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Scientists are closely watching SARS-CoV-2 to track mutations and see if it's developed into different strains. So, has it?

Hosted by: Hank Green

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Sources:

https://www.cdc.gov/flu/prevent/vaccine-selection.htm
https://www.theatlantic.com/health/archive/2020/05/coronavirus-strains-transmissible/611239/
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https://news.cornell.edu/stories/2020/04/why-covid-19-mild-some-deadly-others
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This episode was filmed on May 12th, 2020.

If we have more recent episodes about the COVID-19 pandemic, we’ll include them in the description. Every year, we need to make a new flu vaccine.

That’s because there are multiple strains of the flu, and that one most likely to become a problem changes from year to year. SARS-CoV-2, the virus that causes COVID-19, is much newer than the flu. But as it’s been spreading, scientists have been watching how the virus is mutating to see if it will also develop into different strains.

And knowing whether it has could help us understand how the virus has spread. So, has it? It’s hard to answer this question, partly because “strain” isn’t a super solid concept.

The word doesn’t have a strict definition like, “If its genome is some percent different, it’s a different strain.” Instead, a strain generally refers to an evolutionary lineage of a virus that’s picked up enough mutations that it does... something differently than its cousins. That could be infecting a new species, or spreading faster, et cetera. Now, there are distinct lineages of SARS-CoV-2.

Note that we’re still working with fairly squishy language here; by a lineage we mean any subgroup of the virus we can trace, whether it’s functionally different from its cousins or not. As any virus spreads and reproduces, it naturally picks up mutations. Experts have crunched some numbers from a shared database and found that the virus SARS-CoV-2 actually seems to be mutating relatively slowly, at less than half the rate of the flu.

But mutations are happening. And, actually, studying them can be pretty useful for us. By sequencing and comparing samples of the virus from patients, we can track how different lineages spread over time.

And that can tell us where those lineages have come from. For example, one paper from mid-April found that the genomes of viruses on the West Coast of the United States tend to code for a particular amino acid, aspartic acid, at a certain point in their genome. On the other hand, virus samples on the East Coast tended to have a different amino acid there, called glycine.

This suggested that the viruses on the two sides of the country actually come from two different lineages, named D and G based on the single-letter code biochemists use to refer to those amino acids. And actually, in general, it’s now thought that the virus has been introduced to the US multiple times. Based on following these kinds of changes, it’s now thought the first cases on the West Coast were linked to China, while many early cases on the East Coast may have been more linked to Europe.

Worldwide, there may be several distinct lineages of the virus going around. But whether these lineages act differently from each other, that’s hard to say. It is possible.

Mutations could have all kinds of functional consequences for the virus, if they affect the sequence of its proteins. A mutation could hypothetically make the virus harder to detect, more resistant to certain therapies, or better at infecting host cells. The D to G mutation, for example, affects what scientists call the spike protein, which the virus uses to infect cells.

So it’s been suggested that this mutation could affect the virulence of SARS-CoV-2 — essentially how much damage it does to the human body. A recent preprint paper backed up the idea that this mutation was significant, though they instead claimed it could make the virus more transmissible. And this has been widely reported -- pardon the pun, but it went viral.

However, other scientists have strongly disagreed with both ideas. See, we can’t actually say that the mutation does something… because we don’t know what it does yet. And these papers have left that to other scientists.

Both studies looked at the genetic sequence of the virus. But most molecular biologists will be quick to point out that knowing the sequence of a mutation doesn’t tell you what it does -- what we call functional significance. Instead, they just looked at how those lineages have spread around the world.

While the D lineage is the older one, the G lineage seemed to take over as the predominant lineage in Europe, North America, and Australia after it first appeared in February. This could suggest the G lineage is better at spreading itself around. But not necessarily.

There are lots of other factors that could affect this -- like differences in public health measures between states, and even pure coincidence. Also, the second D-to-G study, as well as some others that have claimed to find a significant change, haven’t gone through peer review at the time we’re making this video. This doesn’t mean they’re wrong, but it means nobody’s really checked their work yet.

See, researchers are in a hurry to understand this virus and save as many lives as soon as possible. That means a lot of papers are being posted to preprint servers and getting a lot of attention before peer review. But that process regularly catches mistakes or shortcomings with the original work, so think of these preprints as sort of a first draft -- one that may never actually get published.

So we really can’t draw conclusions about this mutation yet, because even if a virus has acquired some new mutation in an important protein, a good rule of thumb in biology is that mutations are more likely to break something than be beneficial. And it’s hard to say how any one change can affect complex traits like virulence, which can depend on multiple genes as well as how the host acts. All in all, it’s really hard to say if a mutation will affect how a virus acts or spreads without experiments explicitly designed to investigate this.

In the end, a lot of experts say there just isn’t strong enough evidence to count any branch on SARS-CoV-2’s family tree as a new strain. There are distinct lineages we can pinpoint through genetic sequencing. It’s possible that could complicate vaccine development, though the fact that this virus is mutating relatively slowly hopefully means any vaccine we create now will remain useful for a relatively long time.

But those lineages don’t act differently enough to count as new strains, as far as we know right now. And through careful examination, we can use this to our advantage, helping scientists and health officials understand how the virus is spreading. Thank you for watching SciShow News We already know you like science, because you’re here, so maybe you like SCIENCE PINS?

If so, may I direct your attention to our Pin of the Month. This month, it’s Freedom 7 -- the space capsule that took Alan Shepard safely to space and back in the US’s very first spaceflight. It’ll be available through the end of May and ship at the end of June to give everyone a chance to order.

After that, we’ll reveal a new pin and retire this one -- so keep your eyes peeled. And thanks for your support! [ outro ].