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Ancient Y. Pestis Genome Analyses ID Early Diversification During First Plague Pandemic

NEW YORK (GenomeWeb) – A group led by researchers from the Max Planck Institute for the Science of Human History in Germany has identified early genetic diversification in the Justinianic Plague across Western Europe, including the British Isles, Germany, France, Spain, and other regions.  

Yersinia pestis — the main cause of plague — infects rodents and humans via flea transmission, appearing as bubonic, septicemic, or pneumonic plague. In Europe, the first historically reported pandemic caused by Y. pestis (the Justinianic Plague) began in the fifth century and lasted over 200 years. However, only one strain from the pandemic had been reconstructed using ancient DNA.

In a study published today in PNAS, the researchers screened 183 human remains from 21 sites with multiple burials in Austria, the UK, Germany, France, and Spain for Y. pestis, successfully reconstructing eight of the bacteria's genomes. By assessing single nucleotide polymorphisms in the genomes, the group identified the earliest genetic evidence of plague in Britain from the Anglo-Saxon site of Edix Hill.

The researchers began by using a qPCR assay targeting the Y. pestis-specific pla gene to test 171 teeth from 20 sites, spanning from 300 to 900 AD. For the remaining site — Edix Hill, Britain — the team had only shotgung sequencing data available and applied the metagenomic tool MALT.

Following an in-solution capture approach, the researchers turned the Y. pestis-positive samples into double-stranded, double-indexed, and UDG-treated DNA libraries enriched for Y. pestis, which they sequenced on Illumina NextSeq 500 or HiSeq4000 platforms.

Applying an approach called "SNPEvaluation," the researchers authenticated SNPs found in the samples by establishing three criteria for SNP exclusion: they had higher coverage when mapped with less strict parameters, had "heterozygous" positions in proximity, or were flanked by gaps in the genome.

"The retrieval of genomes that span a wide geographic and temporal scope gives us the opportunity to assess Y. pestis' biodiversity present in Europe during the First Pandemic," co-first author and Max Planck Institute student Marcel Keller explained in a statement.

Keller and his team also found that a single diversification event led to the previously published Y. pestis species, as well as three of the additional branches identified in the current study. Two of the branches contained single genomes with two to three derived SNPs, and one branch diversified into three distinct strains. 

The researchers believe the diversification event may have occurred either in Europe, the Mediterranean basin, or the Middle East during the Justinianic Plague. They offered two different reasons for the scenario. First, they identified four European strains with short genetic distances from the genetic branching using three rural Bavarian genomes. They also identified an almost direct ancestor of the branching in Europe during the sixth century in a British genome.

The study authors highlighted evidence they found that the Justinianic Plague first reached the British Isles in the sixth century. Based on archaeological dating, the researchers believe the strain found at Edix Hill is linked to the very first presence of plague in Britain, previously noted for 544. Because it was a Roman settlement, the researchers speculate that the disease was introduced through sea communications with Brittany after an outbreak in Central Gaul in 543.

The team also identified a 45-kb deletion region recovered from human victims during the first and second pandemics that involved the same two virulence factors, demonstrating an example of potential convergent evolution of the bacteria during large-scale epidemics.

The researchers found that the genomes indicated that several closely related strains of Y. pestis existed during the sixth to eighth centuries in Europe. 

"We interpret the current data as insufficient to resolve the origin of the Justinianic Plague as a human epidemic, before it was first reported in Egypt in 541 AD," the study authors noted. "However, the fact that all genomes belong to the same lineage is indicative of a persistence of plague in Europe or the Mediterranean basin over this time period, instead of multiple reintroductions."

The authors believe that future studies will need to sample putative plague burials more extensively in order to develop a more detailed picture of the onset and persistence of the Justinianic Plague. By doing so, they will be able to track Y. pestis' microevolution and human impact during past and present pandemics.