eLife
ISSN 2050-084X
2026
Shared — curated by The Gufo editorial team
Inferring variant-specific effective reproduction numbers from combined case and sequencing data
Marlin D Figgins*, Trevor Bedford
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
Received: 2026-10-22 · Published: 2026-07-09
© 2026 The Author(s) and the original publisher.
Abstract
Accurately estimating relative transmission rates of SARS-CoV-2 variants remains a scientific and public health priority. Recent studies have used the sample proportions of different variants from genetic sequence data to describe variant frequency dynamics and relative transmission rates, but frequencies alone cannot capture the rich epidemiological behavior of SARS-CoV-2. Here, we extend methods for inferring the effective reproduction number of an epidemic using confirmed case data to jointly estimate variant-specific effective reproduction numbers and frequencies of co-circulating variants using cases and sequences across states in the United States from January 2021 to March 2022. Our method can be used to infer structured relationships between effective reproduction numbers across time series, allowing us to estimate fixed variant-specific growth advantages. We use this model to estimate the effective reproduction number of SARS-CoV-2 variants of concern and variants of interest in the United States, and to estimate consistent growth advantages of particular variants across different locations.
Summary
Public health researchers want to know not just which SARS-CoV-2 variants are becoming more common, but how much faster they are actually spreading. Earlier studies have typically used genetic sequencing data to track the changing proportions of different variants over time, but this approach based on frequencies alone misses important details about how an epidemic actually behaves, such as overall case numbers and transmission dynamics.
This paper presents a new method that combines case count data with sequencing data to estimate both the frequency of circulating variants and their effective reproduction numbers, a measure of how quickly a variant is spreading. The approach allows researchers to model structured relationships between different variants' reproduction numbers across time, which makes it possible to estimate a fixed growth advantage for a given variant. The authors applied this method to data from US states collected between January 2021 and March 2022, examining variants of concern and variants of interest.
Plain-language summary by The Gufo; the paper is the authors’ own text.
Key findings
- The study introduces a method that jointly estimates variant-specific effective reproduction numbers and variant frequencies by combining case and sequencing data, rather than relying on sequence frequencies alone.
- The method can model structured relationships between the reproduction numbers of different variants over time, enabling estimation of a fixed growth advantage for a variant.
- The approach was applied to case and sequencing data from US states between January 2021 and March 2022 to estimate effective reproduction numbers of SARS-CoV-2 variants of concern and variants of interest.
- The analysis found consistent growth advantages for particular variants across different locations in the United States.
