Published March 6, 2024 | Version v1
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Endemic does not mean constant as SARS-CoV-2 continues to evolve

  • 1. University of British Columbia
  • 2. ROR icon Simon Fraser University

Description

Supplementary Mathematica files for "Endemic does not mean constant as SARS-CoV-2 continues to evolve" (Evolution 2024)

Contents (each provided in Mathematica .nb and PDF .pdf formats)

"OttoEtAl_Analysis_Endemic2024.nb" - Design and analysis of SIRn compartment model (for Figures 5, 7, and 8): Impact of variants and NPI measures

"OttoEtAl_Dynamics_Endemic2024.nb" - Diffusion dynamics of SIRn compartment model (for Figures 3, 4, 6, and S1-S4): Exploring transients around steady state

"OttoEtAl_CaseCountTrends_Endemic2024.nb" - Analysis of SARS-CoV-2 data from Canada (for Figure 1): To illustrate the evolutionary dynamics of COVID-19, variant designations of each virus sample were obtained from the Canadian VirusSeq Portal from each province of Canada (VirusSeq 2023) and processed as a part of the duotang project (CAMEO, CoVarr-Net, funded by CIHR).  Modifications of the duotang code on github and generation of Figure 1 were conducted in Mathematica. To show overall trends in incidence, we focused on the sub-set of COVID-19 cases among individuals over aged 70, as they were a more consistently tested age group. 

COVID-19 case count data for Figure 1 were obtained from these publicly accessible data portals (a permanent record of these data are also included in the Mathematica file "OttoEtAl_CaseCountTrends_Endemic2024.nb"): 

Mathematica files (Wolfram Research, Inc., Mathematica, Version 12.0, Champaign, IL (2024)) can be seen in read-only mode using Wolfram’s Mathematica player or re-analysed with a low-cost version of Mathematica using a Raspberry Pi installation. PDF versions are also included.

Files

OttoEtAl_Analysis_Endemic2024.pdf

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Additional details

Related works

Is supplement to
Preprint: 10.1101/2023.09.28.23296264v1 (DOI)

Funding

Natural Sciences and Engineering Research Council

Dates

Accepted
2024-03
Supplementary Mathematica files for Otto et al. (2024) Evolution

Software

Programming language
Mathematica