In silico characterization of Tomato Leaf Curl New Delhi Virus in Manipur: Evidence for its global expansion and future threat

Abstract

Tomato leaf curl New Delhi virus (ToLCNDV) is a whitefly-transmitted bipartite ssDNA virus causing worldwide havoc to the tomato production. The present study addresses first report for the existence of ToLCNDV at Manipur region of North East India. Sequence comparison of DNA A (MG649330) and DNA B (OM752176) genomes showed close homogeneity of about 98% and 100% with Bangladesh isolates, but revealed only 84–96% (DNA A) and 81–100% (DNA B) similarity with other isolates of ToLCNDV. Phylogenetic relationship of global ToLCV species showed interchangeable results, substantiating that the isolate belonged to the old world bipartite group. Significant recombination events were ascertained around the intergenic region and the 5’end of the AC1 gene implicating a constant driving force for evolution and emergence of the strain. Population dynamics of global ToLCNDV isolates and other dominant ToLCV species within India were determined based upon several parameters i.e. genetic diversity, historic demographic events including neutrality test, Fst distance, Mismatch distribution plot, Haplotype network yielding significant results. Population genetics analysis overall showed low nucleotide diversity indicating recent population expansion. The dominant species of ToLCV in India also reinforced similar results where all the population showed diversifying selection constraint for the coat protein genes. Population dynamics of these viruses portrays Indian subcontinent as the possible hotspot for rapid demographic expansion from a small virus population size, indicating probability for rapid spread and emergence of distinct strains which may assist in future to signal the emergence of new threats to tomato production.