LNA-ASOs targeting conserved SARS-CoV-2 single-stranded regions reduce viral load and reshape inflammatory macrophage responses
The COVID-19 crisis is now over, but new viral strains of SARS-CoV-2 that evade immunity from previous infection or vaccination 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 LNA-modified ASOs 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 LNA-ASOs delivered intranasally can reach lung tissue and are preferentially internalized by alveolar macrophages, and modulate the inflammatory response to viral exposure. Taken together, our findings show that LNA-ASO targeting the viral RNA are a promising approach to the development of antiviral therapies.