During infectious disease outbreaks, early warning is crucial to prevent and control the further spread of the disease. While the different waves of the Covid-19 pandemic have demonstrated the need for continued compliance, little is known about the impact of warning messages and risk perception on individual behavior in public health emergencies. To address this gap, this paper uses data from the second wave of Covid-19 in China to analyse how warning information influences preventive behavior through four categories risk perception and information interaction. Drawing on the protective action decision model (PDAM) and the social amplification theory (SARF), warning risk information, risk perception (threat perception, hazard- and resource-related preparedness behavior perception and stakeholder perception), information interaction, and preparedness behavior intention are integrated into a comprehensive model. To test our model, we run a survey with 724 residents in Northern China. The results show that hazard-related preparedness behavior perception and stakeholder perception act as mediators between warning and preventive action. Stakeholder perception had much stronger mediating effects than the hazard-related attributes. In addition, information interaction is effective in increasing all categories risk perception, stimulating public response, while functioning as a mediator for warning. The warning risk information content, channel, and type are identified as key drivers of risk perception. The research found that information channel was more related to different risk perception than other characteristics. Overall, these associations in our model explain core mechanisms behind compliance and allow policy-makers to gain new insights into preventive risk communication in public health emergencies.

COVID-19 is primarily known as a respiratory disease caused by the virus SARS-CoV-2. However, neurological symptoms such as memory loss, sensory confusion, cognitive and psychiatric issues, severe headaches, and even stroke are reported in as many as 30% of cases and can persist even after the infection is over (so-called ‘long COVID’). These neurological symptoms are thought to be caused by brain inflammation, caused by the virus infecting the central nervous system of COVID-19 patients, however we still don’t understand the molecular mechanisms that trigger these symptoms. The neurological effects of COVID-19 share many similarities to neurodegenerative diseases such as Alzheimer’s and Parkinson’s in which the presence of cytotoxic protein-based amyloid aggregates is a common etiological feature. Following the hypothesis that some neurological symptoms of COVID-19 may also follow an amyloid etiology we performed a bioinformatic scan of the SARS-CoV-2 proteome, detecting peptide fragments that were predicted to be highly amyloidogenic. We selected two of these peptides from the open reading frame 6 (ORF6) and open reading frame 10 (ORF10) proteins. The amyloidogenic virus-derived proteins studied in this work did not include spike (S) protein or any other proteins that have been modified to function as antigens in any current vaccines. We discovered that these ORF protein fragments rapidly self-assemble into amyloid aggregates. Furthermore, these amyloid assemblies were shown to be highly toxic to a neuronal cell line. We introduce and support the idea that cytotoxic amyloid aggregates of SARS-CoV-2 proteins are causing some of the neurological symptoms commonly found in COVID-19 and contributing to long COVID.

ABSTRACT Interferon lambda (IFN-λ, type III IFN) is constitutively secreted from human placental cells in culture and reduces Zika virus (ZIKV) transplacental transmission in mice. However, the roles of IFN-λ during healthy pregnancy and in restricting congenital infection remain unclear. Here we used mice lacking the IFN-λ receptor ( Ifnlr1 -/- ) to generate pregnancies lacking either maternal or fetal IFN-λ responsiveness and found that the antiviral effect of IFN-λ resulted from signaling exclusively in maternal tissues. This protective effect depended on gestational stage, as infection earlier in pregnancy (E7 rather than E9) resulted in enhanced transplacental transmission of ZIKV. In Ifnar1 -/- dams, which sustain robust ZIKV infection, maternal IFN-λ signaling caused fetal resorption and intrauterine growth restriction. Pregnancy pathology elicited by poly(I:C) treatment also was mediated by maternal IFN-λ signaling, specifically in maternal leukocytes, and also occurred in a gestational stage-dependent manner. These findings identify an unexpected effect of IFN-λ signaling specifically in maternal (rather than placental or fetal) tissues, which is distinct from the pathogenic effects of IFN-αβ (type I IFN) during pregnancy. These results highlight the complexity of immune signaling at the maternal-fetal interface, where disparate outcomes can result from signaling at different gestational stages. IMPORTANCE Pregnancy is an immunologically complex situation, which must balance protecting the fetus from maternal pathogens with preventing maternal immune rejection of non-self fetal and placental tissue. Cytokines, such as interferon lambda (IFN-λ), contribute to antiviral immunity at the maternal-fetal interface. We found in a mouse model of congenital Zika virus infection that IFN-λ can have either a protective antiviral effect or cause immune-mediated pathology, depending on the stage of gestation when IFN-λ signaling occurs. Remarkably, both the protective and pathologic effects of IFN-λ occurred through signaling exclusively in maternal immune cells, rather than in fetal or placental tissues, or in other maternal cell types, identifying a new role for IFN-λ at the maternal-fetal interface.

The emergence of Zika virus (ZIKV) infection, which is unexpectedly associated with congenital defects, has prompted the development of safe and effective vaccines. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has emerged as a versatile and highly effective platform for delivering target proteins for vaccines. In this article, we developed a bacterium-like particle vaccine ZI-△-PA-GEM based on the GEM-PA system. The fusion protein ZI-△-PA, which contains the prM-E-△ protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3, was expressed. The fusion protein was successfully displayed on the GEM surface, forming ZI-△-PA-GEM. Moreover, when BALB/c mice were immunized intramuscularly with ZI-△-PA-GEM combined with 201 VG and poly(I:C) adjuvants, durable ZIKV-specific IgG and protective neutralizing antibody responses were induced. Potent B cell/DC activation was also be stimulated early after immunization. Remarkably, splenocyte proliferation, the secretion of multiple cytokines, T/B cell activation and central memory T cell responses were elicited. These data indicate that ZI-△-PA-GEM is a promising bacterium-like particle vaccine candidate for ZIKV.

Background: Historical institutionalism (HI) determines that institutions have been transformed by a pattern of punctuated evolution due to exogenous shocks. Although scholars frequently emphasize the role of agency - endogenous factors – when it comes to institutional changes, but the HI analytic narratives still remain in the meso-level analysis in the context of structure and agency. This article provides domestic and policy-level accounts of where biodefense institutions of the United States and South Korea come from, seeing through emergency-use-authorization (EUA) policy, and how the EUA policies have evolved by employing the policy-learning concepts through the Event-related Policy Change Model. Results: By employing the Birkland’s model, this article complements the limitation of the meso-level analysis in addressing that the 2001 Amerithrax and the 2015 Middle East Respiratory Syndrome (MERS) outbreak rooted originations and purposes of the biodefense respectively. Since the crisis, a new post-crisis agenda in society contributed to establishing new domestic coalition, which begin to act as endogenous driving forces that institutionalize new biodefense institutions and even reinforce them through path dependent way when the institutions evolved. Therefore, EUA policy cores (Post-Exposure Prophylaxis (PEP) in the United States and Non-Pharmaceutical Intervention (NPI) in South Korea keep strengthened during the policy revisions. Conclusions: The United States and South Korea have different originations and purposes of biodefense, which are institutions evolving through self-reinforce dependent way based on the lessons learned from past crises. In sum, under the homeland security biodefense institution, the US EUA focuses on the development of specialized, unlicensed PEP in response to public health emergencies; on the other hand, under the disease containment-centric biodefense institution, the Korean EUA is specialized to conduct NPI missions in response to public health emergencies.

ABSTRACT Accumulating evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes various neurological symptoms in coronavirus disease 2019 (COVID-19) patients. The most dominant immune cells in the brain are microglia. Yet, the relationship between neurological manifestations, neuroinflammation, and host immune response of microglia to SARS-CoV-2 has not been well characterized. Here, we report that SARS-CoV-2 can directly infect human microglia, eliciting M1-like pro-inflammatory responses, followed by cytopathic effects. Specifically, SARS-CoV-2 infected human microglial clone 3 (HMC3), leading to inflammatory activation and cell death. RNA-seq analysis also revealed that ER stress and immune responses were induced in the early and apoptotic processes in the late phase of viral infection. SARS-CoV-2-infected HMC3 showed the M1 phenotype and produced pro-inflammatory cytokines such as interleukin (IL)-1β, IL-6, and tumour necrosis factor α (TNF-α), but not the anti-inflammatory cytokine IL-10. After this pro-inflammatory activation, SARS-CoV-2 infection promoted both intrinsic and extrinsic death receptor-mediated apoptosis in HMC3. Using K18-hACE2 transgenic mice, murine microglia were also infected by intranasal inoculation of SARS-CoV-2. This infection induced the acute production of pro-inflammatory microglial IL-6 and TNF-α and provoked a chronic loss of microglia. Our findings suggest that microglia are potential mediators of SARS-CoV-2-induced neurological problems and, consequently, can be targets of therapeutic strategies against neurological diseases in COVID-19 patients. IMPORTANCE Recent studies reported neurological manifestations and complications in COVID-19 patients, which are associated with neuroinflammation. As microglia are the dominant immune cells in brains, it needs to be elucidate the relationship between neuroinflammation and host immune response of microglia to SARS-CoV-2. Here, we suggest that SARS-CoV-2 can directly infect human microglia with cytopathic effect (CPE) using human microglial clone 3 (HMC3). The infected microglia were promoted to pro-inflammatory activation following apoptotic cell death. This pro-inflammatory activation was accompanied by the high production of pro-inflammatory cytokines, and led to neurotoxic-M1 phenotype polarization. In vivo , murine microglia were infected and produced pro-inflammatory cytokines and provoked a chronic loss using K18-hACE2 mice. Thus, our data present that SARS-CoV-2-infected microglia are potential mediators of neurological problems in COVID-19 patients. In addition, HMC3 cells are susceptible to SARS-CoV-2 and exhibit the CPE, which can be further used to investigate cellular and molecular mechanisms of neuroinflammation reported in COVID-19 patients.

Background The purpose of this study was to manually and semi-automatically curate a database and develop an R package that will provide a comprehensive resource to uncover associations between biological processes and environmental factors in health and disease. We followed a two-step process to achieve the objectives of this study. First, we conducted a systematic review of existing gene expression datasets to identify those with integrated genomic and environmental factors. This enabled us to curate a comprehensive genomic-environmental database for four key environmental factors ( smoking, diet, infections and toxic chemicals ) associated with various autoimmune and chronic conditions. Second, we developed a statistical analysis package that allows users to interrogate the relationships between differentially expressed genes and environmental factors under different disease conditions. Results The initial database search run on the Gene Expression Omnibus (GEO) and the Molecular Signature Database (MSigDB) retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 186 studies were selected. From those, 243 individual sets of genes, or “gene modules”, were obtained. We then curated a database containing four environmental factors, namely cigarette smoking, diet, infections and toxic chemicals , along with a total of 25789 genes that had an association with one or more of these gene modules. In six case studies, the database and statistical analysis package were then tested with lists of differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, COVID-19, cobalt exposure and smoking. On testing, we uncovered statistically enriched biological processes, which revealed pathways associated with environmental factors and the genes. Conclusions A novel curated database and software tool is provided as an R Package. Users can enter a list of genes to discover associated environmental factors under various disease conditions.

Red blood cells (RBCs) express the nucleic acid-sensing toll-like receptor 9 (TLR9) and bind CpG-containing DNA. However, whether human RBCs express other nucleic acid-sensing TLRs and bind RNA is unknown. Here we show that human RBCs express the RNA sensor, TLR7. TLR7 is present on the red cell membrane and associates with the RBC membrane protein Band 3. RBCs bind synthetic single-stranded RNA and RNA from pathogenic single-stranded RNA viruses. RNA acquisition by RBCs is attenuated by recombinant TLR7 and inhibitory oligonucleotides. Thus, RBCs may represent a previously unrecognized reservoir for RNA, although how RNA-binding by RBCs modulates the immune response has yet to be elucidated. These findings add to the growing list of non-gas exchanging RBC immune functions. Significance Red blood cells interact with pathogens, cytokines, and CpG-containing DNA; however, their immune functions remain largely unexplored. Here, we report that RBCs can bind synthetic or viral RNA and express TLR7. TLR7 interacts with the RBC membrane protein Band 3 and this interaction is increased during acute infection with SARS-CoV-2. Our study suggests that RBCs may have immune functions mediated by viral RNA, and RNA-carrying RBCs can potentially be a reservoir for RNA-based diagnostics.

Cell death by apoptosis is a major cellular response, in the control of tissue homeostasis and as a defense mechanism in case of cellular aggression like an infection. Cell self-destruction is part of antiviral responses, aimed at limiting the spread of a virus. Although it may contribute to the deleterious effects in infectious pathology, apoptosis remains a key mechanism for viral clearance and resolution of infection. The control mechanisms of cell death processes by viruses have been extensively studied. Apoptosis can be triggered by different viral determinants, through different pathways, as a result of virally induced cell stresses and innate immune responses. Zika virus (ZIKV) induces Zika disease in humans which has caused severe neurological forms, birth defects and microcephaly in newborns during the last epidemics. ZIKV also surprised by revealing an ability to persist in the genital tract and in semen, thus being sexually transmitted. Mechanisms of diverting antiviral responses such as the interferon response, the role of cytopathic effects and apoptosis in the etiology of the disease have been widely studied and debated. In this review, we examined the interplay between ZIKV infection of different cell types and apoptosis and how the virus deals with this cellular response. We illustrate a duality in the effects of ZIKV-controlled apoptosis, depending on whether it occurs too early or too late, respectively in neuropathogenesis, or in long-term viral persistence. We further discuss a prospective role for apoptosis in ZIKV-related therapies, and the use of ZIKV as an oncolytic agent.

The Zika virus (ZIKV) caused neurological abnormalities in more than 3500 Brazilian newborns between 2015 and 2020. Data have pointed to oxidative stress in astrocytes as well as to dysregulations in neural cell proliferation and cell cycle as important events accounting for the cell death and neurological complications observed in Congenital Zika Syndrome. Copper imbalance has been shown to induce similar alterations in other pathologies, and disturbances in copper homeostasis have already been described in viral infections. For this reason, we investigated copper homeostasis imbalance as a factor that could contribute to the cytotoxic effects of ZIKV infection in iPSC-derived human astrocytes. Our results show that ZIKV infection leads to a downregulation of one of the transporters mediating copper release, ATP7B protein. We also observed the activation of mechanisms that counteract high copper levels, including the synthesis of copper chaperones and the reduction of the copper importer protein CTR1. Finally, we show that chelator-mediated copper sequestration in ZIKV-infected astrocytes reduces the levels of reactive oxygen species and improves cell viability, but does not change the overall percentage of infected cells. In summary, our results show that copper homeostasis imbalance plays a role in the pathology of ZIKV in astrocytes, indicating that it may also be a factor accounting for the developmental abnormalities in the central nervous system following viral infection. Evaluating micronutrient levels and the use of copper chelators in pregnant women susceptible to ZIKV infection may be promising strategies to manage novel cases of congenital ZIKV syndrome.

Interferon-induced transmembrane proteins (IFITM1, 2 and 3) are important antiviral proteins that are active against many viruses, including influenza A virus (IAV), dengue virus (DENV), Ebola virus (EBOV), Zika virus (ZIKV) and severe acute respiratory syndrome coronavirus (SARS-CoV). IFITMs exhibit isoform-specific activity, but their distinct mechanisms of action and regulation are unclear. Since S -palmitoylation and cholesterol homeostasis are crucial for viral infections, we investigated IFITM interactions with cholesterol by molecular dynamic stimulations, nuclear magnetic resonance analysis in vitro and photoaffinity crosslinking in mammalian cells. These studies suggest that cholesterol can alter the conformation of IFITMs in membrane bilayers and directly interact with S -palmitoylated IFITMs in cells. Notably, we discovered that the S -palmitoylation levels regulate differential IFITM isoform interactions with cholesterol in mammalian cells and specificity of antiviral activity towards IAV, SARS-CoV-2 and EBOV. Our studies suggest that modulation of IFITM S -palmitoylation levels and cholesterol interaction may influence host susceptibility to different viruses.

Background: The epidemic of 2019 novel coronavirus (SARS-CoV-2) is challenge to the world which was at first confirmed in the Wuhan city of China in December 2019. It was declared a pandemic by the World Health Organization (WHO) in March 2020. In the current work we evaluated effect of health policy of Saudi Arabia for the management of COVID-19 pandemic in early phase and compared to other four countries. Method: Based on the Ministry of Health, Kingdom of Saudi Arabia (KSA) data, the summary of daily report of COVID-19 was prepared from 02 March to 30 April 2020. Further, the daily report of enhancement in cases and recovery of the patients was also summarized. Moreover, the incidence, death and recoveries of COVID-19 cases in KSA were compared with major infected country including China, Italy, Spain and United State of America (USA). The important role of artificial intelligence was shown for the development of drug targets against to infectious diseases Results: In KSA, the first case of COVID-19 was reported on 02 March 2020. Since then, it has affected 22,753 persons till the end of the April 2020. Also, the results showed that the infection rate of COVID-19 increased continuously during the current period of study in KSA. Nevertheless, the rate of death due to COVID-19 is much less with comparison to China, Italy, Spain, and USA due to good medical facilities along with quick action by the government of KSA after the emergence of first case. There is a dire need to develop new platforms and approaches to combat new and old diseases including COVID-19 at warp speed when compared to traditional approaches. DeepDrug’s approach to drug discovery and development showed brighter future towards the discovery of novel drugs against infectious diseases including COVID-19. Conclusion: Currently, there is higher probability of COVID-19 spread at any place. Therefore good health policy, precautionary measures and medical facility of whole nations should be excellent to combat against the COVID-19 pandemic until the reliable vaccine or antiviral drug developed for the proper treatment of virus. The artificial intelligence (AI) based available process might be very helpful for the drug discovery and development against of old and newly discovered diseases including COVID-19.

The current entry discusses several linkages between infectious or communicable diseases and human rights issues. First, the entry puts forward a brief historical note on how international law in the field of the cross-border spread of disease emerged in parallel to international human rights law. Far from being a recent phenomenon, infectious disease outbreaks have long raised questions of which legal measures by national authorities are adequate to respond to these threats. Although the global burden of disease posed by infectious diseases receded in the course of the 20th Century, events such as the HIV/AIDS pandemic and, currently, the COVID-19 pandemic, gave way to questions on the extent of states' health-related human rights obligations. Second, the entry examines the interpretation of states' concrete obligations by international and regional quasi-judicial and judicial human rights bodies. Striking the right balance between protecting persons from the spread of diseases, while at the same time safeguarding individual rights and freedoms, has been a staple of debates in legal doctrine and practice. The entry shows how infectious disease-related events lie beyond the divide between civil and political rights, on the one hand, and economic, social and cultural rights, on the other hand. The analysis concludes by pondering whether the COVID-19 pandemic will be a human rights crucible, posing a series of open questions for further research.

ABSTRACT Strong evidence suggests that human human RNA-binding proteins (RBPs) are critical factors for viral infection, yet there is no feasible experimental approach to map exact binding sites of RBPs across the SARS-CoV-2 genome systematically at a large scale. We investigated the role of RBPs in the context of SARS-CoV-2 by constructing the first in silico map of human RBP / viral RNA interactions at nucleotide-resolution using two deep learning methods (pysster and DeepRiPe) trained on data from CLIP-seq experiments. We evaluated conservation of RBP binding between 6 other human pathogenic coronaviruses and identified sites of conserved and differential binding in the UTRs of SARS-CoV-1, SARS-CoV-2 and MERS. We scored the impact of variants from 11 viral strains on protein-RNA interaction, identifying a set of gain-and loss of binding events. Lastly, we linked RBPs to functional data and OMICs from other studies, and identified MBNL1, FTO and FXR2 as potential clinical biomarkers. Our results contribute towards a deeper understanding of how viruses hijack host cellular pathways and are available through a comprehensive online resource ( https://sc2rbpmap.helmholtz-muenchen.de ).

Aedes aegypti can transmit dengue fever, yellow fever, Chikungunya fever, Zika virus disease and vector density control is the most effective way to prevent these infectious diseases. However, the extensive use of chemical pesticides has caused a series of problems, such as environmental pollution, killing non-target organisms and so on. In this study, a parasitic nematode, Romanomermis wuchangensis was used in the larviciding evaluation of Ae. aegypti , while the activity of four chemical insecticides and biological control agents were tested. Besides, Mentha haplocalyx essential oil was isolated and its olfactory physiological function with OBP1 protein of Ae. aegypti antenna was measured by the prokaryotic expression and fluorescence competitive binding assay. Compared with the control group, R. wuchangensis indicated high efficiency and environmental friendliness in the control of Ae. aegypti. After the second instar larvae were parasitized, the mortality of two treatment groups exceeded 75%. Compared to control group, the quantitative real-time PCR analysis results demonstrated that SOD , POD and CAT genes had obvious high expression levels in the nematodes parasitic groups. The antioxidant enzyme test results also exhibited obvious difference of SOD, CAT and POD during the nematode parasitic period. Besides, Bacillus thuringiensis (Bti) and chemical insecticide experimental results also showed great insecticidal efficacy against mosquito larvae. Five chemical components including Menthol, Pinene, Limonene, Isopulegol and Pulegone were identified from M. haplocalyx and exhibited great binding ability with AaegOBP1 protein. Present results illustrated that the integrated application of these various mosquito vector control methods in the future has broad prospects.

Abstract The US Zika Pregnancy and Infant Registry (USZPIR) monitors infants born to mothers with confirmed or possible Zika virus (ZIKV) infection during pregnancy. The surveillance case definition for Zika-associated birth defects includes microcephaly based on head circumference (HC). We assessed birth and follow-up data from infants with birth HC measurements <3 rd percentile and birthweight ≥10 th percentile to determine possible misclassification of microcephaly.We developed a schema informed by literature review and expert opinion to identify possible HC measurement inaccuracy using HC growth velocity and neuroimaging results. Two or more HC measurements between 2-12 months of age were required for assessment. Inaccuracy in birth HC measurement was suspected if growth velocity was >3 centimeters/month in the first three months or HC was consistently >25 th percentile during follow-up. Normal neuroimaging was considered supportive of HC measurement inaccuracy. Of 6,799 infants, 351 (5.2%) had Zika-associated birth defects, of which 111 had birth HC measurements <3 rd percentile and birthweight ≥10 th percentile. Of 84/111 infants with sufficient follow-up, 38/84 (45%) were classified as having possible inaccuracy of birth HC measurement, 19/84 (23%) had HC ≥3 rd percentile on follow-up without meeting criteria for possible inaccuracy, and 27/84 (32%) had continued HC <3 rd percentile. After excluding possible inaccuracies, the proportion of infants with Zika-associated birth defects including microcephaly decreased from 5.2% to 4.6%.About one-third of infants with Zika-associated birth defects had only microcephaly, but indications of possible measurement inaccuracy were common. Implementation of this schema in ZIKV infection during pregnancy studies can reduce misclassification of microcephaly.

Mosquito-borne flaviviruses (MBFs) adapt to a dual-host transmission circle between mosquitoes and vertebrates. Dual-host affiliated insect-specific flaviviruses (dISFs), discovered from mosquitoes, are phylogenetically similar to MBFs but do not infect vertebrates. Thus, dISF-MBF chimeras could be an ideal model to study the dual-host adaption of MBFs. Using the pseudo-infectious reporter virus particle and reverse genetics systems, we found dISFs entered vertebrate cells as efficiently as the MBFs, but failed to initiate replication. Exchange of the un-translational regions (UTRs) of Donggang virus (DONV), an dISF, with those from Zika virus (ZIKV) rescued DONV replication in vertebrate cells and critical secondary RNA structures were further mapped. Essential UTR-binding host factors were screened for ZIKV replication in vertebrate cells, displaying different binding patterns. Therefore, our data demonstrate a post-entry cross-species transmission mechanism of MBFs, while UTR-host interaction is critical for dual-host adaption. Significance Statement Most viruses have a relatively narrow host range. In contrast, vector-borne flaviviruses, such as dengue virus and Zika virus, maintain their transmission cycle between arthropods and vertebrates, belonging to different phyla. How do these viruses adapt to the distinct cellular environments of two phyla? By comparing the single-host insect specific flavivirus and dual-host Zika virus, we identified three key molecular factors that determine MBF host tropism. This study will greatly increase the understanding of entry, replication, and cross-species evolution of mosquito-borne flaviviruses.

SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evo-lution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic. Graphical Abstract

The COVID-19 pandemic has severely impacted health systems and economies worldwide. Significant global efforts are therefore ongoing to improve vaccine efficacies, optimize vaccine deployment, and develop new antiviral therapies to combat the pandemic. Mechanistic viral dynamics and quantitative systems pharmacology models of SARS-CoV-2 infection, vaccines, immunomodulatory agents, and antiviral therapeutics have played a key role in advancing our understanding of SARS-CoV-2 pathogenesis and transmission, the interplay between innate and adaptive immunity to influence the outcomes of infection, effectiveness of treatments, mechanisms and performance of COVID-19 vaccines, and the impact of emerging SARS-CoV-2 variants. Here, we review some of the critical insights provided by these models and discuss the challenges ahead.

COVID-19 and influenza are both highly contagious respiratory diseases with a wide range of severe symptoms and cause great disease burdens globally. It has become very urgent and important to develop a bivalent vaccine that is able to target these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant VSV (rVSV) vaccine candidates. These rVSV-based vaccines co-express SARS-CoV-2 Delta variant spike protein (SP) or the receptor binding domain (RBD) and four copies of the highly conserved M2 ectodomain (M2e) of influenza A fused with the Ebola glycoprotein DC-targeting/activation domain. Animal studies have shown that immunization with these bivalent rVSV vaccines induced efficient but variable levels of humoral and cell-mediated immune responses against both SARS-CoV-2 and influenza M2e protein. Significantly, our vaccine candidates induced production of high levels of neutralizing antibodies that protected cells against SARS-CoV-2 Delta and other SP-pseudovirus infections in culture. Furthermore, vaccination with the bivalent VSV vaccine via either intramuscular or intranasal route efficiently protected mice from the lethal challenge of H1N1 and H3N2 influenza viruses and significantly reduced viral load in the lungs. These studies provide convincing evidence for the high efficacy of this bivalent vaccine to prevent influenza replication and initiate robust immune responses against SARS-CoV-2 Delta variants. Further investigation of its efficacy to protect against SARS-CoV-2 Delta variants will provide substantial evidence for new avenues to control two contagious respiratory infections, COVID-19 and influenza.

Vaccination against viruses has rarely been associated with Guillain-Barré syndrome (GBS). An association with the COVID-19 vaccine is unknown. We performed a population-based study of National Health Service data in England and a multicentre surveillance study from UK hospitals, to investigate the relationship between COVID-19 vaccination and GBS. Firstly, case dates of GBS identified retrospectively in the National Immunoglobulin Database from 8 December 2021 to 8 July 2021 were linked to receipt dates of a COVID-19 vaccines using data from the National Immunisation Management System in England. For the linked dataset, GBS cases temporally associated with vaccination within a 6-week risk window of any COVID-19 vaccine were identified. Secondly, we prospectively collected incident UK-wide (four nations) GBS cases from 1 January 2021 to 7 November 2021 in a separate UK multicentre surveillance database. For this multicentre UK-wide surveillance dataset, we explored phenotypes of reported GBS cases to identify features of COVID-19 vaccine-associated GBS. 996 GBS cases were recorded in the National Immunoglobulin Database from January to October 2021. A spike of GBS cases above the 2016-2020 average occurred in March-April 2021. 198 GBS cases occurred within 6 weeks of the first-dose COVID-19 vaccination in England (0.618 cases per 100,000 vaccinations, 176 ChAdOx1 nCoV-19 (AstraZeneca), 21 tozinameran (Pfizer), 1 mRNA-1273 (Moderna)). The 6-week excess of GBS (compared to the baseline rate of GBS cases 6-12 weeks after vaccination) occurs with a peak at 24 days post-vaccination; first-doses of ChAdOx1 nCoV-19 accounted for the excess. No excess was seen for second-dose vaccination. The absolute number of excess GBS cases from January-July 2021 was between 98-140 cases for first-dose ChAdOx1 nCoV-19 vaccination. First-dose tozinameran and second-dose of any vaccination showed no excess GBS risk. Detailed clinical data from 121 GBS patients were reported in the separate multicentre surveillance dataset during this timeframe. No phenotypic or demographic differences identified between vaccine-associated and non-vaccinated GBS cases occurring in the same timeframe. Analysis of the linked NID/NIMS dataset suggests that first-dose ChAdOx1 nCoV-19 vaccination is associated with an excess GBS risk of 0.576 (95%CI 0.481-0.691) cases per 100,000 doses. However, examination of a multicentre surveillance dataset suggests that no specific clinical features, including facial weakness, are associated with vaccination-related GBS compared to non-vaccinated cases. The pathogenic cause of the ChAdOx1 nCoV-19 specific first dose link warrants further study.

Various immunomodulatory therapies have been explored to manage the dysregulated immune response seen in severe COVID-19 infection. The objective of this study was to evaluate the efficacy of intravenous immunoglobulin (IVIG) in severe and critical COVID-19 disease. This retrospective study included 535 patients with severe and critical COVID-19 admitted to the intensive care unit (ICU) of a tertiary care hospital, from May 2020 to December 2020. Primary outcome was the percentage of patients requiring mechanical ventilation. Secondary outcomes were a) in-hospital mortality, b) 28-day mortality, c) ICU-length of stay (ICU-LOS), d) days to discontinuation of supplemental oxygen, and e) days to COVID-PCR negativity. Logistic regression and linear regression were performed using the adjusted and unadjusted analysis. We analyzed a total of 535 patients out of which 255 (47.7%) received IVIG along with standard treatment and 280 (52.3%) received only standard treatment. Two groups were similar in terms of COVID-19 severity, APACHE II score, oxygen requirements, and initial management. The requirement of invasive ventilation was significantly less in the IVIG group compared to the Non-IVIG group (32.2% vs 40.4%, p<0.05). In-hospital mortality, 28-day mortality, and ICU-LOS were also significantly less in the IVIG group (all p<0.05). Subgroup analysis within the IVIG group showed that early administration of IVIG (≤ 7 days from ICU admission), old age (≥ 65 years), and obesity were associated with better outcomes (need for mechanical ventilation and in-hospital mortality) (all p<0.05). High-dose IVIG improves outcomes in severe and critical COVID-19 patients. The study also underscores the importance of timing and patient selection when administering IVIG.

Glioblastoma (GBM) is one of the most common brain tumors in adults. Despite the presence of available treatments, it remains one of the most lethal and difficult tumors to treat such that most patients die within two years. Studies reported that infection with Zika virus (ZIKV) causes inhibition of cell proliferation as well as induction of apoptosis; moreover, these manifestations show a predilection for developing neuronal cells. In the present study, two GBM cell lines U-138 and U-251 were infected with ZIKV at multiplicities of infection (MOI) 0.1, 0,01 and 0.001 and tested for cell viability, cell migration, cell adhesion, induction of apoptosis, interleukin levels, and cell surface markers (CD14 and CD73). Our study demonstrated that the ZIKV infection promotes loss of cell viability and increased apoptosis potential. It was not evidenced changes in cell migration, however, the two glioblastoma cell lines displayed increased the cell adhesion behavior. There was small increase in the IL-4 level in the U-251 cell line after exposure to ZIKV, with no change in relation to INF-γ levels. Furthermore, we observed an increase in the percentage of cells expressing the CD14 surface marker in both cell lines and increased CD73 expression in the U-251 cell line. Our results suggest that ZIKV may be associated with decrease of cell viability and increased CD73 expression, enhanced adherence, as well as increased apoptosis rates. Further investigations are required to explore the potential use of ZIKV in the treatment of GBM.

Zika virus (ZIKV) NS4B protein is a membranotropic protein having multifunctional roles such as evasion of host-immune system, and induction of host membrane rearrangement for viral genome replication and processing of polyprotein. Despite its versatile functioning, its topology and dynamics are not entirely understood. Presently, there is no NMR or X-ray crystallography-based structure available for any flaviviral NS4B protein. Therefore, in this study, we have investigated the structural dynamics of Zika Virus NS4B protein through 3D structure models using molecular dynamics (MD) simulations approach and experiments. Subsequently, we employed a reductionist approach to understand the dynamics of ZIKV NS4B protein. For this, we studied its N-terminal (residues 1-38), C-terminal (residues 194-251), and cytosolic (residues 131-169) regions in isolation. Further, we have performed experiments to prove the maximum dynamics in its cytosolic region. Using a combination of computational tools and circular dichroism (CD) spectroscopy, we validate the cytosolic region as an intrinsically disordered protein region (IDR). The microsecond-long all atoms molecular dynamics and replica-exchange MD simulations complement the experimental observations. We have also analysed its behaviour under the influence of differently charged liposomes and macromolecular crowding agents which may have significance on its overall dynamics. Lastly, we have proposed a ZIKV NS4B protein model illustrating its putative topology consisting of various membrane-spanning and non-membranous regions. Highlights Microsecond simulations of NS4B N-terminus and cytosolic regions exposed their dynamic nature. C-terminal region remains intact in presence lipid bilayer during 1 μs simulations. Spectroscopic results also reveal the cytosolic region as an intrinsically disordered region. Cytosolic region exhibits gain-of-structure property under helix inducing solvents.

ABSTRACT An enormous global effort is being made to study SARS-CoV-2 and develop safe and effective treatments. Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify host factors and treatments to combat the infection. However, quantification of released virus often requires lengthy procedures, such as endpoint dilution assays or reinfection with engineered reporter viruses. Quantification of viral RNA in cell supernatant is faster and can be performed on clinical isolates. However, viral RNA purification is expensive in time and resources and often unsuitable for high-throughput screening. Here, we show a direct lysis RT-qPCR method allowing sensitive, accurate, fast, and cheap quantification of SARS-CoV-2 in culture supernatant. During lysis, the virus is completely inactivated, allowing further processing in low containment areas. This protocol facilitates a wide array of high- and low-throughput applications from basic quantification to studying the biology of SARS-CoV-2 and to identify novel antiviral treatments in vitro.