Continuing coronavirus happenings (Part 2)

However, the Pima County Health Department has notified TUSD there may not be enough vaccine supply to vaccinate the hundreds of thousands who qualify for the vaccine in phase 1B, which includes prioritized essential workers in education and protective services, essential workers in fields like transportation and government, adults in congregate settings with high-risk medical conditions and individuals older than 75.

Sigh.

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It boggles the mind. You have to put effort into it to achieve this level of callousness with what is going on in California right now.

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Another story about how Ellen loves her staff and how much they love her back

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Here’s the thing, due to the way viruses replicate, and the numbers involved, there are mutations arising pretty much constantly.

SARS-CoV-2 (COVID-19) by the numbers (nih.gov)

7. What can we learn from the mutation rate of the virus?

Studying viral evolution, researchers commonly use two measures describing the rate of genomic change. The first is the evolutionary rate, which is defined as the average number of substitutions that become fixed per year in strains of the virus, given in units of mutations per site per year. The second is the mutation rate, which is the number of substitutions per site per replication cycle. How can we relate these two values? Consider a single site at the end of a year. The only measurement of a mutation rate in a β-coronavirus suggests that this site will accumulate ~10exp–6 mutations in each round of replication. Each replication cycle takes ~10 hr, and so there are 10exp3 cycles/year. Multiplying the mutation rate by the number of replications, assuming neutrality and neglecting the effects of evolutionary selection, we arrive at 10exp–3 mutations per site per year, consistent with the evolutionary rate inferred from sequenced coronavirus genomes. As our estimate is consistent with the measured rate, we infer that the virus undergoes near-continuous replication in the wild, constantly generating new mutations that accumulate over the course of the year. Using our knowledge of the mutation rate, we can also draw inferences about single infections. For example, since the mutation rate is ~10exp–6 mutations/site/cycle and an mL of sputum might contain upwards of 10exp7 viral RNAs, we infer that every site is mutated more than once in such samples.

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Just to clarify, my thinking there is that with enough data points, it might become apparent over time that people with rheumatoid arthritis might enjoy one vaccine less than the others, or some such. Not that I believe any of them will eventually turn out to have serious issues, or that I’d skip vaccination entirely; fuck all that.

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But also:

How to square this circle? My interpretation (and mine alone) is that this variant is more effective in infecting children, but does not cause any more severe illness. Yielding an increased number of pediatric patients, but not necessarily more critically ill pediatric patients. That increases strain on the healthcare system, and gives more fodder for those very rare but devastating complications among kids. Not great, I think.

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That’s promising. My only concern would be other interferon treatments are insanely expensive, but I like the progress.

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… aaaaand Tucker Carlson’s blood pressure just reached steam-engine level.

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Don’t stop.

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Extremely. And if I read that right, the E484K mutation is present in the otherwise not closely/recently related South African strain as well.

Both NPS positive specimens presented a high viral load, presumed by the low cycle threshold (Ct) values in the real time RT-PCR.

Wait, viral load is guesstimated solely by how many amplification runs are required?!?!? Is that the norm?

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In a PCR test, yes. More details here:

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That article keeps mentioning “10 days since the onset of symptoms” but if someone is symptomatic for three weeks, I would doubt they’re safe to make out with for half that time. Or is my first, overly literal reading actually the correct one?

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“Symptomatic” for this illness is not correlated very well with “infectious,” which is the question being looked at. So many symptoms of Covid are related to immune response rather than viral load, and there are folks still symptomatic after months, so yeah, it’s not a great endpoint, but it is reasonable.

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Better late than never…

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that only took … a year

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Well, with Mrs McTurtle gone, things are happening.

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