This track displays amino acid mutations in SARS-Cov-2 strains of high interest, as of January 2021. The mutations were obtained from community annotation (see Credits below).
Track colors are based on strain coloring at Nextstrain.org.
Resources for creating this track from Angie):
Genomic coordinates for 3 of the 4 strains, and it includes deletions: https://virological.org/t/genomic-coordinates-for-b-1-1-7-p-1-and-b-1-351/606 Other: South Africa: https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1 UK: See also: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=lineageB_1_1_7_US#Description B.1.1.7 * also known as "the UK strain" and "Variant of Concern (VOC) 202012/01" (Public Health England) and "501Y.V1" (shortened version of Nextstrain name) * Nextstrain has gone through a couple names for this one: first 20B/501Y.V1, and then it was promoted to its own letter (I), so now it's 20I/501Y.V1. * initial report on virological.org which lists the protein-changing mutations: https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 B.1.351 * also known as "the South Africa strain"; Nextstrain 20H/501Y.V2 * initial report on virological.org: https://virological.org/t/a-preliminary-selection-analysis-of-the-south-african-v501-v2-sars-cov-2-clade/573 P.1 * also known as "the Brazil strain" or sometimes even "the Japan strain" since it was also detected in Japan in some travelers returning from Brazil, and maybe some journalists' attention spans were too short to catch the Brazil part? Another reason that naming a strain after one of the places it's detected is not ideal. * Nextstrain: 20J/501Y.V3 * initial report on virological.org: https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586 B.1.429 * also known as "the California strain"; initially said (in NYTimes and Washington Post) to come from Denmark, I believe because of this tweet. The part of that tweet about Michigan and Denmark was incorrect; each of those sequences had only one of the "triad" of Spike mutations. Earliest appearance of triad, at least in the 493 sequences that I downloaded from GISAID a couple days ago, included quite a few other mutations and was first seen in a couple sequences from LA collected in July (if we can believe the dates... those samples were already as diverged from the base branch as other samples from November and December). * If there's a Nextstrain designation for it, I don't know of it. It's a tiny little slice of 20C. * AFAIK Cedars-Sinai beat UCSF to releasing a pre-print if not Twitter, the medRxiv manuscript we looked at: https://www.medrxiv.org/content/10.1101/2021.01.18.21249786v1.full.pdf * The authors of that manuscript made up their own name "CAL.20C". I'll follow up with an email about the commands that I ra
Virological.org: A discussion forum for analyosis and interpretation of virus molecular evolution and epidemiology Andrew Rambaut, ARTIC Network
Wenjuan Zhang and colleagues at Eric Vail Lab, Cedars Sinai Medical Center, Los Angeles