Open AccessNearly complete genome sequence of one GII .17 Norovirus identified by direct sequencing from HuZhou, China
Author(s) -
Ji Lei,
Chen Liping,
Xu Deshun,
Wu Xiaofang,
Han Jiankang
Publication year - 2018
Publication title -
molecular genetics and genomic medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.765
H-Index - 29
ISSN - 2324-9269
DOI - 10.1002/mgg3.446
Subject(s) - norovirus , genbank , biology , whole genome sequencing , genome , sanger sequencing , primer (cosmetics) , genotype , virology , genetics , sequence analysis , phylogenetic tree , strain (injury) , gene , dna sequencing , virus , chemistry , organic chemistry , anatomy
Background Human norovirus is the leading cause of acute gastroenteritis worldwide. However, in vitro culture system is complicated for human norovirus. Sequence analysis became more useful for norovirus research, particularly when using complete genomic sequences. Methods Real‐time RT ‐ PCR ( qPCR ) was performed for norovirus detection. Three modified paris of PCR primes were designed based on the alignment of the novel GII .17 norovirus complete sequence available in Genbank., which could amplify three overlapping fragments cover the whole genome. The PCR fragments were sequencing by Sanger sequence with Primer walking methods. Genogroup and genotype were assigned using the Norovirus Noronet typing tool and the strains were named according to the time of isolation. The phylogenetic analysis was conducted using MEGA software (ver. 6.06). Results One nearly complete genome sequence were obtained from sample collected from Huzhou, China. The partial genome sequence of the Huzhou NS 2014603 strain is composed of 7556 nucleotides (nt).The strain was classified as GII .17 genotype both in ORF 1 and ORF 2, and was most closely related to the LC 037415.1/Hu/ GII .17/Kawasaki308 strain. Within the GII .17 cluster, the 2013/14 season strains were grouped separately from the GII .17 strains detected in 2014/15. Huzhou NS 2014603 was clustered with the 2014/15 season strains. Compared with other strains selected, there are 98 variable residues across the VP 1 domain. Among the 98 variable amino acids, 13 (13.3%) were observed in the shell domain and 22 (22.4%) in the P1domain; most of the substitutions and insertions were located in the P2 domain, account for 63 (64.3%). Conclusions This is the first report of the nearly complete genome of the novel GII .17 by direct sequencing method in the Huzhou area. The results of this study could be helpful for the study of the genetic evolution of the virus, the development of rapid diagnostic reagents and the design of vaccine.