NEW CORONAVIRUS VARIANTS - EXPLAINED SIMPLY

This video explains coronavirus variants, mutations, PCR tests in simple terms, so that you can make more sense of media reports and the changing restrictions to our daily lives. You will also learn some cool molecular biology! The video is intended for a wide audience.
The video will cover four areas of science so you will be able to follow the facts behind the global pandemic:
• The main features of the SARS-CoV2 virus, which causes the COVID19 pandemic.
• How the main PCR test for COVID19 works, as unexpected results in these tests are linked to the rapid spread of a new variant of COVID19 in the United Kingdom.
• How mutations arise and how they can affect the behaviour of the virus.
• The two mutations found in rapidly spreading coronavirus variants that are causing concern and a new wave of strict lockdown restrictions
You can use these timestamps to jump to any section to watch it again.
1:56 The SARS-CoV2 virus, its life cycle and genome
7:37 Summary of the tests for COVID19
12:00 A description of the genetic material, DNA and RNA
17:17 How the PCR assay works
28:31 How the clinical COVID19 PCR test works
30:50 Overview of SARS-CoV2 mutations
32:06 The Central Dogma of Biology - How DNA codes for proteins
36:12 The Genetic Code
38:26 Why some mutations matter more than others
45:35 Mutations of the SARS-CoV2 spike protein
50:01 The “S dropout” in PCR tests caused by variant
This presentation is brought to you by Dr Adam West in the College of Medical Veterinary and Life Sciences at the University of Glasgow, Scotland. We hope you found this video useful. Please support us by liking the video and consider subscribing for more informative content. Feel free to ask questions or provide feedback in the comments section below. Thank you.
www.gla.ac.uk/...
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Introduction video clips from Pixabay
SARSCoV2 model from Sketchfab by Annabel Slater, MRC-University of Glasgow Centre for Virus Research
Graphics © Adam West and Biorender.com

[@emmaconway5109]

Excellent video - I have learned a lot from watching this!

[@GenomicsGurus]

Great to hear Emma. Thanks for the feedback!

[@choralvoice]

Wow. I know nothing about molecular biology and am blown away. Makes me believe in God even more, because how else can all this exist and work so precisely? Thanks for an amazing presentation. I’ll check out the other videos.

[@hallohallo1332]

Thank you so much for putting this excellent piece of work together. It's brilliant.

[@GenomicsGurus]

That's very kind of you. Glad you found it useful!

[@margrettaylor2228]

Great lesson, extremely informative. I can't wait to learn more.

[@GenomicsGurus]

Glad you found it helpful!

[@rk1356]

Fascinating. I teach a&p and pathophysiology and there are several key concepts I’d like to use from your presentation, along with the visuals. This was an excellent presentation.

[@GenomicsGurus]

Thanks for your kind feedback. Glad it is useful

[@charlesrones7221]

Great video. Can you tell me more about variants? Where do they come from as in when a normal COVID 19 virus infects someone, can that person’s body create the mutation or does the mutation happen more in the atmosphere? Where are these proteins being introduced that are causing the mutations coming from? Thanks

[@GenomicsGurus]

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.

[@SchuboxProductions]

Simplified and explained well. Thanks for taking the time

[@GenomicsGurus]

Glad it was helpful!

[@Gemini535]

Sitting here waiting to go in and get my vaccination. I'm very nervous. I'm going through these videos to tell myself I'm playing my part in helping

[@milakohen630]

ACE 2 receptors!!!! Bingo! Thank you soooo much . now it makes a perfect sense !

[@GenomicsGurus]

Glad it helped!

[@paulsterman7169]

How would the single amino acid substitutions in the spike proteins be expected to affect the antibody response to the current vaccines as of 5/1/21? What are the chances that the changes can be so little that the virus can still bind to the ACE receptor, but the changes still large enough to elude the effects of the vaccine?

[@GenomicsGurus]

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.

[@coachking5208]

Could you please explain why you use DNA in the example @ 32:26 when it's an RNA genome in the virus. Would it not be easier to understand if you used the RNA on it's own?

[@kingsta4145]

Great video. Thanks so much! I found it very valuable.

[@GenomicsGurus]

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

[@____Ann____]

Thank you! Can you explain why one mutation becomes a competitor to another? Why is a variant taken over by another one? They seem to not exist one next to another. People are not infected with multiple variants at the same time. Nor there are local variants. I don't understand how omicron will take over delta. Edit: I just saw you have another video about exactly that topic. Off to watch that one now.

[@GenomicsGurus]

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.

[@praeteritus2218]

Brazil has already applied 45,136,000 vaccines by May 5, 2021!

[@trollpotato8942]

First, great job of explaining these complex mechanisms. However, I have a few questions (as I am no expert, I’m sorry if they are broadly known or not; or if I have just missed the explanation): 1. Do the primers have to be able to attach on the start of the DNA, or would it still work if they are located somewhere else? 2. How come the fluorescent reporter is released by the polymerase, but the quencher is not? Thanks in advance.

[@GenomicsGurus]

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!

[@trollpotato8942]

@@GenomicsGurus Thanks for the explanation!

[@j-j-j6]

Thank you very much. Great presentation.

[@GenomicsGurus]

Glad it was helpful!

[@henrymarshpoetry1916]

Really well explained!

[@GenomicsGurus]

I'm glad it helped to explain things for you

[@friggenbears]

Very well explained and important video. Thank you so much for making it! A couple of questions: 1. What causes bases in DNA and RNA codons to change/move, resulting in mutations? 2. Is opportunity for mutations to occur higher in unvaccinated individuals as they haven't been given a 'head start' in immunity, and therefore take longer to fight off the virus. Thus allowing more time for replication?

[@GenomicsGurus]

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.

[@genecollinge1265]

Really informative video, thanks a million

[@GenomicsGurus]

Glad it was helpful Gene!

[@genecollinge1265]

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

[@GenomicsGurus]

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

[@genecollinge1265]

Excellent article thanks a million

[@qnxduwnj9997]

great explanation!! Thank you!

[@GenomicsGurus]

Glad it was helpful!

[@orcreep1492]

Thank you for the video, great work

[@GenomicsGurus]

Thanks for your feedback. Glad you found it useful

[@pinchofsalt1277]

So this is just like a football match; Team A tries to score a goal but Team B has a great keeper whom has managed to deny any opportunity. So Team A needs to re-strategise game play or even substitute players, so that they may even get a chance to beat the keeper to score a goal.

[@pushpendrajain9774]

very nice and informative video..

[@GenomicsGurus]

Glad you found it useful

[@lucabarsotti1409]

Could you kindly explain whether vaccination during plandemic selects variants? This is an objection to covid vaccines, often raised, to which i do not have an answer. Thank you...

[@GenomicsGurus]

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.

[@lucabarsotti1409]

@@GenomicsGurus Thanks for the elaborate answer...

[@lynnbennett6848]

Can you update this? Thank you. Mass Jabs, Super Covid. INDIA. I am very worried. Not the worry type. Thank you.

[@scottjames6037]

We are in a war an the variants are winning. Great vid. Thanks

[@GenomicsGurus]

Thanks Scott. The vaccines are winning...

[@nosuchthing8]

Yes but the phizer vaccine works well for the current variants

[@vf5126]

Got it(!), thank you ~

[@GenomicsGurus]

Glad you found it useful!

[@blueskiesandfairwinds3804]

Excellent work, thank you!

[@GenomicsGurus]

Glad you found it useful!

[@chintanmehta4695]

Hats off sir! Your information is really good.

[@GenomicsGurus]

Thanks for your feedback. Glad you found it useful!

[@CraigDaly]

Great video 👍

[@GenomicsGurus]

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

[@chloereciakortje2699]

What a great video! Great explanation! Thank you!!!!

[@GenomicsGurus]

Thanks a lot. Glad you found it useful!

[@alexandrejulio]

How many different RT-PCR S protein probes will Brazil need until 2022?

[@GenomicsGurus]

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)

[@edgerck3924]

Excellent video. Can alpha particles, as in silicon chips, create mutations? They can knock off electrons.

[@GenomicsGurus]

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.

[@edgerck3924]

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

[@jenniferjohnston9429]

Will the vaccine kill the virus or do we need another shot

[@GenomicsGurus]

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.