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SARS-CoV-2 Genomes, Mobility Patterns Point to Broad Interconnections in COVID-19 Spread

NEW YORK – With the help of genomic surveillance, a research team from the US and Mexico retraced SARS-CoV-2 transmission patterns in the San Diego-Baja California region over the first five waves of the COVID-19 pandemic, uncovering extensive and complex connections between locations that shifted to reflect pandemic control measures and related human movements.

The researchers' results, published in Cell on Thursday, pointed to apparent containment at early points of the pandemic when stay-at-home orders, travel restrictions, or other mandates were in place. In contrast, mobility, viral genome, and epidemiology data suggested significant SARS-CoV-2 spread took place in the summer of 2020, when various regions lifted some of the pandemic mandates and travel began to resume.

"[W]e were able to qualify how transmission of the virus within North America changed over time and space in response to the implementation and relaxation of specific COVID-19 mandates," co-first author Nathaniel Matteson, an immunology and microbiology researcher at Scripps Research, explained in an email, adding that "movement of people between locations blurred the boundary between apparently separate epidemics."

Within genome surveillance performed between March 2020 and the end of 2022, the investigators sequenced more than 82,000 SARS-CoV-2 isolates collected in San Diego and Baja California, analyzing the sequences alongside cell phone tracking-based human movement data, epidemiological insights, and SARS-CoV-2 genomes from other parts of North America and beyond.

"By studying locations along international borders and comparing transmission in border regions with that in other US locations, we were able to investigate the effect of travel restrictions across the country and to isolate the impact of restrictions on international borders," the authors explained.

The team's analyses — which included network analysis as well as phylogenetics- and epidemic simulation-based connectivity clues — argued against the notion that COVID-19 cases in a given geographic area mainly reflected viral circulation and transmission in that region, particularly as the pandemic progressed. Instead, the work highlighted transmission between regions, which ratcheted up as mandates began lifting.

"We saw loads of transmission between neighboring, but administratively distinct, locations through the entire pandemic and an increase in transmission between more distant locations over time," Matteson said.

Overall, the investigators estimated that roughly half of COVID-19 cases stemmed from strains circulating locally, while the remaining 50 percent of cases appeared to involve forms of SARS-CoV-2 linked to outbreaks or circulating in adjacent areas or from more distant parts of the country or world.

"Our findings indicate that connectivity between locations plays an increasingly important role in maintaining local epidemics, which highlights the need for collaboration between regional and international governments to enact effective prevention strategies," the authors wrote.

Even so, the investigators noted travel restrictions such as closing the international border to nonessential travel tended to have relatively muted effects on viral spread in the San Diego area, as viral connections with other international locations or domestic locations such as Los Angeles and other American cities became increasingly common.

Together, the authors explained, such findings underlined the potential importance of consistent or coordinated policies for dealing with infectious disease outbreaks across regional, national, or international government organizations.

"[I]t is a necessity that the international community equitably distributes surveillance infrastructure and enacts travel restrictions collaboratively," the authors wrote, calling it "vital that the effects of such restrictions, particularly when they are not equally experienced, be carefully weighed against their quantitative benefit."

While the latest findings illustrate the potential for combining cell phone-based human mobility and epidemiological data to track infectious disease circulation and influx in a region, Matteson noted, they also suggested that genome sequence insights may reflect viral transmission and related human movements in situations where mobility data is not available.

"[I]f mobility data is lacking … we found that the similarity between virus genomes collected in two different locations is a useful proxy for how connected those locations are in terms of the movement of people," Matteson explained, adding that "genomic surveillance can provide useful insight into questions that are usually answered with time- and resource-consuming contact tracing."