Estimating individuals’ genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data

Individuals differ widely in their contribution to the spread of infection within and across populations. Three key epidemiological host traits affect infectious disease spread: susceptibility (propensity to acquire infection), infectivity (propensity to transmit infection to others) and recoverability (propensity to recover quickly). Interventions aiming to reduce disease spread may target improvement in any one of these traits, but the necessary statistical methods for obtaining risk estimates are lacking. In this paper we introduce a novel software tool called SIRE (standing for “Susceptibility, Infectivity and Recoverability Estimation”), which allows for the first time simultaneous estimation of the genetic effect of a single nucleotide polymorphism (SNP), as well as non-genetic influences on these three unobservable host traits. SIRE implements a flexible Bayesian algorithm which accommodates a wide range of disease surveillance data comprising any combination of recorded individual infection and/or recovery times, or disease diagnostic test results. Different genetic and non-genetic regulations and data scenarios (representing realistic recording schemes) were simulated to validate SIRE and to assess their impact on the precision, accuracy and bias of parameter estimates. This analysis revealed that with few exceptions, SIRE provides unbiased, accurate parameter estimates associated with all three host traits. For most scenarios, SNP effects associated with recoverability can be estimated with highest precision, followed by susceptibility. For infectivity, many epidemics with few individuals give substantially more statistical power to identify SNP effects than the reverse. Importantly, precise estimates of SNP and other effects could be obtained even in the case of incomplete, censored and relatively infrequent measurements of individuals’ infection or survival status, albeit requiring more individuals to yield equivalent precision. SIRE represents a new tool for analysing a wide range of experimental and field disease data with the aim of discovering and validating SNPs and other factors controlling infectious disease transmission.
Author summary Effective approaches to reduce the spread of infectious disease transmission in populations are urgently needed. Reduction in disease spread is most effectively achieved by reducing, separately or in combination, individual (i) “susceptibility”, i.e. the relative risk to become infected when exposed to infectious individuals or material, (ii) “infectivity”, i.e. the propensity to transmit infection to others when infected, and/or by (iii) improving “recoverability”, i.e. the propensity to recover. However, to date it is impossible to assess how these three key epidemiological traits controlling disease transmission in a population are regulated by specific genes or interventions, as the necessary statistical methods for estimating genetic and non-genetic effects from available disease surveillance data don’t exist. This paper introduces a novel statistical method that can estimate, for the first time, genetic and non-genetic effects for host susceptibility, infectivity and recoverability simultaneously from a wide range of realistic disease surveillance data. The method has been incorporated into a user-friendly, freely available software tool called SIRE. SIRE can be applied to a range of experimental and field data and will help to move disease control significantly forward by simultaneously targeting multiple host traits affecting infectious disease spread.