Ancient Yersinia pestis genomes lack the virulence-associated YpfΦ prophage present in modern pandemic strains.

Yersinia pestis is the causative agent of at least three major plague pandemics (Justinianic, Medieval and Modern). Previous studies on ancient Y. pestis genomes revealed that several genomic alterations had occurred approximately 5000-3000 years ago and contributed to the remarkable virulence of this pathogen. How a subset of strains evolved to cause the Modern pandemic is less well-understood. Here, we examined the virulence-associated prophage (YpfΦ), which had been postulated to be exclusively present in the genomes of strains associated with the Modern pandemic. The analysis of two new Y. pestis genomes from medieval/early modern Denmark confirmed that the phage is absent from the genome of strains dating to this time period. An extended comparative genome analysis of over 300 strains spanning more than 5000 years showed that the prophage is found in the genomes of modern strains only and suggests an integration into the genome during recent Y. pestis evolution. The phage-encoded Zot protein showed structural homology to a virulence factor of Vibrio cholerae. Similar to modern Y. pestis, we observed phages with a common origin to YpfΦ in individual strains of other bacterial species. Our findings present an updated view on the prevalence of YpfΦ, which might contribute to our understanding of the host spectrum, geographical spread and virulence of Y. pestis responsible for the Modern pandemic.

Human bony labyrinth as a sex indicator in subadults.

Due to the durability and good preservation of the petrous bone in archaeological and forensic contexts, the value of the inner ear as a sex indicator has been evaluated in various studies. Previous findings suggest that the morphology of the bony labyrinth is not stable in the postnatal period. In this study, we aim to assess the sexual dimorphism of the bony labyrinth via analysis of computed tomography (CT) data obtained from 170 subadults (birth to 20 y.o.) and test whether the postnatal changes of the bony labyrinth affect the level of dimorphism in the inner ear. A set of 10 linear measurements of 3D labyrinth models as well as 10 size and shape indices were analyzed. Sexually dimorphic variables were used to produce sex estimation formulae with discriminant function analysis. The produced formulae allowed for the correct classification of up to 75.3 % of individuals aged from birth to 15 years old. Sexual dimorphism was not significant for individuals between 16 and 20 years of age. This study suggests that the morphology of the subadult bony labyrinth exhibits significant sexual dimorphism in individuals under 16 years of age, which can aid the forensic identification process. Although postnatal growth of the temporal bone seems to affect the level of sexual dimorphism present in the inner ear, the formulae created in this study could be used as an additional tool for sex estimation of subadult (<16 y.o.) remains.

Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.

BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically. RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK. CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.

Ancient DNA Study in Medieval Europeans Shows an Association Between HLA-DRB1*03 and Paratyphoid Fever.

Outbreaks of infectious diseases repeatedly affected medieval Europe, leaving behind a large number of dead often inhumed in mass graves. Human remains interred in two burial pits from 14th century CE Germany exhibited molecular evidence of Salmonella enterica Paratyphi C (S. Paratyphi C) infection. The pathogen is responsible for paratyphoid fever, which was likely the cause of death for the buried individuals. This finding presented the unique opportunity to conduct a paratyphoid fever association study in a European population. We focused on HLA-DRB1*03:01 that is a known risk allele for enteric fever in present-day South Asians. We generated HLA profiles for 29 medieval S. Paratyphi C cases and 24 contemporaneous controls and compared these to a modern German population. The frequency of the risk allele was higher in the medieval cases (29.6%) compared to the contemporaneous controls (13%; p = 0.189), albeit not significantly so, possibly because of small sample sizes. Indeed, in comparison with the modern controls (n = 39,689; 10.2%; p = 0.005) the frequency difference became statistically significant. This comparison also suggested a slight decrease in the allele's prevalence between the medieval and modern controls. Up to now, this is the first study on the genetic predisposition to Salmonella infection in Europeans and the only association analysis on paratyphoid fever C. Functional investigation using computational binding prediction between HLA variants and S. Paratyphi and S. Typhi peptides supported a reduced recognition capacity of bacterial proteins by DRB1*03:01 relative to other common DRB1 variants. This pattern could potentially explain the disease association. Our results suggest a slightly reduced predisposition to paratyphoid fever in modern Europeans. The causative allele, however, is still common today, which can be explained by a trade-off, as DRB1*03:01 is protective against infectious respiratory diseases such as severe respiratory syndrome (SARS). It is thus possible that the allele also provided resistance to corona-like viruses in the past.

Sexual dimorphism of the lateral angle: Is it really applicable in forensic sex estimation?

OBJECTIVE: The aim of this study was to test the validity of a previously proposed lateral angle (LA) method for sex assessment of human skeletal remains in the forensic setting. MATERIAL AND METHODS: Computed tomography (CT) scans of 102 crania of Greek adults were used to test the validity of the LA method for sex estimation. The measurement procedure used in this study is a modified version of a method previously proposed by Akansel et al. (2008). RESULTS: Despite the LA values being larger for females, the difference was not found to be statistically significant. Sectioning point of 45° provided a low accuracy rate of 53 %. CONCLUSIONS: The poor accuracy of the LA method obtained in this study proved it to be of no value in sex estimation. Future studies should examine a broader aspect of the petrous portion morphology in order to establish a more accurate method of forensic sex estimation.

Yersinia pestis strains from Latvia show depletion of the pla virulence gene at the end of the second plague pandemic.

Ancient genomic studies have identified Yersinia pestis (Y. pestis) as the causative agent of the second plague pandemic (fourteenth-eighteenth century) that started with the Black Death (1,347-1,353). Most of the Y. pestis strains investigated from this pandemic have been isolated from western Europe, and not much is known about the diversity and microevolution of this bacterium in eastern European countries. In this study, we investigated human remains excavated from two cemeteries in Riga (Latvia). Historical evidence suggests that the burials were a consequence of plague outbreaks during the seventeenth century. DNA was extracted from teeth of 16 individuals and subjected to shotgun sequencing. Analysis of the metagenomic data revealed the presence of Y. pestis sequences in four remains, confirming that the buried individuals were victims of plague. In two samples, Y. pestis DNA coverage was sufficient for genome reconstruction. Subsequent phylogenetic analysis showed that the Riga strains fell within the diversity of the already known post-Black Death genomes. Interestingly, the two Latvian isolates did not cluster together. Moreover, we detected a drop in coverage of the pPCP1 plasmid region containing the pla gene. Further analysis indicated the presence of two pPCP1 plasmids, one with and one without the pla gene region, and only one bacterial chromosome, indicating that the same bacterium carried two distinct pPCP1 plasmids. In addition, we found the same pattern in the majority of previously published post-Black Death strains, but not in the Black Death strains. The pla gene is an important virulence factor for the infection of and transmission in humans. Thus, the spread of pla-depleted strains may, among other causes, have contributed to the disappearance of the second plague pandemic in eighteenth century Europe.

The posterior portion of the ilium as a sex indicator: A validation study.

Establishing a biological profile of skeletal remains is a key task of forensic anthropologists. Sex estimation is essential in forensic examination, as other elements of the biological profile, such as age at death or stature, are sex dependent. Visual assessment is considered low-cost and quick, therefore it is a commonly applied method of sex estimation. The most reliable results can be obtained with the analysis of the anterior part of the pelvis, however, these skeletal elements are fragile and prone to destruction. In contrary, the more robust posterior portion of the pelvis is often recovered. Several features of the posterior pelvis have been explored in the context of sexual dimorphism. The aim of the present study was to test three previously published methods of sex assessment based on the analysis of the inferior shape of the auricular surface (Novotný, 1975), the greater sciatic notch shape (Walker, 2005 (revised)) and overall morphology, apex morphology and inflection of the auricular surface (Luna et al., 2017). The sample consisted of 194 individuals of Greek origin from a documented modern collection. Four features of the auricular surface and shape of the greater sciatic notch were examined. Logistic regression analysis was applied to produce a sex discriminatory formula. The method proposed by Luna et al. (2017) failed to produce satisfactory results with overall accuracies of 36%, 50% and 53% for overall morphology, apex morphology and inflection respectively. Slightly better results (64%) were obtained with the inferior shape morphology (Novotný, 1975). However, the highest accuracy rate of 81% was noted for the greater sciatic notch shape (Walker, 2005 (revised)). The formula produced in this study allowed correct classification of 83.2% of the sample. This study illustrates that in spite of the presence of sexual dimorphism in the posterior portion of ilium, features of the auricular surface proposed as sex indicators by Novotný (1975) and Luna et al. (2017) should not be used for sex estimation purposes in the Greek population. The formula produced in this study and the greater sciatic notch shape should only be used as additional methods in cases where neither the cranium nor the anterior portion of the pelvis is present.