SARS-CoV-2 can infect even more lung cells than we thought

US and Australian scientists have reported that more lung cell types can be infected by SARS-CoV-2 than previously thought, including those without known viral receptors. The research team also reported that the lung is capable of independently mustering an inflammatory antiviral response without help from the immune system when exposed to SARS-CoV-2.

The news comes as more than half of the states in the US report ‘very high’ or ‘high’ levels of COVID-19 infection, according to the US Centers for Disease Control and Prevention. As noted by Professor Evan Snyder from Sanford Burnham Prebys, “Headlines have come and gone, but SARS-CoV-2 and COVID-19 have never left — and neither have the scientists studying it.”

In making the new discoveries, Snyder and his collaborators at Sanford Burnham Prebys, the University of California San Diego and elsewhere used a technique to transform cells taken from patients into cells resembling stem cells. These embryonic-like cells — known as induced pluripotent stem cells (iPSCs) — can then be turned into other types of human cells.

The team caused the cells to develop into a grouping of various lung cell types in a pattern that mimics the human lung at a smaller scale. The advantage of this, as noted by Snyder, is, “With most models for studying respiratory infections, you can’t isolate a specific cellular response because you have all the immune system cells rushing in to help deal with the invaders.”

Another benefit, according to Associate Professor Sandra Leibel from UC San Diego, is that “we can choose the sex of the cells so we’re not just studying male-dominant or female-dominant lung tissue” — which is important as the lung responds differently during disease depending on a person’s sex. In addition, the team could make iPSCs from patients of different racial and ethnic groups to try to understand the disparity in this and other diseases in terms of susceptibility to infection, severity and responsiveness to various medications.

As reported in the journal PNAS, SARS-CoV-2 was able to acutely infect many previously undescribed cell types in the mini lungs. This held true when testing different strains of SARS-CoV-2, although it was clear that certain strains were more effective at infecting specific cell types.

“People used to say that SARS-CoV-2 only infects cells with certain receptors, especially those with the ACE2 receptor known to interact with the infamous SARS-CoV-2 spike protein,” Snyder said. “We demonstrated that when a direct entry point was unavailable, the virus just punches through the cell membrane instead.”

“With the Delta variant having produced more severe symptoms, and the Omicron variant being less deadly but more contagious, we hypothesised that Delta may prefer the alveolar cells deeper in the lungs, while Omicron sticks more to the upper airways,” Leibel added. “While all strains were capable of infecting many lung cell types, we did see a distinct preference for these strains, as predicted.”

In fact, as the strains changed over time, the scientists could see what was reported in patients as the character of the pandemic changed. Earlier strains such as Delta caused more deadly pneumonias because they affected lower lung cells. Later strains like Omicron affected more upper lung cells and led to clinicians seeing less pneumonia and more airway problems and sore throats. So, the mini-lung system may help the team predict patient outcomes.

In addition to demonstrating how the virus infects cells previously thought to be safe, the scientists found a way to block the virus’s unexpected flanking manoeuvre. The team demonstrated that apilimod — a drug currently being studied for potentially treating cancer, ALS, dementia and various viral infections — effectively blocked the backdoor entry of SARS-CoV-2 into cells lacking traditional entry points.

“Our data suggest that apilimod could be an adjunct therapy given early on to slow down the infection and enhance the effectiveness of other medicines and the innate immune response,” Snyder said.

In another surprising result, the team discovered that the mini lungs have their own intrinsic ‘first response’ system in reaction to sensing SARS-CoV-2. Even though the mini lungs lack any connection to an immune system, this study shows that lung cells can initiate many of the same biologic and cell signalling changes in response to a viral threat that are observed when the immune system is present.

“We found that lung cells are capable of autonomously reacting to infection immediately while also subsequently calling for reinforcements from the immune system,” Snyder said.

“We showed that it’s not just the immune cells that are becoming over-activated and secreting too much of the pro-inflammatory cytokines that contribute to severe cases of COVID-19,” Leibel added. “The lung cells do this as well.”

The scientists learned that this inherent antiviral response system in the mini lungs was orchestrated by an unlikely source: one of the four proteins that mix with fats to form a soapy substance in the lungs’ air sacs that helps keep them open as we breathe. This detergent-like substance is called surfactant, and its constituent protein surfactant protein B (SP-B) turned out to be the most important player in the mini lungs’ attempts to ward off SARS-CoV-2. No prior research had suggested that SP-B played any cellular signalling roles.

“When we tested mini lungs genetically engineered to not express SP-B, we saw triple the number of cells infected with SARS-CoV-2,” Leibel said. “When we followed that up by treating these engineered mini lungs with SP-B in a similar way to how premature newborns with surfactant deficiency are treated, we noted a reduction in viral infectivity.”

“These findings suggest not just one but two potential novel drug applications with the possible clinical use of surfactant early in COVID-19 cases,” Snyder said. “This is important, as we only have two current proven antiviral drugs in Paxlovid and remdesivir.”

The team plans to follow up these findings with studies to determine exactly how surfactant is so effective at protecting cells against viral invasion. They are also investigating whether a rapid test for SP-B as well as certain characteristic pro-inflammatory cytokines may help quickly determine which people are at greater risk of more severe forms of COVID-19.

“This would help people make more informed decisions about travelling and attending public events during spikes of COVID-19, and it also would help physicians tailor treatments for those at an increased risk of serious disease,” Leibel said.

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