Viewing a single comment thread. View all comments

NotAnotherEmpire t1_j7hccp7 wrote

Reply to comment by atred in (Virology) Has SARS-CoV-2 outcompeted all the other coronaviruses which have been called the ‘common cold’? by jsgui

Confidence in how it would behave in humans was too high.

It was mostly stable. The problem is that it also seems likely the virus can chronically infect people with a compromised immune system, producing evolution that wouldn't occur going from host to host. That's very likely how Alpha and Omicron came out of nowhere.

Original Omicron isn't competitive evolution gradually picking up changes to evade immunity to the others. It was isolated from the rest of the pandemic and then appeared with a very different spike.

133

Seicair t1_j7hp047 wrote

Alpha came from an immunocompromised individual? I thought alpha and beta were pretty close to the original strain?

20

PHealthy t1_j7hqjrj wrote

It's thought Delta evolved within an immunocompromised person(s) and Omicron was likely a spillover from humans to mice and back to humans.

https://www.nejm.org/doi/full/10.1056/NEJMsb2104756

https://www.sciencedirect.com/science/article/pii/S1673852721003738

110

Seicair t1_j7i6fy4 wrote

Both of those links were fascinating, I hadn’t heard that omicron probably jumped species!

36

NotAnotherEmpire t1_j7hzrjv wrote

If Alpha had evolved gradually the UK or Denmark would have seen it with their massive surveillance programs. No one's reported an Alpha-in-progress.

Alpha had far more than the expected number of mutations and was materially different in behavior. Fortunately it didn't matter for vaccine targeting.

31

Seicair t1_j7i4yh9 wrote

I somehow never heard that. I remember hearing Omicron came out of left field and it was thought to have evolved in an immunocompromised patient due to the sheer number of mutations. I thought Alpha and Beta were two notable strains that were more successful than other small mutations. Now that I look though, I see AB both have a significant number of mutations, just the spike was mostly unchanged.

Fascinating. I studied some microbiology/immunology in school, I would’ve liked to have delved deeper.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8714679/#:~:text=delta)%2C%20B.-,1.1.,of%20these%20variants%20%5B1%5D.

15

jayhillcpa t1_j7ix4s8 wrote

How are the mutations identified when testing? Wouldn’t the mechanisms need to change every time a new variant popped up?

6

gengengis t1_j7jjmf6 wrote

Genetic testing. The viral genome is sequenced and edits between specimens are catalogued.

There are a shitload of mutations between most specimens. Many of these might be single amino acid flips which might not do anything at all. But the viral genome has certain core regions essential to its function. For instance, with Covid, one of these regions codes for the spike protein necessary for infecting host cells.

We can then count up the major core mutations and get an idea of how different one specimen is from another. And indeed, because this science has advanced so much, we can even make predictions about how certain mutations will affect the viral proteins, and how those changes might affect transmissibility and immune evasion.

4

jayhillcpa t1_j7jtuap wrote

So if I drive through one of the mobile testing sites, sequencing and editing occurs all within minutes whilst I’m waiting in my car? Wouldn’t it behoove the individuals by specifying the variant they tested positive for? How does the (what sounds like splicing) categorization occur with the home testing kits - the testing kits that clearly state it cannot and does not differentiate between SARS-COV-1 and COV-2?

As far as predictions go, the “science” apparently isn’t that advanced. It’s as if I were to propose the following, because I can count to 100, I can predict the winning power ball numbers.

By the way thank you for the response.

−4

sirgog t1_j7jussa wrote

A small percentage of people who are tested have their sample sequenced as well.

If a lab performs 250000 PCR tests a week and gets 20000 positives, it will likely sequence 100 of the positives.

This then shows trends across the population in which variants are dominating.

6

GaitAtaxia t1_j7jso9t wrote

It was actually always known to halve a relatively high point mutation rate, giving it a higher rate of genetic drift. It does NOT have the same mechanism as influenza for allowing genetic SHIFT.

We focussed on talking about its low rate of genetic shift and ignored the high rate of genetic drift when making claims of low mutability, but it was really only a half truth at best.

3