SAN 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 their genetic footprints.

While much is unknown, hidden in the virus's unique microscopic fragments are clues to the origins of its original strain, how it behaves as it mutates and which strains are turning into conflagrations while others are dying out thanks to quarantine measures.

Huddled in once bustling and now almost empty labs, researchers who oversaw dozens of projects are instead focused on one goal: tracking the current strains of the SARS-CoV-2 virus that cause the illness COVID-19.

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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 similar but new subtypes.

While researchers caution they're only seeing 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 disease at the University of California, San Francisco School of Medicine.

A map of the main known genetic variants of the SARS-CoV-2 virus that causes COVID-19 disease. The map is being kept on the nextstrain.org website, which tracks pathogen evolution. More

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The SARS-CoV-2 virus first began causing illness in China sometime between mid-November and mid-December. Its genome is made up of about 30,000 base pairs. Humans, by comparison, have more than 3 billion. So far even in the virus's most divergent strains scientists have found only 11 base pair changes.

That makes it easy to spot new lineages as they evolve, said Chiu.

“The outbreaks are trackable. We have the ability to do genomic sequencing almost in real-time to see what strains or lineages are circulating,” he said.

So far, most cases on the U.S. 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’ epicenter, and returned home on 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.

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Charles Chiu, MD, PhD, director of the UCSF-Abbott Viral Diagnostics and Discovery Center, inserts a tray of Universal Transport Medium (UTM) or vials for the collection, transport, maintenance and long term freeze storage of viruses into a Biomatrix sorter that the Chiu Lab will be using, starting Monday to study the genes of the Coronavirus. More

Beware pretty phylogenetic trees

This isn’t the first time scientists have scrambled to do genetic analysis of a virus in the midst of an epidemic. They did it with Ebola, Zika and West Nile, but nobody outside the scientific community paid much attention.

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