1. Epidemiology and Global Health
  2. Microbiology and Infectious Disease
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Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

  1. Kirsten I Bos
  2. Alexander Herbig
  3. Jason Sahl
  4. Nicholas Waglechner
  5. Mathieu Fourment
  6. Stephen A Forrest
  7. Jennifer Klunk
  8. Verena J Schuenemann
  9. Debi Poinar
  10. Melanie Kuch
  11. G Brian Golding
  12. Olivier Dutour
  13. Paul Keim
  14. David M Wagner
  15. Edward C Holmes
  16. Johannes Krause  Is a corresponding author
  17. Hendrik N Poinar
  1. University of Tübingen, Germany
  2. Northern Arizona University, United States
  3. McMaster University, Canada
  4. The University of Sydney, Australia
  5. Université Bordeaux, France
Research Article
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Cite this article as: eLife 2016;5:e12994 doi: 10.7554/eLife.12994

Abstract

The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death.

Article and author information

Author details

  1. Kirsten I Bos

    Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Alexander Herbig

    Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Jason Sahl

    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Nicholas Waglechner

    Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Mathieu Fourment

    Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
    Competing interests
    The authors declare that no competing interests exist.
  6. Stephen A Forrest

    Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Jennifer Klunk

    McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Verena J Schuenemann

    Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Debi Poinar

    McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  10. Melanie Kuch

    McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  11. G Brian Golding

    Department of Biology, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.
  12. Olivier Dutour

    Laboratoire d'anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, PACEA, Université Bordeaux, Bordeaux, France
    Competing interests
    The authors declare that no competing interests exist.
  13. Paul Keim

    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. David M Wagner

    Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Edward C Holmes

    Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
    Competing interests
    The authors declare that no competing interests exist.
  16. Johannes Krause

    Department of Archeological Sciences, University of Tübingen, Tübingen, Germany
    For correspondence
    johannes.krause@uni-tuebingen.de
    Competing interests
    The authors declare that no competing interests exist.
  17. Hendrik N Poinar

    Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Richard A Neher, Max Planck Institute for Developmental Biology, Germany

Publication history

  1. Received: November 12, 2015
  2. Accepted: January 19, 2016
  3. Accepted Manuscript published: January 21, 2016 (version 1)
  4. Version of Record published: March 11, 2016 (version 2)

Copyright

© 2016, Bos et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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Further reading

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    Influenza pandemics pose public health threats annually for lacking vaccine that provides cross-protection against novel and emerging influenza viruses. Combining conserved antigens that induce cross-protective antibody responses with epitopes that activate cross-protective T cell responses might be an attractive strategy for developing a universal vaccine. In this study, we constructed a recombinant protein named NMHC that consists of influenza viral conserved epitopes and a superantigen fragment. NMHC promoted the maturation of bone marrow-derived dendritic cells and induced CD4+ T cells to differentiate into Th1, Th2, and Th17 subtypes. Mice vaccinated with NMHC produced high levels of immunoglobulins that cross-bound to HA fragments from six influenza virus subtypes with high antibody titers. Anti-NMHC serum showed potent hemagglutinin inhibition effects to highly divergent group 1 (H1 subtype) and group 2 (H3 subtype) influenza virus strains. Furthermore, purified anti-NMHC antibodies bound to multiple HAs with high affinities. NMHC vaccination effectively protected mice from infection and lung damage when exposed to two subtypes of H1N1 influenza virus. Moreover, NMHC vaccination elicited CD4+ and CD8+ T cell responses that cleared the virus from infected tissues and prevented virus spread. In conclusion, this study provides proof of concept that NMHC vaccination triggers B and T cell immune responses against multiple influenza virus infections. Therefore, NMHC might be a candidate universal broad-spectrum vaccine for the prevention and treatment of multiple influenza viruses.

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    2. Microbiology and Infectious Disease
    Mark Ferris et al.
    Research Advance Updated

    Background:

    Respiratory protective equipment recommended in the UK for healthcare workers (HCWs) caring for patients with COVID-19 comprises a fluid-resistant surgical mask (FRSM), except in the context of aerosol generating procedures (AGPs). We previously demonstrated frequent pauci- and asymptomatic severe acute respiratory syndrome coronavirus 2 infection HCWs during the first wave of the COVID-19 pandemic in the UK, using a comprehensive PCR-based HCW screening programme (Rivett et al., 2020; Jones et al., 2020).

    Methods:

    Here, we use observational data and mathematical modelling to analyse infection rates amongst HCWs working on ‘red’ (coronavirus disease 2019, COVID-19) and ‘green’ (non-COVID-19) wards during the second wave of the pandemic, before and after the substitution of filtering face piece 3 (FFP3) respirators for FRSMs.

    Results:

    Whilst using FRSMs, HCWs working on red wards faced an approximately 31-fold (and at least fivefold) increased risk of direct, ward-based infection. Conversely, after changing to FFP3 respirators, this risk was significantly reduced (52–100% protection).

    Conclusions:

    FFP3 respirators may therefore provide more effective protection than FRSMs for HCWs caring for patients with COVID-19, whether or not AGPs are undertaken.

    Funding:

    Wellcome Trust, Medical Research Council, Addenbrooke’s Charitable Trust, NIHR Cambridge Biomedical Research Centre, NHS Blood and Transfusion, UKRI.