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Data — sequence accessions and reproduction

Raw nucleotide sequences are not redistributed in this repository (they exceed GitHub size limits and, for SARS-CoV-2, are subject to GISAID terms of use). Instead, the exact accession lists used in the manuscript are provided in accessions/ so the analysis can be reproduced from public databases.

Accession files

File Rows Source Class label
accessions/sars_cov2.tsv 278,738 NCBI GenBank variant
accessions/hiv1.tsv 12,223 Los Alamos National Laboratory HIV Sequence Database (also indexed in GenBank) subtype
accessions/hcmv_UL55.tsv 399 NCBI GenBank genotype
accessions/hcmv_UL73.tsv 646 NCBI GenBank genotype
accessions/hcmv_US28.tsv 443 NCBI GenBank genotype

For SARS-CoV-2 and HIV-1 the accession lists are shared across all analysed genes (one TSV per virus). For HCMV the genotype assignment depends on the gene, so each gene has its own TSV.

Reproducing the FASTA files

A helper script downloads the genomes and extracts each gene region using the GenBank annotation already shipped under data/<Virus>/<Gene>/:

pip install -r requirements.txt           # includes biopython
python scripts/fetch_sequences.py --email you@example.com --virus hcmv
python scripts/fetch_sequences.py --email you@example.com --virus hiv1
python scripts/fetch_sequences.py --email you@example.com --virus sars_cov2

Outputs are written to data/<Virus>/<Gene>/sequences.fasta with the header format expected by the pipeline:

>accession|Virus|Gene|class

NCBI rate limits apply (3 requests/sec without an API key, 10/sec with). For the SARS-CoV-2 dataset (≈278k sequences) consider supplying an API key via --api-key or, for production-scale runs, the NCBI datasets CLI or the EBI ENA bulk download.

Reference annotations

Each gene folder contains the GenBank annotation file used as the alignment target:

Virus Reference accession File
SARS-CoV-2 (Wuhan-Hu-1) NC_045512 data/Severe_acute_respiratory_syndrome_coronavirus_2/<Gene>/NC_045512.gb
HIV-1 (HXB2) AF033819 data/Human_immunodeficiency_virus_1/<Gene>/AF033819.gb
HCMV (Merlin) FJ616285 data/Human_betaherpesvirus_5/<Gene>/FJ616285.gb

Extraction date

Accession lists were extracted on 2026-02-27. Public databases evolve; some accessions may have been updated, suppressed, or merged since this date.