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Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.

The CRISPR-Cas13 system has been proposed as an alternative treatment of viral infections. However, for this approach to be adopted as an antiviral, it must be optimized until levels of efficacy rival or exceed the performance of conventional approaches. To take steps toward this goal, we evaluated the influenza viral RNA degradation patterns resulting from the binding and enzymatic activity of mRNA-encoded LbuCas13a and two crRNAs from a prior study, targeting PB2 genomic and messenger RNA. We found that the genome targeting guide has the potential for significantly higher potency than originally detected, because degradation of the genomic RNA is not uniform across the PB2 segment, but it is augmented in proximity to the Cas13 binding site. The PB2 genome targeting guide exhibited high levels (>1 log) of RNA degradation when delivered 24 hours post-infection in vitro and maintained that level of degradation over time, with increasing multiplicity of infection (MOI), and across modern influenza H1N1 and H3N2 strains. Chemical modifications to guides with potent LbuCas13a function, resulted in nebulizer delivered efficacy (>1–2 log reduction in viral titer) in a hamster model of influenza (Influenza A/H1N1/California/04/09) infection given prophylactically or as a treatment (post-infection). Maximum efficacy was achieved with two doses, when administered both pre- and post-infection. This work provides evidence that mRNA-encoded Cas13a can effectively mitigate Influenza A infections opening the door to the development of a programmable approach to treating multiple respiratory infections. Author summary: For the CRISPR-Cas13 system to be adopted as an alternative treatment of viral infections, it must reach levels of efficacy that rival or exceed the performance of conventional approaches. We evaluated the degradation patterns resulting from the binding and enzymatic activity of mRNA-encoded LbuCas13a and two previously identified crRNAs, targeting conserved PB2 genomic and messenger RNA sequences. The genome targeting guide displayed higher potency than originally detected, because RNA degradation was augmented near the guide binding site, leading to 1-log of RNA degradation in vitro, which persisted over time, with increasing multiplicity of infection (MOI), and across modern influenza H1N1 and H3N2 strains. The addition of chemical modifications to the guide resulted in 1-2-log reduction in viral titer upon nebulizer delivery prophylactically or as a treatment in a hamster model of influenza. Maximum efficacy was achieved with two doses administered pre- and post-infection. [ABSTRACT FROM AUTHOR]

Current seasonal influenza virus vaccines induce responses primarily against immunodominant but highly plastic epitopes in the globular head of the hemagglutinin (HA) glycoprotein. Because of viral antigenic drift at these sites, vaccines need to be updated and readministered annually. To increase the breadth of influenza vaccine–mediated protection, we developed an antigenically complex mixture of recombinant HAs designed to redirect immune responses to more conserved domains of the protein. Vaccine-induced antibodies were disproportionally redistributed to the more conserved stalk of the HA without hindering, and in some cases improving, antibody responses against the head domain. These improved responses led to increased protection against homologous and heterologous viral challenges in both mice and ferrets compared with conventional vaccine approaches. Thus, antigenically complex protein mixtures can at least partially overcome HA head domain antigenic immunodominance and may represent a step toward a more universal influenza vaccine. Editor's summary: A major goal for next-generation influenza vaccines is to elicit antibody responses to more conserved regions, such as the hemagglutinin (HA) stalk. To accomplish this, Luo et al. used a mutagenesis approach to generate a mixture of recombinant HAs that could be used as a vaccine. The mutations were limited to the immunodominant Sb site of the HA head, which the authors hypothesized would push the antibody response to favor immunosubdominant domains. The authors found that vaccination with the HA mixture could boost immune responses against the stalk without negatively affecting head-specific responses. This translated into superior protection against homologous and heterologous influenza challenges in mice and ferrets, supporting further development of this remixed influenza vaccine. —Courtney Malo [ABSTRACT FROM AUTHOR]