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Sarah Otto

4 Sep, 3 tweets, 2 min read

1/3 Looking over Alberta’s recently released modelling, I am concerned that policies were based on parameter estimates made back in June, rather than updated to reflect realized rates of COVID-19 transmission following re-opening Stages 1/2/3 and observed impacts of Delta

2/3 It’s important that models be updated regularly to reflect changes in people’s behaviour & the impact of variants. Underestimating transmission rates has two effects: it underestimates cases in the near future & it suggests a population is closer to herd immunity than it is.

3/3 Using out-of-date parameter estimates appears to explain why ICU and hospitalization rates have been much higher than projected in #Alberta. If we wanted to predict the weather, we wouldn’t use model parameters from June. Same goes for #COVID19. alberta.ca/assets/documen…

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More from @sarperotto

Sarah Otto

@sarperotto

2 Apr

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

This preprint describes how BC is typing VOC by PCR. From their data, we can compare the number of VOC cases publicly reported per week to their best estimate from PCR for that week. medrxiv.org/content/10.110… 3/n

Read 6 tweets

Sarah Otto

@sarperotto

6 Jul 20

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.

3/n To keep the disease from spreading in a population, the fraction of susceptible individuals has to be reduced by a factor 1/R0 to exactly balance out the new infections. That means that if a fraction 1-1/R0 were immune (vaccinated or recovered), the disease would peter out.

Read 14 tweets

Sarah Otto

@sarperotto

12 Dec 19

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

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...

and selection. For example if there’s an extra fitness boost for having two good alleles (positive epistasis), positive LD tends to build, so good-good combos are found more often than expected (as are bad-bad): the loci become positively correlated in which alleles they carry.

Read 4 tweets

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