One thing isn't clear to me, for lack of background knowledge: have there been several strains since the beginning of the pandemic, or is this study based on evidence of mutation in the wild?
It sounds like the former, but since it wasn't explicitly addressed in the abstract, I thought I'd ask.
This is not my area of expertise, but I think I can help answer the question. Everything mutates a lot, so there is a lot of genetic variability. These are usually pretty minor, but really help with tracing, as you can correlate "family trees" of mutations. The big one early in the pandemic was you could see the difference in the genome between the China/West Coast USA and Europe/East Coast USA infections.
I'm not sure of the strict scholastic definition of a strain, but I think they're derived from branches of that family tree. Most of those branches behave pretty similarly as they have mutations that aren't really impactful, but some of those behave differently, and those are the "strains/variants" we're talking about.
On an interesting note on how genetics are used to target therapies, what researchers can do is look at all the different mutations and they can find parts of the genome that change a lot, and parts that change very little. The parts that change very little are often critical for the function of the virus. Mutations to those still happen, but because of the critical nature of the part that mutated, the virus isn't able to reproduce as effectively and so doesn't show up as often. Researchers can use those as targets for treatments, as disrupting those can impact the effectiveness of the virus.
If I got any of that wrong (or I'm using the wrong vocabulary), I'd love to hear from someone with an actual background in this stuff.
With our current knowledge we can only say that there's only one strain, but they are accumulating changes randomly. Usually those changes are deletereous (bad for the virus), some are neutral and a very minor amount increase the fitness of the virus (good for the virus).
It has been proposed that one of those mutations (D614G) increases the fitness of the virus. If that was the case, viruses with D614G would slowly take over the population. The problem here is that if some "founder effect" [1] happens, it will appear exactly like some mutation gives an increased fitness but what happened in reality was that some guy travelled to a meeting and infected 100 people.
This mutation was first reported in january-2020 in Germany (AFAIK), so it's a very posible that it was just one of the very first viruses to arrive in Europe and "founded" a new population when the virus was spreading almost freely. Then some scientist noted that a lot of european sequences included the mutation and hipotesized that the change was behind the quick spreading of march and april.
Right now, about 80% of the sequences reported to Gisaid include that mutation, but that is about the same percentage than in april/may. I'm personally inclined to believe that D614G is close to have neutral effects, as other variants of the virus without the mutation are also being quite successful in spreading and keeping themselves in the population.
There are thousands of mutations which have been observed. Some are consequential - changing the virus' behaviour - others are not. What constitutes a "strain" is fuzzy, since viruses are constantly evolving and it's an artificial category or human construct. To get away from that, it's often helpful to think in terms of phylogeny or genetic relationships.
You can see a phylogenetic tree of the clades (essentially a "family tree" determined through mutations of the virus) & a map showing the distribution of the different clades of the virus worldwide on GSAID platform:
There have been variants but none so dissimilar that they are considered a new strain. The terminology is very precise here but the media have been mixing it up, causing confusion.
Thanks for this link. From the article she states:
“Mutations that alter any of the following can lead to a new strain:
pathogenicity
virulence
immunogenicity.”
And
“ Another way that the term strain is used is when a particular variant of the virus (the virus with a specific set of mutations) ”
This sounds like the mutation referenced in the paper could be considered a “new strain” given the above?
“ Until there is clear evidence supporting functional or immunogenic differences among the variants, it is appropriate to consider all of these lineages of the same virus.”
It sounds like the former, but since it wasn't explicitly addressed in the abstract, I thought I'd ask.