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Explaining Mutations and Variants

Summary:
Blogger and Commenter Professor Joel Essenberg addresses Covid variants being called mutations. As a geneticist, I am troubled by the promiscuous use of the word “mutation” to describe amino acid or nucleotide differences from a reference sequence. In nearly all cases, there is no known functional significance attached to these differences. Accordingly, the differences are best referred to as “variants,” not mutations. I’ve had my genome sequenced and I have a variant call file based on that sequence. I know all the amino acid variants in my genome compared to the reference human genome And I’ve checked for variants associated with risk for disease (mutations); so far, none have been detected. But our ability to detect variants runs far ahead of

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Blogger and Commenter Professor Joel Essenberg addresses Covid variants being called mutations.

As a geneticist, I am troubled by the promiscuous use of the word “mutation” to describe amino acid or nucleotide differences from a reference sequence. In nearly all cases, there is no known functional significance attached to these differences. Accordingly, the differences are best referred to as “variants,” not mutations.

I’ve had my genome sequenced and I have a variant call file based on that sequence. I know all the amino acid variants in my genome compared to the reference human genome And I’ve checked for variants associated with risk for disease (mutations); so far, none have been detected. But our ability to detect variants runs far ahead of our ability to assign significance to them (or alternatively, to confidently say they are neutral).

run75441: At this point I went back to Professor Joel Eissenberg asking him to explain the above paragraph.

Prof. Joel: I’m making an analogy between my genome and a COVID genome. Sequencing my own genome revealed many differences between my genes and the ‘human genome.’ Of course, I’m pretty normal, so most of these differences are probably not contributing to my health. So, I wouldn’t classify these differences as ‘mutations’ but just inconsequential variants.

Similarly, some, many or most of the differences in the spike protein that have been detected by sequencing Omicron virus could be inconsequential ‘variants’ and not ‘mutations’ in the sense that they change the virus behavior (infectiousness, ability to replicate, ability to evade vaccine antibodies). As it is, it is really fast and cheap to obtain COVID virus sequence information and to classify new variants, but it slower to determine which of the variants constitute ‘mutations’ or are inconsequential in terms of virus behavior in an epidemiological sense.”

There’s a lot of concern and chin scratching over the Omicron variant of COVID that was recently discovered in Africa:

Dr. Dan Barouch, head of the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center, said: ‘he was concerned because the new variant has 30 mutations, a large number, in the spike protein that the virus uses to infect human cells. His researchers first saw Omicron’s genetic sequence on Thanksgiving after South African scientists posted it online. The mutations are concentrated at a location on the virus that antibodies target, he said, which “raises the question as to whether the virus will still be covered by the vaccines.'”

At this point, most of these amino acid changes should be called variants, not mutations. We don’t yet know which, or how many, of these difference from the reference COVID spike protein sequence have functional significance. They might make the virus more infectious. They might make infection more severe. They might allow the virus to elude antibodies made to current vaccines. Time will tell. This is the best advice right now:

Dr. Ashish Jha, Dean of the Brown University School of Public Health, wrote on Twitter. “We’ll know more in coming days to weeks. There will be those who will spread fear ― and those who downplay it. Please ignore both groups.'”

Worrisome new COVID variant prompts travel restrictions from Africa – The Boston Globe (Account Required)

New ‘omicron’ variant prompts global travel restrictions | PBS NewsHour

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