Design of antiviral AGO2-dependent short hairpin RNAs

The increasing emergence and re-emergence of RNA virus outbreaks underlines the urgent need to develop effective antivirals.RNA interference(RNAi)is a sequence-specific gene silencing mechanism that is triggered by small interfering RNAs(siRNAs)or short hairpin RNAs(shRNAs),which exhibits significant promise for antiviral therapy.AGO2-dependent shRNA(agshRNA)generates a single-stranded guide RNA and presents significant advantages over traditional siRNA and shRNA.In this study,we applied a logistic regression algorithm to a previously published chemically siRNA efficacy dataset and built a machine learning-based model with high predictive power.Using this model,we designed siRNA sequences targeting diverse RNA viruses,including human enterovirus A71(EV71),Zika virus(ZIKV),dengue virus 2(DENV2),mouse hepatitis virus(MHV)and severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),and transformed them into agshRNAs.We validated the performance of our agshRNA design by evaluating antiviral efficacies of agshRNAs in cells infected with different viruses.Using the agshRNA targeting EV71 as an example,we showed that the anti-EV71 effect of agshRNA was more potent compared with the corresponding siRNA and shRNA.Moreover,the antiviral effect of agshRNA is dependent on AGO2-processed guide RNA,which can load into the RNA-induced silencing complex(RISC).We also confirmed the antiviral effect of agshRNA in vivo.Together,this work develops a novel antiviral strategy that combines machine learning-based algorithm with agshRNA design to custom design antiviral agshRNAs with high efficiency.

Interferon-induced MXB protein restricts vimentin-dependent viral infection

Type I interferon(IFN)inhibits a wide spectrum of viruses through stimulating the expression of antiviral proteins.As an IFN-induced protein,myxovirus resistance B(MXB)protein was reported to inhibit multiple highly pathogenic human viruses.It remains to be determined whether MXB employs a common mechanism to restrict different viruses.Here,we find that IFN alters the subcellular localization of hundreds of host proteins,and this IFN effect is partially lost upon MXB depletion.The results of our mechanistic study reveal that MXB recognizes vimentin(VIM)and recruits protein kinase B(AKT)to phosphorylate VIM at amino acid S38,which leads to reorganization of the VIM network and impairment of intracellular trafficking of virus protein complexes,hence causing a restriction of virus infection.These results highlight a new function of MXB in modulating VIM-mediated trafficking,which may lead towards a novel broad-spectrum antiviral strategy to control a large group of viruses that depend on VIM for successful replication.

Antiviral strategies:What can we learn from natural reservoirs?

Viruses cause many severe diseases in both plants and animals,urging us to explore new antiviral strategies.In their natural reservoirs,viruses live and replicate while causing mild or no symptoms.Some animals,such as bats,are the predicted natural reservoir of multiple viruses,indicating that they possess broad-spectrum antiviral capabilities.Mechanisms of host defenses against viruses are generally studied independently in plants and animals.In this article,we speculate that some antiviral strategies of natural reservoirs are conserved between kingdoms.To verify this hypothesis,we created null mutants of 10-formyltetrahydrofolate synthetase(AtTHFS),an Arabidopsis thaliana homologue of methylenetetrahydrofolate dehydrogenase,cyclohydrolase and formyltetrahydrofolate synthetase 1(MTHFD1),which encodes a positive regulator of viral replication in bats.We found that disruption of AtTHFS enhanced plant resistance to three different types of plant viruses,including the tomato spotted wilt virus(TSWV),the cucumber mosaic virus(CMV)and the beet severe curly top virus(BSCTV).These results demonstrate a novel antiviral strategy for plant breeding.We further discuss the approaches used to identify and study natural reservoirs of plant viruses,especially those hosting many viruses,and highlight the possibility of discovering new antiviral strategies from them for plant molecular breeding and antiviral therapy.