Distribution, molecular characterization and diversity of banana bunchy top virus in Tripura, India

A sensitive batch detection of banana bunchy top virus using SYBR® Green real-time PCR

Banana bunchy top virus (BBTV) is the most destructive viral disease of banana crop in the Philippines. The disease causes heavy damage to important local varieties, 'Lakatan' and 'Cavendish'. Infected planting materials can cause long-term disease transmission causing geographical location to dictate genetic variation among viral strains. Hence, there is a need for an efficient and reliable quarantine detection procedure. This study developed a high-throughput real-time PCR protocol for batch detection of BBTV. A primer set derived from the DNA-R region of the virus was designed for specific BBTV detection. Tests for optimal annealing temperature, sample load, and sensitivity were performed. Finally, the cost per sample was compared to conventional end-point PCR. Optimization of the annealing temperature, from 55.5 ℃ to 63.5 ℃, yielded virus detection. The detection protocol developed was efficient to detect BBTV from a leaf disc measuring up to 5 mm diameter and weight of approximately 3 mg. DNA from infected leaf discs was detectable up to 1:10000 dilution. Sample pooling was detectable up to 1:99 infected to healthy leaf disc ratio. This sensitive and cost-efficient batch detection method for BBTV detection will be useful for quarantine services and various diagnostic applications.

Detection and in silico characterization of banana bunchy top virus in West Bengal, India: relevance to global genetic diversity and population structure

Banana bunchy top disease is one of the major prevailing virus diseases associated with banana cultivation, spreading rapidly within a small scale of time. Till date there are only few extensive reports of completely sequenced isolates in India. A study was conducted to detect BBTV infection across 12 districts in West Bengal (WB) where extensive prevalence of the disease was ascertained. In silico characterization of the six genome components were accomplished which showed 84.90-99.86% similarity with other BBTV isolates reported worldwide. The phylogenetic analysis based upon DNA R and DNA S suggested formation of monophyletic cluster of majority of the WB isolates and its close association with Tripura, Manipur, Australia and Africa isolates indicating diversion from geographical differentiation. Dynamics of evolutionary pattern such as genetic diversity including Tajima's D test and Fu Li's Fs test, average number of nucleotide differences (K), Polymorphic sites (S); Fst distance; Mismatch distribution plot; Haplotype network, and selection pressure were performed based upon geographical distribution of the virus. Population genetics analysis of both Pacific Indian Ocean group and South East Asian group of the global BBTV population revealed low nucleotide diversity, high haplotype diversity, high gene flow within the group, and negative or purifying selection constraint indicating recent population expansion. Hence, this study portrays Indian subcontinent as the possible hotspot for rapid demographic expansion from a small virus population size, contributing valuable addition to the currently available information on BBTV worldwide.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-023-00815-0.

Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes

Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.