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Tom Peacock Profile picture
@PeacockFlu
Nov 23, 2021 • 9 tweets • 3 min read • Read on X
Just spotted: very small cluster of variant associated with Southern Africa with very long branch length and really awful Spike mutation profile including RBD - K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H

github.com/cov-lineages/p…
Full Spike profile: A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
For those interested this has an NTD insertion at the NTD insertion hotspot (at aa214) which shows high likelihood of being host-derived (from host TMEM245 mRNA) Image
Worth emphasising this is at super low numbers right now in a region of Africa that is fairly well sampled, however it very very much should be monitored due to that horrific spike profile (would take a guess that this would be worse antigenically than nearly anything else about)
for this interested in the relevence/prevenece of similar insertions in SARS2 we wrote a short report on this a few months ago: virological.org/t/putative-hos…
A final observation - this variant contains not one, but two furin cleavage site mutations - P681H (seen in Alpha, Mu, some Gamma, B.1.1.318) combined with N679K (seen in C.1.2 amongst others) - this is the first time I've seen two of these mutations in a single variant...
Small update: this lineage has now been assigned as B.1.1.529:
github.com/cov-lineages/p…
Update on South African situation from @Tuliodna (Who is absolutely the best person to follow for updates on this) - bottom line is B.1.1.529 may already be quite widespread in SA.
*Q493R - rather, not Q493K

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More from @PeacockFlu

Tom Peacock Profile picture
Apr 20
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...
So instead this will mostly be updates on previous (putative) mammal to mammal H5N1 clusters. What do we think now? Whats the state of the evidence.
Read 36 tweets
Tom Peacock Profile picture
Jan 2
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…
Swine influenza viruses with pandemic potential more or less come in two flavours - those with haemagglutinin (HA) and other genes from historic human seasonal influenza viruses - often from 'reverse zoonotic' (human to pig) events from the 1970-1990s
Read 19 tweets
Tom Peacock Profile picture
Jul 22, 2023
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)
Beyond birds though, we're seeing more and more infections in wild mammals that we've ever seen before. This is particularly widespread in scavengers and predators (for example foxes in Europe)
Read 33 tweets
Tom Peacock Profile picture
Jun 28, 2023
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.
We also found that these viruses apparently cant use the ACE2 from the species they were isolated from. This isnt unheard of with sarbecos (particular clade 2) but is a little surprising I think?
Read 11 tweets
Tom Peacock Profile picture
Apr 26, 2023
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-…
Dominant XBB.1 lineages mostly also have a truncated ORF8 (due to a premature stop codon).

As well as this we noticed BA.5 lineages had a mutation in a regulatory sequence that likely stopped ORF8 being expressed Image
Read 6 tweets
Tom Peacock Profile picture
Apr 22, 2023
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...
Avian influenza cannot generally infect and replicate within mammals very efficiently. Because flu is an RNA virus and mutates very fast, it can quickly pick up adaptations. Sometimes these adaptations are enough to even transmit between mammals. Cumulative influenza virus ...
Read 26 tweets

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