How the common cold persisted throughout COVID-19 lockdowns

For those who have been coughing and sneezing this autumn, the culprit may have been a rhinovirus (RV). Unlike other respiratory viruses, there are over 100 different types of RVs, with many circulating concurrently. Their vast diversity poses a challenge for researchers hoping to study how RVs spread and evolve.

In a recent study published in The Journal of Infectious Diseases, researchers focused on how RVs spread during and after the COVID-19 lockdowns in Washington State (1). The study analyzed over 1,000 samples of RV from nasal swabs taken at COVID-19 testing sites. The team produced the largest collection of newly sequenced RV genomes yet, which currently makes up half of the publicly available rhinovirus data.

While circulation of other respiratory viruses decreased in response to restrictions and masking efforts during the pandemic, “RVs just kept circulating as if nothing happened,” said Stephanie Goya, a postdoctoral researcher at the University of Washington and coauthor of the study.

The hardest part about rhinovirus is getting people to include it in their surveillance.
- Alex Greninger, University of Washington

The team looked at samples gathered during the spring and summer of 2021 as well as the fall and winter of 2022. They sequenced 1,078 genomes from both symptomatic and asymptomatic people from both periods. With these sequences, the team constructed phylogenetic trees to better understand how the different RV genotypes evolved.

“It’s a huge dataset. I’ve never seen that many nearly complete genome sequences before, so that’s a unique feature of this work,” said Yury Bochkov, a virologist at University of Wisconsin-Madison. “I really appreciate their effort.”

They found 99 different RV genotypes in their samples, and no single genotype was particularly prevalent. The most common genotypes in the 2021 samples appeared to be largely replaced by other genotypes in 2022, suggesting that there was some immunological pressure on RVs to evolve.

The team had plenty of samples from both symptomatic and asymptomatic people but did not find any genotypes that were more likely to cause symptoms. However, they did find that higher viral loads correlated with symptomatic status, in line with previous research (2).

“What is challenging is to continue this analysis in time and to be able to have colleagues around the world that also try to do this type of analysis,” said Goya. Further work analyzing these and other genotypes may help researchers understand the extent to which infection with one RV type provides immunological protection against another type.

There is currently no vaccine for RVs, and the path for developing one is unclear. Addressing all 168 RV genotypes in one vaccine would be challenging, if not impossible. Detailed genome sequences, like the ones included in this dataset, could help future researchers design an effective vaccine for at least a subset of genotypes.

Overall, researchers need more data to better understand RVs. “The hardest part about rhinovirus is getting people to include it in their surveillance,” said Alex Greninger, an epidemiologist at University of Washington and coauthor on the study. “Despite this effort, when you divide it all up over all the genotypes, we still have laughably small amounts of data for many of these genotypes.”