1 December 2025

plague: first pandemic

  • Yersinia pestis
  • causative agent of the Black Death
  • Plague of Justinian (541) - approx. 750 (ancient DNA)

Harbeck et al. (2013)

second pandemic

  • Black Death! 1347 onward
  • human pop 450M → 350-375M by 1400
  • continues until late 18th c.
  • Shakespeare, Isaac Newton, etc. etc.
  • also validated from ancient DNA

acceleration (Earn et al., 2020)

  • get historical details on plague from wills, parish records, London Bills of Mortality …

acceleration: conclusions

  • wills seem to be an adequate (if noisy) proxy for parish records/plague-specific mortality records (London Bills)
  • epidemic speed (\(r\)) increased from \(\approx\) 10/year to 20/year (doubling time from \(\approx\) 4 weeks to \(\approx\) 2 weeks)

Y. pestis transmission

  • Classic story: rat-flea transmission, human spillover
  • Possible pneumonic transmission

Human-ectoparasite transmission

Human-to-human transmission via ectoparasites (e.g. lice)

data fits (Dean et al., 2018; Dean, 2019)

combined model

box diagram

priors

results (example)

results (all)

virulence evolution

  • Sidhu et al. (2025)
  • repeated evolution of PLA (plasminogen activator) depletion across pandemics

PLA results: first pandemic

second pandemic

third pandemic

PLA phenotypes

evolutionary mechanisms?

  • tradeoff theory doesn’t work
  • most transmission is via fleas leaving dying rats
  • ‘infectious period’ is a burst at the end of the infection
  • how can PLA-depleted strains evolve (repeatedly)?

burnout theory

Parsons et al. (2024)

metapopulation model

metapopulation results

References

Dean, K. R. (2019). The epidemiology of plague in Europe: Inferring transmission dynamics from historical data [Doctoral Thesis].

Dean, K. R., Krauer, F., Walløe, L., Lingjærde, O. C., Bramanti, B., Stenseth, N. C., & Schmid, B. V. (2018). Human ectoparasites and the spread of plague in Europe during the Second Pandemic. Proceedings of the National Academy of Sciences, 201715640. https://doi.org/10.1073/pnas.1715640115

Earn, D. J. D., Ma, J., Poinar, H., Dushoff, J., & Bolker, B. M. (2020). Acceleration of plague outbreaks in the second pandemic. Proceedings of the National Academy of Sciences, 117(44), 27703–27711. https://doi.org/10.1073/pnas.2004904117

Harbeck, M., Seifert, L., Hänsch, S., Wagner, D. M., Birdsell, D., Parise, K. L., Wiechmann, I., Grupe, G., Thomas, A., Keim, P., Zöller, L., Bramanti, B., Riehm, J. M., & Scholz, H. C. (2013). Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague. PLOS Pathogens, 9(5), e1003349. https://doi.org/10.1371/journal.ppat.1003349

Parsons, T. L., Bolker, B. M., Dushoff, J., & Earn, D. J. D. (2024). The probability of epidemic burnout in the stochastic SIR model with vital dynamics. Proceedings of the National Academy of Sciences, 121(5), e2313708120. https://doi.org/10.1073/pnas.2313708120

Sidhu, R. K., Mas Fiol, G., Lê-Bury, P., Demeure, C. E., Bougit, E., Beau, R., Balière, C., Kwasiborski, A., Caro, V., Klunk, J., Salkeld, D. J., Carmichael, A., Varlık, N., Poinar, D., Earn, D. J. D., Bolker, B. M., Dushoff, J., Golding, G. B., Rascovan, N., … Poinar, H. N. (2025). Attenuation of virulence in Yersinia pestis across three plague pandemics. Science, 388(6750), eadt3880. https://doi.org/10.1126/science.adt3880

Last updated: 2025-11-30 20:41:32.558256