Neolithic and medieval virus genomes reveal complex evolution of hepatitis B

Abstract

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genome by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results demonstrated that HBV has circulated in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. The ancient viruses appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses.

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

“…2b, Table 1). To determine the phylogenetic placement of Abusir1543, phylogenetic analyses were [63,64]. More precisely, Abusir1543 falls basal to the subclades A1 and A3, representing modern genomes from Asia and Africa, respectively.…”

The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections

“…However for some rapidly evolving viruses such as hepatitis B [ 106 ], aDNA calibration points do not appear to improve the accuracy of estimates of the age of currently circulating viral diversity [ 107 ]. Recent studies of HBV aDNA have produced conflicting results as to whether molecular clock-based approaches to dating how long HBV has been a human pathogen are suitable [ 106 , 108 , 109 ]. They have also emphasized the power of direct dating of HBV from ancient human remains to demonstrate how long HBV has infected humans, its diversity and distribution in past populations, and the possibility of transmission from nonhuman primates [ 108 , 109 ].…”

“…Recent studies of HBV aDNA have produced conflicting results as to whether molecular clock-based approaches to dating how long HBV has been a human pathogen are suitable [ 106 , 108 , 109 ]. They have also emphasized the power of direct dating of HBV from ancient human remains to demonstrate how long HBV has infected humans, its diversity and distribution in past populations, and the possibility of transmission from nonhuman primates [ 108 , 109 ]. Another issue in molecular dating of pathogen origins and divergence is cross-validation [ 110 ] to evaluate the differential fit of the alternative models [ 72 , 111 , 112 ].…”

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

“…Ancient DNA (aDNA) has become a widely accepted source of biological data, helping to provide new perspectives for a range of fields including archaeology, cultural heritage, evolutionary biology, ecology, and palaeontology. The utilisation of short-read high-throughput sequencing has allowed the recovery of whole genomes and genome-wide data from a wide variety of sources, including (but not limited to), the skeletal remains of animals [1,2,3,4], modern and archaic humans [5,6,7,8], bacteria [9,10,11], viruses [12,13], plants [14,15], palaeofaeces [16,17], dental calculus [18,19], sediments [20,21], medical slides [22], parchment [23], and recently, ancient ‘chewing gum’ [24,25]. Improvement in laboratory protocols to increase yields of otherwise trace amounts of DNA has at the same time led to studies that can total hundreds of ancient individuals [26,27], spanning single [28] to thousands of organisms [18].…”

“…Yet, neither of these genome reconstruction pipelines have had major updates to bring them in-line with current routine aDNA analyses. Meta genomic screening of off-target genomic reads for pathogens or microbiomes [18,19] has become particularly common in palaeo- and archaeogenetics, given its role in revealing widespread infectious disease and possible epidemics that have sometimes been previously undetected in the archaeological record [12,13,37,42]. Without easy access to the latest field-established analytical routines, ancient genomic studies risk being published without the necessary quality control checks that ensure aDNA authenticity, as well as limiting the full range of possibilities from their data.…”