Genetic diversity analysis reveals new badnaviruses infecting banana in South China

Abstract

Banana streak virus (BSV) is the causal agent of the most prevalent diseases in banana and causes serious economic losses to banana production worldwide. To examine variability in BSV, 65 isolates were obtained from 99 samples collected from Guangdong, Hainan, Guangxi and Yunnan provinces in South China. The 65 BSV isolates shared 62.8–97.8% nt identity over the RT/RNase H regions when compared to eight BSV species with published complete genomes. Sequence and phylogenetic analyses based on the RT/RNase H region indicated that there was great genetic diversity among BSV isolates in South China, and some isolates belonged to species of badnavirus that had never before been reported in China, including banana streak OL virus (BSOLV) (DN6–2), banana streak IM virus (BSIMV) (DN1–7 and DN5–1), and banana streak VN virus (BSVNV) (YLJ-8). The full genomes of two isolates (DN5–1and DN5–4) were cloned and sequenced. The genetic characteristics of both isolates were very close to those of typical badnaviruses. Based on percentage nucleotide sequence identity and phylogenetic relationships, DN5–1 was categorized as BSIMV. Interestingly, while DN5–4 was similar to both sugarcane bacilliform viruses (SCBVs) and BSVs based on sequence identities of the RT/RNase H region, analysis of its complete sequence and genome organization revealed that it can be further classified as sugarcane bacilliform Guadeloupe A virus-2 (SCBGAV-2). To our knowledge, this is the first report of natural infection of banana by SCBGAV-2 in China. In addition, our results suggest that considering the complete genomic sequence rather than the RT/RNase H region alone is important when classifying badnavirus isolates.