Phylogeny and recombination of papaya begomoviruses in Northern and Central-East India

AARSHI SRIVASTAVA (Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University. Gorakhpur 273009, Uttar Pradesh, India)
VINEETA PANDEY (Zonal Agricultural Research Station, Indira Gandhi Krishi Vishwavidyalaya. Jagdalpur 494001, Chhattisgarh, India)
RAKESH KUMAR VERMA (Department of Biosciences, SLAS, Mody University of Science and Technology. Sikar Rd, Laxmangarh, Narodara Rural 332311, Rajasthan, India)
AVINASH MARWAL (Department of Biotechnology, Mohanlal Sukhadia University. Vigyan Bhawan, Block-B, New Campus, Udaipur 313001, Rajasthan, India)
RAMWANT GUPTA (Department of Botany, Deen Dayal Upadhyaya Gorakhpur University. Gorakhpur 273009, Uttar Pradesh, India)
MUHAMMAD SHAFIQ SHAHID (Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University. Al-Khoud 123, Muscat, Oman)
R. K. GAUR (Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University. Gorakhpur 273009, Uttar Pradesh, India)

Nusantara Bioscience
Vol. 17 No. 2 (2025)

Abstract. Srivastava A, Pandey V, Verma RK, Marwal A, Gupta R, Shahid MS, Gaur RK. 2025. Phylogeny and recombination of papaya begomoviruses in Northern and Central-East India. Nusantara Bioscience 17: 298-312. Papaya plants exhibiting characteristic leaf curl symptoms were surveyed in 2022 across Uttar Pradesh, Delhi, and Chhattisgarh, India. Begomovirus infection was suspected based on symptomatology and confirmed in 11 of 47 collected samples using PCR with Begomovirus-specific primers. This study aimed to elucidate the diversity and distribution of begomoviruses infecting papaya in these regions. Full-length viral genomes were amplified through Rolling Circle Amplification (RCA), and associated alphasatellites and betasatellites were detected using PCR with universal primers. The amplified viral genomes (~2.7 kb), betasatellites (~1.4 kb), and alphasatellites (~1.3 kb) were cloned and sequenced. Sequence analysis revealed 94.57-99.46% nucleotide identity of DNA-A with known isolates of Papaya Leaf Curl Virus (PaLCuV), Cotton Leaf Curl Virus (CLCuV), Croton Yellow Vein Mosaic Virus (CYVMV), Tomato Leaf Curl New Delhi Virus (ToLCNDV), and Cotton Leaf Curl Multan Virus (CLCuMuV). The DNA-B component exhibited 98.33% identity with ToLCNDV. Ten betasatellites shared 86.81-99.71% identity with related species, whereas two alphasatellites showed approximately 98.5% identity with PaLCuA and PaLCVSA. One betasatellite (PL36) displayed 86.81% identity and was identified as a novel Papaya Leaf Curl Raipur Betasatellite (PaLCuRPRB). Furthermore, six PaLCuV isolates showing <91% identity was classified as new PaLCuV variants.