NEW CORONAVIRUS VARIANTS - EXPLAINED SIMPLY 

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I'm glad it helped to explain things for you

You’re welcome. Glad you found it helpful Stacey!

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Thanks a lot Craig. My Dad understood it. Hopefully other non-scientists will too!

The mutations occur when the virus makes new copies of its RNA genome in human cells. A viral enzyme called a polymerase is used to make these RNA copies. This enzyme lacks "proof reading" activity. If it makes a mistake, it cannot correct it. This is deliberate as it allows the virus to mutate relatively quickly so it can adapt to a new host, which is exactly what is happening in the pandemic now. The mutations are largely random and fall anywhere in the virus genome. Most are meaningless, many make the virus less effective and are lost, while a tiny fraction improve the virus. If a mutation changes a protein in a manner that improves viral fitness, it will get selected for. So, over time with many rounds of infection the virus steadily improves its ability to infect and replicate in a new host.

Glad it was helpful Gene!

A little unrelated but I would love to know if possible ,why do our memory cytotoxic T cells not attack the muscle cell itself ,into which the booster/2 vaccine is injected

Have a look at this article. www.nytimes.com/interactive/2020/health/pfizer-biontech-covid-19-vaccine.html

Excellent article thanks a million

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Thanks for watching. 1) Primers only pair up with the matching sequence through DNA base pairing. So they only help to amplify a chosen specific DNA sequence. 2) The flourophore dye and quencher are both released when the polymerase chews through the flourescent probe. But they are no longer positioned next to each other as the both float away freely. The quencher now has little influence and you can visualise the free flourophore, which allows quantification of the polymerase event and thus the amount of target DNA to start with. A really neat trick!

@@GenomicsGurus Thanks for the explanation!

Very hard to say, but PCR primers are easy to produce and validate, so suppliers of clinical grade kits will be able to update reagents quickly if mutations overlap primer sites (as happened with the B.1.1.7 variant in the UK and the Thermo kit)

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Only a small surface of the spike protein interacts with ACE2. There are many other surfaces that can be targeted by antibodies. So, no one mutation is going to wipe out our immune response to the virus. However, depending on the amino acids at the spike's surfaces, some are more immunogenic (easier to make antibodies against) than others. Antibodies that are commonly raised in the whole population target these immunogenic surfaces. E484K is a prime example of a mutation that falls within such a surface, taking out a subset of antibodies. Variants carrying E484K won't completely evade our immunity, created by previous infections or vaccination, but they will face a lower level of immunity. Experiments have shown that the existing vaccines to prove immunity to the variants of most concern, so the goal remains to vaccinate everyone asap. Booster vaccinations that incorporate the dominant variants will probably be necessary in the coming months. To summarise, there is a balance between immunity and susceptibility. No one thing tips the balance completely one way. New mutations can tip the balance more in the viruses favour, whereas vaccines and lockdowns heavily tip the balance in our favour.

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Hi Ann. Omicron is about 10 times more transmissible than Delta. It just outcompetes all other variants. Once you’ve had Omicron, you are resistant to the other variants, so they just fade away into history.

Yes, but remember alpha particles are stopped by a piece of paper or the outer surface of your skin. Will have no bearing on COVID mutatgenesis. COVID mutations arise because it's RNA polymerase enzyme that makes new copies of its genome in human cells is designed to make errors and not correct them.

Alpha particles affect Si computer memory, deeply protected inside. Any one particle, also cosmic rays, will provide mutagenesis. Or, start a ... fluorescent lamp.

Thanks for watching. Glad you found it useful. 1. The virus uses its own RNA-dependent RNA polymerase enzyme to make copies of its RNA genome. It lacks proof-reading activity, so it deliberately makes mistakes to allow for adaptation to hosts an evasion of immunity. 2. Possibly. It is thought that the sudden accumulation of many beneficial mutations all at once occurs in patients with chronic infections that linger for months. Ravi Guptra’s group in Cambridge reported evidence for this. Mutations that benefit the virus accumulate before the person clears the infection and they become reinfected by the new variant and the process repeats itself. It’s hard to say how non or incomplete vaccination might affect this, but full, boosted vaccination and self isolation clearly reduce the chances of new variants developing and spreading.

Hi Luca. It depends what you mean by "selects". Can vaccination change which variants are more dominant in a population? Probably yes, as there will be more immunity against earlier variants, so newer variants with improved evasion of immunity will dominate. This happens naturally anyway, but vaccination programs might speed it up. Now, does vaccination create new variants? The answer from science is clearly no. What we are concerned about is evolution of the virus to form complex variants that now start to evade the immunity built up against the original virus. This appears to happen in individuals who have chronic infections that last for months. They are often hospitalised, get better for periods but never clear the virus completely. The mutations that occur in that individual's virus population accumulate with time. Almost all of the mutants will be defective virus and have no selective advantage as they occur randomly in the virus genome. However, if the early mutations in this person improve the virus' ability to evade our antibodies, bind cells, infect them or replicate more productively, then there is a risk that these can accumulate and we get a new "variant of concern" carrying multiple mutations that evade antibodies and make fitter virus. The scenarios where individuals are host to the creation of complex new variants are rare. The big risk is when very large numbers of people are infected as you increase the probability of these chronic infection events. Vaccination itself does not create this risk. Ideally, a good vaccine is reducing infections and reducing the likelihood of persistent infections. However, we are vaccinating against the original strain and now have much fitter variants like Delta that are dominant. This risk now - is that removal of all restrictions after a vaccination program is deemed sufficiently complete leads to a big rise in cases, as is the case in the UK at present. What we don't know is whether this increases the risk of the chronic infection events or whether the immunity we have gained form vaccination will prevent this from being a problem. This is a complex problem. We are not epidemiologists, so perhaps follow some people in that field to see what they are saying.

@@GenomicsGurus Thanks for the elaborate answer...

Thanks Scott. The vaccines are winning...

Yes but the phizer vaccine works well for the current variants

Most of the vaccines require two doses, separated by 3-12 weeks for full protection. There is only partial protection against the variants of concern after one dose. Booster doses will likely be required in the coming years to maintain protection.