@Simmonds_Lab

Peter Simmonds runs a research group in University of Oxford. Very interested in the broader evolution of viruses and constraints under which they are placed.

 Oxford, England
ndm.ox.ac.uk/principal-investigators/researcher/peter-simmonds
Joined June 2017
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Peter Simmonds@Simmonds_Lab
23 Jun 2024
Here is my re-visiting of the C->U hypermutation phenomenon in SARS-CoV-2 genome 4 years from the start of the COVID pandemic: tinyurl.com/mw3ezp6c A trajectory of loss of C's / gain of U's, but weak 5' context effect and RNA structure dependence on edited sites. APOBEC 3A??
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Peter Simmonds@Simmonds_Lab
19 Feb 2023
Replying to @AdrianJ44426152 @simroux_virus
The downloadable ICTV Virus Metadata Resource contains information of virus names and the taxon they are assigned to: ictv.global/vmr As an example, here is the listing for members of the genus Hepacivirus. Is this what you meant?
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Peter Simmonds@Simmonds_Lab
16 Feb 2023
We believe these principles can be used to create a coherent and logical organisational structure for virus taxonomy that can incorporate the vast diversity of viruses that exist in the world.
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Peter Simmonds@Simmonds_Lab
16 Feb 2023
Four principles to establish a universal virus taxonomy journals.plos.org/plosbiolog… It was a wonderful experience to share a workshop with world experts on virus diversity, genomics and classification.

Four principles to establish a universal virus taxonomy

Transforming an existing phenotypic classification of viruses into one based on evolutionary relationships that can accommodate the vast number of viruses characterized in metagenomics and environm...

journals.plos.org
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Peter Simmonds@Simmonds_Lab
23 Sep 2022
Replying to @ArisKatzourakis @OxfordBiology @alexander_suh
Many congratulations @josegabrielnb , not just for the fascinating and enlightening discussion during the viva, but also for that body of great work on mavericks and virus evolutionary history. A fantastic DPhil! Great also to meet with Alex @alexander_suh, many shared interests
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Peter Simmonds@Simmonds_Lab
23 Sep 2022
Replying to @ArisKatzourakis
Well, the Oxford comma does prevent this (published!) book dedication being misunderstood: To my parents, Ayn Rand and God. Spiritual ancestry indeed! or: Among those interviewed were his two ex-wives, Kris Kristofferson and Robert Duvall I never knew! Thanks Wikepedia,
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Peter Simmonds@Simmonds_Lab
25 Nov 2021
We will be starting a major project to apply genomics to blood and transplant donor microbiology screening. We have project manager, post-doctoral and several funded PhD positions in Oxford and UCL - Apr/22. Great collaborative work with NHSBT: Links to follow Please RT!
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Peter Simmonds@Simmonds_Lab
22 Jun 2021
Very nice article comprehensively reviewing aspects of compositional bias in RNA viruses & interrelationships with still poorly characterised cellular mechanisms responding to RNA sequence motifs - ZAP, APOBECs, ADAR & many more, and selection biases from effects on translation
Elly.Gaunt_lab 💙@GauntLab
22 Jun 2021
1/2 Our review article about genome composition biases in RNA viruses is now online: onlinelibrary.wiley.com/doi/…. TL:DR (it is long): 1. Composition biases occur at mono- and di- nucleotide level and beyond, at amino acid level and codon pairs.
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Peter Simmonds@Simmonds_Lab
2 Jun 2021
Very experimental but also very surprising, here is some evidence for excess C->U changes in a range of mammalian RNA viruses, potentially related to the much discussed phenomenon in SARS-CoV-2: doi.org/10.1371/journal.ppat… Consequences for virus evolution: interesting.....
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Peter Simmonds@Simmonds_Lab
30 May 2021
As some may know, Finnish doesn't have separate b's and p's, so new words may be a bit of a guess - usually right but not always!
Heli Harvala@HarvalaHeli
30 May 2021
Holiday week has started - trying out our new baddleboard and canoe in the Thames. Beautiful day!
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Peter Simmonds@Simmonds_Lab
27 Apr 2021
This adaptive compromise of genome compositions in dual host viruses suggests a potential role for ZAP in defence against arboviruses but is that really all it's there for? Given its evolutionary history, ZAP must have a much more fundamental role in innate immunity but what?
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Peter Simmonds@Simmonds_Lab
27 Apr 2021
We certainly found that for arboviruses, there is is evidence for conflicting evolutionary selection pressures - CpG-high mutants of Zika virus grow better in mosquito cells that WT virus: doi.org/10.1371/journal.pbio…

The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary...

The genome of the flavivirus Zika virus is stuck in a tug-of-war between two directly opposing evolutionary pressures that are present in the cells of mammalian host organisms and mosquito vectors;...

journals.plos.org
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Peter Simmonds@Simmonds_Lab
27 Apr 2021
A fascinating, thoughtful analysis of ZAP evolution, and informative comparative approach across verterbrate lineages. I'm sure I'm missing something here, but you have to wonder what else is involved in its antiviral role if RNA viruses circumvent it by simply suppressing CpG?
Paul Bieniasz@PaulBieniasz
27 Apr 2021
New Paper from @DanSalves and colleagues in #PLOSPathogens: Origin and evolution of the zinc finger antiviral protein dx.plos.org/10.1371/journal.…
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Peter Simmonds@Simmonds_Lab
22 Apr 2021
Job available on Oxford: 1 year post-doc investigating neutralising antibody responses to SARS-CoV-2 infections, serological assay comparisons and their application for COVID plasma and immune Ig treatment. Training in BSL3 working provided - contact [email protected]
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Peter Simmonds@Simmonds_Lab
5 Mar 2021
Some interesting new data on SARS-CoV-2 B.1.1.7 infections from @jeremyratcliff and the lab, @HarvalHeliand & UK REMAP-CAP team medrxiv.org/content/10.1101/… Compared to WT, B.1.1.7 shows no intrinsic replication advantage but viral loads remain high even after Ab seroconversion
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Peter Simmonds@Simmonds_Lab
10 Feb 2021
One of the fascinating implications of the model is how it redates the LCA of HCV to >300,000 BP before humans' Out-of-Africa migration. Maybe HCV did evolve within humans - genotype distributions may partly reflect geograhical /migrational separations doi.org/10.1101/2021.02.09.4…
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Peter Simmonds@Simmonds_Lab
10 Feb 2021
Great to see Mahan @Mahan_Ghafari, Aris Katzourakis's @ArisKatzourakis brilliant PhD student taking on ideas in the Prisoner of War model of virus evolution and putting them into a mathematical framework: doi.org/10.1101/2021.02.09.4… Vastly expanded evolutionary time frames.....
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Peter Simmonds@Simmonds_Lab
18 Jan 2021
Extraordinary data, I do wonder how much long COVID disease is post-replication inflammatory damage and how much originates from ongoing viral replication See our review: doi.org/10.1099/jgv.0.001545 Great to see further virological investigations with more intensive sampling

Understanding the outcomes of COVID-19 – does the current model of an acute respiratory infection...

microbiologyresearch.org
Gisli Jenkins@IPFdoc
17 Jan 2021
Eye watering numbers from Ayoubkhani et al. medrxiv.org/content/10.1101/… 12.7% diagnosed with NEW respiratory disease post discharge (I wonder what that cud b🤔) Readmission & mortality rates post discharge r way 2 high. Need urgent interventional trial! @charlot_summers @mark_toshner
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Peter Simmonds@Simmonds_Lab
17 Dec 2020
I don't think persistent replication of SARS-CoV-2 directly causes "long COVID": ons.gov.uk/news/statementsan… but clearly COVID-19 isn't a typical respiratory infection either. See our review of prolonged infections and mechanisms: microbiologyresearch.org/con…
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Peter Simmonds@Simmonds_Lab
3 Jun 2020
Shared SARS-CoV-2 diversity suggests localised transmission of minority variants biorxiv.org/content/10.1101/…
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