Unusual Events Involved in Banana bunchy top virus Strain Evolution

Abstract

Banana bunchy top virus (BBTV) can be transmitted by aphids and consists of at least six integral components (DNA-R, -U3, -S, -M, -C, and -N). Several additional replication-competent components (additional Reps) are associated with some BBTV isolates. A collected BBTV strain (TW3) that causes mild symptoms was selected to study the processes in BBTV evolution. Southern blot hybridization, polymerase chain reaction (PCR), and real-time PCR did not detect DNA-N in TW3. Real-time PCR quantification of BBTV components revealed that, except for the copy number of TW3 DNA-U3, each detected integral component of BBTV TW3 was at least two orders lower than that of the severe strains. No infection was observed in plants inoculated with aphids, which were first given acquisition access to the TW3-infected banana leaves. Recombination analysis revealed recombination between the integral component TW3 DNA-U3 and the additional Rep DNA-Y. All BBTV integral components contain a replication initiation region (stem-loop common region) that share high sequence identity. Sequence alignment revealed that TW3 DNA-R, -S, -M, and -C all have a stem-loop common region containing a characteristic 9-nucleotide deletion found only in all reported DNA-N. Our data suggest that the additional Rep DNAs can serve as sources of additional genetic diversity for integral BBTV components.

High Variability and Rapid Evolution of a Nanovirus

“…In addition to elevated rates of nucleotide changes, recombination has been identified as another major driving force for the evolution of ssDNA viruses (31,49,50,57,59, 72), including the nanovirus BBTV (30). In the three FBNSV populations analyzed here, we detected 12 clear intragenomic recombination events between different individual DNA components, two of which became established as consensus (Fig.…”

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites

“…Furthermore, it was isolated from a monocotyledonous host. Two geminialphasatellites have been isolated from monocotyledonous plants and both of these have features typical of the Geminialphasatellitinae [24]; and twelve have been isolated from bananas and cardamom, all of which have similarities to other nanoalphasatellites [2,11,18,25,53]. We therefore propose this molecule to represent an unassigned species in the family Alphasatellitidae.…”

Identifying geographic hot spots of reassortment in a multipartite plant virus

“…CBDV is an aphid-borne nanovirus within the Babuvirus genus (Mandal et al 2004(Mandal et al , 2013. Nanoviruses have multipartite genomes, consisting of up to 12 individually encapsidated, circular, singlestranded DNA (ssDNA) genome components (Mandal 2010), and are known to undergo reassortment (Timchenko et al 2000;Hu et al 2007;Fu et al 2009;Hyder et al 2011;Stainton et al 2012;Grigoras et al 2014;Savory and Ramakrishnan 2014). CBDV infects large cardamom, Amomum subulatum, a crop of considerable economic importance in sub-Himalayan regions of Northeast India, Nepal, and Bhutan.…”