Preprint (version 1)

Background

Repeated measurements of cross-sectional prevalence of Polymerase Chain Reaction (PCR) positivity or
seropositivity provide rich insight into the dynamics of an infection. The UK Office for National Statistics
(ONS) Community Infection Survey publishes such measurements for SARS-CoV-2 on a weekly basis based
on testing enrolled households, contributing to situational awareness in the country. Here we present esti-
mates of time-varying and static epidemiological quantities that were derived from the estimates published
by ONS.

Methods

We used a gaussian process to model incidence of infections and then estimated observed PCR prevalence by
convolving our modelled incidence estimates with a previously published PCR detection curve describing the
probability of a positive test as a function of the time since infection. We refined our incidence estimates using
time-varying estimates of antibody prevalence combined with a model of antibody positivity and waning that
moved individuals between compartments with or without antibodies based on estimates of new infections,
vaccination, probability of seroconversion and waning.

Results

We produced incidence curves of infection describing the UK epidemic from late April 2020 until early 2022.
We used these estimates of incidence to estimate the time-varying growth rate of infections and combined
them with estimates of the generation interval to estimate time-varying reproduction numbers. Biological
parameters describing seroconversion and waning, while based on a simple model, were broadly in line with
plausible ranges from individual-level studies.

Conclusions

Beyond informing situational awareness and allowing for estimates using individual-level data, repeated
cross-sectional studies make it possible to estimate epidemiological parameters from population-level mod-
els. Studies or public health surveillance methods based on similar designs offer opportunities for further
improving our understanding of the dynamics of SARS-CoV-2 or other pathogens and their interaction with
population-level immunity.

Release details

This is a code release that matches the first release of the preprint of this work.