SARS-CoV-2 variation data

Data used in The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Darren P Martin, Steven Weaver, Houryiah Tegally, Emmanuel James San, Stephen D Shank, Eduan Wilkinson, Alexander G Lucaci, Jennifer Giandhari, Sureshnee Naidoo, Yeshnee Pillay, Lavanya Singh, Richard J Lessells, NGS-SA4, COVID-19 Genomics UK (COG-UK), Ravindra K Gupta,, Joel O Wertheim, Anton Nekturenko, Ben Murrell, Gordon W Harkins, Philippe Lemey, Oscar A MacLean, David L Robertson,Tulio de Oliveira, Sergei L Kosakovsky Pond

This repository contains compressed and anonymized meta data and sequence variants for SARS-CoV-2 genomes. It is used by as data source by a variety of visualization notebooks, including

1. https://observablehq.com/@spond/sc2-selection-trends
2. https://observablehq.com/@spond/sc2-temporal-selection-trends
3. https://observablehq.com/@spond/spike-trends
4. https://observablehq.com/@spond/sars-cov-2-selected-sites
5. https://observablehq.com/@spond/sc2-prioritization

The contents of the directory are as follows.

1. sequence-info.json : compressed partial sequence metadata.
2. gene/variants-clear.json : unique haplotypes variation for a given gene
3. gene/duplicates-compressed.json : sequence identifiers mapping to a unique haplotype
4. windowed-sites-fel-*.csv: site-level selection analysis results (FEL) for GISAID data analyzed in three-month intervals.

The windowed-sites-fel-current.csv file contains site-level selection data computed with FEL (3-month windows) and that have been found under selection at least once (p≤0.05). Column headers are as follows

1. gene : gene/ORF
2. site : site in gene
3. seqs : number of representative sequences used for analysis
4. from : start of the time interval
5. to: end of the time interval
6. p: p-value for non-neutrality (positve if alpha < beta, negative otherwise)
7. alpha : site MLE estimate for the synonymous rate
8. beta : site MLE estimate for the non-synonymous rate
9. T_int: total length of internal branches in the gene tree used for inference (subs/site)
10. T_total: total length of all branches in the gene tree used for inference (subs/site)

Evolutionary prediction

The file ncov-predictions.json contains evolutionary predictions for codons that are expected to occur in SARS-CoV-2 based on the evolution of nCOV bat/pangolin viruses; this is based on the alignment from Lytras et al This JSON file contains records like

"274": [
  "CTT",
  {
   "CTA": 0.0009359560817146797,
   "CTC": 0.003176408584479247,
   "CTG": 0.0005105015949308743,
   "CTT": 0.995375735314138
  }
 ]

This means that at site 274 (nucleotide coordinates in the SARS-CoV-2 genome), the genomic reference for the virus (Wuhan-1 strain) has codon CTT and the four codons predicted to occur at this codon are CT* with corresponding imputed probabilities (evolutionary "likelihood") shown. When a codon is invariable in nCOV sequences, the second entry will be "null". Sites in SARS-CoV-2 that lack homologous sites in nCOV sequences will not be present (e.g. insertions).