Purpose: Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a great impact on human survival and a great threat to public health in countries all over the world. The link between COVID-19 and ocular illness has received increasing attention due to SARS-CoV-2 infection can be transmitted through eye contact. Using bioinformatics methods, we sought to investigate the potential molecular mechanisms between uveitis and COVID-19, providing rationales and directions for further exploration. Methods Transcriptomic data of uveitis and COVID-19 patient blood samples were accessed from the Gene Expression Omnibus public database. Common differentially expressed genes were identified. Genetic Ontology analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, Protein-Protein Interaction network analysis were performed on intersected genes. We screened 5 hub genes by using the maximum clustering centrality algorithm. The Least Absolute Shrinkage and Selection Operator regression analysis identified the potential biomarkers for uveitis and COVID-19. Finally, the expression level and diagnostic value of the biomarker in the two diseases were determined. Results 50 intersected genes were extracted from differential expression analysis in uveitis and COVID-19. These genes were functionally enriched in cytokine-mediated signaling pathway, vesicle lumen, receptor ligand activity. Through KEGG analysis, these genes were found to be involved in viral protein interaction with cytokine and cytokine receptor, and cytokine-cytokine receptor interaction. HORMAD1 was obtained by Least Absolute Shrinkage and Selection Operator regression analysis, which was high expression in both uveitis and COVID-19 when compared to controls. Receiver Operating Characteristic values and AUC statistics indicated that HORMAD1 had diagnostic value for uveitis and COVID-19. Conclusions Bioinformatic analysis predicts HORMAD1 involvement in etiology and therapeutic targets of uveitis and COVID-19. However, additional clinical trials and studies are needed to confirm the role of HORMAD1.

Point-of-care diagnosis is crucial to control the spreading of viral infections. Here, universal-modifiable probe-gated silica nanoparticles (SNPs) based lateral flow assay (LFA) is developed in the interest of the rapid and early detection of viral infections. The most superior advantage of the biosensor is its utility in detecting various sides of the virus directly from the human swab samples and its adaptability to detect various types of viruses. For this purpose, high concentration of fluorescein and rhodamine B as a reporting material was loaded into SNPs with excellent loading capacity 21 µM and 6.2 µM, respectively. As a model organism, severe acute respiratory syndrome coronavirus-2 (CoV-2) infections were selected by targeting its nonstructural (NSP9, NSP12) and envelope (E) genes as target sites of the virus, we showed that NSP12-gated SNPs-based LFA significantly outperformed detection of viral infection in 15 minutes from a dilution of 1:103 of unprocessed human samples with an increasing test line intensity compared to steady state (n=12). Compared to the RT-qPCR method, sensitivity, specificity, and accuracy of NSP12-gated SNPs were calculated as 100%, 83%, and 92%, respectively. Finally, this modifiable nanoparticle system is a high-performance sensing technique that could take advantage of upcoming point-of-care testing markets for detection of viral infection.

Background: Chikungunya virus (CHIKV) diagnosis have become a challenge for primary care physicians in areas where zika virus and/or dengue virus are present. Case definitions for the three arboviral infections are overlapping. Methods: A cross-sectional analysis was carried out. A bivariate analysis was made using confirmed CHIKV infection as the outcome. Variables with significant statistical association were included in an agreement consensus. Agreed variables were analyzed in multiple regression model. The area under the receiver operating characteristic (ROC) curve was calculated to determine a cut-off value and performance. Results: 295 patients with confirmed CHIKV infection were included. A screening tool was made using symmetric arthritis (4 points), fatigue (3 points), rash (2 points) and ankle joint pain (1 point). The ROC curve identified a cut-off value and a score ≥ 5.5 was considered positive to identify CHIKV patients with a sensibility of 64.4% and a specificity of 87.4%, positive predictive value of 85.5%, negative predictive value of 67.7%, area under the curve of 0.72, and an accuracy of 75%. Conclusion: We developed a screening tool for CHIKV diagnosis using only clinical symptoms as well as proposed an algorithm to aid the primary care physician.

ABSTRACT Vaccination is critical for the control and prevention of viral outbreaks, yet conventional vaccine platforms may involve trade-offs between immunogenicity and safety. Insect-specific viruses have emerged as a novel vaccine platform to overcome this challenge. Detailed studies of humoral and T-cell responses induced by new insect-specific flavivirus (ISFV)-based vaccine platforms are needed to better understand correlates of protection and improve vaccine efficacy. Previously, we used a novel ISFV called Aripo virus (ARPV) to create a Zika virus (ZIKV) vaccine candidate (designated ARPV/ZIKV). ARPV/ZIKV demonstrated exceptional safety and single-dose efficacy, completely protecting mice from a lethal ZIKV challenge. Here, we explore the development of immune responses induced by ARPV/ZIKV immunization and evaluate its correlates of protection. Passive transfer of ARPV/ZIKV-induced immune sera to naïve mice prior to challenge emphasized the importance of neutralizing antibodies as a correlate of protection. Depletion of T-cells in vaccinated mice and adoptive transfer of ARPV/ZIKV-primed T-cells to naïve mice prior to challenge indicated that ARPV/ZIKV-induced CD4 + and CD8 + T-cell responses contribute to the observed protection but may not be essential for protection during ZIKV challenge. However, vaccination of Rag1 KO, Tcra KO, and muMt − mice demonstrated the critical role for ARPV/ZIKV-induced T-cells in developing protective immune responses following vaccination. Overall, both humoral and T-cell-mediated responses induced by ISFV-based vaccines are important for comprehensive immunity, and ISFV platforms continue to be a promising method for future vaccine development.

We reported the first case of Guillain-Barré syndrome that is associated with COVID-19 and malaria coinfection. The current report demonstrates diagnostic challenge to identify GBS case in a country like Sudan that is endemic with several infectious diseases associated with developing GBS.

Aedes mosquitoes transmit pathogenic arthropod-borne (arbo) viruses, putting nearly half the world's population at risk. Blocking virus replication in mosquitoes is a promising approach to prevent arbovirus transmission, the development of which requires in-depth knowledge of virus-host interactions and mosquito immunity. By integrating multi-omics data, we find that heat shock factor 1 (Hsf1) regulates eight small heat shock protein (sHsp) genes within one topologically associated domain in the mosquito genome. This Hsf1-sHsp cascade acts as an early response against chikungunya virus (CHIKV) infection and shows pan-antiviral activity in cell lines of three vector mosquitoes, Aedes aegypti, Aedes albopictus, and Anopheles gambiae. Our comprehensive in vitro data suggest that Hsf1 could serve as a promising target for the development of novel intervention strategies to limit arbovirus transmission by mosquitoes.

Type I interferons (IFNs) are the major host defence against viral infection and are induced following activation of cell surface or intracellular pattern recognition receptors, including retinoic-acid-inducible gene I (RIGI)-like receptors (RLRs). All cellular processes are shaped by the microenvironment and one important factor is the local oxygen tension. The majority of published studies on IFN signalling are conducted under atmospheric (18%) oxygen conditions, that do not reflect the physiological oxygen levels in most organs (1-5% O 2 ). We studied the effect of low oxygen on IFN induction and signalling in induced Pluripotent Stem Cell (iPSC)-derived macrophages as a model for tissue-resident macrophages and assessed the consequence for Zika virus (ZIKV) replication. Hypoxic conditions dampened the expression of interferon-stimulated genes (ISGs) following RLR stimulation or IFN treatment at early time points. RNA-sequencing and bio-informatic analysis uncovered several pathways including changes in transcription factor availability, the presence of HIF binding sites in promoter regions, and CpG content that may contribute to the reduced ISG expression. Importantly, hypoxic conditions increased ZIKV replication at early time points, emphasizing the importance of understanding how low oxygen conditions in the local microenvironment affect pathogen sensing and host defence.

Background Dengue is a major public health challenge and a growing problem due to climate change. The release of Aedes aegypti mosquitoes infected with the intracellular bacterium Wolbachia is a novel form of vector control against dengue. However, there remains a need to evaluate the benefits of such an intervention at a large scale. In this paper, we evaluate the potential economic impact and cost-effectiveness of scaled Wolbachia deployments as a form of dengue control in Vietnam – targeted at the highest burden urban areas. Methods Ten settings within Vietnam were identified as priority locations for potential future Wolbachia deployments (using a population replacement strategy). The effectiveness of Wolbachia deployments in reducing the incidence of symptomatic dengue cases was assumed to be 75%. We assumed that the intervention would maintain this effectiveness for at least 20 years (but tested this assumption in the sensitivity analysis). A cost-utility analysis and cost-benefit analysis were conducted. Results From the health sector perspective, the Wolbachia intervention was projected to cost US$420 per disability-adjusted life year (DALY) averted. From the societal perspective, the overall cost-effectiveness ratio was negative, i.e. the economic benefits outweighed the costs. These results are contingent on the long-term effectiveness of Wolbachia releases being sustained for 20 years. However, the intervention was still classed as cost-effective across the majority of the settings when assuming only 10 years of benefits. Conclusion Overall, we found that targeting high burden cities with Wolbachia deployments would be a cost-effective intervention in Vietnam and generate notable broader benefits besides health gains.

Introduction: Zika virus (ZIKV) caused an outbreak in Brazil, in 2015, being associated to microcephaly. ZIKV has a strong neurotropism leading to death of infected cells in different brain regions, including the hippocampus, a major site for neurogenesis. The neuronal populations of the brain are affected differently by ZIKV from Asian and African ancestral lineages. However, it remains to be investigated whether subtle variations in the ZIKV genome can impact hippocampus infection dynamics and host response. Objective This study evaluated how two Brazilian ZIKV isolates, PE243 and SPH2015, that differ in a single missense amino acid substitution in the protein NS1, affect the hippocampal phenotype and transcriptome. Methods Organotypic hippocampal cultures (OHC) from infant Wistar rats were infected with PE243 or SPH2015 and analyzed in time series using immunofluorescence, confocal microscopy, RNA-Seq and RT-qPCR. Results Unique patterns of infection and changes in neuronal density in the OHC were observed for PE243 and SPH2015 between 8 and 48 hours post infection (p.i.). Phenotypic analysis of microglia indicated that SPH2015 has a greater capacity for immune evasion. Transcriptome analysis of OHC at 16 hours p.i. disclosed 32 and 113 differentially expressed genes (DEGs) in response to infection with PE243 and SPH2015, respectively. Functional enrichment analysis suggested that infection with SPH2015 activates mostly astrocytes rather than microglia. PE243 downregulated biological process of proliferation of brain cells and upregulated those associated with neuron death, while SPH2015 downregulated processes related to neuronal development. Both isolates downregulated cognitive and behavioral development processes. Ten genes were similarly regulated by both isolates. They are putative biomarkers of early hippocampus response to ZIKV infection. At 5, 7, and 10 days p.i., neuronal density of infected OHC remained below controls, and mature neurons of infected OHC showed an increase in the epigenetic mark H3K4me3, which is associated to a transcriptionally active state. This feature is more prominent in response to SPH2015. Conclusion Subtle genetic diversity of the ZIKV affects the dynamics of viral dissemination in the hippocampus and host response in the early stages of infection, which may lead to different long-term effects in neuronal population.

Airborne virus, such as COVID-19, caused pandemics all over the world. Virus-containing particles produced by infected individuals are suspended in the air for extended periods of time, actually results in viral aerosols and the spread of infectious diseases. Aerosol collection and detection devices are essential for limiting the spread of airborne virus diseases. This review provides an overview of the primary mechanisms and enhancement techniques for collecting and detecting airborne viruses. Indoor virus detection strategies for scenarios with varying ventilations are also summarized based on the excellent performance of existing advanced comprehensive devices. This review provides guidance for the development of future aerosol detection devices and aids in the control of airborne transmission diseases, such as COVID-19, monkeypox, and other airborne transmission viruses.

Abstract Background: Genomic surveillance, with the aid of next-generation sequencing (NGS) technologies, revolutionized the SARS-CoV-2 pandemic. Coupled with high-performance analysis software, methodologies such as the Ion Torrent S5 and Illumina MiSeq dramatically improved the genomic surveillance capacity within South Africa during the height of the pandemic. Using de-identified remnant samples collected from Eastern Cape and analysis software, Genome Detective and NextClade, we compared the sequencing process, genomic coverage, quantification of mutations, and clade classification from sequence data generated by these two common “benchtop” NGS platforms. Results: Sequence data analysis revealed success rates of 175/183 (96%) and 172/183 (94%) on the Ion Torrent S5 and Illumina MiSeq, respectively. Internal quality metrics were assessed in terms of genomic coverage (>80%) and the number of mutations identified (<100). A greater number of higher-genomic coverage sequences were generated on the Ion Torrent S5 (99%) than on the Illumina MiSeq (80%) and <100 mutations was obtained by both platforms. Ion Torrent S5 generated high coverage sequences from samples having a broader range of viral loads (VL) compared to the Illumina MiSeq, which was less successful in sequencing samples with lower viral loads. Clade assignments were comparable across platforms which accurately differentiated between Beta (<45%) and Delta (≤30%) VOCs. A disparity in clade assignment was observed in <10% of sequences due to poor coverage obtained on the Illumina MiSeq, followed by a failure rate of ≤6% across the two platforms. Manual library preparation found both methods similar in terms of sample processing, handling of larger sample quantities, and clade assignment for SARS-CoV-2. Variability between the Ion Torrent S5 and Illumina MiSeq was observed in sequencing run duration (3,5 hrs vs 36 hrs), sequencing process (semi-automation vs manual), genomic coverage (99% vs 80%), and viral load requirements (broad range vs high VL). Conclusion: The Illumina MiSeq and Ion Torrent S5 are both reliable platforms capable of performing WGS with the use of amplicons and providing specific, accurate, and high throughput analysis of the SARS-CoV-2 whole viral genomes. Both sequencing platforms are feasible platforms for the genomic surveillance of SARS-CoV-2, each with its specific advantages and trade-offs.

Viruses with encephalitogenic potential can cause neurological conditions of clinical and epidemiological importance, such as Saint Louis encephalitis virus, Venezuelan equine encephalitis virus, Eastern equine encephalitis virus, Western equine encephalitis virus, dengue virus, Zika virus, Chikungunya virus, Mayaro virus and West Nile virus. The objective of the present study was to determine the number of arboviruses with neuroinvasive potential isolated in Brazil that corresponds to the collection of viral samples belonging to the Section of Arbovirology and Hemorrhagic Fevers (SAARB/IEC) of the Laboratory Network of National Reference for Arbovirus Diagnosis from 1954 to 2022. A total of 1,090 arbovirus samples with encephalitogenic potential were isolated from mice. From a total of 7,054 samples intended for cell culture. The isolates from mosquitoes totaled 659 viruses. The emergence of new arboviruses may be responsible for diseases still unknown to humans, making the Amazon region a hotspot for infectious diseases due to its fauna and flora species characteristics. The detection of circulating arboviruses with the potential to cause neuroinvasive diseases is constant, which justifies the continuation of active epidemiological surveillance work that offers adequate support to the public health system regarding the virological diagnosis of circulating arboviruses in Brazil.

Neurotropic viruses can cross the otherwise dynamically regulated blood-brain barrier (BBB) and affect the brain cells. Zika virus (ZIKV) is an enveloped neurotropic Flavivirus known to cause severe neurological complications, such as encephalitis and foetal microcephaly. In the present study, we used human brain microvascular endothelial cells (hBMECs) and human progenitor derived astrocytes to form a physiologically relevant BBB model. We used this model to investigate the effects of ZIKV envelope (E) protein on properties of cells comprising the BBB. E protein is the principal viral protein involved in interaction with host cell surface receptors, facilitating the viral entry. Our findings show that ZIKV E protein results in activation of both hBMECs and astrocytes. hBMECs showed reduced expression of endothelial junction proteins - ZO-1, Occludin and VE-Cadherin, which are crucial in establishing and maintaining the BBB. As a result, ZIKV E protein triggered alteration in BBB integrity and permeability. We also found upregulation of genes involved in leukocyte recruitment along with increased proinflammatory chemokines and cytokines upon exposure to E protein. Furthermore, E protein resulted in astrogliosis as seen by increased expression of GFAP and Vimentin. Both BBB cell types exhibited inflammatory response following exposure to E protein which may influence viral access into the central nervous system (CNS), resulting in infection of other CNS cells. Overall, our study provides valuable insights into the transient changes that occur at the site of BBB upon ZIKV infection.

In the recent days, lipid nanoparticles have been successfully emerged as one of the most advanced technology for highly efficient in vivo delivery of exogenous mRNA, especially for delivery of COVID-19 vaccines. For the vaccines to be successful or protective, they require highly efficient mRNA delivery systems. However, developing effective, translatable vaccines with better safety against some of the SARS‐CoV‐2 variants is still a challenge. Lipid nanoparticles (LNPs) are composed of four different types of lipids including ionizable lipids, helper or neutral lipids, cholesterol and polyethylene glycol (PEG) attached lipids. In this review, we present recent advancements and insights in designing the advanced LNPs and their composition and properties, with a subsequent discussion on the development of COVID-19 vaccines. In particular, as the ionizable lipids are most important drivers for complexing the mRNA and in vivo delivery, the role of ionizable lipids in mRNA vaccines discussed in detail. Furthermore, the use of LNPs as effective delivery vehicles for vaccination, genome editing, and protein replacement therapy were discussed. Finally, expert opinion of LNPs for mRNA vaccines were discussed which might address the future challenges in the development of mRNA vaccines employing highly efficient LNPs using novel set of ionizable lipids.

Zika virus (ZIKV) is a recently re-emerged flavivirus transmitted primarily through the bite of an infected mosquito, Aedes aegypti being the main vector. ZIKV infection is associated with a range of adverse effects; infection during pregnancy can lead to foetal abnormalities, including microcephaly. Lacking a licensed vaccine, or specific therapeutics, control of ZIKV transmission focuses on vector control. However, in most transmission settings, current methods are insufficient to successfully control ZIKV, or other similarly-transmitted arboviruses such as dengue and chikungunya viruses. This has stimulated interest in genetics-based methods, either to reduce the number of mosquitoes (“population suppression”), or to make mosquitoes less able to transmit (“population modification”). Here, we describe a method to selectively eliminate infected mosquitoes, using a virus sensor inserted into the mosquito genome and coupled to a quorum-counting lethal effector. In mosquitoes, ZIKV normally establishes persistent, lifelong infection; survival of these infected mosquitoes is crucial to transmission potential. Correspondingly, removal of infected mosquitoes can reduce vectorial capacity of a mosquito population, i.e. ability to transmit. Since relatively few mosquitoes become infected, typically <2%, engineered hypersensitivity to ZIKV would have only a modest population-level fitness cost, and lower still if transmission were successfully reduced by such means.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused 2019 coronavirus disease (COVID-19) poses a serious threat to global public health security. SARS-CoV-2, like other coronaviruses, has evolved many strategies to inhibit interferon (IFN) production. Here, we identify that SARS-CoV-2 Nsp15 suppresses IFN production by antagonizing the RLR-mediated antiviral signaling pathway. Overexpressed Nsp15 obviously reduced mRNA levels of IFN-β and IFN-stimulated genes ( ISG56, CXCL10 ), and also inhibited IRF3 phosphorylation and nuclear translocation. Mechanically, the poly-U-specific endonuclease domain (EndoU) of Nsp15 directly associates with the kinase domain (KD) of TBK1, thereby Nsp15 interfered TBK1 interacting with IRF3 and reduced TBK1-mediated IRF3 phosphorylation. In addition, Nsp15 also prevented nuclear translocation of phosphorylated IRF3 via binding and reducing the nuclear import adaptor karyopherin α1 (KPNA1) protein. Collectively, this data revealed the novel mechanism of Nsp15 antagonizing the innate immune pathway and provided an optional target for drug development against COVID-19 disease.

More than 6.6 million Covid-19 deaths have been recorded worldwide, with over one million of those in the United States, and the pandemic death toll continues to climb by approximately 335 deaths each day in the U.S. The pandemic has disrupted families, schools, the health care system, employers, and the supply chain. And the hardest hit continues to be the most vulnerable populations. It unlikely that the full extent of the physical, mental, social, and economic consequences directly or indirectly caused by the Covid-19 public health emergency will be understood for decades. On September 18, 2022, we heard from President Biden: “the pandemic is over.” The Covid-19 pandemic, however, is morphing into an endemic while outbreaks of other contagious diseases, like respiratory syncytial virus (RSV), influenza, Mpox and polio, have dominated the news cycles and received their own public health emergency designations. On January 30, 2023, the World Health Organization's International Health Regulations Emergency Committee voted to renew the Public Health Emergency of International Concern for now. On that same day, however, the White House announced that the Covid-19 public health emergency status in the U.S. is expected to end on May 11, 2023. The vast majority of states have already terminated their public health emergency status, with the remaining few likely to do so shortly. Establishing the conditions under which declarations, continuations, and terminations of public health emergencies ought to be made is particularly important given the implications such decisions have and the competing interests that underlie them. Declarations of public health emergencies are what noted philosopher and scholar J.L. Austin called performative utterances, which are statements that have the effect to act or cause an action, or change social reality, such as “time of death 4:12 pm,” rather than descriptive phrases that are simply true or false statements, like “the sky is blue.” Declaring public health emergencies are critical performative utterances as emergency powers provide a wide range of resources from providing grants and funding to deploying the military, waiving, or modifying regulations and requirements, curtailing certain civil liberties and shuttering businesses. When invoked, many times executive emergency powers negate the need for legislative authorization during the span of the emergency. As we saw in March 2020, public health emergency declaration—described in detail in this article—are performative utterances that changed our world. Such declarations necessarily shift the balance of power toward the executive action. Terminating public health emergencies, however, are also critical performative utterances. And if we presume that ordinary laws, regulations, and procedures appropriately balance government power with individual rights, then our default should be a clear understanding of when we can return to those laws, regulations, and procedures. Currently, the U.S. laws fail to provide consistency or clear guidance on procedures or conditions public health emergency declarations and terminations. Because the stakes are so high—and affect the fundamental structure of our government—we should be intentional in developing procedures and establishing criteria for declaring, continuing, and terminating public health emergencies. Instead of simply accepting lengthy unfettered executive public health emergency powers or enacting strict legislative limitations on executive authority that could hinder an effective public health response, or create chaos in our health care systems and with government operations, a diverse, multi-disciplinary team of scholars and stakeholders should examine the existing web of public health emergency legislation and provide input and guidance on felicity conditions for declaring, continuing and terminating specific public health emergencies that build in relevant, appropriate checks and balances.

COVID-19 caused by novel corona virus (SARS-CoV-2) is the major pandemic of the decade claiming millions of lives causing severe disruptions to society. Despite rapid development of COVID-19 vaccines, condition is still not under control and newer antiviral drugs are required. In the present work, we describe the design and synthesis of Diphenyl-1 H -imidazole derivatives as a potential lead series for SARS-CoV-2 3CLpro enzyme inhibition. The synthesized molecules were screened for SARS-CoV-2 3CLpro enzyme inhibition at 20µM concentration. All the synthesized compounds ( 6-14 ) showed inhibition in the range of 88 to 99%. They were further tested for anti-SARS-CoV-2 activity against ancestral Wuhan and the Delta variants in virus infected cells. The compounds 4-(4-hlorophenyl)-2-(3,4-dimethoxyphenyl)- 1H -imidazole (9) , 4-(2,4-dichlorophenyl)-2-(3,4-dimethoxyphenyl)- 1H -imidazole (10) , 4-(4-(2,4-dichlorophenyl)- 1H -imidazol-2-yl)benzene-1,2-diol (14) showed promising activity against both Wuhan (IC 50 7.7 µM, 12.6 µM and 11.8 µM, respectively) and Delta (IC 50 7.4 µM, 13.8 µM and 12.1 µM, respectively) variant of COVID-19. Our results demonstrate efficacy of diphenyl-1 H -imidazole derivatives as promising ligands for further development and optimization against COVID-19.

ABSTRACT Bacteria have evolved a wide range of defense strategies to protect themselves against bacterial viruses (phages). However, the known mechanisms almost exclusively target phages with DNA genomes. While several bacterial toxin-antitoxin systems have been considered to cleave single-stranded bacterial RNA in response to stressful conditions, their role in protecting bacteria against phages with single-stranded RNA genomes has not been studied. Here we investigate the role of a representative toxin-antitoxin system, MazEF, in protecting Escherichia coli against two RNA phages – MS2 and Qβ. Our population-level experiments revealed that a mazEF deletion strain is more susceptible to RNA phage infection than the wild-type. At the single-cell level, deletion of the mazEF locus significantly shortened the time to lysis of individual bacteria challenged with RNA phage. At the genomic level, we found that the adenine-cytosine-adenine sequence, directly recognized and cleaved by the MazF toxin, is systematically underrepresented in the genomes of RNA phages that are known to infect E. coli , indicating selection for decreased probability of cleavage. These results suggest that in addition to other physiological roles, RNA-degrading toxin-antitoxin modules can function as a primitive immune system against RNA phages.

Most existing studies characterising SARS-CoV-2-specific T cell responses are peptide based. This does not allow evaluation of whether tested peptides are processed and presented canonically. In this study, we used recombinant vaccinia virus (rVACV)-mediated expression of SARS-CoV-2 spike protein and SARS-CoV-2 infection of ACE-2-transduced B cell lines to evaluate overall T cell responses in a small cohort of recovered COVID-19 patients and uninfected donors vaccinated with ChAdOx1 nCoV-19. We showed that rVACV expression of SARS-CoV-2 antigen can be used as an alternative to SARS-CoV-2 infection to evaluate T cell responses to naturally processed spike antigens. In addition, rVACV system can be used to evaluate the cross-reactivity of memory T cells to variants of concern (VOCs) and to identify epitope escape mutants. Finally, our data showed that both natural infection and vaccination could induce multi-functional T cell responses with overall T cell responses remaining despite the identification of escape mutations.

Background: The COVID-19 pandemic exposed the vulnerability of the world to emerging infectious disease threats. An epidemic preparedness and response (EPR) plan gives decision-makers a framework within which they can focus outbreak response strategies. We performed a systematic review of literature reviews on interventions in infectious disease outbreaks in low- and middle-income countries (LMICs) to assess key gaps in evidence for informing EPR plans. Methods: Six databases [MEDLINE, Embase, Cochrane Register, Cochrane Database of Systematic Reviews (CDSR), Epistemmonikos and Global Index Medicus] were searched systematically up to 23/09/2021. Studies were screened based on pre-determined eligibility criteria. Data extraction and quality assessment were conducted by two reviewers. Conflicts were resolved by a third reviewer. The Joanna Biggs Institute Critical Appraisal checklists was used for quality assessment of studies. A formal narrative synthesis approach was used to summarise findings. Findings: Of 122 literature reviews included, the largest proportion concerned COVID-19 (43.4%), followed by Ebola virus and influenza (6.6% each), and tuberculosis (4.9%) [25.4% covered multiple infections]. The majority (77.0%) spanned multiple geographical regions, 9.8% covered specific geographic regions, and 13.1% were country specific. 65 (53.3%) reviews focussed on outbreak response and only 17 (13.9%) on outbreak detection. There was limited evidence on key EPR components, notably logistics and supply chains; risk communication and community engagement (RCCE) and infodemic management; and international travel and mass gatherings. Only 43 (35.2%) reviews were assessed as high quality. Interpretation: This review highlights considerable gaps in evidence for informing EPR plans in LMICs. While evidence could be strengthened in all areas, research focussing on high consequence outbreak-prone pathogens other than SARS-CoV-2, improving effectiveness of outbreak detection systems and strengthening key response pillars on logistics, RCCE and international travel, should be a priority. Funding: UK Public Health Rapid Support Team Declaration of Interest: The lead author conducted this research as part of a broader consultancy for the UK Public Health Rapid Support Team (UK-PHRST). The interventions and outcomes under which the research gaps were categorized were decided based on discussions with the UK-PHRST team led by GH and ASh.

Zika virus (ZIKV) contains multiple conserved RNA structures in the viral 3’ untranslated region (UTR), including the structure known as dumbbell-1 (DB-1). Previous research has shown that the DB-1 structure is important for flavivirus genome replication and cytopathic effect (CPE). However, the role of the DB structure and the mechanism by which it contributes to viral pathogenesis is not known. Using recently solved flavivirus DB RNA structural data, we designed two DB-1 mutant ZIKV infectious clones termed ZIKV-TL.PK, which disrupts DB-1 tertiary folding and ZIKV-p.2.5’, which alters DB-1 secondary structure formation. In cell culture, we found that viral genome replication of both mutant clones is not significantly affected compared to ZIKV-WT, but viral CPE is considerably decreased. We investigated sub-genomic flaviviral RNA (sfRNA) formation by both DB-1 mutants following A549 infection and found both mutant clones have decreased levels of all sfRNA species compared to ZIKV-WT during infection. To investigate the mechanism of decreased CPE in our DB-1 mutant clones, we assayed ZIKV DB mutant-infected A549 cells for cell viability and caspase activation. We found that cell viability is significantly increased in DB-1 mutant-infected cells compared to ZIKV-WT due to reduced caspase 3 activation. We also show that replication of the ZIKV-P.2.5’ mutant was significantly restricted by type I interferon treatment without altering interferon stimulated gene expression. Using a murine model of ZIKV infection, we show that both ZIKV-DB-1 mutants exhibit reduced morbidity and mortality compared to ZIKV-WT virus due to tissue specific attenuation in ZIKV-DB viral replication in the brain tissue. Overall, our data show that the flavivirus DB-1 RNA structure is important for maintaining sfRNA levels during infection which supports caspase-3 dependent, viral cytopathic effect, type 1 interferon resistance, and viral pathogenesis in a mouse model.

Innate immune signaling in the central nervous system (CNS) exhibits many remarkable specializations that vary across cell types and CNS regions. In the setting of neuroinvasive flavivirus infection, neurons employ the immunologic kinase receptor-interacting kinase 3 (RIPK3) to promote an antiviral transcriptional program, independently of the traditional function of this enzyme in promoting necroptotic cell death. However, while recent work has established roles for neuronal RIPK3 signaling in controlling mosquito-borne flavivirus infections, including West Nile virus and Zika virus, functions for RIPK3 signaling in the CNS during tick-borne flavivirus infection have not yet been explored. Here, we use a model of Langat virus (LGTV) encephalitis to show that RIPK3 signaling is specifically required in neurons of the cerebellum to control LGTV replication and restrict disease pathogenesis. This effect did not require the necroptotic executioner molecule mixed lineage kinase domain like protein (MLKL), a finding similar to previous observations in models of mosquito-borne flavivirus infection. However, control of LGTV infection required a unique, region-specific dependence on RIPK3 to promote expression of key antiviral interferon-stimulated genes (ISG) in the cerebellum. This RIPK3- mediated potentiation of ISG expression was associated with robust cell-intrinsic restriction of LGTV replication in cerebellar granule cell neurons. These findings further illuminate the complex roles of RIPK3 signaling in the coordination of neuroimmune responses to viral infection, as well as provide new insight into the mechanisms of region-specific innate immune signaling in the CNS. Importance Interactions between the nervous and immune systems are very carefully orchestrated in order to protect the brain and spinal cord from immune-mediated damage, while still maintaining protective defenses against infection. These specialized neuro-immune interactions have been shown to vary significantly across regions of the brain, with innate antiviral signaling being particularly strong in the cerebellum, although the reasons for this are poorly understood. Here, we show a specialized adaptation of programmed cell death signaling that uniquely protects the cerebellum from tick-borne flavivirus infection. These findings provide important new insight into the molecular mechanisms that promote the uniquely robust antiviral immunity of the cerebellum. They also provide new clues into the pathogenesis of tick-borne encephalitis, a zoonosis of significant global concern.

In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing SARS-CoV-2 pandemic has made the importance of such efforts especially clear. New biotechnological advances in vaccinology allow for recent advances that provide only the nucleic acid building blocks of an antigen, eliminating many safety concerns. During the COVID-19 pandemic, these DNA and RNA vaccines have facilitated the development and deployment of vaccines at an unprecedented pace. This success was attributable at least in part to broader shifts in scientific research relative to prior epidemics; the genome of SARS-CoV-2 was available as early as January 2020, facilitating global efforts in the development of DNA and RNA vaccines within two weeks of the international community becoming aware of the new viral threat. Additionally, these technologies that were previously only theoretical are not only safe but also highly efficacious. Although historically a slow process, the rapid development of vaccines during the COVID-19 crisis reveals a major shift in vaccine technologies. Here, we provide historical context for the emergence of these paradigm-shifting vaccines. We describe several DNA and RNA vaccines and in terms of their efficacy, safety, and approval status. We also discuss patterns in worldwide distribution. The advances made since early 2020 provide an exceptional illustration of how rapidly vaccine development technology has advanced in the last two decades in particular and suggest a new era in vaccines against emerging pathogens.

ABSTRACT BACKGROUND Zika virus (ZIKV) is highly teratogenic, in contrast with dengue virus (DENV) or the yellow fever virus vaccine (YFV-17D). The mechanisms employed by ZIKV to cross the placenta need to be elucidated. METHODS Parallel infections with ZIKV, DENV and YFV-17D were compared in terms of efficiency, activation of mTOR pathways and cytokine secretion profile in human cytotrophoblastic HTR8 cells (CTB), and monocytic U937 cells, differentiated to M2 macrophages (M2-MØ). RESULTS In CTB, ZIKV replication was significantly more efficient than DENV or YFV-17D. In M2-MØ, ZIKV replication continued to be more efficient, although differences between strains were reduced. Significantly greater activation of Phospho-S6r and Phospho-AKT/Ser473 fractions in CTB infected with ZIKV than with DENV or YFV-17D, was observed. CTB treated with the mTOR inhibitors rapamycin or AZD8055, showed a 20-fold-reduction in ZIKV yield, versus 5 and 3.5-fold for DENV and YFV-17D, respectively. Finally, we detected that ZIKV infection, but not DENV or YFV-17D, efficiently inhibited the interferon response of CTB cells. CONCLUSIONS These results suggest that CTB cells are permissive and act favoring ZIKV entry into the placental stroma, over DENV and YFV-17D and that the mTOR complex is a switch that enhances the replication of ZIKV in CTB cells.