Trevor Bedford Profile picture
May 11, 2021 10 tweets 4 min read Read on X
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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More from @trvrb

Dec 5, 2022
Currently, the US is reporting about 54k daily cases of COVID-19 (16 per 100k per capita) and the UK is reporting about 4k (6 per 100k). This seems comfortingly low compared to even this summer's BA.5 wave and let alone last winter's BA.1 wave. Figure from @OurWorldInData. 1/16
However, at this point, nearly all infections will be in individuals with prior immunity from vaccination or infection and this combined with a roll back in testing makes it unclear how to interpret current case counts compared to previous time periods. 2/16
We're interested in the case detection rate or the ratio of underlying new infections compared to reported cases. Throughout much of 2020 and 2021, I had a working estimate of 1 infection in ~3.5 getting reported as a case. 3/16
Read 16 tweets
Aug 16, 2022
Largely through partial immune escape, lineage BA.5 viruses resulted in sizable epidemics throughout much of the world. However, in most countries these epidemics are now beginning to wind down. What do we expect after BA.5? 1/10
Lineage BA.2.75 (aka 'Centaurus') has been high on watch lists due to sustained increase in frequency in India combined with the presence of multiple mutations to spike protein. We now have enough sampled BA.2.75 viruses from outside India to make some initial conclusions. 2/10
If we look at frequency data we see sustained logistic growth of BA.2.75 in India, Japan, Singapore and the US. Critically, in India it is clearly displacing BA.5. 3/10
Read 10 tweets
Aug 3, 2022
Based on the experience in winter 2020/2021, seasonal influence on SARS-CoV-2 transmission is quite clear, but much of the Northern Hemisphere is currently experiencing large summer epidemics driven the spread of evolved BA.5 viruses. 1/11
It's necessarily fraught to try to make predictions of seasonal circulation patterns going forwards, but we can gain some intuition from simple epidemiological models. 2/11
In particular, we can use an SIRS system in which individuals go from Susceptible to Infected to Recovered, and then return to the Susceptible class due to immune waning / antigenic drift of the virus. 3/11
Read 12 tweets
Jul 20, 2022
There seems to be a worry that telling people we've exited the "pandemic phase" will lead to further reduced precautions. As always however, I think it's best not to conduct messaging for intended behavioral effect and just try to make scientifically accurate statements. 1/5
Given vaccination and infection, the US and global population now has widespread immunity to SARS-CoV-2 and deaths per-infection are about 10 times lower than they were pre-immunity in 2020 with a ballpark IFR of 0.05% (though this will vary by immunity and age demographics). 2/5
You can see this reduction in mortality rate in looking at projections of deaths from lagged-cases keyed to early case fatality rate. 3/5
Read 5 tweets
Jun 27, 2022
The @US_FDA VRBPAC committee will be meeting tomorrow to discuss variant-specific COVID-19 vaccines (fda.gov/advisory-commi…). Based on present observations, I would argue that the most important metric to optimize are titers against BA.4/BA.5 viruses. 1/10
We've seen repeated replacement of SARS-CoV-2 variants during 2022, first of Delta by Omicron BA.1 and then by sub-lineages of Omicron, with BA.2 replacing BA.1 and now with BA.4/BA.5 replacing BA.2. 2/10
Viruses have been evolving to be higher fitness through both increases in intrinsic transmissibility (seen in BA.2 vs BA.1) as well as escape from existing population immunity (seen in Omicron vs Delta as well as BA.4/BA.5 vs BA.2). 3/10
Read 10 tweets
Jun 3, 2022
Global monkeypox confirmed and suspected cases compiled by @globaldothealth show initial rapid increase as case-based surveillance comes online, followed by slower continued growth. 1/10
This is data from github.com/globaldothealt… and has had a 7-day smoothing applied and all y-axes are shown on a log scale. 2/10
If we focus on the last 11 days, we can see steady exponential growth in global cases with a ~7.7 day doubling. 3/10
Read 11 tweets

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