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Theo Sanderson Profile picture
Theo Sanderson
@theosanderson
Scientific researcher in pathogen genetics. Previously: @GoogleAI, @sangerinstitute 🧪 🤖 🖥️ @theosanderson@mstdn.science / @theo.io on bluesky
2 subscribers
Sep 25, 2023 • 22 tweets • 5 min read
📄 📄 Our molnupiravir work is now out after peer-review! We definitively demonstrate that molnupiravir has resulted in viable SARS-CoV-2 viruses with significant numbers of mutations, in some cases with onwards transmission of mutated viruses. nature.com/articles/s4158… Molnupiravir is an antiviral drug. It works by creating mutations in the virus genome. Since many of these mutations will stop virus proteins from working correctly, molnupiravir can reduce viral load.
Jan 27, 2023 • 18 tweets • 7 min read
💥 New preprint out today

We conclusively demonstrate that mutational events caused by molnupiravir treatment can be seen in globally sequenced SARS-CoV-2 genomes, in some cases with onwards transmission.
🧵
medrxiv.org/content/10.110… Molnupiravir is a drug used to treat COVID-19. Tens of millions of doses have been sold, although recent studies have case doubt on its effectiveness. It works by creating mutations in the virus as it replicates. Image
Jan 11, 2023 • 13 tweets • 7 min read
Now out in journal form: sciencedirect.com/science/articl…

Malaria parasites replicate asexually in the bloodstream, however a subset form ♂️ and ♀️ sexual cell types that when sucked up by a 🦟 undergo sexual reproduction. But how?
🧵 We already knew that a single transcription factor, called AP2-G, is necessary and sufficient to move asexual cells onto a sexual developmental pathway. But why and how do these cells decide whether to become male and female, in the absence of – for example – sex chromosomes?
Aug 5, 2022 • 4 tweets • 1 min read
Anti-nucleocapsid seropositivity (i.e. antibodies that can be acquired only from infection) has gone up from 25% at the start of the year to almost 70% now.

(This underestimates cumulative infection due to waning, and some people not producing measurable anti-N antibodies.) Source: assets.publishing.service.gov.uk/government/upl…
Aug 4, 2022 • 4 tweets • 1 min read
in my continuing quest to describe SARS-CoV-2 sequencing artifacts.. nt:nt:A14960T / ORF1b:N498I / ORF1ab:N4899I looks like it is caused by a primer artifact that affects a small number of sequencing sites sometimes. Looking at the reads it looks like it can sort of be explained by a homodimer, (although I know the mechanism below doesn't quite work)
Jan 13, 2022 • 7 tweets • 2 min read
Today's ONS Infection Survey antibody data breaks up people who are positive into those who have lower (>42 ng/ml) and higher (>179 ng/ml) levels of antibodies, and reveals the effect of boosting A) It's great that they've been agile and are providing this analysis
B) It shows to an extent a limitation of the public data previously available: a large set of continuous datapoints revealing *levels* of antibodies, and how they vary across a population have until now
Jan 10, 2022 • 5 tweets • 2 min read
Rise and fall of SARS-CoV-2 dynasties Methodological details: estimated cases are from covid19.sanger.ac.uk, which (thanks @richgoater) combines genome proportions by local authority with case counts from coronavirus.data.gov.uk (UKHSA). Estimates under 10 cases per week are not plotted.
Jan 5, 2022 • 7 tweets • 2 min read
Interesting paper comparing LFD and PCR performance and finding low sensitivity in first days after positivity even where saliva Cts are low medrxiv.org/content/10.110…

On the face of it, results confusing because sensitivity appears better at higher Cts, but.. [1/3] The Ct data are from saliva, and the LFD results are from nasal swabs. For a small proportion of samples they have paired data from nasal and saliva samples, and those show much higher Cts for nasal than saliva samples very early in infection. [2/3]
Jan 5, 2022 • 5 tweets • 2 min read
Latest release of ONS Infection Survey in London suggests rates in younger people might have peaked (though accompanying text cautions that it is too early to be sure).

Plotted below are central modelled estimates. See ONS data for confidence intervals. ons.gov.uk/peoplepopulati… Data in pivotted form for analyses: gist.github.com/theosanderson/…
Dec 16, 2021 • 6 tweets • 2 min read
71.9% of cases in London with specimens from 13 December were Omicron.

Overall London cases are already reaching the maximum values ever seen in the pandemic. Omicron waves are rising fast throughout England
Dec 16, 2021 • 5 tweets • 2 min read
60% of cases in London for specimens taken on 12 December were Omicron Rising waves in other regions also:
Dec 15, 2021 • 9 tweets • 2 min read
Delta may be decreasing somewhat in incidence in the UK. Is this a direct result of people becoming immune after being infected by Omicron?

An attempt to think through how we could we go about analysing this 🧵 It looked like Delta R might be below 1 in London in data up to specimens taken on 11 December:
Dec 15, 2021 • 4 tweets • 2 min read
Most cases in London with swabs taken on 11 December were caused by Omicron. Caveats around weekday effects and potentially testing capacity, but strong suggestion of R < 1 for Delta (not unexpected given significant NPI changes, and boosting).

R>>1 for Omicron.
Dec 14, 2021 • 4 tweets • 2 min read
Cases in London broken down into separate Omicron/Delta epidemics Code for this: gist.github.com/theosanderson/… Traced data: Source for traced graph: assets.publishing.service.gov.uk/government/upl…
Dec 13, 2021 • 7 tweets • 2 min read
Reckon Omicron as 50% of global cases is only a few days away
Dec 10, 2021 • 6 tweets • 2 min read
UKHSA Technical Briefing 31 reports 3-fold higher risk of houshold transmission for Omicron index case

gov.uk/government/pub… Image Substantially reduced VE vs. symptomatic infection in early data Image
Dec 3, 2021 • 6 tweets • 2 min read
SGTF:
Oct 29, 2021 • 5 tweets • 2 min read
The demise of B.1.1.7 is I think particularly strikingly seen on the timetree mode of Cov2Tree.org And if you're wondering about this grey wave, that extends into the future:

it turns out that sequences arrive on GenBank a little before their metadata. So these are recent sequences without metadata, so the algorithm is estimating a date for them. [1/2]
Oct 29, 2021 • 16 tweets • 5 min read
I have a new preprint out. It describes Chronumental, a tool I've developed that estimates time-trees from very large phylogenies.

Quick 🧵on what that means below, or read the preprint:
biorxiv.org/content/10.110… Trees are a great way to analyse sequence data. A typical phylogenetic tree uses the x-axis to represent the genetic distance between a sequence and its ancestor.

Here is such a tree, from the wondrous @nextstrain.
Oct 26, 2021 • 6 tweets • 1 min read
For the seq geeks: we are seeing a rise in calls of orf1ab:F5086Y / ORF1b:F685Y (&some other mutations - orf1ab:V2857A) this seems to be related to the rollout of ARTIC V4, and to be an artefact. Mostly posting this so people who search for those mutation strings find this info) thanks @alexselby1770 for flagging this
Oct 18, 2021 • 17 tweets • 6 min read
Just out: a dive into the apparent weirdly goings-on at positions 142 (G142D) and 95 (T95I) of Delta SARS-CoV-2 (spoiler: amplicon 72 dropout).

medrxiv.org/content/10.110… One of several mutations found in the Delta lineage is at Spike 142 from G to D. But at first glance it exhibits really weird patterns. For example a recent preprint (medrxiv.org/content/10.110…) points to trees apparently showing mutation back and forth at this pos. within Delta.