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Infectious Disease Sequencing Service, Training Launched

Aedes albopictus mosquito

Aedes albopictus mosquito, responsible for spreading West Nile and chikungunya viruses (CDC.gov)

16 Oct. 2018. A cloud-based open-source genomic sequencing program is underway to identify the source and nature of infectious diseases anywhere in the world. The service known as IDseq is provided by the Chan Zuckerberg Biohub, and unveiled today at the Gates Grand Challenges meeting in Berlin, where a competition to learn about IDseq with training in molecular biology and bioinformatics was also announced.

IDseq is an open-source platform enabling labs and clinics worldwide to connect with large-scale databases of metagenomics — genomics data taken directly from microorganisms and other environmental sources — and analytical algorithms to identify disease-causing microbes. The service reads a specimen sample, from bacteria, viruses, or other pathogens, and returns an actionable report for labs and physicians. The analyzed data are then added to IDseq’s knowledge base of infectious diseases, which in turn makes the system more valuable for physicians, clinics, and public health authorities.

The idea for IDseq originated in research conducted at the precision diagnostics lab of biochemist and biophysicist Joseph DeRisi at University of California in San Francisco. Derisi and colleagues study the genomic bases of infectious diseases, particularly malaria, but also identifying the nature of unknown conditions. “The global health community needs the ability to share data quickly to track outbreaks or emerging diseases,” says DeRisi in a Chan Zuckerberg Biohub statement. “With IDseq, we hope to empower data-driven decisions about how to better manage antibiotics, where to prioritize immunization campaigns, how to shape vector control and surveillance efforts.” DeRisi also shares scientific leadership duties at Chan Zuckerberg Biohub.

IDseq was put to work in a test of the technology to identify an unknown mystery pathogen at Dhaka Shishu Hospital in Bangladesh. Senjuti Saha of the Child Health Research Foundation in Dhaka, Bangladesh used IDseq to reveal a mosquito-borne viral chikungunya disease in the spinal fluid of patients. “Chikungunya was previously thought to be neuroinvasive only in very rare instances,” notes Saha. “But the data from IDseq suggested otherwise. It helped shed light on what were otherwise mysterious brain infections. This will help inform policy makers and initiate appropriate evidence-based case management.”

Training in IDseq is made available in a competition arranged through the Bill and Melinda Gates Foundation. The challenge competition is seeking proposals for projects to use IDseq for infectious disease identification. Winners of the challenge will receive hands-on training in best practices and standards for sample processing, DNA and RNA extraction, library preparation, and data analysis on IDseq software. Data generated by challenge participants will be added to the IDseq knowledge base to help process future queries. The deadline for challenge entries is 6 December 2018.

Chan Zuckerberg Biohub is rolling out IDseq in stages, with implementation expected to be completed next year. Biohub is a medical research organization collaborating with University of California in Berkeley, Stanford University, and the University of California in San Francisco. The program was started by Priscilla Chan and her husband Mark Zuckerberg, founder and CEO of Facebook, to make discoveries and develop new technologies that cure, prevent, or manage all diseases during our children’s lifetime. Chan and Zuckerberg committed $600 million to launch Biohub two years ago.

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