In late February, when researchers at the University of Washington in Seattle were analyzing the genetic sequence of a SARS-CoV-2 novel coronavirus sample, they realized it had clearly descended from a different patient sample they had seen six weeks earlier.
Genetic sequences from both virus samples contained a rare change that they had only seen in two out of 59 sequenced strains from China — the likelihood that these samples were not related was extremely low. This relatedness is typical for transmission through a community as the virus moves from one person to another; however, these two patients did not have contact with one another, and the second patient’s sample was collected six weeks after the first patient had been contagious. Patient 1 had passed the virus to Patient 2 through an unknown chain of people.
This finding had staggering public health implications — it meant that the virus had been traveling undetected in the community for six weeks. Overnight, we learned that the Seattle area had been almost certainly experiencing the start of its now significant outbreak for over a month without any awareness.
This genomic analysis was an essential piece of information for informing officials in Washington State that they needed to change the scope of their response immediately, and this approach serves the same purpose in every community where it is deployed.
Labs and public health organizations across the world are sequencing samples of SARS-CoV-2 to create an enormous family tree of how all of the strains we have seen so far are related. This tree can be seen at Nextstrain.org, an analytic and visualization project helping scientists realize the full potential pathogen genome data and improve outbreak response. Nextstrain and its data repository contain sequence information for 59 BC strains of SARS-CoV-2, sequenced through a rapid genomic analysis initiative led by researchers at the BC Centre for Disease Control (BCCDC) and the University of British Columbia (UBC) and funded by Genome BC.
For each new strain they sequence, the BCCDC is able to ask whether it is more closely related to strains from other countries or to strains they have already seen in BC. Knowing whether a strain is a new arrival or being passed through the community helps public health agencies decide what types of interventions are likely to be most effective and see where existing interventions are successful or failing.
A March 20th situation report on Nextstrain highlighted how the BC sequence data can cross-check travel histories collected through more traditional means. A patient who reported travel to Europe also had a strain of the virus most closely genetically related to strains reported from England and the Netherlands, meaning that they likely contracted the virus abroad and not in BC. This is useful information for public health agencies because their approach to the case and community management would have been different if the results of genomic analysis didn’t match the travel history.
This was the situation for another strain from BC in which a patient reported travel to Iran, but their viral strain wasn’t closely related to other strains from Iran, indicating they potentially contracted the virus while traveling elsewhere or once they had returned to BC.
In addition to helping us understand how a virus is spreading through a community, genomic analysis can help scientists determine the origins of a virus and predict what treatments will be effective against it now and in the future. These are all genetic clues scientists will follow as they work to manage this pandemic.
Resources:
Dr. Trevor Bedford , University of Washington, @trvrb, announcing findings about community spread in Washington State: https://twitter.com/trvrb/status/1233970271318503426
Coronavirus May Have Spread in U.S. for Weeks, Gene Sequencing Suggests. New York Times, March 9, 2020, Sheri Fink and Mike Baker: https://www.nytimes.com/2020/03/01/health/coronavirus-washington-spread.html
BCCDC to track origins and spread of new coronavirus with genomic technology, Genome BC https://www.genomebc.ca/blog/bc-to-track-origins-and-spread-of-new-coronavirus-with-genomic-technology
BC data featured on Nextstrain
Europe: https://nextstrain.org/narratives/ncov/sit-rep/2020-03-20?n=6
Iran: https://nextstrain.org/narratives/ncov/sit-rep/2020-03-20?n=7
For more about how to read relatedness or “phylogenetic” trees, a resource here: https://nextstrain.org/narratives/trees-background/