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…
This should provide at least an initial guide to how a virus (or a virus sequence) might be assigned. It also provides downloadable alignments of informative genes used for classification.
Each chapter is regularly updated, and most virus families are now included.
The online (10th) ICTV Report:
ictv.global/report
provides comprehensive information on the assignment criteria for species and other ranks that are used for each virus family, and a description of the properties of members of each.
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?
I'll let the experts comment here on alignments, but I don't think there is any doubt that RNA viruses possess a homologous RdRp. As described, there is clearly scope for structure-based or other analyses to better define deeper phylogenies. As for cellular reconstructions.....
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.
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
In the end, through collective efforts at the meeting and during writing up, we made some major steps towards understanding each others’ points of view, creating consensus and developing a coherent set of principles that will hopefully guide the wider virology community”
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.
The RdRp is the hallmark gene used for classification of most RNA viruses, homologous and distinct from cellular polymerases. Other realms are based on other gene sets. Analogous to the use of evolutionarily conserved ribosomal genes for deeper taxonomy of cellular organisms?
RdRp is the hallmark gene for the realm of most RNA viruses, clearly homologous and distinct from cellular polymerases. Other gene sets are used for other realms. Analogous to constructing deeper phylogenies of prokaryotes, eukaryotes and archaea using ribosomal genes?
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
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,
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…
Project background:
Genomic Revolutions in Donation Screening and Safety (GRiDDS) is funded NIHR for 5 years and providing resources for a major expansion of genomics-based technologies in blood and transplant donation screening and emerging virus / pandemic preparedness .
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