Ancient viral genomes reveal introduction of HBV and B19V into Mexico during the transatlantic slave trade

Abstract

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 (16th c. – 18th c.) hospital and a Colonial chapel 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.

Transoceanic pathogen circulation in the age of sail and steam

“…Our analysis indicates that historical processes involving large-scale movement of people were potential watersheds for transoceanic pathogen ecology. This mirrors a longstanding historical literature demonstrating links between war, colonialism, and infectious disease [27,75], as well as recent phylogenetic work indicating that the transatlantic slave trade introduced parvovirus and hepatitis-B virus to Mexico [41]. In the case of 1850s California, ship population size could easily have been the difference between plausible introduction and epidemiological isolation.…”

Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts

“…The phylogenetic placement of our Paratyphi C genome from 1652 Barcelona basal to the diversity observed in post-contact Mexican strains supports one of two scenarios: (i) an introduction of S. Paratyphi C strains from Europe or (ii) an extensive geographic range of S. Paratyphi C prior to the colonial period. Given that other cases of introduction of pathogens in the Americas during the colonial period have been recently proposed, aided by the analysis of ancient microbial genomics, including parvovirus and hepatitis B virus, leprosy, syphilis, and malaria ( Yalcindag et al., 2012 ; Schuenemann et al., 2013 ; Guzmán-Solís et al., 2020 ; Majander et al., 2020 ; Van Dorp et al., 2020 ), it is plausible that colonial migrations contributed to the distribution of past Paratyphi C observed. The continental origin of some infectious diseases putatively associated with colonial settlement, such as syphilis, has been debated for decades with little progress from the analysis of modern strains alone.…”