Pipeline followed for ancient viral genomes reconstruction.
Teeth were fragmented into small pieces to extract DNA from which next-generation sequencing (NGS) libraries were constructed. Reads were separated into human and non-human for downstream analysis. After metagenomic analysis, samples were chosen for viral DNA enrichment and sequencing. Two independent viral DNA capture rounds were joined to reconstruct the ancient genome and estimate damage patterns. Consensus genomes were constructed and aligned to a viral dataset with sequences from different genotypes and geographic regions to perform phylogenetic analysis.