New paper: Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny Philip Fowler, 9th February 20269th February 2026 Zam Iqbal, at the University of Bath, led this epic study published today in Nature Methods where we assembled all SARS-CoV-2 genomes deposited in the European Nucleotide Archive before 2 March 2023. In total a staggering 4,395,655 samples were processed. Since SARS-CoV-2 was almost always sequenced using tiled amplicons (e.g. ARTICv3), he and his team wrote viridian which is a variant caller that identifies the amplicon scheme used and then uses that information to avoid making spurious calls. The resulting phylogenetic tree is much more consistent than other trees built from publicly-available consensus sequences. You can explore the huge phylogenetic tree in detail here. Share this: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Related clinical microbiology publication
computing New Publication: Predicting affinities for peptide transporters 29th January 201629th September 2018 PepT1 is a nutrient transporter found in the cells that line your small intestine. It… Share this: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance New publication: Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex 9th March 202016th March 2020 Although the population structure M. tuberculosis is clonal, one must be careful when inferring the… Share this: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance New paper: predicting pyrazinamide resistance 20th March 202420th March 2024 This paper has finally been published and you can find it here. It had a… Share this: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Read More