Zika virus (ZIKV) outbreaks in Central and South America caused severe public health problems in 2015 and 2016. These outbreaks were finally contained through several methods, including mosquito control using insecticides and repellents. Additionally, the development of herd immunity in these countries might have contributed to containing the epidemic. While ZIKV is mainly transmitted by mosquito bites, mucosal transmission via bodily fluids, including the semen of infected individuals, has also been reported. We evaluated the effect of mucosal ZIKV infection on continuous subcutaneous challenges in a cynomolgus monkey model. Repeated intravaginal inoculations of ZIKV did not induce detectable viremia or clinical symptoms, and all animals developed a potent neutralizing antibody, protecting animals from the subsequent subcutaneous superchallenge. These results suggest that viral replication at mucosal sites can induce protective immunity without causing systemic viremia or symptoms.

Informed consent (IC) is key to generating and maintaining research participants’ trust and upholding the ethical principle of autonomy. Broad consent for future use, wherein researchers ask participants for permission to share participant-level data and samples collected within the study for purposes loosely related to the study objectives, is central to enabling ethical data and sample reuse. Ensuring that participants understand broad consent-related language is key in maintaining trust in the study itself and in public health research generally. Therefore, we conducted 52 cognitive interviews with the help of semi-structured interview guides to explore cohort research participants’ understanding of the broad consent-related language in the University of California at Berkeley template IC form for biomedical research with participants from long-standing infectious disease cohort studies in Nicaragua and Colombia. After the first round of interviews, we used participants’ explanations to modify the broad consent-related language in the IC template and consequently re-evaluated participants’ understanding of and agreement with the new consent form. Participants generally supported data and sample sharing but expressed concerns about the intentions of for-profit groups as well as misuse of data or samples. Moreover, they felt uncomfortable not receiving information about incidental findings and results from future studies. Cohort participants did not understand abstract concepts including the collection and reuse of genetic data in either version of the IC. Trust in the research team and the belief that data and sample sharing could lead to new scientific insights and improved treatments were key to participant support for data and sample sharing. The study findings and research participants’ language to describe broad consent provide essential insights for researchers who want to include broad consent and ethics review committees (ERCs) working to ensure research is conducted in keeping with the ethical principle of respect for persons. Author Summary This is the first study to apply cognitive interviewing to evaluate participants’ understanding of broad consent. We found that cohort participants did not well understand the broad consent-related language in the UCB template IC. When broad consent was reworded with language from the community, difficult to process concepts, like genetic studies, were better understood. Many ethics review committees (ERCs) and universities require researchers to use a template when consenting participants for participation in biomedical research. Our finding that key concepts in the broad consent section of the template, including genetic studies and sample collection, were not well understood suggests that ERCs must allow researchers flexibility to alter IC template language to ensure participant understanding. While, like many ERCs, the University of California at Berkeley (UCB) recommends that researchers not communicate incidental findings, participants did not understand that incidental findings would not be shared and universally wanted to learn about incidental findings. Participants generally believed in the utility of data and sample reuse but expressed concerns about reuse by commercial groups and wanted to better understand who and what the future users were. Participants did not mention privacy as a concern in data and sample sharing. Informing participants about incidental findings and future uses and users is an important part of maintaining trust in data and sample sharing.

The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.

The Zika virus (VZIK) is a Flavivirus of the Flaviviridae family. With the ability to infect neural progenitor cells, microcephaly is the most serious and irreversible neurological complication associated with ZIKV. In this work, we evaluated the mRNA expression of cytokines involved in the inflammatory process that occurred during Zika virus infection in Mesocricetus auratus . The samples came from the real tissue of animals infected through sexual transmission and comprising 3 different groups of animals (TS-01, TS-02 and ZP-01).The project started with the extraction of viral RNA and mRNA from the kidneys of ZIKV-infected animals. After this step, RT-qPCR was carried out to quantify both the viral load and the expression of cytokines associated with the inflammatory process that occurred during the ZIKV infection. As can be seen in our results, this work corroborates different studies that demonstrate that ZIKV can infect and cause an inflammatory response to the kidneys, even causing a high viral load.

SARS-CoV2 is a positive-strand RNA virus in the Coronaviridae family that has caused world-wide morbidity and mortality. While much progress has been made we still need expanded rapid anti-virals. The top advanced antiviral candidates all target stages of RNA replication, leaving virus assembly an unexplored avenue of antiviral research. To address this gap, and explore the biochemical and cell biological features of viral assembly, we have employed an improved virus-like particle (VLP) system. We exploited the small nanoLuciferase protein for enhanced signal and surprisingly found that the protein itself appears to be packaged into both SARS CoV2 VLPs and virions and secreted from cells. Interestingly, nLuc is not co-secreted with dengue or Zika infection, suggesting the large virion of Coronavirus can encaspidate and secrete a cellularly expressed reporter protein. Our findings open the way for powerful new approaches to measure viral particle production, egress and viral entry mechanisms.

Most of the cholesterol in the plasma membranes (PMs) of animal cells is sequestered through interactions with phospholipids and transmembrane domains of proteins. However, as cholesterol concentration rises above the PM’s sequestration capacity, a new pool of cholesterol, called accessible cholesterol, emerges. The transport of accessible cholesterol between the PM and the endoplasmic reticulum (ER) is critical to maintain cholesterol homeostasis. This pathway has also been implicated in the suppression of both bacterial and viral pathogens by immunomodulatory oxysterols. Here, we describe a mechanism of depletion of accessible cholesterol from PMs by the oxysterol 25-hydroxycholesterol (25HC). We show that 25HC-mediated activation of acyl coenzyme A: cholesterol acyltransferase (ACAT) in the ER creates an imbalance in the equilibrium distribution of accessible cholesterol between the ER and PM. This imbalance triggers the rapid internalization of accessible cholesterol from the PM, which is sustained for long periods of time through 25HC-mediated suppression of SREBPs. In support of a physiological role for this mechanism, 25HC failed to suppress Zika virus and human coronavirus infection in ACAT-deficient cells, and Listeria monocytogenes infection in ACAT-deficient cells and mice. We propose that selective depletion of accessible PM cholesterol triggered by ACAT activation and sustained through SREBP suppression underpins the immunological activities of 25HC and a functionally related class of oxysterols.

Zika virus (ZIKV), an arbovirus transmitted by mosquitoes, was identified as a cause of congenital disease during a major outbreak in the Americas in 2016. Vaccine design strategies relied on limited available isolate sequence information due to the rapid response necessary. The first-generation ZIKV mRNA vaccine, mRNA-1325, was initially generated and, as additional strain sequences became available, a second mRNA vaccine, mRNA-1893, was developed. Herein, we compared the immune responses following mRNA-1325 and mRNA-1893 vaccination and reported that mRNA-1893 generated comparable neutralizing antibody titers to mRNA-1325 at 1/20 th of the dose and provided complete protection from ZIKV challenge in non-human primates. In depth characterization of these vaccines indicated that the observed immunologic differences could be attributed to a single amino acid residue difference that compromised mRNA-1325 virus-like particle formation.

This paper aims to develop a hybrid method for emergency decision making (EDM) by combining the best-worst method (BWM), multi-attributive border approximation area comparison (MABAC) and prospect theory (PT) in trapezoidal interval type-2 fuzzy rough (TrIT2FR) environment. In this hybrid method, the decision information is represented by trapezoidal interval type-2 fuzzy rough numbers (TrIT2FRNs). Firstly, this paper gives the definition of TrIT2FRN and analyzes its desirable properties. Then, the TrIT2FR-BWM is developed to determine criteria weights. In the development of the TrIT2FR-BWM, this paper completes the following three core issues: (i) propose an effective theorem to normalize the TrIT2FR weights; (ii) build a crisp mathematical programming model to transform the minmax objective of weight-determining model for the TrIT2FR-BWM; (iii) design a consistency ratio for the TrIT2FR-BWM to check the reliability of the determined criteria weights. Afterwards, this paper extends the classical MABAC into TrIT2FR environment to calculate the border approximation area (BAA). Subsequently, the PT is used to rank the alternatives, in which the calculated BAA is selected as the reference point. Lastly, the validity of the proposed method is certificated with a real site selection case of makeshift hospitals on COVID-19. Sensitivity analysis and comparative analyses are conducted to illustrate the robustness and superiorities of the proposed method.

Monkeypox is an emerging, rapidly spreading disease with pandemic potential. It is caused by the monkeypox virus (MPXV), a dsDNA virus from the Poxviridae family, that replicates in the cytoplasm and must encode for its own RNA processing machinery including the capping machinery. Here, we present the crystal structure of its 2′-O-RNA methyltransferase (MTase) VP39 in complex with the pan-MTase inhibitor sinefungin. A comparison of this 2′-O RNA MTase with enzymes from unrelated ssRNA viruses (SARS-CoV-2 and Zika) reveals a surprisingly conserved sinefungin binding mode implicating that a single inhibitor could be used against unrelated viral families.

Being able to train Named Entity Recognition (NER) models for emerging topics is crucial for many real-world applications especially in the medical domain where new topics are continuously evolving out of the scope of existing models and datasets. For a realistic evaluation setup, we introduce a novel COVID-19 news NER dataset (COVIDNEWS-NER) and release 3000 entries of hand annotated strongly labelled sentences and 13000 auto-generated weakly labelled sentences. Besides the dataset, we propose CONTROSTER, a recipe to strategically combine weak and strong labels in improving NER in an emerging topic through transfer learning. We show the effectiveness of CONTROSTER on COVIDNEWS-NER while providing analysis on combining weak and strong labels for training. Our key findings are: (1) Using weak data to formulate an initial backbone before tuning on strong data outperforms methods trained on only strong or weak data. (2) A combination of out-of-domain and in-domain weak label training is crucial and can overcome saturation when being training on weak labels from a single source.

After severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) made the world tremble with a global pandemic, SARS-CoV2 vaccines were developed. However, due to the coronavirus’s intrinsic nature, new variants emerged, such as Delta and Omicron, refractory to the vaccines derived using the original Wuhan strain. We developed an HERV-enveloped recombinant baculoviral DNA vaccine against SARS-CoV2 (AcHERV-COVID19S). A non-replicating recombinant baculovirus that delivers the SARS-CoV2 spike gene showed a protective effect against the homologous challenge in a K18-hACE2 Tg mice model; however, it offered only a 50% survival rate against the SARS-CoV2 Delta variant. Therefore, we further developed the AcHERV-COVID19 Delta vaccine (AcHERV-COVID19D). Cross-protection experiments revealed that mice vaccinated with the AcHERV-COVID19D showed 100% survival upon challenge with Delta and Omicron variants and 71.4% survival against prototype SARS-CoV2. These results support the potential of the viral vector vaccine, AcHERV-COVID19D, in preventing the spread of coronavirus variants such as Omicron and SARS-CoV2 variants. Author Summary After the SARS-CoV2 pandemic, it is known that the existing vaccine has diminished efficacy against the emerging variants. We developed a baculoviral COVID19 DNA vaccine for the Delta variant (AcHERV-COVIS19D). Compared to AcHERV-COVID19S, designed to protect from the prototype of SARS-CoV2, AcHERV-COVID19D elicited higher humoral and cellular immunity and showed perfect protection against SARS-CoV2 delta strain and Omicron challenge. The broad and robust cellular immunity of the AcHERV-COVID19D vaccine appears to have played a significant role in the cross-protection of the Omicron variant. Our AcHERV-COVID19D can be a potential vaccine against emerging SARS-CoV2 variants.

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed the world’s unpreparedness to deal with the emergence of novel pathogenic viruses, pointing to the urgent need to identify targets for broad-spectrum antiviral strategies. Here, we report that proteins encoded by Minor Intron-containing Genes (MIGs) are significantly enriched in datasets of cellular proteins that are leveraged by SARS-CoV-2 and other viruses. Pointing to a general gateway for viruses to tap cellular machinery, MIG-encoded proteins (MIG-Ps) that react to the disruption of the minor spliceosome are most important points of viral attack, suggesting that MIG-Ps may pan-viral drug targets. While contemporary anti-viral drugs shun MIG-Ps, we surprisingly found that anti-cancer drugs that have been repurposed to combat SARS-CoV-2, indeed target MIG-Ps, suggesting that such genes can potentially be tapped to efficiently fight viruses.

ABSTRACT Zika virus (ZIKV) is a mosquito-borne flavivirus that causes neurological disorders and microcephaly. Recent research has shown that ZIKV causes cell cycle arrest and DNA damage response in neuronal progenitor cells that potentially leads to congenital neurodevelopmental defects. However, the specific role of regulators that control DNA damage response to ZIKV infection and the related mechanisms remain largely unknown. Here through both in vitro and in vivo studies, we observe that ZIKV induces DNA damage response in both human cell line and mouse embryo. When CHK2 dependent DNA damage response pathway is inhibited by a small molecule inhibitor or genetic deletion, ZIKV production is reduced and the embryonic developmental defects are rescued. Furthermore, we demonstrate that in ZIKV infected Chk2-/- mice, the reduced viral load correlates with elevated antiviral innate immune response which is found to be dependent on the STING signaling pathway. Collectively, our study reveals a specific role of CHK2 for ZIKV infection and pathogenesis, demonstrating a mechanism that inhibition of the CHK2 axis suppresses ZIKV infection through the STING-dependent antiviral pathway, thus providing a new therapeutic strategy against ZIKV. These findings also suggest the intriguing possibility that ZIKV evolved to orchestrate DNA damage response factors to create a beneficial environment for its infection in the host cells.

A detailed understanding of host fitness changes upon variation in microbe density is a central aim of infection biology. Here, we applied dose-response curves to study Aedes aegypti survival upon exposure to different microbes. We challenged female mosquitoes with Listeria monocytogenes , a model bacterial pathogen, Dengue 4 virus and Zika virus, two medically relevant arboviruses, to understand the distribution of mosquito susceptibility and net fitness (survival) following microbe exposure. By correlating microbe loads and host health, we found that a blood meal promotes survival in our systemic bacterial infection model and that mosquitoes orally infected with bacteria had an enhanced defensive capacity than insects infected through injection. We also showed that Aedes aegypti has a higher survival profile upon arbovirus infection but, under the conditions tested, was more susceptible to Zika virus when compared to Dengue virus. Here, we applied a framework for the study of microbe-induced mosquito mortality detailing how Aedes aegypti lifespan varies upon different inoculum sizes of bacteria and arboviruses.

The study was conducted to assess the impact of macro factors on economic growth in emerging and growth-leading economies (EAGLEs) during the COVID-19 pandemic. The study applied a Bayesian simulation method, and the empirical results exhibited an ambiguous impact of trade openness and the number of internet users on economic growth in these countries during the COVID-19 outbreak. Besides, in response to the economic downturn caused by the COVID-19 pandemic, countries have loosened monetary and fiscal policies simultaneously. However, policy rate reduction was found to be less efficient in the countries previously applying low-interest rates. The evidence showed that reasonable pandemic control measures formed a basis for fastening economic recovery.

Background: Coronavirus disease 2019 (COVID-19) pandemic is still raging worldwide, while the treatment of human coronaviruses (HCoVs) infections remains limited. Qingfeipaidu decoction (QFPDD), formulated by four classical prescriptions, was the most widely used prescription for COVID-19 containment and exhibited positive effects in China. As one critical prescription in QFPDD, Xiaochaihu decoction (XCHD) could relieve the symptoms of fever, fatigue, anorexia, sore throat in TCM theory. To explore the role and mechanisms of XCHD against HCoVs, we presented an integrated systems pharmacology framework in this study. Methods We constructed a global herb-compound-target network of XCHD against HCoVs. Subsequently, multi-level systems pharmacology analyses highlighted the key regulatory proteins of XCHD, and revealed that XCHD may affect multiple biological functions related to HCoVs. We further applied network-based prediction, drug-likeness analysis, combined with literature investigation to uncover the key ani-HCoV constituents in XCHD, while in vitro HCoV-229E virus-induced cytopathic effect assay was carried out to verify our prediction. Finally, we proposed molecular mechanism hypothesis for these compounds against HCoVs via subnetwork analysis. Results Based on the systems pharmacology framework, we identified 163 XCHD constituents connecting to 37 HCoV-associated genes. And an integrated pathway comprising TLR signaling pathway, RIG-1-like receptor signaling pathway, cytoplasmic DNA sensing pathway, and IL-6/STAT3 pro-inflammatory signal transduction axis was further proposed, revealing the mechanism of action of XCHD against HCoVs. Through in vitro assay, several constituents (e.g. betulinic acid, chrysin, isoliquiritigenin, schisandrin B, and (20R)-Ginsenoside Rh1) in XCHD exerted good inhibitory activity against HCoV-229E virus. Conclusion Our work presented a comprehensive systems pharmacology approach to explore the molecular mechanism and effective substances of XCHD against HCoVs.

Bat-borne emerging zoonotic viruses cause major outbreaks, such as the Ebola virus, Nipah virus, severe acute respiratory syndrome (SARS) coronavirus, and SARS-CoV-2. Pteropine orthoreovirus (PRV), which spillover event occurred from fruit bats to humans, causes respiratory syndrome in humans widely in South East Asia. Repurposing approved drugs against PRV is a critical tool to confront future PRV pandemics. We screened 2,943 compounds in an FDA-approved drug library and identified eight hit compounds that reduce viral cytopathic effects on cultured Vero cells. Real-time quantitative PCR analysis revealed that six of eight hit compounds significantly inhibited PRV replication. Among them, micafungin used clinically as an antifungal drug, displayed a prominent antiviral effect on PRV. Highlights A library of 2,943 FDA-approved drugs was screened to find potential antiviral drugs of Pteropine orthoreovirus. Six hit compounds dramatically inhibited viral replication in vitro . Micafungin possessed antiviral activity to multiple strains of PRV.

A bstract SARS-CoV-2, the causative agent of covid-19, is known to exhibit secondary structure in its 5’ and 3’ untranslated regions, along with the frameshifting stimulatory element situated between ORF1a and 1b. To identify further regions containing conserved structure, multiple sequence alignment with related coronaviruses was used as a starting point from which to apply a modified computational pipeline developed to identify non-coding RNA elements in vertebrate eukaryotes. Three different RNA structural prediction approaches were employed in this modified pipeline. Forty genomic regions deemed likely to harbour structure were identified, ten of which exhibited three-way consensus substructure predictions amongst our predictive utilities. Intracomparison of the pipeline’s predictive utilities, along with intercomparison with three previously published SARS-CoV-2 structural datasets, were performed. Limited agreement as to precise structure was observed, although different approaches appear to agree upon regions likely to contain structure in the viral genome.

The consequences of Zika virus (ZIKV) infections were limited to sporadic mild diseases until almost a decade ago, when epidemics outbreaks took place and were followed by virus introduction and quick spread into the Americas. Simultaneously, novel severe neurological manifestations for ZIKV infections were identified, including congenital microcephaly. However, the complete understanding of why the epidemic strains behave differently from previously circulating variants is still missed and many questions still remain about the actual significance of ZIKV genetic variations in the epidemiology and biology of ZIKV. Here, we attained to analyze a high number of sequences to identify genes with different levels of variability and patterns of genomic variations that could be associated with ZIKV diversity. We compared numerous epidemic strains with the pre-epidemic ones from both the Asian and the African lineages, while we also investigated special variations among the epidemic ZIKV strains derived from microcephaly cases. We identified several viral genes with dissimilar mutation rates among the ZIKV strain groups. Moreover, we found novel protein variation profiles that might be associated with the epidemiological particularities of each category of ZIKV strains. Finally, we assessed the impact of the detected changes on the structure and stability of the corresponding viral proteins, finding some interesting non synonymous variations which could help to explain the heterogeneous features among the diverse ZIKA strains. Altogether, this work contributes to identify ZIKV genetic variations that might have a phenotypical impact, as a basis for future experimental analysis to elucidate the recent ZIKV emergency.

Abstract: It is assumed that upon SARS-CoV-2 infection granulocytes can undergo potentially destructive oxidative burst. Therefore, the aim of this study was to evaluate some parameters of redox and inflammatory signaling in granulocytes of recovered and of deceased COVID-19 pa-tients. Granulocytes were isolated from the blood of 32 COVID-19 patients on admission to the hospital (16 survived and 16 died within a week). The levels of proteins (immunoassay), eico-sanoids (UPLC-MS) and antioxidants activity (spectrophotometry) were examined. Enhanced activation of Nrf2 and NFκB and the levels of heme oxygenase and proinflammatory cytokines where found in granulocytes of all COVID-19 patients, while Cu,Zn-SOD and Mn-SOD activities were decreased, especially in deceased patients. Moreover, in patients who died increased levels of pro-inflammatory eicosanoids (PGE2 and TXB2) and decreased of anti-inflammatory (15d-PGJ2 and 5-HETE) were observed. However TXB2 was decreased, and IL-2 and IL-10 levels were in-creased in survivors, if compared both to healthy subjects and deceased patients, who did not change their cytokine generation. Therefore, it seems that by triggering transcription factors granulocytes activate redox signaling, leading to the production of pro-inflammatory eicosanoids, while reducing cellular antioxidant capacity via SOD, they express altered response to COVID-19, which might result in the onset of the vicious cycle of systemic oxidative stress in deceased patients.

Background CRISPR-Cas based diagnostic assays provide a portable solution which bridges the benefits of qRT-PCR and serological assays in terms of portability, specificity and ease of use. CRISPR-Cas assays are rapidly fieldable, specific and have been rigorously validated against a number of targets, including HIV and vector-borne pathogens. Recently, CRISPR-Cas12 and CRISPR-Cas13 diagnostic assays have been granted FDA approval for the detection of SARS-CoV-2. A critical step in utilizing this technology requires the design of highly-specific and efficient CRISPR RNAs (crRNAs) and isothermal primers. This process involves intensive manual curation and stringent parameters for design in order to minimize off-target detection while also preserving detection across divergent strains. As such, a single, streamlined bioinformatics platform for rapidly designing crRNAs for use with the CRISPR-Cas12 platform is needed. Here we offer PrimedSherlock, an automated, computer guided process for selecting highly-specific crRNAs and primers for targets of interest. Results Utilizing PrimedSherlock and publicly available databases, crRNAs were designed against a selection of Flavivirus genomes, including West Nile, Zika and all four serotypes of Dengue. Using outputs from PrimedSherlock in concert with both wildtype A.s Cas12a and Alt-R Cas12a Ultra nucleases, we demonstrated sensitive detection of nucleic acids of each respective arbovirus in in-vitro fluorescence assays. Moreover, primer and crRNA combinations facilitated the detection of their intended targets with minimal off-target background noise. Conclusions PrimedSherlock is a novel crRNA design tool, specific for CRISPR-Cas12 diagnostic platforms. It allows for the rapid identification of highly conserved crRNA targets from user-provided primer pairs or PrimedRPA output files. Initial testing of crRNAs against arboviruses of medical importance demonstrated a robust ability to distinguish multiple strains by exploiting polymorphisms within otherwise highly conserved genomic regions. As a freely-accessible software package, PrimedSherlock could significantly increase the efficiency of CRISPR-Cas12 diagnostics. Conceptually, the portability of detection kits could also be enhanced when coupled with isothermal amplification technologies.

Summary Zika virus (ZIKV) is an arthopod-vectored flavivirus that disseminates from the infection site into peripheral tissues, where it can elicit virus-induced pathology. To move through the body, ZIKV is thought to exploit the mobility of myeloid cells, in particular monocytes and dendritic cells. However, multiple distinct steps during viral spread culminate in peripheral tissue infection, and the timing and mechanisms underlying mobile immune cell shuttling of virus remain unclear. To understand the very early steps in ZIKV dissemination from the skin, we kinetically and spatially mapped ZIKV-infected lymph nodes (LNs), an intermediary stop en route to the blood. Contrary to dogma, migratory immune cells were not required for large quantities of virus to reach the LN or blood. Instead, ZIKV rapidly infected a subset of immobile macrophages in the LN, which shed virus through the lymphatic pathway into the blood. Importantly, infection of LN macrophages alone was sufficient to initiate viremia. Together, our studies indicate that sessile macrophages that live and die in the LN contribute to initial ZIKV spread to the blood. These data build a more complete picture of ZIKV movement through the body and identify an alternate anatomical site for potential antiviral intervention. Highlights ZIKV infects and replicates in distinct LN macrophage populations LN macrophage infection results in infectious virus in the blood Virus reaches the blood in the absence of DC migration or monocyte infection Nodal macrophage infection does not sustain viremia or induce morbidity Graphical abstract Caption: ZIKV infects lymph node macrophages, which shed infectious virus into the lymph and then blood.

Oxysterols (i.e., oxidized cholesterol species) have complex roles in biology. 25-hydroxycholesterol (25HC), a product of activity of cholesterol-25-hydroxylase (CH25H) upon cholesterol, has recently been shown to be broadly antiviral, suggesting therapeutic potential against SARS-CoV-2. However, 25HC can also amplify inflammation and tissue injury and be converted by CYP7B1 to 7α,25HC, a lipid with chemoattractant activity via the G protein-coupled receptor, EBI2/GPR183. Here, using in vitro studies and two different murine models of SARS-CoV-2 infection, we investigate the effects of these two oxysterols on SARS-CoV-2 pneumonia. We show that while 25HC and enantiomeric-25HC are antiviral in vitro against human endemic coronavirus-229E, they did not inhibit SARS-CoV-2; nor did supplemental 25HC reduce pulmonary SARS-CoV-2 titers in the K18-human ACE2 mouse model in vivo . 25HC treatment also did not alter immune cell influx into the airway, airspace cytokines, lung pathology, weight loss, symptoms, or survival but was associated with increased airspace albumin, an indicator of microvascular injury, and increased plasma pro-inflammatory cytokines. Conversely, mice treated with the EBI2/GPR183 inhibitor NIBR189 displayed a modest increase in lung viral load only at late time points, but no change in weight loss. Consistent with these findings, although Ch25h was upregulated in the lungs of SARS-CoV-2-infected WT mice, lung viral titers and weight loss in Ch25h −/– and Gpr183 −/– mice infected with the beta variant were similar to control animals. Taken together, endogenous 25-hydroxycholesterols do not significantly regulate early SARS-CoV-2 replication or pathogenesis and supplemental 25HC may have pro-injury rather than therapeutic effects in SARS-CoV-2 pneumonia.

Abstract The full text of this preprint has been withdrawn by Resarch Square. Please do not cite this preprint as it contains ethical issues with infringement of the author list and conflict of interest.

Since the outbreak of the COVID-19 pandemic, the rapid development of new drug candidates has been demanded. To satisfy such demand, various deep generative models have been applied to drug generation techniques, and recurrent neural networks (RNNs) based models have achieved the state-of-the-art performance. Since the RNNs architecture suffers from the long-term dependency problem, recently Transformer-based models have been proposed to address the problem with the self-attention mechanism. However, the Transformer models showed worse performance than the RNNs models in the drug generation task, and we believe it is because the Transformer model is over-parameterized with the over-fitting problem. In this paper, we propose to replace the large decoder with simple feed-forward layers to avoid the problem. In our experiments, we demonstrate that our proposed model outperforms the previous state-of-the-art baseline in major evaluation metrics while preserving other minor metrics with a similar level of performance. Furthermore, when we apply our models to generate candidate molecules against the SARs-CoV-2 (COVID-19) virus, the generated molecules are more effective than the drugs in commercial market like Paxlovid, Molnupiravir, and Remdesivir.