The Analytic Garden

I have thought for a long time that the most likely virus  that might cause a new pandemic would be a coronavirus. We don't yet know how contagious it (SARS-CoV-2) is. We know that it is being spread person to person, but we don't know to what extent.   ~ Eric Toner  I think, with every kind of creature and every kind of human, there is no better. We're all just mutations, and I think that each mutation should be celebrated. ~ Arca The D614G Sars-CoV-2 mutation, mentioned in a previous post , has been in the news again.  The mutation is a single nucleotide change of a A to an G at position 23403 in the reference sequence,  NC_045512 , that causes a non-synonymous  amino acid change from Aspartic acid (D) to Glycine (G). In that previous post, I mention a pre-print describing the mutation. The full article has now been published in Cell. They present some in-vitro data showing possible increased transmissability of  the mutated virus...

Mutation is random; natural selection is the very opposite of random ~ Richard Dawkins Mutations merely furnish random raw material for evolution, and rarely, if ever determine the course of the process. ~ Sewall Wright A specific mutation in the Sars-CoV-2 genome has been in the news lately. This preprint  by Korber et al. describes a mutation, D614G, in the Sars-CoV-2 spike protein. The D614G notation describes a change from the reference sequence Aspartic Acid base to a Glycine at position 614 in the protein amino sequence. This is a non-synonymous substitution caused by a single nucleotide change from an A to a G at position 23,403 in the genome. The position refers to the location in the reference sequence, NC_045512 . The article makes some strong claims, including that this is a new strain and that the mutation make the virus more transmissible and perhaps more deadly. The paper was subject to some debate on scientific twitter and blogs, with a fair amount of push ba...

All countries need to review their strategies now. ~ Dr. Michael J. Ryan, WHO It's literally a new world now, so either we adapt to it collectively as one species or only the privileged healthy will be left to live. And the only way to adapt to a new world is to keep working through mistakes, failures and changes, driven by a sense of community. ~  Abhijit Naskar The NY Times published a great article by   Jonathan Corum and Carl Zimmer describing the  SARS-CoV-2 proteins. It's some of the best popular science writing we have seen.  SARS-CoV-2 genome data keeps arriving at NCBI. This data is extremely important for tracking the mutational history of the virus. On April 4, we downloaded 417 full  SARS-CoV-2  genome sequences from NCBI Virus  in FASTA format along with the corresponding full GenBank files.  We analyzed it right away, but because life under social distancing sometimes requires some tricky management, we haven't...