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High-Coverage Genome Offers Peek at Justinian Plague Genetics

NEW YORK (GenomeWeb) – In a study published online today in Molecular Biology and Evolution, a German-led team teased apart subtle genetic differences that distinguished Yersinia pestis bacteria involved in a plague during that spanned the sixth to eighth century and the forms of Y. pestis bacteria behind the 14th century scourge known as Black Death.

Using samples obtained from a burial site near present-day Munich, the researchers put together a high-coverage genome assembly for a Y. pestis strain infecting a woman who died in the sixth century during the so-called Justinian plague. Results from the analysis suggest Justinian plague-causing forms of Y. pestis had significant divergence from strains associated with the Black Death, though the diversity of Justinian plague strains documented in southern Germany so far appears limited.

"Our research … provides new insights into the evolutionary history of Yersinia pestis, illustrating the potential of ancient genomic reconstructions to broaden our understanding of pathogen evolution and of historical events," co-corresponding author Michal Feldman, a medical anthropology and archaeology researcher affiliated with the Max Planck Institute for the Science of Human History and the University of Tübingen, said in a statement. 

Due to epidemiological differences between the Justinian plague, Black Death, and a more recent pandemic in China during the 19th century, some investigators previously suspected distinct pathogens were behind each pandemic.

With molecular evidence placing Y. pestis behind ancient and modern plagues, the team explained, there is interest in teasing apart genetic features associated with historical Y. pestis samples and characterizing pathogens with the potential for re-emergence from persisting reservoirs around the world.

For the current study, Feldman and colleagues focused on male and female remains found together at a burial site in the medieval town of Altenerding in southern Germany during the Justinian plague, which persisted for more than 200 years, affecting populations in Egypt, eastern portions of the Roman Empire, and Europe and ultimately petering out in the eighth century.

The team initially identified the two Y. pestis-positive samples through PCR-based screening on 20 tooth samples from skeletons at the Bavarian burial site.

After doing DNA array hybridization-based target enrichment in samples from the deceased woman, who appears to have died between 426 and 571 A.D., the researchers used the Illumina HiSeq 2500 to sequence the Y. pestis genome to an average depth of nearly 18-fold coverage.

Across a set of more than 100 available Y. pestis genomes, they uncovered nearly 3,100 SNPs not present in the Y. pestis reference genome. In contrast, the newly sequenced Justinian plague pathogen differed from that reference at fewer than 200 chromosomal or plasmid SNPs.

Compared with a Justinian plague pathogen draft genome from a nearby burial site in Germany, described by another team in Lancet Infectious Diseases in 2014, the new genome assembly had new and known alterations that appeared to be distinct to strains obtained from Justinian plague-affected individuals, including substitutions affecting genes implicated in plague virulence.

But while their phylogenetic analyses of the Justinian plague-causing Y. pestis was consistent with that proposed in the earlier draft genome analysis, the researchers' re-analysis of reads from the Justinian plague pathogen from the nearby Aschheim site suggests that substitutions identified in the prior study may have false positives due to insufficient sequence coverage.

"Excluding the … putative false-positive SNPs, no difference was found between the Aschheim genome and the Altenerding genome reported here, supporting that both genomes represent the same bacterial strain and that the infected individuals were victims of the same outbreak," Feldman and co-authors wrote, arguing that this is consistent with low genetic diversity within Y. pestis in the German region considered during that portion of the Justinian plague.