Supplementary materials and Matlab code for "Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses" (doi:10.21979/N9/H73L8Y)

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Supplementary materials and Matlab code for "Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses"

doi:10.21979/N9/H73L8Y

DR-NTU (Data)

2019-03-22

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Chen, Haifen; Zhou, Xinrui; Zheng, Jie; Kwoh, Chee Keong, 2019, "Supplementary materials and Matlab code for "Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses"", https://doi.org/10.21979/N9/H73L8Y, DR-NTU (Data), V1

Supplementary materials and Matlab code for "Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses"

doi:10.21979/N9/H73L8Y

Chen, Haifen

Zhou, Xinrui (Nanyang Technological University)

Zheng, Jie (Nanyang Technological University)

Kwoh, Chee Keong (Nanyang Technological University)

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Matlab

Academic Research Fund Tier 1 grant MOE2014-T2-2-023

DR-NTU (Data)

Zhou Xinrui

Zhou Xinrui

2019-03-22

https://doi.org/10.21979/N9/H73L8Y

Computer and Information Science, Medicine, Health and Life Sciences, Other, Computer and Information Science, Medicine, Health and Life Sciences, Other, Influenza viruses, Co-occurring mutations, A/H3N2/H1N1 and B, Antigenic evolution, Co-occuring mutation, Influenza vaccine

Background <br> The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune system. Therefore, the vaccine has to be updated every year to stay effective. There is a need to characterize the evolution of influenza viruses for a better selection of vaccine candidates and the prediction of pandemic strains. Studies have shown that the influenza hemagglutinin evolution is driven by simultaneous mutations at antigenic sites. Here, we analyze simultaneous or co-occurring mutations in the HA protein of human influenza A/H3N2, A/H1N1 and B viruses to predict potential mutations, characterizing the antigenic evolution. <br><br> Methods<br> We obtain the rules of mutation co-occurrence using association rule mining after extracting HA1 sequences and detect co-mutation sites under strong selective pressure. Then we predict the potential drifts with specific mutations of the viruses based on the rules and compare the results with the “observed” mutations in different years. <br> <br> Results<br> The sites under frequent mutations are in antigenic regions (epitopes) or receptor binding sites. <br><br> Conclusions<br> Our study demonstrates the co-occurring site mutations obtained by rule mining can capture the evolution of influenza viruses and confirms that cooperative interactions among sites of HA1 protein drive the influenza antigenic evolution. <br><br> Electronic supplementary material<br> The online version of this article (doi:10.1186/s12920-016-0230-5) contains supplementary material, which is available to authorized users. <br><br> Code and data are also available at: https://github.com/Xinrui0523/comutation

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Matlab code

10.1186/s12920-016-0230-5

Chen, H., Zhou, X., Zheng, J., & Kwoh, C. K. (2016). Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses. BMC Medical Genomics, 9(Suppl 3), 229-240.

10356/83926

Chen, H., Zhou, X., Zheng, J., & Kwoh, C.-K. (2016). Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses. BMC Medical Genomics, 9(Suppl 3), 229-240.

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main_transform_data.m

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