. 2022 Apr 1;11(7):1960. doi: 10.3390/jcm11071960

Table 3.

Infectious diseases studied using molecular techniques including metagenomics.

Time Frame of Disease Appearance	Archaeological Discovery and Pathogen Identification	Method of Retrieval	References
4900 BCE	Different individuals at Fralsegarden in Gokhem parish, Falbygden, western Sweden. Identification of the presence of Y. pestis DNA	Genotyping of Y. pestis strain, phylogenetic and molecular clock analyses, heatmaps and functional classification of variants, and admixture analyses of human genomes	[8]
4800 to 3700	563 tooth and bone samples from Russia, Hungary, Croatia, Lithuania, Estonia	Shotgun screening sequencing, in silico screening, deep shotgun sequencing, Y. pestis in-solution capture, genome reconstruction and authentication, individual sample treatment due to laboratory preparation and sequencing strategies, SNP calling, heterozygosity and phylogenetic analysis, dating analysis, SNP effect analysis, virulence factor analysis, and indel analysis	[88]
	Latvia, and Germany.
	Identification of the presence of extinct clade in the Y. pestis phylogeny
3250 BCE to 700 CE	Different individuals from Abusir el-Meleq, located in Middle Egypt.	Metagenomic screening and SNP typing	[89]
3250 BCE to 700 CE	Identification of Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus	Metagenomic screening and SNP typing	[89]
3500 BCE to 300 CE	Mummies from Upper and Lower Egypt.	PCR amplification and sequencing	[90,91,92]
3500 BCE to 300 CE	Identification of Falciparum malaria (Plasmodium Falciparum) and human tuberculosis (Mycobacterium tuberculosis)	PCR amplification and sequencing	[90,91,92]
430 BCE	Dental pulp in Kerameikos mass burial of putative victims of the plague.	PCR amplification and sequencing	[32]
430 BCE	Identification of Salmonella enterica serovar Typhi	PCR amplification and sequencing	[32]
541–543 CE	Radiocarbon dating of individuals to 533 AD (plus or minus 98 years) from the Aschheim-Bajuwarenring, Bavaria, Germany.	PCR amplification and sequencing reconstructed draft genomes of the infectious Y. pestis strains, comparing them with a database of genomes from 131 Y. pestis strains from the second and third pandemics, and constructing a maximum likelihood phylogenetic tree.	[22]
541–543 CE	Identification of Y. pestis		[22]
13th and beginning of the 14th century to 19th century	Different subjects from different places in Europe. Identification of Y. pestis	PCR and sequencing SNP calling and evaluation	[93,94,95,96]
1630–1632	Different subjects from Imola Northern Italy. Identification of Y. pestis	Genomic and metagenomic analysis of sequencing data	[97]
16th century	Italian mummy from the 16th century.	Genomic and metagenomic analysis of sequencing data	[98]
16th century	Identification of intact smallpox virus particles	Genomic and metagenomic analysis of sequencing data	[98]
1580–1630 VARV	Different subjects from Vilnius, Lithuania.	PCR and sequencing	[99,100]
1580–1630 VARV	Identification of smallpox	PCR and sequencing	[99,100]