Complete sequence analysis of norovirus strain NHBGR59 of Hebei Lulong

Abstract

Objective To study the gene and evolution of the complete sequence of NHBGR59 strain isolated from children with diarrhea in Hebei Lulong. Methods The full-length genome was amplified based on the two contigs and reference sequence of strain of 30443 (KM198534) by methods of reverse transcription PCR and rapid-amplification of cDNA ends. The PCR products was cloned and sequenced. HBGR59 was performed on sequence analysis and phylogenetic tree. Results The complete sequence of NHBGR59 was 7 563 bp (excluding PolyA tail), including three open reading frames (ORFs): ORF1 (5-5 098 nt), ORF2 (5 079-6 731 nt) and ORF3(6 731-7 510 nt), with 20 nucleotide (nt) overlapping in ORF1 and ORF2, and 1 nt overlapping in ORF2 and ORF3. By sequence analysis, NHBGR59 showed the highest homology in complete sequence with norovirus strain 30443 (98% identity), and the ORF2 and ORF3 also showed the highest identity to strain 30443 (97.0% and 99.0% in nt; 98.0% and 98.0% in amino acid (aa)), while the ORF2 displayed the highest homology (99.0% in nt, 99.3% in aa) with the strain 11-FJ-5 (KM461694), which was related to GII.6 norovirus gastroenteritis outbreaks in Taiwan in 2014, and only one amino acid was different (aa308D→N in P2 region) between them. The phylogenetic analysis showed NHBGR59 clustered tightly with strains of 30443 and 11-FJ-5 in norovirus genogroup II genotype 6 (GII.6). Conclusions NHBGR59 belongs to norovirus GII.6, which is the mostly close to the recently reported strain 30443 and 11-FJ-5. Key words: Norovirus; Genogroup II genotype 6; Phylogenetic tree; Genome