@Simmonds_Lab
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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
Joined June 2017
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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??
Peter Simmonds retweeted
Before #COVID19, when was the last #coronavirus #pandemic? Some have argued for 1889-1892 for the zoonosis of human #OC43 from bovine coronavirus, but in our new paper: journals.plos.org/plosone/ar…, we suggest 1899-1900, based on a review and replication of existing molecular data.
Peter Simmonds retweeted
Have you ever wondered how nucleic acid editing pathways (APOBEC, ADAR, and epitranscriptomics) might impact the adaptation of zoonotic viruses to humans? Of course you have! Lucky for you, we have a new review in COVIRO considering just that issue: authors.elsevier.com/c/1gtX3…
Peter Simmonds retweeted
The largest study to date on the viruses residing within our tissues
Unmasking the tissue-resident eukaryotic DNA virome in humans academic.oup.com/nar/advance…
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.
These principles traverse a range of seemingly intractable points of disagreement and contention that have bedevilled virus classification since its inception in the 1960s. Resolution of these conflicts provides a clear strategy for harnessing the genomics revolution in virology
Peter Simmonds retweeted
Come and work with some fantastic people (Oxford/UCL) on using genomics to improve safety of transfusion and transplantation: jobs.ac.uk/job/CKU178/projec…
jobs.ac.uk/job/CKV942/post-d…
Fully funded Oxford PhDs:
ndm.ox.ac.uk/study/dphil-the…
Fully funded UCL PhD:
jobs.ac.uk/job/CKJ558/phd-st…
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!
Links for the posts:
In Oxford:
tinyurl.com/6tvz4r8c
tinyurl.com/5b2dvpnh
in UCL:
tinyurl.com/hf2xh6d8
and the PhDs for Oxford:
tinyurl.com/kh822v9v
and UCL:
tinyurl.com/39u2wkpr
Peter Simmonds retweeted
Fantastic thread - we report here a total of 139 EV-D68 cases from Europe, most of them in September and numbers are likely to increase. A timely reminder that you will only find what you are looking for!
1. Europe is seeing an upswing in cases of an infection that has been linked to a polio-like phenomenon called #AFM — acute flaccid myelitis — according to a report today in @Eurosurveillanc. Enterovirus D68 is thought to trigger AFM in some kids. eurosurveillance.org/content…
Peter Simmonds retweeted
Are you ready and looking for it! Did you know EV-D68 is back?
Thankful for the great collaboration! @ENPEN_ESCV @KimBenschop
@TheaKFischer @Simmonds_Lab
@ESCVirology @Eurosurveillanc
eurosurveillance.org/content…
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
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.
Peter Simmonds retweeted
Our review of the ZAP antiviral pathway and how it specifically targets viruses is out in @AnnualReviews. Thank you to @stuartjdneil & @Swanson_Chad. annualreviews.org/doi/abs/10…
Peter Simmonds retweeted
See you there!
The #ESCV2021 Conference is coming to you!
Wherever you are, we can learn together, reshaping our community and raising standards of #ClinicalVirology. More of what you can expect from the #ESCV2021 programme below : ow.ly/L6g450FbmyH
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.....
