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Published February 16, 2022 | Version These data correspond to the third version of the preprint (10.1101/2021.11.11.21266068v3) and the published paper (https://www.science.org/doi/10.1126/science.abn4947).
Dataset Open

Data for Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa

Creators

  • 1. South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa
  • 2. National Institute for Communicable Diseases, Division of the National Health Laboratory Service, South Africa
  • 3. National Institute for Communicable Diseases, Division of the National Health Laboratory Service, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
  • 4. South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa; McMaster University, Canada
  • 5. National Health Laboratory Service, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), South Africa

Description

Data files for Pulliam, JRC, C van Schalkwyk, N Govender, A von Gottberg, C Cohen, MJ Groome, J Dushoff, K Mlisana, and H Moultrie. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. DOI: 0.1126/science.abn4947

For code and more details see: https://github.com/jrcpulliam/reinfections/releases/tag/v3.0 or 10.5281/zenodo.5807591

  • ts_data.csv - national daily time series of newly detected putative primary infections (cnt), suspected second infections (reinf), suspected third infections (third), and suspected fourth infections (fourth) by specimen receipt date (date)
  • demog_data.csv - counts of individuals eligible for reinfection (total), who have 0 suspected reinfections (no_reinf) or >0 suspected reinfections (reinf) by province (province), age group (5-year bands, agegrp5), and sex (M = Male, F = Female, U = Unknown, sex)
  • posterior_90_null.RData - posterior samples from the MCMC fitting procedure (as used in the manuscript)
  • sim_90_null.RDS - simulation results (as used in the manuscript)
  • emp_haz_sens_an.RDS - output of sensitivity analysis of relative empirical hazard estimation to assumed observation probabilities (as used in the manuscript)

Note: There may be some inconsistencies with the numbers of infections through time in earlier versions of this data set due to back-filling of late-arriving data.

Notes

The data provided here cover the period from 2021-03-04 to 2022-01-31.

Files

demog_data.csv

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Additional details

Related works

Is supplement to
Preprint: 10.1101/2021.11.11.21266068v3 (DOI)
Software: https://github.com/jrcpulliam/reinfections (URL)
Journal article: https://www.science.org/doi/10.1126/science.abn4947 (URL)
Software: 10.5281/zenodo.5807591 (DOI)
Software: 110.5281/zenodo.6347439 (Handle)

Funding

Characterization of SARS-CoV-2 transmission dynamics, clinical features and disease impact in South Africa, a setting with high HIV prevalence 221003
Wellcome Trust