When people talk about variants of the COVID-19 virus, called SARS-CoV-2, we tend to use very broad terms like omicron and delta. But scientists who track the virus can get a lot more specific.
San Diego-based Scripps Research has released a study of how the virus was transmitted though the San Diego region and beyond. It found that while social distancing and some travel restrictions held the virus in check, some did not.
Scripps scientists compared data from more than 82,000 COVID-19 samples from the region. And the viruses they examined were constantly on the move, replicating and mutating.
“This sort of adds up to about one mutation every ten days or so. Based on this information we can build a sort of family tree of all the virus sequences we have.” said Scripps Research epidemiologist Mark Zeller, a senior author of the study that appeared in the journal Cell.
In the study, researchers also wanted to determine how travel patterns affected the virus. They did that by examining cell phone data that showed where people were and where they were going.
“And we show a really good correlation between the connectedness, based on the viral genome data and the travel data, based on the cell phones,” Zeller said.
The movement of these viral variants depended on what part of the pandemic you’re looking at.
Scripps researchers examined infections from the pandemic’s beginning in 2020 until midway through 2022. Early on, travel restrictions and stay-at-home orders were common in San Diego County and around the country. Add to that the reluctance of people to travel and you have a very limited geographic spread of viruses.
When those local mandates were lifted, it became a different story. New variants were showing up in San Diego frequently and spreading rapidly.
“So typically when a new wave comes in the local transmission increases, right? Because, well, there’s a new variant that has lots of susceptible hosts in San Diego County so it can just burn through those,” Zeller said.
By late in the pandemic about 50% of the viruses circulating were established local variants. The other half were recently introduced, due to travel outside the region.
One finding in the study showed that banning non-essential travel across the U.S.-Mexico border had little-to-no effect on COVID-19 risk in San Diego. Zeller said, in general, that targeted measures that try to stop the flow of people from a specific place are quite ineffective.
“Because by the time you have detected these variants, it is probably already too late. And the variant has already escaped the targeted area or targeted country,” he said.
Zeller compared the partial closure of the U.S. - Mexico border to the effort to ban travel from South Africa, after the omicron variant emerged. It also was ineffective.
But there’s no question that restrictions on travel and social distancing regulations can and do limit disease transmission in an epidemic. But Zeller said in an interconnected world viruses will ultimately travel as freely as we choose to.
