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

RichHTML

4

PDF (PC)

252

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 — —
1 Ratnamohan VM , Zeng F , Donovan L , et al. Phylogenetic analysis of human rhinoviruses collected over four successive years in Sydney, Australia[J]. Influenza Other Respir Viruses, 2016, 10 (6): 493- 503.
doi: 10.1111/irv.12404
2 Ahn JG , Kim DS , Kim KH , et al. Clinical characteristics and cytokine profiles of children with acute lower respiratory tract infections caused by human rhinovirus[J]. PLoS One, 2018, 13 (7): e0198624.
doi: 10.1371/journal.pone.0198624
3 McKnight KL , Swanson KV , Austgen K , et al. Stimulator of interferon genes (STING) is an essential proviral host factor for human rhinovirus species A and C[J]. Proc Natl Acad Sci U S A, 2020, 117 (44): 27598- 27607.
doi: 10.1073/pnas.2014940117
4 Bizot E , Bousquet A , Charpié M , et al. Rhinovirus: a narrative review on its genetic characteristics, pediatric clinical presentations, and pathogenesis[J]. Front Pediatr, 2021, 9, 643219.
doi: 10.3389/fped.2021.643219
5 Ko FW , Chan PK , Chan RWY , et al. Molecular detection of respiratory pathogens and typing of human rhinovirus of adults hospitalized for exacerbation of asthma and chronic obstructive pulmonary disease[J]. Respir Res, 2019, 20 (1): 210.
doi: 10.1186/s12931-019-1181-0
6 李洪军, 崔燕, 杨艳娜, 等. 2011-2018年北京通州儿童急性呼吸道感染九种病毒性病原体监测研究[J]. 中国感染控制杂志, 2019, 18 (8): 713- 718.
LI Hongjun , CUI Yan , YANG Yanna , et al. Surveillance of nine viral pathogens of acute respiratory tract infection in children in Tongzhou District, Beiing, 2011-2018[J]. Chinese Journal of Infection Control, 2019, 18 (8): 713- 718.
7 吴家敏, 林广裕, 蔡晓莹, 等. 鼻病毒所致儿童中枢神经系统感染的感染学及临床特点分析[J]. 中华传染病杂志, 2015, 33 (9): 527- 532.
doi: 10.3760/cma.j.issn.1000-6680.2015.09.004
8 Soma N , Aizawa Y , Matsunaga M , et al. Clinically mild encephalitis/encephalopathy with a reversible splenial lesion associated with rhinovirus[J]. Pediatr Infect Dis J, 2021, 40 (3): e122- e125.
doi: 10.1097/INF.0000000000002995
9 Palmenberg AC , Rathe JA , Liggett SB . Analysis of the complete genome sequences of human rhinovirus[J]. J Allergy Clin Immunol, 2010, 125 (6): 1190- 1201.
doi: 10.1016/j.jaci.2010.04.010
10 da Costa Souza L , Bello EJM , Dos Santos EM , et al. Molecular and clinical characteristics related to rhinovirus infection in Brasília, Brazil[J]. Braz J Microbiol, 2021, 52 (1): 289- 298.
doi: 10.1007/s42770-020-00411-0
11 Fall A , Dia N , Kébé O , et al. Enteroviruses and rhinoviruses: molecular epidemiology of the most influenza-like illness associated viruses in Senegal[J]. Am J Trop Med Hyg, 2016, 95 (2): 339- 347.
doi: 10.4269/ajtmh.15-0799
12 Linster M , Donato C , Mah MG , et al. Genetic diversity of respiratory enteroviruses and rhinoviruses in febrile adults, Singapore, 2007-2013[J]. Influenza Other Respir Viruses, 2020, 14 (1): 67- 71.
doi: 10.1111/irv.12662
13 Stepanova E , Isakova-Sivak I , Rudenko L . Overview of human rhinovirus immunogenic epitopes for rational vaccine design[J]. Expert Rev Vaccines, 2019, 18 (9): 877- 880.
doi: 10.1080/14760584.2019.1657014
14 Esposito S , Daleno C , Tagliabue C , et al. Impact of rhinoviruses on pediatric community-acquired pneumonia[J]. Eur J Clin Microbiol Infect Dis, 2012, 31 (7): 1637- 1645.
doi: 10.1007/s10096-011-1487-4
15 Ledford RM , Patel NR , Demenczuk TM , et al. VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds[J]. J Virol, 2004, 78 (7): 3663- 3674.
doi: 10.1128/JVI.78.7.3663-3674.2004
16 Fendrick AM , Monto AS , Nightengale B , et al. The economic burden of non-influenza-related viral respiratory tract infection in the United States[J]. Arch Intern Med, 2003, 163 (4): 487- 694.
doi: 10.1001/archinte.163.4.487
17 To KKW , Yip CCY , Yuen KY . Rhinovirus-From bench to bedside[J]. J Formos Med Assoc, 2017, 116 (7): 496- 504.
doi: 10.1016/j.jfma.2017.04.009
18 Lewis-Rogers N , Seger J , Adler FR . Human rhinovirus diversity and evolution: how strange the change from major to minor[J]. J Virol, 2017, 91 (7): e01659- 16.
doi: 10.1128/JVI.01659-16
19 Kennedy JL , Turner RB , Braciale T , et al. Pathogenesis of rhinovirus infection[J]. Curr Opin Virol, 2012, 2 (3): 287- 293.
doi: 10.1016/j.coviro.2012.03.008
20 Glanville N , Johnston SL . Challenges in developing a cross-serotype rhinovirus vaccine[J]. Curr Opin Virol, 2015, 11, 83- 88.
doi: 10.1016/j.coviro.2015.03.004
21 Papadopoulos NG , Megremis S , Kitsioulis NA , et al. Promising approaches for the treatment and prevention of viral respiratory illnesses[J]. J Allergy Clin Immunol, 2017, 140 (4): 921- 932.
doi: 10.1016/j.jaci.2017.07.001
22 Sherry B , Mosser AG , Colonno RJ , et al. Use of monoclonal antibodies to identify four neutralization immunogens on a common cold picornavirus, human rhinovirus 14[J]. J Virol, 1986, 57 (1): 246- 257.
doi: 10.1128/jvi.57.1.246-257.1986
23 Sam Narean J , Glanville N , Nunn CM , et al. Epitope mapping of antibodies induced with a conserved rhinovirus protein generating protective anti-rhinovirus immunity[J]. Vaccine, 2019, 37 (21): 2805- 2813.
doi: 10.1016/j.vaccine.2019.04.018
24 周豪, 夏冬, 夏志强, 等. 鼻病毒全球研究现状分析[J]. 中华实验和临床病毒学杂志, 2018, 32 (4): 411- 415.
doi: 10.3760/cma.j.issn.1003-9279.2018.04.017
[1] Xiaoxu ZENG,Heng ZHANG,Ming JIAO,Tao CHEN,Xiyan LI,Weijuan HUANG,Jing YANG,Dayan WANG. Genetic characteristics of H10 subtype avian influenza virus in three southern provinces of China [J]. Journal of Shandong University (Health Sciences), 2021, 59(5): 52-59.
[2] Hengyun GUAN,Chunrong WANG,Lanzheng LIU,Huailong ZHAO,Aiying BAI,Huiyu JIANG,Hua DONG,Na LI,Xiaoying SHAN,Hongqi CHENG. Positive distribution of four dominant enteroviruses associated with hand, foot and mouth disease and VP1 genotypes in Jinan, China, 2012-2017 [J]. Journal of Shandong University (Health Sciences), 2021, 59(5): 60-67.
[3] SUN Yu, CHEN Na, MA Aihua. A case of congenital disorder of glycosylation caused by SLC35A2 gene mutation [J]. Journal of Shandong University (Health Sciences), 2021, 59(4): 113-116.
[4] HUANG Xiuli, LIU Bingju, SUN Lifeng. Activated phosphoinositide 3-kinase δ syndrome caused by a mutation in PIK3CD gene: a case report and literature review [J]. Journal of Shandong University (Health Sciences), 2021, 59(3): 107-112.
[5] HU Sicui, SUN Qing, WANG Yibing, SUN Lili, SUI Yanxi, LI Tang. Analysis of CLCNKB gene mutation in two families with Bartter syndrome [J]. Journal of Shandong University (Health Sciences), 2020, 1(9): 64-70.
[6] XU Jixi, CHEN Weijian. Diffuse midline glioma with H3 K27M mutation in the spinal cord: a case report [J]. Journal of Shandong University (Health Sciences), 2020, 1(7): 96-101.
[7] LIU He, LIU Fuqiang, HOU Xinguo, CHEN Li. A study of 11β-hydroxylase defect induced by a novel CYP11B1 gene mutation in one family [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2017, 55(9): 85-89.
[8] CHEN Wenbiao, YU Xiangqi, DAI Yong. Different expressions of novel microRNAs of iPSCs from Alport syndrome [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2015, 53(9): 80-85.
[9] LU Min, CHEN Yun, DING Botong, CHANG Yali, ZHOU Yawei, ZHAO Aiping, GUO Nongjian. Gene detection and analysis for hemophilia B among populations in Shandong Province [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2015, 53(3): 87-92.
[10] SUN Jie, MU Xiaoyan, DONG Xueli. Combinational and sequential effect of sunitinib and gemcitabine on K-RAS mutant A549 cells [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2014, 52(3): 45-49.
[11] YANG Shulin, YANG Fan, ZHAI Jing, LIU Jintong, ZHANG Yan, CHEN Gang. Genome-wide association study of autism in Shandong Province [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2014, 52(11): 92-96.
[12] ZHU Famei, ZHENG Jiafa, XIE Dinghua, HU Peng. Analysis of SLC26A4 gene mutations in 5 families associated with enlarge vestibular aqueduct syndrome [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2014, 52(10): 90-95.
[13] SUN Jin, HAN Bo, WEI Mei-li, YANG Wen-wei, WANG Jie-zhong, LIU Yong-jiao. Mutation screening of TFAP2B gene in children with patent ductus arteriosus [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2013, 51(3): 72-75.
[14] LIU Chen-fan1, WANG Zhen-ying2, SONG Huai-dong3, PAN Chun-ming3, ZHANG Li2. Mutation screening of candidate genes causing disseminated superficial porokeratosis [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2013, 51(1): 93-97.
[15] SU Lei1, GUO Shu-ling1， FENG Yu-xin2, XIAO Ke-yuan1, ZHU Xiao-li1, YUAN Fang-shu1. Determination of Demodex genome size by flow cytometry [J]. JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCES), 2013, 51(06): 57-60.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
[1] SUO Dongyang, SHEN Fei, GUO Hao, LIU Lichang, YANG Huimin, YANG Xiangdong. Expression and mechanism of Tim-3 in animal model of drug-induced acute kidney injury[J]. Journal of Shandong University (Health Sciences), 2020, 1(7): 1 -6 .
[2] MA Qingyuan, PU Peidong, HAN Fei, WANG Chao, ZHU Zhoujun, WANG Weishan, SHI Chenhui. Effect of miR-27b-3p regulating SMAD1 on osteosarcoma cell proliferation, migration and invasion[J]. Journal of Shandong University (Health Sciences), 2020, 1(7): 32 -37 .
[3] XU Yuxiang, LIU Yudong, ZHANG Peng, DUAN Ruisheng. A retrospective analysis of risk factors of cerebral microbleeds in 101 patients with cerebral small vessel disease[J]. Journal of Shandong University (Health Sciences), 2020, 1(7): 67 -71 .
[4] LUO Xin, HE Bing, NIE Qingsheng, HOU Zhenbo, DONG Jun, LI Yuhua, ZENG Xiangqin, LIU Wei, KONG Demin, CAO Jinfeng. Comparison of the value of mono-exponential mode and diffusion kurtosis imaging mode in grading clear cell renal cell carcinoma using magnetic resonance diffusion-weighted imaging[J]. Journal of Shandong University (Health Sciences), 2020, 1(7): 89 -95 .
[5] Di ZHANG,Meng YU,Xia LIU. A general overview of neuromodulation[J]. Journal of Shandong University (Health Sciences), 2020, 1(8): 50 -60 .
[6] Wei ZHANG,Wenhao TAN,Yibin LI. Locmotion control of quadruped robot based on deep reinforcement learning: review and prospect[J]. Journal of Shandong University (Health Sciences), 2020, 1(8): 61 -66 .
[7] Anjing CHEN,Xun ZHANG. The new strategies of targeting SUMOylation in the treatment of glioma[J]. Journal of Shandong University (Health Sciences), 2020, 1(8): 88 -94 .
[8] ZHANG Hongbin, ZHAO Hanhui, WANG Suxia, ZHOU Peng, HE Qingqing, WANG Yanqun, DING Weiping, LIU Gang. Perioperative observation and postoperative risk factors of severe hypocalcemia after parathyroidectomy: a report of 303 cases[J]. Journal of Shandong University (Health Sciences), 2020, 1(9): 14 -20 .
[9] SUN Yifeng, GAO Yu, LIANG Yongyuan, GAO Yang. Expression of CPLX2 and its in vitro effects on the proliferation migration and invasion of hepatocellular carcinoma cells[J]. Journal of Shandong University (Health Sciences), 2020, 1(9): 34 -39 .
[10] LI Yinglin, SONG Daoqing, XU Zhonghua. Identification of FKBP11 expression in clear cell renal cell carcinoma using bioinformatics analysis[J]. Journal of Shandong University (Health Sciences), 2020, 1(9): 45 -51 .
Copyright 2018 © Editorial office of Journal of Shandong University (Health Sciences)
Supported by Beijing Magtech Co.Ltd