利用系统进化树对H7N9大数据预测传播模型的评估

doi:10.13523/j.cb.20141103

中国生物工程杂志

2014, Vol. 34

Issue (11): 18-23 DOI: 10.13523/j.cb.20141103

计算生物学与生物信息学专辑

利用系统进化树对H7N9大数据预测传播模型的评估

杜鹏程^1,2, 于伟文^1,2, 陈禹保³, 闫鹏程³, 安云鹤⁴, 陈晨^1,2

1. 中国疾病预防控制中心传染病预防控制所传染病预防控制国家重点实验室北京 102206;
2. 感染性疾病诊治协同创新中心杭州 310003;
3. 北京市计算中心北京 100094;
4. 北京市理化分析测试中心北京 100089

Evaluation of the H7N9 Transmission Model Predicted by Big Data by Phylogenetic Tree

DU Peng-cheng^1,2, YU Wei-wen^1,2, CHEN Yu-bao³, YAN Peng-cheng³, AN Yun-he⁴, CHEN Chen^1,2

1. State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
2. Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China;
3. Beijing Computing Center, Beijing 100094, China;
4. Beijing Centre for Physical & Chemical Analysis, Beijing 100089, China

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摘要：

活禽贸易和H7N9禽流感病毒传播之间存在关联,应用大数据技术分析活禽交易网络数据,可进行疫情溯源并预测未来传播趋势。从流感研究数据库中获取了截止至2013年分离得到的H7N9毒株的血凝素基因核酸序列,构建系统进化树推断2013年上半年疫情中H7N9在各省及城市间的传播情况,并与大数据推断结果进行对比分析。结果表明,系统进化树推断结果更为准确,但大数据分析能够提供更多地区的信息且具有更好的时效性,同时推断的传播模型准确度较高,在H7N9疫情的应对中具有较高的应用价值。

关键词： H7N9型禽流感; 系统进化树; 大数据; 传播模型

Abstract:

It has been widely proved that the emergence and transmission of H7N9 avian influenza in China 2013 is closely associated with the live poultry trading all over the mainland China. By analyzing the poultry trading information in mainland China from websites using big data analysis technology, we could perform the work of H7N9 outbreak tracing,transmission analysis and trend prediction. In current study, we obtained the nucleotide sequences of hemagglutinin gene of H7N9 avian influenza virus isolates collected before 2013 from the Influenza Research Database firstly, and then conducted phylogenetic analysis using maximum likelihood method by RAxML software. A phylogenetic tree was constructed and then based on the phylogenetic relationship and isolate background including sources, time and locations of collection, we built several transmission routes of H7N9 between provinces and cities during the outbreak emerged in China in the first half of 2013. The results from phylogenetic analysis were compared with the ones from big data analysis to modify the transmission model which has been built by the big data method in our previous research. It revealed that the phylogenetictree could provide more accurate transmission information to trace the real route which could be used to complete and modify the model from big data, but the connection and transmission model from big data analysis could provide nearly accurate information from larger areas in time, which is meaningful in facing the H7N9 outbreak and could provide valuable basis for setting up and carrying out health policy and measures of disease control and prevention.

Key words: H7N9 avian influenza Phylogenetic tree Big data Transmission model

收稿日期: 2014-09-20 出版日期: 2014-11-25

ZTFLH:

R181

基金资助:

国家"863"计划(2014AA021505),国家自然科学基金(81201322,81301402)资助项目

通讯作者: 陈晨,chenchen@icdc.cn E-mail: chenchen@icdc.cn

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引用本文:

杜鹏程, 于伟文, 陈禹保, 闫鹏程, 安云鹤, 陈晨. 利用系统进化树对H7N9大数据预测传播模型的评估[J]. 中国生物工程杂志, 2014, 34(11): 18-23.

DU Peng-cheng, YU Wei-wen, CHEN Yu-bao, YAN Peng-cheng, AN Yun-he, CHEN Chen. Evaluation of the H7N9 Transmission Model Predicted by Big Data by Phylogenetic Tree. China Biotechnology, 2014, 34(11): 18-23.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20141103 或 https://manu60.magtech.com.cn/biotech/CN/Y2014/V34/I11/18

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