Taking on the coronavirus with a new next-generation sequencing strategy
Monday, February 10, 2020
The Centers for Disease Control (CDC) is closely monitoring an outbreak of respiratory illness caused by a new coronavirus named first started in Wuhan, China, but cases have been identified in a growing number of other international locations, including the United States.
On Jan. 21, 2020, the first case of 2019-nCoV in the U.S. was diagnosed in the state of Washington. While originally thought to be spreading from animal-to-person, there is growing concern that limited person-to-person spread is happening.
Over the past several weeks, the CDC has been proactively preparing for the introduction of 2019-nCoV, including the following:
- Alerting clinicians on Jan. 8 to be on the watch for patients with respiratory symptoms and a history of travel to Wuhan, China.
- Developing guidance for clinicians for testing and managing 2019-nCoV and providing guidance for home care of patients with 2019-nCoV.
- Developing a diagnostic test to detect this virus in clinical specimens, accelerating the time it takes to detect infection. Currently, testing for this virus must take place at CDC, but now the CDC will share these tests with domestic and international partners.
- Implementing public health entry screening at San Francisco (SFO), New York (JFK), Los Angeles (LAX), Atlanta (ATL), and Chicago (ORD) airports. The last two airports were added on Jan. 17.
- Activating its Emergency Operations Center to better provide ongoing support to the 2019-nCoV response.
In the meantime, to monitor how viruses like this one spread and evolve in animal populations, researchers are exploring next-generation sequencing (NGS). However, NGS can be costly and laborious, so geneticists are developing less expensive and more efficient NGS strategies.
One such strategy uses enrichment for monitoring coronaviruses, especially those originating in bats. The NGS is enriched with probes or baits, tiny fragments of genetic material that find and bind to the viral DNA, which could be a quick way to identify where the viral genetic material might be hiding.
According to Lin-Fa Wang, Ph.D., who directs the Program in Emerging Infectious Diseases at Duke-NUS Medical School, in Singapore, coronaviruses in bats are important to monitor because these viruses, such as the outbreak of severe acute respiratory syndrome (SARS) in 2003 and swine acute diarrhea syndrome (SADS) in 2018, have the potential to infect other animal populations and maybe even people.
When the world is free of outbreaks, called peace time, researchers build data banks of probes associated with known forms of coronaviruses. During outbreaks, or war time, researchers use that information to track the evolution of viruses and spread of infections both in animal and human populations. Of course, the bat coronavirus is constantly changing, so for the enrichment NGS to be successful, the probe library will need frequent updates.
While the researchers are working to understand 2019-nCoV, the World Health Organization (WHO) is working closely with global experts, governments, and partners to rapidly expand scientific knowledge on this new virus, to track the spread and virulence of the virus, and to provide advice to countries and individuals on measures to protect health and prevent the spread of this outbreak.
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