Who's ready for some molecular virology?*

SARS-CoV-2, the coronavirus that's causing this pandemic – evolves VERY SLOWLY for an RNA virus. You've probably seen headlines like "There are now 3 strains of the coronavirus" or "8 strains are now circulating the globe."

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All total bullshit.

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TL;DR: SARS-CoV-2 is so far very stable around the world, similar in NYC as it is to Europe and China.

The differences in outcome are not because the virus is different, but because the political leadership in the US sucks and our system wasn't built to handle any shock.

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There is one 'strain' of SARS-CoV-2, and it's everywhere around the world. The image below is of a phylogeny organized as a molecular clock view.

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The x-axis is the time of a viral sample being taken. The y-axis is the number of mutations that virus has from an inferred ancestor, our best guess at the original sequence of SARS-CoV-2 virus in humans.

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The colors denote the geography of where the virus was sequenced (blues: Asia; reds: The Americas; yellows/greens: Europe).

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Please notice the scale on the y-axis. These are individual mutations, single base changes. There are – on average – only about 10-15 single letter changes between any two viruses in the world.

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There are around 30,000 bases – or letters – total in the viral RNA. The level of molecular similarity between these viruses then is 99.95%.

Wow.

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We don't yet understand the effect of selection on the virus. When the virus meets our immune systems, it's under a TON of pressure to evade the response. Get around the immune response and it will make a ton more copies of itself, and that's how evolution occurs.

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There are already clear viral hotspots of evolution, and we need to keep a close eye on any potential differences in viral replication in humans that correlate with mutations at these (or other) locations.

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In this graph, the y-axis denotes the likelihood of a mutation, spikes are 'hot spots'.

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This is especially important due to the sheer number of infections around the world. This gives the virus lots of evolutionary 'space' to try new mutations for phenotypic differences.

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There's a molecular explanation for why this virus evolves so slowly. It's replication machinery, which is uses to copy itself, encodes an error checking domain, which viruses like HIV and flu do not.

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This makes its large genome (30,000 versus around 10,000 for HIV and flu both) much more stable, but also makes the virus evolve MUCH more slowly.

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