California and Zuckerberg lab team up to map coronavirus genome, one of the largest efforts to discover how it spreads – San Francisco Chronicle

Health officials and scientists believe genome sequencing of the coronavirus could hold great promise. The technique today helps trace where infections began, and perhaps one day it could help shape the way doctors treat COVID-19 patients.

A new initiative between California and the San Francisco research institution funded by Facebook CEO Mark Zuckerbergs philanthropic organization could bring them one step closer.

The Chan Zuckerberg Biohub will offer free genome sequencing for lab samples that have tested positive for the coronavirus from all California counties, the institution is slated to announce Thursday.

It is one of the largest statewide, coordinated efforts to do genome sequencing for COVID-19, said Dr. Joe DeRisi, co-president of the Chan Zuckerberg Biohub. Genome sequencing helps determine what strain of the virus people have, which helps public health officials trace how transmission occurred and where it came from.

The Biohub had already been doing genome sequencing on samples from many California county public health departments on a smaller scale since March. Now, it is formally partnering with the state Department of Public Health to expand the work.

Sequencing is not necessary for all samples, but can be useful to determine the source of an outbreak in some settings or to rule out a suspected pattern of transmission. For example, if sequencing found that similar strains of the virus are rampant at two different nursing homes, and the two facilities share staff, that may indicate a staffer brought the virus from one home to the other. Or if one factory employee has a strain that is similar to that of a coworker, it may indicate the virus spread at work; but if strains found in one workplace are vastly different, it indicates the employees likely got sick from interactions outside of work.

Where its the most helpful is understanding the number of circulating strains in a given community, to understand if theres been a new introduction of a strain to a particular geographic area or facility, DeRisi said. That establishes whether youre looking at ongoing, in-community transmission, or whether theres been an outside introduction that was unbeknownst to you.

Sequencing involves putting a sample that has tested positive for the coronavirus into a lab machine that analyzes the viral genetic material and identifies where mutations occur.

A strain is a group of viruses with similar mutations. SARS-CoV-2, the virus that causes COVID-19, has 30,000 letters of RNA, genetic material that includes instructions on how to make new copies of the virus. When the virus spreads from cell to cell and person to person, it passes on small changes, or mutations, in the viral information. Some of those mutations are then passed on to the next person. A strain is a product of a long chain of transmission, and the cumulative changes that occurred over time.

The Biohub will not sequence every single sample. But it will sequence samples when the work can help answer critical questions about some outbreaks and how they started. Biohub has sequenced about 1,600 samples from nursing homes, packing plants and prisons from 20 California counties. It is sequencing samples from San Quentin State Prison to determine whether the outbreak there came in from one source and then spread, or if it came in from multiple sources carrying different strains.

Sequencing has helped scientists determine that the East Coast has largely been hit with a European strain of the virus, while California has been hit by many strains, including from Europe and China.

One of the potential promises of genome sequencing is that it could eventually help scientists learn whether certain strains of the coronavirus are resistant to certain drugs. That could help doctors pick which drugs, or cocktail of drugs, to administer to patients. With HIV, for instance, sequencing helped researchers glean that some strains of the virus respond well to certain drugs while other strains are resistant to the same drugs.

Ultimately, we might be able to use this data for things like susceptibility to drugs or a vaccine, said Dr. Robert Siegel, a Stanford infectious disease expert. Were not there yet.

It is too early with the coronavirus to know whether some strains are resistant to drugs. There have not been many drugs that have successfully treated COVID-19. But a few, including remdesivir, appear to help some very sick patients.

Imagine that you took all the patients on remdesivir, and you had good clinical data on them, and it turns out some people responded to remdesivir and some didnt, Siegel said. Its possible that is either a function of the viral strain or of the genetic makeup of the host, or a combination of the two. Or it could be luck. ... If we started seeing remdesivir resistance, almost certainly wed be able to tell what mutations gave rise to remdesivir resistance.

It costs about $15 to $20 to sequence each sample, DeRisi said.

The sequencing will be done at a lab at the Biohub, which is financed by the philanthropic organization Chan Zuckerberg Initiative in San Franciscos Mission Bay. The initiative was created in 2015 by Zuckerberg and his wife Dr. Priscilla Chan, who pledged $600 million over 10 years to help advance medical research.

The initiative has also committed $13.6 million to fund large, long-term COVID-19 studies in the Bay Area and a $4 million UCSF lab to process coronavirus tests.

Catherine Ho is a San Francisco Chronicle staff writer. Email: cho@sfchronicle.com Twitter: @Cat_Ho

Here is the original post:
California and Zuckerberg lab team up to map coronavirus genome, one of the largest efforts to discover how it spreads - San Francisco Chronicle