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SARS-CoV-2 variant A.30 is heavily mutated and evades vaccine-induced antibodies
- whatanorigtht 5y agoHahahah sucks to be vaxxtarded.
- inglor_cz 5y agoSo, they detected this variant half a year ago, and yet it didn't become prevalent. Delta rules the roost. Is it possible that the heavy mutations detected on the A.30 variant also make it less contagious?
- grillvogel 5y agogenuinely asking, how do we actually know the delta variant is real, and is the dominant variant causing the current cases? do people actually get tested for specific variants, or is it just a generic covid test?
- depereo 5y agoNZ had until recently sequenced 100% of its cases, and used that sequencing information to map person to person infection linkages. This included all of the people in the mandatory 2-week quarantine at the border. So in NZ, yes, every case was tested for specific variants. Delta does seem to be real.
- black6 5y agoSome small subset of COVID tests are sent to larger labs to perform a more detailed genetic test to determine specific variants. The prevalence of different variants within that set is extrapolated to the population of the region from which it originated. If the lab finds that 87% of the samples from Adam's College are of the Omega Mu strain, then it's assumed 87% of total cases at Adam's College to be Omega Mu variant.
- kadoban 5y agoNot every test will tell you which variant it is, but they do some extra testing here and there to track which variants are spreading.
- roywiggins 5y agoIt depends where you live. The UK was an early[0] leader in sequencing a lot of their cases. They hit 600,000 sequenced cases in July[1]. That said, if you just want to know what proportion of the population has delta, you don't need to sequence that many cases. The point of sequencing a large fraction of cases is to catch emerging variants, that wouldn't be likely to be caught otherwise. But to know whether Delta is 30%, 50%, or 70% of cases, you just need a good random sample, not a particularly large one, and I imagine you can do that at the labs where the PCR tests are being run. (at one point, I recall that the UK had a test that matched on three distinct sites on the virus, and they found that one of those sites would turn up negative for a particular variant, so they were able to use that as a proxy for the spread of the variant. I don't remember if that was Alpha or Delta though, and obviously it's no replacement for sequencing) [0] https://cen.acs.org/analytical-chemistry/sequencing/200000-counting-UK-sequenced-cases/99/web/2021/02 https://cen.acs.org/analytical-chemistry/sequencing/200000-c... [1] https://www.gov.uk/government/news/uk-exceeds-600000-covid-19-tests-genomically-sequenced https://www.gov.uk/government/news/uk-exceeds-600000-covid-1...
- walterbell 5y agoUK publishes detailed reports on variant surveillance via genetic sequencing, https://www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings https://www.gov.uk/government/publications/investigation-of-... US does statistical sampling and also prevents patients from being told about variants, https://news.ycombinator.com/item?id=28419280 https://news.ycombinator.com/item?id=28419280
- _3u10 5y agoThey sample the swabs and do full sequencing for those selected.
- ceejayoz 5y agoGenomic surveillance; separate from the routine COVID tests, performed on a statistically significant sampling of them. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-surveillance.html https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-s... https://www.cdc.gov/coronavirus/2019-ncov/variants/cdc-role-surveillance.html https://www.cdc.gov/coronavirus/2019-ncov/variants/cdc-role-...
- 323 5y agoThere are multi tests today which can differentiate between variants without sequencing. There is also a way to differentiate on some RT-PCR tests (but not all), depending on how they are made.
- mewpmewp2 5y agoAlso see nextstrain.org for interesting data.
- slimeballsz 5y agoDelta is fake. The whole fucking thing is fake. Branch Covidians should be thrown out of airplanes at 30k feet over the Pacific.
- Herodotus38 5y agoIn Washington state, a percent of positive tests are sent to the dept of health for variant sequencing. You can see the published results by week. Delta has outcompeted every other variant for several months. All covid is essentially delta. See page [pdf] 5 on this: https://www.doh.wa.gov/Portals/1/Documents/1600/coronavirus/data-tables/420-316-SequencingAndVariantsReport.pdf https://www.doh.wa.gov/Portals/1/Documents/1600/coronavirus/... It is updated every Wednesday
- kjaftaedi 5y agoNot all cases are tested for which variant, but those that are are catalogued. I've been watching the delta variant take over the world over the past several months here: https://covariants.org https://covariants.org (dark green is delta)
- dragontamer 5y agoEven if A.30 was "more contagious", like Alpha, it isn't as contagious as Delta and thus would get outcompeted. There's a lot of variants of concern. Its important to keep an eye on new variants, but don't worry about them until they cross the 1% or 5% mark. At that point, you can better theorize that they might be outcompeting the dominant strain. You _really_ don't know that something is outcompeting until it reaches 50%. But by then its too late. The 1% or 5% points are still a month or two in advance of the 50% crossing, in both Alpha and Delta. So that's where I keep my attention: at the 1% and 5% points. A variant gotta get to 1% before it can reach 50% of the world ya know?
- FooBarWidget 5y agoHow does viral outcompetion work? How would Delta prevent A.30 from thriving? Why won't we become infected by Delta and A.30?
- deleted 5y ago[deleted]
- polote 5y agoSame question, especially that if someone is infected with delta he can only infect someone with delta. So delta can be outperformed at the person level only if the person is infected by both variant at the same time. For me the only way a variant can be outperformed is that all people who get infected get also infected with the other variant OR the first variant for whatever reason stop being transmissible
- greg5green 5y ago>For me the only way a variant can be outperformed is that all people who get infected get also infected with the other variant OR the first variant for whatever reason stop being transmissible What you are saying isn't logically sound.
- JamesBarney 5y ago> How does viral outcompetion work? Basically one spreads faster than the other so after a few iterations almost all of new cases are the new variant. > How would Delta prevent A.30 from thriving? Directly by driving up immunity, indirectly by coercing people to take steps to slow the spread of delta, which also slows the spread of a.30. Things like vaccination, social distancing, mask wearing etc... > Why won't we become infected by Delta and A.30? Because Delta probably give you significantly more immunity than a vaccine. Specifically infection gives both more robust and stronger immunity than the vaccines.
- rolph 5y agothe results in the paper suggest, the mutations facilitate viral mechanisms of entry and antibody evasion. efficacy of Oxford, Pfizer, and hetero-innoculation with both were examined, indications were given of reduced efficacy of either vaccine alone vs CoV A.30. The combination of both vaccines[hetero-inocculation] was associated with higher efficacy vs A.30 the mutations appear in vitro; to confer inhibition of vaccine induced antibody binding; enhanced cellular entry; enhanced pulmonary[lung] trophicity[targeting] relative efficacies of moderna; Johnson&johnson; vs Oxford; Pfizer were not examined.
- orra 5y ago> Is it possible that the heavy mutations detected on the A.30 variant also make it less contagious? That wouldn't surprise me. The spike is central to how SARS-CoV-2 is so infectious. If the virus mutates the spike too much, it might evade the vaccines, but at the cost of being less infectious. What's surprising is this research says, in vitro, A.30 is more infectious. Regardless, as you and others say, in real world conditions A.30 doesn't appear to out compete Delta.
- greg5green 5y ago>Is it possible that the heavy mutations detected on the A.30 variant also make it less contagious? 100%. This strain hasn't been seen since May. It has already died out because of Delta. All of these discussions are academic -- we really are only talking about if a Delta variant can gain these mutations and really wreck havoc. And the answer is "probably not" (for a while, anyways)
- bydo 5y agoI hadn't seen these names before, so: ChAdOx1 nCoV-19 is AstraZeneca BNT162b2 is Pfizer/BioNTech
- deleted 5y ago[deleted]
- throwawayswede 5y agoBoth of these look like “cool hacker names” from a movie…
- _3u10 5y agoChAdOx1 is the guy who gets the girl lol.
- throwawayswede 5y agoOnly initially, then he turns out to be a douche.
- deleted 5y ago[deleted]
- orra 5y agoFrankly, I think the names are terrible. Great vaccines and all, but terrible branding.
- michaelmior 5y agoNeither names are really intended to be the "brand" of the vaccine. That said, I don't think Comirnaty is really much better.
- orra 5y agoNo, I don't think Comirnaty is any better! I am however relatively partial to Spikevax, aka Moderna: at least Spikevax is easily pronounceable. I suppose you mean the vaccine names are mainly useful for regulatory purposes, because the general population will continue to name the vaccines after the manufacturer or researchers?
- venomsnake 5y agoThe question is are outcomes in vaccinated people comparable to flu - if yes - we can freely ignore it. Or people that have natural immunity. Or unvaccinated. I have a bad feeling that with focus just on antibodies we're ignoring the important metrics. Which is outcomes.
- Jabbles 5y agoBut that question is far harder to answer than testing the viral proteins in a lab. You seem to be dismissing this research whilst suggesting they concentrate on something that is probably impossible, thankfully, due to the fact that this variant hasn't spread much.
- SketchySeaBeast 5y agoIt is possible to determine, but only in hindsight, which is really the worst sort of possible.
- orra 5y agoSure, it's hard to test things in real world conditions, but that doesn't mean we should over extrapolate from in vitro findings. In particular, infecting cells easier in a lab doesn't mean the virus spreads from person to person easier. Besides, the fact this variant hasn't spread much is telling in and of itself! Maybe we got 'lucky'. But maybe it just isn't that contagious, compared to Delta.
- 323 5y agoThe outcomes are pretty clear already, 10 times more official deaths globally compared to a bad flu. And we know the official death counts is under-counted by a 4x-10x factor.
- Jensson 5y ago> And we know the official death counts is under-counted by a 4x-10x factor. Not even California undercounted that much and they are among the worst under counters in the western world, if we compare Covid deaths to excess mortality. Death undercounts are closer to 30% at worst.
- JPKab 5y agoI didn't see any information about this variant's ability to infect those with immunity from previous infection. Did I miss it, or was this rather important question completely out of the scope of this study?
- encryptluks2 5y agoI remember getting downvoted a while back, but my suggestion has been to have people get vaccinated and then give them a small dose of coronavirus thereafter. At the time it may have seemed wild, but now it has been proven to be the most effective immunity.
- SketchySeaBeast 5y agoHas it? I thought there was promising result with catching COVID and then being vaccinated (though you've already caught COVID, so you've failed the whole "don't catch COVID" objective), I wasn't aware there was good research for the opposite.
- encryptluks2 5y agoLike most things with COVID they didn't test the other way, but it is thought to be as effective and more so in order to prevent an initial serious infection, especially if timed adequately with the body has produced maximum resistance.
- orra 5y ago> At the time it may have seemed wild, but now it has been proven to be the most effective immunity. It's wild because immunity is useful for preventing infection (also, reducing the severity of infection). There's little point catching the thing you don't want to catch in order to prevent you catching it, because you still. suffer. the. harm. of having been infected. There are way better options, like third doses of vaccines. Or revising the vaccines for Delta. Besides, if you want something 'like' a small dose of coronavirus, it would be far safer to attenuate the coronavirus first. Then you just have a classic vaccine.
- chme 5y agoA.30 seems to be one of the very minor lineages: https://cov-lineages.org/lineage.html?lineage=A.30 https://cov-lineages.org/lineage.html?lineage=A.30 compared to others https://cov-lineages.org/lineage_list.html https://cov-lineages.org/lineage_list.html
- greg5green 5y agoI can't even find it on Nextstrain
- 323 5y agoThe title is more bombastic than their conclusion. TL;DR: it's just a bit worse than the Beta variant.
- listless 5y agoThank you. I came looking for the truth behind the click. Of course, the truth is much less interesting.
- MuffinFlavored 5y agoIs the Beta variant worse than the Delta variant?
- e40 5y agoI believe Delta is worse than Beta.
- revolvingocelot 5y agoThe real question is "can I even find a Beta variant to get infected by, given the steady global dominion of Delta"? [0] https://covariants.org/per-variant https://covariants.org/per-variant
- r00fus 5y agoThanks for that link. Seems Delta and P681 are the "winners" in this environment (but it seems on further research P681 is itself a variant of Delta).
- Kenji 5y agoThat moment when after 20 months of nothing happening, other than human rights being abolished across the planet, you're still scared of a common cold virus.
- uuddlrlr 5y agoI guess there might be a point where strictly vaccinated populations are less protected than populations with more natural antibodies. Where I live is >80% double dosed, however there are far less than 5% that have been naturally infected.
- barbazoo 5y agoWhat do you base your guess on?
- dev_tty01 5y agoIs there any significantly contagious and deadly disease where natural antibodies have proven more protective than large-scale vaccination? Measles? Polio? Diptheria? Flu? Mumps? Rubella? Hepatitis? ...
- uuddlrlr 5y agoI worded it poorly (and it wasn't really anything worth saying in the context of COVID), but: A population with 5% naturally-induced/80% vaccine-induced immunity might see more spread of a new variant than a population with 25%/60%, however the total outcomes would still be better in the first population; so "less protected" was definitely the wrong thing to say. Naturally-induced immunity for COVID is stronger because it targets more than just the spike protein, and it presumably[0] grants better mucosal immunity than our current vaccines induce, but of course the risk/cost of natural infection is very high. [0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8358136/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8358136/
- bserge 5y agoThe great imbecility pandemic of 2020-2021. People who have experienced severe symptoms, hospitalization and deaths of relatives came out smarter than those who didn't.
- dudeofea 5y agoDengue. The initial vaccine did not target all subtypes of dengue, causing "severe dengue" in infections after a naive individual was vaccinated. The same could happen if someone moved from one region to another, since the subtypes inhabit different regions. Your body will respond to one subtype's antigens primarily with it's initial conditioning. If you weren't conditioned with that subtype, you get original antigenic sin / severe dengue https://www.cdc.gov/dengue/prevention/dengue-vaccine.html https://www.cdc.gov/dengue/prevention/dengue-vaccine.html The worst-case scenario for a vaccine is not "no immunity", it is negative immunity. If your adaptive immune response outcompetes your innate immune response in binding to antigens, but does not neutralize them, then your immune system will struggle to fight off an infection
- c7DJTLrn 5y agoJust saying, now is the perfect time for countries to stealthily unleash biological warfare upon their enemies. Mutated or engineered?
- CoastalCoder 5y agoQuestion from a non-molecular-biologist: IIUC, when COVID first gained notoriety, there was a large public effort to solve its molecular structure [0]. Articles like this seem to imply that they've solved the structure of numerous variants, making me think we (collectively) can do it much more quickly now. If that's really true, what's changed? Does knowing the structure of other COVID variants give us a massive head start? Or has there been a massive investment in computing power for solving COVID-variant stuctures? [0] https://foldingathome.org/diseases/infectious-diseases/covid-19/?lng=en-US https://foldingathome.org/diseases/infectious-diseases/covid...
- timr 5y agoNo, there are not solved structures for these variants (in general). They're using computer modeling. Even if there were, changes of a single amino acid that don't induce significant conformational (shape) change are the sort of thing that you'd need a very good structure to discern, since they're mostly on the surface of the spike, and probably spin around a lot. The most relevant thing to know is what a mutation / mutations looks like in the context of antibody binding, but that's even harder to get a good structure. It's not something that can be done quickly.
- rolph 5y agowhen the focus is on individual molecules it is about a statistical measure of bond angle, distance, resonanceforms, charge distribution, and rotational freedom. this ends up looking like the quantum physics conundrum where there is a central tendency rather than certainty, until you pin it down in some way. this is why we have a vaccine to begin with, the realization that there are conformational frequencies to the S protien, and a particular locus in the sequence is associated with the conformational change that sequesters the binding domain of S protien. thus the 2proline version of S was used in subsequent vaccines, allowing the ACE2 binding domain to remain exposed to the PAMP recognition machinery. it takes months or weeks depending on how well the supervising scientist receives a request, it used to take years and decades in many cases.
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- angelzen 5y ago"[...] the variant A.30 [...] was detected in several patients in Angola and Sweden in spring 2021 and likely originated in Tanzania". As Western liberal democracies can't outcast "the unvaccinated" fast and hard enough, nobody cares to explain what exactly is the plan to timely vaccinate billions of people living in poor countries.
- lol768 5y agoI've not seen much reported in the way of clinical trials / peer-reviewed publications for modified vaccines that target (the spike protein of) these variants of concern that are actively circulating. Is there ongoing work here I'm missing? What progress has been made? I'm somewhat surprised that almost a year on from the initial vaccination roll-out in the UK we're now dishing out boosters which are .. identical to the vaccinations given out initially.
- angelzen 5y agoThat is a fantastic question. We are still vaccinating & boosting against the original variant. Would "the experts" please demonstrate that vaccines against variants are effective, given that original antigenic sin is a long known and well documented phenomenon? https://en.wikipedia.org/wiki/Original_antigenic_sin https://en.wikipedia.org/wiki/Original_antigenic_sin https://www.jstor.org/stable/985534 https://www.jstor.org/stable/985534
- belltaco 5y agoHow is OAS related to ADE?
- angelzen 5y agoA South Korea paper from 2016 argues they are related "sometimes". Note that coronaviruses are RNA viruses. Now, all the epi data we have indicates that the covid mRNA vaccines are effective against covid variants of concern. No need to panic. "Original Antigenic Sin Response to RNA Viruses and Antiviral Immunity" "Abstract: The human immune system has evolved to fight against foreign pathogens. It plays a central role in the body's defense mechanism. However, the immune memory geared to fight off a previously recognized pathogen, tends to remember an original form of the pathogen when a variant form subsequently invades. This has been termed 'original antigenic sin'. This adverse immunological effect can alter vaccine effectiveness and sometimes cause enhanced pathogenicity or additional inflammatory responses, according to the type of pathogen and the circumstances of infection. Here we aim to give a simplified conceptual understanding of virus infection and original antigenic sin by comparing and contrasting the two examples of recurring infections such as influenza and dengue viruses in humans." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5086450 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5086450
- jjtheblunt 5y agoI think these headlines, possibly purposefully, overlook the possibility that vaccine antibodies eased acquisition of infection induced antibodies to the point of being subclinical events. That is, a vaccinated person could be exposed to a variant for which they are partially protected, not notice clinical symptoms, while the person's immune system still remembers the details of the variant. As an iterative process, this is akin to software updates (for a running immune system). So to say that variant A.30 isn't covered by the mRNA induced spike protein antibodies is a very different statement than to say it's able to evade an immune system primed by mRNA antibodies which then re-entered daily life and thereby was able to continuously adapt to variants.
- chicorea 5y agoIt depends if the person who got vaccinated was exposed to the virus before the vaccination. If not, it is very likely that these variants will escape the vaccine induced immunity due to original antigenic sin, especially considering that mRNA vaccines only stimulate the production of spike ABs and not other ABs such as nucleocapsid ABs which target proteins that do not mutate as much as spike.
- christkv 5y agoAntibodies is also just one part of the immune response, memory T cells are just as important. We know the vaccines are not sterilizing so you can still catch and spread it. They do reduce the likelihood of hospitalization and that seems to be about that.
- feanaro 5y agoNot sterilising, but they do reduce viral load and hence also the probability of spreading.
- christkv 5y agoI don't think there is consensus about that unfortunately. I see plenty of pre-prints going both ways. https://www.medrxiv.org/content/10.1101/2021.09.28.21264262v1 https://www.medrxiv.org/content/10.1101/2021.09.28.21264262v... I think the only conclusion that can be supported truly at this point is that you seem to be less likely to get a severe disease progression. And before anyone jumps on the whole political thing. Yes I have taken two doses of the biogen vaccine.
- slimeballsz 5y agoFAKE NEWS FAKE NEWS FAKE NEWS
- slimeballsz 5y agoTLDR: The puppy torturers want you to keep submitting to their totalitarian fascist wishes. Branch Covidians: We are preparing your chopper ride. You will go down.
- slimeballsz 5y agoStop lying you fascist fuck.
- hammock 5y agoHow well does this variant evade natural immunity-induced antibodies, which includes not only antibodies vs. the spike protein but vs. the body of the virus as well?
- gzer0 5y agoHeterologous ChAdOx1 nCoV-19/BNT162b2 vaccination, which was previously shown to augment neutralizing antibody responses against VOCs compared to corresponding homologous vaccinations [7, 10], might offer robust protection against the A.30 variant. There's hope!
- cryptica 5y agoIt's important to point out that many scientists were called conspiracy theorists by mainstream media after predicting (long before the vaccine rollouts) that mass vaccinations would cause the virus to mutate faster and that we'd all be worse off (as is clearly the case)... Mainstream media and big pharma are corrupt. The people responsible are criminals and should be brought to justice. COVID19 is not lethal for the majority of people. We will all die of something eventually but if some people are particularly fixated on COVID19, they are welcome to spend more time at home (instead of going out to meet people) and they can try to find remote work or some job which doesn't require so much contact with other people. Anyone could easily bring their risk of catching COVID19 to nearly 0% by limiting social contact, proper distancing, hand-washing, mask-wearing, choosing the right kind of job (or retiring), getting plenty of sunlight, vitamin D supplements, living outside of urban centers, not travelling too much, etc... All of these things are going to be way more effective at protecting individuals from COVID19 than any vaccine and these things don't require ruining other people's lives. Also, if you don't want to risk dying of COVID19, you can just go live in a remote village/town; nobody is forcing you to live in a densely populated city. Big cities are reservoirs for the COVID19 virus. Other people can kill you; this is a fact of life which we have to accept. If you choose to constantly surround yourself with many people, then you're taking the risk, nobody else owes you protection from whatever viruses they may harbor inside their bodies without their knowledge. The hospital system will be fine. If hospitals become too crowded with COVID19 patients; they can just start turning them away! People will come up with solutions; temporary/makeshift COVID19 hospitals, home-delivered ventilators, etc... Maybe governments can fund this if it comes to that?
- JJzD 5y agoThere is so much wrong with this. Let's start with the apparent numbers you are accepting. Millions of Americans will die directly from infections, millions will need life support, and an additional ten million will die as a direct consequence of an overwhelmed health care system. With those numbers it's hard to imagine a family not hit with these enormous consequences, where you seem to gloss over. Secondary, the virus has no will of it's own, it will just randomly mutate, and if a stronger variant appears it will do so, if there are vaccins or not. However, you are advocating to roll the dice millions time more, just because there was already a very small chance this gets worse, and you think that is a good idea?
- zzutz 5y agoHail Fauci! Hail Fauci! Hail Fauci! Have you been a good little nazi? Hail Fauci!
- InInteraction 5y agoA.30 is basically dead, well outcompeted by Delta etc. The UK don't report on it now. "VUI-21FEB-01 (A.23.1 with E484K), VOC-21FEB-02 (B.1.1.7 with E484K), VUI-21MAR-01, (B.1.324.1 with E484K), A.30, B.1.633, B.1.214.2 and B.1.1.7 with S494P have not been observed in the UK or within the international GISAID dataset within the last 12 weeks. These variants are no longer included in the data update."
- q1w2 5y agoThe biggest pressure on variant mutation right now is vaccine-evasion - so the reason the Delta variant has out-competed it is likely because the Delta variant does an even better job of evading the vaccine. In general, I'm disappointed that we are not rolling out updated boosters with variant protection. Flu vaccines are updated each year - and here we are almost two years from the initial outbreak, and we're still vaccinating people against the original form of the virus - which isn't even spreading anymore That's not to say that it's not still lifesaving to get the current vaccine - but F - we can do better!
- b0sk 5y agoThe silver lining with Delta is it's such a transmissible variant that it out-competes the more slowly spreading but more vaccine evasive variants. I hope we never see a more transmissible one than Delta
- m0zg 5y agoWe're also about to discover what happens when people don't exercise their immune systems for 2 years. There's a "super cold" of some sort going around in the UK [1] which, while not COVID (and therefore is probably not vaccine-sensitive wrt vaccines designed for COVID), has similar symptoms and is a lot more severe than a normal cold. Normally you'd get colds 2-3 times a year (there are over a billion cases per year in the US alone), sometimes without noticing. These would "boost" your immune system from time to time and afford some limited protection against severe disease. That did not happen over the past 18 months for a lot of people, especially in countries like UK/NZ/Australia which went way overboard on lockdowns, to the point where there was no "flu season" last year. I bet US will fare better just because enforcement is relatively lax, and 190M people already had COVID [2] (probably due to not really observing any lockdowns or whatever). [1] https://www.bbc.com/news/newsbeat-58624295 https://www.bbc.com/news/newsbeat-58624295 [2] https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/burden.html https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/burd...