At this point, the countries with most genomic data to analyze spread of the variant virus belonging to https://t.co/ImaHU6Jxdv B.1.1.7 lineage or @nextstrain clade 20I/501Y.V1 are the UK, Denmark and the USA. Here I compare growth rates of B.1.17 across these countries. 1/13

Working from @GISAID data, the UK has 18776 genomes, Denmark has 6089 genomes and the USA has 3093 genomes from specimens collected after Dec 15, 2020. Here, I'm looking at daily genomes with collection dates up to Jan 6 that were not pre-screened by "S dropout". 2/13
For the UK, we can see a steady increase in the frequency of sequenced variant viruses belonging to the B.1.1.7 lineage, reaching ~70% frequency at the end of December. Solid line is a 7 day sliding window average. 3/13
We can fit a logistic growth model to the frequency of B.1.1.7 in the UK data to estimate the rate of frequency increase through time. 4/13
And following @erikmvolz et al (https://t.co/l2ElhJVk8b) we can convert from a measured frequency growth rate to an estimate of increased transmissibility by assuming a particular generation time, which I take to be between 5 days and 6.5 days. 5/13
Doing so gives the following result where the observed saturation of variant frequency is well matched by the logistic growth model with an estimate of logistic growth rate of B.1.1.7 of 0.08 per day corresponding to an increase in transmission rate of 40-52%. 6/13
This result fits with more rigorous modeling studies by Vöhringer et al (https://t.co/i2vY5tp9f9) and @_nickdavies et al (https://t.co/gStjq57mQD), and the 30-50% increase in transmission is supported by secondary attack rate estimates from @PHE_uk (https://t.co/v9WzAaxEC2). 7/13
We can do a similar analysis of genomic data from Denmark where we see an increase in B.1.1.7 frequency to ~3% over the course of December. Sparser bars are due to Denmark releasing specimen collection dates by week rather than by day. 8/13
Using the same logistic growth model, we get a logistic growth rate of B.1.1.7 of 0.07 per day in Denmark corresponding to an increase in transmission rate of 34-44%. 9/13
At the end of December the US frequency of B.1.1.7 was approximately ~1%. Recent samples used in this estimate are largely from New York, California, Wisconsin, Wyoming, Maryland and New Mexico. 10/13
The logistic growth model gives a logistic growth rate of B.1.1.7 of 0.08 per day in the US which corresponds to an increase in transmission rate of 42-55% although this estimate is noisy at this point. 11/13
Similar rates of frequency growth of lineage B.1.1.7 in different geographic contexts support biological increase in transmission rate of the 501Y.V1 variant. 12/13
Near real-time tracking of the spread of B.1.1.7 is possible due to efforts of @covidgenomicsuk in the UK, https://t.co/kTUi50z50e in Denmark and @HealthNYGov, @CedarsSinai, @HealthNYGov, @CedarsSinai, @tcflab, @dho_lab, @health_wyoming, @NMDOH among others in the US. 13/13
Follow up #1: There was a typo in tweet 4/13. The correct logistic growth model is what's shown here (multiply by e^ rather than add by e^ in the denominator). Code is correct, typesetting was off.

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Brief thread to debunk the repeated claims we hear about transmission not happening 'within school walls', infection in school children being 'a reflection of infection from the community', and 'primary school children less likely to get infected and contribute to transmission'.

I've heard a lot of scientists claim these three - including most recently the chief advisor to the CDC, where the claim that most transmission doesn't happen within the walls of schools. There is strong evidence to rebut this claim. Let's look at


Let's look at the trends of infection in different age groups in England first- as reported by the ONS. Being a random survey of infection in the community, this doesn't suffer from the biases of symptom-based testing, particularly important in children who are often asymptomatic

A few things to note:
1. The infection rates among primary & secondary school children closely follow school openings, closures & levels of attendance. E.g. We see a dip in infections following Oct half-term, followed by a rise after school reopening.


We see steep drops in both primary & secondary school groups after end of term (18th December), but these drops plateau out in primary school children, where attendance has been >20% after re-opening in January (by contrast with 2ndary schools where this is ~5%).

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@EricTopol @NBA @StephenKissler @yhgrad B.1.1.7 reveals clearly that SARS-CoV-2 is reverting to its original pre-outbreak condition, i.e. adapted to transgenic hACE2 mice (either Baric's BALB/c ones or others used at WIV labs during chimeric bat coronavirus experiments aimed at developing a pan betacoronavirus vaccine)

@NBA @StephenKissler @yhgrad 1. From Day 1, SARS-COV-2 was very well adapted to humans .....and transgenic hACE2 Mice


@NBA @StephenKissler @yhgrad 2. High Probability of serial passaging in Transgenic Mice expressing hACE2 in genesis of SARS-COV-2


@NBA @StephenKissler @yhgrad B.1.1.7 has an unusually large number of genetic changes, ... found to date in mouse-adapted SARS-CoV2 and is also seen in ferret infections.
https://t.co/9Z4oJmkcKj


@NBA @StephenKissler @yhgrad We adapted a clinical isolate of SARS-CoV-2 by serial passaging in the ... Thus, this mouse-adapted strain and associated challenge model should be ... (B) SARS-CoV-2 genomic RNA loads in mouse lung homogenates at P0 to P6.
https://t.co/I90OOCJg7o
I'm going to do two history threads on Ethiopia, one on its ancient history, one on its modern story (1800 to today). 🇪🇹

I'll begin with the ancient history ... and it goes way back. Because modern humans - and before that, the ancestors of humans - almost certainly originated in Ethiopia. 🇪🇹 (sub-thread):


The first likely historical reference to Ethiopia is ancient Egyptian records of trade expeditions to the "Land of Punt" in search of gold, ebony, ivory, incense, and wild animals, starting in c 2500 BC 🇪🇹


Ethiopians themselves believe that the Queen of Sheba, who visited Israel's King Solomon in the Bible (c 950 BC), came from Ethiopia (not Yemen, as others believe). Here she is meeting Solomon in a stain-glassed window in Addis Ababa's Holy Trinity Church. 🇪🇹


References to the Queen of Sheba are everywhere in Ethiopia. The national airline's frequent flier miles are even called "ShebaMiles". 🇪🇹
A THREAD ON @SarangSood

Decoded his way of analysis/logics for everyone to easily understand.

Have covered:
1. Analysis of volatility, how to foresee/signs.
2. Workbook
3. When to sell options
4. Diff category of days
5. How movement of option prices tell us what will happen

1. Keeps following volatility super closely.

Makes 7-8 different strategies to give him a sense of what's going on.

Whichever gives highest profit he trades in.


2. Theta falls when market moves.
Falls where market is headed towards not on our original position.


3. If you're an options seller then sell only when volatility is dropping, there is a high probability of you making the right trade and getting profit as a result

He believes in a market operator, if market mover sells volatility Sarang Sir joins him.


4. Theta decay vs Fall in vega

Sell when Vega is falling rather than for theta decay. You won't be trapped and higher probability of making profit.