“Once the virus gets through that barrier,” he said, “it can replicate freely in underlying cells.”

The researchers also found that SARS-CoV-2, once inside the cell, induces activity on the part of intracellular enzymes that causes microvilli to enlarge and branch, like crazy cactus plants, until their tips poke out above the mucus barrier. Their numbers increase. As soon as 24 hours post-inoculation, many altered microvilli, ordinarily less than half the length of cilia, have turned into huge, branching, tree-like structures the size of cilia or larger, and they’re decorated with attached viral particles that can shove off into the mucus-mucin layer, where they can float down the mucus river and infect other, more-distant cells.

The researchers pinpointed enzymes in the cell, massively switched on by SARS-CoV-2 infection, that were causing the microvilli’s transformation. Inhibiting these enzymes ground that aberration to a halt and greatly diminished the virus’s spread to other cells.

One spray to bind them all?

Jackson and his colleagues had similar results when they incubated airway organoids with either of two other respiratory viruses — the now-surging respiratory syncytial virus and the less-common parainfluenza virus — as well as with BA.1, a variant of the omicron strain.

Omicron is more contagious, and, as expected, it infected airway-organoid multiciliated cells more quickly than the older strain used for the other SARS-CoV-2 experiments. But inhibiting viral entry or exit in airway cells still proved effective, even for this highly infectious variant.

These viral entry mechanisms may be a general property of many respiratory viruses, Jackson said.

The findings identify new targets for a nasally applied drug that, by impeding ciliary motion or microvilli gigantism, could prevent even unknown respiratory viruses — the kind you meet, say, at a pandemic — from making themselves at home in your nose or throat.

Jackson said substances used in these experiments could perhaps be optimized for use in, say, nasal sprays soon after a respiratory viral exposure, or as prophylactics.

“Delaying viral entry, exit or spread with a locally applied, short-duration drug would help our immune systems catch up and arrive in time to stop full-blown infection and hopefully limit future pandemics,” he said.

Other researchers from UCSF, the Jikei University School of Medicine in Tokyo and the Texas Biomedical Research Institute contributed to the work.

The study was funded by the National Institutes of Health (grants R01DK127665, R01HD085901, R01GM121565, P30DK116074, R01AI149672-01, U54-CA209971, R01 AI36178, AI40085, P01 AI091575, 5T32GM007276 and 1S10RR026780-01), the Stanford Diabetes Research Center, Fast Grant, the Bill and Melinda Gates Foundation, Defense Advanced Research Project Agency, the California Institute for Regenerative Medicine, Stanford Respond Innovate Scale Empower, and the Stanford Maternal and Child Health Research Institute.

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