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Invasion and Eradication

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Epidemics

Part of the book series: Use R! ((USE R))

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Abstract

Pathogens invade new host niches all the time. The global invasion of the human niche by SARS-CoV-2 during the 2020–22 pandemic is the most recent example, but cross-species transmission is ubiquitous. In 2009 Influenza A/H1N1pdm09 emerged and spread globally most likely after a triple recombination of human, avian, and porcine viral segments (Smith et al., 2009a). The HIV-1 pandemic started in the mid-twentieth century probably from bushmeat spillover of chimpanzee simian immunodeficiency virus, which itself is thought to have originated from spillovers from other primates, to go global in the 1970s (Hemelaar, 2012). Cross-species transmission is not just an issue of zoonotic spillover or anthropogenic spillback, it is equally important as spillover among animal species.

This chapter uses the following R packages: scatterplot3d, raster, gdistance, maptools, rgdal, maps and ncf.

A five minute epidemics MOOC on spatial spread can be seen on YouTube: https://www.youtube.com/watch?v=WPjsAdyD1Gg

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Notes

  1. 1.

    A kin to the failure of persistence of measles in human communities below the critical community size (Bartlett, 1960b; Grenfell & Harwood, 1997, Sect. 1.3).

  2. 2.

    Engen et al. (2021) discuss an alternative diffusion approximation approach to study this issue.

  3. 3.

    Though there are Cetacean morbilliviruses documented from rare species of toothed whales which mode of persistence is not understood (Van Bressem et al., 2014).

  4. 4.

    Manipulation of geospatial data is an enormous field and the R community has generated a lot of resources beyond the scope of this text. The code is adopted from https://stackoverflow.com/questions/69258889.

  5. 5.

    Conventional usage is to use “eliminate” for regional control and “eradicate” for global control; smallpox and Rinderpest are the only two viruses that have been eradicated through vaccination.

  6. 6.

    https://tinyurl.com/msszkdjw links to visualization of the invasion and elimination of fox rabies across Switzerland between 1967 and 1999.

  7. 7.

    The code is actually vectorized so can accommodate N as a vector of varying population sizes.

  8. 8.

    So for this code to work the previous susceptible reconstruction must be available.

  9. 9.

    As described by watchmakers centuries ago who noted how clocks hanging on a common wall would lock-step.

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  1. Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA

    Ottar Bjørnstad

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Bjørnstad, O. (2023). Invasion and Eradication. In: Epidemics. Use R!. Springer, Cham. https://doi.org/10.1007/978-3-031-12056-5_15

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