Together these characteristics enable Influenza A to evolve relatively rapidly in non-human hosts, then re-adapt to humans through exchange of segments (reassortment) in a host co-infected with a human and, e.g., an avian strain. the mutation rate in the genome is high in influenza viruses, and particularly high in Influenza A, since their RNA polymerase lacks exonuclease activity necessary for proof-reading.consist of several (eight in the case of Influenza A and B) distinct pieces of RNA, which typically encode just one, sometimes two viral proteins. the linear negative-sense single-stranded RNA genomes of influenza viruses (and of all viruses of the Orthomyxoviridae family) are segmented, i.e.Reassortment events are a key trait of Influenza A made possible by its wide range of natural hosts combined with two molecular characteristics of the species: Importantly, all flu pandemics of the last century have been triggered by reassortment events between avian and human Influenza A strains (although at least the 2009 swine flu pandemic involved an additional mixing event with an Influenza A strain from pigs). The different influenza species infect distinct animal hosts (though all of them can infect humans and pigs) and the most important natural reservoir for Influenza A are birds (in particular, wild aquatic birds), in which it causes Avian influenza. Of the four species of influenza viruses (Influenza A-D), Influenza A is the most virulent in human hosts and subtypes of it have been responsible for all historic flu pandemics. Generate per-segment phylogenetic trees of AIV consensus sequences Use a collection of per-segment reference sequences to construct a hybrid reference genome that is sufficiently close to a sequenced sample to be useful as a reference for mappingĬonstruct a sample consensus genome from mapped reads How can we obtain meaningful phylogenetic insight from AIV consensus sequences?ĭetermine how reassortment impacts reference-based mapping approaches Is it possible to reuse existing tools and workflows developed for the analysis of sequencing data from other viruses? With reassortment of gene segments being a common event in avian influenza virus (AIV) evolution, does it make sense to use a reference-based mapping approach for constructing consensus genome sequences for AIV samples?
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