Indian scientists flag virus mutations that could ‘evade immune response’ | Hacker News Reader

Indian scientists flag virus mutations that could ‘evade immune response’

reuters.com

One positive side effect of the non vaccine measures being taken, social distancing, wearing masks and increased hand washing is it’s cutting down on the ability for any pathogen to spread around. Pathogens we ignored and tolerated before such as influenza are being effected too. The spread of any airborne pathogen is going to have record low numbers as people adopt these as lasting life styles. The idea that we were comfortable sitting on an international airline in closed space with strangers breathing the same air before is sort of alarming in retrospect. We are in need of modernization of our public interaction facilities and transit. Simply having strong ventilation and extremely fine particulate filtration everywhere to mimic the particulate diffusion/vacuum effect of being outdoors would probably do wonders to prevent airborne pathogens.

Creating humans so weak that they instantly fall sick as soon as they leave sterilized environments (or are getting mouth-to-mouth when needed).

We need good functioning immune systems. We also need close human contact. We need to shake hands with strangers. If we don't do that we will estrange from each other and conflict will ensue.

We should treat our immune systems like we should treat our children: train them to withstand the outer world, not keep it away.

I think we can agree that sterile environments affecting a population's immune system was not a factor in 1918.

There's a big difference between a sterile environment and plonking 100s of people from different places into a pressurised tube for a few hours before releasing them into another city a thousand miles away. The type of behaviour we accepted as "normal" was anything but.

People have always travelled and shared their germs. Some of them probably worse than what we have now. I think it’s perfectly natural for 100s of people to get together and travel. Sailors are a good example of how this relates to the past. Going to Mars will be the future. We cannot isolate as tribes.

Just because it’s always been done or natural doesn’t make it a good idea. Plagues were pretty terrifying events throughout history until we became aware of how they spread. The advantage we have over our animal counterparts is our ability to learn from our mistakes and upgrade our culture to decrease the chance of causing unnatural deaths in our populations. You are right we definitely shouldn’t isolate as tribes. This should be on the individual level when being exposed to anyone you aren’t around daily. This doesn’t constitute a tribe. If someone carelessly takes part in the spread of a pathogen without attempting to prevent it from using their body to get to other human hosts who are perhaps more vulnerable, they are ethically responsible for the death of every individual that is infected and does not recover as a result of that carelessness.

I'm not saying that because we did it in the past, we should continue doing it. Knowledge is power, and we have concrete evidence that herd immunity works. We need germs to work as a species at the moment, so let's find a way forward that doesn't restrict air travel or blame the butterfly for the monsoon, right?

There is a line between exposing yourself to a little bit of something that you're like to catch anyway, and sticking the world into a blender and expecting every organism to come out stronger. Life is always at risk from pests and diseases that evolved in other ecosystems. Always will be, unless we destroy the boundaries between ecosystems and create a single worldwide ecosystem (which would be fucked).

I diagree that we have to find a way forward that doesn't restrict air travel. Worldwide air travel for the masses is a very recent fad. It's a terrible co2 emitter and was bound to trigger an event like this.

Travel in a book?

> We also need close human contact. We need to shake hands with strangers. If we don't do that we will estrange from each other and conflict will ensue.

For me, hand shaking has always been uncomfortable, and let's not speak of places where they greet by kissing. I don't see physical contact outside of your intimate circle as a human need, but as a political move to fake friendliness. I will keep greeting people politely, and after this pandemic I won't feel guilty again for not having physical contact forced upon on me.

Not so. There are plenty of things in your home environment to keep your immune system busy. Most of its activity appears like nothing is attacking you because it’s just so good at what it does most of the time. Without humans to infect, there really isn’t a way for new pathogens to readily emerge naturally that are able to infect humans. Anytime you let a pathogen use your body to reproduce then pass it to someone else you are taking part in its evolution and adaptation to the human immune system which does not really change much unless there is a big human extinction like the Black Plague. Western Native tribes were highly susceptible to European pathogens not because they were isolated but because the pathogens had a lot of time to evolve various nasty traits by freely spreading throughout the European and other populations prior to being introduced to the natives. Viruses don’t just become highly lethal to humans without spending considerable amount of time being spread around by humans or an organism very closely related to humans.

A virologist, along with an evolutionary biologist, here explain, in depth and for layperson, why that is perhaps exactly what we need to primarily be focusing on - and by targeting the immune system in a rigid way with mRNA - it's allowing more slight variants to escape immune response, that existing mRNA vaccine will still target some of the variants but at a lower efficacy (which seems to match the real world findings as well); virus attenuated vaccines would have avoided this - where if the vaccine included dead virus for the body to respond to: https://youtu.be/BNyAovuUxro

We may be growing the perfect variants to escape and may need to be getting non-mRNA vaccines for years to come, for multiple variants that become too broad difference wise from each other, to allow our innate immune system to develop a spread of variants it will target to stop the efficient development of even more variants.

> Unless you culture those viruses and test them in the lab, you can't say for sure. At this point, there is no reason to believe that they are expanding or if they can be dangerous, but we flagged it so that we keep our eye on the ball

The headline is only responsible if you interpret "could", as "yes, literally it could, just like many other other spike protein mutations"

Variants are dangerous and research should be done, but it's not responsible to indicate that every variant is uniquely dangerous. It will weaken the response when/if a true escape variant emerges.

Trying to understand something here: when COVID-19 first came out, there were reports that it would be difficult to produce vaccines for it because it is was a mRNA virus (as opposed to a DNA virus for which it is easier to produce a vaccine for.) One of the reasons I remember reading was that a vaccine could work for one mRNA variant, but not for the multiple variants that mRNA viruses are known to mutate into.

Is this what is happening? The current vaccines are effective against existing / known variants, but the new variations / mutations would require new vaccines?

Sort of. The thing is, while there are already variants out there that impact immune response, it's not like a single mutation is a vaccine escape. It's more like the vaccines go from 95% efficacy to 75% efficacy.

Now, I'm no biologist but I would imagine DNA viruses are easier to vaccinate primarily because they have lower mutation rates than RNA viruses. However, even within RNA viruses, there's differences in mutation rates. Influenza mutates so fast (and is allowed to replicate out-of-control most of the time) to the point that vaccine escape happens within a year or so - that's why you need a new flu shot every year. As far as I'm aware, COVID-19 mutates slower than the flu, so vaccine escape will take longer.

Out of the three COVID-19 vaccines out there, two of them use an mRNA vaccine platform. This isn't because you need to match mRNA viruses with mRNA vaccines, but because it's just an extremely versatile platform to work with. In fact, for Moderna, stopping a worldwide pandemic was just a side project. Their actual goal was to produce custom cancer vaccines tailored to an individual patient's tumors. You can do this because the vaccine is just some genetic material and some nanoparticles to get it into cells. Your body itself makes the actual antigens that your immune system then fights.

So what will ultimately happen in the event of a vaccine escape is that Moderna and Pfizer will tweak their vaccines a little and the FDA will fast-track a new roll-out of the modified shot after Stage 1 testing. They already do this for flu vaccines - it's the only reason why we can even vaccinate against the flu in the first place. And as far as I'm aware, Moderna and Pfizer are both already trialling booster shots. Not so much because they expect a vaccine escape, but because they expect immunity to wane regardless of how fast the virus mutates.

> Influenza mutates so fast (and is allowed to replicate out-of-control most of the time) to the point that vaccine escape happens within a year or so - that's why you need a new flu shot every year.

No, it's because the yearly flu shot only includes a couple of the viruses out there. They take a best guess in the spring as to which ones will be the most prevalent in the fall and start production on those.

From what I remember it's limited to only a few for two main reasons: Cost and some of the vaccines aren't actually compatible with each other (so you can't put them in the same shot).

This. The influenza variants that "arise" next year are almost certainly circulating at low level now, and not targeted by this year's vaccines.

If we vaccinate everyone, aren't we selecting for the virus mutations in which the vaccine doesn't work, can we possibly make virus more advance this way?

It depends on what you mean by “more advanced”. More lethal? Easier to transmit?

In any case, the answer is “maybe”. By vaccinating, we cannot be sure of what is actually being selected for. We only have an idea of what is being selected against.

Being a novel (new) Corona-virus, nobody actually knows the extent of possible mutations. This is a strong argument against it being a weapon. However, it's impossible to contain everywhere, though we should perhaps make the attempt.

My understanding is that lethality and transmisability are typically a one or the other type situation. Viruses like HIV and to some extent COVID that kill their host effectively but slowly are rare. The typical case is to either multiple quickly inside one host (i.e. kill the host quickly) or move quickly from host to host (i.e. spread rapidly without killing the host because you need the host to be a vector)

You got it right. Generally speaking, RNA viruses (without the “m”) have higher mutation rates than DNA ones. Therefore the possibility of a vaccine-evading mutation arising in their genome is higher as well. However, predicting a priori the effect of such a mutation is difficult, because it depends on many factors.

For instance, the mRNA vaccines are optimized to generate antibodies against the SARS-CoV-2 spike protein in the prefusion state. If a mutation alters this conformation the immune response elicited by the vaccine might be reduced or even abolished.

In addition to that, mapping the mutational space of the virus is experimentally challenging and computationally expensive, so there’s no easy way to be prepared against potentially detrimental mutations.

> but the new variations / mutations would require new vaccines?

I'll just poke at this part since the other responses are good on the rest:

It's not "would", it's "might". The mRNA vaccines, for example, train your body against the spike protein - a very specific piece of the virus. The vaccines would still work against any mutations that don't change that piece of the virus, and even for the mutations that do change it, the change might not be big enough to have an effect.

TL;DR mutations happen.

The key paragraph is the following: "We are seeing some mutation coming up in some samples that could possibly evade immune responses," said Shahid Jameel, chair of the scientific advisory group of INSACOG and a top Indian virologist. He did not say if the mutations have been seen in the Indian variant or any other strain.

This could be anecdotal but several of my distant family and their friends in India have tested positive for COVID even after full inoculation. I wouldn't be surprised if it's true.

There are many such anectodes. For another one - my girlfriend had covid, but no loss of smell or taste, a doctor thought it was a normal infection, so she didn't do any tests (we don't have easy access to tests). When coughing didn't stop, she tested and was positive. I was sleeping with her, she even coughed on my face once, but I didn't have any symptoms. Three weeks later her daughter had loss of smell and taste but no coughing, she tested positive too, I've taken test too but still, my test was negative. When gf was still coughing (before test), we travelled in car with 2 more people, none of them tested positive after that. Consultant from local disease control center said that currently tests will show positive results even for throat infections other than covid. One of my friends said (a rumour) that at those test sites, they don't have enough of thinning agent, so need to thin with physiological salt and then such tests come back positive 7/8 times.

Conclusion: it's all a big mess. When you can't have cold straight facts about transmission, you won't have effective responses.

Depending on the vaccine, they are all only X% effective, so this type of thing is expected. I think too many people try to use these cases as “evidence” that the vaccines are fake, or the government is just trying to control people, but some just not being effective is really just how it’s expected to work.

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