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Tom Peacock Profile picture
Tom Peacock
@PeacockFlu
Virologist. Influenza and Coronaviruses. Typos are intenitonal. Fellow at @Pirbright_Inst and @ImperialInfect
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Apr 20 • 36 tweets • 11 min read
It's been getting on for a year since I wrote this thread - heres a bit of an update of where we are with the evidence for mammal-to-mammal transmission of H5N1s.
What I'm not really able to cover yet is the North American cattle situation - not enough sequencing or epidemiological data has been shared to draw any strong conclusions - see this recent piece by @HelenBranswell This is frustrating to say the least...
Jan 2 • 19 tweets • 6 min read
Thinking about pandemic preparedness, H5N1 has (rightfully I think?) recieved a lot of attention over the last couple of years.

However I think there is another group of flu viruses that most folks working on flu might say pose a higher pandemic risk - swine influenza viruses. Image Swine influenza viruses have recieved a bit of attention recently - with 'cryptic' (ie no know contact with pigs) infections found in the UK and the Netherlands in the last few months
gov.uk/government/new…
Jul 22, 2023 • 33 tweets • 9 min read
There have been some interesting developments with the panzootic (aka a pandemic of animals) H5N1 in mammals over the last few months.

Though I'd write a brief thread covering Polish cats, South American sealions and European fur farms. Image Firstly, a quick situational update on the panzootic in birds. We're now 3 years into this outbreak and the virus is continuing to spread across the world, largely impacting waterfowl and seabirds (including many that are endangered)
Jun 28, 2023 • 11 tweets • 3 min read
Excited to see our paper on coronavirus discovery in UK bats out. Its a cool story with some great multidisciplinary work between conservationists, molecular biologists, bioinformaticians, virologists, structural biologists, and more.

A few things I found interesting below: First off we did find some sarbecoviruses (distantly related to sars1 and 2) that had detecatable human ace2 binding, however this was pretty weak. We also know that it doesnt take that much go switch from weak to strong binding with sarbecos though.
Apr 26, 2023 • 6 tweets • 4 min read
Inspired by some recent discussion we wrote a short report for virological about how one of SARS-CoV-2's accessory proteins (called ORF8) appears to have gone missing over the last year (with @LongDesertTrain and @siamosolocani) What does ORF8 do?

Good question... if you ask 10 different virologists they may give you 20 different answers... in animal models it doesnt seem that important, and variants such as Alpha were missing most of it (but still did fine)...

virological.org/t/preliminary-…
Apr 22, 2023 • 26 tweets • 10 min read
With our new paper just out thought I'd write a brief thread about one of the ways avian influenza virus ('bird flu') adapts to mammals (with a focus on the polymerase).

Will aim to start off simple then get into the weeds!
journals.asm.org/doi/10.1128/jv… The natural host of influenza viruses is wild aquatic birds - ducks, geese, gulls, etc.

Flu is very good at jumping into other species, including mammals like pigs, dogs, horses, and of course humans. Ecology of influenza viruse...
Jan 28, 2023 • 7 tweets • 3 min read
Our preprint laying out the evidence for molnupiravir associated sequences in global sequencing data is now out! medrxiv.org/content/10.110… We believe we've seen strong evidence for onwards transmission of molnupiravir-treated viruses including some quite large clusters.
We would strongly urge public health/genomics bodies to investigate these clusters as this has major implications for any continued use of MOV.
Nov 26, 2022 • 16 tweets • 8 min read
Over the past few months something interesting has happened with the evolution of SARS-CoV-2 - rather than discrete clonal(ish) waves of BA.1, BA.2 and BA.5 we've seen huge diversification of lineages - to explain whats going on we've written a report:
virological.org/t/sars-cov-2-e… First off we've seen continued emergence of 'variant' or 'saltation' lineages - ie lineages with long branch lengths, rooted in older sequences, no genetic intermediates - similar to the origional Alpha, Beta, Gamma and Omicron itself.
Oct 29, 2022 • 6 tweets • 5 min read
Monoclonal antibody (mAb) therapies have been one of the most successful and effective treatments against SARS-CoV-2 during the pandemic. However with the emergence of of variants thier effectiveness has gradually diminished with each new wave. This is exemplified by the most recent batch of variants such as BA.2.75.2, XBB and BQ.1.1 showing resistance to nearly all approved mAbs.

Oct 16, 2022 • 8 tweets • 3 min read
Thread of avian influenza virus (AIV).

First off a PSA - DO NOT touch, handle or attempt to treat suspected sick or dead birds yourself - particularly poultry, waterfowl (ducks, geese, etc) or seabirds. These are VERY dangerous viruses that can infect people and be deadly! Instead if you suspect wild birds or domestric poultry might be infected either call your vet or approapriate veternary health body (for example Defra in the UK - see advice here). rspca.org.uk/adviceandwelfa…
Sep 7, 2022 • 15 tweets • 5 min read
With the BA.5 in the rearview mirror in most places I thought I'd do a quick thread on 'whats next for SARS-CoV-2 variants?' (TL:DR - not really sure but probably a BA.2 offshoot?) First off: BA.2.75 - this is by far the most prevelent new variant out there - its caused a bit of a wave in India but I'm not sure it has the right combination of properties to cause a global wave like BA.5 did.. Image
Jun 30, 2022 • 6 tweets • 3 min read
Surveillence minded folks - worth keeping a close eye on BA.2.75 - lots of spike mutations, probable second generation variant, apparent rapid growth and wide geographical spread...
github.com/cov-lineages/p… Spike mutation-wise its got normal BA.2 mutations + K147E, W152R, F157L, I210V, G257S, G339H, G446S, N460K and reversion of R493Q - none of these individually really flag as that worrying but all appearing together at once is another matter...
Jun 21, 2022 • 4 tweets • 2 min read
Delighted to be a small part of this new consortium trying to work out what on earths been going on with H5N1 avian influenza viruses the last few years! Some context - the last few years have seen mass wild bird die offs and some of the highest numbers of jumps into poultry farms ever seen across Europe (in particular in the UK) nature.com/articles/d4158…
Jun 8, 2022 • 22 tweets • 11 min read
Been a hectic month but we had some new SARS-CoV-2/Omicron preprints out in the last few weeks! going to do a 'quick' thread of some of the highlights from these recent studies... First off we updated our Omicron entry preprint: biorxiv.org/content/10.110…
Headline is - in our hands the entry pathway and antigenicity of Omicron are completely independently encoded by different domains of Spike
Mar 20, 2022 • 5 tweets • 1 min read
Stray thought on what the next variant ('Pi/Rho/Tau') might look like (assuming it eventually comes along).

Heard a few people say 'the only thing we know for sure is it wont look like Omicron' - I think this is largely correct on one level, but maybe an oversimplification... ...I suspect, superficially, the next variant *might* look quite a bit like Omicron - similar numbers of mutations at similar/same amino acid positions - at first glance it might be quite hard to tell apart from Omicron mutation-wise...
Mar 16, 2022 • 34 tweets • 15 min read
With three Omicron-related recombinants getting assigned Pango lineages I'm going to write a thread covering:
- What are recombinants?
- Why are we seeing so many now?
- What exactly are the new lineages XD, XE and XF?
- How concerned should we be about them? Image First off, what are recombinants?
When two related viruses infect the same cell (ie during a coinfection) the viral replication machinery can accidentally switch from one genome to the other resulting in a mixed genome - this is viral recombination. Jackson et al, Cell, 2021
Mar 3, 2022 • 8 tweets • 3 min read
Proud to have been a small part of this really important work that, I think, adds to the body of evidence that chronic infections are potential sources of SARS2 variants. Lots of evidence here but I'm going to write a short thread on one aspect I think is interesting... One of the mutations that repeatedly, independently, arises during known chronic infections is E:T30I, after Spike: E484K, it is the most common mutation we saw in this dataset. (though worth saying it arises during *many*, but not *all* chronic infections) Image
Feb 12, 2022 • 6 tweets • 4 min read
Our paper risk assessing the zoonotic threat from mink/ferret-adapted SARS-CoV-2 is now out in cell reports! Here's a thread I made when it preprinted summarising the paper for those interested in the full details
Jan 19, 2022 • 22 tweets • 6 min read
As its been getting increasing attention recently, I'm going to write a short thread on what we currently know about BA.2.
-what is BA.2?
-what is BA.2 doing currently?
-Should we be concerned about it? First off - what is BA.2?

BA.2 is a sister lineage to BA.1. Currently both lineages are defined as the Omicron variant.

As @shay_fleishon shows - BA.2 shares a lot of mutations with BA.1, but it also has many differences
Jan 9, 2022 • 8 tweets • 3 min read
If anyone wants to check our working out on this (and I encourage people to do so if you are able to!) heres the phylogenetic tree of the sequences not clustering at all: In comparison the actually real recombinant lineage XC (an Alpha/Delta recombinant found in Japan a few months back) forms a really nice, single cluster (in red)
nextstrain.org/fetch/genome.u…
Jan 3, 2022 • 4 tweets • 1 min read
Lots of chat about B.1.640.2 in the last few days - just a few points to keep in mind:
- B.1.640.2 actually predates Omicron
- in all that time there are exactly... 20 sequences (compared to the >120k Omis in less time)
Def not one worth worrying about too much at the mo... and as @shay_fleishon pointed out there havent been any new sequences uploaded since before Christmas... this virus has had a decent chance to cause trouble but never really materialised (as far as we can tell at least...)