Inferring risks of coronavirus transmission from community household data

Abstract

The response of many governments to the COVID-19 pandemic has involved measures to control within- and between-household transmission, providing motivation to improve understanding of the absolute and relative risks in these contexts. Here, we perform exploratory, residual-based, and transmission-dynamic household analysis of the Office for National Statistics COVID-19 Infection Survey data from 26 April 2020 to 15 July 2021 in England. This provides evidence for: (i) temporally varying rates of introduction of infection into households broadly following the trajectory of the overall epidemic and vaccination programme; (ii) susceptible-Infectious transmission probabilities of within-household transmission in the 15-35% range; (iii) the emergence of the Alpha and Delta variants, with the former being around 50% more infectious than wildtype and 35% less infectious than Delta within households; (iv) significantly (in the range of 25-300%) more risk of bringing infection into the household for workers in patient-facing roles pre-vaccine; (v) increased risk for secondary school-age children of bringing the infection into the household when schools are open; (vi) increased risk for primary school-age children of bringing the infection into the household when schools were open since the emergence of new variants.

Keywords: COVID-19; Epidemic; infection; model; risk factors.

Figure 1.

Schematic diagram of a hypothetical but realistic data pattern for a four-person household in the first 2 months after recruitment. Each negative test is shown as a blue circle containing $\times$ and each positive test is shown as a red circle containing $+$ . One potential route for infection coming into and transmitting within the household is shown as through a series of red arrows. This is not directly observed in the study design, and in fact other transmission trees (for example, one in which PID2 is infected before PID3) are consistent with the data that would be obtained from this household.

Figure 2.

Histograms of household attack rates. (a) Tranche 1, (b) Tranche 2, (c) Tranche 3, (d) Tranche 4, (e) Tranche 5, and (f) Tranche 6.

Figure 3.

Kernel density plots showing proportion of positives in different age classes in households. (a) Tranche 1, (b) Tranche 2, (c) Tranche 3, (d) Tranche 4, (e) Tranche 5, (f) Tranche 6, and (g) Legend.

Figure 4.

Pair counts for PCR gene positivity patterns. (a) Tranche 1, (b) Tranche 2, (c) Tranche 3, (d) Tranche 4, (e) Tranche 5, and (f) Tranche 6.

Figure 5.

Residual plots for PCR gene positivity patterns. (a) Tranche 1, (b) Tranche 2, (c) Tranche 3, (d) Tranche 4, (e) Tranche 5, and (f) Tranche 6.

Figure 6.

Visualisation of the fitted model. Top: Baseline probability of infection from outside. Bottom: Per-pair baseline probabilities of secondary transmission within the household, not including tertiary transmission effects.

Figure 7.

Visualisation of the fitted model. Relative effects on transmission, susceptibility and external exposure compared to baseline of an adult not working in a patient-facing role with OR $+$ N $+$ S maximal PCR gene positivity pattern if positive. ‘Trans.’ stands for relative transmissibility, ‘Susc.’ for relative susceptibility and ‘External’ for relative external exposure.