Gapmers targeting conserved SARS-CoV-2 single-stranded regions reduce viral load and reshape inflammatory macrophage...

The COVID-19 crisis is now over, but additional viral strains of SARS-CoV-2 that evade immunity are continuously emerging. We explored the design, evaluation, and optimization of anti-sense oligonucleotides (ASOs) targeting SARS-CoV-2 RNA, with the aim of providing a scalable strategy capable of responding to emergent outbreaks. Twenty-four ASOs were designed to target highly conserved, single-stranded regions of the SARS-CoV-2 genome. Extensive in vitro screening led to the identification of gapmers that exhibited high efficacy against four selected SARS-CoV-2 variants, significantly reducing intracellular viral RNA and virus production. Importantly, the antiviral efficacy correlates with viral RNA accessibility and is not due to activation of antiviral host responses. Finally, naked gapmers delivered intranasally can reach lung tissue, are preferentially internalized by alveolar macrophages, and modulate the inflammatory response to viral exposure. Taken together, our findings show that gapmers targeting the viral RNA are a promising approach to the development of antiviral therapies.