Pathogen screening of the community buried at the early medieval settlement Lauchheim “Mittelhofen” revealed that more than 30% of the population was positive for least one pathogen at the time of death. We identified seven individuals with concurrent infections with two viruses (G16, G27, G29, G31, G46, G66, and G79) and one individual with a triple infection of HBV, B19, and M. leprae (G83) (Table 1).
Seven percent of adults and 26.6% of subadults had an HBV infection (Table 1), a prevalence which today is considered endemic [10]. Furthermore, the proportion of HBV-infected subadults in Lauchheim was over three times as high as that of adults, which is in accordance with the age-related infection pattern in endemic areas [10]. Although today most HBV infections are asymptomatic or cause mild symptoms, individuals with a compromised immune system are at risk of developing severe complications such as liver failure, cirrhosis, and liver cancer. All HBV genomes were of sub-genotype D4—as previously found in eleventh–twelfth century Petersberg (Germany) [11]. To date, sub-genotype D4 is mainly found in Australasia and Northern America. Thus, the available data point to a temporal change in the geographical distribution of HBV genotype D sub-genotypes in Europe—with early medieval D4 subtypes being replaced with those that are prevalent today, such as D1, D2, and D3 [12]. Interestingly, in sixteenth century Italy, an HBV strain of genotype D3 was already present [13] (Fig. 2). Two pairs (G78 and G79; G27 and G83) of identical genomes were reconstructed (based on sequence comparison). Although the diversity of HBV at the time is unknown, this finding could possibly suggest a direct transmission between these individuals or a common source of infection.
In comparison to HBV, B19 was more abundant, with 30% of the Lauchheim community identified as positive. The CPP estimated for subadults (40%) falls within the prevalence seen today (15-60%). The adult CPP of 27.3% is slightly below the rate expected in the present day (30-60%), suggesting that it might likely be an underestimate. B19 infections can lead to a mild disease in children (fifth disease) and serious fetal conditions in pregnant women. In immunocompromised individuals, the infection may lead to anemia and life-threatening aplastic crisis [14]. Thirteen out of the 21 B19-positive individuals in Lauchheim died before reaching an estimated 30 years of age (62%, in comparison to 41% in the overall population). Although not particularly likely, premature death could have possibly occurred due to complications developed after a B19 infection. In the phylogenetic analysis, the G83 strain (genotype 2) is basal to all modern and ancient genotype 2 genomes recovered to date. Genotype 2 is today mainly found in elderly northern Europeans [15].
Variola virus (VARV) was detected in one individual (G31). VARV is the causative agent of the now-eradicated smallpox. The disease is characterized by high mortality (reaching up to 30%), with symptoms including fever, vomiting, and skin rash [16]. In the phylogenetic analysis, the G31 strain clustered within the known diversity of early medieval VARVs from northern and eastern Europe [3]. These VARVs are distinguished from modern VARVs by a larger number of intact genes. G31 exhibits a pattern of gene loss that is a combination of unique features found in both the VK382-VK388 and VK281-VK470 branch of the medieval VARV clade, showing that viruses with different gene compositions were circulating in the Early Middle Ages. The reductive evolution in modern VARVs is thought to be a result of changed selection pressures due to adaptation to humans as exclusive hosts [17]. Given the transmissibility of modern VARV, it is interesting that we only detected a VARV infection in one Lauchheim inhabitant. The absence of additional VARV-positive samples in Lauchheim may be due to a lower fatality rate [18], or the fact that viremia is not thought to last for the duration of infection [19], and thus the viral DNA was not preserved. Furthermore, genomic differences between the modern and medieval VARVs (Fig. 4 and Additional File 1: Fig. S3) could possibly reflect a reduced efficiency of human-human transmission in ancient VARVs. The epidemiology of VARV in the Early Middle Ages, however, remains unknown.
In addition to viral infections, the pathogen screening revealed the presence of M. leprae (causative agent of leprosy) in an adolescent male (G83). Leprosy mainly affects the skin, mucous membranes, and peripheral nerves. Subsequent sensory loss in the hands and feet makes these areas susceptible to injuries and secondary infections, usually leading to deformation and in some cases even loss of extremities. Leprosy per se is not deadly and only approximately 5% of infected individuals exhibit clinical symptoms. As leprosy can cause severe disability as well as visible disfigurement of the limbs and face [20], social stigma of the disease likely surpassed its clinical outcome in terms of suffered consequences. The skeleton of individual G83 exhibits signs suggestive of lepromatous leprosy that take years to develop. Although the adolescent likely had visible facial disfigurement caused by leprosy, he was buried together with the rest of the community, indicating that he might not have been ostracized. Although leprosy was already present in Europe in the Early Middle Ages [21, 22], its prevalence peaked between the twelfth and fourteenth centuries CE. The G83 strain is the oldest found in Germany to date. Two British strains dating to a similar time period were included in the phylogenetic analysis (GC96, fifth–sixth century and EDI006, sixth–seventh century CE). The Lauchheim strain groups in branch 3 together with both British strains, suggesting low diversity of M. leprae in the Early Medieval Period [23]. Based on the observed variation (Fig. 5) as well as the temporal and geographic distribution of the medieval strains (Additional file 1: Fig. S7), we can hypothesize an early appearance of branch 3 strains in Europe. The spread may have been facilitated by the expanding Roman Empire [22, 23].
Although the dating of the Lauchheim settlement abuts the Justinian plague (541–543 CE), no traces of the causative Yersinia pestis (Y. pestis) were found in any of the analyzed samples. Moreover, in the case of the Lauchheim settlement, most likely not all inhabitants were buried within its borders and part of the population might have been buried in the traditional graveyard situated nearby or at another unknown location. Overall, the burials may not be representative of the general Lauchheim population. Excavation and preservation bias also influence the amount of data available for analysis. Inherent limitations of the collected molecular evidence must also be considered. Lack of infection cannot be inferred from pathogen-negative DNA samples as degradation of the genetic material could have erased traces of the microorganism. Thus, the observed infectious disease prevalence in Lauchheim is probably an underestimate.
In the early medieval community of Lauchheim, we observed a high prevalence of infectious diseases caused by four different pathogens. Pathogens were detected in all six burial groups, indicating a broad distribution of infections across the population. The extent of the disease burden becomes even more apparent when considering the fact that pathogens which do not enter the bloodstream are most likely undetectable, due to lack of DNA preservation. Moreover, other types of diseases, such as hereditary, metabolic, and nutritional diseases or cancer, were not accounted for in this investigation. Interestingly, 95.5% of the pathogen-positive individuals (Table 1) and 84.4% of the individuals with no molecular sign of infection exhibited skeletal lesions suggestive of physiological stress. This extremely high burden of lesions indicates poor health in Lauchheim. In one scenario, malnutrition could have increased the level of physiological stress, which in turn resulted in a weakened immune system and a higher probability of successful pathogen transmission and zoonoses. In another scenario, a high burden of infectious diseases in the community compromised the immune system leading to increased physiological stress and metabolic disturbances. The cause-and-effect relationship is unclear and it is likely that multiple factors simultaneously contributed to the elevated stress in the Lauchheim community. Interestingly, Europe experienced a major climate decline between the fifth and seventh century CE, i.e., the Late Antique Little Ice Age (LALIA), which was likely an environmental driver of crop failure, famine, and disease [24]. Although the degree to which LALIA affected the Lauchheim community is unknown, it presents one possible explanation for the high disease burden. The far-reaching contacts and networks during that time, also documented for Lauchheim [25], might have contributed to the spread of infections.
It is notable that LALIA coincides with several changes in the pathogen landscape. A case in point is the Justinian plague (541-543 CE) that affected millions of people across Europe. Another example is that the dating of the G31 VARV genome together with VK388 and VK382 (Fig. 4A) falls within LALIA. Moreover, the early medieval M. leprae infections were the starting point of the leprosy epidemic during the eleventh–fourteenth centuries CE. This scenario is supported by the ancestral positions of the early Lauchheim (G83) and the British (GC96) genomes in clade 3 of the phylogeny (Fig. 5), which were to dominate the later epidemic (Additional file 1: Fig. S7) [23]. Taken together, we would like to hypothesize that LALIA may have created an ecological context in which persistent outbreaks set the stage for severe epidemics hundreds of years later. This speculation, however, needs corroboration.
The pathogens detected in Lauchheim are responsible for some of the most feared diseases of the last millennium and, with the exception of variola virus, still represent major health burdens today.
