PALAEOGENOMICS OF PATHOGENS QUIZ k. What is biocodicology? What can we learn from it? 1. What is necrobiome and where do we find it? Group of organisms associated with decay of other organisms' remains. It's present in all our samples from remains (both skeletal and mummified) 2. What ways of parchment sampling are used? Eraser rubbings Fragments of the parchment 3. What are museomics? Omics used for the analyses of historical biomolecules from museum collections. Biocodicology is an emerging field that studies the biological information stored in ancient manuscripts and is currently revolutionizing the field of codicology (Fiddyment et a!., 2019) by incorporating high-throughput molecular techniques such as proteomics (Fiddyment et al., 2015), genomics and metagenomics (Teasdale et erf., 2015, 2017). These technologies make it possible to extract the biological information stored for centuries in ancient manuscripts, especially in parchment objects. What was the parchment made from, species, sex and population affinity. Fragment relationship. Origin of stains. Pathogens. Preservation and organisms that could endanger the document. Parchment Quality Index. Treatment. Human handling.... 5. What are some of the steps for validation? Authentication based on damage Competitive mapping Good reference, database choice!! Unique markers Does it make biological and historical sense? 6. Write at least 5 examples of sources for metagenomics of ancient samples. PALAEOGENOMICS OF PATHOGENS EVA CHOCHOLOVA LABORATORY OF BIOLOGICAL AND MOLECULAR ANTHROPOLOGY DEPARTMENT OF EXPERIMENTAL BIOLOGY Time of death Endogenous DNA microbiome & pathogens Burial history \ |f*j Endogenous Environmental factors 5 104 Endogenous 'total' DNA Pathogen DNA 10 bp Degradation and preservation of host DNA [including the microbiome and circulating pathogens] occurs rapidly after death. DNA degrades in an environmentally informed manner, where water, temperature, pH, microbial soil content and other factors shorten the remaining endogenous DNA but most is lost. At the same time, environmental (exogenous) DNA swamps out the original signal, with fragment-length distributions that both overlap and extend beyond the ancient DNA in the sample. Medieval peoples were well acquainted with death as the 15th century manuscript illustration on the left suggests (image: © British Library Board: Add MS 37049). Here, a recently buried noblewoman [endogenous) sits atop the worms and other vermin (exogenous], who will soon set upon her corpse. The image accompanies a Middle English poem relating a discussion between the decaying woman and eager worms [138]. 100 bp 10 bp 1000 bp Current Biology Curr Biol. 2020 Oct 5; 30(19): R1215-R1231. Published online 2020 Oct 5. doi: 10.1016/i.cub.2020.08.081 PMCID: PMC7534838 PMID:33022266 The Recovery, Interpretation and Use of Ancient Pathogen Genomes Sebastian Duchene.11 Simon Y.W. Ho.2 Ann G. Carmichael.3 Edward C. Holmes.4" and Hendrik Poinar5 6 Duchéne et at, 2020 DOI: 10.1016/j.cub.2020.08.081 Virulence and transmission Sample collection from archaeological remains Recovery and sequencing of DNA/RNA from pathogen I Phylogenetic analysis and comparative genomics Origins and geographic spread Vectors and host reservoirs ft Evolutionary rates and genetic diversity Ttemfari Micro biology Figure 2. Overview of Microbial Genomics of Ajicier 11 Palhoyens. Studying ancient pathogens can be a vaLiaCte tool In answering many historical and biological questions. Those nouoe what could have, caused the high mortality of past diseases, how Iriey spread across continents, haw '.octets and host reservoirs conlrbuted to their vlrulenoe and transmission, and the origins and diversity of pathogens in Ihe past. For a more delated explanation a' 1he methods used In ancient pathogen genomics vva refer Ihe reader to an excalent review by Dranccurt and Raotit [79]. Fig. 1 I Methods for the detection and isolation of pathogen DNA From ancient m etagenomlc spec linens. The diagram provides an overview of techniques used foi pathogen DNA detection in ancient remains by distinguishing between laboratory and computational methods. In both cases, processing begins with the extraction of DNA from ancient sped mens1 ".As part of the laboratory pipeline, direct screening of extracts can be performed by PGR (quantitative (qPCRlor conventional!againsc species-specific genes, as done previously1 riLQ*1. PGR techniques alone, however, can suffer from frequent false-positive results and should therefore always be coupled with further verification met Nods such as downstream genome enrichment and/or n*Kt-generation sequencing (NGS) in oidcr to ensure ancient DNA (a DNA) authentic at ion of putativcly positive samples. Alternatively, construction of NGS Libraries1^1 y' lui enabled pathogen si.ic-ciiiuc via fluorcsr.enr.e-basod iur on microarrays'7andvia DNA enrichment approaches1 . Tlie latter has been achieved, through single locus in-solution capture '■" or through simultaneous screening for multiple pathogens using micioarray-based enrichment of species-specific loci and l: rabies. poM-NGS aDNA authentication. In addition, data produced by direct (shotgun) sequencing of N GS libraries before enrichment can also be used for pathogen screen ing using computational tools. After pre-processing, reads can be directly mapped against a target reference genome (in cases for which contextual information is suggestive of a causative organism) 01 against a mult igc no me reference composed of closely related species to achieve increased mapping specificity of ancient reads. Alternatively, ancient pathogen DNA can also be detected using niciagenomic profiling methods, as presented elsewhere""iJ, through tanonomie assignment of shotgun NGS reads. Both approaches allow for subsequent assessment of aDNA authenticity andean be followed by whole patliocenceuoineiwiieyal ih ouc 11 targeted mik.l runt 01 dheci sccuci icii ic ulpos t vc sample libraries. \\ Archaeological or \\ historical sped men qPCR screening ass-ay of DNA extracts DNA extraction NGS library preparatio 4 Amplification basEd Laboratory methods Capture based Further verification necessary for samples gelding amplification products rurther ■ Library indexing and amplihcatio -I =1 _ J Pathogen screening array Single locus in-soLution capture Computational methods Broad approach Post-enrichment NGS Single reference read mapping Reference Ml Iti referenee read mapping Reference A Reference B Reference C .Metagenomic profiling Tasonornic assignment and relative abundance Putative ancient Bacteria -* pathogen —» reads 5driipleA sampleB SampLe-C Ancient pathogen read authentication: deamination, depurination, read Length, coverage distribution and edit distance Whole-genome capture and/or NGS of positive or putative Ly positive samples Spyrou et al., 2019; DOI: 10.1038/s41576-019-0119-1 Table 1 I Ancient pathogen genomic data recovered from archaeological or historical specimens Pathogen Infectious disease Method of retrieval Number of genomes1' Biological insights Rets Bacterial pathogens Borre\\a rnecurrentii Kelapsinq lever Shotgun sequencing 1 * Isolation: from 15th-century Ce human remains from Norway * Genome signatures of reductive evolution, associated with typical virulence profile, and recent ecological adaptation flrucetfa Brucellosis Shotgun sequenci ng 1 * Isolation from a calcified nodule identified in an meiitensis individual's pelvic gird le * Presence ofiJ. melitensus in Sardinia during the 14th century Ct GardnereJfa vaginalis Bacterial vaginosis Shotgun sequencing 1 * Identified in human remains from Troy dating to 13th century C£ * Association with women's mortality during childbirth in the past * The identified strain clusters among modern G. wioinalis diversity Helicobacter pytori ■ Ulcers of the upper qastroincesrinal tract In-solution capture followed by WCft 1 * Isolation from European Copper Age, 5,3CiQ-year-oLd mummy (Otzi) ■ Increased rkkof gas-trie carcinoma * Unadmixed strain, contrary to-modern European strains, which are hybrids of two ancestral populations leprae Lepromatous leprosy ■ Shotgun sequencing ■ Microanay-based capture followed by 27 * First de novo-assembled ancient pathogen genome * Estimated emergence >5,Qf)i} years ago * European origin of leprosy in the Americas * High M. leprae diversity in medieval Europe Mycobacterium mrWtufosis Tuberculosis ■ Shotgun sequencing ■ Microarray-based capture followed byNCS 19 *Genome5 from pre-Columbian human infections show phylogenetic clustering within animal-adapted lineage present today in sea Is * Molecular dating analysis suggests emergence of Ml HC <; 6,000 years ago * Analysis ol E uropean genomes shows past occurrence of multiple infections and suggests origin of lineage 4 during the4th to 5th century Ce i'ii enierica iubip-enterica serovar Paratyphi C Enteric (paratyphoid) fever ■ Shotgun sequencing ■ Microarray-based capture followed byNGS ■ In-solurion capture followed by HCS 11 •5. entente subsp. entencaserovar feratyphi C presence in 12th-century Ce Norway * Paratyphi Cserovar wasaIso identified among 16th-century individualism Mexico that were associated with the major post-contact 'cocoliz tli" epidemic SrophyJococeus Wf '-. I.i i- ■ Lrrinarytract infections ■ Puerperal fever Shotgun Lequencing 1 * Identified in '-SOO-year-old human remains from Troy * Association with women's mortality during childbirth in the past \ \ - identified lineage is not commonly associated with human disease today TdnnerefJa Jonyth\a Periodontal disease Shotgun sequencing 1 * Isolation from medieval human remains (circa gM-i2MCE) * First pathogen genome reconstructed from ancient dental calculus Treponema pallidum ■ Syphilis (Treponema ■ i.jl.-:.=■*:■■ Ii:!^i■ ■ Yaws (Treponema pa 1 du m su bs p. perten u e\ ■ Bejel [Trepcmema pallidum subsp. endemkum) Microarray-ba5ed capture fo J owed byNGS 5 * Isolated from individuals who Lived in Mexico City between the 17th and 19th centuries Ce * Different Treponema subspecies (T. pa J fitfum subsp. lid Ifidum and subsp. penenue) caused similar stele taL lesions usually identiliable as skeletal syphilis in infants Mb™ dwlerae Cholera Microarray-hased capture fo LI owed byNGS 1 * Isolation from 19th-century akohol-pre served intestinal specimen from an individual affected during the second cholera pandemic •The identified strain shows highest similarity with the classic pathogenic biotype Ol yersinia :■!-::- Bubonic, pneumonic and septicaemic plague ■ Shotgun sequencing ■ Microanay-based capture followed byNGS ■ In-solution capture followed by NCS 5S * Bacterium affected humans as early as 5,000 years ago * Both flea-adapted and non-adapted varia nts were present in Eurasia during the Bronze Age * Causative agent ol the Plague oF Justinian (6th century ce} * Causative agent ol Black Death and persistence in Europeduring the second plague pandemic (14th to loth century Ce) •Possible European origin ol third plague pandemic lineage Pathogen Infectious disease Method of retrieval, Number of genomes' Biological insights Rets Viral jHiŕnogerts HSV Viral hepatitis ■ Shotgun sequencing ■ In-solution capture followed by NCS ■ Whole-genome PCR" 17 * Identified in ancient human specimens as early as 7r0lK years ago * Neolithic genome lineage related to contemporary strains identilied in Alrican non-human primates * Complex evolutionary history of HBV and identification of ancient recombination event giving rise to genotype A strains HIV AIDS Whole-genome PCftb 1 •Analysis of HIV ftNA from archival specimens of seropositive individuals enrolled in HE5V studies during the Late 1970s * HlVwas introduced into the Americas from the Caribbean inthe early 1370,5 B19-V ■ Erythema inlectiosum (filth disease} in children ■ Arthropathies in adults ■ Hydropsfetalisorfetal death in pregnant women ■ Pure red-cell aplaiia In-solution capture followed by MGS 10 •Genomic signatures of ES19V identified in human remains dating as early as -7,000 years ago ■ Contrary to previous estimates of a most recent common ancestor younger than 200 years, phylogenetic and molecula r daring analysis ol ancient genomes showed a much lengthier association of B19V with human papulations Influenza virus Influenza Whole-genome PCftb 1 * First reconstructed genome from historical RNA virus * Avian source oil 913 influenza pandemic (Spanish flu, 1913-1520) * Reconstructed virus particle displayed increased virulence under laboratory conditions VARV Smallpox In-solution capture followed by MC£ 1 •Genome reconstruction from a 17th-century mummy from Lithuania • Recent emergence of Iftth century VARV Lineages (divergenceduring the 13th century CeJ Li. k niyor.."c pathogens Phytophtfiora Late blight (also known as potato blight) Shotgun sequencing 13 • First sequenced ancient eukaryotk.(plant>pathogen genomes • Isolated from historical herbarium specimens •A unique fttyrophrhora injesrons genotype caused the Irish potato famine and during the 1900s became replaced by the Ui-l lineage thatdominated worldwide untilthe 19705 Plasmodium falciparum and /tasmodi um vtmK Malaria In-solution capture followed by MGS • Oldest Plasmodium falciparum detection from southern ltaLy(lstto 2nd century Ce) •Plasmodium falciparum and Plasmodium viva* mitochondrial genome isolation from 20thcentury microscopy slides * Possible introduction of Plasmodium wax in the Americas through European contact Bl9V,humanuarTOnrukbig;CE, lurrcnl Era; HßV hcuatiLit, EíviruiL.ViTfiC. ilf>-:i>LiJĽlrr.'iľr: I u úľ,-iĽlut-ifr-rumples: NCt,ne vir ui .'Tlie ii-idkale-d numbers include whirls pathogen yĽ-iiunici-an-J ipccimcriiyielding yennn-ie-widL-dLl-a.1 Wlwls-ysr infucnmvirui , HIV and HĎV ' that wereiiNqutnLed uiiriy c apillary lequenc iny I Sanger methndX .t-yerierationLcuucncinu,; VAAYI vdrioL jmtfPCR ainpLiĽun^frnmlhtfLtudipujl Spyrou et al. 2019 D01:10.1038/s41576-019-0119-1 Present Schematic phvlogenetic tree showing how ancient genomes can provide information on key various aspects of the evolutionary history of pathogens. An ancient pathogen genome can potentially be placed as (A) an extinct sister lineage to the modern diversity (e.g., ancient variola virus from 7th- 10rh century [ 103]; image: teeth from an East Smithfield individual used to indicate source from which ancient variola-like sequences have been isolated, courtesy of Sharon DeWitte, Museum of London); (B) an extinct sister lineage to a modern haplogroup or genotype, but still falling within the modern clade of the pathogen (e.g.. variola virus from the 17th century; image: VD21 child mummy from Vilnius, Lithuania, from which smallpox was detected, from [ 10]); (C) belonging to a present-day MpJogroup. or genotype (e.g., hepatitis B virus from the lSth century [9,125]; image: child mummy from Naples, Italy, with HBV detected, © 2018 Patterson Ross etal. CC BY 4.0); or (D) at the base of the modern clade, possibly as a direct ancestor (e.g., Y.pestis from 134S [5]; image: skull of an individual from East Smithfield that yielded a Black Death genome, courtesy of Jelena Bekvalac, Museum of London (M1N86)). The square symbol denotes the common ancestor of modern pathogen samples. Importantly, the emergence of a pathogen in its present host could have occurred at any point along the branch between the divergence from its closest extant or extinct relative and the most recent common ancestor of the sampled isolates (branch in blue). Ancient pathogen genomes can help narrow this window of emergence [90] while also shedding light on any gain or loss of function along the branches leading up to the modern clade (branch in orange). Past *•— Closest extant group A Gam or loss D Emergence of pathogen Common ancestor of modern samples Phylogenetic placements of ancient pathogen genomes A Extinct sister lineage to modern diversity (e.g., ancient VARV ~7-10th c) B Extinct sister lineage to a modern haplogroup or genotype (e.g., variola virus ~17th c) C Belonging to a present-day haplogroup or genotype (e.g.. Hepatitis B virus 16th c) D Base of the modern clade, possibly a direct ancestor (e.g.. Yersinia pestis 1348) Duchene et al., 2020 D01:10.1016/j.cub.2020.08.081 Current Biology PALEOGENOMICS IN PATHOGEN RESEARCH • Fast rate of evolution • Pathogen morphology often inaccessible or insufficient • Presence of pathogen not necessarily associated DISEASE-RELATED CHANGES tiff #c . ft tiff AAA M A AAA AM. —— n. a —- .hah. Pathogen exerts A A A A selective pressure AAA A AAA Pre-epidemic Post-epidemic Contemporary Ancient humans humans ^ Absence of risk-associated mutation Presence of risk-associated mutation Protective variants in e.g. TLR10-TLR1-TLR6gene cluster, human leukocyte antigen-associated PPT2and EGFL8 Kerner et al., 2023; DOI: 10.1038/s41591-023-02244-4 PALEOGENOMICS IN PATHOGEN RESEARCH ACTIVE? LATENT? NON-PATHOGENIC? A ntonin-e plague [165-iSOf Suspected Lo be smallpox Cyprian plague 1.250-275 ^ Suspected to be either i-.;l dz-■ or measles Roman fever Suspected to be malaria Pharaoh's plague ("lS-iSth century BC| Suspected to be snail fever (also called blond fluke disease er schistosomiasis] First Yersinia plague pandemic 1541-543}_ I Leprosy 116—17th centunlesf h English sweat |14S5-1551) Suspected to be hantavirus Second Yersinia plague pandemic [1346-135^ Smallpox (16-lSth century) The scale of the epidemic among Native American popular on upon European contact remains uncertain., but the disease nevertheless- played an important role in the population history erf the American continent. Third yera'rrJo plague pandemic (l£S3s| Plcardy sweat |18-19th century! Suspected tobe hantavirus Spanish flu (lMfr-lMS) The flu pandemic appeared to have rapidly spread in three distinct waves within a year in Europe. Asia and Americas. _ H'ttite plague (14th century EC) Suspected to be tularemia Plague of Athens [427-430 3C| Suspected to be typhus, typhoid fever, me-asles or smallpo* Leprosy \ 12- 14th century] Syphilis 1,15th century] The Columbian hypothesis on the origin of syphilis posits that European exploration of the Americas introduce syphilis into Europe, while the pre-Columbian hypothesis suggests that the d ise a se has a much older history in the Old World. Typhus (14fi9-14SÜr< Also called war Fever, prison fever and ship Fever, typhus epidemic was recorded in Spain during the Spanish war against the Moors in Granada. Cholera \ 19th century) A total of seven pandemics have been recorded since the 19th century. Tuberculosis JlS-lfrh century) One oF the oldest diseases known to humanity, tuberculosis has been previously called by numerous names such as phthisis, Pott's disease, King's evil, scrofula, consumption and white plague. Typhus <1S12} Typhus epidemic was recorded during the French war against Russia. Trends in Micrabtclagy Figure 1. Overview and Timeline of Hialoricalfy tollable Disease Outbreaks in Human History. Colored dels represent dfffareni outbreaks and epiderics. Black dels tfidlcaledis6a3&outtraa^s of unresolved on^ins[1.£7-75]. The origin of syphlfe rerinflJnscontentlouG. win two hypotheses put forward to explain the epldamlc In Eunopa In the 12tfi-l4u1 canturlas [1.76-78]. Mot shownare seven Bronze Age (-^3000 EC) Yersinia plague slralns [46]. Locatlonof dots reprffientB apr^rcrtdiriatetima and should not be laken as precise estimates of ihe time, of occurence of ihe disease. Andam et al.p 2016 D01:10.1016/j.tim.2016.08.004 DOMESTICATION, AGRICULTURE • Increase in pathogens, including those affecting plants and animals • Changes in human genome associated with pressure from pathogen spread • Further changes with urbanisation • Anthroponosis - human to human (rubella, smallpox, gonorrhea...) • Zoonosis - between animal and human in any direction • Anthropozoonosis - animal to human (hemorrhagic fevers) • Zooanthroponosis - human to animal (influenza, tuberculosis) • Synanthropic - from animals with us (urban, domestic - urban rabies, cat scratch disease) • Exoanthropic - animals living in the wild (Lyme disease, wildlife rabies...) • Sapronosis - abiotic environment (e.g., soil, decaying plant or animal remains) to living host (legionellosis, nontuberculous mycobacterioses, Yersinia pseudotuberculosis) Hubálek, 2003; DOI: 10.3201/eid0903.020208 MASS GRAVES INJURY FAMINE INFECTIOUS EPIDEMIC DISEASES Example: iScience. 2021 May 21; 24(5): 102419. Published online 2021 Apr20. doi: 10.1016/j.isd 2021 102419 PMCID: PMC8100618 PMID: 33997698 Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lübeck Magdalena Haller.1 Kimberly Callan.1'2 Julian Susat.1 Anna Lena Flux.3 Alexander Immel.1 Andre Franke.1 Alexander Herbia.4 Johannes Krause.4 Anne Kupczok 56 Gerhard Fouquet.7 Susanne Hummel 3 Dirk Rieaer.8 Almut Nebel.19 and Ben Krause-Kvora1'9'10^ ---- piri pi rrrjr^vi-i- WAYS TO STUDY CIVILIZATIONS DECLINE/COLLAPSE • Possible epidemics • Famine due to plant pathogens Article I Published: 15 January 2018 Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico As-ilc J vcce-e A exčrdeľ He'j :i ľ diad G carps-B. Ne v VI. Rubles Gar:'a. Christina Wannner. Jcihannes Krause Natuľe Ecology &Evcliit\an 2, 520-528 [2013] | Cite this article 9523 Accesses | 147 Citations | 1275 Altmetric | Metrics Abstract Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many o ľ which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of anew metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enierica in individuals buried in an early contact era epidemic cemetery atTeposcolula-Yucimdaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 ce epidemic that affected large parts of Mexico. Locally, this epidemic was known as 'cocoltztli, the pathogenic cause of which has been debated for more than a century. Here, we present genome-wide data from ten individuals for Salmonella enteäca subsp. tviŕericííserovar Paratyphi C, a bacterial cause of enteric fever. We propose LhaLi. Paratyphi C be considered a strong candidate for the epidemic population decline d u ri ng th e 1545 cocolitt ti outbrea k at Teposco I ul a -Yucundaa. Article | Open access | Published: 06 February 2014 A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus O Ve' S n't-. Alan C Pbit Rose. Y^a" Liu -li- 1 -: i-. A a jy Scientific Reports 4, Article num bsr: 4003 (2014) | Cite this article 6439 Accesses | 66 Citations | 57 Altmetric | Metrics Abstract The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain -750 years of age. Phylogenetic analysis of BSMVthat includes this genome indicates the divergence of BSMVand its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa and spread to North America and East Asia with their hosts along historical trade routes. 750 yBP A PALAEOVIROLOGY • Research of ancient viruses and their co-evolution with hosts • Small genome, often tissue specific • RNA and ssDNA challenging • Ancient viruses, ancient host genomes • Modern genomes of hosts • Endogenous viral element (EVE) - viral sequences integrated into genome through various mechanisms, including transposition • Endogenous retrovirus (ERV) - subset of EVEs, retroviruses in the genome of their hosts -evolutionary history Baltimore Classification of Viruses Group Example Genetic Material Processing microbenotes.com Group 1 dsDNA Group 2 +ssDNA Group 3 dsRNA Group 4 +ssRNA Group 5 -ssRNA Group 6 +SSRNA-RT Group 7 dsDNA-RT Smallpox Parvovirus Rotaviruses Coronaviruses Measles HIV Hepatitis B dsDNA mRNA +SSDNA dsDNA mRNA y*y*y* dsRNA +SSRNA -SSRNA +SSRNA dsDNA-RT mRNA S\S\s\ —► '-!\/\/\/®®® -SSRNA mRNA mRNA RT dsRNA dsDNA !{WV"" mRNA +SSRNA RT y?^yxy?<; —► y*y*yx —► "\/\/\/" * " dsRNA dsDNA mRNA https://microbenotes.com/what-are-viruses/ PALAEOVIROLOGY 1997 2003 2005 2012 2014 First ancient RNA viral study First ancient DNA viral study First complete ancient RNA virus First complete ancient DNA virus First ancient virome study 2020 Oldest complete ancient RNA virus Oldest viral detection 1999 First NGS platform on the market 2005 First ancient DNA study using NGS 2006 First ancient viral study using NGS 2014 > Oldest complete ancient DNA virus 2021 Nishimura et al., 2022; DOI: 10.3390/v14061336 VARIOLA VIRUS Research articles Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox Giada Ferrari'''E37 Judith Neukammf H7 Helle T. Baalsrud, Abagail M. Breidenstein, Mark Ravi net, Carina Phillips. Frank Ruhli, Abigail Bouwmair'-Hand Verena J. Schuenemann-'-H Published: 05 October 2020 https://doi.org/10.1098/rstb.20l9.0572 • Was thought to originate around 3000-4000 years ago Sbpbna - James Gathany Ferrari et al., 2020 D01:10.1098/rstb.2019.0572 iß) -fr- -fr- VA P-II VD21 -P328 - camelpox taterapox cowpox mulfordsl902 - horsepox monkeypox - volepox skunkpox raccoonpox (b) 1908-1915 AD 1797-1820 AD 1678-1714 AD 1639-1662 AD -EE 1877-1893 AD 4 p-i DQ441417.1 .Botswana. 1972 DQ441418.1 _Bolswana_ 1973 DQ441436.1 .South.Africa. 1965 DQ441435.1 _South_ Africa. 1965 DQ437583. I.Congo. 1970 DQ441423.1 _Congo9_ 1970 DQ441443. l_Tanzania_1965 DQ441438.l_Somalia_1977 DQ441439.1 _Somalia_ 1977 DQ441425.1 .Ethiopia. 1972 DQ441440.1 Sudan_l 947 DQ44144 I.I.Sudan. 1947 DQ437581.1 .Bangladesh. 1975 DQ441421.1 .Bangladesh. 1974 DQ441420.1 .Bangladesh. 1974 DQ437588.l_Nepal.1973 DQ437584.1 .Germany. 1958 DQ441446.1 .United.Kingdom. 1947 DQ44l427.l_India.l953 NC_001611.l_major_lndia.1967 DQ437587.1 .Iran. 1972 DQ437592.l_Syria.1972 DQ441448.1 .Yugoslavia. 1972 DQ437589.1 .Pakistan. 1969 DQ437580.1 .Afghanistan. 1970 DQ44l433.l_Kuwait.1967 DQ437585.l_India.l964 DQ437586.1 .India. 1964 DQ437591.1 .Sumatra. 1970 DQ441445.1 .United.Kingdom. 1946 DQ441444.1 .United.Kingdom. 1946 LT706528.l_Czcch.V563 DQ44l428.l_lndia.1953 DQ441429.1 Japan. 1946 DQ441430.1 .Japan. 1951 DQ441431.1 .Japan. 1951 DQ437582.l_China.l948 DQ441432.l_Korea.1947 DQ441426.1 .Guinea. 1969 DQ441437. l.Sierra.Leone.l 969 DQ441416.Uenin.1968 DQ441434. I.Niger. 1969 D TT DQ441419.l_Brazil.1966 T -11 Y16780.1 .minor.Garcia.l 966 DQ441447.1 .United.Kingdom. 1952 LT706529.1_Czech.V1588 l'328J.ondon BK010317.1 _VD21 .Lithuania 1600 1650 1700 1750 1800 1850 1900 1950 1977 Ferrari et al., 2020 D01:10.1098/rstb.2019.0572 THE SPREAD AND ERADICATION OF SMALLPOX https://wwwxdc.gov/smallpox/history/smallpox-origin.html A container used to store the powdery variolation material in Ethiopia. West African god of smallpox Shapona wi thought to force the disease upon humar due to his 'divine displeasure ." Smallpox Is present In the Egyptian Empire. 3ü£ CENTURY BCE increased trade with China and Korea Introduces smallpox Into Japan. Smallpox goddess Shitala Mata. worshipped in northern India, was considered both the cause and cure of smallpox disease. Smallpox spreads to Asia Minor, the area of present-day Turkey. Population expansion and more frequent travel renders smallpoi endemic In previously unaffected Central and North Europe, with severe epidemics occurring as far as Iceland. 412 CENTURY BCE A written description of a disease that clearly resembles smallpox appears In China. European colonization and the African slave trade Import smallpox Into the Caribbean and Central and South America. Variolation—a process of grinding up dried smallpox scabs from a smallpox patient and Inhaling them or scratching them Into an arm of an uninfected person—is being used in China and India to control smallpox. Variolation Is Introduced Into England by Lady Mary Wort ley Montagu, a wife of the British ambassador in Turkey. In 1796, Edward Jenner, an English doctor, shows the effectiveness of previous cow pox infection In protecting people from smallpox, forming the basis for vaccination. 6- CENTURY 7IÜ CENTURY 10- CENIURY TIH CENTURY 13" CENTURY CENTURY 16- CENTURY 1712 CENTURY 18Ti CENTURY Smallpox is widespread In India. Arab expansion spreads smallpox Into northern Africa, Spain, and Portugal. Crusades further contribute to the spread of smallpox In Europe with the European Christians moving to and from the Middle East during the next two centuries. Portuguese expeditions to African west coast and new trade routes with eastern parts of Africa introduce the disease into West Africa. Traces of smallpox pustules were found on the head of a 3.000-year-old mummy of the Pharaoh Ramses V. Variolation is a commonly used method for preventing smallpox In the Ottoman Empire (former Asia Minor, present-day Turkey) and North Africa. European colonization Imports smallpox Into North America. The Ottoman Empire in 1801 extended from Turkey (Anatolia) to Greece. Hungary. Bulgaria. Romania, northern Africa and parts of Middle East Smallpox is thought to arrive here from Asia through major trade routes, like the Silk Road. Lady Mary Wortley Montagu, a survivor of smallpox herself, had both of her children variolated and was the foremost advocate of the technique in England. n defeats the "smallpox demon" In Japan, families who fell sick * up shrines in their homes to :ion of smallpox into Mexico by the Spanish around 1520 was one of the factors that led to the demise of Aztec Empire. Franciscan missionary Bernardino de Sahagun. who lived there from 1545 until his death in 1590. illustrated this in his accounts of the Aztec history entitled "General History of the Things of 201 CENTURY Smallpox Is widespread In Africa, Asia, and South America In the early 1900s, while Europe and North America have smallpox largely under control through the use of mass vaccination. After a global eradication campaign that lasted more than 20 years, the 33rd World Health Assembly officially declares the world free of smallpox In 1980. Edward Jenner (1749-1823) SMALLPOX ORIGIN NORTHEAST AFRICA c. 10,000 k Smallpox is believed to have first appeared with early agricultural settlement Incidents, of major smallpox otitbrealcs stretch from Europe all the way to Siberia fS SIBERIA One of two remaining stocks of smallpox is IwH under lock and kc>' to prevent possible use as biological weapon 340 Earliest written account of using the plant qing-liao for treatment of malarial fever CARIBBEAN IS1-\ND5 ami SOI Til AMERICA 18th century I .eprosy crosses Atlantic Ocean with West African slaves J6S0 Medicinal hark used by Incas is adopted by Jesuits for treatment r>f malaria INDIA r. 1500 fK Egyptian merchants arrive hearing smallpox Oldest documented skeletal evidence of leprosy ■ 30.000.000 st Malaria plasmodii is traced to a mosquito found in a piece of amber Doug Belshaw blog HEPA r/T/S B VIRUS • Best studied virus in aDNA • Global prevalence around k % • Oldest ca 10000 BP Ten millennia of hepatitis B virus evolution arthur kocher 0 , ujka papac 0, rodrigo barquera ffi„fei_ixm. key ^g) „maria a. spyrou, ron hübler ^ „ adam b. rohrlach ^ , franziska arqn (jS^ . Raphaela stahl ffi.[...], and de mise Kuhnert ^ +160 authors Authors Info & Affiliations £C likely present in human populations before farming. Furthermore, the virus was i o present in the Americas by about 9000 years ago, representing a lineage sister to g the viral strains found in Eurasia that diverged about 20,000 years ago. — LMZ 12000 9000 6000 3000 0 Years BP 11000-9000 BP 9000-7500 BP J f> 7500-5000 BP 3000-1500 BP ? 5000-3000 BP 5 ♦ • 1500-0 BP HBV lineage Mesolithic 1 Mesolithic 2 Anatolian Early Neolithic 9 WENBA Genotype A Genotype D Kocher et al., 2021; DOI: 10.1126/science.abi5658 2149 HBV lineage Date range (BP) • Mesolithic 1 O 11000-7500 Anatolian Early Neolithic □ 7500-5000 • Mesolithic 2 <-> 5000-3000 • WENBA • Genotype A • Genotype D • Undetermined Prev. published A 3000-1500 V 1500-0 B HBV lineage • Ancient American 1 Ancient American 2 • Ancient American 3 Genotype F • Genotype H • Genotype A Date range (BP) O 11000-7500 A 3000-1500 V 1500-0 Prev. published A, , .D A,D A,D A, D A,D D H A,D F,A E A,E p E A,D B,C A,D A,E,D A E,D A,D B,C A,B,C B.C F,A,D B,C ,D Kocher et al., 2021; D01:10.1126/science.abi5658 HEPA r/T/S B VIRUS Letter | Published: 09 May 2018 Ancient hepatitis B viruses from the Bronze Age to the Medieval period Barbara Mühlernann, Terry C. Jones, Peter de Barros Damqaard, Morten E. Allentoft, Irina Shevnina, Andrey Logvin, Emma Usmanova, Irina P. Panyushkina, Bazartseren Boldgiv, Tsevel Bazartseren, Kadicha Tashbaeva, Victor Merz, Nina Lau, Vaclav Smrčka. Dmitry Voyakin. Egor Kitov, Andrey Epirnakhov, Dalia Pokutta, Magdolna Vicze, T, Douglas Price, Vyacheslav Moiseyev, Anders J. Hansen, Ludovic Orlando, Simon Rasmussen, Martin Sikora, Lasse Vinner, Albert D. M. E. Osterhaus, Derek J, Smith, Dieter Glebe, Ron A. M, Fouchier, Christian Prosten, Karl-Goran Sjögren, Kristián Kristiansen & Eske Willerslev^ A3 FJ692611 11 HI1 Caribbean A3_FJ692598_11_HTl_Canbbean A FN545831 10 CMR Middle Africa A3_FJ692556_13_NIG_ Western Africa A3 0O161813 11 GIN West em Africa A3_AY934764_12_GMB Western Africa A1 AB453988.12 JPN Eastern Asia A1 AB116084 14 BGD Southern Asia A1_AB076679_20_MWI_Eastem Africa A EU859952 19 BEL Western Europe A4_GQ331047.19.BEL.Western Europe A4 GQ331046 11 BEL Western Europe S_l567_SVK_Eaaiem Europe A2 GQ477499 11_POL Eastern Europe A2 AY738142 12 GER Western Europe -IA_DA195 2645 HUN Eastern Europe RISE386 4160 RUS Central Asia RISE387_4282 RUS Central Asia C4.AB04870S. C4_AB048704 b5_AB287321 B5_AB287320 B5 DQ463789~ B5.AB287318. B5 AB287316 b5 DQ463792 b3 AB219430 B3_AB033555 B3_AP011089 B AB241117 1 B3.AB219429. B1 KP341007 b1 AB073858 25.AUS Australia 25_AUS_ Australia 19_GRL_ Northern America 19_ GRL.. Northern Amenca 38 CAN Northern America 12 _ USA_ Northern Amenca 12 USA Northern America 38 CAN Northern Amenca 12_PHL_South eastern Asia l8_IDN_Soulh eastern Asia 19_DN_South eastern Asia 2 PHL South eastern Asia 12.PHL.South eastern Asia 4 JPN Eastern Asia 16.JPN.Eastern Asia 6 DQ993686 11 VNM South eastern Asia B4_AB073835J6_VNM_South eastern Asia 335 0 XB0925 22 GRC Southern Europe — D_AY796031_13_TUR_WesternAaa 02 GCM774S5 11 POL Eastern Europe D2_JN642163_7_LBN_ Western As«a D2GQ477453 11 POL.Eastem Europe D2 JN642160 7 LBN Western Asia D_AB2l08l8_12_JPN_EastemAsia D1 KP322600 4 NA Western Asia D1_FJ899792_t0_CHN_Eastem Asia D1 JN642140 7 LBN Western Asia D_AY902768_12_USA_Northem America D3 KC875319 7 IND Southern Asia D3 KP322602 4 IND Southern Asia D3 JN688711 6 ARG South America 03 JN688710 7 ARG South Amenca DA222_1l67_KAZ_Central Asia D AB048702_25 AUS Australia D_ABO48701 25 AUS Australia O AB033559 29 PNG Melanesia D4 HE974378 14 MTQ Caribbean D4_GQ922005_33_CAN_Northem Amenca D4 KJ47089I 8 BRA South Amenca D4_KJ470893_B_BRA_South America D4 KJ47089B 7 BRA South America 07 FJ904436 10 TUN Northern Africa 07 FJ904430 12 TUN Northern Africa O AM494716 10 CAF Middle Africa D_GQ2O5378_10 IND_Southem Asia O GQ205377 10 INO Southern Asia O5GQ205385 9 INO Southern Asia D GQ205389 9 IND Southern Asia D5 KP322603 4 IND Southern Asia D_GO?05382.9_IND_Southern Asia D GO205384 9 IND Southern Asia D_DQ3l5779_t2JND_Southem Asia D AB033558 29 JPN Eastern Asia DAZr_1610_KAZ_Central Asia DA51 2397 KGZ Central Asm Vg Gorilla AJ131S67 18 CMR Middle Africa Chimp_AY330911_14_CMR_M*ddle Africa Chimp AF222323 17 NA NA Cnimp_A8032433_35_LBR_Western Africa BA RISE563 4488 Ell Western Europe BA RISE254 4009 I UN Eastern Lurope BA RISF154 3851 fOl Easlem Europe Oratxj EU155B24 10 THA South eastern Asa Orang_AF 193863_ 18_NA_NA J AB486012 11 JPN Eastern Asia GiMx»r>_FM209516_11_TWN^Eastern Asia Gibbon U46935 27 NA NA re Í Q. o E 87 .AJndbnes la JZM4-4 & 6 straln£.5»»crieHas x 8 s 4 -i_2BQ6 _A_ tflel nam jiHI'-^H.....<,h.>_ a... ■icrpa- -^&3 il_China l>w -;;w.i9rj3ji_ci'ni ■52-S5_28«ejl_VitilnBm JK1*6-ít.l«8Jk.Ph1lfcl ■' "■ Mmn JJM3-W-WT7_A_ Ta iwa r Jľ B G7-B 4_! B B 6 A-Vie I n am . ..HI:,-1 W_:'MMi_m_V~-,.i-, jHaai-«4_i9a &_a_c m™ CF&P-iSSS 4 3 wreiní.New-Z«ii#iw JK14&-C1 1950 A_MaLays1a . i;i;jh ..i.-. -ChlOT-KLÍSOT _a_1 n*ici in J K145-BL1 í 98_A_M ala wii a :l . ■ ■í-Yí.^F'ji ..■.f. MJflHJ I'l-i.b.)-rii1. lpib ? J2 81 ?Xfa tiSaii _P-B6_2617_A_Paltislan JJZSfl 80." í B7_A_ MalH iva _ JJ23a-11_ľJB7_A_Val:JW_i MCPPB-3&18-TW8 JU nfli« Jja36.-fli S 5 _1rain__M_,ldi.«-; _P2.34-§3 2317 a Pakistan ■•■ ľ. =4jtii;|:iii J. U I ■'>{»> A PaK-SILir-LC1B3 2BB6_A3angLade5 h . :Jľfj..'KWi).^Bangl«te3h ,ll:fl ■ . - I a lim :1 LE11&-U*BB_A.Mal' .p.' I ^KfJfi ŕ. Mil-_l-3í-l_2s-G_/i Scicgn. 1CPP1a-3él2_HeS_ít_lnaia HERB «M /■ inoia - G f, Bäľ'íani'sN ii mi iíj? r. cnlm _G115JSe7JmJrdia I 'ť.ľl,:'---Jt.sí.-9fla_*»fJnilia _f;b-ŕ Ií^í.jlw.Oman k i- m .j ;_Mia».Cer">vT« Ai>u„ T, .Kl.;j s ,-,.,i:,r "K, _D-71a.2sb7.Ailu- Cíii i jl-Jiŕi .ľ''|. .'.:!■'''."l'i "" ----19Ba_Astar_lndia IIIIB 1817 1217 1317 1417 1517 1617 BIOSAFETY • Should such research take place? • Should the methodology and genome be published? (Critique surrounding 1918 influenza virus) Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology Matthieu Leeendre, |ulia Bartoll. Lvubov Shmakova, +10. and |ean-Michel Claverie B Authors Info & Affiliations Edited by James L. Van Eden, University of Nebraska-Lincoln, Lincoln, NE, and approved January 30, 2014 (received for review November 7, 2013) March 3, 2014 111 (11) 4274-4279 https://clQi.ora/10.1073/pnas.1320670111 Pithovirussibericum resurrection - infection of Acanthamoeba, >30,000-y-old Global warming, mining and drilling - potential threat from frozen viruses > \ ^0% Ír VF 1" • 4 2prn J f^^lOorari O 200 nm ■ 200 nm lOOnm YERSINIA PESTIS Volume 35, Issue 13,29June2021,109278 Rodent reservoir, flea as a vector After infection • pathogen travels to lymph nodes causing bubonic plague (swelling - buboes) • lung infection - pneumonic • disseminated - septicemic Oldest case 5000 BP, probable emergence of this lineage 7000 BP during Neolithic Report A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis lulian SusQt111, Harald Liibke 2 n, Alexander Immel1, Ute Brinker2, Aifo. Macäne 3, lohn Meadows 1 4, Britta Steer5. Andreas Tholey5, Ilqa Zaqorska s, Guntis Gerhards 6; Ulrich Schrnolcke 2, Märcis Katrins 6, Andre Franke Elina Petersone-Gordina 6, Barbara Tefjman 7, Mari Tory 8. Stefan Schreiber19, Christian Andree 10i Valdis Berzins 6, >lmut Nebell. Ben Krause-Kyora 111 £ B Yersinia pestis BALTIC SEA Susat et al., 2021 DOI: 10.1016/j.celrep.2021.109278 Fig. S | yersinia pestis ecology and transmission cycle. A simplified version of the Yersinia pestis enzootic cycle, during which the bacterium is maintained among wild rodent populations through a flea-dependent transm ission mechanism. Under poorly understood circumstances, plague epizootics, which are best explained as animal epidemics,can occur among susceptible rodent populations. During those periods, humans and other mammals are at highest risk of becoming infected with Y. pestis. Plague can manifest in humans in the bubonic, pneumonic and septicaemic forms. Pneumonic plague is the only form that can result in airborne transmission between humans. Spyrou et al., 2019; DOI: 10.1038/s41576-019-0119-l Modern Y. pestis genomes Branches 0,1, 2, 3 and 4 A Middle Neolithic strain (4,900 y bp) ▲ Late Neolithic/Bronze Age strains (4.800-3,500 yBP) A Late Bronze Age/Iron Age strains (3,800-2,900 yBP) A DA101 Tian Shan strain (2nd to 3rd century CE) ▲ First-plague-pandemic strains (6th to 8th century CE) A Second-plague-pandemic strains (14th century ce) A Second-plague-pandemic strains (16th to 18th century CE) % Spyrou et al, 2019; D01:10.1038/s41576-019-0119-1 Fig. 4 | Map of published modern and ancient Yersinia pestis genomes. Published ancient specimens that have yielded whole Yersinia pestis genomes and genome-wide data are shown in triangles (n = 38). and their different colours indicate time period distinctions, A set of modern V. pestis genomes (n = 336J. from the following publications (released until 2013)^" i1'-1"1^-1^^ are shown as grey circles within their geographical country or region of isolation, and the size of*aeh circle is p ro parti on al to th^numbw of strains sequenced from each location (number indicated when more than one genome is shown). The areas highlighted in brown are regions that contain active plague loci as determined by contemporary or historical data, yap, years before present. Adapted with permission from the "Global distribution of natural plague foci as of March 2016'from htlps://www.who.int/csr/disease/plague/Plague-ma p-Z016.pdf- Branch 1 (2nd and 3rd pandemics) Branch 0 branch 2 branch 3 branch 4 1 Ancient genomes y-v Second pandemic genomes (Europe) u (post-Black Death 16th to 18th century ce) Second pandemic genomes (Europe) * (Black Death until late 14th century ce) OFirst pandemic genomes (Germany) (6th to 8th century CE) » DA101 (Tian Shan region) (2nd to 3rd century ce) f-\ Late Bronze Age (Samara region) u (3,800yBP) OLate Neolithic/Bronze Age (Eurasia) (4,800-3,500 yBP) Middle Neolithic (Scandinavia) ^ (4,900 yBP) ^ ^ ^ Non-flea adapted 3,500—5,000 yBP J 5f> y Flea adaptation in Y. pestis: acquisition of ymt and pseudogenization of FDE2, PDE3, rcsA and ureD genes I yersinia pseudotuberculosis Spyrou et al., 2019; D01:10.1038/s41576-019-0119-1 Fig. 6 I Evolutionary history of yersinia pestis. A phylogenetic tree graphic depicting trie evolutionary history of Versinia pestis based on both ancient and modern genomes. Ancient strains that have been previously characterized by phylogenetic anaLysis are represented with coloured circles among the tree branches as follows: a Middle Neolithic genome is shown in yellow; tate Neolithic and Bronze Age (LNBA) genomes are shown in purple; a Late Bronze Age genome (RTS) encompassing signatures of flea adaptation is shown in blue; a pre-Justinian, 2nd century of the current era (ce), genome is shown in green; first-plague-pandemic genomes are shown in black; second plague pandemic, 14th-century genomes are shown in red; and post-BLack Death (up until 18th century ce) genomes are shown in grey. Modern lineages are simplified and shown as branches of equaL Length in order to enhance the clarity of the graphic. The geographical distribution of modern strains is as follows (using universal country abbreviations): branch 1 (UGA, DRC, KEN. DZA. MDG.CHN, IND, IDN, MNM, USA and PER), branch 2 (RUS, AZE. KAZ, KGZ, UZB, TKM, CHN. IRN and NPL). branch 3 (CHN and MNG), branch 4 (RUS and MNG) and branch 0, including lineages 0.ANT3 (CHN and KGZ), 0.ANTS (KGZ and KAZ), 0.ANT2 (CHN), 0.AIMT1 (CHN), 0.PES (MNG), 0.PE4 (TJK, UZB, KGZ, RUS, CHN and MNG), 0.PE2 (GEO, ARM, AZE and RUS) and 0.PE7 (CHN). yBP, years before present. YERSINIA PESTIS Volume 26, Issue 5, 19 May 2023, 1067E7 Improving the extraction of ancient Yersinia pestis genomes from the dental pulp Pierre Clave! 1„ Lexane Louis L, Clio Per Sarkissian 1, Catherine Theves L, CLaudia Gillet 1, Lorelei Chauvey - Gcigt" ~suls-^s he nie Schiavinato Laure Calviere-Tonasso Norbert Telmon \ BenoTt CLrjvel2, Richard jonvel3, StefanTzortzis 4, Laetitia Bouniol5, lean-Marc Femolant 5> )ennifer Klunk 6. Hendrik Poinar7 3 9h Michel Siqnoli 10< Caroline Costedoat10, Maria A, Spvrou 11, Andaine Sequin-Orlando V Ludovic Orlando 112 E ■ 18" century CE • Thirty Years' War ▲ Black Death ♦ Post-Black Death • 1300-1400 CE o 1400-1650 CE • 1600-1800 CE • Our sludy Ancient DNA Extraction from Dental Pulp Yersinia pestis Host Contaminant \ / 1 hour pro-digestion Ö Overnight digestion O Clavel et at, 2023 DOI: 10.1016/j.isci.2023.106787 MYCOBACTERIUM TUBERCULOSIS Home > Genome Biology > Article A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex Research | Open access | Published: 10 Augu5t2020 Volume21, article number201,(2020) Cite this article L2 (1036-2356) Background Although tuberculosis accounts for the highest mortality from, a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000ycars. Here, we aim to address tills discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Pcdcr Winstrup of Lund (b. 1605-d.l679). Results Ametagcnomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Baycsian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategics more realistically than those based on the coalcscent. Conclusions The results of our nietagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, wc estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC. i54U animal Jüan lineages M. canettH -3000 -2000 -1000 Years Before Present ^62438917^5016344516 MYCOBACTERIUM LEPRAE Detection and Strain Typing ofAncient Mycobacterium leprae from a Medieval Leprosy Hospital G. Michael Taylor |5|, Katie Tucker, Rachel Butler, Alistair W. G. Pike: Jamie Lewis, Simon Roffey, Philip Marter, Oona Y-C Lee: Houdini H. T. Wu, David E. Minnikin, Gurdyal S. Besra, Pushpendra Singh: Stewart T. Cole. Graham R. Stewart Published: April 30.2013« A. https://doi org/10.137iyjournal.pone.0062406 It May also Strike the EYES and the Thin Tissue Lining the Inside of the NOSE, KIDNEYS, and MALE REPRODUCTIVE ORGANS Blindness or Glaucoma Kidney Failure Muscle Weakness Inability to Flex Erectile Dysfunction VectorMine Taylor et al., 2013 DOI: 10.1371/journal.pone.0062406 SMALLPOX ORIGIN NORTHEAST AFRICA c. 10,000 k Smallpox is believed to have first appeared with early agricultural settlements Incidents, of major small'*ix outbreak* stretch from Europe all the way to Siberia fS SIBERIA One of two remaining stocks of smallpox' is IwH under lock and kcj' to prevent possible use II biological weapon 340 Earliest written account of using tlic plant (|ing-liao for treatment of malarial fever CARIBBEAN ISl-\NDe ami SOI Til AMERICA 18th century I -eprnsy ČNÍM Atlantic Ocean with West African slaves J6S0 Medicinal hark used by Incas is adopted by Jesuits for treatment of malaria INDIA r. 1500 fK Egyptian merchants arrive hearing smallpox Oldest documented skeletal evidence of leprosy ■ 30.000.000 st Malaria plasmodii is traced to a mosquito found in a piece of amber Doug Belshaw blog Fig 3 Dissemination of leprosy in the world, based on the analysis of single-nucleotide polymorphisms. The ovals indicate the country of origin of the samples examined and their distribution into four SNP types: yellow, type 1: orange, type 2: pink, type 3: green, type 4. The coloured arrows indicate the direction of human migrations predicted by. or inferred from SNP analysis: white dotted arrows correspond to the migration routes of humans derived from genetic, archaeological and anthropological studies, with the estimated time of migration in years. From Monot etal (2005). Reproduced with permission from AAAS. Washington. DC. USA. SNP. single-nucleotide polymorphisms. EMBO Reports, 2007; DOI: 10.1038/sj.embor.7400908 TREPONEMA PALLIDUM • Syphilis (Treponema pallidum subsp. pallidum) • Yaws (Treponema pallidum subsp. pertenue) • Bejel (Treponema pallidum subsp. endemicum) • Low pathogen load in tertiary stage Journal of Archaeological Science Volume 32, Issue 5, May 2005, Pages 703-713 ELSEVIER The limits of biomolecular paleopathology: ancient DNA cannot be used to study venereal syphilis ^^^^ Abigail 5. BQuwrnan, Terence A, Brown s Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe Graphical Abstract Treponema pallidum in early modern Europe * A Example: Tp ssp. paHtóum Tp ssp-perfentw T. pallidum [new lineage! Authors Kerttu Majander, Saskia Pfrengle, Arthur Kocher.....Denise Kuhnert, Johannes Krause, Verena J. Schuenemann Correspondence kerttu.majander'ttuzh.ch (K.M.). krause@shh.mpg.de (J.K.), verena. schuenemann@iem.uzh.ch (V.J.S.) In Brief Majander et al. find a high diversity among the first ancient European treponemal genomes, including a newly discovered lineage. Dated around Columbus' contact with the Americas, these lineages and their overlapping spatial distributions suggest a possible Old-World origin of syphilis and the existence of endemic treponematoses in Europe. Highlights • Four ancient Treponema pallidum genomes from early modern Europe were reconstructed • The genomes are highly diverse and include syphilis, yaws, and an unknown lineage • The new ancient T. pallidum lineage is a basal sister group to yaws and bejel Molecular clock dating would allow a pre-Columbian origin of T. pallidum in Europe SALMONELLA ENTERICA Article I Published: 24 February 2020 Emergence of human-adapted Sa Imonella enterica is linked to the Neolithization process Felix M, Key Cosimo Posth, Luis R. Esquivel-Gomez, Ron Hübler, Maria A. Spyrou, Gunnar U, Neumann, Anja Furtwängler, Susanna Sabin, Marta Burri, Antje Wissgott, Aditya Kumar Lankapalli, Ashild J. Vägene, Matthias Meyer, Sarah Nagel, Rezeda Tulchbatova, Aleksandr Khokhlov, Andrey Chizhevsky, Svend Hansen, Andrey B, Belinsky, Alexey Kalmykov, Anatoly R. Kantorovich, Vladimir E. Maslov, Philipp W, Stockhammer, Stefania Vai, Monica Zavattaro, Alessandro Riga, David Caramelli, Robin Skeates, Jessica Beckett, Maria Giuseppina Gradoli, Noah Steuri, Albert Hafner, Marianne Ramstein, Inga Siebke, Sandra Losch, Yilmaz Selim Erdal, Nabil-Fareed Alikhan, Zhemin Zhou, Mark Achtman, Kirsten Eos, Sabine Reinhold, Wolfgang Haak, Penise Kuhnert, Alexander Herbig ^ 81 Johannes Krause^ — Show fewer authors Nature Ecology & Evolution 4, 324-333 (2020) | Cite this article 0 £. entertca /□mg« 4? ill 1 ■ - ■-11 -'.ll : 1 ~t t t i j ami: Prasad Others enterica f*\ (Typhi, Errteritidis etc.) Pig and human-adapted d-iolaraasuls Human-adapted Paratyphi c Key et al., 2020 DOI: 10.1038/s41559-020-1106-9 (••) ETR001 | 1,813-1,618 cal yr bp Danube J 5^ (••) IV3002 | 5,578-5,077 cal yr bp (••) MK3001 | 2,994-2,873 cal yr bp IKI003 | 5,290-5,048 cal yr bp (••) Recovered ancient Salmonella genomes (••) Previously published ancient Salmonella genomes Key et at, 2020 DOI: 10.1038/s41559-020-1106-9 Ag ro paste ralist economy Transiional forager economy Smcrdhan & e-BG 4Ju Errlcfilins Pl2510* Key et al., 2020 DOI: 10.1038/s41559-020-1106-9 PLANT PATHOGENS Phytophthora infestans as one of the deadliest oomycetes - Irish potato famine caused death and emigration of >2 mil people Article | Open access | Published: 13 July 2013 Reconstructing genome evolution in historic samples of the Irish potato famine pathogen Michael D. Martin^, Enrico Cappellini, Jose A, Samaniego, M. Lisandra Zepeda, Paula F, Campos, Andaine Seguin-Orlando, Nathan Wales, Ludovic Orlando, Simon Y. W, Ho, Fred S. Dietrich, Piotr A, Mieczkowski. Joseph Heitman, Eske Wi Hers lev. Anders Krogh, Jean B, Ristaino & M. Thomas P. Gilbert Nature Communications 4, Article number: 2172 (20131 | Cite this article 6524 Accesses | 85 Citations | 74 Altmetric | Metrics Abstract Responsible for the Irish potato famine of 1845 49, theoomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. Infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multipledistinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenoty pe in modern strains, which helps explain the20th century's episodic replacements of Europeans infestans lineages. PHYTOPHTHORA INFEST ANS eLife 2013:2 e00731. PMCID: PMC3667578 Published online 2013 May 28. doi: 10.7554/eLife 00731 PMID: 23741619 The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine Kentaro Yoshida.1-* Verena J Schuenemann.2''1' Liliana M Cano.1 Marina Pais.1 Baqdevi Mishra.3;4;5 Rahul Sharma.3'4'5 Chirsta Lanz.6 Frank N Martin.7 Sophien Karnoun.1-* Johannes Krause,2-^ Marco Thines 3A-5$'$ Detlef Weiqel9* and Hernän A Burbano9;' Genetic epidemiology of late blight in Australia using ancient DNA Biitlrey M.Caruana1,2• Rudolf F de Boer2 • Brendan Rodoniu • Noel O.I. Cogan12 • Jacqueline Edwards12 Received: 20 October íall i Accented: 1 Anauit 20211 PuWiiheJ oni ine: 9 August lůl i o Crawrt 2023 MORE TO LOOK INTO • Bacteriophages (currently most studied in calculus and coprolites) • Borrelia recurrentis • Plasmodium falciparum • Mycobacterium tuberculosis • Treponema pallidum Why should we study ancient pathogens? • RNA and ssDNA viruses worst preservation • Goddess of smallpox • Domestication • Spread of pathogens accross populations and continents and everything • Phylogenetic trees • Ways to study past diseases • Ethical questions, biosafety • Visible pathology and pathogens relationship, different load of pathogen in different stages