Diversity and Evolution Trend of Protein Types of Human Influenza A (H1N1) Virus HA Segment

Junpeng Bao, Fangfang Huang, Hui He, Ke Yang, Zhonghui Feng, Yu Wang

Abstract: The Influenza A virus is prone to mutation and the ongoing research on its evolution is of great significance to its prevention and control. The WHO did not update the recommended vaccine after A/California/07/2009 was recommended as the vaccine strain, but the virus has been mutating. This paper proposes an Integrated-Clustering-Analysis (ICA) model to study the distribution and evolution of the influenza A (H1N1) virus. We discover the following interesting facts. Every year there is one major type of virus sequences, the number of which is the overwhelming majority of all sequences. Viral sequences after 2009 undergo cumulative changes as they deviate from the viral vaccine strain over time. According to the drift rate, the evolution process can be divided into three stages. The first stage is a high-speed mutation period from 2009 to 2011. In the second stage, from 2012 to 2014, the mutation speed drops continuously and keeps at a low level. The third stage, from 2015 to 2017, the mutation speed starts with a year jump and follows by two years trough. It seems that the evolution of the influenza A virus has a three years cycle, so we cautiously guess that the drift rate in 2018 would jump up again. The ICA model proposed in this paper can intuitively observe the process of virus type change.