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Dozens of Introduction Events Sparked SARS-CoV-2 Spread in Oregon, Sequence Data Suggests


NEW YORK - SARS-CoV-2 was introduced to Oregon dozens of times between March and July, according to researchers from Oregon Health and Science University (OHSU), the Knight Cancer Institute, and the Oregon National Primate Research Center.

Using sequences for 537 SARS-CoV-2 isolates linked to the region from late February to July, focusing on samples with more than 90 percent genome coverage, the multidisciplinary team of sequencing, pathology, and clinical experts tracked the introduction and infection dynamics of lineages in the region, identifying a super-spreader event as well as a handful of strains that seem to have been stamped out.

"One of our main projects has been to identify and track viral transmission chains in Oregon through the use of residual clinical samples, doing whole-genome sequencing," explained post-doctoral researcher Brendan O'Connell, who shared data from the study at the American Society of Human Genetics virtual meeting on Wednesday.

When the OHSU shut down on-campus research on March 23rd, he recalled, 191 cases of COVID-19 had been reported in Oregon, but no SARS-CoV-2 genomes from state had yet been sequenced. Inspired by the success of viral sequencing programs in Washington State, the team submitted a proposal to start its own sequencing analysis at the burgeoning "Oregon SARS-CoV-2 Genome Sequencing Center," and began processing samples in mid-April.

By that time, the University of Washington had sequenced 10 SARS-CoV-2 genomes from Oregon, and the US Centers for Disease Control and Prevention had generated sequences from two Oregon isolates, including the first case identified in the state on February 27th.

O'Connell and his colleagues went to work generating hundreds more SARS-CoV-2 genomes using RNA extraction and RT-PCR to identify SARS-CoV-2-positive swab samples before converting the viral RNA to complementary DNA for amplification, indexed library preparation, Illumina short-read sequencing, and assembly.

The team's genome analyses ramped up considerably between March and July as the scale of the pandemic increased, from three SARS-CoV-2 genomes in March to 250 viral genomes generated in July.

More than 92 percent of the genomes analyzed by the Oregon SARS-CoV-2 Genome Sequencing Center originated in Oregon, though the researchers also took a look at a handful of SARS-CoV-2-positive samples from southern Washington, California, Alaska, Idaho, and Texas.

"We've tried to keep up with the spread of the pandemic in Oregon," O'Connell said, noting that a custom Oregon-centered Nextstrain analysis helped in untangling introductions to the state and placing them within a larger pandemic context.

Based on 685 available viral genomes generated at OHSU and elsewhere from samples in Oregon, the researchers narrowed in on 29 likely SARS-CoV-2 introductions to that state, including 14 unambiguous introductions between February and April that were marked by multiple isolates. O'Connell explained that a few more suspected introductions were suspected, though not as well supported by the sequence data, since they each involved a single SARS-CoV-2 genome.

Just four main transmission clusters appeared to contribute to many of the cases detected in the first few months of the pandemic in Oregon, the team suggested. These transmission events were linked to some two-thirds of the SARS-CoV-2 genomes sequenced from Oregon during that time.

As the pandemic progressed from May to July, the researchers saw three more multiple-member introductions to the state and another major transmission chain, O'Connell explained, along with eight more potential introduction events represented by individual SARS-CoV-2 genomes. Notably, only a dozen of the strains that were introduced to the region were still being picked up by viral sequencing by July, he added, suggesting "a number of those transmission chains appear to have been broken."

With the genome sequences on hand, the team also investigated an apparent super-spreader event at the Portland VA Medical Center in early May, where at least six patients, 24 staff members, and one medical trainee were infected with SARS-CoV-2 on two in-patient wards.

Using a triplet mutation shared by all but one of the SARS-CoV-2 samples from that outbreak, along with additional sub-clonal mutations, the researchers retraced transmission events at the hospital, linking the outbreak to a sub-strain that was apparently circulating in the community at the time.

"In the 400-plus samples we've sequenced since May, we don't see any of this outbreak signature," O'Connell said, noting that "the VA has been working on linking our genomic data with their contact tracing data and so far, those accord very well."

Together, O'Connell said, findings from a single state over a few months highlight the potential for using SARS-CoV-2 genome sequencing to not only identify introductions and monitor the spread of new viruses, but also for finding and following COVID-19 outbreaks, all while getting a closer look at SARS-CoV-2 biology, evolution, and potential vulnerabilities.

So far, the investigators have identified "strains from every continent showing up in Oregon," he said, though domestic travel appears to have been a large contributor to viral spread in the region.

"Overall, these data strongly support the major source of new viral introductions in Oregon are from domestic travel," O'Connell and his co-authors wrote in the presentation's abstract, adding that the data are expected to "provide a valuable resource for tracking existing and new introductions of SARS-CoV-2 within our region."