It sounds like the former, but since it wasn't explicitly addressed in the abstract, I thought I'd ask.
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.
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.
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:
https://medium.com/swlh/variants-lineages-and-strains-of-cor...
“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.”