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REVIEW: Genomics of Ancient Pathogens: First Advances and Prospects

Alexandra B. Malyarchuk1,a*, Tatiana V. Andreeva1,2, Irina L. Kuznetsova2,3, Svetlana S. Kunizheva2,3, Maria S. Protasova2, Lev I. Uralsky2,3, Tatiana V. Tyazhelova2, Fedor E. Gusev2, Andrey D. Manakhov2,3, and Evgeny I. Rogaev2,3,4,b*

1Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia

2Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia

3Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia

4Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA

* To whom correspondence should be addressed.

Received December 14, 2021; Revised January 8, 2022; Accepted January 21, 2022
Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today’s world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.
KEY WORDS: human populations, ancient DNA, paleopathology, paleogenomics, pathogen, plague, cholera, leprosy, syphilis, smallpox, tuberculosis

DOI: 10.1134/S0006297922030051