2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals

Neukamm, Judith; Pfrengle, Saskia; Molak, Martyna; Seitz, Alexander; Francken, Michael; Eppenberger, Partick; Avanzi, Charlotte; Reiter, Ella; Urban, Christian; Welte, Beatrix; Stockhammer, Philipp W.; Teßmann, Barbara; Herbig, Alexander; Harvati, Katerina; Nieselt, Kay; Krause, Johannes; Schuenemann, Verena J.

doi:10.1186/s12915-020-00839-8

Cited by 40 publications

(54 citation statements)

References 126 publications

(262 reference statements)

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“…This dataset contains genomes from A–J genotypes as well as non-human primate HBV genomes (gibbon, gorilla, and chimpanzee). Additionally, 19 ancient HBV genomes ( Barquera et al, 2020 ; Kahila Bar-Gal et al, 2012 ; Krause-Kyora et al, 2018 ; Mühlemann et al, 2018a ; Neukamm et al, 2020 ; Patterson Ross et al, 2018 ) and 1 ancient HBV genome from this study (HSJN194) were included.…”

Section: Methodsmentioning

confidence: 99%

“…The study of ancient viral genomes has revealed important insights into the evolution of specific viral families ( Barquera et al, 2020 ; Duggan et al, 2016 ; Düx et al, 2020 ; Kahila Bar-Gal et al, 2012 ; Krause-Kyora et al, 2018 ; Mühlemann et al, 2018a ; Mühlemann et al, 2018a ; Mühlemann et al, 2018b ; Neukamm et al, 2020 ; Pajer et al, 2017 ; Patterson Ross et al, 2018 ; Xiao et al, 2013 ), as well as their interaction with human populations ( Spyrou et al, 2019 ). To explore the presence of viral pathogens in circulation during epidemic periods in New Spain, we leveraged the vast historical and archeological information available for the Colonial HSJN.…”

Section: Introductionmentioning

confidence: 99%

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Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Guzmán-Solís

Villa-Islas

Bravo-Lopez

et al. 2021

eLife

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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 to 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.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Guzmán-Solís

Villa-Islas

Bravo-Lopez

et al. 2021

eLife

View full text Add to dashboard Cite

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“…HBV-Dataset-2 (HBV/DS2): comprises 593 whole genomes downloaded from the NCBI database in August 2020, that included genomes from A-J genotypes as well as non-human primates HBV genomes (gibbon, gorilla, and chimpanzee), 19 ancient HBV genomes (Barquera et al, 2020; Kahila Bar-Gal et al, 2012; Krause-Kyora et al, 2018, p.; Mühlemann, Jones, et al, 2018; Neukamm et al, 2020; Patterson Ross et al, 2018) and one ancient HBV genome from this study (HSJN194).…”

Section: Methodsmentioning

confidence: 99%

“…The study of ancient viral genomes has revealed important insights into the evolution of specific viral families (Barquera et al, 2020; Duggan et al, 2016; Düx et al, 2020; Kahila Bar-Gal et al, 2012; Krause-Kyora et al, 2018, p.; Mühlemann, Jones, et al, 2018, 2018; Mühlemann, Margaryan, et al, 2018; Neukamm et al, 2020; Pajer et al, 2017; Patterson Ross et al, 2018; Xiao et al, 2013), as well as their interaction with human populations (Spyrou et al, 2019). To explore the presence of viral pathogens in circulation during epidemic periods in New Spain, we leveraged the vast historical and archeological information available for the Colonial HSJN.…”

Section: Introductionmentioning

confidence: 99%

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

Guzmán-Solís

Blanco-Melo

Villa-Islas

et al. 2020

Preprint

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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.

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“…Uncovering such high diversity raises important questions about whether the origin of the disease may in fact be in Eurasia, but the lack of ancient data from outside Europe and the resulting potential sampling bias do not yet allow precise conclusions [ 45 ]. Even the recently published oldest genome from an ancient Egyptian mummy from Abusir el-Meleq, thereby representing the only ancient M. leprae genome outside Europe, does not further refine the localization of leprosy’s origin [ 49 ]. Furthermore, the identification of M. leprae in modern red squirrels in Britain [ 50 ], genetically closely related to a branch 3 strain isolated in a fifth–sixth century male from the Essex/Cambridgeshire border, eastern England, highlights the possibility that there may be important animal reservoirs that could add a further layer of complexity to the identified diversity [ 51 ].…”

Section: Introductionmentioning

confidence: 99%

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

et al. 2021

Self Cite

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Background Hansen’s disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease’s complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. Results Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae’s genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. Conclusions Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease’s global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy’s global history and can contribute to current models of M. leprae’s worldwide dissemination, including interspecies transmissions.

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2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals

Cited by 40 publications

References 126 publications

Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

Ancient viral genomes reveal introduction of human pathogenic viruses into Mexico during the transatlantic slave trade

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

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

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