Rapid Response

The Rapid Response team is made up of researchers and physicians involved in our infectious disease efforts and in support of establishing sustainable capabilities in laboratories in the US and around the world. We strive to enable data-driven decision-making by providing access to advanced molecular tools and methodologies, unique reagents, deep expertise in data science, and training within low-resource settings. Our work encompasses infectious disease surveillance, outbreak response, and capacity building to facilitate more agile triage and identification of (re)emerging infections and inform transmission dynamics through the application of genomic epidemiology. We enable strategies that are broadly applicable for a “One Health” approach to public health, facilitating more informed decision-making and resource allocation for implementing effective public health initiatives.

To cultivate global equity in basic and translational research for improved surveillance and response to emerging infectious diseases within underserved geographies.

Our surveillance projects have encompassed vector, syndromic, and SARS-CoV-2 efforts.

• The focus of our vector surveillance activities is to study and understand the dynamic between the disease reservoir, transmission of infection, and resulting morbidity. We aim to develop better molecular methods to evaluate potential risk for zoonoses, by exploring the microbial metagenomes particular to a variety of known vectors of infectious disease, such as mosquitoes, ticks, and bats.
• For syndromic surveillance cohorts we strive to provide insight into potential etiologies for better health care decisions and improvement of public health and patient care.
• We have also established a genomic surveillance system for SARS-CoV-2 with health departments throughout California.

Our outbreak response activities are meant to achieve impact through the use of our genomics approaches for rapid data generation and analyses for real-time investigations and retrospective interrogation of outbreaks. By improving the analysis of hospital or community outbreaks we can better understand the factors involved with both their occurrence and persistence, in order to improve response efforts and decrease morbidity and mortality. Finally, through the distribution of unique reagents and methodologies for antimicrobial resistance detection we can improve data collection and elicit higher resolution data.

For capacity building, the centerpiece of our efforts involves providing access to CZ ID, which is an open-source pipeline developed by the Chan Zuckerberg Initiative (CZI) for processing and analyzing metagenomic sequencing data combined with high-performance computing in the cloud. Ideally, use of this platform can be combined with our hands-on training of investigators on technique, methodologies, SOPs, and best practices for performing next-generation sequencing. Training investigators, and providing access to an analytical pipeline, elevates both the research and clinical care capacity within country.

We provide support to groups around the world to facilitate successful establishment of their own self-sustaining sequencing platforms. This is made possible, in part, through partnerships with both public and private organizations, regional network organizations, such as National reference labs, academic institutions, and CZI, and in support of establishing sustainable capabilities in laboratories in the US and around the world.