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Genetic Linkage

Omicron Evolves and the Covidization of Scientific Publishing

Just as we thought Omicron was rolling across the US and into oblivion, a new "subvariant" has arrived and is, again, taking over. At the same time Moderna is announcing dosing of the first participant in its phase 2 study of an Omicron-specific booster. But Omicron's evolution wasn't unexpected – the World Health Organization's recent update cites four lineages of Omicron, dubbed BA.1 through BA.4.


"So it goes," to quote Kurt Vonnegut in Slaughterhouse Five. But that statement was in response to death among the Tralfamadorians – not the robust activity of a tiny virus.


It seems to me that the continual categorization of SARS-CoV-2 reflects the human urge to group, categorize, and name things to help us understand them. I think the situation is eventually going to dissolve into a continuum of genetic flux as the tango of mutation and selection continues. That's what nucleic acids do.


Since it still new days for Omicron 2.0, here's a snapshot:




To continue reading go to DNA Science, where this post first appeared.

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Pandemic Too Fast to Follow as Three Waves of Infection Wash Over the US: Delta, Omicron, and Flu

Next Tuesday, December 21, marks two years since the China CDC Weekly acknowledged the first "cluster of pneumonia cases with an unknown cause … in Wuhan."


On the Origin of COVID


Half of the two-page report from China is an illustration of seven colored ovals, each enclosing symbols for closely-related viruses. Within one oval, 3 of the 7 viral lineages bear asterisks. The trio includes what was then called 2019-nCoV.


In that initial report, China claims that the origin of the novel coronavirus "is still being investigated … all current evidence points to wild animals sold illegally in the Huanan Seafood Wholesale Market."


That's a little like saying the Beatles came from Hamburg because they played there often in their early days – rather than from Liverpool.


An alternate hypothesis of the possible origin, based on genome sequence evidence, unfolds in a report on bats from Cambodian caves collected in 2010, published recently in Nature. Predecessors of SARS-CoV-2 might have arisen in many places, such as southeast Asia, where investigators weren't looking. (I covered the bats in April when the study appeared in preprint form – the pandemic has instilled a never-ending sense of déjà vu to science journalists.)


The Cambodian bats are the closest known relatives to the enemy, yet they are curiously missing the precise part of the genome that encodes the region of the spike protein that the virus uses to grab onto and slip into our cells. Coincidence? Perhaps. Genetic material is well known to flit from genome to genome, crossing what we humans call species boundaries. But there are other hypotheses.


As Fox Mulder said often in The X Files era, the truth is out there. But we may never know it.


To continue reading, go to DNA Science, my blog for Public Library of Science, where this post first appeared.

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