Isolation, Identification and Analysis of the Complete Genome Sequence of Black Queen Cell Virus Strain China-JL1 / 病毒学报

ABSTRACT

Honeybee pupae were collected from Jilin apiaries and RNA was extracted for use as a tefnplate for amplification. Based on the complete genome sequences of black queen cell virus (BQCV) published on GenBank, we designed 10 pairs of primers to amplify genes by reverse transcription-polymerase chain reaction (RT-PCR). Using this approach, we have obtained the first complete genome sequence of a BQCV isolate in China. The genome of the isolated strain, named BQCV-JL1, is composed of 8358 nucleotides and shares between 86% and 93% homology with the complete genome sequences of the other six BQCV strains published on GenBank. ORF 1 of BQCV-JL1 is positioned between nucleot ides (nt) 546 and 4676 (4131 nt), while ORF 2 is located between nt 5750 and 8203. Between the two ORFs of BQCV-JL1 there is a short ORF, called ORF 3, between nt 4891 and 5433 (543 nt). The first functional gene ex- pression domain of the BQCV-JL1 strain is positioned between nt 546 and 5 429, encompassing both ORF 1 and ORF 3. There is an internal ribosome entry site (IRES) located before ORF 2, the last three bases of which are CCU (nt 5642-5644). These bases act as an initiation.codon facilitating the translation of ORF 2. The second functional gene expression domain of the BQCV-JL1 strain is located between nt positions 5642 and 8203. The BQCV-JL1 strain was found to share high sequence identity (93%) with the Hungary 10 genotype at the whole-genome level and analysis of the nucleotide and amino acid sequences revealed that the BQCV-JL1 strain also shows close genetic relationships with the South Korea strain, suggesting that both the BQCV-JL1 and South Korea strains may have migrated from European countries. BQCV-JL1 strain was different from the other 6 strains in dividing the nucleotides positions of QRF, which vqs because of the gene mutation.