2022 Project: Scripps Research Institute

SEARCH alliance, San Diego — genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread using viral phylodynamics

What to know

In March 2020, Scripps Research Institute, together with the University of San Diego and public health partners, established the San Diego Epidemiology and Research for COVID Health Alliance (SEARCH), which has conducted sequencing and wastewater surveillance for SARS-CoV-2 and developed widely used analytical tools for genomic epidemiology.

Decorative image with words "2022" and "SARS-CoV-2"

Findings on SARS-CoV-2 surveillance and investigations

This project described drivers of local COVID-19 epidemics, including regional transmission across international boundaries.1

New and improved sequencing software tools

Substantial improvements have been made to software packages iVar, Freyja, and outbreak.info, which are regularly updated and can be found on a GitHub repository: https://github.com/andersen-lab.

New SARS-CoV-2 dashboards and websites

In partnership with SEARCH alliance, this project conducts clinical genomic surveillance to incorporate into the SEARCH dashboard. This is used to display genomic data obtained from wastewater in multiple wastewater treatment plants in San Diego County.

Awarded in 2022, this project is still in progress.

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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)
  1. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics - PubMed (nih.gov) Cell