Ancient Viruses: How infectious diseases arrived in the colonial Americas

Analysis of viral DNA from human remains suggests that the transatlantic slave trade may have introduced new pathogens that contributed to the devastating disease outbreaks in colonial Mexico.
  1. Ville N Pimenoff
  2. Charlotte J Houldcroft  Is a corresponding author
  1. Department of Laboratory Medicine, Karolinska Institutet, Sweden
  2. Department of Cultures, University of Helsinki, Finland
  3. Faculty of Medicine, University of Oulu, Finland
  4. Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, United Kingdom

When European colonisers arrived in the Americas in the 16th and 17th centuries, they brought with them multiple infectious diseases which led to massive outbreaks that killed millions of indigenous people. However, it is unclear which pathogens were responsible for these devastating epidemics that are generally referred to as the Cocoliztli, meaning ‘pest’ in the Nahuatl language (Acuna-Soto et al., 2004).

Most research in this area has focused on diseases that arrived in the Americas from Europe, and do not factor in another horrific part of European colonial history: the transatlantic slave trade that forcibly transported West Africans – who carried unique genotypes of the disease-causing pathogens – to the Americas (Diamond, 1998). Now, in eLife, María C. Ávila-Arcos from Universidad Nacional Autónoma de México and colleagues – including Axel A Guzmán-Solís as first author – report the first likely evidence of viruses that originated in Africa circulating in Mexico during the colonial period (Guzmán-Solís et al., 2021).

The team (who are based in Mexico, Denmark and the United States) studied human remains that were found in two burial sites in Mexico City: one was associated with a colonial hospital and chapel, and the other a hospital that treated Native Americans during the 1576 Cocoliztli outbreak. Archaeological analysis of the remains from the latter site suggested that 21 of the individuals studied were of West African ancestry, despite their presence in a hospital associated with the treatment of indigenous people. Viral DNA was then extracted from these remains and analysed using various genetic sequencing tools.

The data identified an ancient strain of parvovirus B19 in three of the individuals studied, and an ancient strain of hepatitis B in one other individual. The genome of the discovered parvovirus was highly similar to a strain called genotype 3, which is sporadically found in Africa and is extremely rare in modern Europe and the Americas. This suggests that the transatlantic slave trade imposed by European colonization may have introduced new viral pathogens or genotypes into colonial Mexico.

Guzmán-Solís et al. also found the genotype 3 strain in the human remains of an indigenous person, suggesting that the virus may have spread to local individuals and contributed to the disease outbreaks that affected millions of people. The researchers then carried out genealogical DNA testing of the four individuals to study whether being infected with a specific pathogen genotype was associated with their genetic ancestry. These data helps build on a previous study revealing how different viral genotypes are distributed among modern Native Americans with African ancestry related to European colonial history (Lopera et al., 2014).

Although the study provides an important glimpse into the existence of these ancient viral strains in the colonial Americas, there are some limitations. First, the historical global distribution of the genotypes discovered is still largely unknown. Second, the conclusions are based on pathogens isolated from only four individuals, although it is common for these kinds of studies to have small amounts of genetic data due to limited number of samples.

Nevertheless, a global dataset with more genotype 3 sequences needs to be retrieved and analysed to confirm or refute the hypothesis that B19 genotype 3 was first brought to the Americas by enslaved Africans during the transatlantic slave trade. Indeed, a previous study found this strain of B19 in the remains of North European soldiers from the Second World War (Toppinen et al., 2015), and the genotype has also been observed in India (Jain et al., 2015) and the Brazilian Amazon (Freitas et al., 2008). Lastly, very few viral strains of African origin have been isolated from modern or ancient remains of African individuals, which will be needed to fully understand the genetic history and genotype distribution of these human infecting pathogens (Figure 1).

The evolution of parvovirus B19.

In modern society, there are three main genotypes of parvovirus B19: genotype 1 (GT1), the most predominant strain around the world; genotype 2 (GT2) which is more commonly found in Europe; and genotype 3 (GT3) which has been sporadically observed worldwide, including in Ghana, Brazil and India (Jain et al., 2015; Freitas et al., 2008; Candotti et al., 2004). Previous studies have shown that the three genotypes likely emerged in human populations around five thousand years before present day (BP) from a common ancestor that arose ten thousand years ago. This divergence happened before the arrival of Columbus in the Americas (dashed line) and therefore pre-dates the European colonisation of the Americas and subsequent transatlantic slave trade.

Image credit: Ville N Pimenoff (based on data from Mühlemann et al., 2018).

Previous studies have found other ancient pathogens in the human remains of individuals who were alive during the colonial period in Mexico, some of whom were buried in a manner associated with an epidemic event. The work by Guzmán-Solís et al. suggests that parvovirus B19 can be added to this growing list of microbes, which includes the viruses and bacteria responsible for the skin disease yaws, hepatitis B, syphilis, salmonella and paratyphoid fever (Barquera et al., 2020; Schuenemann et al., 2018; Vågene et al., 2018). The study also provides historical evidence of viruses being transmitted between geographically distant human populations, which likely led to the emergence of related infectious diseases in populations that were previously naïve to the pathogen.


  1. Book
    1. Diamond J
    Guns, Germs and Steel

Article and author information

Author details

  1. Ville N Pimenoff

    Ville N Pimenoff is in the Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden, and the Department of Cultures, University of Helsinki, Helsinki, Finland and Faculty of Medicine, University of Oulu, Oulu, Finland

    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0813-7031
  2. Charlotte J Houldcroft

    Charlotte J Houldcroft is from the Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom

    For correspondence
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1833-5285

Publication history

  1. Version of Record published: September 9, 2021 (version 1)


© 2021, Pimenoff and Houldcroft

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.


  • 1,616
  • 111
  • 1

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Ville N Pimenoff
  2. Charlotte J Houldcroft
Ancient Viruses: How infectious diseases arrived in the colonial Americas
eLife 10:e72791.

Further reading

  1. The transatlantic slave trade introduced dangerous human pathogens into Mexico

    1. Genetics and Genomics
    Doo Eun Choi, Jun Wan Shin ... Jong-Min Lee
    Research Article

    An expanded CAG repeat in the huntingtin gene (HTT) causes Huntington’s disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and guide RNAs (gRNAs) efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without altering HTT mRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased in the liver by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion strategies in HD and potentially other repeat expansion disorders.