DOI: 10.5061/dryad.5x69p8d2s
title: Ancient viral genomes reveal introduction of HBV and B19V into Mexico during the transatlantic slave trade

description: After the European colonization of the Americas there was a dramatic
 population collapse of the Indigenous inhabitants caused in part by the
 introduction of new pathogens. Although there is much speculation on the
 etiology of the Colonial epidemics, direct evidence for the presence of
 specific viruses during the Colonial era is lacking. To uncover the
 diversity of viral pathogens during this period, we designed an enrichment
 assay targeting ancient DNA (aDNA) from viruses of clinical importance and
 applied it on DNA extracts from individuals found in a Colonial hospital
 and a Colonial chapel (16th c. – 18th c.) where records suggest victims of
 epidemics were buried during important outbreaks in Mexico City. This
 allowed us to reconstruct three ancient human parvovirus B19 genomes, and
 one ancient human hepatitis B virus genome from distinct individuals. The
 viral genomes are similar to African strains, consistent with the inferred
 morphological and genetic African ancestry of the hosts as well as with
 the isotopic analysis of the human remains, suggesting an origin on the
 African continent. This study provides direct molecular evidence of
 ancient viruses being transported to the Americas during the transatlantic
 slave trade and their subsequent introduction to New Spain. Altogether,
 our observations enrich the discussion about the etiology of infectious
 diseases during the Colonial period in Mexico.
description: Dental samples (premolars and molars) from archeological remains
 in Mexico were superficially cleaned with NaClO (70%) and ethanol (70%)
 and later exposed to UV light for 1.5 minutes. The teeth were sectioned
 from the crown and fragmented by mechanical pressure. aDNA was extracted
 from 200 mg of teeth powder by EDTA and proteinase K treatment followed by
 DNA purification by binding to silica in the presence of high
 concentrations of guanidinium thiocyanate
 (https://www.nature.com/articles/nprot.2007.247). NGS libraries were
 constructed following the protocol in Meyer and Kircher 2010
 (https://doi.org/10.1101/pdb.prot5448). Capture-enrichment was performed
 on the indexed libraries using custom designed biotinylated probes to
 pull-down viral aDNA (hybridization at 60ºC during 48h).  Enriched
 libraries were amplified by PCR (18-20 cycles), pooled and deep sequenced
 on an Illumina NextSeq550 (2x75 mid-output). Resulting sequencing reads
 were merged (&gt;11bp overlap) and trimmed with AdapterRemoval 1.5.4.
 Overlapping reads (&gt;30 bp in length, quality filter &gt;30)
 were kept and mapped to the human genome (hg19) using BWA 0.7.13. Unmapped
 reads were mapped to HBV or B19V publicly available genomes using BWA.
 Genome sequences with the most hits (for HBV) or that were covered
 &gt; 50% (B19V) were selected as reference sequence. Unmapped reads
 were aligned to the correspondent reference sequence using BWA. The
 alignment was rescaled for damaged sites using mapDamage 2.0 and a
 consensus genome was produced using SAMtools 1.9.
description: FASTQ files contain the reads mapped to HBV (Ref: GQ331046) or
 B19V (Ref: AB550331) and used to construct ancestral consensus
 genomes.