Semiparametric inference of effective reproduction number dynamics from wastewater pathogen surveillance data

TL;DR

This paper introduces a novel semiparametric model to estimate the effective reproduction number of infectious diseases from wastewater pathogen data, avoiding complex assumptions about susceptible populations, and demonstrates its application to SARS-CoV-2 in Los Angeles.

Contribution

We develop a new semiparametric inference framework for estimating the effective reproduction number from wastewater data, validated through simulations and real-world SARS-CoV-2 analysis.

Findings

Successfully estimated SARS-CoV-2 R effective in Los Angeles

Validated model with agent-based simulation data

Provided a flexible approach avoiding susceptible population assumptions

Abstract

Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective reproduction number, the average number of individuals a newly infected person will infect. We propose a model where new infections arrive according to a time-varying immigration rate which can be interpreted as an average number of secondary infections produced by one infectious individual per unit time. This model allows us to estimate the effective reproduction number from concentrations of pathogen genomes while avoiding difficult to verify assumptions about the dynamics of the susceptible population. As a byproduct of our primary goal, we also produce a new model for estimating the effective reproduction number from case data using the same framework. We test this modeling framework in an agent-based simulation study with a realistic data generating mechanism which accounts for the time-varying dynamics of pathogen shedding. Finally, we apply our new model to estimating the effective reproduction number of SARS-CoV-2 in Los Angeles, California, using pathogen RNA concentrations collected from a large wastewater treatment facility.