11 votes

Weekly coronavirus-related chat, questions, and minor updates - week of July 4

This thread is posted weekly, and is intended as a place for more-casual discussion of the coronavirus and questions/updates that may not warrant their own dedicated topics. Tell us about what the situation is like where you live!

6 comments

  1. eladnarra
    Link
    Connecticut Patient Had COVID for 471 Days, Evolved 3 New Lineages: Study: The Connecticut cancer patient continuously tested positive for COVID-19 at high levels and appeared to evolve multiple...

    Connecticut Patient Had COVID for 471 Days, Evolved 3 New Lineages: Study: The Connecticut cancer patient continuously tested positive for COVID-19 at high levels and appeared to evolve multiple new lineages of the virus

    5 votes
  2. [3]
    Autoxidation
    Link
    Some extra bad news came from a paper late last month (still in preprint, but the authors are very notable). Research is beginning to get published about multiple covid infections, and early...

    Some extra bad news came from a paper late last month (still in preprint, but the authors are very notable). Research is beginning to get published about multiple covid infections, and early indications look like that damage to the body is cumulative. Reinfection brings greater chance of issues and ultimately death, contrary to other diseases where antibodies generally provide additional protection from further infections. Coupled with the insane increase in immunity escape BA.5 brings, reinfection is possible every 2 to 3 weeks.

    Eric Topol has a concerning article about it here.

    5 votes
    1. eladnarra
      Link Parent
      Yeah, I've been following this type of research relatively closely, and honestly it makes a lot of sense to me. A single COVID infection can often leave you with one or more new medical conditions...

      Yeah, I've been following this type of research relatively closely, and honestly it makes a lot of sense to me. A single COVID infection can often leave you with one or more new medical conditions or exacerbate existing ones, and you might not know at first whether that's happened. COVID hits those of us who have other conditions harder, so anyone who's had COVID once is potentially now in that higher risk group to some degree.

      Not good news, indeed!

      4 votes
    2. FluffyKittens
      Link Parent
      Totally makes sense that damage would be cumulative if you accept the mainstream hypothesis that the majority of long-term sequelae are the product of microthrombi. However, given that they’re...

      Totally makes sense that damage would be cumulative if you accept the mainstream hypothesis that the majority of long-term sequelae are the product of microthrombi. However, given that they’re using purely observational data, there’s some guaranteed heavy sampling bias happening here. The more severe someone’s case is, the more likely it is to get documented.

      I say this not as a criticism or dismissal of the paper, but rather to contextualize it; just take the precise magnitude of the effects they’re reporting with a grain of salt.

      1 vote
  3. skybrian
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    We could have universal COVID vaccines very soon — if we urgently reform the process (Patrick Collision) [...]

    We could have universal COVID vaccines very soon — if we urgently reform the process (Patrick Collision)

    We already have quite good evidence that such approaches can work based on initial mouse and non-human primate data, where robustly protective responses have been generated against a broad variety of sarbecoviruses. (The virus that causes COVID is part of this family.) Furthermore, the underlying nanoparticle platform used in one group’s work, David Veesler’s nanoparticle-based vaccine, has been validated in humans, and just finished a successful Phase 3 trial in South Korea. (The nanoparticle in this trial used a part of the spike protein from the original COVID strain, and isn’t itself a pan-variant vaccine.) But simply embedding slightly different proteins on its surface stands an excellent chance of conferring much broader protection.

    We (Fast Grants) are in touch with a number of these groups. Despite excellent technology and promising early results in animal models, we estimate that the very earliest we will have access to these vaccines in humans is 2024. These groups need to run primate trials, then run human clinical trials, and then ramp manufacturing and distribution. Beyond having to jump through a lot of hoops, we’ve observed that they’re frequently tripped up by stupid things outside of their control, any one of which may hold their work back by months. (One group’s monkeys have been delayed by US Customs, which will push the start of their primate trial back ‘till September. Another is struggling to obtain necessary adjuvants. Multiple groups are unable to get access to current mRNA vaccines for research purposes because of legal barriers.) All groups we’ve interacted with are underfunded compared to what would be ideal.

    Broadly speaking, the holdups involve some combination of logistical challenges and regulatory requirements, and the intersection between both. (You don’t in principle have to run a primate trial, but the FDA makes it harder to run a human trial if you don’t. You don’t in principle need to use “acute infection” as a trial endpoint; you could also use neutralizing antibody titers, which would be much faster and simpler.)

    [...]

    Pan-variant vaccines are a $1 trillion dollar bill on the sidewalk. Some combination of a lack of basic institutional seriousness and self-imposed straightjackets mean that we will probably get these vaccines much later (perhaps years later) than we otherwise could. It is intellectually internally consistent to believe that COVID doesn’t matter and that we consequently shouldn’t care about any of this. But it is not consistent to think that COVID matters and that this situation is anything other than crazy.

    5 votes
  4. skybrian
    Link
    COVID State of Affairs: July 7 (Your Local Epidemiologist) [...] [...]

    COVID State of Affairs: July 7 (Your Local Epidemiologist)

    In India, all eyes are on a new variant: BA.2.75. After first being discovered at the end of May, it quickly took hold and now accounts for 25% of cases, with most samples reported from Maharashtra (Mumbai). There is sparse testing data in India (see the grey bar charts in the figure below), but BA.2.75 appears to be outcompeting BA.5 and BA.2 (with a growth advantage of 17% thus far). This means it has the potential to cause a wave and is important to follow. BA.2.75 cases have been identified in other countries, like Australia, New Zealand, U.K., and Germany, but remain low at this time.

    [...]

    In four short months, four Omicron sub-lineages have come and gone in the U.S. Currently, BA.4/5 made a fast entrance and now accounts for more than 70% of tests. Interestingly, BA.4 stopped (or substantially slowed) growth, so this is really now a story about BA.5. It’s not clear whether BA.5 will result in a wave in the U.S. given our BA.2.12.1 history that other countries did not experience. If we do get a BA.5 wave, it would start about now, so all eyes are on epidemiological trends.

    The U.S. holds a steady state of ~100,000 reported cases per day. This equates to about 1M “true” cases per day, using back of the napkin math. (At the height of the first Omicron wave, we experienced ~3.9M true cases per day). The steady state is reflected in national wastewater with plateauing trends across every region.

    [...]

    The disagreeing patterns between cases/wastewater and TPR could mean that a wave is about to come (historically, TPR trends upwards first). Or it’s a reflection that cases are just a terrible measure of community transmission. Lack of testing, lack of reporting antigen tests, and biased testing (some groups are more likely to get tested than others) are creating really weird trends in metrics. This begs the question: How do we detect a wave at this point in the pandemic?

    4 votes