Molecular epidemiological characterization for VP1 region gene of coxsackievirus A6 in China
-
摘要:
目的 分析我国2010―2018年柯萨奇病毒A组6型(Coxsackievirus A6,CV-A6)毒株VP1区基因流行和进化规律,为手足口病的防治提供科学依据。 方法 从GenBank获得2010―2018年我国CV-A6病毒全长VP1区核苷酸序列,用MEGA V7.0和Interactive Tree of Life V5(iTOLV5)软件构建进化树,用DNAstar V8.1.3软件对核苷酸同源性进行分析。 结果 880条序列来源的CV-A6毒株以D3亚型为主,占毒株总数的95.45%,不同基因型核苷酸同源性为80.8%~86.0%,同基因型内核苷酸同源性为88.1%~100.0%。D2亚型VP1区相对稳定,无整体氨基酸变异情况;而D3毒株VP1区发生多点氨基酸替换,其中A5T、T283A、N137S、V242I、A30V、I174V氨基酸替换循环出现,这种进化模式与越南地区相似,但与日本地区却不同。VP1区5T、30A、137N、242V比例逐年增加,可能与CV-A6引起我国手足口的轻症和重症病例比例上升有关。 结论 具有VP1区遗传多样性的CV-A6 D3株的出现可能是CV-A6在反复流行的一个重要因素,这有助于解释我国CV-A6的流行情况和流行特点。 Abstract:Objective To analyze the epidemic and genetic evolution principals of Coxsackievirus group A type 6 (CV-A6) VP1 region from 2010 to 2018 in China so as to provide scientific basis for the prevention and treatment of Hand-foot-mouth disease (HFMD). Methods The full-length VP1 nucleotide sequence of CV-A6 virus from 2010 to 2018 in China was obtained from GenBank. The phylogenetic trees based on VP1 sequences of CV-A6 were constructed by the MEGA V7.0 and Interactive Tree of Life V5 (iTOLV5) software, and the nucleotide homology was analyzed with DNAstar V8.1.3. Results The CV-A6 D3 was the main sub-genotype, accounting for 95.45% of the total 880 strains. The homology of nucleotides sequences in different genotype was between 80.8% and 86.0% while the homology of nucleotides sequences in the same genotype was between 88.1% and 100.0%.The VP1 sequences of D2 was relatively stable without any global amino acid variation. However, the VP1 sequences of D3 had multi-point amino acid substitutions, in which A5T, T283A, N137S, V242I, A30V and I174V amino acid substitution occurred circularly. This evolutionary pattern was similar to that in Vietnam but different from that in Japan. The proportion of 5T, 30A, 137N and 242V in the VP1 region increased year by year, which may be related to the increasing proportion of the mild and severe cases of HFMD caused by CV-A6 in China. Conclusions The emergence of CV-A6 D3 Sub-genotype strains with high genetic diversity in VP1 region could be a factor associated with the repeated epidemics, which helps to explain the epidemics and characteristics of CV-A6 in China. -
Key words:
- Coxsackievirus group A type 6 /
- VP1 region gene /
- Molecular epidemiology
-
表 1 CV-A6原型毒株及参考株
Table 1. CV-A6 prototype strain and reference strain
序号 GenBank
登录号菌株名称 来源 年份 基因型
/亚型1 AY421764 Gdula 美国 1949 A 2 JQ364886 92022/SD/CHN/1992 中国 1992 B1 3 KP143075 AFP262/GD/CHN/2005 中国 2008 B2 4 JQ364887 96188/SD/CHN/1996 中国 1996 C1 5 JN203517 N-313 印度 2008 C2 6 FR797988 ESP08/54698 西班牙 2011 D1 7 KC86690 JB14080448 中国 2008 D2 8 KC86616 JB143090122 中国 2009 D2 9 JQ364889 10032/SD/CHN/2010 中国 2010 D2 10 KM114057 Finland/2008 芬兰 2008 D3 11 AB779618 Kyoto5 日本 2009 D3 12 HE572906 CF140007_FRA10 法国 2010 D3 13 JN582001 TW/1537/2011 中国台湾 2011 D3 表 2 2010-2018年不同省/自治区/直辖市CV-A6 VP1区序列分布情况
Table 2. CV-A6 VP1 sequences in different province from 2010 to 2018
地区 序列数量(条) 合计(%) 2010年 2011年 2012年 2013年 2014年 2015年 2016年 2017年 2018年 上海 2 30 66 87 19 17 221(25.11) 云南 9 50 8 42 63 43 215(24.43) 广西 1 2 7 5 10 17 8 51 101(11.48) 北京 2 3 17 19 29 19 89(10.11) 河南 3 9 30 13 24 79(8.98) 江西 23 20 5 3 51(5.80) 江苏 28 28(3.18) 山东 1 4 5 14 24(2.73) 河北 1 1 4 7 13(1.48) 新疆 2 4 3 1 10(1.14) 甘肃 1 1 2 5 9(1.02) 吉林 6 1 7(0.80) 辽宁 1 1 5 7(0.80) 山西 2 4 6(0.68) 广东 3 2 5(0.57) 湖南 3 2 5(0.57) 四川 2 1 1 4(0.45) 浙江 4 4(0.45) 重庆 2 2(0.23) 合计 6 42 108 229 128 127 69 114 57 880(100.00) 表 3 CV-A10病毒VP1区核苷酸序列同源性比对分析
Table 3. The homology analysis of CV-A6 VP1 nucleotide acid sequences
参考株/各年度毒株 基因型/亚型 核苷酸同源性(%) 2010年 2011年 2012年 2013年 2014年 2015年 2016年 2017年 2018年 Gdula A 81.4~83.7 80.8~83.7 81.5~83.5 81.3~83.6 81.7~84.2 81.9~84.2 82.0~83.7 81.5~83.9 82.0~83.8 92022/SD/CHN/1992 B1 82.5~83.6 82.2~83.7 82.7~84.0 82.3~84.4 82.2~84.5 82.2~84.5 82.6~84.2 82.4~84.5 82.7~84.2 AFP262/GD/CHN/2005 B2 83.6~84.6 83.1~84.6 82.8~84.8 83.0~85.0 83.1~85.1 83.1~85.1 83.4~84.7 83.1~85.0 83.6~85.2 96188/SD/CHN/1996 C1 84.6~85.7 84.5~85.6 84.3~85.6 83.5~86.0 83.4~85.9 83.7~85.9 84.2~85.8 84.0~85.7 83.9~86.0 N~313 C2 84.3~85.4 84.5~85.6 83.9~85.8 83.5~85.8 83.6~86.0 83.6~86.0 83.3~85.7 83.3~85.4 83.1~84.7 ESP08/54698 D1 90.4~100.0 90.6~91.7 90.6~92.3 89.0~92.3 89.0~92.3 90.5~92.3 89.8~91.9 89.5~91.7 90.2~91.8 JB14080448 D2 91.0~98.0 90.2~97.2 89.9~97.7 89.9~97.0 89.6~95.5 89.6~91.5 88.9~91.3 88.6~90.5 88.3~90.8 JB143090122 D2 91.1~98.3 90.3~98.1 90.1~98.3 89.7~96.7 89.8~94.5 89.6~91.6 89.0~91.6 88.7~91.6 88.9~91.3 10032/SD/CHN/2010 D2 90.3~100.0 89.6~97.2 89.5~97.0 89.3~98.1 89.2~94.6 89.8~90.8 88.2~90.7 88.0~90.5 88.2~90.5 Finland/2008 D3 90.6~96.8 90.7~97.0 90.7~96.8 89.3~96.8 89.3~96.4 94.6~96.4 94.2~95.7 93.7~95.4 92.8~95.3 Kyoto5 D3 90.3~96.9 89.9~97.2 90.2~96.9 88.1~96.7 88.3~96.5 94.6~96.5 93.6~96.2 93.7~95.6 93.7~95.4 CF140007_FRA10 D3 90.8~96.2 91.1~96.0 90.9~96.5 89.5~96.4 89.5~96.2 94.2~96.2 93.6~95.5 93.2~95.2 92.8~95.3 TW/1537/2011 D3 90.8~99.6 90.6~97.8 90.7~98.8 89.0~99.1 89.1~98.9 95.2~98.9 94.1~98.8 94.5~98.0 95.5~97.9 2010年 D2/D3 90.3~98.3 89.6~99.7 89.5~99.2 88.5~99.1 88.5~98.7 88.7~98.4 88.2~97.7 88.0~96.3 88.2~96.3 2011年 D2/D3 89.0~99.9 88.8~99.6 88.0~99.6 88.0~99.1 88.2~98.9 87.8~98.1 87.4~96.6 87.1~96.5 2012年 D2/D3 89.7~100.0 87.5~100.0 89.4~99.8 89.3~99.6 89.1~99.5 89.0~99.5 88.1~99.6 2013年 D2/D3 88.0~100.0 87.8~99.6 87.1~99.6 87.2~99.5 86.1~99.1 86.1~98.6 2014年 D2/D3 88.0~100.0 87.5~99.9 92.3~99.6 86.9~99.5 86.1~98.3 2015年 D3 92.0~100.0 91.5~99.8 91.8~99.5 91.1~98.5 2016年 D3 91.5~100.0 90.9~99.9 91.1~99.0 2017年 D3 92.2~100.0 91.1~99.7 2018年 D3 93.9~100.0 -
[1] 国家卫生健康委员会.手足口病诊疗指南(2018年版) [J].传染病信息, 2018, 31(3), 193-198. DOI: 10.3969/j.issn.1007-8134.2018.03.001.National Health Commission of the People's Republic of China. Diagnosis and treatment guideline on hand-foot-mouth disease (2018) [J]. Infect Dis Info, 2018, 31(3), 193-198. DOI: 10.3969/j.issn.1007-8134.2018.03.001. [2] Osterback R, Vuorinen T, Linna M, et al.Coxsackievirus A6 and hand, foot, and mouth disease, Finland [J]. Emerg Infect Dis, 2009, 15(9):1485-1488. DOI: 10.3201/eid1509.090438. [3] Kelly F, Ilan Y, Jennifer H, et al. Hand, foot, and mouth disease caused by Coxsackievirus A6 [J]. Emerg Infect Dis, 2012, 18(10):1702-1704. DOI: 10.3201/eid1810.120813. [4] Cisterna DM, Lema CL, Martinez LM, et al. Atypical hand, foot, and mouth disease caused by Coxsackievirus A6 in Argentina in 2015 [J]. Rev Argent Microbiol, 2019, 51(2):140-143. DOI: 10.1016/j.ram.2018.05.003. [5] Fujimoto T, Iizuka S, Enomoto M, et al. Hand, foot, and mouth disease caused by Coxsackievirus A6, Japan [J]. Emerg Infect Dis, 2012, 18(2):337-339. DOI: 10.3201/eid1802.111147. [6] Li Y, Chang Z, Wu P, et al. Emerging enteroviruses causing hand, foot and mouth disease, China, 2010-2016 [J]. Emerg Infect Dis, 2018, 24(10):1902-1906. DOI: 10.3201/eid2410.171953. [7] 于方圆, 朱汝南, 钱渊.手足口病相关病原体柯萨奇病毒A6的研究进展[J].中国病毒病杂志, 2017, 7(6):472-477. DOI: 10.16505/j.2095-0136.2017.06.015.Yu FY, Zhu RN, Qian Y. Hand, foot and mouth disease associated coxsackievirus A6:recent progress [J]. Chin J Viral Dis, 2017, 7(6):472-477. DOI: 10.16505/j.2095-0136.2017.06.015. [8] Oberste MS, Maher K, Kilpatrick DR, et al. Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification [J]. J Virol, 1999, 73(3):1941-1948. doi: 10.1128/JVI.73.3.1941-1948.1999 [9] Xing W, Liao Q, Viboud, C, et al. Hand, foot, and mouth disease in China, 2008-12: an epidemiological study [J]. Lancet Infect Dis, 2014, 14(4):308-318. DOI: 10.1016/S1473-3099(13)70342-6. [10] Zhi CZ, Zeng QK, Yong JB, et al. Epidemiological research on hand, foot, and mouth disease in mainland China [J]. Viruses, 2015, 7(12):6400-6411. DOI: 10.3390/v7122947. [11] He S, Chen M, Wu W, et al. An emerging and expanding clade accounts for the persistent outbreak of Coxsackievirus A6-associated hand, foot, and mouth disease in China since 2013 [J]. Virology, 2018, 518:328-334. DOI: 10.1016/j.virol.2018.03.012. [12] Wang H, Yu W, Xu T, et al. Molecular characteristic analysis for the VP1 region of coxsackievirus A6 strains isolated in Jiujiang area, China, from 2012 to 2013 [J]. Medicine, 2019, 98(14):e15077. DOI: 10.1097/MD.0000000000015077. [13] Chen M, Zuo X, Tan Y, et al. Six amino acids of VP1 switch along with pandemic of CV-A6-associated HFMD in Guangxi, southern China, 2010-2017 [J]. J Infect, 2019, 78(4): 323-337. DOI: 10.1016/j.jinf.2019.02.002. [14] 卞莲莲, 姚昕, 毛群颖等.江苏省2012-2013年柯萨奇病毒A组6型分子流行特征分析[J].中国病毒病杂志, 2015, 5(5):361-367. DOI: 10.16505/j.2095-0136.2015.05.007.Bian LL, Yao X, Mao QY, et al.Genetic characteristics of coxsackievirus A6 circulated in Jiangsu Province of China from 2012 to 2013 [J]. Chin J Viral Dis, 2015, 5(5):361-367. DOI: 10.16505/j.2095-0136.2015.05.007. [15] Song Y, Zhang Y, Ji T, et al. Persistent circulation of Coxsackievirus A6 of genotype D3 in mainland of China between 2008 and 2015 [J]. Sci Rep, 2017, 7(1):5491. DOI: 10.1038/s41598-017-05618-0. [16] 袁芳, 陈慧, 马江涛, 等. 2013~2015年宁夏地区手足口病柯萨奇病毒A组6型基因特征分析[J].病毒学报, 2016, 32(6):702-706. DOI:10.13242/j.cnki.bingduxuebao. 003065.Yuan F, Chen H, Ma JT, et al. Genetic characteristics of 6 Coxsackivirus A6 of hand-foot-mouth disease in Ningxia from 2013 to 2015 [J]. Chin J Viro, 2016, 32(6):702-706. DOI:10.13242/j.cnki.bingduxuebao. 003065. [17] 邓红, 冀天娇, 黄永迪, 等. 2012~2016年新疆柯萨奇病毒A6的分子流行病学特征分析[J].病毒学报, 2018, 34(6):839-843. DOI: 10.13242/j.cnki.bingduxuebao.003475.,Deng H, Ji T J, Huang Y D, et al. Genetic Characteristics of coxsackievirus circulated in Xinjiang, China from 2012 to 2016 [J]. Chin J Viro, 2018, 34(6):839-843. DOI: 10.13242/j.cnki.bingduxuebao.003475. [18] To AN, Truc NN, Tu VHM, et al. Emerging Coxsackievirus A6 causing hand, foot and mouth disease, Vietnam [J]. Emerg Infect Dis, 2018, 24(4):654-662. DOI: 10.3201/eid2404.171298. [19] Hideaki Y, Yuki A, Sachiko I, et al. Molecular epidemiology of coxsackievirus A6 derived from hand, foot, and mouth disease in Fukuoka between 2013 and 2017 [J]. J Med Virol, 2018, 90(11):1712-1719. DOI: 10.1002/jmv.25250. [20] Du J, Zheng B, Zheng W, et al. Analysis of enterovirus 68 strains from the 2014 north American outbreak reveals a new clade, indicating viral evolution [J]. PLoS One, 2015, 10(12):e0144208. DOI: 10.1371/journal.pone.0144208. [21] Wang SH, Wang A, Liu PP, et al. Divergent pathogenic properties of circulating coxsackievirus A6 associated with emerging Hand, Foot, and Mouth Disease [J]. J Virol, 2018, 92(11):e00303-18. DOI: 10.1128/JVI.00303-18.