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??

@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?

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/journa…
Consequences for virus evolution: interesting.....

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 Peter.Simmonds@ndm.ox.ac.uk

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/10.110…

Compared to WT, B.1.1.7 shows no intrinsic replication advantage but viral loads remain high even after Ab seroconversion

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/10.1101/2021.0…

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/10.1101/2021.0…

Vastly expanded evolutionary time frames.....

I don't think persistent replication of SARS-CoV-2 directly causes "long COVID":

ons.gov.uk/news/statement…

but clearly COVID-19 isn't a typical respiratory infection either. See our review of prolonged infections and mechanisms:

microbiologyresearch.org/content/journa…

Recent analysis of SARS-CoV-2:
- Rampant C->U transitions
- high rates of non-synonymous change
- a mutational process likely driven by the host
- APOBEC-like context
- Potential widespread homoplasy

doi.org/10.1101/2020.0…

Spock: It's evolution, Jim, but not as we know it

A low seroprrevalence of SARS-CoV-2 in Scotland - Only 6 from 1000 blood donors screened between the 15th - 23rd March were reactive in pseudotype assay or anti-spike protein ELISA. A great team effort to get this data out

Plant viruses, such as, potato virus Y don't like CpG or UpA dinucleotides inserted into their genomes either.

nature.com/articles/s4159… …

Great work by Ahmad and nice collaborative work with Richard Kormelink and colleagues in Wageningen. The mechanism? ... it can't be ZAP!

How many post-docs does it take to produce a 23 page monster paper in Nucleic Acids Research? Quite a few, a really great team effort and some fascinating new data on CpG, UpA, ZAP, OAS33 and RNAseL - you thought it was simple?
doi.org/10.1093/nar/gk…

Here's a little article we wrote recently. This tries to make sense of the receding timelines of virus evolution - every time a new technology comes along to investigate more and more ancient viruses, the less rapidly they seem to have changed from contemporary populations.

Just finished reading this fascinating book. Ostensibly a whole book exposing the factual / methods flaws in ncbi.nlm.nih.gov/pubmed/22923579 . Not exactly a diatribe but any reader would agree it's focussed.

Luckily Bayesian phylogeographic methods work perfectly for virus evolution...

Finally published - fantastic to have worked with Evelien @EvelienAdri
, Rob @RobLavigne1 and Andrew on how phage and eukaryotic taxonomy matches up - using GRAViTy genomics-based assignments as a common benchmark. jgv.microbiologyresearch.org/content/journa…

A further amazing ancient DNA based study from Terry Jones, Barbara Muehlemann and others on the origins and evolution on human parvovirus B19 - close to contemporary strains of B19 were alive and kicking in Eurasia in the early Neolithic. TDRP anyone?
pnas.org/content/early/…

EUROPIC 2018 at Egmond an Zee.
Important session on poliovirus eradication. And a great meeting ahead.

What do you do on a sunny bank holiday? Spend the day at an ENPEN enterovirus workshop. Fantastic meeting thanks Heli, Eeva and Thea.

@Paleovirologist @edwardcholmes I'm sot sure dinucleotide composition metrics are very trendy, but here is the analysis of group II RNA viruses (including flaviviruses) in Colmant et al. mSphere from 2017. Tamana bat virus (arrowed) is clearly associated with the mammalian virus cluster, a long way from ISFs,

Finally published, a relatively robust bioinformatic way to classifiy viruses at the Family level in the ICTV taxonomy

rdcu.be/HpD3

Including a working machine, as imagined by Pakorn (Gahn) Aiewsakun

A small philosophical discussion into the use of the "species" term in virology and perhaps why views are so polarised about it!!

jgv.microbiologyresearch.org/content/journa…