Abstract
Different subtypes of Influenza A virus are associated with species specific, zoonotic or pandemic Influenza. The cause of its severity underlies in complicated evolution of its segmented RNA genome. Although genetic shift and genetic drift are well known in the evolution of this virus, we reported the significant role of unique RNA palindromes in its evolution. Our computational approach identified the existence of unique palindromes in each subtype of Influenza A virus with its absence in Influenza B relating the fact of virulence and vigorous genetic hitchhiking in Influenza A. The current study focused on the re-assortment event responsible for the emergence of pandemic-2009 H1N1 virus, which is associated with outgrow of new palindrome and in turn, changing its RNA structure. We hypothesize that the change in RNA structure due to the presence of palindrome facilitates the event of re-assortment in Influenza A. Thus the evolutionary process of Influenza A is much more complicated as previously known, and that has been demonstrated in this study.
Highlights
Influenza A viruses are single-stranded RNA viruses of negative sense with an eight-segmented genome and belong to the family Orthomyxoviridae [1]
This correlates the palindromic occurrence with the event of expedited gene exchange in Influenza A termed as reassortment, which is a special mechanism of producing new subtype, since Influenza B lacks both palindromes and the reassortment event
We hypothesize that palindromes play a significant role in the re-assortment of Influenza A virus
Summary
Influenza A viruses are single-stranded RNA viruses of negative sense with an eight-segmented genome and belong to the family Orthomyxoviridae [1]. Positive selection has taken place that could be the cause of new subtypes [7] Besides these concepts, we performed a computational approach to study the evolution of Influenza virus from a different point of view, by investigating the presence of palindromes in the gene of Influenza viruses, each from different subtypes. Some previous statistical and experimental studies of palindromes in other classes of viral genomes, such as the double stranded DNA viruses, bacteriophages, retro viruses, etc., have been performed [8-12], this is a novel approach to analyze the gene pattern and evolution of Influenza A. The structural changes among the HA gene segments involved in re-assortment were identified using M-fold [14] program for the comparative folding pattern in the palindromic site, to analyze the influence of palindrome in the folding pattern of the RNA of the virus
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