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Selection in Within-Host Evolution of Influenza Virus - Coggle Diagram
Selection in Within-Host Evolution of Influenza Virus
Intro
Influenza virus, H7N9, is arising as a pandemic due to the two steps, infection humans using localized and sporadic tactics and then emerging to humans all around the globe. A perfect example of evolution in nature.
The first step is already occurring but for a virus to reach global proportions it must undergo phenotypic evolutionary transmissibility.
This experiment explain the transmission evolution of influenza using observations, a model that is used is the H5N1 strand of influenza and its evolution with its increase or decrease of mutations and its selection.
The main method to take into account is to understand how selection through the technique of maximum likelihood method
Results
Using animals, in a previous experiment focusing on transmission taking 2 uninfected pigs and 2 infected pigs and placing them in the same environment. This showed limiting transmission also observed non-neutral behavior as well as selection became a rare occurrence.
18 alleles were non-neutral, 9 were under selection and the other 9 were experiencing linkage disequilibrium.
18 pigs under non-neutral behaviors found selection that includes time-dependent selection occurring all at once with more than 1 loci.
Pig 104 observed negative selection upon allele G to A, mutation occurring in loci with large selection. This mutation is synonymous and also strongly deleterious.
Pig 109 has a positive selection in three different locus spots, 553 and 914 had changes in alleles G to A and loci 696 going from A to G mutations. Pairs of mutant alleles under selection are linked but the mutations at loci 696 and 914 are only joint on sequences but are not isolated, this shows that selection will only favor multiple locus.
Pig 405 showed strong evidence occurs through positive selection on alleles G to A located on locus 844. At the same time, time-dependent selection is occurring on A to G at locus 553. Both mutations are nonsynonymous.
Pig 410 showed a time-dependent selection located on locus 447 using a synonymous C to T allele.
Discussion
This experiment shows understanding of the evolution of the within-host influenza virus.
This experiment took into account that linkage disequilibrium ocurred between alleles but at different locus, considering in this case multiple changes of alleles occurred at the same time in a non-recombinant gene.
Even with dN/dS ratios being acceptable at codons 204 and 257, there was no siting of selection for alleles at these codons.
Now that it is known that the time frame when a mutation occurs it becomes easier for the mutation to be understood.
Between the linkage disequilibrium of a pair of alleles there was no siting of recombination and no decay within a larger distance of alleles.
Mutations occur at high frequencies which in hand give a greater change for mutations to be under selection. counting mutations there was found to be a large transition transversion ratio that has a positive correlation with the values of RNA in viral populations.
Pig 412 showed an example of selection acting on polymorphism in a time-dependent selection which could be caused by interference of a mutation.
Methods
Quasispecies Theory and model expalins the evolution of an organism that self-replicates and contains mutations with a despcription that includes the set of locus that is spanned using haplotypes.
This quasispecies model included an evolutionary model, identification of alleles under selection, and the description of the extent of support.
Mutation models occurring with haplotypes were used with the constant being the rate of mutation and comparing the probability of a mutation occurring between different haplotypes.
Selection was compared in each haplotype with a constant selection coefficient. Taking into account the evolutionary time frame of influenza, there needed to be 12- hour intervals as well as how selection only acted once the cell was excited.
Conclusion
Continuation between the transmitted and native population needs to occur. This causes the allele frequencies to change after and before transmission which is the result from selection. The action of bottle necking could change the structure of the population
The course of infection needs to be known, without this the rate of selection occurring in transmission will remain unknown.
With the use of modernized technology and more data collection will increase the understanding of infections even more.
Citation
Illingworth CJR, Fischer A, Mustonen V. 2014. Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data. Wilke CO, editor. PLoS Computational Biology. 10(7):e1003755. doi:10.1371/journal.pcbi.1003755.