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Sort of. Sometimes. Viruses evolve according to evolutionary pressures. I'm surprised we don't see Covid mutations that invalidate PCR tests - perhaps it's too

Sort of. Sometimes. Viruses evolve according to evolutionary pressures. I'm surprised we don't see Covid mutations that invalidate PCR tests - perhaps it's too soon, or even, who knows, maybe they are there and we don't know? The common trope is that if the virus is too deadly, then it doesn't have a chance to find new hosts. This is kind-of what happened to "SARS-1" - it tended to kill its hosts before they could pass it on. Unfortunately, this is only a weak effect in Covid. Most of the spread happens well before people are very ill; in terminal stages of severe Covid, many people in fact would test negative for virus presence. So there is little evolutionary pressure on the virus to be less deadly - by the time it kills people, we are spent vessels from its point of view. I suppose a mutation that makes it completely benign would be beneficial, as current rules on self-isolation curb the spread of strains causing symptomatic disease. There are pressures that make it more deadly: a mutation leading to higher viral load is both more deadly and more transmissible. So unless the transmissibility increases too much (and virus is way too deadly), we might even expect the virus to become more deadly. This hasn't happened yet, thankfully. An example I used elsewhere was the introduction of Myxomatosis in Australia, to control the invasive rabbit population. Over time, the local strain evolved to be more deadly, but with a longer incubation periods. This way, bunnies had more time to pass the virus around, then once that job was done, the virus was happy to kill them off. On the flipside (and very long timescales), since some people appear to be genetically more resistant to the virus, you can expect natural selection to do its job. But since overall death rate from Covid is low-ish (no more than 1%, you'd say, and skewed towards older, non-reproducing individuals) this would take a long time. Another hope is that, if the disease is less serious in children, perhaps immunity it built up during the usual period of childhood infections. There is another coronavirus, which causes a mild cold in children, but can be very serious in adults (apologies, I can't remember what it's called). Thankfully, a single infection gives more-or-less complete lifetime protection - so most people have it as children and never worry about it again. In either of these cases, we're talking about generational timescales.

ufo 5y ago
Apparently there are some variants of Omicron that can't be detected with current PCR tests. We may need to update the list of primers at some point. https://www.theguardian.com/world/2021/dec/07/scientists-find-stealth-version-of-omicron-not-identifiable-with-pcr-test-covid-variant https://www.theguardian.com/world/2021/dec/07/scientists-fin...
- _Wintermute 5y ago
  Just to clarify, as it's not clear from that sentence: it can still be detected with PCR, just not distinguished from other variants as easily.
dtech 5y ago
> I'm surprised we don't see Covid mutations that invalidate PCR tests PCR tests for RNA or DNA, that's not something a mutation can change. I don't know for Covid, but usually a PCR test targets something fundamental & stable. That might need to be updated with new variants.
- rich_sasha 5y ago
  They test for particular fragments, not the whole thin. 3 fragments usually in the UK.
- chki 5y ago
  Isn't that the only thing a mutation can change? What is mutating in the virus if it's not the DNA?
323 5y ago
> I'm surprised we don't see Covid mutations that invalidate PCR tests The people who design the tests know which parts of the sequence are more likely to mutate, so they pick the more conserved parts. Also, most PCR tests check for 3 different parts of the sequence. Which is why Omicron can still be detected even if there is a mutation in one part checked by the test, since the other 2 parts still match (the so called S-gene-dropout).
makomk 5y ago
The current PCR tests detect three different regions of RNA that are expected to be relatively well conserved, so there's no single mutation that can cause PCR tests to not detect them and we'll hopefully get a substantial early warning that allows the tests to be adapted if they ever head in that direction. One of the three markers detected by some of the PCR tests is actually invalidated by Omicron and some other variants but it's likely either bad luck or the result of some other benefit this mutation gives the virus. In order to get much benefit the virus would basically have to dodge all the things the PCR tests check for at once and that's hard to evolve.
- rich_sasha 5y ago
  Yeah, Alpha had the same mutation as Omicron too. I'm not a virologist by any stretch of imagination. Mutations seem to come in bundles; I'm just surprised that, given typical PCR tests only test for three RNA fragments, that we don't see mutations that evade it. The main evolutionary pressure on Covid in developed countries is Public Health clamping down on it like a ton of bricks. A variant that quietly evades PCR tests, self-isolation etc. is set up for life.
hackinthebochs 5y ago
> So there is little evolutionary pressure on the virus to be less deadly - by the time it kills people, we are spent vessels from its point of view. A variant that infects more people from a single host (assuming everything else held constant) is a positive selective pressure. So increasing the contagious period is beneficial. But the length of the contagious period is inversely related to the timing and strength of the immune response. So we should expect the virus to become less deadly over time, assuming there's a hard limit to its ability to evade a typical immune system.
lovecg 5y ago
Viruses that evade the PCR test for Covid would be a different species almost by definition, and with enough mutations that could happen. These tests don’t detect other common cold causing coronaviruses for example.
def_true_false 5y ago
> An example I used elsewhere was the introduction of Myxomatosis in Australia, to control the invasive rabbit population. Over time, the local strain evolved to be more deadly, but with a longer incubation periods. This way, bunnies had more time to pass the virus around, then once that job was done, the virus was happy to kill them off. Do you have other examples besides Myxomatosis?
zamfi 5y ago
> This is kind-of what happened to "SARS-1" - it tended to kill its hosts before they could pass it on. Quick nit: while this is true, SARS-1 was also not particularly transmissible before symptoms appeared, in contrast to Covid, which made control much easier (in addition to the much higher fatality rate causing everyone to take it much more seriously).

ufo 5y ago

Apparently there are some variants of Omicron that can't be detected with current PCR tests. We may need to update the list of primers at some point. https://www.theguardian.com/world/2021/dec/07/scientists-find-stealth-version-of-omicron-not-identifiable-with-pcr-test-covid-variant https://www.theguardian.com/world/2021/dec/07/scientists-fin...

_Wintermute 5y ago
Just to clarify, as it's not clear from that sentence: it can still be detected with PCR, just not distinguished from other variants as easily.

dtech 5y ago

> I'm surprised we don't see Covid mutations that invalidate PCR tests PCR tests for RNA or DNA, that's not something a mutation can change. I don't know for Covid, but usually a PCR test targets something fundamental & stable. That might need to be updated with new variants.

rich_sasha 5y ago
They test for particular fragments, not the whole thin. 3 fragments usually in the UK.
chki 5y ago
Isn't that the only thing a mutation can change? What is mutating in the virus if it's not the DNA?

323 5y ago

> I'm surprised we don't see Covid mutations that invalidate PCR tests The people who design the tests know which parts of the sequence are more likely to mutate, so they pick the more conserved parts. Also, most PCR tests check for 3 different parts of the sequence. Which is why Omicron can still be detected even if there is a mutation in one part checked by the test, since the other 2 parts still match (the so called S-gene-dropout).

makomk 5y ago

The current PCR tests detect three different regions of RNA that are expected to be relatively well conserved, so there's no single mutation that can cause PCR tests to not detect them and we'll hopefully get a substantial early warning that allows the tests to be adapted if they ever head in that direction. One of the three markers detected by some of the PCR tests is actually invalidated by Omicron and some other variants but it's likely either bad luck or the result of some other benefit this mutation gives the virus. In order to get much benefit the virus would basically have to dodge all the things the PCR tests check for at once and that's hard to evolve.

rich_sasha 5y ago
Yeah, Alpha had the same mutation as Omicron too. I'm not a virologist by any stretch of imagination. Mutations seem to come in bundles; I'm just surprised that, given typical PCR tests only test for three RNA fragments, that we don't see mutations that evade it. The main evolutionary pressure on Covid in developed countries is Public Health clamping down on it like a ton of bricks. A variant that quietly evades PCR tests, self-isolation etc. is set up for life.

hackinthebochs 5y ago

> So there is little evolutionary pressure on the virus to be less deadly - by the time it kills people, we are spent vessels from its point of view. A variant that infects more people from a single host (assuming everything else held constant) is a positive selective pressure. So increasing the contagious period is beneficial. But the length of the contagious period is inversely related to the timing and strength of the immune response. So we should expect the virus to become less deadly over time, assuming there's a hard limit to its ability to evade a typical immune system.

lovecg 5y ago

Viruses that evade the PCR test for Covid would be a different species almost by definition, and with enough mutations that could happen. These tests don’t detect other common cold causing coronaviruses for example.

def_true_false 5y ago

> An example I used elsewhere was the introduction of Myxomatosis in Australia, to control the invasive rabbit population. Over time, the local strain evolved to be more deadly, but with a longer incubation periods. This way, bunnies had more time to pass the virus around, then once that job was done, the virus was happy to kill them off. Do you have other examples besides Myxomatosis?

zamfi 5y ago

> This is kind-of what happened to "SARS-1" - it tended to kill its hosts before they could pass it on. Quick nit: while this is true, SARS-1 was also not particularly transmissible before symptoms appeared, in contrast to Covid, which made control much easier (in addition to the much higher fatality rate causing everyone to take it much more seriously).