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Thread: The Black Death Has Been Traced Back to Russia6 days old

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    Default The Black Death Has Been Traced Back to Russia

    The Black Death was only the beginning. Countless millions perished in this terrible early wave – an estimated 60 percent of Europe was wiped out – but the virulent bacterium responsible was never actually contained.

    When the Black Death of the mid–14th century was over, Yersinia pestis was far from done, laying waste to human life for another 500 years. This grim, recurring saga of outbreaks – called the second plague pandemic – lasted until the 19th century. But where did its deadly antagonist originate?

    In a new study, an international team of scientists reconstructed 34 Y. pestis genomes sourced from the teeth of 34 individuals who died in 10 different countries – tracing a kind of genetic family tree of shadowy pestilence spanning the 14th to 17th centuries.

    The family tree, encompassing the remains of people who were infected by the bacterium in England, France, Germany and elsewhere, reveals a diversification of the Y. pestis lineage over time into multiple genetically distinct clades. Nonetheless, these clades appear to have one common starting point.

    "These findings indicate a single entry of Y. pestis into Europe through the east", says archaeogeneticist Maria Spyrou from the Max Planck Institute for the Science of Human History, on the basis that one strain in particular looks to be the ancestor of all the second plague pandemic strains that came after it.

    The precursor, the researchers say, came from Russia, specifically a town called Laishevo in the historical Volga region, based on the evidence of a sample known as LAI009.

    "Our phylogenetic reconstruction shows that the LAI009 isolate from Laishevo is ancestral to the Black Death isolates from southern, central, western and northern Europe, as well as to the previously published late 14th-century isolates from London and Bolgar City," the researchers explain in their paper.
    The Nature study (Spyrou et al. 2019) identified LAI009 from Laishevo as the most ancestral form of the strain that entered Europe during the initial wave of the second pandemic. Laishevo is the administrative center of Laishevsky District in the Republic of Tatarstan, Russia. It was previously thought that the Black Death originated in Central Asia and was carried to Europe by fleas living on black rats that travelled on all merchant ships. But the most likely source is the southern Russian region where Kazan Tatars historically inhabited. The first historically documented outbreaks of the second pandemic occurred in 1346 in the Lower Volga and Black Sea regions.

    Our phylogenetic reconstruction shows that the LAI009 isolate from Laishevo is ancestral to the BD isolates from southern, central, western and northern Europe, as well as to the previously published late 14th-century isolates from London (6330)10 and Bolgar City9 (Fig. 2). This genome possesses only one derived SNP distinguishing it from the N07 polytomy that gave rise to Branches 1–4 (Fig. 2; Supplementary Data 1)23. Since all other second pandemic genomes share an additional derived SNP on Branch 1, we interpret LAI009 as the most ancestral form of the strain that entered Europe during the initial wave of the second pandemic that has been identified to date. Regarding the central and western European genomes, NAB003 from Nabburg does not show differences compared to previously published BD genomes from London and Barcelona9,10. In addition, NMS003 from Cambridge was genotyped based on inspection of its SNP profile, despite it not fulfilling the genomic coverage criteria for inclusion in our phylogenetic analysis (Supplementary Table 3), as its archaeological context makes it distinct from other Y. pestis-positive individuals from the same site (see Supplementary Note 1). As a result, SNP inspection classified it as potentially identical to other BD genomes (Supplementary Data 3). By contrast, certain isolates associated with the BD period are seemingly distinct. For example, TRP002 from Toulouse, which dates to 1347–1350 based on archaeological evidence, forms its own unique branch (Fig. 2; Supplementary Data 1). Qualitative assessment of eight unique SNPs in TRP002 with SNPEvaluation28 classified them as potential false-positives (see Methods, Supplementary Data 2). In addition, after visual inspection, all such variants appear in regions of the genome where reads from diverse sources seem to be mapping (Supplementary Fig. 17) and, therefore, were considered to be of exogenous origin. Similarly, we assessed one unique SNP identified in our re-analysis of the recently published OSL-1 genome from Oslo, Norway8 (Fig. 2). Visual inspection revealed it as a low-quality C-to-T transition that could be confined by aDNA damage (Supplementary Fig. 18). Finally, despite exclusion of BSS31 (Siena, Italy) from phylogenetic analysis, two previously identified unique SNPs in this genome were manually inspected, since they were presented as evidence for Y. pestis genetic diversity in Europe during the BD8. Importantly, BLASTn analysis of reads overlapping those regions (Supplementary Fig. 18, Supplementary Data 4 and 5) showed a 100% identity to environmental or other enteric bacterial species, but not to Y. pestis. We, hence, conclude that apart from LAI009 all reconstructed genomes associated with the initial pandemic wave have identical genotypes. In addition, we note that structural rearrangements could provide alternative means of genetic diversity. Although architectural differences are vastly abundant among modern Y. pestis genomes34, their assessment in ancient Y. pestis is limited by the short read aDNA data produced here.

    Based on historical sources alone, it has been difficult to determine the time at which Y. pestis first reached different parts of western Russia7. A commonly accepted view dates its arrival in the southwest, particularly in cities of Astrakhan and Sarai, in 13461,44 with subsequent spread into southern Europe from the Crimean peninsula. On the other hand, the dispersal of plague into northwestern Russia (i.e. in the cities of Pskov and Novgorod7,44) may have followed an alternative route via the Baltic Sea, occurring at the end of the BD between 1351 and 13531,7,44. Such a notion of plague’s expansion from northern Europe eastwards is also supported by published ancient genomic data from the late 14th-century Middle Volga region of Russia9, though other scenarios may come to light with incorporation of additional genomic and historical data. Importantly, through analysis of our new strain from Laishevo (LAI009), which is phylogenetically ancestral to all second pandemic strains sequenced to date (Fig. 2), we provide evidence for the bacterium’s presence in the same region, ~2000 km northeast of the Crimean peninsula, prior to reaching southern Europe in 1347–13481 (currently represented by strains from Siena, Saint-Laurent-de-la-Cabrerisse, Barcelona and Toulouse8,9). These results suggest that the N07-derived SNP previously termed “p1”9 (Fig. 2, Supplementary Fig. 12), that is common to all other second pandemic strains, was likely acquired within Europe during the onset of the BD. In addition, given the proximity of the LAI009 genome to the N07 node often associated with the initiation of the BD (Fig. 2, Supplementary Fig. 12)23, further data will be necessary to accurately re-evaluate the geographic origin of Branch 1. Previous analyses have proposed East Asia as the mostly likely candidate for the N07 polytomy10,23 (Fig. 2). Such claims, however, cannot yet be verified given; (1) the apparent East Asian sampling bias of modern isolates23,45, (2) the lack of molecular evidence from East Asia dating to the early 14th century and (3) the scarcity of historical documentary sources from this region describing precise disease symptoms46. In addition, recently published modern Y. pestis genomes from Central Asia show a rich diversity in the local plague foci26,27, and further sampling from these regions has the potential to inform hypotheses on plague movement and evolution.
    Last edited by ThirdTerm; 2019-10-09 at 22:38.

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