Genetic Surveillance of SARS-CoV-2 Spread in Wisconsin to Inform Outbreak Control
At a Glance
This project aimed to genetically characterize SARS-CoV-2 in Wisconsin to estimate infection parameters and evaluate the effectiveness of interventions. In March 2020, little was known regarding the true extent of SARS-CoV-2 transmission in Wisconsin. Researchers used genomic surveillance, tracking of different SARS-CoV-2 strains through space and time, to inform decisions on public health measures and aid the transition between mitigation and containment strategies. Preparing the genetic epidemiology infrastructure was crucial for tracking the local SARS-CoV-2 epidemic through 2020.
The project was successful in understanding and tracking SARS-CoV-2 transmission in Wisconsin. The team utilized genomic surveillance to identify patterns in SARS-CoV-2 transmission and sequenced over 5,000 viral genomes. The establishment of a sequencing program played a vital role during the emergence of the Delta variant, contributing to its early detection in Wisconsin. This project was also one of the first to show that vaccinated people who became infected with Delta variants could transmit the virus to others. Results from this project established a vigorous new research program that attracted significant extramural support, including three new CDC-funded projects using SARS-CoV-2 genome sequences to reveal patterns in virus transmission and evolution.
The Challenge
In March 2020, little was known regarding the true extent of SARS-CoV-2 in Wisconsin. Molecular epidemiology methods were leveraged to better understand patterns of viral evolution. The virus rapidly accumulated mutations as it spread, generating genetic fingerprints that could be used to track individual viruses as they caused outbreaks over time in different places. This information was used to estimate epidemiological parameters, including how many genetically distinct viral clusters were being transmitted through the state, how many infections occurred and how quickly those infections were doubling. Results from this work could also inform decisions on public health measures, aiding the transition between mitigation and containment strategies. Preparing the genetic epidemiology infrastructure was crucial for tracking the local SARS-CoV-2 epidemic through 2020.
Project Goals
The goals of this project were to genetically characterize SARS-CoV-2 in Wisconsin, estimate infection parameters and evaluate the effectiveness of interventions. These goals were addressed through two specific aims:
- Define SARS-CoV-2 transmission clusters throughout Wisconsin for the rest of 2020.
- Ascertain SARS-CoV-2 prevalence independent of, and complementary to, direct case testing.
Results
The project was successful in understanding and tracking SARS-CoV-2 transmission in Wisconsin. Utilizing genomic surveillance, the team identified transmission clusters and supported outbreak investigations, for example identifying likely sources of infection among healthcare workers. The project also used modeling approaches that demonstrated the effectiveness of public health measures in Dane and Milwaukee Counties early in the pandemic.
Key to the project’s success was the establishment of a successful SARS-CoV-2 sequencing program, sequencing over 11,000 genomes and garnering additional support from various funding sources. The data generated proved invaluable during the emergence of the Delta variant, enabling the rapid documentation of its arrival and spread. This project was among the first in the world to demonstrate that vaccinated people infected with Delta viruses could transmit those viruses to others. The researchers developed new collaborations with public health entities to share and interpret these and other findings, influencing key decisions such as the reimposition of mask mandates. These successes have not only contributed to ongoing SARS-CoV-2 monitoring but also positioned the team to successfully compete for federal and foundation funding for new projects aimed at using SARS-CoV-2 sequence data to understand patterns of viral transmission and evolution. They have also enhanced collaborations between UW investigators and state and local public health officials, leading to new approaches to collect, interpret and publicly share data on respiratory infections.