SARS-CoV-2 Sequence Analysis pipeline
Archived news

Oct 3, 2022
We have released a new update to our listings of SARS-CoV-2 Spike Variants.

Aug 15, 2022
We have released a new update to our listings of SARS-CoV-2 Spike Variants.

Jun 8, 2022
We continue to provide ongoing updates to our listings of SARS-CoV-2 Spike Variants.

Jun 5, 2022
We now provide detailed information about WHO Reference Strains of SARS-CoV-2. This information includes both a spreadsheet describing each sequence, and curated alignments of the reference sequence genomes and Spike proteins.

Jan 9, 2022
Our updated variant reference sequence fasta files for Spike and the full length genome are available through the GISAID downloads, in the LANL folder. These fasta files include reference sequences representative of the most common form of several Omicron variants. The updated spreadsheet describing the sequences and mutations, as well as notes regarding the Omicron updated sequences are available both here in “Curated Variants" and through the LANL page at GISAID.

Dec 5, 2021
Variant forms of Spike among B.1.1.529 complete genome alignments can be found summarized in our Most common spike forms based on Pango lineage designations listings.
Updated notes on Omicron variant dynamics based on GISAID sequences are now available at under the Spike Variants: Notes on Specific Variants. Reference sequence alignments are provided at GISIAD.org. After logging in, they can be found under “Downloads” and “LANL alignment”.

Dec 5, 2021
The issue we were having with consistency of Omicron Spike NTD indel alignments has been resolved. Variant forms of Spike among intact B.1.1.529 complete genome alignments can be found summarized in our Most common spike forms based on Pango lineage designations listings.

Nov 30, 2021
An updated list of Spike variant mutations at the protein level is now available. These are offered as suggestions for reference reagents for experimental testing of commonly circulating Spike variants. The most common forms of Spike for the Omicron variant lineage (B.1.1.529), as well as for the B.1.640 lineage, are now included. See “Spike variants” on blue bar at the top of the pages.
The alignments (fasta files) of natural sequences corresponding to our suggestions for variant reference sequences are now available through the GISAID initiative, for both Spike and for full length coding regions: GISAID.org -> EpiCoV -> Downloads -> LANL alignments.

Nov 29, 2021
Please note: Our automated alignments are currently problematic for Omicron, B.1.1.529, in the regions neighboring the Spike NTD insertions and deletions. We hope resolve this issue by our next update of GISAID data, and apologize for any inconvenience.

Oct 29, 2021
Updated listings of mutations in common Spike Variants are available here, including a brief summary of Delta variants of Spike, including AY.4.2.

Oct 3, 2021
Updated listings of Spike Variants are available here, including a brief summary of Delta variants, Mu, C.1.2, and Gamma variants

Sep 17, 2021
New listings of Spike Variants are available here, including C.1.2, and new interest variants of Delta, Gamma, and Mu.

Aug 22, 2021
Table of the most common natural forms of spike representing variants of interest

• Our cov.lanl.gov listing of commonly found Spike forms of variants of interest and variants of variants that are currently circulating or have transiently emerged in 2021 can be found here.
• A description of the contents and useful addendums can be found here.

Jul 21, 2021
Variant Visualizer is a new tool that provides multiple options and output styles for visualizing CoV-2 variants. Variant Visualizer graphical output is provided as a png or pdf, and the appearance of the output can be refined interactively.

Jul 20, 2021
Three new methods of analysis have been released recently:

• Geographically Restricted Embers
• Geographically Restricted Shiver
• Geographically Restricted Xspike

Jul 7, 2021
Updated Color key to variant forms. This key is used by several of the tools and analytical resources on this site, and is updated regularly.

Jun 20, 2021
Updated Color key to variant forms. This key is used by several of the tools and analytical resources on this site, and is updated regularly.

May 20, 2021
New resources were added:
Geographical Distribution of hCoV-19 variants, tracking the global geographical distribution over time of circulating variants of interest and concern.
Rainbow tree of variants, displaying color-coded variants of interest and concern on a global phylogeny.

Nov 16, 2020
We have added new antibody features to the Variation Summaries (.xlsx) spreadsheet.

Nov 9, 2020
The slides of a talk given Nov. 5, 2020 as part of the Immune Epitope Database (IEDB) annual workshop are available. The slides describe the data included at cov.lanl.gov, and examples of how to use the analyses and tools provided.

Nov 3, 2020
We have released an updated summary of SARS-CoV-2 variation.

Sep 3, 2020
We have released a summary of SARS-CoV-2 variation, with a focus on Spike mutations that might impact antibodies, and considerations for vaccine reagents.

Aug 25, 2020
FAQs and answers regarding the D614G mutation in the Spike protein

May 11, 2020

1. The observation in our preprint, that the D614G mutation was associated with higher viral loads in subjects, but not associated with greater disease severity (indicated by fewer PCR cycles needed for detection, Fig. 5C and 5D of Korber et al., based on clinical data from Sheffield), has recently been repeated by the Bedford lab in Washington: https://github.com/blab/ncov-D614G. So some progress on this issue, of course more work will need to be done.
2. The global pattern of repeated shifts over time from the D614 to G614 variant continues to be supported as data accrues, in dozens of regions in parallel throughout the globe. There is an interesting exception in California, where sequences of the original D614 are currently dominant. That could be explained by a bolus of available sequences from Santa Clara county in late April; D614 is the local epidemic form in Santa Clara county. To see what is happening in California at the county level go to the Tracking Mutations tool, but here is a summary as of today:
   California, a county breakdown: May 11, 2020
3. In our original bioRxiv preprint, we noted that a mutation in Spike at position 943 seemed to be accruing. This position turned out to be a sequence processing artifact, which we have corrected in our bioRxiv preprint.