Concerned about the new coronavirus, James Lee and his wife sought testing after returning home to Oakland from a trip last month to Wuhan, China, the center of the fast-spreading outbreak that has sickened 17,391 people in 24 nations, killing 361.
For six hours, the couple was quarantined in a local urgent care facility and hospital emergency room, not returning home until 1 a.m. Their samples were sent to the Centers for Disease Control in Atlanta for testing. Then they waited two days to see if they were safe.
There’s a better and faster way, say Bay Area scientists.
Racing to build a test to diagnosis coronavirus and other deadly pathogens, UC San Francisco’s Dr. Charles Chiu and the San Francisco biotech company Mammoth Biosciences are enlisting CRISPR, the famed gene-editing tool.
Quick, accurate and inexpensive, the tool will use CRISPR’s ability to detect snippets of a virus’s genetic material to detect infection early and help rein in the spread of disease. They hope to have it ready within several weeks.
Fast turnaround time is essential in an emergency like coronavirus, when patients need to be isolated or quarantined immediately. The infection is dispersing into more remote parts of China and the globe. On Monday, there were 11 confirmed cases in the U.S., including four in the Bay Area, two in Southern California, two in Illinois and one each in Washington, Arizona and Massachusetts.
These cases could be the tip of an iceberg, according to a paper recently published in the journal Lancet. Using mathematical models, it predicted that over 75,000 people in Wuhan may have been infected with the virus of January 25th — and outbreaks in other Chinese cities will sustain exponential spread outside Wuhan.
“Large cities overseas with close transport links to China could also become outbreak epicenters, unless substantial public health interventions at both the population and personal levels are implemented immediately,” wrote lead researcher Joseph T. Wu of the University of Hong Kong. “Self-sustaining outbreaks in major cities globally could become inevitable … in the absence of large-scale public health interventions. Preparedness plans and mitigation interventions should be readied for quick deployment globally.”
In Wuhan, residents report that it is nearly impossible to get the health care they need to diagnose the disease. Doctors say there is a shortage of testing kits and other medical supplies.
Moreover, there is emerging evidence that some patients spread the virus during its incubation period, which may last 14 days, before symptoms emerge. Last week, scientists reported in the New England Journal of Medicine that a Shanghai businesswoman who did not feel sick transmitted the virus while on a January trip in Germany.
This raises the possibility that people could spread the virus before they know they’re infected.
“What you want to do is test people at a point-of-care setting — like a doctor’s clinic, emergency room or even an airport,” said Chui. “That is the motive for this test.”
In practice, it would work like a pregnancy test, with results in one to two hours. A strip of special paper would be dipped into a sample containing the CRISPR system. If the sample contains the virus’s genetic sequence, it would change color.
It might even be linked to a smart phone application. The person could take the test at home, upload a picture of the testing strip once it changes color, get results from the app and then be connected to a doctor.
For the San Francisco team, the next step is to demonstrate that CRISPR diagnostic kit is effective in living coronavirus-infected cells. They’re waiting to acquire cells from the CDC or state. Thus far, they’ve only been able to study the virus by analyzing the genetic code published by Chinese scientists. Research, thus far, has been conducted in synthetic cells designed in the lab.
Competitive tests are also in development by other companies, such as the Cambridge-based biotech company Sherlock Biosciences. It uses CRISPR-based technology developed by Feng Zhang and his colleagues at the Broad Institute of MIT and Harvard.
Currently all potential coronavirus specimens are sent to U.S. CDC labs in Atlanta.
The government’s test uses a large, expensive and sophisticated tool called Reverse Transcriptase PCR (RT-PCR), which measures the amount of viral RNA, a chain of cells that carry genetic information, in a patient’s sputum, serum or blood.
It takes time to ship a patient’s sample to Atlanta, then process it and release results.To help expedite detection, the government is improving and standardizing its test and plans to release it to a limited number of state health departments. But still that test will take time.
That’s one reason why news about suspected cases has been slow to confirm.
CRISPR, conceived by UC Berkeley’s Jennifer Doudna, has shown potential to fix genes that cause deadly disease, as well as alter plants, improve food, create biofuels and even revive extinct mammals.
She discovered that bacteria use CRISPR — an acronym for “clustered regularly interspaced short palindromic repeats,” those weird repetitive and mysterious sequences in genetic code — to recognize the genetic sequences of invading viruses so they could chop them up.
But it can be a diagnostic tool, not just a chopping tool. It can be programmed to act like a homing beacon on invading viruses, rather than molecular scissors.
CRISPR has the advantage of being easy to tweak as needed, if a virus evolves and mutates. Although the virus has not evolved substantially over the course of this outbreak, scientists want to watch if its genome could change over time, perhaps affecting its lethality or capacity to spread. The CRISPR test could also reveal how the virus interacts with the immune system.
After their long wait, James Lee and his wife were relieved to learn that they were negative for the virus. Indeed, she was sick — but her illness was Type A influenza, not coronavirus.
03 Jun, 2020  0  Comments
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