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Trevor Bedford Profile picture
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11 May, 10 tweets, 4 min read
The drivers of the #COVID19 epidemic in India are certainly multifactorial, but we have now seen the viral lineage B.1.617 linked to this epidemic continue to increase in frequency in India and spread rapidly outside of the country. 1/10
Looking within India there are three primary viral lineages of consequence: B.1.1.7 (in blue) and B.1.351 (in green) introduced into India repeatedly from outside the country and B.1.617 (in yellow) emerging endogenously from within India (nextstrain.org/ncov/asia?c=em…). 2/10
Tracking frequencies over time in sequence data shared to @gisaid shows a continued increase in B.1.617, while recent weeks have shown a decline in B.1.1.7. 3/10
Frequency estimates for April are noisy and end on April 22 due to data availability. There are 883 sequenced genomes for April, but are not strictly in proportion to cases and have a particular geographic focus of Gujarat, Karnataka, Maharashtra and West Bengal. 4/10
Unlike B.1.1.7 and P.1 where mutations comprising the new variant all appeared more-or-less in tandem, the B.1.617 lineage has shown continued evolution since its emergence in mid-2020. 5/10
Basal mutations L452R and P681R exist across the lineage, while sub-lineage B.1.617.1 possesses additional mutations E154K and E484Q and sub-lineage B.1.617.2 possesses additional mutation T478K and commonly 157-158del. 6/10
Looking at frequencies of sub-lineages of B.1.617 shows that the overall increase of B.1.617 is driven by sub-lineage B.1.617.2. Here, we see B.1.617.1 declining at a similar pace as B.1.1.7. 7/10
If we look more broadly, B.1.617 has started to spread beyond India and we observe that among clades in the @nextstrain globally subsampled view, B.1.617 is now the most rapidly expanding clade as measured by logistic growth rate (nextstrain.org/ncov/global?br…). 8/10
This spread can also be seen in frequency trajectories in individual countries. This is particularly striking in the UK where B.1.617.2 was just announced as a variant of concern by @PHE_uk. 9/10
The observed rapid growth of this (sub)-lineage in India and elsewhere would suggest that this virus is potentially highly transmissible. If faster growth than B.1.1.7 in India and in the UK is conclusive, it would suggest that this lineage will spread widely. 10/10

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Trevor Bedford Profile picture
7 May
From Aug 2020 to Mar 2021, the lagged case fatality rate (CFR) of the US #COVID19 epidemic had remained largely constant at ~1.5% and provided a simple method to predict subsequent deaths from current cases. 1/6
I've rerun the previous analysis correlating state-level reported cases with state-level reported deaths with different lags. Using @CDCgov data since Aug 2020, I find that a 19 day lag of cases to deaths maximizes average state-level correlation coefficient. 2/6
This shows the resulting projection for deaths where the gray dashed line shows a lookahead projection where 1.5% of reported cases result in reported deaths 19 days later. This can be compared to the solid red line showing realized 7-day average of reported deaths. 3/6
Read 6 tweets
Trevor Bedford Profile picture
3 May
Just as we can decompose the US #COVID19 epidemic into a B.1.1.7 epidemic and a non-B.1.1.7 epidemic, we can further partition by variants of concern B.1.1.7, B.1.351 and P.1, where it's clear that P.1 has been gaining ground. 1/13
Here, using data from @GISAID, we see that in terms of frequencies across the US, P.1 has been undergoing more rapid logistic growth in frequency than B.1.1.7, while B.1.351 has been slower than B.1.1.7. 2/13
I'm plotting this with the unusual "logit" y-axis (with 1%, 10%, 50%, etc...) because a straight line in logit space is indicative of logistic growth. This sort of plot makes it easy to compare logistic growth rate of frequency between lineages with different frequencies. 3/13
Read 13 tweets
Trevor Bedford Profile picture
26 Apr
There are effectively two #COVID19 epidemics in the US at this moment; one largely resolving epidemic comprised of non-variant viruses and one growing epidemic of B.1.1.7. Together they have resulted in a near-plateau of cases throughout much of the spring. 1/10
If we look at virus frequencies in the US using data in @GISAID, we can see that the 7-day weighted frequency of B.1.1.7 has been growing consistently since January and is now over 50% in the US. 2/10
This pattern is repeated across individual states. These six were chosen as states with plentiful genomic data and to provide geographic diversity. B.1.1.7 is dominating throughout the US, except for New York and surroundings where B.1.526 is co-circulating. 3/10
Read 10 tweets
Trevor Bedford Profile picture
23 Apr
It's hard for me to infer the degree to which new variants are driving the surge in cases in India, but we are seeing rapid growth in frequency of multiple viral variants. 1/5
Here is a @nextstrain view of @GISAID data that focuses on viruses from India and highlights emerging lineages B.1.1.7 (in blue), B.1.351 (in green) and B.1.617 (in orange). Interactive version at nextstrain.org/ncov/asia?c=em…. 2/5
We can fit a logistic growth model to the full genomic dataset from India for these three lineages, where we see logistic growth as "linear on a logit scale". Each of these lineages is estimated to have similar logistic growth rates of ~0.3 per week. 3/5
Read 5 tweets
Trevor Bedford Profile picture
23 Apr
When variants of concern were first identified in late Dec, the US was not where it needed to be in terms of genomic surveillance. However, with considerable ramp up by the CDC, state labs and academic groups, we now have a remarkable genomic surveillance system. 1/14
My favorite metric for genomic surveillance is the number of cases that have been sampled, sequenced and shared publicly to @GISAID in the previous 30 days. By incorporating both sequencing volume and turnaround time, it tells you how much is known about current circulation. 2/14
Throughout the fall, the US had just 100-300 genomes available that were sampled, sequenced and shared in the previous 30 days. 3/14
Read 14 tweets
Trevor Bedford Profile picture
14 Apr
Since their recognition in the UK, South Africa and Brazil in Dec 2020 and Jan 2021, the variant of concern lineages B.1.1.7, B.1.351 and P.1 have continued to spread throughout the world with B.1.1.7 so far the most successful of the three. 1/15
These lineages first received attention due to large numbers of mutations to the spike protein along with rapid increases in frequency in the UK, South Africa and Manaus, Brazil, but much subsequent attention has focused on key mutations E484K and N501Y. 2/15
This figure shows genotype at sites 484 and 501 mapped onto a reference phylogeny of ~4k viruses sampled from all over the world with 484K viruses in light orange, 501Y viruses in blue (including B.1.1.7) and 484K+501Y viruses in dark orange (including B.1.351 and P.1). 3/15
Read 16 tweets

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