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

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.