Synonymous codon usage pattern and genetic polymorphism analysis of a novel reassortant avian-origin influenza A (H7N9) virus in China
H7N9 avian flu infecting humans for the first time and showing high death rates in China arises world-wide concern.Codon usage and genetic polymorphismon on this new reassortant virus remains unknown.CDC (Codon Deviation Coefficient) values, RSCU (relative synonymous codon usage) values, ENC (effective number of codons) values, nucleotide contents, CAI (codon adaption index) and CBI (codon bias index) of novel H7N9 sequences were investigated and compared with the ”classical H7N9”.Calculation on DNA sequences for genetic polymorphism analysis was performed.Results showed that novel H7N9 virus is AT rich in base composition and the whole codon usage bias is low (mean ENC=51.5000 > 50).ENC-plot revealed that mutational pressure is the most important factor in codon usage pattern of novel H7N9.Haplotype diversity index ranked high in eight genes (Hd: 0.8607 ±-0.16060) while nucleotide diversty index was very low in all (π: 0.0043 ± 0.00207).Phylogenetic analysis identified that A/Shanghai/1/2013 strain was different from remaining novel H7N9 strains and great disparities existed in novel and classical H7N9 genomes.Neutrality tests indicated that population expansion or purifying selection would act in virus” evolution.
H7N9 Codon usage bias Correspondence analysis GC content Phylogenetic tree
Huang ZM Chen RP Chen C Hu CY Ye XH Wang ZB I.LONGO PHEMBA Lu DY Li QF
国内会议
第八届浙江国际消化病学术大会暨美国胃肠病协会第二届中国学术论坛
浙江绍兴
英文
187-194
2015-10-30（万方平台首次上网日期，不代表论文的发表时间）