Complete sequencing the genome and taxonomic clarification of Sacbrood virus collected from honey bee in Vietnam

Abstract

The entire genome (8779 nucleotides) of a strain of Sacbrood virus (SBV) isolated in Vietnam, designated as HY (Hung Yen province), has been determined. The complete sequence of this strain was obtained by PCR and direct sequencing, using 5 primer pairs with template of cDNA converted from genomic RNA by random hexamers. The generated sequence for each PCR fragment overlapped each others at 5’ and 3’ ends. Genomic arrangement of the SBV-HY strain includes 3 main regions, of which the first part consists of a non-coding region, namely 5'UTR (181 nucleotides (nt) in length), followed by an open reading frame (ORF) with 8532 nt in size, encoding a polypeptide of 2843 amino acids, and the third part is another non-coding region termed 3' UTR (64 nt). Comparative analysis of nucleotide sequences collected from GenBank revealed that the HY strain showed the lowest (89%) to the UK (GenBank: AF092924) and the highest identity to the Korean strains of KorAC (HQ322114) and Kor19 (JQ390592), 94.1% and 93.4%, respectively. Analysis of deduced amino acid sequences showed that the HY strain is similar to the Korean Kor19 and KorAC strains, missing 17 amino acids at positions 712-728, in comparison with strains of SBM2 (KC007374), Kor21 (JQ390591), SXnor (KJ00692), BJ (GKF960044), K3A (JX270798), S2 (JX270799) and UK (AF092924). Phylogenetic analysis showed that 15 sequences formed four groups (clades 1-4), where the HY strain is placed in same group (clade 3) with the genetically most related strains of Kor19 and KorAC of Korean origins.