Scientists hunting down eight coronavirus strains
SAN FRANCISCO – At least eight strains of the novel 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’s 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, said Chiu.
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 Wuhan, China, the virus’s epicenter, and returned home Jan. 15.
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.
Different symptoms, same strains
COVID-19 hits people differently, with some feeling only slightly under the weather for a day, others flat on their backs sick for two weeks and about 15% hospitalized. Currently, an estimated 1% will die. The rate varies greatly by country; experts say it is likely tied to testing rates rather than actual mortality.
Chiu said it appears unlikely the differences are related to people being infected with different strains of the virus.
The COVID-19 virus does not mutate very fast. It does so eight to 10 times more slowly than the influenza virus, said Anderson, making its evolution rate similar to other coronaviruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS).
It’s also not expected to spontaneously evolve into a form more deadly than it already is to humans. SARSCoV-2 is so good at transmitting itself between human hosts, said Andersen, that it is under no evolutionary pressure to evolve.
Shelter in place working in California
Chiu’s analysis shows California’s strict shelter in place efforts appear to be working.
Over half of the 50 SARS-CoV-2 virus genomes his San Francisco-based lab sequenced in the past two weeks are associated with travel from outside the state. About 30% are associated with health care workers and families of people who have the virus.
“Only 20% are coming from within the community. It’s not circulating widely,” he said.
That’s good news, he said, indicating the virus has not been able to gain a serious foothold because of social distancing.
The virus, he said, can be stopped.