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Nanobodies Against the Coronavirus: Something New

So let’s talk about nanobodies – there’s a coronavirus connection to this, but it’s a good topic in general for several reasons. We begin at the beginning: what the heck is a “nanobody”?

Antibody Structure

The name is derived, rather loosely, from “antibody”. So let’s spend a minute on what antibodies actually look like. What you see at right is the three-dimensional structure of a typical one – you have a ridiculous number of these things circulating in your blood right now, nearly all of them subtly different from each other. The color codes are the two “heavy chains”, in red and blue, and the two “light chains”, in green and yellow. It all adds up to about 150 kilodaltons, a bit on the chunky side as proteins go.

It’s a bit easier to picture this stuff in schematic, so the next picture is general layout of these chains and domains. I’ve retained the same color scheme, but with some added information

There are the heavy chains and the light chains, as in the protein structure picture, but you’ll notice that the ends of both of those are variable regions, while the rest stay as a constant platform. Those variable ends (the “Fab”, for “fragment antigen binding” regions) are actually the part that recognizes antigens, as you would figure. You never know what sort of antigen you’re going to encounter next, and thus the insanely large collection of different antibodies that all of us are walking around with, produced “on spec” in hopes that one or another of them will happen to recognize what turns up. The two heavy chains are almost always identical in any given antibody, as are the two light chains (the antibody structure is symmetrical). All of this is held together by disulfide bonds between Cys amino acids and some other polar interactions between the constant regions.

I’m leaving out a lot. In any discussion of immunology that runs to less than about 500 pages in 6-point type you’ll be leaving out a lot. For example, antibody proteins have various sugar molecules attached to their surface at key points, and those are really important to their function. What’s more, there are actually five distinct types of heavy chain and two types of light chain – they’re mostly about the same size (a couple of the heavy ones are noticeably heavier) and they all fit into this same arrangement, but you can distinguish them by their amino acid sequences. That “base” at the bottom with the two heavy chains is called the Fc (“fragment, crystallizable”) region, and binds to various immune cells to regulate function. Meanwhile, the working details of the binding up in the variable Fab regions just get finer and grainer the closer you look at them; there are whole careers of work up there. Different classes of antibodies can also have these individual “Y” structures arranged further into pairs, for example, or into cycles with five of them in each unit. And so on.

Camelids and Nanobodies

And with that, we shall now abruptly veer off into talking about camels, llamas, alpacas and their kin, because they have their own variety of antibody. No one knew that they had a different system going until 1989, when a student-run project at the Vrije Universiteit Brussel was trying to come up with a diagnostic test to check camels for trypanosome infection. They discovered that camel antibodies were. . .weird. Some of them were just like the ones above, but about 75% of the camel antibodies (and up to 50% in the New World species like llamas) have no light chains at all. They just have the variable parts of the heavy chain stuck directly onto the “base” constant region. Sharks and their relatives, as it turns out, have something similar going on with a different sort of base region, in what are clearly two different evolutionary events: at least 220 million years ago for the cartilaginous fish and 25 million years ago for the camelids. Both sets of animals seem to work just fine with their proprietary systems – before these discoveries, most immunologists would have said that that such modifications would be likely to cripple the antibody response, but not so. That led to thoughts of clipping things down to just that heavy-chain variable chunk to see if those would recognize targets as well (i.e., having just one of those light-blue or light-red pieces in the above schematic by itself).

That they did, and “nanobodies” were born. Not only can they bind with high affinity to all sorts of antigen targets, but they do so via binding modes that have never been observed with real antibodies (which means that they might be able to recognize all those targets in new ways). They’re also much smaller than antibodies per se, which leads to some interesting properties. Nanobodies can have a wide range of stability and half-lives, which is tunable with some experimentation, and they often demonstrate much greater penetration into tissues and many other features. People have been investigating their properties and uses for over 25 years now. The Belgian researchers formed a company (Ablynx) in 2001 that has led the way, thanks to their solid patent positions in the area, but there have been so many twists and turns in the story that the first actual nanobody drugs have appeared just as their early patents have begun to expire (more on this timeline in that earlier link). With some irony in hindsight, some of those early investments in nanobodies were made in order to try to avoid the serious patent-licensing headaches with traditional antibodies.

Coronavirus Nanobodies

There is now a preprint describing a screen for such nanobodies binding to the coronavirus. Update: the folks at VIB have also been working in this area, getting into it quickly, and I’ll be highlighting their efforts in another post. The team (a large multicenter effort led out of UCSF) had a yeast-displayed library of billions of potential heavy-chain fragments (prepared earlier in collaboration with the Kruse lab at Harvard), 21 of which ended up showing strong binding to the coronavirus Spike protein. These fell into two classes: Class I bound directly to the receptor-binding domain (RBD) and competed with the ACE2 from the surface of human cells. Class II, though, didn’t hit the RBD, but instead bound somewhere else and changed the conformation of the RBD so that it can’t recognize ACE2 when it’s available. When these nanobodies were put into an assay that measured the binding of fluorescent-labeled Spike protein and HEK293 cells expressing ACE2, the Class 1 species were active, but the Class II ones did nothing, weirdly.

Further work yielded cryo-EM structures for two of the best Class I candidates bound to the RBD, but they couldn’t get any such data for a Class II. That was worked out (partially) by another technique, where the complex was exposed to extremely reactive hydroxyl radicals (generated by synchroton X ray beams). You then look over the proteins to see what didn’t get eaten by the radicals. Those experiments showed a protected area on the Spike protein well away from the RBD, which is presumably where that particular Class II nanobody was binding.

The team went on to take one of the Class I candidates (designated Nb6) and make dimers and trimers of it, separated by inert Gly-Ser linking chains. The idea was that the Spike protein, which has a three-fold repeated architecture, could be inhibited even more strongly by binding to more than one RBD on its surface. And that proved to be the case: using surface plasmon resonance (SPR) assays, which let you follow on- and off-rates in detail, it became clear that the dimeric and trimeric forms of Nb6 occasionally bound with just one of its nanobody ends, in which case it could fall off again reasonably quickly, and also showed binding with all of its nanobody regions at once, in which case it came off much more slowly. The trimeric form showed subpicomolar affinity for the Spike protein in this assay, although the exact binding constant is so tight that it hasn’t even been quantified.

These various forms were taken into a pseudovirus cell infection assay (that’s where you rig up a harmless virus to use the coronavirus’ infection machinery, Spike and all). Plain Nb6 had an IC50 of 2 micromolar, and another Class I nanobody (Nb11) was almost the same. The best Class II nanobody (Nb3) was 3.9 micromolar. But that trimeric form of Nb6 (Nb6-tri) was 1.2 nanomolar in the assay, a two-thousand-fold-improvement. Trimer forms of Nb11 and Nb3 also improved, but not as much. In a test of Vero cell infection with real SARS-Cov-2 coronavirus (done at the Pasteur Institute in France), Nb6-tri prevented viral attack with an IC50 of 160 picomolar, which is truly impressive.

They didn’t stop there, though. A “saturation mutagenesis” experiment around the sequence of Nb6 was then tried, with new rounds of assays, and this yielded a mutant nanobody that was still more potent. You might wonder about trying to make things even better when you started out with billions of nanobody candidates in the first round, but a quick look at the math shows that a couple of billion nanobodies are just a speck compared to the total number of possibilities (around 110 amino acids, 20 variations per!) This one was trimerized as before, and the new mNb6-tri, when put into the SPR assay, showed no off-rate at all during the limits of the experiment, putting its binding constant somewhere in the femtomolar range at worst. It comes in with IC50s of 120 picomolar in the pseudovirus assay and about 50 picomolar in the wild-type infection assay, but those are probably at the limit of detection for both. Basically, we don’t actually know how potent this nanobody construct is, because we don’t have assays good enough to read out a number (!)

Potential Therapeutic?

OK, now things get interesting. The authors tested the stability of mNb6-tri, and found that it can be heated, lyophilized (freeze-dried, basically), and nebulized into an aerosol with no loss of potency. It’s a very stable species that can put up with all sorts of handling and processing. You could certainly inject this material, just as you’d administer monocolonal antibodies. But there are more possibilities. How about formulating it as a nasal spray? Or in a nebulizer, to be breathed into the lungs, or even sprayed out into the room air? How about impregnating filter material with this protein so it pulls coronavirus particles out of the air as they pass through it? The extreme stability of nanobody proteins gives all of these a real shot, and they’re under serious consideration for development. The team says that they’re in discussion with several commercial partners to take this technology into human trials (and presumably medical-device trials, for the filtration idea), and I think that’s an excellent idea. This has real public-health potential, from the looks of it, and could be just the backup that we may need for the existing vaccine programs if they come in less effective than we’d like (or are rolled out more slowly than we’d like!) I hope that the money and resources are rounded up quickly.

 

122 comments on “Nanobodies Against the Coronavirus: Something New”

  1. Assay Person says:

    Worth mentioning: The reported of on-rate of 1.4E6 M^-1 s^-1 is likely to be transport limited and might appear higher in homogeneous assays.

  2. Toni says:

    Are camels protected against MERS?

    1. MTK says:

      Was about to mention that.

      I believe the animal host for MERS is indeed camels. Seems like a good place to look for relevant nanobodies.

  3. David G. Whiteis says:

    Even assuming they live up to their hype, AreoNabs would ostensibly be sold as over-the-counter meds. This means that people would have to pay out-of-pocket for them, immediately making them unavailable to many of our most high-risk populations (low-income people, the frail elderly, etc.)

    How can this problem be addressed?

    1. zero says:

      A competent insurance company would recognize that the cost of a safe, effective OTC treatment/preventative is far less than the cost of treating the infection itself. Such a firm would cover the treatment.

      Lacking sane insurers, a competent administration (or the legislature) would mandate that this be so in the name of public health. The process would be ugly (perhaps even ghoulish) but the result would be effective.

      Lacking a competent administration, aid organizations, employers and municipalities would have to try to make up the difference, probably with the manufacturer throwing in a PR-friendly discount.

      1. David G. Whiteis says:

        A “competent administration”?

        Gee — what a concept!

        I do seem to remember, once upon a time, in a remote galaxy far away . . .

        1. x says:

          As far as the wealthy elite are concerned, every administration is competent. We’re the only ones who suffer from their “incompetence”.

      2. Kerry Lewis McCarthy says:

        Has anyone mentioned nebulizer pricing yet? I wonder if the Chinese are in production?

    2. confused says:

      Lots of ways. The simplest might be an act of Congress, equivalent to CARES — Something outside our general healthcare system, just as the payments and such are outside our usual economic system.

      Or a bunch of local measures of varying effectiveness toward more or less the same end.

      1. gippgig says:

        A pandemic is a global problem. It cannot be dealt with by nations. A global approach is required.

        1. An engineer says:

          I don’t know what you mean by this:

          “A global approach is required.”

          This is not an attack. I would honestly like to know what a “global approach” refers to.

          Are you referring to a desire for global cost sharing? If so why? It would seem that the rich prosperous places are going to foot the bill on R&D this time around (mostly because others can’t) and when the cure or vaccine is available other places will then buy the product or be given it or the instructions to make it.

          Are you referring to some sort of global information sharing? If so why? It already happened/is happening. My understanding of the state of information sharing is that this crisis has increased the flow of emails and papers between labs in different countries by a factor of 10 or more vs pre-crisis levels.

          Are you referring to a global manufacturing supply chain? If so why? From my work in Pharmaceutical manufacturing I can say that every large manufacturer I have worked for or with is already very global (ever tried to support IQ on a skid on another continent? I have it sucks when the locals forget to plug in the charger for the remote engineering workstation and are all asleep when you get to work).

          Basically I have trouble understanding how the industry I work in could be any more “global”. But if you have a different approach then the current strategy please explain, maybe it’s good /shrug.

          Sorry if this comes off as abrasive I really do want to understand what people mean when they use this phrase and I could be totally wrong about the above.

          Best

          1. Metaphysician says:

            I assume the underlying sentiment is “a pandemic needs a single transnational government to deal with it, rather than individual nation states”. Which, beyond just the fact that no such thing exists and there is no way to establish such without World War Three…

            Why would anyone assume a single world government would be any less susceptible to bad leadership than any single national government? A single global authority might be a good thing if it makes the optimal decision against a crisis. It would be a very, very bad thing if it makes a bad decision against a crisis… and without any competition or comparison, what incentive would such a global government have to improve?

            ( I find it bemusing how the same people who passionately support the idea of ever centralizing governance, often cry bloody murder about actual or perceived monopolies in business. . . )

          2. gippgig says:

            By global approach I mean the world’s top epidemiologists & public health experts get together, come up with the best possible recommendations (& how to change them as new data becomes available) on what should be done, and tell the world that the best chance of stopping the pandemic is to follow those recommendations (regardless of what governments say).

        2. Uncle Al says:

          https://www.ratburger.org/wp-content/uploads/2020/08/DemSoc01.jpg

          Pictures do not lie. The world can never have too much government.

    3. wilhelm Cody says:

      The FDA would likely first approve such a product by prescription only. Only after years of use showing general safety would they then accept over the counter sales.

      So now the criticism becomes that folks who do not have effective pharmaceutical coverage could not afford it.

      1. David G. Whiteis says:

        To say nothing of the fact that getting that prescription would require seeing a physician, which automatically adds layers of time and inconvenience (to say nothing of expense) even for people fortunate enough to have access to a physician in the first place.

        Hardly a “quick-fix.”

    4. Driving, may stay a while says:

      Seriously, this sort of whinging is getting old.

      The hard parts are inventing the appropriate nanobodies and manufacturing them. The harder parts are determining safety and ferreting out rare effects.

      Distribution is not a hard problem. It’s a public policy issue; some (probably most) governments may find it worthwhile to distribute it with indirect payment, or what AOC would call “free”. Gov picks up the check, then taxes everyone a trivial amount to cover it. There are good reasons not to do that except on rare occasions; a case where you daily life is crippled due to some real hazard and much hype and hysteria.

      One way or another, everyone who needs this will get it. I want to hear from the lab people, not the complaining chorus.

    5. TallDave says:

      lol no, even it was expensive Feds would give it away for free… if it works

      price of keeping economy closed is estimated around a trillion a month

      anyways highly speculative, tech has potential but still far from market… let’s at least see some animal data before we start planning the pandemic victory parades 🙂

      1. x says:

        The “price” of shutdown is irrelevant. Money is fake to begin with, merely lube for the market. We could shut down the country cold for a year, and while millions might starve, the wealthy would have a virtually inexhaustible reserve to survive comfortably on, and would retain ownership of all their capital; after the “dead year” ended they could simply pick up where they left off, albeit with a slightly dearer labor larket – of course, there’s no shortage of potential immigrants to repopulate the domestic workforce if needed.

        Perhaps some medium-sized businesses would be destroyed, but they’re just fodder for the big guys anyway – and we’re all fine with that, right? A few might make tepid objections about this mega-merger or that buyout, but on the whole, no one actually seems to care about our march toward monopoly.

    6. loupgarous says:

      Oseltamivir didn’t live up to its hype, but has a good enough benefit-risk ratio during influenza pandemics that physicians prescribe it to high-risk patients. There doesn’t seem to be an overwhelming issue of availability with oseltamivir because most physicians know how to stratify risk and benefit in their patients.

      I don’t think that AeroNabs will “make PPE obsolete”, but I can see how AeroNabs would have a place in COVID-19 prophylaxis if it lives up to its promise. If it just frees up a certain number of ICU beds and lowers demand for medical interventions by reducing severity of COVID-19 infection in the populace among the high-risk population, AeroNabs will have done its job. If not, then there’s room for it on the pharmacy shelf next to remidesivir.

  4. Kenneth Crook says:

    Nice piece as usual. Beyond nanobodies, I see that trispecific DARPins have been generated against multiple viral epitopes and are also being touted as a treatment.

    1. anon says:

      Yes, I heard also the Centyrin platform is suited for this approach. Can easily make bi and tri specifics.

  5. David G. Whiteis says:

    . . . and just so I understand this fully — the nanobody nasal spray / aerosol would be a preventive, not a “treatment,” right? In other words, this would be a protection for people not yet infected, not be something administered to a patient who presented with mild symptoms (or one who tested positive but was asymptomatic) to keep the symptoms from getting worse?

  6. anon says:

    Would a vaccine even be necessary after AeroNabs are marketed? The nanobodies would act like herd immunity; the R0 would decline rapidly possibly almost to near 0. COVID might then essentially go extinct within 2 weeks of introduction. Might also use these as sensitive COVID viral detectors.

    1. David G. Whiteis says:

      In theory, you’re right, although (unless the nanobody treatment could be thoroughly covered by all insurance, both public and private, which would be highly unusual for an over-the-counter med), a lot of people wouldn’t be able to access it. In addition, unless I’m misunderstanding something, AeroNabs wouldn’t lead to actual “immunity” at all; it would apparently have to be inhaled daily, and at least 70 or 80% of the world’s population would probably have to do it to bring the R0 down to anything approaching 0. Would this be feasible? After all, we’re already fretting about whether people will be able to take an annual booster shot for a vaccine.

      1. David G. Whiteis says:

        . . . and of course we’re also looking at extremely daunting production and distribution logistics (COVID is, of course, a worldwide crisis, so we’re talking about upwards of 7.5 billion people here). That would take months, at best, probably over a year, and since this is a privately marketed product, there would be huge political / economic hurdles in getting it distributed and marketed worldwide.

      2. Charles H. says:

        Of course, even an R of 0.9 would quickly lead to the extinguishing of the pandemic. Even 0.95.

        OTOH, it seems quite possible that it *could* be used effectively at first symptoms. Not certain…but… Well, there are already enough cases that are asymptomatic, and there’s *some* evidence that this is due to a SMALL initial exposure. Perhaps the immune system can detect it quickly, and needs time to ramp up the response, so the doubling time from a small population gives it enough time to respond. In that case suppressing it in the lung and nasal cavities might suffice to turn potentially serious cases into mild cases.

        (Of course, there are those reports of heart damage in even mild cases….but that study explicitly said that this wasn’t proof of permanent damage, so perhaps it isn’t.)

        1. eub says:

          Really not quickly at all. If you have a million active cases, a blanket Re of 0.9 takes 131 serial transmission periods — just call it two years — to get down to 1 active case, after which you can talk “go extinct” as anon looks for. If 80% of the population takes this per David Whiteis, you have Re of something like 2.5 * (1 – 80%) = 0.5, you need only 19 ~weeks. (But there are likely well more than a million active cases even in the U.S. if you include unrecognized ones.)

    2. Pedwards says:

      And that also assumes that everyone would freely and enthusiastically use such medication/devices at a high enough rate to create effective herd immunity. Given the resistance to uptake on things as simple as wearing a mask (or as effective as getting a vaccine), I don’t think that’s an accurate assumption.

      1. David G. Whiteis says:

        Well, the reasons for resistance are somewhat different — masks are alienating, they can be uncomfortable, and some people (whether rightly or wrongly) see them as a violation of personal freedom; there are legitimate and not-so-legitimate reasons to fear a vaccine, especially one that’s been developed rapidly. In the case of a nanobody spray or aerosol, though, it wouldn’t be quite as intimidating to spritz your nose at home as it would be to get jabbed by a needle in a doctor’s office or a clinic, and as a society we’re used to seeing and using nasal sprays and aerosols on a daily basis.

        On the other hand, even given the legitimate misgivings about “rushed” science, COVID seems to have unleashed an almost Luddite-like distrust of scientific medicine — in both the U.S. and other places — until we seem to be descending into a new Dark Age of superstition and fear. I honestly wonder if it will spill over into other areas of medical practice and health care. In such an atmosphere, even something as seemingly benign as a new nasal spray could, indeed, meet with some pretty fierce resistance.

    3. Ian Malone says:

      Well, we don’t know efficacy or safety in people yet. What if they trigger an allergic reaction in 5% of people? What if your immune system just sweeps them up? It’s exciting, I’ve seen some buzz on twitter too, but don’t take any silver bullet for granted based based just on binding potentials.

  7. steve says:

    Immunologist here. The issue with nanobodies (which, as Derek said are from camelids, not just camels, so including llama, alpaca etc) is that they are foreign proteins. So eventually people will make antibodies to the and their efficacy will fail. This is why we moved to humanized antibodies from mouse – because of the Human AntiMouse Antibody (HAMA) effects. With nanobodies that might be mitigated by cloaking them with PEG or something but as far as I know none have ever been approved for clinical use so we don’t really know whether repeat dosing is possible.

    1. Nanobuddy says:

      Per Derek’s post-there is an approved nanobody therapeutic with several more candidates in clinical trials (link in name). Immunogenicity is a concern but not prohibitive it seems

    2. cole j batty says:

      I find these comments to be illustrative of the tendency of people to see one highly impressive number (as these constructs’ binding affinities really are) and start jumping to absurd conclusions about this being the Ultimate Fix. These things are expensive and in their early stages of development and evaluation. I think there is a lot of potential but it needs to be borne out before people start saying this is the 100 trillion dollar magic solution. There could be major issues with safety.

      Especially with the ‘no off rate’ construct, you are literally attaching your large foreign protein construct to a viral protein/particle with known immunogenicity. This is a known strategy to increase vaccine response to antigens. What’s to stop nanobodies from being those antigens?

    3. Anonymous says:

      Excellent point, steve! I’d hope with an anti-viral nanobody that the treatment time would be short enough that even if anti-drug antibodies did develop, they would be late enough that they wouldn’t impact treatment efficacy – if there’s a 5 day window of treatment to ameliorate infection immediately post-exposure or right when people come in with symptoms (as opposed to, say, a prophylactic given to healthcare workers every week), that’s short enough to not worry about ADAs. It’s also possible to humanize nanobodies (e.g. https://pubmed.ncbi.nlm.nih.gov/19010777/) although I don’t know if that was done in this case.

  8. anon says:

    AeroNabs are orders of magnitude off the chart. How much of this will even be needed at 50 picomolar dosing? A kitchen scale lab? This is science at its most powerful. Reasonably this technology has an economic impact on the scale of $100 trillion.

    There is, of course, an effective, cheap and low tech solution to COVID, everyone could simply lock themselves in their homes and have food delivered for a year or two. This strategy has largely flattened the first wave, though what about the next wave and the next wave? People have not been overly enthusiastic about option number 1. Option number 2: Inhale relatively inexpensive AeroNabs for about 2 weeks and COVID rapidly disappears on a global scale. If you do not have the money, then stay bunkered down for the 2 weeks and the pandemic is over. The combination of physical containment along with AeroNabs should rapidly extinguish this pandemic. The doomsday scenario of the virus sickening front line workers is also avoided. With nanobody treatment these workers would then in essence (though not technically) be immune.

    AeroNabs could turn around this pandemic almost over night. The timeline probably is no longer on the order of ~ a year, but probably ~ weeks.

    1. confused says:

      >>everyone could simply lock themselves in their homes and have food delivered for a year or two.

      Part of the issue has been that everyone *can’t*; food delivery to your door is not available everywhere in the world, and billions of people couldn’t pay for food for a year without working at their (non-work-from-home) jobs.

      Nor could the food & other essentials supply chains survive this.

      1. Ian Malone says:

        Yes, very easy to believe this, but those delivery drivers, people in the depots, those providing care, maintaining infrastructure, there are lots of pools of people whose work is keeping the rest of us comfortable who simply can’t hole up for two years and keep doing what they’re doing. (Also, ultimately physical and mental health will deteriorate if you try to maintain an absolute “don’t leave home” lockdown for that long.)

        1. confused says:

          >>ultimately physical and mental health will deteriorate if you try to maintain an absolute “don’t leave home” lockdown for that long

          Oh, that too.

          I would argue that the results of that would ultimately be worse *long-term* than the results of an unrestrained COVID pandemic. (In terms of quality of life lost, too… I’d argue that the quality of life lost by *everyone* strictly staying home for a year or two would probably be worse than the life-years lost to disease.)

          But that’s much more arguable; it’s easier to demonstrate that it’s just not possible in the first place.

  9. David G. Whiteis says:

    “. . . If you do not have the money, then stay bunkered down for the 2 weeks and the pandemic is over. . .”

    A lot easier for some folks than others. Many of the world’s poor (and, for that matter, many of America’s poor) don’t have anywhere to “bunker down” in the first place, and many who do can’t do so in isolation. Then there are the countless low-income working people who’ll lose their jobs if they don’t show up (this has already been a major contributing factor to the disproportionately high rates of COVID infections and deaths in communities of color in the U.S.). Social inequality, ultimately, is a far more powerful risk factor than non-compliance to masking and “distancing” mandates.

    1. steve says:

      You’re aware, right, that “AeroNabs” have never gone through GLP tox, never mind completed clinical trials. Even if you’re from UCSF your claims are a bit over the top. It’s amazing how 160,000 people have died in the US alone and there have been multiple failed clinical trials of much touted therapeutics but some (incredibly naive) people still think the solution is trivial and if people only would listen to them….

  10. Nathan Williams says:

    Isn’t one of the big questions here going to be “what *else* does this bind to and foul up?”

  11. anon says:

    Thank you steve, it’s always appreciated having adults on board.

    Apparently, a nanobody technology has already been approved for acquired thrombotic thrombocytopenic purpura: caplacizumab. This is not as obscure a technology as I had thought. http://hugin.info/152918/R/2233733/878824.pdf

    1. wilhelm Cody says:

      Reading the reference gives the relevant information that “…Cablivi targets von Willebrand factor (vWF), a protein in the blood involved in hemostasis. It is designed to inhibit the interaction between vWF and platelets. Cablivi is an anti-vWF Nanobody …”.
      There is an hypothesis that some of the more lethal effects of COVID-19 induces high levels of von Willebrand factor, leaving to disseminated clotting (https://www.youtube.com/watch?v=kK-DNyKnb5c). So the approved product could be tested in clinical tries with patients with severe cases.

    2. steve says:

      Thanks; I wasn’t aware of that. Evidently it’s humanized so I guess they removed any camelid epitopes that might invoke the kind of immune response I was talking about. Good to know!

      1. Marko says:

        The nanobody therapy included immunosuppression and plasma exchange. I don’t see where they humanized anything.

        1. Omar Stradella says:

          From: https://www.medpagetoday.com/Cardiology/VenousThrombosis/56154

          “For acquired thrombotic thrombocytopenic purpura (TTP), an anti-von Willebrand factor humanized immunoglobulin resolved acute episodes faster, the phase II TITAN trial showed.
          Daily subcutaneous shots of caplacizumab (Nanobody) reduced median time to normalization of platelet count by 39% compared with placebo during acute episodes of TTP requiring plasma exchange (P=0.005), Filip Callewaert, PhD, of trial sponsor Ablynx, and colleagues reported in the Feb. 11 issue of the New England Journal of Medicine.”

          1. Marko says:

            The point is that the approval of Caplacizumab for this indication , and the PII and Plll data the approval was based on , do little to allay the fear that anti-drug antibodies could inhibit the success of nanobodies used for other indications.

            For their first FDA approval , they picked the one indication that would minimize any potential problems with anti-drug antibodies , one in which the nanobody drug would be combined with immunosupressives – which would reduce such antibody formation – along with plasma exchange , which would clear any such antibodies that were produced. Even with these advantages , drug-induced antidrug antibodies were detected in a subset (9%) of patients , though it was not sufficient to inhibit drug activity.

            https://www.nejm.org/doi/full/10.1056/NEJMoa1505533

          2. anon says:

            Great point Marko, very astute. You wouldn’t really expect much ADA with daily plasma exchange and immunosuppressive therapy, so I am amazed that it even appeared in the trial. It does seem suggestive of problems down the line for this modality.

  12. Vaudaux says:

    Are we talking about a drug or a disinfectant? If a drug, would it not have to go through preclinical studies and clinical trials like any other new drug? How could it be on the market before vaccines? From the bioRxiv article, these nanobodies neutralize coronavirus in Vero cells but there is no mention of protecting or treating mice or any other animal.

  13. Dr. Manhattan says:

    “The team (a large multicenter effort led out of UCSF) had prepared a yeast-displayed library of billions of potential heavy-chain fragments, 21 of which ended up showing strong binding to the coronavirus Spike protein.”

    A small correction. The yeast surface display library was created in Andrew Kruse’s lab at Harvard Medical School. It is an all purpose nanobody library, and by its synthetic variation of 3 regions, obviates the necessity of having to raise antibodies in llamas, etc. In theory, due to the numbers, it could be used to find nanobodies against any antigen screened. Dr. Manglik was a coauthor on the original Kruse lab publication, which describes the nanobody library creation. Originally publication is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5839991/

    1. Andrew Kruse says:

      In the interest of giving full credit, the nanobody library in our 2018 paper was the result of a close and equal collaboration between my group and the Manglik lab, so I wouldn’t consider the it to be an exclusive product of either of our groups. We want this resource to be broadly available to the research community, details on obtaining the library are available here: https://www.kerafast.com/item/1770/yeast-display-nanobody-library-nblib.

      1. Derek Lowe says:

        I’ll make a note in the main text – thanks!

    2. Nanobuddy says:

      It’s interesting that the monomeric anti-RBD nanobodies from the yeast display platform are low affinity by antibody standards (low micromolar), which is pretty typical for nanobodies from synthetic libraries. A nanobody from alpaca immunization comes out of the gate at <100 nM (link in name). If formatting nanobodies into multimers proves to be a challenging part of optimizing for therapeutic application then immune-derived nanobody monomers might be a better way to go

  14. Christophe L Verlinde says:

    Pubmed lists 8 papers in which specific nanobodies for parts of SARS-CoV2 are described. Google Scholar lists 17 papers on this topic.

    Maybe it is useful to inform the reader of this blog that a nanobody just has about 100 amino acid residues.

    1. Derek Lowe says:

      That’s mentioned in passing near the end.

  15. Anon says:

    I remember when domain antibodies were the future… Whatever happened to them? Then came the adnectins…. Call me skeptical but I think I’ll stick to immunoglobulins. BTW I’ve clinical experience of both platforms to bolster my skepticism. The situation is not dissimilar to the vaccine platforms being tested at the moment. Many platforms bur little precedence. Evidence of pharmacology is likely to be the lowest entry point. Then it comes down to ease of manufacture, stability, immunogenicity, route of delivery, etc. And what happens for your own host immunity when you develop neutralizing antibodies against a nanobody binding region that targets the spike protein?

    1. Adnectins have not completely disappeared. BMS, which acquired the platform back in 2007, are currently sponsoring two PD-L1 imaging studies using an adnectin radioconjugates. Significantly faster clearance rates than full-length antibody, potentially bringing SPECT/CT down to a couple of hours or less.

      There’s also a slew of anti-PD-L1 nanobodies in the works (one of which has completed a clinical POC study), and one in pivotal solid tumours study in China, earlier stage in US (more accurately, a nanobody-human Fc fusion protein), suitable for subcut administration.

  16. Marko says:

    “And what happens for your own host immunity when you develop neutralizing antibodies against a nanobody binding region that targets the spike protein?”

    NDE ? ( nanobody-dependent enhancement of disease )

    These things have been studied long enough that it seems to me there should have been some animal model studies for other viral infectious diseases to show some proof-of-concept. I hope it all pans out , but it’s going to take more than pseudovirus / Vero cell assays to get me much excited.

  17. LikeMike says:

    Anyone have thoughts on MSC’s? Interesting piece in WSJ.

    The Treatment That Could Crush Covid https://www.wsj.com/articles/the-treatment-that-could-crush-covid-11597360709

    1. Oudeis says:

      I saw that. I found the article less than perfectly lucid about what exactly is involved in the treatment. I guess I’ll have to look into it sometime.

  18. A Nonny Mouse says:

    I see that Peru has told its population to eat llamas on the basis of this study as a cure!

  19. Laura says:

    I have one degree in English and one in Theology, got a C- in college Bio, and never took another science class again, so please forgive my n00b questions as I try to understand this!

    So the bits of the antibodies that get broken off to make nanobodies — ordinarily, they’re the ones that recognize antigens. But then you break them off, and the heavy parts that are left actually do just fine on their own going after the antigens. (Have I got that right-ish so far?) And then they… what? You say they “bind” to them; what does that binding do to the antigens? Does it kill/neutralize/destroy/something else? Given that the “hey I worked out what this Thing is” bits of the antibodies have been removed to make the nanobodies, is there not a risk that the nanobodies are going to, like, bang into a piece of healthy tissue and bind to IT, thus doing (whatever bad thing binding does)?

    Your writing here is an absolute joy, even though I only understand parts of it. Thanks for your work, which I look forward to continuing to follow long after this verkakte pandemic is behind us.

    1. x says:

      First off all, understand how an antibody works – I’ll use a goofy example.

      Imagine you want to pick trash up off the ground at a distance. So you use a long handle with a spike on the end. (You’ve probably actually seen these in pictures or movies, if not in person.)

      That works great for trash, but what if you wanted to pick up other things? Instead of a spike, you might have one of those grabby pincers. Or a hook. Or a glue blob. Magnet. Suction cup. One side of velcro. (Useless for picking up almost anything except the other side of velcro, but oh boy, is it ever good at that.)

      Your body comes with a vast library of possible sticky ends, encoded in your genes, and as a toddler, you make a zillion of them in crazy random combinations. This antibody has a barbed needle and a magnet on it! This other one has a jigsaw puzzle piece and a sticky hand from a vending machine! This other one has a lot of little magnets glued onto a ping-pong ball and a hook with another, smaller hook coming off of it! …and so on. Your body doesn’t yet know what, exactly, these will be good for, but it makes them anyway.

      The reason none of these antibodies stick to parts of you is because very early in life your immune system kills off every cell that produces self-harming antibodies. (Occasionally one slips through, or develops later in life, and voila! autoimmune disease.)

      So, the antibodies that bind to things like the coronavirus generally don’t bind to anything else, because their particular combination of sticky parts are great for picking up coronavirus but lousy for picking up anything else.

      Normally, antibodies have four sticky bits: those are the two light chains, plus the variable ends of the two heavy chains. If you take off the light chains, the heavy chains can still stick to things. You’d think they wouldn’t stick as well with only two sticky bits, and you’d be half-right; the thing is that a normal antibody can have its sticky bits get in each others’ way, too. So it’s possible for a nanobody to actually work better than an antibody that has a useless end getting in the way. It all depends on how well the sticky bits match the thing they stick to.

      A couple things happen when antibodies bind to antigens. First, the spike protein on the coronavirus that attaches to the ACE2 receptors on human cells works the same way, with sticky bits that match the receptor. If you gum up all the sticky bits on the virus, it just becomes a useless lump of protein and lipids floating around that can’t infect anything.

      Second, the handle ends of antibodies have some biological functions, one of which is to signal to white cells “HEY I GOT SOMETHING PLEASE DESTROY WHATEVER IT IS”. So once you have a bunch of antibodies sticking to things, your neutrophils, macrophages, and T-lymphocytes go to work ruthlessly eating, puncturing, and poisoning whatever has some of those convenient handles stuck to it – all the while spewing clouds of chemicals that tell other white cells “HEY WE’VE GOT A SITUATION, GET OVER HERE”, which is one of the things that generates the inflammatory response.

      Interestingly, after eating the antigens and breaking them into bits, some of these cells actually stick the bits to their outside, like trophies. Or evidence. These are generically called “antigen presenting cells”, and there are other cells that recognize these bits and then tell your immune system to make a billion more of whatever sticks to them, which is how you develop immunity. Of course, once the infection is eliminated, your body ramps antibody production back down to normal levels, but the best antibody-producing cells become “memory cells” that can be rapidly activated if the same antigen is ever seen again, which is how you stay immune to things like chickenpox.

  20. Craig says:

    Derek –

    I just want to say, as someone who enjoys reading about science but who was a C student in chemistry many, many, many years ago… thanks for this blog. It’s great to have a place to read this kinda stuff where it’s actually understandable for us non-science types, but also not oversimplified to the point of being fluff.

    I will admit that I most often come here hoping for a new “Things I Won’t Work With” – but I’ve really enjoyed reading your stuff regarding COVID over the past year. It helps me to filter and put in perspective the stuff I’m seeing on various news sites, etc.

  21. idiotraptor says:

    These are exciting proof of principle data. Translating them into a potential human therapeutic will be a difficult and not necessarily rapid process. Whether based on camelid or wholly synthetic sequences, nanobodies will almost certainly be no potential substitute for an efficacious prophylactic vaccine. The immunogenicity of nanobodies in vivo, either as free polypeptides, complexed with high avidity to targets antigens, or associated non-specifically with self-proteins will probably limit their use to one or two administrations before evoking an immune response. As already noted, SARS-CoV2 directed nanobodies might result in ADE or, if administered prior to receiving a prophylactic vaccine, induction of antibodies that antagonize or inhibit development of protective immunity. Obvious there are lots of moving parts here. I’d much rather have the benefit of a prophylactic vaccine. Maybe nanobodies could be used acutely if unvaccinated individuals had a confirmed exposure to COVID19 or, as an adjunct treatment of a vaccinated person developed severe COVID19 symptoms. Repeated administration may be problematic. Nanobodies might be more immediately useful in the development of high sensitivity diagnostics or environmental biosensors to SARS-CoV2 and other airborne pathogens.

    In no way do I mean to minimize or trivialize the results of Schoof et al. This is an important data set. The gulf between proof of principle data and having a clinically tested and validated therapeutic is wide and deep.

  22. idiotraptor says:

    On reflection, proof of concept is the more appropriate term.

  23. idiotraptor says:

    On reflection, me thinks proof of concept is the more appropriate term.

  24. eub says:

    “a student-run project at the Vrije Universiteit Brussel”

    That’s a fun part of the story. Heck of a student project, eye-opening to just how little we know about biology.

  25. Bryon Wasserman says:

    When might we plausibly see these available these if they work? If they’re not starting human trials for a few months, it seems like it could be a long while before phase 3 trials are completed. I think that EIDD-2801 went into phase 1 trials in April and aren’t even set to start phase 3 trials until September.

    1. Bryon Wasserman says:

      To follow up, assuming phase 1 trials start in October, probably phase 2 trials in December at the earliest with phase 3 trials starting in February and approval late spring/early summer? Is there something about the nature of the product that might let them move faster?

  26. anon says:

    “… the treatment (AeroNabs) could be available to the public as an over-the counter medication in three or four months.” San Francisco Chronicle

    1. Bryon Wasserman says:

      I hope that you’re right-I just don’t see how they get there. Maybe the approval process is faster because it’s an inhaled spray and doesn’t go into the body?

  27. anon says:

    That was exactly what I was thinking! Keep the AeroNabs outside of the body! End-run the FDA.

    The problem with COVID has been that there is no widely used diagnostic test. It’s hopeless if only 1 in ~1,000 is tested everyday. How could we test 1 in 1 at every point of contact? If there were a cheap ubiquitously embedded technology that could rapidly identify those who were infected the pandemic would immediately stop. As it is now, there is no effective population scale identification of those who are or are not infected.

    AeroNabs could do the trick. Detection = Elimination. If AeroNab filters/… could capture and report COVID, then they could be deployed everywhere. Everyone could have their own portable Corona stopper. No treatment required; perhaps not even FDA authorization required. Posters on thread with more technical skill are encouraged to respond.

  28. David G. Whiteis says:

    “Gloomy Gus” here . . . I still worry about distribution and affordability / access. Someone correct me if I’m wrong — has the Fed. govt. ever taken it upon itself to subsidize the distribution and sale of a privately marketed over-the-counter med? Does most private insurance cover the cost of non-prescription medications? And if it’s taken as an aerosol / inhaler, not a conventional nasal spray, that means additional expense to purchase the necessary device. (The suggestion that it could actually be pumped into offices, hotel rooms, and other public spaces sounds risky to me — all it would take would be one allergic reaction, and the lawsuits would kill both the company marketing AeroNabs and whatever business was unfortunate enough to have been involved.)

    If, as suggested here, an immune response might develop in the user after just a few administrations, then its efficacy as a preventive will be extremely limited. It might be useful as an intervention for people who’ve tested positive and/or developed symptoms, but the idea that it might be carried around and used daily to prevent infection on an everyday basis is probably over-optimistic, to say the least. (Of course, we won’t know this for sure until the results of the human trials come in.)

    I also have a question that probably reflects my medical ignorance, for which I apologize — but a lot of people already use nasal sprays, inhalers, aerosols, etc. for sinus problems, respiratory issues, etc. Would it be possible to used AeroNabs on top of this? Or would this be strictly contraindicated?

  29. anon says:

    Dave, if we had had an effective detector of COVID near the beginning of this pandemic, there never would have been a pandemic. Simply detecting the virus would have been enough to almost immediately move down R0 to 0. Imagine how powerful an infectious prevention technology could be if everyone had X-Ray vision and could instantly identify those who were infected. Any time an infected person entered a building, a bus, or even just walked down a street an alarm could sound.

    With such a technology vaccines would be obsolete. As it is the pandemic is costing the global economy $5 trillion per month and a vaccine has still to be distributed. If AeroNabs could offer such a detection feature, then there would be no obvious reason not to market them immediately on production. What public safety concern would be present when no treatment was involved? From first characterization of a new infectious illness to mass production possibly only 1 month would be required. Many nations had 3 months warning of the arrival of COVID and now still have barely controlled local epidemics. An AeroNab detection system (perhaps with a glowing florescent label etc.) would be an ideal technology to protect us from yet another recurrence of the current pandemic.

    1. David G Whiteis says:

      Thank you for your reponse, but I’m confused — I understand that the nanobody treatment can “detect” the COVID virus in order to do its job (so to speak), but how would that affect peope’s everyday life outside of a clinical setting? It won’t be as if someone inhales it and an alarm will go off. (I admit I don’t understaand your “glowing flourescent label” idea.). Only if a person has prsented at a medical facdility, is administered the nanobody solution, and then is assessed to see whether COVID has been “discovered,” will this be effective.

      In other words, what you’re describing is basically another form of “testing.” It’s a lot more efficient than the testing procedures we have right now, but until there’s some kind of mandatory testing for every man, woman, and child in the U.S., I don’t see how it’s going to make all that much difference. Most people don’t go in to get tested unless (1) they think they have symkptoms, and/or (2) they’re planning to visit an elderly relative or someone else whom they know is high-risk and they want to be sure they’re safe.

      Either way, this discussion is a long way frolm the hype we’re getting from UCSF about how AeroNabs will make PPE obsolete, how people will be able to virtually [if temporarily] immunize themselves from COVID with a daily spritz, how it will “reshape the course of the pandemic worldwide,” etc. From what you’re describing here, it will basically serve as a new, improved diagnostic tool that people will have to consult a medical professional to effectively use.

  30. David G Whiteis says:

    ” . . .symptoms,” of course (I DO wish there was an “edit” function here!)

  31. anon says:

    Dave, I am not thinking about treatment at all. “Treatment” is the limiting step in the process. Any treatment typically requires years and years (in actuality decades) of consideration before regulatory approval. Indeed in the current era of clinical trials we are migrating to upwards of 10 years for phase 1 clinical trials. How happy would the people be if this same standard were applied to COVID treatments and vaccines? Avoiding “treatment” means that there are virtually no barriers to entry. It would be highly instructive to see how fast the capitalist system could respond to the opportunity of COVID detectors under such an incentive structure. Turn it in a month? Or less?

    Clearly from the perspective of COVID, AIDS and others the focus on “treating” infectious illness has largely been an abysmal failure. The provocative speculation that I am advancing is to reimagine the problem as something that needs to be treated to something that needs to be detected early. If everyone did have X-Ray vision to detect COVID (even in asymptomatics), then obviously there would never have been a COVID pandemic. More particularly, if ubiquitous COVID detectors were present in the community (e.g., every building entrance, every person with a handheld unit, etc.), then COVID and perhaps all other infectious illnesses could never go viral.

    Essentially the entire community would be under continuous surveillance by everyone else. As soon as an infected person breathed their viral particles into the AeroNab impregnated membrane and this was identified by the detector a five alarm siren could sound, perhaps with an accompanying kaleidoscopic pulsing disco ball, quickly accompanied by arrest and detention in a military hospital until the virus had cleared. Under this scenario, there would not be millions (or more) potential infectees, but perhaps dozens. With intensive, continuous surveillance pandemics essentially become impossible.

    Admittedly, the idea of an AeroNab detector is something of a black box. Anyone with technical insight into how this could actually be realized are encouraged to post. What is also of interest is that such a detector could be constructed such that it could be universal detector of any virus (or possibly other infection). Perhaps one could simply swap out one AeroNab filter for COVID and replace it with one for influenza. I suspect that those in positions of leadership are now highly aware that the tolerance for infectious illness can shift rapidly. How long will it be before people respond to typical “flu” as they have to COVID? Embracing the detection strategy would seem to be one way to demonstrate progressive leadership.

    1. drsnowboard says:

      Not really a ‘land of the free’ solution , is it? Maybe just a twitching stick to wave at everyone over 70 (presidential candidates exempt obviously) or who votes a different way.

  32. As still a newcomer to this blog, one of my more enjoyable pastimes is ascertaining the med chem community’s collective reaction to news items.

    1) Repurposing of existing drug candidates with known safety profiles:
    ( https://blogs.sciencemag.org/pipeline/archives/2020/04/10/more-on-screening-for-coronavirus-therapies )
    Community reaction: ‘Bearish, unwishful thinking’

    2) A completely new drug _class_ with totally
    unknown safety profile and immunogenicity:
    ‘Let’s get this into a therapeutic form and marketed right behind vaccines’

    I would love a social psychologist’s take on what we’re observing here.

    1. Derek Lowe says:

      Your point has something to it. But at the same time, we know from past experience that single-compound antiviral therapies generally have limited efficacy. And the paper you reference is about in vitro screening, and pulled out a lot of frequent hitters, which many of us have been burned by in the past. So that first category is not as intrinsically attractive as it might appear.

      As for the second category, nanobodies are not completely new – there’s one already on the market and several in trials for other indications. And some of the applications for this one don’t even involve systemic human dosing, which helps a great deal.

  33. anon says:

    drsnowboard, the key concession here is that the above suggestion would be a solution. The centuries old default of physical distancing (and possibly in a few months a vaccine) hardly can be described as effective solutions (21st Century or otherwise). Of course, walking back infringements to liberty becomes all too easy when one has a ubiquitous technology with the power of picomolar (or better) potency. Heavy handed responses are more a sign of weakness than strength. Population scale infection detection would not be a weak strategy. Ubiquitous detection technology largely would forestall the emergence of any future pandemic. Humanity could finally enter a post-infectious era which would in itself be a substantial step forward for human freedom.

    What is actually quite astonishing has been how far what would have been until recently considered essentially sacrosanct rights (such as freely walking in one’s own neighborhood) could be compromised by the COVID pandemic (especially as this relates to the solutions that we have applied to counter the pandemic). We followed the prescribed game plan and
    yet our rights still have been widely overridden. Within the conception of universal disease surveillance such infringements could never recur because pandemics could not occur.

    Of further interest is the assumption of who US is (‘land of the free’). If the putative nation of origin for COVID had applied the detection system suggested, then there would never have even been a global pandemic; we probably would not have even been made aware of it. Uncloaking the virus’s identity shield might mean that the dozens of infectees that I referred to above could have actually represented the entire global infection count for COVID. They would have received considerable global esteem if they had actually applied such a tactic. Instead of such a response from fifth dimensional hyperspace, what we have been left with have been the usual list of banalities including the heavy hand of big government and rewriting the rules of regulatory approval: Less of an inspiration, more of a yawn.

    I greatly wish that this suggestion is given at least some consideration by those with the needed technical skills. Can humanity truly not respond more effectively against what might be best described as biological automatons? There have been multiple instances of such pandemics over the last 100 years. In fact, this is the third corona outbreak in the last 20 years. This is our best response after two previous warnings? Would we truly be satisfied to reapply our current “strategy” with similar results if a fourth corona virus pandemic were to emerge?

    It is not entirely obvious, however, whether we will even have a fourth chance. As students experience the freedoms of home schooling and workers avoid the grind of the commute, the un-competitiveness of bricks and mortar reality is becoming all to self-apparent.

  34. Marko says:

    This could be important , if it works :

    “Coronavirus: Test for Covid-19 T cells immunity developed”

    https://www.bbc.com/news/uk-wales-53764640

  35. Marko says:

    Move along , hydroxychloroquine ( and forsythia ). There’s a new miracle cure in town :

    “Trump eyes new unproven coronavirus “cure” ” :

    https://www.axios.com/trump-covid-oleandrin-9896f570-6cd8-4919-af3a-65ebad113d41.html

    1. drsnowboard says:

      Great, Trump moves from The Apprentice mode to ‘Shark Tank’ mode… Supplements industry on a charge to get a piece of the action.

  36. artificial chemist says:

    (Na)Nobodies against the Coronavirus. An adequate description how some countries act against the Pandemic.

  37. exGlaxoid says:

    There is a good summery article in the NY Times about Covids interaction with the immune system, which is a good start for lay persons. It is better than 99% of the news articles that I have seen in terms of having real science in it.

    https://www.nytimes.com/2020/08/11/magazine/covid-cytokine-storms.html

  38. RandomWok says:

    “and found that it can be heated, lyophilized (freeze-dried, basically), and nebulized into an aerosol with no loss of potency”

    That last part, “nebulized” without denaturing the protein can be the tricky show stopper.

  39. anon says:

    Whoa! Whoa! Whoa!

    It might not be progressive anymore to keep score, though here goes.
    I am crediting UCSF with a touchdown for AeroNabs.
    Yet, I am scoring Yale with a grandslam homerun in the bottom of the 9th to push it over the top for the win for SalivaDirect. Good one!

    This is more or less exactly what I was thinking about: a reasonably fast, fairly inexpensive ( a little cheaper would be better) COVID detector (and no nasal surgery required; it’s a saliva test!). Applied at population scale, this could rapidly eliminate the pandemic. Perhaps they could use the ole pooling the sample technique for additional cost savings. Time line? Um, days! Yeah! Life resumes.
    This might be applied to all school children every day at the start of classes with results e

    1. David G Whiteis says:

      Okay, “Stupid Question” time.

      Ideally, at least, people should be tested and re-tested on a regular basis (e.g., I’m tested today, the results come back negative; I’m exposed to the virus next week, but I’m still assuming, on the basis of my “old” test, that I’m safe. You know the rest). How will something like this stop the pandemic unless every person gets tested, re-tested, etc.?

      AND — what good will testing really do if we don’t have quick and efficient contact tracing, as well? If I test positive, I can be quarantined — but what about the dozen or so people I came into contact with in the meantime?

  40. anon says:

    Emergency Use FDA authorization granted August 15th for SalivaDirect.

  41. anon says:

    Great one, Dave!
    Whoa! x 4.

    I had thought that a grand slam in the bottom of the ninth was the zenith.
    I wasn’t expecting something better.
    Heat it for half an hour? No lab? How much?

    Time for the Na Na Na Na Na Na Na Na A A A Goodbye song.

    Basically, if we could all agree to press this for two weeks, it’s over.

  42. anon says:

    Dave, I find it surprising that the conversation has shifted back to vaccines. With a good detection technology there might be no great need for a vaccine. By deploying these diagnostic tests, the pandemic might largely be over before vaccines are approved. All that is needed is a detector that is cheap and convenient; the examples that we have posted largely fulfill these requirements. If they could only be even cheaper and even more convenient, then the pandemic would almost surely disappear as quickly as it appeared (probably even quicker)i.

    Diagnostics have such an overwhelming advantage over medical interventions: There is no treatment involved and therefore no human treatment clinical trials. The test that you mentioned apparently requires no lab; simply heat the sample. This is nearly ideal.

  43. Kris M says:

    It sounds like a great discovery (which my science fiction loving a** automatically ran with and went ‘really hope nobody decides to find a way to weaponized this so it turns against us instead of helping us’… *facepalm* shut up, brain).
    The vaporisation of a room could potentially work wonders in an hospital wings for patient afflicted with the virus

    1. David G Whiteis says:

      . . . and, in theory, hotel/motel rooms, classrooms, offices, etc. Maybe, depending on how concentrated the aerosol would need to be, even larger spaces such as restaurants, lobbies, stores, etc.

      I fear, though, that this is probably one of those “too-good-to-be-true” scenarios. And, again, if even one or two indivduals had an adverse reaction, the resulting lawsuits would be enough to annihilate both the business itself and whatever pharma comany ends up marketing and distributing the AeroNabs.

      The best we could probably do would be for most people to simply have a nasal inhaler or an aerosol device on hand on a daily basis. Ideally, this would be most efficacious for people who weren’t vaccinated, or for whom the vaccine had less-than-optimal efficacy. And again, this would depend upon whether AeroNab would remain effective over multiple administrations/inhalations, which is far from certain.

      1. David G Whiteis says:

        . . . and again, RE: testing — It seems to me that testing is only part of the solution. What good will testing ultimately do without contact tracing? For every “one” person tested, a minimum of two or three others have probably been infected, and then each of them will infect two or three more, etc. ad nauseum/pandemicum. Even with testing, only subsequent contact tracing followed by strict quarantining can stop this endless spiral of contagion.

    2. loupgarous says:

      Tom Mangold’s documentary Plague War refers, I think, to mass immunization using inhaled matter sprayed from an one or more atomizers of some sort developed at a Soviet biowarfare facility in Stepnogorsk, Kazahkstan.

  44. anon says:

    Dave,

    the Yale test would dramatically clear COVID from communities within days if it were applied at population scale. Consider a population of 1 million with COVID prevalence of 1 in a thousand (i.e., 1,000 prevalent infectees). Testing all 1 million in the population would detect 950 of these infectees, while 50 would go undetected (i.e., a 5% false negative rate). Those who tested positive could then isolate until they tested negative.

    The article noted that there was a 0% false positive rate. If the test results are independent, then a second round of testing would find 47 more infectees, while 3 would go undetected again (i.e., double false negatives). So, with one round of population scale double testing the number of prevalent COVID remaining undiscovered is reduced by over 300 fold and has almost reached non-existence.

    Yet, given a daily R0 = 0.1 (i.e., R0 = 1.4/14 days = 0.1/ 1 day), upwards of 100 daily incident infections from the original 1,000 infectees could be expected to continue to incubate and then become infectious for 2 weeks after the double testing were conducted. However, then testing with a single round each day 95 of these new infections would be detected on the first day of conversion to infection. On the second day almost all of those who tested false negative on the first round would be identified. By the above logic, after 2 weeks less than 10 prevalent COVID infectees would remain in the community.

    This would be a remarkably powerful example of reverse exponential growth. We are so accustomed to exponential growth that it is almost difficult to imagine what would happen if it could be put into reverse. For example, the new infections that you noted would not spin out of control ad nauseum/pandemicum as you suggested. With 95% detection and only R0 =0.1 infections/day, population scale with the Yale test would rapidly result in viral extinction.

    The only question that remains is who has enough bandwidth to move this forward and get their society back on track. I suspect Asia could move on this and possibly also Australia/ New Zealand.

    While there is a considerable amount of testing involved, it might not be overly expensive plan. The saliva sample kits only cost ~ $1.5. The cost for the lab work was reported as ~$10. Yet if the process were automated and the samples diluted 10 fold, then the cost might drift down to ~ $1.

    With the above scenario the testing expense could be very reasonable. One might choose to first double test with a non-diluted sample ($10) and on second testing use 10 fold dilution ($1). Regular population screening might then be able to use daily 10 fold dilution ($1). Perhaps even 10 fold dilution would not even be necessary. With only ~ 100 prevalent infections at any given time in the community after the first double round, pooling of 1,000 samples would be expected to have no reported infectees 90% of the time. If the test could give accurate results with 1,000 fold dilution, then the marginal cost for the lab chemical processing could approach ~ $0.01 per test.

  45. David G Whiteis says:

    I will say, though, that I’m irritated with the way most of the “mainstream” media are reporting things like Americans’ willingness to be vaccinated. The latest from NBC — “Less Than Half of Americans Say They’ll Get A Coronavirus Vaccine” — is actually misleading. The data show that Forty-four percent of American adults say they would get the vaccine, 22 percent say they wouldn’t and 32 percent sayi they “aren’t sure” — which, of couse, leaves the possibility open that if a significant number of “undecideds” change their mind, the total uptake rate could be upwards of 70% .

    If that headline had been “Only 22 Percent of Americans Will Refuse a Vaccine,” how much different might the reaction be among readers and viewers? I won’t go so far as to call this “irresponsible reporting,” but with lives on the line, I think it is the responsibiilty of jounralists to give a full and accurate picture, including the nuances.

    1. x says:

      You may as well call it irresponsible reporting; a headline like that has an evident editorial slant, especially viewed in the contexts of thousands of other headlines that also have an evident editorial slant. The pattern becomes too strong to ignore.

  46. Gayle Ashton says:

    AeroNab would be a Godsend for the immune suppressed like a relative who has had a lung transplant. He, and his family, have been in lockdown since the virus arrived. He could use AeroNab and the rest of the family receive a vaccine.

    I understand the concern of those who voiced concerns about availability but first let us make it available and ramp up supply.

    In my youth the thalidomide disaster surfaced. Harm can manifest itself in unexpected ways. AeroNab could be restricted to those who are willing to take a risk, older folks for whom other medications are not suitable.

  47. anon says:

    Ashton, this is a very exciting development. An article linked in the blog post noted that the intention is to move this into a clinical trial with the sickest coronavirus patients. It had been unclear to me whether such treatment potential exists for AeroNabs; apparently it does. If AeroNabs could demonstrate magical levels of clinical efficacy on very ill patients then a months to market might not be entirely unrealistic.

    What is perhaps even more exciting is the idea that this could included as part of a mask. Many of the articles about AeroNabs have emphasized that this is molecular PPE, though what’s so bad about PPE? People are already largely wearing masks. What if they could wear masks with picomolar (or less) potency AeroNab filters? There is some legitimate doubts about how effective cloth masks are in keeping corona away. Absolute protection from an AeroNab mask would crush the virus almost immediately. The bonus is that as a non-medical treatment, the clinical trials that could lead to FDA approval would take considerably less time to complete.

    1. David G Whiteis says:

      Perhaps — but I do believe that a lot of people who are “already” wearing masks would concur that they’re terribly alienating and depressing (it’s “emotional distancing”, just the same way as having to stay physically apart from other people is so-called “social distancing”), and if there were a way to safely replace them with something else that would allow people to see each another’s faces and actually smile at each other again, they’d jump at the chance.

      After all, research makes it very clear that a significant proportion of human communication — especially when it comes to conveying (and feeling) empathy — derives from facial expressions. It isn’t just a matter of person preference — we’ve evolved that way over millennia. It wouldn’t hurt at all to be able to get it back, if we can do so safely.

  48. anon says:

    Dave, I really do not understand what is going on here. The Yale test would rapidly extinguish the COVID pandemic. Basically, buy 10 Yale testing kits for $20 for each member of your household. Everyone in your residence tests last thing on the Thursday before the labor day long weekend and then maximally isolate for the next 4 days. Make it a super long weekend by also taking off the Tuesday and then everyone test again late Tuesday or early Wednesday morning. If everyone tests clear again, then continue with your life with distancing and masking. Test again on Thursday. Take a long weekend on the Friday and lock down until Monday and test again before continuing with life. Test on Tuesday, Wednesday and Thursday and take another long weekend on the Friday. Test again on the Monday and Tuesday of the following week. 10 tests = $100. 5 days of holiday.

    The virus has now been almost completely eliminated from the community. All that is left are the third generation infectees which might amount to a handful of new infections per day. Testing once or twice per week from then on would prevent exponential growth until the vaccine arrives.

    If the test is sensitive enough to detect those who are shedding viruses before they actually become infectious then there might be close to zero infections after 2 weeks of intensive testing. If everyone entering the nation or perhaps passing through internal checkpoints were also screened and tested, then the pandemic could almost be completely halted. Why not at least try this Yale protocol? It’s only 10 saliva samples to start and it could be done largely anonymously. Machine learning and linking the identifiers of the test kits during each testing round, linking the kit numbers for each member of the household along with skill testing questions might allow artificial intelligence to find interesting patterns in the data and optimize the response. Once there were only a handful of remaining infectees extensive contact tracing could be deployed. It is possible that this could entirely stop transmission even before the arrival of the vaccine.

    This is a solid plan. Why is everyone talking about how we will need to bunker down for the next 4 or 5 months, when this could be over in ~2 weeks?

    1. David G Whiteis says:

      What percentage of the population would have to purchase and use this test in order for it to achieve the results you’re suggesting? Remember, we’re talking a GLOBAL pandemic here, which includes millions of people without the wherewithal to purchase ANYTHING. For that matter, that $100.00 price tag you mention would be well beyond the means of most people I know, incuding most of my neighbors here on the West Side of Chicago (to say nothing of the homeless folks sleeping in the alleys and jones-ing on the sidewalks a couple of block south of me).

      With all respect, your constant allusions to “days off,” “long weekends,” “holiday,” etc. make it seem as if you’re suggesting that only employed, financially stable, middle-class folks are giong to be eligible for this.

      Also, even if the kits were given away, this would take a unified mobization unprecedented in human history in order for it to work. Right now, in countries like the U.S. and the U.K., it’s doubtful that more than 50% of the population will agree to get vaccinated, even if it’s free. So now they’re all going to rush out and buy testing kids (which have miraculously all become available at the same time) and immediately start using them (and know exactly how to do so without any instruction or training)?

      And then there are the logistics of making it work. “Machine learning and linking the identifiers of the test kits during each testing round, linking the kit numbers for each member of the household along with skill testing questions might allow artificial intelligence to find interesting patterns in the data and optimize the response” — really? Remember the computer crashes and techno-chaos that occurred when the previous administration in the U.S. tried to roll out the Affordable Care Act? And they had months to set that up. This would have to be operationalized in a matter of weeks in orderc for it to work as rapidly as we’re suggesting here. Redirecting the Normandy Invasion would have been a more feasible project than this.

  49. anon says:

    Dave, each double test removes nearly 100% of the prevalent infectees among the tested. If 90% of the population complied with testing, then even a single double round would remove 90% of those with infection (assuming that those who tested were at similar risk as those who did not test). After this initial testing round, each test during the first two weeks is finding the ~10% background emerging infections every day. By careful testing of the herd and removing those infected through isolation, the herd never experiences run away infection. The Yale test gives the opportunity to rapidly extinguish COVID. Perhaps if people saw how effective testing was then even the COVID dissenters could buy in. It would be a win for everyone.

    There again the days off idea is not an entirely necessary part of the process. I only included that to try and reduce testing days. It would depend on how cost sensitive people were. It
    likely make a great deal of sense for most people to pay even $10 per day than take the day off. If the true test cost was only $1 day with dilution, then the 5 days off plan could be reconsidered. Yet, trying to find a way to make this pleasant might help with compliance.
    I was reading today that for most people after they have the Q-tip rammed 10 inches into their nasal cavity that they usually are not seen or heard from again. If this can be designed
    as a non-medieval torture experience, then people might buy in. Giving a few saliva samples and dropping off the sample in a local easily accessible collection location seems fairly reasonable.

    The $100 is probably as you suggested somewhat steep cost-wise at population scale. The important thing is that it should be affordable across income levels. Yet, the $100 was more about putting the bad news out front and then walking it back. If 10 fold dilution could be used in the testing, then the marginal cost for the lab component of the testing moves towards $1 per test. You could well imagine that at population scale and with dilution that the cost is no longer $100 per capita but perhaps $30. For those who needed some help with the cost assistance could be made available.

    One thing that could also be helpful is that with the skill testing questions one could probably learn a great deal of interesting information that would allow for strategic testing that would optimize the results at a community level. For example, asking about social interactions during the day could allow for stratifying people into risk tiers. There are quite probably people who are orders of magnitude more at risk for infection than others. An optimized testing strategy could be developed through machine learning.

    Even with anonymous testing one could find other patterns that would be helpful for infection control. Consider the drop off point of the sample. If one found that a cluster of infections were occurring in a neighborhood, then this knowledge could feedback to the testers through their web account.

    At $20 for 10 testing kits there would be $3 billion of profit for those interested in supplying the kits. Aside from the saliva collection container the article only mentioned $ .10 worth of chemical. Some of the other commentary on this site about companies not being motivated by profit but by an interest in helping others. I would feel much more comfortable if there were a more visible “invisible hand” at play. I suspect that there might be people who could be motivated to wake up early in the morning to cash in their check for $3 billion to supply the tests. A typical city of 1,000,000 people might only need a minimum of ~100 points of distribution to make the kits widely accessible. Capitalism is a self-organizing system: it is not necessary to have some grand theory directed on a big map. All that needs to happen is that self-interested parties find a mechanism of establishing and fulfilling a contract.
    I want 10 Yale testing kits for $20 — from the article there should be a reasonable profit for whoever can supply me with what I want; how difficult can this be?

    The lab testing might be a little bit trickier. I am not as entirely sure whether the lab testers in my community are strictly driven by market based logic. I suppose that if I was not able to comprehend their system of rationality that China might be all too willing to accept my sample for testing.

    With the machine learning idea all you need is to have an organization that could analyze the data sets that were produced. Their are probably off the shelf programs that could do this. Basically, give the supercomputer a bunch of data and wait to see what they can find. With AlphaGo it was quite surprising what they did find. You could start off by block chaining all of the testing kits for a given person and tying in the test results for everyone in a household. Could also start asking about typical patterns of behavior etc. The computer could then likely develop a fairly accurate model of risk even without the lab tests. The information from the AI model of the epidemic could give powerful insights into how its was spreading. With the very low level of testing that is happening now most of this level of knowledge is not being captured currently. The system must just see waves of people showing up at hospital without a great understanding of what is driving the underlying process at the community level.

    This testing idea would show the magic of capitalism at work. It would be a big project. Yet as Adam Smith noted the butcher baker and others by doing their jobs create all this utility for others even when it might not be their intention. All that needs to happen is for a market
    demand to be expressed: I want my Yale testing kits. Someone interested in making money and that’s about it. All I need to know is what url to go to give my credit card number.

  50. anon says:

    Sorry everyone, many of my above comments were highly misinformed. I only realized this after some online reading about PCR etc. In the Pipeline readers deserve better!

    For example, the total US PCR capability is not 300 million+ samples per day as I suggested but perhaps closer to 10 million per week. It would obviously be a near trivial problem to solve COVID if the installed infrastructure and supply chains were in place– apparently they are not. Perhaps a strategic decision could be made to make this a priority. PCR could be developed into a highly automated highly efficient and cheap technology at population scale. The infectious epdemics that emerge every year could then be controlled rapidly. Instead of ignoring this market (and opportunity) it could be developed into the next technology growth story.

    On further investigation PCR appears to much simpler and cheaper than I could have imagined — basically, heat cool heat cool (repeat). I had thought that perhaps PCR machines could cost upwards of $100,000 each, yet I saw commercially available PCR thermocylcers for $1,000. Some of the DIY projects were even less than $100. The wholesale cost for a round of PCR reported online was $1.50.

    Even more remarkable was LAMP technology which does not even require a thermocycler. Given how basic this technology is, it was not overly surprising to see that some communities have embraced the daily monitoring that I had anticipated. It is critically necessary that our basic government infrastructure (and those who work in it) do not become a focus of an infectious outbreak. It is comforting to know that science can be used on a wider scale to ensure continuity of core government services. The intuition is that this intensive testing could spread more wider so that more of the community including schools, workplaces etc. might also have stronger safeguards against COVID. With such a strategy, it could be imagined that some communities could defeat their epidemic. As I noted above removing ~95% of infections on each daily round of testing would rapidly bring COVID under control.

  51. anon says:

    Lateral flow assays. Cheap, convenient quick. This could be the one. Rumor mill suggests FDA ready to approve over short term.

  52. David G Whiteis says:

    Yes, lateral flow assays do look enouraging. But (as usual, I know!) I have some
    rather serious questions: These can be self-administered at home, right? How do we ensure that someone without symptoms will (1) self-administer multiple tests over the course of a few days to avoid false negatives (https://www.smithsonianmag.com/innovation/scientists-are-racing-to-develop-paper-based-tests-for-covid-19-180975640/); (2) voluntarily self-quarrantine immediately if found positive, and then (3) contact everyone he or she has been with for past week or two, and then (4) stay home for two weeks, and THEN (5) self-report all this to local health authorities, so data can be kept updated? Even countries like New Zealand, where the “social contract” remains a lot stronger than it is in the U.S., have been forced to take people out of their homes and ensconce them in supervized quarantine centers to ensure compliance. (And, of course, distribution and affordability will be issues, as well.)

    Don ‘t get me wrong — these can do a lot of good. MANY people want to get tested (witness those long lines we see), and even more will do so if they can get quick results. But COVID has taught me to be very skeptical about “game-changer” predictions. Every time we think there’ s a game-changer in sight, the damn thing moves the goalposts on us!

  53. anon says:

    Dave, this is exciting! We all can see a game changer when we see it; this looks like a game changer. Cheap, convenient and quick, what is there not to like? All this fancy high end
    science had not brought us the product we need.

    The important point to keep in mind is that it does not require that 100% of the people comply with testing. There are enough people of conscience who will do the right thing.
    My community is worth at least a $1 day to me. I suspect many others feel likewise and if they do then a good mass tester would end COVID.

    For the test…
    The test needs to be cheap; as soon as the price goes over $10, it’s hopeless. It needs to be a price point where essentially everyone could afford repeat testing.

    The test needs to be convenient. Sure some people will wait hours in line for a test. Yet, to make population scale impact testing needs to be reasonably accessible by all.

    The test needs to be quick. Why even bother if the test is going to require days to read out?

    From previous posts it should be easy to predict that a test that can satisfy the above requirements (while also being at least moderately accurate) could have a substantial effect
    on the pandemic. At 20% false negatives, you are still removing 80% of infectees on each testing round. Mass testing would result in rapid exponential decline in the number infected.
    It is not obvious to me how there could be any debate about moving this technology forward.
    Up till this point we have brought the pandemic under control the hard way: distancing, masking etc.. When you add in mass testing, the pandemic would disappear with much less exertion.

  54. David G Whiteis says:

    No, I agree — we definitely need to move this forward. It can help a lot. And combined with a reasonably effective vaccine and a robust uptake, something like this could, indeed, change the game (especially if an aeronabs-type therapeutic were added to the mix).

    Let’s just hope, as I know we all do, that the ugly and egregious politicization of the vaccine rollout we might see doesn’t do irreperable damage to its acceptance.

  55. anon says:

    Dave, this is great news!

    The FDA is on board with innovating our way out of this pandemic.
    Other nations should be encouraged to take up this lead and try some of their own variations.

    The ability to detect 97.1% of infected is well beyond my wildest dreams.
    My impression was that we would talking about a test perhaps ~80% (or
    less). The amount of test result confusion could then have been substantial.
    97.1% & 98.5%? Those are solid numbers. One sweep of the population could
    remove 97% of infected? Very startling. Is this even better than a ~$50 PCR test?

    It was, though, more than somewhat mysterious to me why they did not double
    test the positives. In a low prevalence environment where you test
    1,000 people at a cost of $5,000 you have ~15 false positives. Why wasn’t the
    protocol to retest these 15 positives at a cost of $75 when the test result
    reported back (i.e., in 15 minutes)? Isn’t the whole point to demonstrate that
    this is a cheap, fast test that you can do without great stress and a comprehensive
    analysis?

    We are all left guessing how many of the false positives would revert to negative on second testing. It has to be worth $75 to know. When I crunched the numbers with the assumption
    that all the false positives reverted to negative in a low prevalence environment, the FP/TP
    (did not see a name for this ratio– This ratio tells you the number of false positives
    for each true positives.) went from 154:1 (Ouch!) with a single round of testing to 2:1 with two rounds.

    The low positive predictive value was the first point everyone talked about. This possibly could be easily, quickly and cheaply resolved; then by all means do the research.
    A PPV of ~0 would be a tough sell. This should be clarified (and soon). The false positives disappeared on second testing. This is a critically important point that needs to be investigated.

  56. Aaron Ruby says:

    Instead of therapeutics, could the nanobodies be used in lateral flow tests?
    Appreciate any responses!

    A rapid antigen test using conjugated nanobodies would work like a “pee on a a stick” pregnancy test.

    Saliva has been shown to contain antigens, so a “spit on a stick” test with very sensitive nanobodies would be cheap and fast.

    Conjugated nanobodies were used to detect a porcine Coronavirus (in an ELISA)
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6745792/

  57. Hopeful Layman says:

    A little difficult for me to tell exactly how these findings tie into the development of Aeronabs (I am, as stated, a layman), but it would appear as if nanobodies may become the next major front line in the attack on COVID. According to one of these articles, a COVID-19 nanobody-based treatment is already in preclinical testing in Australia. (Any idea what the timeline might be on developing an actual vaccine?)

    https://www.genengnews.com/insights/camelid-nanobodies-poised-to-revolutionize-antibody-therapeutics/

    https://www.sciencedaily.com/releases/2020/09/200904090314.htm

  58. Hopeful Layman says:

    Here’s another article on more promising nanobody research.

    https://www.thenakedscientists.com/articles/science-features/nanobodies-llama-key-covid-19-therapy

    I’d love to hear people’s opinion — if it took longer than we’re now anticipating to get an effective vaccine (or if a vaccine were approved, but its effectiveness would be somewhere in the low-50% range), but if a good nanobody therapeutic became available, then the scenario that’s been suggested — COVID basically being reduced to the level of a mild flu — could come to pass. That would still mean that a lot of “new” cases would arise, but the vast majority of them could be treated rather easily, and very few people wouild get critically ill. Do you think this would be sufficient for policy makers, both Federal and local, to consider opening up the economy fully, letting bars reopen and having crowds attend athletic events and concerts, etc., loosening “distancing” and masking requirements in most circumstances? Or would public health officials still hold out for a more drastic reduction in cases before a full reopening could be considered? I’m thinking, I guess, of the logistical and financial difficulties with having a constant supply of nanobody therapeutics on hand, throughout the country, for a pretty significant length of time. How much of a boon to our actual everyday lives might this be?

  59. Yago says:

    The solution is Plitidepsin (Aplidin) Ask Nevan Krogan

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