|A microscopic photo of an Influenza virus positive / Photo by: Dr. Erskine Palmer via Wikimedia Commons|
The influenza virus is routinely responsible for causing flu epidemics seasonally every year. This virus comes in two main types, Type A and Type B. Over the years; the World Health Organization Influenza Surveillance Network reviews the numerous scientific data availed by scientists to predict the best suitable strains of Influenza virus for flu vaccine in the next coming Influenza season. This review by WHO has proved necessary due to the virus rapid way of accumulating new mutations. This has led to a turnover of strains used previously, because of its ability to bypass the immunity provided before. The rate at which these mutations occur profoundly determine the capability of a virus in evading and adapting the host’s immune system. For a long time now, researchers have shown interest in measuring the rate of these mutations.
However, already existing approaches have proved to have shortcomings and biases that are yet to be considered. Nonetheless, the good news is, a report by Megan Procario, Adam Lauring and Matthew Pauly of the University of Michigan indicates that by employing a new twist to an old approach can overcome the shortcomings.
When in a host cell, the influenza virus tricks the cell into copying its genome, which is usually encoded in RNA rather than the DNA while assembling progeny virions, these are new virus particles. An RNA polymerase copies the viral RNA, which is a virus enzyme through molecular machinery in the cell of the host. Nonetheless, the RNA polymerase enzyme often makes mistakes, which lead to high mutation rates in the new RNA molecules.
Over the years, sequencing method has been primarily used to measure mutation rates. According to scientist Sanjua’n, this approach involves sequencing the genome of a virus, afterward, allowing that virus to infect cells, sequencing progeny virions genomes and finally making a comparison between original genome and progeny sequence. This portrays the mutations that have taken place in the cycle of infection. The advantage of this method is that it provides the sum of all mutations and the frequencies of each type. Nevertheless, this approach has two significant shortcomings. First and foremost, differentiation of natural mutations from the errors made during sequencing has proven difficult. Secondly, this approach is likely to miss vital mutations. For instance, the mutations that occur at the beginning of the infection cycle may limit further mutations of the virus.
The three scholars were, however, able to curb the first shortcoming. They sequenced transcripts from an artificial DNA construct known as a plasmid. It is based on RNA encoding some of the virus genomes. The errors made in the plasmoid genome and the virus genome are similar, proving that any other errors that occur in mutation are because of a viral polymerase which copies the viral genome. This procedure showed that sequencing errors are responsible for almost half of the mutations in the Influenza virus using the sequencing approach.
Megan et al. were involved in looking into the extent of the second shortcoming. They examined the number of mutations that cause the production of incomplete proteins. These proteins are harmful to the virus. The result was that there were fewer mutations of the viral genomes produced as compared to the plasmid sequences. They concluded that through the sequencing method, very lethal mutations could be missed.
Mutations rates can also be measured through a fluctuation test. Salvador Luria and Max Delbru`ck are the brains behind this approach which they established in the 1940s. This method involves counting the number of rare mutations to a readily observable phenotype. For instance, the resistance to a drug. This approach has one major problem in that; it cannot be used to determine if mutations change the nucleotides in RNA or DNA. Megan et al. believed that this shortcoming could be overcome if it was possible to point out which exact mutations caused the measured phenotype.
Thus, they established a fluctuation test for the Influenza virus depending on the fluorescence emitted by (GFP) green fluorescent protein. It involved the production of recombinant Influenza viruses that expressed a version of green fluorescent protein with one nucleotide change that removed the fluorescent properties of the protein. With the reverse made by mutations, fluorescence is restored making it possible to count the frequency of occurrence of the reverse mutation.
Megan et al. further constructed 12 different recombinant viruses that required 12 distinct single nucleotide reversion mutations to restore fluorescence for each possible mutation. The positive thing about these mutants GFPs is that they do not affect the virus to infect cells or to replicate. With this new test, these three scholars found out that the rate at which the Influenza virus mutates is faster than any case that was reported previously. With these new findings, it will be easier to establish better models of influenza evolution, making it better to make future predictions of the changes that come with the circulating strains that have enabled the virus to bypass the existing vaccines. The good news on this method is that its applications can work with any virus, so long as it can withstand the gene encoding GFP being inserted into its genome.