SARS-CoV-2 Innovation: Broad Agency Announcement awards
CDC announces awards as a part of the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) Initiative
The Centers for Disease Control and Prevention (CDC) has issued 29 awards as part of the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES) Initiative. These awards are intended to fill knowledge gaps and promote innovation in the U.S. response to the COVID-19 pandemic. Funding awards are determined through a competitive selection process based on scientific needs and available funds.
The AMD program has spent the last seven years investing in the latest next-generation genomic sequencing technologies. It now also has some of the greatest bioinformatics and epidemiology expertise across CDC and the nation. These awards will fund innovative research and collaborative projects to support these advancements in public health. 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.
Arizona State University
SARS-CoV-2 genomic surveillance in Arizona
The Arizona State University (ASU) will conduct viral next-generation sequencing and develop tools to track SARS-CoV-2 in Arizona. This project will sequence 2,000 positive samples over 12 months. Sample criteria include reinfection cases, routine surveillance of low-population counties and vaccinated individuals. ASU will develop a tool for researchers to upload sequences and analyze the data for emerging variant trends.
Northern Arizona University
Viral genomic dynamics in differentially vaccinated populations
Northern Arizona University will monitor populations on varying vaccinations schedules. This study will monitor two populations on opposite vaccination schedules and compare their impact for SARS-CoV-2 transmission. One site will monitor 500 vaccinated residents in two long-term care facilities, and the other site will monitor 2,000 unvaccinated school-aged children in a school setting. The two populations provide an ideal opportunity to explore the impacts of vaccination on viral evolution, infection rates, and transmission.
Translational Genomics Research Institute – Arizona
COVID-19 Genomics in the American Southwest
Translational Genomics Research Institute (TGen North) will expand their analysis of SARS-CoV-2 genomic diversity in the Southwest United States and provide public health with actionable information on how the SARS-CoV-2 virus spreads and evolves. This project aims to conduct multi-level genomic analysis on COVID-19 clinical sample sets. To do this they will form a robust genomic analysis team, consisting of subject matter experts in numerous fields (pathogen genomics, infectious disease epidemiology, virology, human genetics, mathematics, comparative analytics, and bioinformatics). They will also employ validated and published analysis methods in novel ways, with a focus on generating outcomes that are meaningful for public health, clinical medicine, and the COVID-19 research community.
University of California, San Francisco
Actionable real-time genomic surveillance of SARS-CoV-2 in California
The University of California, San Francisco (UCSF) will create an integrated network that combines rapid viral sequencing with epidemiologic and clinical data. The network will connect directly to local, state and federal public health agencies for immediate action. This project will use existing partnerships to establish a real-time network that can track and monitor the evolution and spread of SARS-CoV-2 in California. By using optimized techniques to sequence SARS-CoV-2 genomes from infected patients and then sharing data directly and immediately to public health agencies through an integrated network, UCSF intends to better inform contract tracing and public health responses.
University of California, Santa Cruz
Empowering comprehensive SARS-CoV-2 strain surveillance and transmission pattern inference for public health practitioners
The University of California, Santa Cruz will increase the understanding of SARS-CoV-2 by developing a genomic data platform for both scientists and public health officials. The platform will simplify interactions with genomic data, enabling users to rapidly cross-reference and identify genomic variation data sets in a unified setting. The platform will provide downloads of SARS-CoV-2 evolutionary maps in both scientific diagrams and in plain language to facilitate widespread use. All platform efforts ensure that users have access to complete, accurate, and understandable genome sequence data for all SARS-CoV-2 variants.
J Michael Consulting – Georgia
Implementation of cloud-hosted bioinformatics infrastructure to facilitate standardization, quality and submission of SARS-CoV-2 and other pathogen sequence data to public repositories
J Michael Consulting, LLC will provide a proof of concept bioinformatics platform for use by state and local public health partners. This project will pilot a solution to automate the submission of quality, curated sequenced data directly to the National Center for Biotechnology Information (NCBI) and CDC databases for SARS-CoV-2. These systems will establish the technological foundations of a national network to fully combine next-generation sequencing data into public health surveillance, monitoring, and research efforts.
University of Georgia
Community scaled viral sequence analysis and phylodynamics for SARS-CoV-2 using wastewater-based informatics
The University of Georgia will build and validate a viral sequencing platform to detect SARS-CoV-2 transmission at a community level from wastewater. The project will build, validate, and evaluate a platform that can analyze the characteristics and relationship between viral sequences at the community-level using water-based testing and information science. The University of Georgia will critically compare methods for genomic data extraction, collection, and analysis in order to provide validated methods that can support national surveillance efforts.
Johns Hopkins University – Maryland
SARS-CoV-2 Genome: viral evolution as a factor of sustained community transmission and prolonged infection
Johns Hopkins University will provide data in real-time describing the evolution of the SARS-CoV-2 virus in both the community and individuals. This study will provide real-time viral evolution data to identify whether specific changes in the SARS-CoV-2 genome mean a variant can spread more easily between people. It will also detect if a variant is better adapted to replicate within a host, or can make people more sick. Researchers will use novel methods to study how the virus evolves, not only in the community, but within a patient over a period of time. Through this study they will better understand the effects of SARS-CoV-2.
University of Michigan
SARS-CoV-2 sequencing to study virus evolution in a vaccinated population
The University of Michigan will sequence SARS-CoV-2 samples collected through healthcare networks, and a range of local testing labs in southern Michigan. Their goal is to associate viral sequences with vaccination status and assess changes in the characteristics and evolution of the virus as a result of vaccine campaigns. The study will combine viral genomic data with vaccination status, prior infection status, and antibody data to better understand risk factors and outcomes in SARS-CoV-2 reinfection. The same surveillance system will capture cases of SARS-CoV-2 reinfection.
University of Minnesota
Minnesota sequencing of SARS-CoV-2: a unified state and region-wide SARS-CoV-2 genomic surveillance effort
The University of Minnesota will provide real-time next-generation sequencing and analysis of SARS-CoV-2 in Minnesota. This project will establish the University of Minnesota Genomics Center (UMGC) as a regional SARS-CoV-2 sequencing hub and facilitate a low-cost and high-output genomic sequencing method. In addition, the project will provide research on how the host and virus interact with one another during infection and the potential for reinfection.
University of Mississippi Medical Center
Spatiotemporal sequence analysis of SARS-CoV-2 in Mississippi
The University of Mississippi Medical Center will use genomic sequencing to research viral emergence, evolution, and the spread of SARS-CoV-2 infection with a focus on racial disparities between African Americans and Caucasians. This study will perform genomic sequencing of SARS-CoV-2 samples collected through the state of Mississippi through a partnership with the Mississippi Department of Health. Genomic sequencing will be performed in 81 of the 82 counties across the state. The analysis will include pre- and post-vaccination samples. Data will be shared with national data repositories to provide insight into the SARS-CoV-2 transmission rate based on race.
University of Nebraska Medical Center
SARS-CoV-2 Viral Evolution and Spread within Nebraska and Surrounding States
The University of Nebraska Medical Center will generate genomic and clinical SARS-CoV-2 data. Shared in real-time, this data will support regional and local efforts to combat the SARS-CoV-2 pandemic. The study will provide SARS-CoV-2 whole-genome sequencing support and variant tracking for Nebraska and surrounding states. Sequencing efforts will focus on samples of reinfection cases, vaccine escape cases, and cases in which severe symptoms are present. Data generated from the study will be public and in real-time, so clinicians and researchers can see if they are dealing with similar cases and have access to samples for further testing.
Nevada State Public Health Laboratory
Real-time tracking of COVID-19 cases through rapid sequencing and single nucleotide polymorphism (SNP) analysis
The Nevada State Public Health Laboratory will develop a monitoring system of SARS-CoV-2 genomics in Nevada which will include daily sequencing of SARS-CoV-2 positive specimens with results available within 24 hours. In addition, the project will produce a software pipeline that will convert files into actionable genomic data.
University of New Mexico
Genomic sequencing and phylodynamic analysis of SARS-CoV-2 in the Mountain West USA
The University of New Mexico will support a regional partnership to expand genomic surveillance for SARS-CoV-2 in New Mexico, Wyoming, Montana, and Idaho. This study will generate extensive genomic data for the Mountain West region and provide state public health laboratories with actionable information on patterns of viral transmission and evolution. Researchers will interpret the regional sequences in a national and global context. Using tailored strategies and local knowledge, the consortium can fill critical gaps and improve the stream of surveillance sequencing data enabling them to track the trajectories of known and novel variants.
Oregon Health & Science University
Expanded genomic surveillance of SARS-CoV-2 in Oregon
In partnership with the Multnomah County Health Department and the Oregon State Public Health Lab, the Oregon Health & Science University will monitor emerging variants in the Portland metropolitan area and surrounding region. This project will expand SARS-CoV-2 surveillance efforts with a minimum sequencing capacity of 250 samples per week and establish low-cost sample sequencing pipelines. Emphasis will be placed on the dynamics of existing SARS-CoV-2 linages and the emergence of locally evolving high-impact variants associated with potential vaccine escape, super spreader events, and reinfection cases.
University of Pennsylvania
Whole-genome sequencing to define SARS-CoV-2 variant populations during vaccine rollout in the Philadelphia metropolitan region
The University of Pennsylvania will use genomic data to define clusters of variants in the Philadelphia metropolitan area and how the proportions of variants change as people in the area are vaccinated. This project will define how SARS-CoV-2 variant populations cluster geographically across Philadelphia’s metropolitan region, and how the variants in this area change over time as people are vaccinated. Using these data sets, researchers will develop a model to predict the impact of vaccination campaigns on evolving variants, which could better inform public health interventions related to vaccines.
Children’s Hospital of Philadelphia Research Institute
Monitoring diversity in SARS-CoV-2 genomes for tracking emerging variants, measuring impact of mitigation strategies, and gauging clinical outcomes in pediatric patients
The Children’s Hospital of Philadelphia Research Institute will provide genomic surveillance of SARS-CoV-2 in adults and children by tracking changes in the virus over two years in the greater Philadelphia area. With a weekly collection of a structured sample of isolates, genomic sequencing can detect new or expanding variants. In addition, the project will test the hypotheses that specific variants are more likely to be identified in clusters of cases or linked to “super-spreader” events or that specific viral variants are more associated with severe disease. The Children’s Hospital of Philadelphia Research Institute will build a web-based, user-friendly version of their viral classification tool to be easily accessed by health departments and hospitals.
Rice University – Texas
Harvest variants: enhancing tools for integrated, collaborative variant tracking of SARS-CoV-2
Rice University will enhance current genomic sequencing tools with SARS-CoV-2 tracking and analysis software. This project will design and develop genomic sequencing software that integrate SARS-CoV-2 genomic data sets. The software integration will enable users to download real-time virus data and variant analyses. Users will also have access to support and feedback tools.
University of Texas Medical Branch at Galveston
SARS-CoV-2 sequencing and surveillance at UTMB using “Tiled-Click Seq”
The University of Texas Medical Branch at Galveston will sequence and monitor SARS-CoV-2 for emerging variants. This project will provide genomic surveillance of current and future SARS-CoV-2 variant samples collected in University of Texas Medical Branch clinics. Scientists will focus on samples of individuals who test positive for SARS-CoV-2 but were vaccinated or were previously infected. Samples of individuals with persistent positive and severe or unusual cases of SARS-CoV-2 will be analyzed to provide a better understanding of the cause(s). The design and development of a bioinformatic database will assist in tracking this data and will provide a tool to share large datasets.
University of Washington
Viral genome sequencing and open-source software development to support genetic epidemiology in Washington State
The University of Washington (UW) will provide whole-genome sequencing and phylogenetic analyses of SARS-CoV-2 for the state of Washington and the surrounding region. This project will perform sequencing on an additional 4,400 SARS-CoV-2 virus genomes and analyze their diversity and development. Based on this analysis, the team will report on variants in the area, detect emerging variants, and determine how the variant proportions change as more of the population are vaccinated.
University of Wisconsin-Madison
Impact of immune failure on SARS-CoV-2 evolutionary potential
The University of Wisconsin-Madison (UWM) will analyze data of variants emerging in two Wisconsin regions (Dane County and Milwaukee County) with different demographics and various levels of socioeconomic vulnerability. Also, the study will focus on subpopulations who are at increased risk for immune failure and/or in whom cases of immune failure may be most likely to be contracted: healthcare workers, those who are infected despite vaccination, and people living in high-density settings (prisons, homeless shelters). The project will provide data on the impact of vaccines in community transmission.
Center for Genomic Pathogen Surveillance – Oxford, UK
Data tools to collect, integrate, contextualize, and visualize: transforming disparate datasets into actionable information for public health leaders
The Center for Genomic Pathogen Surveillance at the University of Oxford’s Big Data Institute will develop and enhance software tools to gather, integrate, and visualize pathogen genomic sequence data. These applications will enable researchers to incorporate many different types of data, providing better context and more useful public health information for state and local pandemic response efforts. This project will build customized data roadmaps at state-level laboratories that will act as pilot sites. Researchers will broadly analyze the bioinformatics capacity, data systems, and reporting processes of public health laboratories within strategically identified sites in collaboration with CDC’s Technical Outreach and Assistance for States Team (TOAST). The goal is to develop protocol and training materials for the roll-out of the developed toolchain to support genomic surveillance of SARS-CoV-2 in a wider range of laboratories across the U.S., and define what support is needed and where tools can have the greatest impact.
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.
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.