Mission of randomness

Keywords: :

• influenza A virus
• mutation
• randomness
• protein structure
• genetic reassortments
• analysis of variance (ANOVA)

This article refers to:

Possibility of cross-species/subtype reassortments in influenza A viruses

In order to explore the possibility of cross-species/subtype reassortments in influenza A viruses, in this issue of Virulence Drs Wu and Yan address the reassortment of influenza A virus based on the analysis on nonstructural protein variations from a purely random mechanism viewpoint.¹ This approach is interesting but not widely known in the scientific community. Indeed, an extensive literature search reveals that only this research group, Drs Wu and Yan, has applied it so far.

Why does a mutation occur? What is a driving force behind a mutation? These are the questions that have been puzzling the world for a long time, questions that humans have intended to solve for years. Mutations in the influenza A virus have troubled the world with pain, and even death. According to Drs Wu and Yan’s consideration, one of driving forces behind mutations is randomness existing in protein structure.¹ So what is this mysterious randomness? These are uncharted areas which use undefined and unclear terms that may leave the scientific community at a loss.

However, this is unlikely to be the case, because randomness existing in protein structure is measured by the maximal probability of occurrence.^2-5 Is this a trick to replace a less popular term with a somewhat understandable term? No, it is because the maximal probability can be calculated very simply. For example, there is a bag containing 10 blue and 20 red balls, the maximal probabilities should be 20/30 × 10/29 or 10/30 × 20/29 when you take two balls from this bag. Similarly, an amino acid pair should have a chance to be constructed in the same way. If not, nature should deliberately do so. Otherwise a protein structure would be uncomfortable and would seek to mutate to a structure with the maximal probability of occurrence. How can we measure this mutation tendency? It is the difference between the predicted probability and actual probability measured in a protein structure.⁶ Interestingly enough, a mutation makes a portion of protein approaching to the predicted probability, but also makes other portion of protein away from the predicted probability, which leads to the tendency toward mutation in future. This is the everlasting force driving mutations.

Influenza A viruses have been affecting our world for a long time because influenza is the most commonly infectious disease, whose seasonal epidemics and occasional pandemics have brought about the loss of many lives in humans and other species. The prevention and treatment of influenza is very costly, and presents a huge burden worldwide. All of these results stem from frequent mutations of influenza A viruses, of which the reassortment of genetic segments from different viruses, different species and/or different subtypes, is the most crucial because new strains can be formed and may induce influenza outbreak.⁷ For example, the outbreak of highly pathogenic avian influenza A/H5N1 viruses started in 1996,⁸ the last pandemic of influenza A/H1H1 viruses in 2009,⁹ and the newest atypical influenza A/H7N9 viruses just emerged since early 2013.¹⁰ Unfortunately, these threatening strains continue to circulate in some regions and different populations.

It is clear that influenza A viruses have 8 RNA segments that encode 10 or 11 viral proteins, which provide a foundation for genetic reassortment. There are also some differences between viral genes from different subtypes and species, which is the basis for viral classification. In general, such differences can prevent cross-subtype mutation and cross-species infection, and form the subtype barrier and species barrier. However, frequent reassortment mutations challenge the subtype/species barrier of influenza A viruses, like the strain of influenza A(H1N1)pdm09 whose genetic material came from three different species: human, avian and swine, indicating small difference between species.

Therefore, it is important to estimate the difference of viral proteins from different species and subtypes. Modern technologies have rapidly developed in recent years¹¹ and genomic sequences are very useful for molecular epidemiological analysis These advances also helps our understanding of genetic reassortment events.¹² Although multiple sequence alignment and phylogenetic tree construction showed the low degree of variation within the alleles of some proteins,¹³ it seems that how about the difference between viral proteins has yet be explained. Drs Wu and Yan evaluated this issue from statistical viewpoint. They used the amino acid pair as a measure to quantify each viral protein and then to analyze the difference between subtypes and species for the first time. Their results demonstrate that in general the inter-subtype/species variations are remarkably smaller than the intra-ones and this phenomenon can be found in all ten proteins of influenza A viruses. This sheds some light on explaining the question why genetic reassortments occur frequently in influenza A viruses.

Analysis of variance (ANOVA) has been widely used in almost all of scientific fields for estimating the difference between group means and the variation among and between groups. However, because ANOVA deals with numerical components while proteins are presented by amino acids in alphabet format, it has not been used to compare the differences between the influenza virus proteins from different species and subtypes. It is novel that amino acids or a protein can be converted into numerical characteristics to conduct various statistical analyses and modeling using the computational mutation approach developed by Wu and Yan.⁶ According to their study, one can have a clear concept that there are no statistical differences between most influenza A viruses in terms of subtypes and species, thus genetic reassortment from different subtypes and species is easier to occur during co-infection.

The prevention and treatment of influenza promote further development of virus surveillance, antiviral vaccines, and drugs. Recently it has been revealed that influenza vaccines are not so effective in controlling new outbreaks and partially because their primary target is designed to induce immunity to the hemagglutinin antigen of specific influenza virus strain.¹⁴ To any antiviral therapy, a major drawback is drug resistance, which depends on the degree of reduced fitness of particular mutations.¹⁵ Evidence from phylogenetic and statistical analyses conform that influenza A viruses are susceptible to genetic reassortment because of their small inter-subtype/species variation. Thus, new strategies have been focused on developing universal anti-viral drugs and vaccines¹⁶ which brings about the hope that one can finally defeat the threat of epidemic and pandemic from influenza A viruses.

10.4161/viru.27136

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.