Occurrence, Complete Genome Sequencing, and Development of Diagnostics for Black Pepper Virus F Infecting Black Pepper in India

• Published in: Journal of phytopathology Vol. 172; no. 5
• Main Authors: Malavika, P., Greeshma, M., Bhat, A. I.
• Format: Journal Article
• Language: English
• Published: Berlin Wiley Subscription Services, Inc 01.09.2024
• Subjects: Clustering; Coat protein; crude extract; detection; DNA-directed RNA polymerase; Fabavirus; Gene sequencing; Genomes; Nucleotide sequence; Nucleotides; Phylogeny; Piper nigrum; Polymerase chain reaction; Propagation; Proteins; Recombinase; Reverse transcription; Ribonucleic acid; RNA; RT‐PCR; RT‐RPA; sequence; Vegetables; Viruses; India
• ISSN: 0931-1785; 1439-0434
• DOI: 10.1111/jph.13418

ABSTRACT The occurrence of black pepper virus F (BPVF) was identified for the first time from India, and its complete genome sequence was determined using overlapping fragments obtained through reverse transcription polymerase chain reaction (RT‐PCR). The RNA 1 and RNA 2 of the Indian isolate of BPVF (BPVF‐IND) contained 6376 and 3340 nucleotides potentially coding for proteins of 230.7 kDa and 114 kDa respectively. Comparison of the RNA 1 sequence of BPVF‐IND with that of BPVF from Brazil (BPVF‐ BR‐PA) and China (BPVF‐ ZYP‐1) revealed an identity of 95% and 90%, respectively, while RNA 2 showed an identity of 96% and 90%. The phylogenetic analysis of the Pro‐Pol region of RNA 1 and coat protein region of RNA 2 revealed close clustering of all three BPVF isolates well separated from other species of the genus, Fabavirus. Diagnostics assays based on the RT‐PCR and RT‐recombinase polymerase amplification (RT‐RPA) were developed for the sensitive detection of the virus that will help in the identification and propagation of virus‐free black pepper plants.