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 39 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 eight 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 fund innovative research and collaborative projects to support advancements in public health. 

Broad Institute, Massachusetts Department of Public Health, and Fathom Information Design

Enabling integrated analysis of multi-modal data for state epidemiologists

The Broad Institute will work to develop a system for integration, storage, analysis, and visualization of genomic and other data types. A team from the Broad Institute, Massachusetts Department of Public Health, and Fathom Information Design will collaborate to address three main challenges: identify public health use cases where improved tools for data analysis and visualization could guide public health; determine and implement solutions for data transfer and storage; and create relevant, real-time data visualization tools for the data. The over-arching goal is to provide relevant and timely information to guide public health decision making.

Helix OpCo, LLC - California

Genomic surveillance of respiratory pathogens with an integrated clinical dataset across a multi-site network of health systems

Helix OpCo, LLC (Helix), as part of efforts to create and support a national pandemic early warning system, is building a pan-respiratory virus surveillance program. The surveillance program involves linking virus genomes to key clinical and demographic data across a multi-site network. Additionally, Helix is creating an infrastructure to not only standardize the process of patient consent, sample collection, and data reporting, but also to return data back to each site to ensure that those site’s analyses and decisions are based on locally gathered information. This project is jointly supported by the Center for Forecasting Analytics and the Office of Advanced Molecular Detection.

Helix OpCo, LLC - California

Identifying viral and host genetic determinants of vaccine efficacy

Helix OpCo, LLC will establish a large-scale registry of COVID-19 breakthrough and reinfection cases and perform both virus and host genetic sequencing. This study aims to characterize viral and host genetic factors associated with efficacy of vaccines against infection and against severe disease, as well as factors associated with waning immunity. Results from this study may help to better predict breakthrough infections and poor outcomes of SARS-CoV-2 infection and to better tailor the time between vaccine doses and boosters.

Scripps Research – California

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

In March 2020, Scripps Research, together with the University of San Diego and public health partners, established the San Diego Epidemiology and Research for COVID Health Alliance (SEARCH) that has conducted sequencing and wastewater surveillance for SARS-CoV-2 and developed widely used analytical tools for genomic epidemiology. SEARCH will expand its large-scale surveillance activities to develop and implement real-time sequencing workflows and investigate spread and diversity of SARS-CoV-2 across the entire US-Mexico border. As part of the work, they will continue to develop and expand the open-source vital software and tools.

University of California, San Francisco

Characterization of host and immune responses to different SARS-CoV-2 variants and association with disease severity

The team plans to combine whole-genome sequencing for SARS-CoV-2 variants with host transcriptome and antibody analyses to develop models for predicting poor outcomes of SARS-CoV-2 infection and likelihood of vaccine breakthrough or re-infection. The intention is to uncover key biomarkers that can be used in assays in the future to improve diagnostic capabilities and monitor clinical course and outcomes in severely ill patients with pneumonia or other complications of COVID-19. This project also aims to further understand correlates between variant infection and clinical, immunological, and patient host responses, especially in vaccinated and/or boosted individuals.

J Michael Consulting – Georgia

Improving open source bioinformatic tools to provide better genomic data for pathogens of public health concern

J Michael Consulting will expand on previous work to develop and use CDC-driven standards, which are intended to connect public health laboratories (PHLs) to a secure national data sharing network so they can rapidly share sequence and other data for SARS-CoV-2 and other pathogens confidently and securely. While there is widespread access to sequencing technology, this network is intended to fully integrate advanced molecular detection (AMD) testing for the public health mission and wide data sharing.

University of New Mexico

Genomic Surveillance of SARS-CoV-2 in New Mexico and the Mountain West

A joint venture between the state public health laboratories of New Mexico, Wyoming, Idaho, and Montana, the UNM Health Sciences Center, and TriCore Reference Laboratories (NM), the group intends to gather and use data from the genomic sequencing of SARS-CoV-2 in the Mountain West region to provide the respective state public health laboratories with actionable information on patterns of viral transmission and evolution. The targeted focus enhances surveillance for a multi-state region and provides ongoing information on novel variants, including those that may be associated with increased clinical severity, and on patterns of viral transmission and evolution.

University of Washington

Collaborative technology development and analyses to support genetic epidemiology in Washington State

Researchers will continue to build on infrastructure built for multi-pathogen respiratory disease surveillance to combine SARS-CoV-2 sequencing data with detailed demographic and behavioral metadata to understand transmission dynamics of SARS-CoV-2 and co-circulating respiratory pathogens. Researchers will continue ongoing collaboration with the Washington Department of Health to understand new SARS-CoV-2 variants and how they relate to severity and transmission dynamics. They will also develop novel wet laboratory methods for sequencing and maintain and improve Nextstrain software that is widely used for phylodynamic analysis.

University of Wisconsin-Madison

Impact of local differences in vaccine uptake on SARS-CoV-2 evolution and spread across three Upper Midwestern states

The researchers will perform genomic surveillance in Wisconsin, Minnesota, and Michigan and analyze these data along with vaccination and demographic data. They will develop two models. One model will illustrate transmission within and between geographic subdivisions. The second model will be used to understand the impacts of factors such as vaccination, population density, and socioeconomic indices on viral diversity and transmission patterns. In addition, they will build and deploy systems to improve local health department integration with statewide public health data.

Yale School of Public Health

Transmissibility and immune escape of emerging SARS-CoV-2 variants

Researchers will combine data from genomic surveillance together with clinical, experimental laboratory, and epidemiological data with the overarching goal to better understand SARS-CoV-2 variant evolution, emergence, and transmission. This research aims to continuously evaluate the influence of SARS-CoV-2 variants on transmission and escape from vaccine-induced immunity to aid response planning and inform vaccine dosing and design strategies in real time.