Ajeje Brazorf
07-08-2024, 02:45 PM
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02806-8
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.
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.
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.
Germany_Lauchheim_EarlyMedieval:G56__AD_750__Cov_3 9.59%,0.127482,0.138112,0.037335,0.003553,0.036007 ,-0.010877,-0.002585,0.001846,0.003477,0.02606,-0.000812,0.007493,-0.010406,-0.004542,-0.010858,0.00716,0.011735,0.005448,0.010684,-0.002126,-0.001747,0.007296,0.003574,0.017713,0.004311
Germany_Lauchheim_EarlyMedieval:G63__AD_750__Cov_2 8.15%,0.110408,0.128972,0.034695,0.007106,0.032314 ,-0.005857,-0.004465,-0.005307,0.008181,0.01713,-0.003897,-0.005245,-0.014717,-0.010597,0.012486,0.009016,0.009257,0.010769,0.005 154,-0.009129,0.010856,0.007543,-0.001232,0.017834,-0.004191
Germany_Lauchheim_EarlyMedieval:G66__AD_750__Cov_1 4.62%,0.125205,0.14319,0.023381,0.000969,0.024004, 0.001952,0.00047,0.002769,0.009817,0.005285,0.0077 95,0.016935,0.001933,-0.015276,0.002579,-0.009149,-0.01004,-0.01799,0.002263,0.005002,-0.021961,-0.007419,-0.002342,0.017231,-0.000239
Germany_Lauchheim_EarlyMedieval:G67__AD_750__Cov_1 3.37%,0.133173,0.132019,0.038466,0.021318,0.032621 ,0.006972,-0.005405,0.003461,0.003477,-0.000364,0.002436,-0.013338,-0.029286,-0.008395,0.005972,0.023203,0.005085,0.004941,0.005 782,0.01138,-0.004492,0.02065,-0.003574,0.007109,0.006945
Germany_Lauchheim_EarlyMedieval:G78__AD_750__Cov_7 2.40%,0.117238,0.149283,0.017725,-0.018734,0.018157,-0.010598,0.00376,0.002538,0.009204,0.021504,0.0081 19,0.01109,-0.002676,-0.004679,-0.002986,-0.014717,-0.009388,0.001647,0.00264,-0.002126,-0.001497,0.003586,0.000123,-0.004217,-0.007784
Germany_Lauchheim_EarlyMedieval:G83__AD_750__Cov_1 8.29%,0.126344,0.147252,0.029415,-0.004199,0.040931,0.013387,0.001645,0.000923,0.013 703,0.010387,-0.013316,-0.001199,-0.019475,0.002752,0.00665,-0.00716,-0.014994,-0.005954,0.002388,0.005253,-0.021587,0.000495,0.007148,0.009037,-0.001317
Distance to: Germany_Lauchheim_EarlyMedieval:G56__AD_750__Cov_3 9.59%
0.02552346 Italian_Veneto:ALP378
0.02786415 Hungary_IA_LaTene:I18834__BC_260__Cov_58.86%
0.02808959 Italian_Friuli_Sappada:GRC14386282
0.02916356 Italian_Bergamo:HGDP01147
0.02941570 Italian_Northeast
0.02952947 Avar:MGS124
0.03008049 European:8324843039_R02C02
0.03009549 Italian_Northeast:ALP093
0.03023990 Italian_Piedmont:Piedmont61
0.03060091 Avar:MGS027
Distance to: Germany_Lauchheim_EarlyMedieval:G63__AD_750__Cov_2 8.15%
0.03150745 French_Provence:S_23_2
0.03254058 Germany_AltInden_Saxon_EMedieval:IND003.A_noUDG__A D_600__Cov_64.86%
0.03504951 Italian_Veneto_Lessinia_Cimbrian:GRC14372326
0.03613650 Italian_Veneto_Lessinia_Cimbrian:GRC14372345
0.03620997 French_Provence
0.03649956 Italian_Aosta_Valley
0.03699680 European:8324843039_R02C02
0.03707264 Germany_AltInden_Saxon_EMedieval:IND014.A_noUDG__A D_600__Cov_59.35%
0.03752336 Italy_South_Tyrol_EMA:2324__AD_512__Cov_25.20%
0.03778340 French_Auvergne:C_9_2
Distance to: Germany_Lauchheim_EarlyMedieval:G66__AD_750__Cov_1 4.62%
0.03767285 Austria_Ovilava_Roman.SG:R10666.SG__AD_709__Cov_85 .27%
0.04040280 Avar:CSK060
0.04201835 Agamemnon_scaled
0.04335725 Camulogène_Rix_scaled
0.04395581 Italian_Northeast:ALP346
0.04399557 British:GRC10044008
0.04421143 Avar:MGS130
0.04436576 nitmarux_scaled
0.04449402 Avar:MGS062
0.04451939 Italian_Piedmont:ItalyPiedmont136
Distance to: Germany_Lauchheim_EarlyMedieval:G67__AD_750__Cov_1 3.37%
0.03736541 German:German55
0.03970674 BelgianC:5434289058_R01C01
0.03970674 European:5434289058_R01C01
0.04027266 Italian_Veneto_Lessinia_Cimbrian:GRC14372326
0.04105960 Czechia_IA_LaTene:I14986__BC_305__Cov_69.56%
0.04179783 BelgianB:5434289058_R03C02
0.04179783 European:5434289058_R03C02
0.04201356 Avar:CSK082
0.04242643 Koolmets21_father_scaled
0.04283865 Spain_Visigoth:I12163__AD_558__Cov_36.14%
Distance to: Germany_Lauchheim_EarlyMedieval:G78__AD_750__Cov_7 2.40%
0.02138988 Hungary_Conqueror_Elite:K2-33.SG__AD_980__Cov_88.64%
0.02258156 Italian_Tuscany:Tuscany74
0.02275955 Greek_Thessaly:GreeceNE144
0.02378573 Italian_Emilia:ALP392
0.02438742 andrearinaldi11_23andMe_scaled
0.02472912 Croatia_Tilurium_Roman.SG:R3544.SG__AD_576__Cov_58 .93%
0.02473408 Italian_Marche:MarABQ080D
0.02510994 andrearinaldi11_AncestryDNA_scaled
0.02565886 Italian_Marche:MarACO060D
0.02567585 loxias_grandmother_scaled
Distance to: Germany_Lauchheim_EarlyMedieval:G83__AD_750__Cov_1 8.29%
0.03331064 Austria_Ovilava_Roman.SG:R10666.SG__AD_709__Cov_85 .27%
0.03522432 Italian_Northeast:ALP280
0.03566573 Italian_Veneto_Lessinia_Cimbrian:GRC14386251
0.03674978 Italian_Northeast:ALP506
0.03683203 Serbia_Kormadin:I27298__AD_500__Cov_69.51%
0.03709337 Italian_Friuli_Timau:GRC14386319
0.03716947 Italian_Veneto_Lessinia_Cimbrian:GRC14386250
0.03725330 Croatia_Mursa_Roman.SG:R3655.SG__AD_221__Cov_42.85 %
0.03735389 Italian_Friuli_Sappada:GRC14372344
0.03751828 Italian_Friuli_Sauris:GRC14415977
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.
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.
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.
Germany_Lauchheim_EarlyMedieval:G56__AD_750__Cov_3 9.59%,0.127482,0.138112,0.037335,0.003553,0.036007 ,-0.010877,-0.002585,0.001846,0.003477,0.02606,-0.000812,0.007493,-0.010406,-0.004542,-0.010858,0.00716,0.011735,0.005448,0.010684,-0.002126,-0.001747,0.007296,0.003574,0.017713,0.004311
Germany_Lauchheim_EarlyMedieval:G63__AD_750__Cov_2 8.15%,0.110408,0.128972,0.034695,0.007106,0.032314 ,-0.005857,-0.004465,-0.005307,0.008181,0.01713,-0.003897,-0.005245,-0.014717,-0.010597,0.012486,0.009016,0.009257,0.010769,0.005 154,-0.009129,0.010856,0.007543,-0.001232,0.017834,-0.004191
Germany_Lauchheim_EarlyMedieval:G66__AD_750__Cov_1 4.62%,0.125205,0.14319,0.023381,0.000969,0.024004, 0.001952,0.00047,0.002769,0.009817,0.005285,0.0077 95,0.016935,0.001933,-0.015276,0.002579,-0.009149,-0.01004,-0.01799,0.002263,0.005002,-0.021961,-0.007419,-0.002342,0.017231,-0.000239
Germany_Lauchheim_EarlyMedieval:G67__AD_750__Cov_1 3.37%,0.133173,0.132019,0.038466,0.021318,0.032621 ,0.006972,-0.005405,0.003461,0.003477,-0.000364,0.002436,-0.013338,-0.029286,-0.008395,0.005972,0.023203,0.005085,0.004941,0.005 782,0.01138,-0.004492,0.02065,-0.003574,0.007109,0.006945
Germany_Lauchheim_EarlyMedieval:G78__AD_750__Cov_7 2.40%,0.117238,0.149283,0.017725,-0.018734,0.018157,-0.010598,0.00376,0.002538,0.009204,0.021504,0.0081 19,0.01109,-0.002676,-0.004679,-0.002986,-0.014717,-0.009388,0.001647,0.00264,-0.002126,-0.001497,0.003586,0.000123,-0.004217,-0.007784
Germany_Lauchheim_EarlyMedieval:G83__AD_750__Cov_1 8.29%,0.126344,0.147252,0.029415,-0.004199,0.040931,0.013387,0.001645,0.000923,0.013 703,0.010387,-0.013316,-0.001199,-0.019475,0.002752,0.00665,-0.00716,-0.014994,-0.005954,0.002388,0.005253,-0.021587,0.000495,0.007148,0.009037,-0.001317
Distance to: Germany_Lauchheim_EarlyMedieval:G56__AD_750__Cov_3 9.59%
0.02552346 Italian_Veneto:ALP378
0.02786415 Hungary_IA_LaTene:I18834__BC_260__Cov_58.86%
0.02808959 Italian_Friuli_Sappada:GRC14386282
0.02916356 Italian_Bergamo:HGDP01147
0.02941570 Italian_Northeast
0.02952947 Avar:MGS124
0.03008049 European:8324843039_R02C02
0.03009549 Italian_Northeast:ALP093
0.03023990 Italian_Piedmont:Piedmont61
0.03060091 Avar:MGS027
Distance to: Germany_Lauchheim_EarlyMedieval:G63__AD_750__Cov_2 8.15%
0.03150745 French_Provence:S_23_2
0.03254058 Germany_AltInden_Saxon_EMedieval:IND003.A_noUDG__A D_600__Cov_64.86%
0.03504951 Italian_Veneto_Lessinia_Cimbrian:GRC14372326
0.03613650 Italian_Veneto_Lessinia_Cimbrian:GRC14372345
0.03620997 French_Provence
0.03649956 Italian_Aosta_Valley
0.03699680 European:8324843039_R02C02
0.03707264 Germany_AltInden_Saxon_EMedieval:IND014.A_noUDG__A D_600__Cov_59.35%
0.03752336 Italy_South_Tyrol_EMA:2324__AD_512__Cov_25.20%
0.03778340 French_Auvergne:C_9_2
Distance to: Germany_Lauchheim_EarlyMedieval:G66__AD_750__Cov_1 4.62%
0.03767285 Austria_Ovilava_Roman.SG:R10666.SG__AD_709__Cov_85 .27%
0.04040280 Avar:CSK060
0.04201835 Agamemnon_scaled
0.04335725 Camulogène_Rix_scaled
0.04395581 Italian_Northeast:ALP346
0.04399557 British:GRC10044008
0.04421143 Avar:MGS130
0.04436576 nitmarux_scaled
0.04449402 Avar:MGS062
0.04451939 Italian_Piedmont:ItalyPiedmont136
Distance to: Germany_Lauchheim_EarlyMedieval:G67__AD_750__Cov_1 3.37%
0.03736541 German:German55
0.03970674 BelgianC:5434289058_R01C01
0.03970674 European:5434289058_R01C01
0.04027266 Italian_Veneto_Lessinia_Cimbrian:GRC14372326
0.04105960 Czechia_IA_LaTene:I14986__BC_305__Cov_69.56%
0.04179783 BelgianB:5434289058_R03C02
0.04179783 European:5434289058_R03C02
0.04201356 Avar:CSK082
0.04242643 Koolmets21_father_scaled
0.04283865 Spain_Visigoth:I12163__AD_558__Cov_36.14%
Distance to: Germany_Lauchheim_EarlyMedieval:G78__AD_750__Cov_7 2.40%
0.02138988 Hungary_Conqueror_Elite:K2-33.SG__AD_980__Cov_88.64%
0.02258156 Italian_Tuscany:Tuscany74
0.02275955 Greek_Thessaly:GreeceNE144
0.02378573 Italian_Emilia:ALP392
0.02438742 andrearinaldi11_23andMe_scaled
0.02472912 Croatia_Tilurium_Roman.SG:R3544.SG__AD_576__Cov_58 .93%
0.02473408 Italian_Marche:MarABQ080D
0.02510994 andrearinaldi11_AncestryDNA_scaled
0.02565886 Italian_Marche:MarACO060D
0.02567585 loxias_grandmother_scaled
Distance to: Germany_Lauchheim_EarlyMedieval:G83__AD_750__Cov_1 8.29%
0.03331064 Austria_Ovilava_Roman.SG:R10666.SG__AD_709__Cov_85 .27%
0.03522432 Italian_Northeast:ALP280
0.03566573 Italian_Veneto_Lessinia_Cimbrian:GRC14386251
0.03674978 Italian_Northeast:ALP506
0.03683203 Serbia_Kormadin:I27298__AD_500__Cov_69.51%
0.03709337 Italian_Friuli_Timau:GRC14386319
0.03716947 Italian_Veneto_Lessinia_Cimbrian:GRC14386250
0.03725330 Croatia_Mursa_Roman.SG:R3655.SG__AD_221__Cov_42.85 %
0.03735389 Italian_Friuli_Sappada:GRC14372344
0.03751828 Italian_Friuli_Sauris:GRC14415977