Non-pharmaceutical interventions and the emergence of pathogen variants

Ben Ashby, Cameron Smith, Robin N Thompson

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Non-pharmaceutical interventions (NPIs), such as social distancing and contact tracing, are important public health measures that can reduce pathogen transmission. In addition to playing a crucial role in suppressing transmission, NPIs influence pathogen evolution by mediating mutation supply, restricting the availability of susceptible hosts, and altering the strength of selection for novel variants. Yet it is unclear how NPIs might affect the emergence of novel variants that are able to escape pre-existing immunity (partially or fully), are more transmissible, or cause greater mortality. We analyse a stochastic two-strain
epidemiological model to determine how the strength and timing of NPIs affects the emergence of variants with similar or contrasting life-history characteristics to the wildtype. We show that, while stronger and timelier NPIs generally reduce the likelihood of variant emergence, it is possible for more transmissible variants with high cross immunity to have a greater probability of emerging at intermediate levels of NPIs. This is because intermediate levels of NPIs allow an epidemic of the wildtype that is neither too small (facilitating high mutation supply), nor too large (leaving a large pool of susceptible hosts), to prevent a novel variant becoming established in the host population. However, since one cannot predict the
characteristics of a variant, the best strategy to prevent emergence is likely to be
implementation of strong, timely NPIs.
Original languageEnglish
Pages (from-to)80-89
Number of pages10
JournalEvolution, Medicine, and Public Health
Issue number1
Early online date19 Dec 2022
Publication statusPublished - 31 Dec 2023

Bibliographical note

BA and CAS are supported by the Natural Environment Research Council (grant numbers NE/N014979/1 [BA] and NE/V003909/1 [BA and CAS]). We acknowledge the support of the Natural Sciences and Engineering Research Council of Canada (NSERC). Nous Remercions le Conseil de Recherches en Sciences Naturelles et en Génie du Canada (CRSNG) de Son Soutien. PIPPS receives funding from the BC Ministry of Health.

Source code for the simulations is available in the online Supplementary Materials and at


  • pathogen evolution
  • transmissibillity
  • immune escape
  • cross-immunity
  • social distancing
  • lockdowns


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