Stalking the coronavirus
Research provides hope that killer can be halted
Scientists have chased global killers before, such as the viruses that cause SARS, MERS and Ebola. Now they’re doing it under a global spotlight as COVID-19 rampages across the globe. In labs around the world, they’re tracking how the virus mutates. The research shows that social distancing and quarantines are helping to slow the spread of the virus’s eight strains.
FRANCISCO – At least eight strains of the coronavirus are making their way around the globe, creating a trail of death and disease that scientists are tracking by genetic footprints.
While much is unknown, hidden in the unique microscopic fragments of the SARS-CoV-2 virus, which causes the illness COVID-19, are clues to the origins of its original strain, how it behaves as it mutates and which strains are turning into conflagrations while others die out because of quarantine measures.
Labs around the world are turning their sequencing machines, most about the size of a desktop printer, to the task of rapidly sequencing the genomes of virus samples taken from people sick with COVID-19. The information is uploaded to a website called NextStrain.org that shows how the virus is migrating and splitting into new but similar subtypes.
While researchers caution they’re seeing only the tip of the iceberg, the tiny differences between the virus strains suggest shelter-in-place orders are working in some areas and that no one strain of the virus is more deadly than another. They also say it does not appear the strains will grow more lethal as they evolve.
“The virus mutates so slowly that the virus strains are fundamentally very similar to each other,” said Charles Chiu, a professor of medicine and infectious diseases at the University of California, San Francisco School of Medicine.
SARS-CoV-2 first began causing illness in China sometime between midNovember and mid-December. Its genome is made up of about 30,000 base pairs. Humans have more than 3 billion. So far scientists have found only 11 base pair changes even in the virus’s most divergent strains.
That makes it easy to spot new lineages as they evolve, Chiu said.
“The outbreaks are trackable,” he said. “We have the ability to do genomic sequencing almost in real time to see what strains or lineages are circulating.”
In the U.S., most cases on the West Coast are linked to a strain first identified in Washington state. It may have come from a man who had been in WuSAN han, China, the virus’s epicenter, and returned home Jan. 15. It is only three mutations away from the original Wuhan strain, according to work done early in the outbreak by Trevor Bedford, a computational biologist at Fred Hutch, a medical research center in Seattle.
On the East Coast, there are several strains, including the one from Washington and others that appear to have made their way from China to Europe and then to New York and beyond, Chiu said.
Chiu’s analysis shows California’s strict shelter in place efforts appear to be working. Over half of the 50 SARSCoV-2 virus genomes his San Francisco-based lab sequenced in the past two weeks are associated with travel from outside the state.