Human pathogenic flaviviruses pose a significant health concern and vaccination is the most effective instrument to control their circulation. How pre-existing immunity to antigenically related viruses modulates immunization outcome remains poorly understood. In this study, we evaluated the effect of vaccination against tick-borne encephalitis virus (TBEV) on the epitope immunodominance and immunogenicity of the yellow fever 17D vaccine (YF17D) in a cohort of 250 human vaccinees. Following YF17D vaccination, all study participants seroconverted and generated protective neutralizing antibody titers. At day 28, TBEV pre-immunity did not affect the polyclonal neutralizing response which largely depended on the IgM fraction. We found that sera from TBEV-immunized individuals enhanced YF17D vaccine virus infection via antibody-dependent enhancement (ADE). Upon vaccination, individuals with TBEV pre-immunity had higher concentrations of cross-reactive IgG antibodies with limited neutralizing capacity against YF17D whereas vaccinees without prior flavivirus exposure showed a non-cross-reacting response. Using a set of recombinant YF17D envelope protein mutants displaying different epitopes, we identified quaternary epitopes as the primary target of neutralizing antibodies. Sequential immunizations redirected the IgG response towards the pan-flavivirus fusion loop epitope (FLE) with the potential to mediate enhancement of dengue and Zika virus infections whereas TBEV naïve individuals elicited an IgG response directed towards neutralizing epitopes without an enhancing effect. We propose that the YF17D vaccine effectively conceals the FLE and primes a neutralizing IgG response in individuals with no prior flavivirus exposure. In contrast, the response in TBEV-experienced recipients favors weakly-neutralizing, cross-reactive epitopes potentially increasing the risk of severe dengue and Zika disease due to ADE.

We present compelling evidence for the existence of an extended innate viperin dependent pathway which provides crucial evidence for an adaptive response to viral agents like SARS-CoV-2. We show the in vivo biosynthesis of a family of endogenous cytosine metabolites with potential antiviral activity. Two dimensional Nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally allowed the characterization and quantification of the most abundant serum metabolites showing potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine and uracil based) analogue structures, eight of which were previously unknown in humans. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ and IL-10, suggest an association with the viperin enzyme contributing to an endogenous innate immune defence mechanism against viral infection.

Understanding the population dynamics of an infectious disease requires linking within-host dynamics and between-host transmission in a quantitative manner, but this is seldom done in practice. Here a simple phenomenological model for viral dynamics within a host is linked to between-host transmission by assuming that the probability of transmission is related to log viral titre. Data from transmission experiments for two viral diseases of livestock, foot-and- mouth disease virus in cattle and swine influenza virus in pigs, are used to parameterise the model and, importantly, test the underlying assumptions. The model allows the relationship between within-host parameters and transmission to be determined explicitly through their influence on the individual reproduction number and generation time. Furthermore, these critical within-host parameters (time and level of peak titre, viral growth and clearance rates) can be computed from more complex within-host models, raising the possibility of assessing the impact of within-host processes on between-host transmission in a more detailed quantitative manner. Author summary For a pathogen to be able to transmit between hosts it must replicate to a sufficiently high level within an infected host. Because of this linking the dynamics of a pathogen within a host to transmission between hosts is important for understanding an infectious disease and its control. In this study I develop a simple mathematical model for the within-host dynamics and combine it with a model relating the probability of transmission to the level of the pathogen. I use the model derive explicit relationships between parameters related to the within-host dynamics, such as viral growth and clearance rates, and summary transmission measures, such as the reproduction number and generation time. I test the assumptions in the underlying model and estimate parameters using data from transmission experiments for two important viral diseases, foot-and-mouth disease virus in cattle and swine influenza virus in pigs. Identifying the critical within host parameters that influence transmission allows the impact of within-host processes on between-host transmission to be investigated in a more detailed quantitative manner.

Zika virus (ZIKV) is spread by mosquitos, sexual intercourse and vertically during pregnancy. The 2015–2016 ZIKV epidemic infected millions in the Americas and resulted in thousands of infants born with malformations. Though the clusters of severe birth defects have subsided since 2017, ZIKV transmission remains a concern throughout Latin America and the Caribbean. Travel-associated and sexually-transmitted Zika, therefore, remain potential routes of transmission for women of reproductive age and their partners. This is particularly true for communities with high immigrant and foreign-born populations in Central Brooklyn, New York. Limited information has been collected on the perception by this population of ZIKV and how high-risk women engage in preventive practices. Using a survey adapted from the WHO, we assessed engagement in mosquito-related preventive practices while traveling. Data from 483 respondents on knowledge and perceived ZIKV concern, along with demographics as correlates of engagement in preventive practices were collected using a convenience sample between September 2020 and January 2021. Data were collected via a multipronged approach using social media in REDCap. Our findings show that being white/not Hispanic, pregnant, knowledgeable and concerned about ZIKV, and having enough information about ZIKV were all significantly associated with an increased likelihood of engaging in preventive practices while traveling. Multivariable logistic modeling revealed that knowledge was significantly associated with an increased likelihood of engaging in preventive practices while traveling (AOR = 1.90, 1.28–2.83). These findings underscore the importance of directing tailored health education efforts to vulnerable populations.

Zika virus (ZIKV) is a mosquito-borne Flavivirus that persistently infects patients, enters protected brain, placental, and testicular compartments, is sexually transmitted, and causes fetal microcephaly in utero . ZIKV persistently infects brain microvascular endothelial cells (hBMECs) that form the blood-brain-barrier and Sertoli cells that form testicular barriers, establishing reservoirs that enable viral dissemination. ZIKV persistence requires inhibiting interferon (IFN) responses that direct viral clearance. We found that ZIKV induces IFN-β and IFN-λ in hBMECs but post-transcriptionally inhibits IFN-β/λ expression. IFNβ/λ mRNAs contain AU-rich elements (AREs) in their 3’ untranslated regions which regulate protein expression through interactions with ARE binding proteins (ARE-BPs). We found that ZIKV infection of primary hBMECs induces the expression of the ARE-BP tristetraprolin (TTP) and that TTP is a novel regulator of endothelial IFN secretion. In hBMECs, TTP knockout (KO) increased IFN-β/λ 1 mRNA abundance and IFN-β/λ 1 secretion in response to ZIKV infection and inhibited viral persistence. In contrast, TTP expression dramatically reduced IFN-β/λ 1 secretion in hBMECs. IFN-β/λ 1 mRNA stability was not significantly altered by TTP and is consistent with TTP inhibition of IFN-β/λ 1 translation. TTP is similarly induced by ZIKV infection of Sertoli cells, and like hBMECs, TTP expression or KO inhibited or enhanced IFN-β/λ mRNA levels, respectively. These findings reveal a mechanism for ZIKV induced TTP to promote viral persistence in hBMECs and Sertoli cells by post-transcriptionally regulating IFN-β/λ secretion. Our results demonstrate a novel role for virally induced TTP in regulating IFN secretion in barrier cells that normally restrict viral persistence and spread to protected compartments. Importance Our findings define a novel role for ZIKV induced TTP expression in regulating IFN-β/λ production in primary hBMECs and Sertoli cells. These cells comprise key physiological barriers subverted by ZIKV to access brain and testicular compartments and serve as reservoirs for persistent replication and dissemination. We demonstrate for the first time that the ARE binding protein TTP is virally induced and post-transcriptionally regulates IFN-β/λ secretion. In ZIKV infected hBMEC and Sertoli cells, TTP knockout increased IFN-β/λ secretion, while TTP expression blocked IFN-β/λ secretion. The TTP directed blockade of IFN secretion permits ZIKV spread and persistence in hBMECs and Sertoli cells and may similarly augment ZIKV spread across IFN-λ protected placental barriers. Our work highlights the importance of post-transcriptional ZIKV regulation of IFN expression and secretion in cells that regulate viral access to protected compartments and defines a novel mechanism of ZIKV regulated IFN responses which facilitate neurovirulence and sexual transmission.

Globally, health promotion measures have been undertaken in preventing the emergence and spread of coronavirus disease 2019 (COVID-19). However, whether these measures influence public awareness and behaviors is unclear and evidence is limited in particular in low-and-middle income country. We conducted an online survey among internet users in Bangladesh to understand the status and attributes of their knowledge, attitudes and practices towards COVID-19 during second wave of the pandemic when COVID educational information was more accessible to the public. Survey data were analyzed using descriptive statistics, Chi-square tests, and multivariate logistic regression analysis. Of 964 respondents, 40.2%, 51.5%, and 64.3% had good knowledge, confident attitudes, and proper practices towards COVID-19, respectively. The multivariate regression analysis found that the knowledge and practice scores were associated (p<0.05) with gender, age, and occupation. Females had better knowledge and practices compared to males (p<0.05). There were major gaps in awareness, attitudes, and practices among internet users in particular males and elders that needs to be addressed to control the further spread of COVID-19 infections before at least COVID-19 vaccine become accessible at population level in Bangladesh.

ABSTRACT Background Zika virus (ZIKV) has emerged as a cause of febrile illness in children and adults globally. West Asian and Middle Eastern countries have not yet experienced the widespread emergence of ZIKV. In Pakistan, detection of ZIKV antibodies have been reported. However, the validity of this data is questionable given the current understanding of flaviviral antigenic cross-reactivity. In order to determine if ZIKV is circulating in the Sindh region of Pakistan, patients presenting to healthcare centers with an acute febrile dengue-like illness were evaluated for ZIKV infection. Methods Dengue virus (DENV) screening in patients was performed using a commercial ELISA Rapid Test NS1 antigen capture test. All DENV negative samples were tested for Zika virus, using a commercial IgM capture ELISA kit. Additionally, a plaque reduction neutralization test (PRNT) was performed to measure neutralizing antibodies. Singleplex, two-step Real-time PCR using general primers and probes was performed for the detection of Zika virus nucleic acid. Results Patients with acute dengue-like illness (DLI) presenting at healthcare centers in different sites throughout the Sindh region of Pakistan were recruited. A total of 745 patient samples were tested for ZIKV via IgM ELISA and RT-PCR. Thirty-seven samples (4.9%) tested positive for ZIKV IgM without any cross-reactivity to other flaviviruses tested simultaneously. These were considered as presumptive positive for ZIKV, selected presumptive positive samples (n=20) were confirmed using PRNT50 using Vero cells. All 20 samples showed ZIKV neutralization at PRNT50. Conclusions Our study provides evidence that ZIKV is circulating in the Sindh region of Pakistan and is a probable cause of clinical dengue-like illness (DLI) cases that are seen seasonally in Pakistan.

SUMMARY In the past decade, Zika virus (ZIKV) emerged as a global public health concern. While adult infections are typically mild, maternal infection can lead to adverse fetal outcomes. Understanding how ZIKV proteins disrupt development can provide insights into the molecular mechanisms of symptoms caused by this virus including microcephaly. In this study, we generated a toolkit to ectopically express Zika viral proteins in vivo in Drosophila melanogaster in a tissue-specific manner using the GAL4/UAS system. We use this toolkit to identify phenotypes and host pathways targeted by the virus. Our work identified that expression of most ZIKV proteins cause scorable phenotypes, such as overall lethality, gross morphological defects, reduced brain size, and neuronal function defects. We further use this system to identify strain-dependent phenotypes that may contribute to the increased pathogenesis associated with the more recent outbreak of ZIKV in the Americas. Our work demonstrates Drosophila’s use as an efficient in vivo model to rapidly decipher how pathogens cause disease and lays the groundwork for further molecular study of ZIKV pathogenesis in flies.

Introduction Needle-stick injuries (NSIs) are defined as the sharp point of a needle puncturing human skin. This article examines the risk and illustrates the burden of NSIs for workers in the healthcare, veterinary and research industries, and includes a sample survey population of workers in workplaces using needles. Methods For the review component of this article, PubMed and Google Scholar were queried within the date range of 1998-2022, retrieving 1,437 results. A publicly available sample population dataset was and analyzed from British Columbia (n=30) on workplace needlestick injuries. The OSHA, WHO, and NIEHS guidelines were reviewed, and the WorkSafe BC injury database was searched using FIPPA requests. Discussion Recapping remains a common practice despite decades of guidelines recommending against recapping. NSI research is underpowered and underrepresented in non-healthcare settings. NSIs lead to heightened anxiety, depression, and PTSD in workers and exposure to pathogens, toxic chemicals and permanent tissue damage. NSI annual reporting is likely an underestimate due to chronic underreporting, and the financial impact including work-loss and healthcare costs continues to rise. Current NSI prevention devices have limited uptake and thus, more affordable, versatile and efficient NSI-prevention devices are needed. Relevance Due to COVID-19, healthcare workers are at a higher risk of receiving NSIs. Emphasis on safe needle handling practices is necessary to maintain workers physical and psychological safety, to protect workers using COVID-19 PPE on long shifts, and to deliver the high volume of vaccinations required to inoculate the global population. Conclusion NSIs are detrimental to healthcare workers wellbeing, chronically underreported, and poorly surveyed. Areas of future research include determining more effective solutions to reduce NSIs, assessing the validity of NSI reporting systems, and integrating solutions with COVID-19 prevention and vaccination protocols.

Background: Mosquito borne pathogens are a threat to human health and can be difficult to detect especially when they cause a high rate of asymptomatic infections in human. The discovery that infected mosquitoes can release viruses in both their saliva and secreta gave rise to low-cost methods for the early detection of arboviruses during entomological surveillance. Methods: Here, we implemented both saliva and excreta-based entomological surveillance during the emergence of Zika virus (ZIKV) in French Guiana in 2016 by trapping mosquitoes around households of confirmed ZIKV symptomatic cases. Results: ZIKV was detected in mosquito excreta and not in mosquito saliva in one trap collection out of 85 (1.2%) throughout the survey. One female Ae. aegypti was found with a ZIKV systemic infection in the corresponding trap. The lag time between symptom onset declared by the ZIKV infected individual living in this site and ZIKV detection detected in this mosquito was one week. Conclusions: Altogether, these results highlight the potential of trapped mosquito excreta as a sensitive and cost-effective method to non-invasively detect arbovirus circulation.

Abstract Introduction : Plants of the genus Phyllanthus ( Euphorbiaceae ), the “stone breaker” has long been used in folk medicine to treat hepatitis B, an important viral disease. In this regard some species of this genus were tested against viruses as Herpes simplex virus type 1 (HSV-1), COVID and Hepatitis C virus (HCV), showing expressive inhibition in some of them, attracting attention to the genus and to its chemical constituents. Although P. brasiliensis has no traditional use as an antiviral plant, these findings urge us to consider whether P. brasiliensis , plant widely distributed in the Brazilian Amazon and its compounds have antiviral activity against Vero cell lines infected with Mayaro, Oropouche, Chikungunya, and Zika viruses. Objectives : Thus, herein we describe a study of extracts' chemical diversity, antiviral activity, and specialized metabolites detected in different parts of the Phyllanthus brasiliensis (Aubl.) Poir., Methods: In this context, liquid chromatography-mass spectrometry is a crucial analytical method to reveal the identity of many drug candidates from extracts from medicinal plants used to treat diseases, including for instance infections by viruses. Results : As result, 44 compounds were annotated by mass spectrometry-based molecular networking approach. Along, the extracts were tested against Vero cell lines infected with Mayaro, Oropouche, Chikungunya, and Zika viruses. Overall, the results revealed that this species is high in fatty acids, flavones, flavan-3-ols, and lignans. Among them, especially lignans are known to have promising antiviral properties. In this context, in vitro assays revealed potent antiviral activity against different viruses, especially lignan-rich extracts MEB (EC 50  = 0.80 µg.mL − 1 , SI = 377.59), MEL (EC 50  = 0.84 µg.mL − 1 , SI = 297.62), and HEL (EC 50  = 1.36 µg.mL − 1 , SI = 735.29) against Zika virus (ZIKV). Conclusions : The potential of lignans was also supported by in silico antiviral prediction, and Tuberculatin (a lignan) stood out with high activity score and as a strong candidate from MEL extract. Therefore, authors believe that P. brasiliensis extracts contain metabolites that could be a new kick-off point with candidates for antiviral drug development, with lignans becoming a promising trend for further virology research.

Viral infections can endanger public health by causing serious illness, leading to pandemics and burdening healthcare systems. Moreover, in the situation of a global spread, disruptions occur in every aspect of life including business, education, and social life. Fast and accurate diagnosis of viral infections has huge implications for saving people’s lives, preventing spread of the diseases, and minimizing social and economic damages. In the last decades, polymerase chain reaction (PCR) based techniques have been frequently used to detect viruses in the clinic. However, in a situation where rapid virus detection is the primary measure in preventing the spread, as in the case of ongoing COVID-19 pandemic, disadvantages of PCR, such as long processing times and requirement of sophisticated laboratory instruments, have been faced. Due to the urgent need for accurate techniques for virus detection, biosensor systems involved in many applications in biological detection are being developed for rapid, real-time, and high-throughput detection of viruses. Among various sensing platforms, optical devices are of great interest due to their advantages such as high sensitivity and direct readout. In the current review, usability of sensing techniques depending on optical phenomena, such as fluorescence-based sensors, surface plasmon resonance (SPR), surface enhanced Raman scattering (SERS), optical resonators and interferometry-based platforms, is discussed for virus diagnostics applications. Then, we focus on an interferometric biosensor developed by our group, single-particle interferometric reflectance imaging sensor (SP-IRIS), which has the capability to visualize single nanoparticles, to demonstrate its application for digital virus detection.

Abstract: Background: Cytidine/uridine monophosphate kinase 2 (UMP-CMP kinase 2, CMPK2) has been reported as an antiviral interferon-stimulated gene (ISG). We previously observed that the expression of CMPK2 was significantly upregulated after Zika Virus (ZIKV) infection in A549 cells. However, the role of CMPK2 in ZIKV replication remains to be determined. Methods: CMPK2 or retinoic acid inducible gene I (RIG-I) was overexpressed by plasmid transfection or knocked down by siRNA, respectively in A549 cells before the cells were infected with ZIKV. ZIKV RNA and NS1 protein were detected by RT-qPCR and Western Blot, respectively. The activation status of Jak-STAT signaling pathway was determined by the evaluation of the phosphorylation level of STAT1 (p-STAT1, by Western Blot), interferon stimulated response element (ISRE) activity (by dual luciferase assay) and interferon stimulated gene (ISG) expression (by RT-qPCR). Results: We found that ZIKV infection induced CMPK2 expression dependent on RIG-I. Overexpression of CMPK2 inhibited while CMPK2 knockdown promoted ZIKV replication. Mechanically, we found that CMPK2 inhibited ZIKV replication probably through the activation of Jak/STAT signaling pathway as shown by the increased level of p-STAT1, enhanced activity of ISRE, and the up-regulated expression of some downstream ISGs. Conclusion: ZIKV infection induced CMPK2 expression, which activated the Jak/STAT signaling pathway to inhibit ZIKV replication. Keywords: CMPK2; ZIKV; Jak/STAT signaling pathway

Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5′ end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach ‘SMART-9N’ and a version compatible rapid adapters available from Oxford Nanopore Technologies ‘Rapid SMART-9N’. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.

Following a number of recent crises, including, amongst others, financial crises, COVID-19, global climate change, and the Ukraine War, this article reviews the main principles guiding crisis management. Our first aim is to sum up the main lessons that these crises have taught or reminded us of. The fire that burned Notre Dame cathedral in Paris is used to present the dynamics of crisis and to provide a context to illustrate the principle. What is particularly painful in the crisis – a fact that motivated the writing of this article - is to see that these principles are regularly ignored. Crisis is not a time for learning or reinventing what should already be known. Crisis management is a time for experienced hands, endowed with healthy doses of both science and “facts,” and, on the other hand, intuition. On the science side, not learning from the past, or the present, can be very costly. One of the overarching characteristics that renders crisis management complex is that the manager faces a great number of dualities, such as continuing the fight or retreat. These act as tensions affecting decision making in an already charged context. When poorly addressed, each of these dualities may lead to failure. This complexity appears not to have been well recognized in the literature. A final duality is that perspectives in the crisis management literature are typically either internal and organizational, or external and stakeholder focused. Integration in time and across organizational and stakeholder boundaries is the suggestion for further conceptual development and empirical work. The current article fills this gap by joining both perspectives. It does so by presenting a general framework for crisis management that consists of 5 phases to be implemented following a virtuous cycle. The framework allows several clear conclusions: framing and reframing of the crisis are key, the way one gets into a crisis is typically not the way one exits a crisis, and that the how in crisis management (process) is as important as the what (outcomes).

Molecular diagnostic methods to detect and quantify viral RNA in clinical samples rely on the purification of the genetic material prior to reverse transcription polymerase chain reaction (qRT-PCR). Due to the large number of samples processed in clinical laboratories, automation has become a necessity in order to increase method processivity and maximize throughput per unit of time. An attractive option for isolating viral RNA is based on the magnetic solid phase separation procedure (MSPS) using magnetic microparticles. This method offers the advantage over other alternative methods of making it possible to automate the process. In this study we report the results of the MSPS method, based on magnetic microparticles obtained by a simple synthesis process, to purify RNA from oro- and nasopharyngeal swab samples of patients suspected of COVID-19 provided by three diagnostic laboratories located in the Buenos Aires Province, Argentina. Magnetite nanoparticles of Fe3O4 (MNPs) were synthesized by the coprecipitation method and then coated with silica (SiO2) produced by hydrolysis of tetraethyl orthosilicate (TEOS). After preliminary tests on samples from the A549 human lung cell line and swabs, an extraction protocol was developed. The quantity and purity of the RNA obtained were determined by gel electrophoresis, spectrophotometry, and qRT-PCR. Tests on samples from naso- and oropharyngeal swabs were performed in order to validate the method for RNA purification in high-throughput SARS-CoV2 diagnosis by qRT-PCR. The method was compared to the spin columns method and the automated method using commercial magnetic particles. The results show that the method developed is efficient for RNA extraction from nasal and oropharyngeal swab samples, and also comparable to other extraction methods in terms of sensitivity for SARS-CoV-2 detection. Of note, this procedure and reagents developed locally are intended to overcome the shortage of imported diagnostic supplies as the sudden spread of COVID-19 required unexpected quantities of nucleic acid isolation and diagnostic kits worldwide.

The coronavirus disease 2019 (COVID-19) pandemic continues to represent a global public health issue. The viral main protease (M pro ) represents one of the most attractive targets for the development of antiviral drugs. Herein we report peptidyl nitroalkenes exhibited enzyme inhibitory activity against M pro (Ki: 1-10 micM) and three of them good anti-SARS-CoV-2 infection activity in the low micromolar range (EC 50 1-12 micM) without significant toxicity. Additional kinetic studies of compounds FGA145, FGA146 and FGA147 show that all three compounds inhibit Cathepsin L, denoting a possible multitarget effect of these compounds in the antiviral activity. QM/MM computer simulations assisted in the design and in elucidating the way of action. Finally, structural analysis shows, in agreement with the computer predictions, the binding mode of FGA146 and FGA147 to the active site of the protein. Our results illustrate that peptidyl nitroalkenes are potent covalent reversible inhibitors of the M pro and cathepsin L, and that inhibitors FGA145, FGA146 and FGA147 prevent infection becoming promising drugs against SARS-CoV-2.

The Zika virus (ZIKV) outbreaks and its co-relation with microcephaly have become a global health concern. It is primarily transmitted by a mosquito, but can also be transmitted from an infected mother to her fetus causing impairment in brain development, leading to microcephaly. However, the underlying molecular mechanism of ZIKV-induced microcephaly is poorly understood. In this study, we explored the role of ZIKV non-structural protein NS4A and NS4B in ZIKV pathogenesis in a well-characterized primary culture of human fetal neural stem cells (fNSCs). We observed that the co-transfection of NS4A and NS4B altered the neural stem cell fate by arresting proliferation and inducing premature neurogenesis. NS4A-NS4B transfection in fNSCs increased autophagy and dysregulated notch signalling. Further, it also altered the regulation of downstream genes controlling cell proliferation. Additionally, we reported that 3 methyl-adenine (3MA), a potent autophagy inhibitor, attenuated the deleterious effects of NS4A and NS4B as evidenced by the rescue in Notch1 expression, enhanced proliferation, and reduced premature neurogenesis. Our attempts to understand the mechanism of autophagy induction indicate the involvement of mitochondrial fission and ROS. Collectively, our findings highlight the novel role of NS4A and NS4B in mediating NSC fate alteration through autophagy-mediated notch degradation. The study also helps to advance our understanding of ZIKV-induced neuropathogenesis and suggests autophagy as a potential target for anti-ZIKV therapeutic intervention.

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learned. As a component of the Platform, the SARS-CoV-2 Data Hubs enabled the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.

During past viral outbreaks, researchers rushed to patent genomic sequences of the viruses as they were discovered, leading to disputes and delays in research coordination. Yet similar disputes did not occur with respect to the genomic sequence of SARS-CoV-2, the virus responsible for COVID-19. With respect to COVID-19, global research collaboration occurred rapidly, leading to the identification of new variants, the ability to track the spread of the disease, and the development of vaccines and therapeutics in record time. The lack of patenting of SARS-CoV-2 is likely due the U.S. Supreme Court’s 2013 ruling in Association for Molecular Pathology v. Myriad Genetics, which established that naturally occurring genomic sequences are ineligible for patent protection, a decision that has had repercussions around the world. Recently, however, legislative proposals have been made in the U.S. to overturn this decision. Such legislation, if enacted, would enable researchers, likely based in countries where pathogenic outbreaks first occur, to obtain U.S. patents on pathogen genomes. Given that ample opportunities exist for patenting of diagnostics, vaccines, therapeutics and other downstream innovations, steps should be taken at national and international levels to ensure that pathogenic sequence data cannot be appropriated by individual researchers, institutions, or states.

Zika virus (ZIKV) is a mosquito-borne flavivirus and causes an infection that is associated with neurological manifestations, including microcephaly and Guillain-Barre syndrome. The mechanism of ZIKV-mediated neuropathogenesis is not well understood. In this study, we discovered that ZIKV induces the degradation of the Numb protein, which plays a crucial role in neurogenesis by allowing asymmetric cell division during embryonic development. Our data show that ZIKV reduced the Numb protein level in a time- and dose-dependent manner. However, ZIKV infection appears to have minimal effect on the Numb transcript. Treatment of ZIKV-infected cells with a proteasome inhibitor restores the Numb protein level, which suggests the involvement of the ubiquitin-proteasome pathway. In addition, ZIKV infection shortens the half-life of the Numb protein. Among the ZIKV proteins, the capsid protein significantly reduces the Numb protein level. Immunoprecipitation of the Numb protein co-precipitates the capsid protein, indicating the interaction between these two proteins. These results provide insights into the ZIKV-cell interaction that might contribute to its impact on neurogenesis.

Abstract Background The effects of in-utero exposure to maternal SARS-CoV-2 infection on the offspring's neurodevelopment are still unknown. Methods We performed a prospective cohort of babies exposed to SARS-Cov-2 during pregnancy, and a control group of unexposed babies in a low-income area in Northeastern Brazil. All data were prospectively collected from medical records. Children’s neurodevelopment was assessed using the guide for Monitoring Child Development in the IMCI context and the Ages & Stages Questionnaire (ASQ-3), at ages 4, 6, and 12 months. Maternal depressive symptoms were assessed using the Edinburgh Postnatal Depression Scale (EPDS). Results We followed 127 children for one year, 69 children in the COVID-19 exposed Group (EG), and 68 in the control group (CG). All mothers were unvaccinated at the time included in the cohort. Maternal demographics were similar in the two groups, but prematurity was more prevalent in mothers infected with COVID-19 (21.7% vs. 8.8%, p = .036) and EPDS scores were also significantly higher among the EG ( M =  11.00, SD =  6.00 vs. M =  8.68, SD =  4.72, p =  0.04). Both groups had similar rates of cesarean delivery, Apgar scores, average birth weight, head circumference and length at birth. 20.3% of EG children and 5.9% of the CG received a diagnosis of neurodevelopmental delay within 12 months of life (p = 0.013, RR = 3.44; 95% CI, 1.19–9.95). 10% of EG children presented abnormalities at the cranial ultrasound. Conclusions COVID-19 exposure was associated with neurodevelopmental impairment. This study highlights the importance of specific guidelines in the follow-up of children exposed to in-utero SARS-CoV-2 in order to mitigate or prevent long-term effects on children’s health.

The Americas, particularly Brazil, were greatly impacted by the widespread outbreak of Zika virus (ZIKV) in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We perform a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA and Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus.

ABSTRACT Toehold switches are biosensors useful for the detection of endogenous and environmental RNAs. They have been engineered to detect virus RNAs in cell-free gene expression reactions. Their inherent sequence programmability makes engineering a fast and predictable process. Despite improvements in the design, toehold switches suffer from leaky translation in the OFF state, which compromises the fold change and sensitivity of the biosensor. To address this, we constructed and tested signal amplification circuits for three toehold switches triggered by Dengue and Sars-CoV-2 RNAs and an artificial RNA. The serine integrase circuit efficientl contained leakage, boosted the expression fold-change from OFF to ON, and decreased the detection limit of the switches by three to four orders of magnitude. Ultimately, the integrase circuit converted the analog switches’ signals into digital-like output. The circuit is broadly useful for biosensors and eliminates the hard work of designing and testing multiple switches to find the best possible performer. GRAPHICAL ABSTRACT

In order to recover from infection, organisms must balance robust immune responses to pathogens with the tolerance of immune-mediated pathology. This balance is particularly critical within the central nervous system, whose complex architecture, essential function, and limited capacity for self-renewal render it susceptible to both pathogen-and immune-mediated pathology. Here, we identify the alarmin IL-33 and its receptor ST2 as critical for host survival to neuroinvasive flavivirus infection. We identify oligodendrocytes as the critical source of IL-33, and microglia as the key cellular responders. Notably, we find that the IL-33/ST2 axis does not impact viral control or adaptive immune responses; rather, it is required to promote the activation and survival of microglia. In the absence of intact IL-33/ST2 signaling in the brain, neuroinvasive flavivirus infection triggered aberrant recruitment of monocyte-derived peripheral immune cells, increased neuronal stress, and neuronal cell death, effects that compromised organismal survival. These findings identify IL-33 as a critical mediator of CNS tolerance to pathogen-initiated immunity and inflammation. Author Summary The central nervous system (CNS) is an extraordinarily complex organ system with limited capacity for repair and renewal. When infectious pathogens invade the CNS, resulting immune responses must clear the pathogen while limiting immune-mediated tissue pathology. IL-33 is an “alarmin” cytokine, whose release from dying cells can promote a variety of immune responses. IL-33 is expressed at high levels in the brain, and previous work has implicated signaling by IL-33 in CNS development as well as in the response to parasitic infection of the CNS. Here, we identify IL-33 as a key mediator of disease tolerance in the context of neuroinvasive infection with the flaviviruses West Nile virus and Zika virus. Notably, we find that IL-33 signaling is not involved in the clearance of virus from the brain; rather, IL-33 is required to promote the survival and reprogramming brain-resident immune cells (microglia). When IL-33 signaling is disrupted in mice, flavivirus infection results in defective microglial activation, increased death of both microglia and neurons, increased invasion of the brain by peripheral immune cells, and increased host death. This work suggests that IL-33 is a key mediator of host tolerance upon neuroinvasive flavivirus infection.