division of Plant PathologyICAR-Indian Agricultural Research InstituteNew DelhiIndia
  2. 2.Division of Fruit Science and TechnologyICAR-Indian Agricultural Research InstituteNew DelhiIndia
  3. 3.Department of Agricultural BiotechnologySardar Vallabhbhai Patel University of Agriculture and TechnologyMeerutIndia
  4. 4.ICAR- Sugarcane Breeding Institute Regional CentreKarnalIndia

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