COVID Transmissions for 2-5-2021
A new variant tracker website, for the data visualization nerds among you
Good morning and welcome to COVID Transmissions.
It has been 445 days since the first documented human case of COVID-19. In the time since COVID-19 first emerged, a typical giant sequoia tree has used about 225,000 gallons of water.
Another weekend is upon us. Enjoy it!
A couple of headlines today about some different online resources regarding COVID-19 and vaccines. And then a reader comment about another online resources. Isn’t the Internet grand?
As usual, bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
Covariants.org
I learned today about a new website that tracks the global distribution of different variants of SARS-CoV-2. Yes, this is super wonky, but it’s also educational. It’s called covariants.org, which you can of course find here: https://covariants.org/
It’ll give you graphs that show the prevalence of different variants over time, in different countries, like this one for 20A.EU1, a variant that emerged in Spain and then became distributed around Europe:
This variant isn’t thought to have any particularly special characteristics. Instead, it is thought to have spread in the way that it did by chance and human behavior. As you can see, the lines are kind of wacky. They look like a kid scribbling on a wall with different crayons—random because there isn’t a clear advantage for this virus lineage over others.
Compare this to the S.N501 mutational cluster, which is associated with a fitness gain for SARS-CoV-2:
See how variants in this group all seem to rise up and then stay high? This is because there is, presumably, some kind of fitness advantage for variants with mutations at position 501.
What this shows me is something that many virologists have been trying to communicate widely since variants first started making the news: that virus mutations are very common, and not all of them are important. Some do have impacts on the fitness of a virus, and some do not. So it’s important that we really make an effort to learn about what a variant does before we start making big claims about it.
Antivax movement misusing the VAERS safety database to undermine public confidence in SARS-CoV-2 vaccines
The US government maintains a database called the Vaccine Adverse Event Reporting System. VAERS is intended to cast a wide net to help find potential safety signals with all vaccines. In order to cast that wide net, it takes any and all reports of safety events, with no confirmation for whether they are true or not. This is important because it helps regulators and manufacturers see what is being most commonly reported without any kind of interference that might discourage reports.
Unfortunately, it also means the database can be abused by bad actors, as is detailed in this piece from Vice: https://www.vice.com/en/article/qjpmp7/anti-vaxxers-misuse-federal-data-to-falsely-claim-covid-vaccines-are-dangerous
I really recommend reading the article, since it spells things out well, but to summarize a take-home point:
Often, antivax agitators will mine this database for the most outrageous events they can find, and then manipulate these unverified reports to scare people. So, if you find anything online that claims unusual adverse events for a COVID-19 vaccine, you need to verify the source. While a government database may appear to have authority, the tool can be abused to serve the cause of misinformation. Be wary.
What am I doing to cope with the pandemic? This:
Annual review time!
I had my annual review at work today, which was my first with this company. It went well, so I’m sort of riding a little high from that.
Carl found us the clinicaltrials.gov page for ENSEMBLE 2:
Don't know if you're interested, but I found the details of the ENSEMBLE 2 trial at clinicaltrials.gov: https://clinicaltrials.gov/ct2/show/NCT04614948
Projected to complete in May. Of course, if they have significant results I'm sure they'll report them early, just like all other vaccine trials to date.
Of course, I had to comment on this and turn it into an opportunity to talk about clinical trial design, because I’m a huge clinical trials nerd:
Cool! You have to be very careful with what you find on clinicaltrials.gov. Not because it contains misinformation, but usually because it contains only the barest bones of information. For example, here it is saying that ENSEMBLE 2 is projected to "complete" in May. Does it say what completion means? Of course not. This may be the longest time they're planning to do solicited safety reporting, or it may be an estimate for when they originally expected to get their full number of disease events. You're right that they may well report earlier than that.
However, it won't be based on whether they have significant results or not. Remember, these are blinded trials. The analyses are prespecified and they are only triggered by prespecified conditions. Usually for a vaccine trial, that condition to trigger analysis is based on a specific number of total disease events, across all trial arms, with the number being chosen based on a desire to achieve about 80% statistical "power" to detect an effect on the primary endpoint. For those who don't read clinical trial statistics all the time, this is a number of events that lets them be about 80% confident that IF there is an effect, they will probably be able to see that effect in the results.
Anyway, they give an estimate for the trial completion, but since it's event-driven, there's no way to know in advance when it will end.
Being event-driven makes the design less prone to bias, though--this way, the folks running the trial don't have any control over the exact period of the trial that is used to analyze the data. The event-driven approach means they must look at a specific period of time, they must perform the analysis they planned before they knew the results, and they cannot manipulate the time window or analysis methods, even subconsciously, to get the result they would prefer to see. Trial sponsors choose this kind of approach in advance to make sure the results are convincing and unbiased.
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See you all next time.
Always,
JS