One mutation vs two amino acid substitutions

By: James V. Kohl | Published on: November 30, 2018

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A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission (2007)

…a predominant human alpha-2,6 sialic acid binding preference is essential for optimal transmission of this pandemic virus. These findings confirm an essential role of hemagglutinin receptor specificity for the transmission of influenza viruses among mammals.

The two amino acid change is food energy-dependent and the food is linked to the creation of receptor specificity.
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution (2013)

Koel et al. (p. 976) show that major antigenic change can be caused by single amino acid substitutions. These single substitutions substantially skew the way the immune system “sees” the virus. All substitutions of importance are located next to the receptor-binding site in the hemagglutinin. Because there are few positions of importance for antigenic drift, there are strict biophysical limitations to the substitutions at these positions, which restricts the number of new antigenic drift variants at any point in time.

One amino acid substitution is the link to virus-driven pathology via the failure to create the species-specific receptor. The virus changes the way the immune system perceives it.
For facts about the molecular mechanisms of glycosylation linked to ecological adaptations via our visual perception of mass and energy in the context of the space-time continuum, see: Identification of Amino Acid Substitutions Supporting Antigenic Change of Influenza A(H1N1)pdm09 Viruses (2015)

Substitution 127DT introduces a glycosylation pattern (N-X-S/T-X) that potentially adds a carbohydrate side chain at position 125. Carbohydrate side chains can mask antibody epitopes and have been shown to change the antigenic properties of influenza viruses (15, 16). Seasonal A(H1N1) viruses that circulated from the 1930s until 1986 had a glycosylation site starting at position 127, while viruses that circulated from 1986 onwards had a glycosylation site starting at position 125.

To see how quickly the energy-dependent molecular mechanisms can alter a functional structure of irreducible complexity, see: Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system (2015)

The mutated bacteria regained the lost flagella, and motility, within 4 days. Two stereotypical mutations diverted an evolutionarily related regulator that normally controls nitrogen uptake to control flagella biosynthesis. The mutations increased the levels of the co-opted regulator, then altered its specificity for the flagella pathway.

To link the potential of hydrogen (pH) and glycosylation to ecological adaptations of functional structures or to virus-driven pathology see: Molecular requirements for a pandemic influenza virus: An acid-stable hemagglutinin protein (2016)

Influenza pandemics occur several times per century, causing millions of deaths. For one of the myriad of zoonotic influenza viruses to do so, a virus containing a hemagglutinin (HA) surface antigen previously unseen by most humans must evolve the necessary, albeit largely unknown, properties for sustained respiratory spread between people. During entry, the prototypic viral fusion protein HA binds receptors and is triggered irreversibly by low pH in endosomes to cause membrane fusion. These studies link a fundamental property, activation energy of a fusion protein measured as its pH of activation (acid stability), to the ability of zoonotic influenza viruses to cause a human pandemic. Monitoring HA stability is expected to enhance prepandemic surveillance and control of emerging influenza viruses.

The activation energy that links the creation of pH-dependent receptors that prevent the ability of zoonotic influenza viruses to cause a human pandemic has been linked from light-activated microRNA biogenesis in plants to all biophysically constrained viral latency in bacteria via the weekend resurrection of the bacterial flagellum in P. fluorescens, which fluoresces when exposed to ultraviolet light.
See also: Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication (2018)

…we applied photoactivatable ribonucleoside enhanced cross-linking and immunoprecipitation (PAR-CLIP) to assess the native-state of NP–vRNA interactions in infected human cells. NP binds short fragments of RNA (~12 nucleotides) non-uniformly and without apparent sequence specificity. Moreover, NP binding is reduced at specific locations within the viral genome, including regions previously identified as required for viral genome segment packaging. Synonymous mutations designed to alter the predicted RNA structures in these low-NP-binding regions impact genome packaging and result in virus attenuation…

You’ve just witnessed how pseudoscientists link synonymous mutations to evolution, while serious scientists link food energy-dependent fixation of amino acid substitutions to light-activated ecological adaptations in species from microbes to humans.
Apparently, many researchers do not understand the difference between a mutation caused by the virus-driven degradation of messenger RNA and the fixation of an energy-dependent amino acid substitution that biophysically constrains viral latency in species from microbes to humans.
For an example of those who do understand the difference: North and South Korea team up to tackle TB and malaria (2018)

…if border restrictions are lifted, the viral infections, such as influenza, that are more common in South Korea will start to hit especially hard in North Korea, where immunity is low and suppressed by malnutrition…

Seeking the foundations of cognition in bacteria: From Schrödinger’s negative entropy to latent information (2006)

…it is widely accepted that there is no need for some unknown laws of physics to explain cellular ontogenetic development. We take a different view and in Schrödinger’s foot steps suggest that yet unknown physics principles of self-organization in open systems are missing for understanding how to assemble the cell’s component into an information-based functioning “machine”.

One mutation vs two amino acid substitutions

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