As reminders…

Alpha–Variant first identified in the UK

Beta–Variant first identified in South Africa

Gamma–Variant first identified in Brazil

Delta–Variant first identified in India

This will be legit short this time–the 4th of July fell on a Sunday this year, and I am sure just about everybody’s work recognized it on the 5th, making this week the prime week for people to be still out on vacation. Many of our Euro readers are also likewise probably fairly focused on the Euro 2020 soccer semi-finals, as the tournament has really seemed like the first semblance of normalcy for the continent since last year.

–So, around the horn, delta variant has come to dominate new cases around the globe (including the US) almost completely as it dominates COVID headlines. That said, at least in the US, overall cases are flat to declining, and headlines are generally emphasizing the occasional hot spot–like one place in Missouri whose hospital beds are fully than they would prefer, but are not overwhelmed yet. Yes, declining, with even Epiforecasts currently showing the r for the US is likely a little under 1.0

We’ll see how that holds up. The next two weeks will be critical, as my gestalt is that most people have been out and about (including the unvaccinated with no known previous infection) around the holiday. If there is going to be any delta bump in the US, we’ll see it over the next two weeks.

–Some sad trombone headlines about the US missing the Biden Administration’s arbitrary vaccination target, and how the much publicized lotteries and the like (such as in Ohio) to encourage vaccination did not have much of an effect on rates. When you drill down on the “vaccine hesitant” population in the US, they are largely young adults and/or Hispanic/African American minorities.

Again, for all the headline and article angst politicizing vaccination, those demographics are not exactly enriched for “red” voters.

Most young adults without underlying conditions don’t feel especially threatened personally by COVID (which, by the numbers, is tough to argue is more than a bad flu for them) but do worry about side effects (despite, for example, the risk of myocarditis from COVID still greatly exceeding the chance of myocarditis from the mRNA vaccines). The other populations are typically hesitant because of rural location and immigration status for themselves and their families, or totally understandable mistrust of anything health related from the government after the Tuskegee Syphilis Study. That’s worth reading if you have never heard of it, because it is the textbook example for everything done wrong ethically in a biomedical study, and is the reason all of us get training in medical school (with frequent mandatory refreshers, especially if you have to submit anything to an institutional review board) on bioethics, and the reason you have 8,000 checklist items on any institutional review board submission for any study you want to run to try make sure this doesn’t happen again.

So yes, it is still very frustrating to read politicization articles again this week, when the media is missing a golden opportunity to focus on disparity of access (rural vs. urban and among demographics), effective and inclusive outreach, and how to build trust in the public health system.

–On the plus side, I’m not convinced the vaccination target even matters. Again, there is good evidence in the literature to suggest that people who have recovered from PCR proven COVID have a panoply of SARS-CoV-2 specific antibody and T-cell responses, similar to those generated by vaccination. It’s not clear, but I think studies that we have linked in prior reports are consistent with the idea that those who have recovered from previous infection have immunity to future infection at a level approximating the most effective vaccines. Still not clear medically if you need a vaccine if you have recovered from bona fide, PCR proven infection. I would still expect many countries, for the near future at least, to want to see proof of vaccination, though, before admission to the country–and are not likely to accept proof of previous infection as good enough. Some of those studies we linked earlier, although small and in healthcare workers, also strongly suggest that recovered patients may really only need one dose of the vaccine as a booster.

So why the vaccine focus? Again, I think it’s because vaccine shots out are easier for the government to count. The PCR data is messy, as a plethora of labs across the country are doing it. The antigen tests work in the right setting, but are not as accurate. And we know that some people who got sick with SARS-CoV-2 were never sick enough to -get- tested, and so the total number of “recovered” patients is a guessing game. Vaccines out is not. So vaccination targets are an easy (-ier) way for the government to guesstimate how close to herd immunity a region or nation is.

This is also why delta variant bumps may not be as pronounced as one would expect by vaccination numbers alone if that undervaccinated region had already had a significant SARS-CoV-2 wave and is at or near herd immunity with recovered+vaccinated.

–Going around the horn real quick, Japan decided today to eliminate spectators for the Olympics as it tries to keep delta variant from penetrating the islands too much while it continues a very deliberately paced vaccination effort. South Africa looks solidly on the downswing of its third big (this time delta variant) wave. Indonesia still climbing–same for Russia. The UK appears to be leveling off its delta heavy wave–we’ll have to see.

–In other vaccine news, some conflicting data on vaccine effectiveness versus the delta variant in Israel. Despite a high vaccination rate, new cases are climbing slightly there, and they estimated that the mRNA vaccines may be only 63% effective in preventing symptomatic COVID after two doses. This is contrast to the UK’s NHS, which estimated 88% effectiveness in stopping symptomatic COVID in their patient population. However, the number of cases among the vaccinated in Israel is still very low, so their estimate has HUGE error bars right now (the real effectiveness percentage could be, and probably is, much higher) and testing is not well distributed among the population there, making statistical sampling an issue.

Regardless, the key takeaway is that the Israeli data confirms the NHS data that the vaccines are still HIGHLY effective in preventing severe (hospitalizing) disease from COVID, even among the delta variant–at least 93% reduction in hospitalizations with two doses of the mRNA vaccines.

–In other vaccine news, there is a pre-print article confirming the intuitive circulating this week online. Spike protein sequencing in patients who were infected, but vaccinated, shows fewer new variants than in patients without vaccination who were infected. Since a vaccinated patient is likely to have very mild disease and impaired viral replication (as the antibodies and T-cells effectively cap the number of new virus particles that will be made in a shorter, milder disease course), the virus has fewer “chances” to come up with something new in the spike protein to escape. In contrast, an unvaccinated patient having to mount a completely new immune response will have a higher viral burden and/or a longer disease course, with more total new virus copies produced. Each of those copies is another chance for a spike protein replication oopsie, or mutation. Thus, the authors conclude, by reducing the total viral load over the course of infection, the vaccines are also reducing the chances of new variants appearing.

–Lastly, on the testing front, internet rumors were confirmed when soft drinks (but, interestingly, NOT their individual components) created false positive COVID antigen tests. Apparently, kids were spreading this rumor on the internet as a way to get out of class with a false positive COVID test. Now, this ONLY works on the rapid antigen tests where you put the sample directly onto the test pad–and highlights the limitation of these we discussed long ago. Anything that can convince the antibodies that make up a rapid antigen test that they are close enough to the spike protein of SARS-CoV-2 for the antibody to bind them (or react the binding confirming reagent) will pop as a false positive. Soft drinks, it turns out, can do that.

PCR, on the other hand, is tested very differently, and is -NOT- fooled by soft drinks. It’s just slower and requires more specialized equipment than the rapid antigen tests. But it’s also more sensitive and specific, and why that is the gold standard. Also why I stress “PCR proven” COVID infection when talking about recovered patients, in case you ever wondered.

–That’s it for this week. Your chances of catching coronavirus, in most places in the world, are equivalent to the chances that you should enjoy your summer vacation, whenever and wherever that might be…

<Paladin>