CoV-SARS-2 Genome Tracker

Abstract: Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus CoV-SARS-2 genomes is critical for disease control, outbreak forecasting, and for developing clinical interventions. With CoV Genome Tracker we trace viral genomic changes in real time using a haplotype network, an accurate and scalable representation of evolutionary changes at micro-evolutionary time scale. We resolve direction of mutations by using a bat-associated genome as the outgroup. At the macro-evolutionary time scale, the Genome Tracker provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular targets of clinical interventions.

This is the repository for the CoV-SARS-2 Genome Tracker http://cov.genometracker.org

Outline

1. Download hCoV-19 genomic sequences from GISAID
2. Parse sequences and meta-data using parse-metadata.ipynb
3. • a. Align each hCoV-19 genome to an NCBI reference genome, Wuhan-Hu-1, accession ID NC_045512 with align-genome.sh
   • b. Identify variation sites with samtools and bcftools, and create a haplotype alignment using bcftools using infer-genome.sh
4. Discard haplotypes with missing 10% or more bases then identify haplotype imputing interior missing bases with closest haplotype
5. Build minimum spanning tree for unique haplotypes using hapnet.pl
6. Create a bootstrap alignments and infer networks using hapnet-boot.pl
7. Get consensus network using net-consense.pl

Workflow

Parse metadata

Reads the GISAID hCov-19 sequence metadata and adds geo-location.

parse-metadata.ipynb

It outputs into the following formats:

• covid-19-[current_date].tsv
• covid-[current_date].fasta

align-genome.sh

Align each CoV-SARS-2 isolates from GISAID to the NCBI reference genome Wuhan-Hu-1 (Genbank accession ID: NC_045512)

input: fasta containing hCov-19 genome, reference seq Wuhan-Hu-1, ploidy file, folder name bamfile for non-human sequences, outgroup (sorted bam file).

infer-genome.bash [ covid-[file_date.fasta] ] [Wuhan-Hu-1 reference sequence] [vcf ploidy file] [folder name that contains non-human cov genome bam files] [outgroup bam file]

impute-hap.pl

Estimating missing genotypes from haplotype or genotype reference panel.

• input:
  • SAM file containing haplotypes with each sequence < 10% gaps (any non-ATGC: "n", "." or "-")

impute-hap.pl [input] []

• output
  • log file with the removed sequences with 10% gaps or more
  • sequence type (ST) alignment

hapnet.pl

Reconstruct a network of unique haplotypes This program calculates the minimum spanning tree of a set haplotype.

hapnet.pl