Thread on COVID-19 variants in Canada 🇨🇦: BQ.1* variants predominate (~85% of lineages estimated today). There are lots of variants circulating in Canada: 289 named PANGO lineages have been posted in the global sequence database (GISAID) since October! Many of the fastest growing lineages in Canada are BQ.1 descendants, such as BQ.1.1.10 with a daily selective advantage of 13%. XBB.1.5, a BA.2* recombinant, is also spreading rapidly, with a selective advantage of 9% (roughly similar to that of Alpha over the original virus).

Variants in Canada update based on GISAID data from today: BQ.1.1 and BF.13 are the fastest growing lineages, each with a selective advantage of 8.5% [95%CI: 6-12%] relative to the main BA.5.2 lineage in 🇨🇦, implying a doubling time of ~8 days. Cautionary notes: Both BQ.1.1 & BF.13 are still rare in 🇨🇦 (<50 sequences) and subject to biased sampling. Other lineages with immune evasion ability are still very rare or not present yet, like XBB (one 🇨🇦sequence in GISAID). 👀

1/ As an evolutionary biologist, I am concerned that Molnupiravir will be a source of multi-step mutations, the effects of which are unknown. Even if most viruses produced are less fit, the concern is the increased risk of a new VOC appearing.

https://twitter.com/sarperotto/status/1457730958619131911

2/ The theory on drugs that increase the mutation rate and push viruses beyond the "error threshold" (where all progeny viruses produced are too riddled with mutations to survive) assume that the virus is already near its fitness peak (not known for SARS-CoV-2) and that

A commentary on #COVID19 Variants of Concern (VOC) in BC. Today's news release reported "90 new confirmed COVID-19 cases that are variants of concern." This severely underreports the actual number. Why? And how bad is it? 1/n The release describes the number of "confirmed" VOC, but with numbers so high BC doesn't have the capacity to confirm so many cases by whole genome sequencing. But we don't need to confirm. Most cases are now screened quickly by PCR for the spike mutation N501Y. 2/n

1/n I've been asked a few times about the math in this recent Science paper, so here's a thread to help unpack it: A mathematical model reveals the influence of population heterogeneity on herd immunity to SARS-CoV-2
science.sciencemag.org/content/early/… 2/n Background: the reproduction number R0 for a disease is how many individuals are infected, on average, by an infected individual, in a fully susceptible population without mitigation measures.

Agreed linkage disequilibrium (LD) is poorly named. LD is a covariance in the alleles found together at two loci. Negative LD refers to a higher chance of carrying a “bad” allele at 2nd locus if a chromosome carries a “good” allele at the 1st locus.

https://twitter.com/rebekahoomen/status/1205112857404334081

Recombination shuffles the loci and breaks down LD (much like shuffling cards randomizes them and breaks down associations, such as clubs being near each other in an unshuffled deck). So what builds LD? Many things - which chromosome a mutation lands on, chance genetic drift...