ena-STUDY-Center for Pathogen Evolution, University of Cambridge-14-03-2018-21:51:36:069-158
Ancient Hepatitis B viruses from the Bronze Age to the Medieval
Hepatitis B virus (HBV) is a major cause of human hepatitis. Approximately 257 million people are chronically infected and around 887,000 died in 2015 due to associated complications. We searched for HBV among 115 billion ancient DNA sequences in shotgun sequencing libraries obtained from 304 Central and Western Eurasian human skeletons, dated from the early Bronze Age to Medieval times. We recovered 12 full or partial ancient HBV genomes aged between 822 and 4488 years old. The ancient sequences group either within or in sister relationship to extant human or other ape HBV clades. With a few exceptions, the genome properties follow those of modern HBV. Different evolutionary models project the root of the heterochronous HBV tree to between 8.6 and 20.9 thousand years ago (kya), and estimate a substitution rate between 8.04x10-6 and 1.51x10-5 nucleotide substitutions per site per year (s/s/y). In several cases, the geographic locations of the ancient genotypes do not match present day distribution. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are here shown to have an early Eurasian presence. The geographic and temporal patterns we observe in ancient and modern HBV genotypes are compatible with well- documented human migrations during the Bronze and Iron Ages. We show evidence for the creation of genotype A via recombination and a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. Taken together, the data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.
Hepatitis B virus (HBV) is a major cause of human hepatitis. Approximately 257 million people are chronically infected and around 887,000 died in 2015 due to associated complications. We searched for HBV among 115 billion ancient DNA sequences in shotgun sequencing libraries obtained from 304 Central and Western Eurasian human skeletons, dated from the early Bronze Age to Medieval times. We recovered 12 full or partial ancient HBV genomes aged between 822 and 4488 years old. The ancient sequences group either within or in sister relationship to extant human or other ape HBV clades. With a few exceptions, the genome properties follow those of modern HBV. Different evolutionary models project the root of the heterochronous HBV tree to between 8.6 and 20.9 thousand years ago (kya), and estimate a substitution rate between 8.04x10-6 and 1.51x10-5 nucleotide substitutions per site per year (s/s/y). In several cases, the geographic locations of the ancient genotypes do not match present day distribution. Genotypes that today are typical of Africa and Asia, and a subgenotype from India, are here shown to have an early Eurasian presence. The geographic and temporal patterns we observe in ancient and modern HBV genotypes are compatible with well- documented human migrations during the Bronze and Iron Ages. We show evidence for the creation of genotype A via recombination and a long-term association of modern HBV genotypes with humans, including the discovery of a human genotype that is now extinct. Taken together, the data expose a complexity of HBV evolution that is not evident when considering modern sequences alone.