Assoc Prof at Harvard T. H. Chan School of Public Health and Gooner. Currently cosplaying Dr Rieux in some weird re-enactment of La Peste. Tweets are personal
There is a new ‘variant’ clearly identified today, P.1. And it is worth saying a little about what we have learned about it, and from the variants we have identified so far virological.org/t/genomic-char…
First these are not simple ‘mutants’. Mutations happen all the time and most mean nothing much and either persist at low levels or are removed by selection. The variants are characterized by *multiple* mutations – one of the reasons we call them variants and not mutants 2/n
Those multiple mutations are in parts of the genomes that are not exactly the same, but they overlap to a really pretty marked degree (esp the receptor binding domain). This looks like convergent evolution in which different lineages find the same solution by different routes 3/n
(Think bats and birds and their wings for an eg of far more distantly related things coming to a similar solution. One of my rules of evolution is there's usually more than one way to skin a cat, and we can learn from the different ways evolution has skinned cats in the past) 4/n
The variants we are thinking about now all arose independently, but they have things in common. Notably a mutation in the spike protein at the 501 amino acid position. We write it N501Y as shorthand 5/n
Now N501Y is a mutation that has been reported lots of times, because it has happened lots of times (the many millions of cases worldwide do provide the opportunity to mutate) but hasn’t always taken off. Why not if it is allegedly so awesome? (<-rhetorical question) 6/n
It is worth noting that in each of the currently identified variants, this mutation exists alongside *many* others in the same protein and elsewhere in the genome. Almost like it’s not strong enough on its own and needs its friends for support 7/n
This is a comment on a couple things in evolution. First if a mutation happens all the time and is good, why is it not everywhere already? It should have outcompeted everything. One possibility why not is, it has negative impacts too and there is a trade off 8/n
And the fact that mutations at one place in a protein have an impact depending on what else is going on in the protein. They can and do interact. A mutation might be awesome in one context, and meh in another 9/n
Jason Kindrachuk, PhD
Wed Jan 13
Excellent thread from Dr. @BillHanage on the roles of complimentary mutations and the roles they may play in the SARS-CoV-2 variants recently described (and the ones yet to be identified) twitter.com/BillHanage/sta…
**Genomic characterization of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings**
New lineage circulating in Manaus, named P.1, has a unique constellation of mutations, including some w potential biological importance 😷🦠🧬. Read here👇
@EvolveDotZoo @WHO @Tuliodna @MarionKoopmans @mvankerkhove Really nice work @nmrfaria, @ingraclaro, @estercsabino and everyone else who pulled the sequencing and analysis together so quickly. Thank you!
With multiple convergent mutations of biological relevance in spike along with evidence of high frequency in Manaus, we have decided to label the emerging variant described by @caddeproject here virological.org/t/genomic-char… as Nextstrain clade 20J/501Y.V3. 1/2 pic.twitter.com/tgwrwocaoq
Mathematician/epidemiologist at @LSHTM. @WellcomeTrust fellow and @TEDFellow. Author of The Rules of Contagion. Views own.
Worth reading this analysis of new SARS-CoV-2 variant in Manaus by @nmrfaria & co. Shares mutations with new variants in UK and South Africa (although arose independently). Found in 0/26 samples collected Mar–Nov 2020, but in 13/31 (42%) collected mid-Dec: virological.org/t/genomic-char…
"The recent emergence of variants with multiple shared mutations in spike raises concern about convergent evolution to a new phenotype, potentially associated with an increased propensity for re-infection of individuals."
Important report. Manaus largest city in Amazon region severely hit COVID-19 pandemic with estimated SARS-CoV-2 attack rate ~75% by Oct 2020. Still suffering & where new variants may emerge & transmit despite high seroprevalence & presumed immunity.
Ch. Julian Villabona-Arenas
Tue Jan 12
Actualización: El estudio liderado por @nmrfaria @CaddeProject muestra q 42% (13/31) de muestras del estado del Amazonas brasileño (15-23 de dic) hacen parte de un linaje descendiente de B.1.1.28 que contiene varias mutaciones de importancia biológica 1/3 virological.org/t/genomic-char…