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Estimating Infection Rates from Serological Data

Source: R/serocalculator-package.R
serocalculator.Rd

This package translates antibody levels measured in a (cross-sectional) population sample into an estimate of the frequency with which seroconversions (infections) occur in the sampled population.

The API for this package includes the following functions:

Function NamePurpose
load_pop_data()loading cross-sectional antibody survey data
check_pop_data()checking antibody data
summary.pop_data()numerical summaries of antibody data
autoplot.pop_data()graphs of antibody data distributions
load_curve_params()loading antibody decay curve models
autoplot.curve_params()graphing antibody decay curves
llik()computing log-likelihoods
graph.loglik()graphing log-likelihood functions
autoplot.seroincidence()graphing log-likelihood functions
autoplot.seroincidence.by()graphing log-likelihood functions
est.incidence()estimating incidence rates
est.incidence.by()estimating incidence rates by strata
summary.seroincidence.by()summarizing stratified incidence rate estimates
autoplot.summary.seroincidence.by()graphing incidence rate estimates
sim.cs()simulating cross-sectional population antibody data using longitudinal seroresponse models

Details

_PACKAGE

References

Methods for estimating seroincidence

  • Teunis, P. F. M., and J. C. H. van Eijkeren. "Estimation of seroconversion rates for infectious diseases: Effects of age and noise." Statistics in Medicine 39, no. 21 (2020): 2799-2814.

  • Teunis, P. F. M., J. C. H. van Eijkeren, W. F. de Graaf, A. Bonačić Marinović, and M. E. E. Kretzschmar. "Linking the seroresponse to infection to within-host heterogeneity in antibody production." Epidemics 16 (2016): 33-39.

Applications

  • Aiemjoy, Kristen, Jessica C. Seidman, Senjuti Saha, Sira Jam Munira, Mohammad Saiful Islam Sajib, Syed Muktadir Al Sium, Anik Sarkar et al. "Estimating typhoid incidence from community-based serosurveys: a multicohort study." The Lancet Microbe 3, no. 8 (2022): e578-e587.

  • Aiemjoy, Kristen, John Rumunu, Juma John Hassen, Kirsten E. Wiens, Denise Garrett, Polina Kamenskaya, Jason B. Harris et al. "Seroincidence of enteric fever, Juba, South Sudan." Emerging infectious diseases 28, no. 11 (2022): 2316.

  • Monge, S., Teunis, P. F., Friesema, I., Franz, E., Ang, W., van Pelt, W., Mughini-Gras, L. "Immune response-eliciting exposure to Campylobacter vastly exceeds the incidence of clinically overt campylobacteriosis but is associated with similar risk factors: A nationwide serosurvey in the Netherlands" Journal of Infection, 2018, 1–7, doi:10.1016/j.jinf.2018.04.016

  • Kretzschmar, M., Teunis, P. F., Pebody, R. G. "Incidence and reproduction numbers of pertussis: estimates from serological and social contact data in five European countries" PLoS Medicine 7, no. 6 (June 1, 2010):e1000291. doi:10.1371/journal.pmed.1000291.

  • Simonsen, J., Strid, M. A., Molbak, K., Krogfelt, K. A., Linneberg, A., Teunis, P. "Sero-epidemiology as a tool to study the incidence of Salmonella infections in humans" Epidemiology and Infection 136, no. 7 (July 1, 2008): 895–902. doi:10.1017/S0950268807009314

  • Simonsen, J., Teunis, P. F., van Pelt, W., van Duynhoven, Y., Krogfelt, K. A., Sadkowska-Todys, M., Molbak K. "Usefulness of seroconversion rates for comparing infection pressures between countries" Epidemiology and Infection, April 12, 2010, 1–8. doi:10.1017/S0950268810000750.

  • Falkenhorst, G., Simonsen, J., Ceper, T. H., van Pelt, W., de Valk, H., Sadkowska-Todys, M., Zota, L., Kuusi, M., Jernberg, C., Rota, M. C., van Duynhoven, Y. T., Teunis, P. F., Krogfelt, K. A., Molbak, K. "Serological cross-sectional studies on salmonella incidence in eight European countries: no correlation with incidence of reported cases" BMC Public Health 12, no. 1 (July 15, 2012): 523–23. doi:10.1186/1471-2458-12-523.

  • Teunis, P. F., Falkenhorst, G., Ang, C. W., Strid, M. A., De Valk, H., Sadkowska-Todys, M., Zota, L., Kuusi, M., Rota, M. C., Simonsen, J. B., Molbak, K., Van Duynhoven, Y. T., van Pelt, W. "Campylobacter seroconversion rates in selected countries in the European Union" Epidemiology and Infection 141, no. 10 (2013): 2051–57. doi:10.1017/S0950268812002774.

  • de Melker, H. E., Versteegh, F. G., Schellekens, J. F., Teunis, P. F., Kretzschmar, M. "The incidence of Bordetella pertussis infections estimated in the population from a combination of serological surveys" The Journal of Infection 53, no. 2 (August 1, 2006): 106–13. doi:10.1016/j.jinf.2005.10.020

Quantification of seroresponse

  • de Graaf, W. F., Kretzschmar, M. E., Teunis, P. F., Diekmann, O. "A two-phase within-host model for immune response and its application to serological profiles of pertussis" Epidemics 9 (2014):1–7. doi:10.1016/j.epidem.2014.08.002.

  • Berbers, G. A., van de Wetering, M. S., van Gageldonk, P. G., Schellekens, J. F., Versteegh, F. G., Teunis, P.F. "A novel method for evaluating natural and vaccine induced serological responses to Bordetella pertussis antigens" Vaccine 31, no. 36 (August 12, 2013): 3732–38. doi:10.1016/j.vaccine.2013.05.073.

  • Versteegh, F. G., Mertens, P. L., de Melker, H. E., Roord, J. J., Schellekens, J. F., Teunis, P. F. "Age-specific long-term course of IgG antibodies to pertussis toxin after symptomatic infection with Bordetella pertussis" Epidemiology and Infection 133, no. 4 (August 1, 2005): 737–48.

  • Teunis, P. F., van der Heijden, O. G., de Melker, H. E., Schellekens, J. F., Versteegh, F. G., Kretzschmar, M. E. "Kinetics of the IgG antibody response to pertussis toxin after infection with B. pertussis" Epidemiology and Infection 129, no. 3 (December 10, 2002):479. doi:10.1017/S0950268802007896.

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