Members of the greater Seattle Coronavirus Assessment Network (SCAN) have published a paper showing how the early outbreak of SARS-CoV-2 in Washington State unfolded.

While the outbreak was characterized by a shift in viral variants, the researchers conclude it was likely a combination local behavior patterns and introduction of viruses into the State that shaped the outbreak.

The paper, “Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State” and published May 3 in Science Translational Medicine, was led by researchers at the Fred Hutchinson Cancer Research Center and the University of Washington School of Medicine.

“Our research shows how we can leverage genomic data to quantify the importance of introductions in driving local outbreaks,” said Nicola F. Müller, one of the lead authors and a post-doctoral fellow in the Bedford Lab at the Fred Hutchison Cancer Research Center. “It also suggests that assessing transmission benefits of novel viral variants has to take local outbreak and introduction dynamics into account.”

This work was based on continuous genomic sequencing of SARS-CoV-2 viruses that SCAN, UW Virology, and the Washington State Department of Health made publicly available throughout the pandemic. This enabled early analyses of potential differences in viral loads of the different spike variants that differed by a substitution in the spike protein, namely D614G.

Cassia Wagner, a PhD Student in the Bedford lab and co-lead author on the project said: “That early data and result sharing helped clue in other researchers that the D614G mutation might confer increased transmissibility, and our GitHub repository was cited in manuscripts studying this substitution in vitro and in vivo,” And further: “This experience taught me how open science, throughout all stages of a research project, can encourage synergistic research, which in this case had global benefit during the pandemic.”

Overall, the researchers sequenced nearly 4,000 viruses collected between February and July 2020 and compared these sequences with others from elsewhere in the world to characterize transmission dynamics. The paper notes that the outbreak in Washington State was caused by repeated introductions of the virus and shaped by temporal differences in mobility reductions across different regions in the State.

“We show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state,” according to the paper. “At an individual level, we observed evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we did not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that with regards to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus.

Access the paper here