Molecular Characterization and Population Structure Analysis of Pepper Mild Mottle Virus Infecting Capsicum in Himachal Pradesh, India

Pepper Mild Mottle Virus (PMMoV) is posing a great threat to capsicum cultivation worldwide. Based on the ability of PMMoV in overcoming L mediated resistance in Capsicum spp., it has been categorized in to five pathotypes. The information of pathotype is crucial in framing sustainable management practices. The surveys conducted in seven districts of Himachal Pradesh (H.P) during 2016 and 2017 revealed maximum incidence of PMMoV in Kullu (88.89%) district followed by Mandi (78.57%) after confirmation through DAS-ELISA and RT-PCR. A total 16 isolates were selected for their pathotype characterization by deducing their Amino Acid (aa) sequence and their pathogenicity on differential capsicum cultivars carrying L1, L2, L+, L3 and L4 genes. None of the test isolates produced visible symptoms on differential cultivarsPI-159236 and PI-260429 carrying L3 and L4 genes, respectively. The aa sequences of all test isolates except PMMoV-16.6, 16.10 and PMMoV-17.1 were 100% similar to the P12 pathotypes available at NCBI database. Additionally, the 3-D structure of PMMoV-16.6, 16.10 and 17.1 isolates constructed using SWISSMODEL affirmed the presence of mutations in the short and long hairpin loops of viral CP corresponding to the inner surface and thus do not contribute to the elicitor activity of CP. Thus, all the present isolates were characterized as P12 pathotype. The full genome sequences of three isolates viz., PMMoV-16.7 (MN496153), 16.9 (MN496154) and 17.3 (MN734123) determined in the present study revealed their maximum similarity with PMMoV-HP1 (P12, KJ631123.1) and a Japanese isolate (P12, AB000709.2) and least with a Korean isolate (LC082100.1). The full genome-based recombination analysis did not show any significant recombination event.