Year: 2022

MUTANT REFRESHERS. "After introduction into the human population, a lineage of influenza generally persists through antigenic drift, in which HA and NA continually accumulate mutations allowing viruses to infect hosts immune to earlier forms of the virus. These lineages of influenza show recurrent seasonal epidemics in temperate regions and less periodic transmission in the tropics." (HA and NA = key antigens). https://lnkd.in/dDjCWve View in LinkedIn

BRANCH SUBPOPULATION EXTINCTIONS. "Of central interest to the study of viral phylodynamics is the distinctive phylogenetic tree of epidemic influenza A/H3N2, which shows a single predominant trunk lineage that persists through time and side branches that persist for only 1–5 years before going extinct." https://lnkd.in/dDjCWve View in LinkedIn

TRUNK EPITOPE SELECTION. "Phylogenetic analysis of H3N2 influenza has shown that putative epitope sites of the HA protein evolve approximately 3.5 times faster on the trunk of the phylogeny than on side branches. This suggests that viruses possessing mutations to these exposed sites benefit from positive selection and are more likely than viruses lacking such mutations to take over the influenza population." https://lnkd.in/dDjCWve View in LinkedIn

BRANCH NONEPITOPE SELECTION. "Conversely, putative nonepitope sites of the HA protein evolve approximately twice as fast on side branches than on the trunk of the H3 phylogeny, indicating that mutations to these sites are selected against and viruses possessing such mutations are less likely to take over the influenza population." https://lnkd.in/dDjCWve View in LinkedIn

HITCHHIKING. "Reassortment between segments occurs slowly enough, relative to the actions of positive selection, that genetic hitchhiking causes beneficial mutations in HA and NA to reduce diversity in linked neutral variation in other segments of the genome." https://lnkd.in/dDjCWve View in LinkedIn

ANTIGENIC EVOLUTION. "Swine influenza A/H3N2 is known to evolve antigenically at a rate that is six times slower than that of the same virus circulating in humans, although these viruses' rates of genetic evolution are similar." https://lnkd.in/dDjCWve View in LinkedIn

RAPID MICROBE EVOLUTION. "In a decade bacteria can produce 200,000 generations — about the number of generations of humans there have been since our lineage split from that of chimpanzees. So it’s hardly surprising that in less than a human lifespan we’ve seen the evolution of new diseases such as HIV and numerous antibiotic-resistant bacteria." https://www.newscientist.com/article/dn13640-evolution-myths-evolution-produces-perfectly-adapted-creatures/ View in LinkedIn

SO ENDS this contemplation of the immensely successful strategy of viruses, the remains of these creatures which litter our genomes and drive evolutionary novelty. Viruses are everywhere. In every habitat, no matter how hostile. In every creature. And in virtually every genome in some form or another. It is preposterous that we have been so slow to recognize that they are very much alive. They simply are an extreme case of outsourcing. View in LinkedIn

DISCRIMINATION LACKING. "One ultimate goal of genomics is to read the code—to be able to predict variation in gene expression levels based on the nucleotide sequence—and this goal remains challenging. The main difficulty is that many changes in TF binding do not seem to result in measurable changes in gene expression levels, and we do not yet know how to distinguish between binding events that affect gene expression and those that do not." (TF = transcription factor). https://lnkd.in/dFv6Tsi View in LinkedIn

NATURAL SELECTION is at the heart of everything that matters, or so it seems. Researchers have devoted an incredible effort to describe it, and it has even been proposed as being anticipatory for conditions it has never seen. But what is this mystical force? Is it not just the population effects of competition between species, between individuals, between sexes, between instars, and the searing effects of death? Death is at its heart, and without death, natural selection does not thrive. View in LinkedIn