DNA & Disease: Facing Pandemics with Pathogen Genomics

Sequencing: Faster, Cheaper, More Available

Every infectious disease agent, from the common cold to exotic brain parasites, has a genome made of DNA or RNA. This genetic material contains instructions that allow a pathogen to attack, reproduce, and move to a new host. It can also be used to fingerprint a pathogen, thanks to advances in sequencing technology that enable scientists to read genetic “barcodes” within the pathogen’s DNA or RNA.

Metagenomics: A Tool for Identification

Consider the task of figuring out what is making someone sick when you don’t have a prior idea of what the cause might be and running tests for every possible pathogen would take too long. This is where sequencing can help by looking at all the different pathogens in a person’s sample, for example their saliva. The fluid likely contains the pathogen behind the illness, with a genomic barcode that can reveal its identity. However, this barcode is also mixed in with lots of other DNA: e.g., the infected person’s own DNA (from cells shed from the throat) and DNA from any other organisms currently infecting that person, as well as from the microbes naturally found in their mouth, known as commensals. In short: The saliva sample contains a cornucopia of genetic material from different sources.

A researcher from Madagascar at the Chan Zuckerberg Biohub, which provides researchers free access, training, and compute on the Chan Zuckerberg ID platform, and the necessary equipment and supplies to begin work in their own countries through the Bill & Melinda Gates Foundation Grand Challenges Explorations Grants.

Genomic Epidemiology: Tracking Disease

Identifying the culprit behind an emerging disease is the first step in tackling an infectious disease outbreak. But as the COVID-19 pandemic has highlighted, being able to monitor the spread of an infectious disease is critical for public health. Epidemiologists use contact tracing to track the transmission of a pathogen in a population. But there are limitations to that approach, namely the reliance on interviewing individuals and being able to gather an accurate history of where they went, who they came into contact with, and when. Enter genomic epidemiology, which helps supplement standard contact tracing by leveraging sequencing data.

Jeremy Corrigan, DrPH, at the Humboldt County Public Health Laboratory. Teams at CZI and the CZ Biohub collaborated to launch Chan Zuckerberg GEN EPI (formerly known as COVID Tracker) — a free, open source software tool to help public health officials analyze their COVID-19 data, track the virus and prepare for future crises.



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Chan Zuckerberg Initiative Science

Chan Zuckerberg Initiative Science


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