Dengue and Zika RNA-RNA interactomes reveal pro- and anti-viral RNA in human cells.

BACKGROUND: Identifying host factors is key to understanding RNA virus pathogenicity. Besides proteins, RNAs can interact with virus genomes to impact replication. RESULTS: Here, we use proximity ligation sequencing to identify virus-host RNA interactions for four strains of Zika virus (ZIKV) and one strain of dengue virus (DENV-1) in human cells. We find hundreds of coding and non-coding RNAs that bind to DENV and ZIKV viruses. Host RNAs tend to bind to single-stranded regions along the virus genomes according to hybridization energetics. Compared to SARS-CoV-2 interactors, ZIKV-interacting host RNAs tend to be downregulated upon virus infection. Knockdown of several short non-coding RNAs, including miR19a-3p, and 7SK RNA results in a decrease in viral replication, suggesting that they act as virus-permissive factors. In addition, the 3'UTR of DYNLT1 mRNA acts as a virus-restrictive factor by binding to the conserved dumbbell region on DENV and ZIKV 3'UTR to decrease virus replication. We also identify a conserved set of host RNAs that interacts with DENV, ZIKV, and SARS-CoV-2, suggesting that these RNAs are broadly important for RNA virus infection. CONCLUSIONS: This study demonstrates that host RNAs can impact virus replication in permissive and restrictive ways, expanding our understanding of host factors and RNA-based gene regulation during viral pathogenesis.

Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions.

SARS-CoV-2 is a major threat to global health. Here, we investigate the RNA structure and RNA-RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 in cells using Illumina and Nanopore platforms. We identify twelve potentially functional structural elements within the SARS-CoV-2 genome, observe that subgenomic RNAs can form different structures, and that WT and Δ382 virus genomes fold differently. Proximity ligation sequencing identify hundreds of RNA-RNA interactions within the virus genome and between the virus and host RNAs. SARS-CoV-2 genome binds strongly to mitochondrial and small nucleolar RNAs and is extensively 2'-O-methylated. 2'-O-methylation sites are enriched in viral untranslated regions, associated with increased virus pair-wise interactions, and are decreased in host mRNAs upon virus infection, suggesting that the virus sequesters methylation machinery from host RNAs towards its genome. These studies deepen our understanding of the molecular and cellular basis of SARS-CoV-2 pathogenicity and provide a platform for targeted therapy.

Efficacy of low-level light therapy for improving healing of diabetic foot ulcers: A systematic review and meta-analysis of randomized controlled trials.

Diabetic foot ulcers are prevalent among patients with diabetes and negatively affect mortality and life expectancy. This study aimed to synthesize and systematically review the best evidence to assess the efficacy of low-level light therapy in improving healing of diabetic foot ulcers. We search CINAHL, Cochrane Library, EMBASE, ProQuest, PubMed, Scopus, and Web of Science from inception until September 30, 2019. Meta-analysis was performed using the Comprehensive Meta-analysis 3.0 software. Overall effect was measured using Hedges' g and determined using the Z-statistic at a significance level of P < .05. Heterogeneity was assessed using χ2 and I2 statistics. Twelve randomized controlled trials were included. Meta-analysis revealed that 30.90% of the ulcer area was significantly reduced in the therapy group compared with the control group (Z = 3.95, P < .001) with a very large effect (g = 2.81). A 4.2 cm2 reduction of the ulcer area was observed in the therapy group compared with the control group (Z = 2.17, P = .03) with a very large effect (g = 1.37). In addition, diabetic foot ulcers in the therapy group was 4.65 times more likely to heal completely than those in the control group (Z = 3.02, P = .003). Low-level light therapy accelerates wound healing and reduces the size of diabetic foot ulcers. However, our review does not allow any recommendation for the best treatment parameters required to achieve improved healing. Future trials need to include a good design and large sample size in defining the optimal treatment parameters for ulcers of different sizes.

Structure mapping of dengue and Zika viruses reveals functional long-range interactions.

Dengue (DENV) and Zika (ZIKV) viruses are clinically important members of the Flaviviridae family with an 11 kb positive strand RNA genome that folds to enable virus function. Here, we perform structure and interaction mapping on four DENV and ZIKV strains inside virions and in infected cells. Comparative analysis of SHAPE reactivities across serotypes nominates potentially functional regions that are highly structured, conserved, and contain low synonymous mutation rates. Interaction mapping by SPLASH identifies many pair-wise interactions, 40% of which form alternative structures, suggesting extensive structural heterogeneity. Analysis of shared interactions between serotypes reveals a conserved macro-organization whereby interactions can be preserved at physical locations beyond sequence identities. We further observe that longer-range interactions are preferentially disrupted inside cells, and show the importance of new interactions in virus fitness. These findings deepen our understanding of Flavivirus genome organization and serve as a resource for designing therapeutics in targeting RNA viruses.