One 5,000-year old individual buried in Riņņukalns, Latvia, was infected with an early Yersinia pestis strain, shortly after it split from its antecessor Y. pseudotuberculosis c. 7,000 years ago.
Neolithic-era human teeth from Eurasia have also shown evidence of some of the oldest strains of Yersinia pestis. The ages of the skeletons identified between 2,800 and 5,000 years old, with seven of the one hundred and one individuals carrying similar sequences of the bacterium. Additionally, studies of the ancient strains discovered show these ancient strains lack the Yersinia murine toxin (ymt), which would have prevented the strains from using fleas as a vector.
A similar site was found in China in 2011; the site Hamin Mangha in northeast China dates back to approximately 5000 years ago and features a small structure filled with almost 100 bodies. Whilst there are several theories as what the reasons are for so many bodies in one location, such as a geological disaster or a ritual sacrifice, a plague is also considered as a hypothesis. In the case of the plague, despite being the weakest of the hypotheses, the placement of the bodies suggesting others carrying them in, alongside being intact before being burned, and the lack of artifacts alongside the bodies. Two other sites like these have been found in Northeast China: Miaozigou and Laijia, but archaeologists did not speculate as to the causal agent.
Some studies, as those from the researchers from the Kiel University, have contested the hypothesis that the plague was responsible for the Neolithic decline. Analysis of the plague bacteria that infected a hunter-gatherer in Latvia during this period indicates that, unlike modern plague strains, the strain which afflicted this man was incapable of causing flea-spread bubonic plague and could only cause septicemic plague via a rodent bite or a largely non-contagious case of pneumonic plague, implying that the disease would have had difficulty spreading across vast distances in a short amount of time. The man identified in this particular case, after being studied, does not have a clear indicator of how much he was actually affected by the bacteria. Importantly, and supported by the results from the gallery graves of the Wartberg Culture, they do not see indications for a mass-outbreak.
Studies of the ancient variations of the bacteria have tried to show connections to the specific strain they studied and the more modern strands, such as ones during the Black Death. Studies in Sweden, on the Gok2 Neolithic Yersinia pestis strain, discovered it to be the basal to all known Y. pestis strains with the use of genome reconstruction, as well as containing plasminogen activators genes that would have allowed it to start a pneumonic plague. Other cases revealed a lack of ability to be able to use fleas as a vector of transmission; the case in Sweden contained Yersinia murine toxin which prevented the use of fleas, alongside a separate case studying late bronze-age bodies revealing the use of fleas in transmission would have occurred around the time after the collapse, being a few hundred years off.
Starting around 5400 BP and ending around 5000 years ago, according to the Rascovan et al. reference.
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Colledge, Sue; Conolly, James; Crema, Enrico; Shennan, Stephen (2019-01-10). "Neolithic population crash in northwest Europe associated with agricultural crisis". Quaternary Research. 92 (3): 686–707. Bibcode:2019QuRes..92..686C. doi:10.1017/qua.2019.42. ISSN 0033-5894. S2CID 202186375. https://www.cambridge.org/core/product/identifier/S0033589419000425/type/journal_article
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Susat, Julian; et al. (2021-06-29). "A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis". Cell Reports. 35 (13): 109278. doi:10.1016/j.celrep.2021.109278. ISSN 2211-1247. PMID 34192537. S2CID 235697166. https://doi.org/10.1016%2Fj.celrep.2021.109278
"Neolithic plague bacterium did not cause mass mortality". Uni Kiel. 2025-01-22. Retrieved 2025-01-22. https://www.uni-kiel.de/en/cluster-roots/details/news/138-plague-dog
Rascovan, Nicolás; Sjögren, Karl-Göran; Kristiansen, Kristian; Nielsen, Rasmus; Willerslev, Eske; Desnues, Christelle; Rasmussen, Simon (2019-01-10). "Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline". Cell. 176 (1–2): 295–305.e10. doi:10.1016/j.cell.2018.11.005. ISSN 0092-8674. PMID 30528431. https://doi.org/10.1016%2Fj.cell.2018.11.005
Rasmussen, Simon; Allentoft, Morten Erik; Nielsen, Kasper; Orlando, Ludovic; Sikora, Martin; Sjögren, Karl-Göran; Pedersen, Anders Gorm; Schubert, Mikkel; Van Dam, Alex; Kapel, Christian Moliin Outzen; Nielsen, Henrik Bjørn; Brunak, Søren; Avetisyan, Pavel; Epimakhov, Andrey; Khalyapin, Mikhail Viktorovich (2015-01-10). "Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago". Cell. 163 (3): 571–582. doi:10.1016/j.cell.2015.10.009. PMC 4644222. PMID 26496604. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644222
Rascovan, Nicolás; Sjögren, Karl-Göran; Kristiansen, Kristian; Nielsen, Rasmus; Willerslev, Eske; Desnues, Christelle; Rasmussen, Simon (2019-01-10). "Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline". Cell. 176 (1–2): 295–305.e10. doi:10.1016/j.cell.2018.11.005. ISSN 0092-8674. PMID 30528431. https://doi.org/10.1016%2Fj.cell.2018.11.005
Rascovan, Nicolás; Sjögren, Karl-Göran; Kristiansen, Kristian; Nielsen, Rasmus; Willerslev, Eske; Desnues, Christelle; Rasmussen, Simon (2019-01-10). "Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline". Cell. 176 (1–2): 295–305.e10. doi:10.1016/j.cell.2018.11.005. ISSN 0092-8674. PMID 30528431. https://doi.org/10.1016%2Fj.cell.2018.11.005
Rasmussen, Simon; Allentoft, Morten Erik; Nielsen, Kasper; Orlando, Ludovic; Sikora, Martin; Sjögren, Karl-Göran; Pedersen, Anders Gorm; Schubert, Mikkel; Van Dam, Alex; Kapel, Christian Moliin Outzen; Nielsen, Henrik Bjørn; Brunak, Søren; Avetisyan, Pavel; Epimakhov, Andrey; Khalyapin, Mikhail Viktorovich (2015-01-10). "Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago". Cell. 163 (3): 571–582. doi:10.1016/j.cell.2015.10.009. PMC 4644222. PMID 26496604. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644222