SPHERES Initiative: SARS-CoV-2 Awards Announced

CDC announces awards as a part of the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) Initiative

SPHERES system logo

The Centers for Disease Control and Prevention (CDC) has issued seven awards as part of the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) Initiative. The awards, totaling nearly $14.5 million over two years, are intended to fill knowledge gaps and promote innovation in the U.S. response to the COVID-19 pandemic. SPHERES builds upon six years of investment by CDC’s Advanced Molecular Detection program. This program integrates next-generation genomic sequencing technologies with bioinformatics and epidemiology expertise across the US public health system. The SPHERES collaboration, which currently includes scientists from nearly 200 public health, academic, clinical, and non-profit laboratories and institutions, aims to accelerate the application of SARS-CoV-2 genome sequencing for genomic epidemiology and pandemic response.

Yale School of Public Health and Johns Hopkins University

Virus genomics and human mobility to reveal the patterns of SARS-CoV-2’s spread.


This genomic epidemiologic study will integrate virus evolution and human behavior on regional and national scales. Revealing SARS-CoV-2 genetic diversity within New England and patterns of virus spread across the region and the country will help assess the effectiveness of intervention strategies for containing SARS-CoV-2. Along with providing continuous monitoring, this study will help inform future decision-making and create a new roadmap for responding to pandemic threats.

Scripps Research Institute

Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread.


Researchers will investigate SARS-CoV-2 genomics and molecular epidemiology in Southern California, collaborating with the CDC SPHERES program, California COVIDNet, and county and local public health laboratories. This project will expand collaboration with California laboratories to improve laboratory and bioinformatic methods for cost-effective, high-throughput sequencing.

Broad Institute, Massachusetts General Hospital, and Massachusetts Department of Public Health

Real-time SARS-CoV-2 genomic surveillance to support clinical and public health response and monitor functionally relevant mutations.


This project will enhance SARS-CoV-2 genomic surveillance in Massachusetts. Coupling a logical sampling plan with epidemiological and clinical data will enhance understanding of regional transmission patterns and link genetic variants to clinical outcomes. It will support the broader public health genomics community by developing bioinformatics tools for open data analysis, easy data sharing, and privacy controls.

University of Wisconsin-Madison, University of Michigan, and City of Milwaukee Health Department

Defining the role of college students in SARS-CoV-2’s spread in the Upper Midwest.


This study will use viral genomics to understand university students’ role in driving the transmission of SARS-CoV-2 within their communities over two years, beginning in fall 2020. The information generated will help inform risk assessments for in-person instruction and other on- and off-campus activities and suggest effective means of interrupting SARS-CoV-2 transmission chains. The study will be positioned to detect the emergence and potential spread of genetic variants over the longer term, such as viruses that could pass from person to person faster or be less recognizable to the body’s immune system.

Vanderbilt University Medical Center

Host-pathogen discovery at an institutional scale: The pathogenomic determinants of SARS-CoV-2 disease manifestations.


This project will fill unmet scientific and public health needs to understand the SARS-CoV-2 viral, host genetic, ecological factors and co-morbidity/co-infections risk factors for 1) symptomatic and asymptomatic infection; 2) prolonged shedding; and 3) acute and chronic sequelae of COVID 19. Further by high-throughput genomic sequencing of SARS-CoV-2 the proposal plans to investigate the evolution, emergence and spread of infections in communities and populations and identify viral signatures of virulence.

Emory University

Genomic, clinical, and phenotypic characterization of SARS-CoV-2 across a clinically and demographically diverse population in the Southeastern United States.


This study will characterize the diversity and evolution of SARS-CoV-2 strains circulating in Georgia, for the purpose of understanding if possible population-level changes in the rates of viral spread and whether there are associations between viral genotype, the viral phenotype in vitro, and clinical phenotype/outcome.

University of Georgia, University of Texas School of Public Health at Houston, and Houston Health Department

Molecular epidemiology and transmission dynamics of SARS-CoV-2 in Houston, TX.


This project will develop a genome sequencing and molecular epidemiology pipeline for SARS-CoV-2 samples collected in Houston, TX, the fourth largest city in the US. The project will develop computational approaches for integrating community-based surveillance and contact tracing with phylogenetic and epidemic network analysis to identify transmission clusters.

Page last reviewed: March 9, 2021