Browsing by Author "Shen, Jun"

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    Diversifying selective pressure on influenza B virus hemagglutinin
    (2009) Shen, Jun; Ma, Jianpeng
    Influenza B virus hemagglutinin (HA) is a major surface glycoprotein with frequent amino-acid substitutions. However, the roles of antibody selection in the amino-acid substitutions of HA were still poorly understood. In order to gain insights into this important issue, an analysis was conducted on a total of 271 HA1 sequences of influenza B virus strains isolated during 1940∼2007. In this analysis, PAML (Phylogenetic Analysis by Maximum Likelihood) package was used to detect the existence of positive selection and to identify positively selected sites on HA1. Strikingly, all the positively selected sites were located in the four major epitopes (120-loop, 150-loop, 160-loop and 190-helix) of HA identified in previous studies, thus supporting a predominant role of antibody selection in HA evolution. Of particular significance is the involvement of the 120-loop in positive selection, which may become increasingly important in future field isolates. Despite the absence of different subtypes, influenza B virus HA continued to evolve into new sublineages, within which the four major epitopes were targeted selectively in positive selection. Thus, any newly emerging strains need to be placed in the context of their evolutionary history in order to understand and predict their epidemic potential.
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    Study of influenza virus hemagglutinin
    (2010) Shen, Jun; Ma, Jianpeng
    The suddenly global outbreak of 2009 H1N1 Flu reminds human being the danger and severity of influenza virus. The gene of the new strain come from five different influenza viruses: North American swine influenza, North American avian influenza, human influenza, and two swine influenza viruses typically found in Eurasia. The recombination of gene in virus evolvement makes it more and more important to understand the evolutionary characteristics of influenza. Hemagglutinin (HA), embedded on the surface of influenza virus, is one of two virally-coded integral envelope proteins of the virus. The three primary functions of hemagglutinin (HA) include receptor binding, membrane fusion, and antigenic variation. Study of HA structure and its evolutionary mechanism is crucial to fully understand influenza virus. In the first chapter, a study of diversifying selective pressure on influenze B virus hemagglutinin was reported. All the positively selected sites were located in the four epitopes (120-loop, 150-loop, 160-loop and 190-helix) of HA, and all of them have been identified in previous studies. This supports a predominant role of antibody selection in HA evolution. In the second chapter, we studied positive selection analysis of 2009 HINT Flu. Among a subgroup of human A(H1N1) HAs between 1918∼2008, we found strong diversifying (positive) selection at HAI 156 and 190. We also analyzed the evolutionary trends at HAI 190 and 225 that are critical determinants for receptor-binding specificity of A(H1N1) HA. Additional analysis of directional selection was also employed for H1N1 gene data.