Journal of Shandong University (Health Sciences) ›› 2021, Vol. 59 ›› Issue (5): 68-72, 81.doi: 10.6040/j.issn.1671-7554.0.2021.0265

• Current Advance of Basic and Clinical Medical Virology • Previous Articles     Next Articles

Genetic characteristics and molecular variation of human rhinovirus genetype B83 in Jinan

Huailong ZHAO,Yan LYU,Hong ZHAO,Baotian ZHAO,Ying HAN,Jing PAN,Xiaoman DING,Chunrong WANG,Xiuyun HAN,Lanzheng LIU*()   

  1. Jinan Center for Disease Control and Prevention, Jinan 250021, Shandong, China
  • Received:2021-03-12 Online:2021-05-10 Published:2021-06-01
  • Contact: Lanzheng LIU E-mail:jncdcllz@jn.shandong.cn

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Abstract:

Objective: To analyze the genetic characteristics and molecular variation of human rhinovirus (HRV) identified in Jinan, 2020. Methods: The samples collected form influenza-like illness were tested by realtime RT-PCR and the HRV nucleic acid positive sample was sequenced with metagenome sequencing technology. Molecular variation and phylogenetic trees of VP4/VP2 coding region were analyzed using the softwares Lasergene 7.1 and MEGA 5.2. Results: The 7 219 nt complete genome sequence of JN909 was obtained. Phylogenetic analysis of VP4/VP2 coding region on HRV positive strain agreed with the serotype HRV B83. The JN909 was genetically closed to the SC0340 strain found in Seattle City of USA (GenBank accession number: MN306025), with a nucleotide similarity of 98.5% and deduced amino acid similarity of 99.7% of ORF, and there were 6 sites mutation between stains, in which substitutions A23T and P275L sites were located in VP1. Conclusion: There is a high homology between JN909 and SC0340 strains, and only 6 sites amino acid mutations occurs.

Key words: Human rhinovirus, Phylogenetic analysis, Genome, Mutation

CLC Number: 

  • R183.3

Fig.1

The phylogenetic tree based on the VP4/VP2 gene regions of HRV strain in Jinan in 2020"

Table 1

Nucleotide and amino acid identities between JN909 and human rhinovirus serotype B83 strains"

GenBank登录号 时间 国别/地区 血清型序列一致性(nt/aa)%
ORF 5’UTR VP4 VP2 VP3 VP1
MN306025 2019 美国 B83 98.5/99.7 99.7 99.0/100.0 99.0/100.0 98.3/100.0 97.5/99.3
MF160982 2014 美国 B83 — — 99.0/100.0 98.2/100.0 — —
FJ445161 2008 美国 B83 91.4/98.2 97.1 94.7/98.6 92.0/98.1 90.8/99.6 90.5/95.5
JN990701 2007 美国 B83 96.4/99.3 99.4 98.1/100.0 97.5/99.6 95.9/100.0 96.7/99.7
JX863847 2010 中国/上海 B83 — — 96.1/98.6 93.9/98.1 — —
MH648108 2010 新加坡 B83 — 87.1 84.1/97.1 83.4/92.5 — —
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