Infection by SARS-CoV-2 leads to diverse symptoms, which can persist for months. While antiviral antibodies are protective, those targeting interferons and other immune factors are associated with adverse COVID-19 outcomes. Instead, we discovered that antibodies against specific chemokines are omnipresent after COVID-19, associated with favorable disease, and predictive of lack of long COVID symptoms at one year post infection. Anti-chemokine antibodies are present also in HIV-1 infection and autoimmune disorders, but they target different chemokines than those in COVID-19. Monoclonal antibodies derived from COVID- 19 convalescents that bind to the chemokine N-loop impair cell migration. Given the role of chemokines in orchestrating immune cell trafficking, naturally arising anti-chemokine antibodies associated with favorable COVID-19 may be beneficial by modulating the inflammatory response and thus bear therapeutic potential. One-Sentence Summary: Naturally arising anti-chemokine antibodies associate with favorable COVID-19 and predict lack of long COVID.

Objectives Identify the association between maternal SARS-CoV-2 infection in pregnancy and individual neonatal morbidities and outcomes, particularly longer-term outcomes such as neurodevelopment. Setting Case-control and cohort studies from any location published after 1st January 2020, including pre-print articles. Participants Neonates born to pregnant women diagnosed with a SARS-CoV-2 infection at any stage during pregnancy, including asymptomatic women. Primary and secondary outcome measures Neonatal mortality and morbidity, including preterm birth, Caesarean delivery, small for gestational age, admission to neonatal intensive care unit, level of respiratory support required, diagnosis of culture-positive sepsis, evidence of brain injury, necrotising enterocolitis, visual or hearing impairment, neurodevelopmental outcomes, and feeding method. These outcomes were selected according to a Core Outcome Set developed between health professionals, researchers and parents. Results The search returned 3234 papers, from which 204 were included with a total of 45,646 infants born to mothers with SARS-CoV-2 infection during pregnancy across 36 countries. We found limited evidence of an increased risk of some neonatal morbidities, including respiratory disease. There was minimal evidence from low-income settings (1 study) and for neonatal outcomes following first trimester infection (17 studies). Neonatal mortality was very rare. Preterm birth, neonatal unit admission and small for gestational age status were more common in infants born following maternal SARS-CoV-2 infection in pregnancy in most larger studies. Conclusions There is limited data on neonatal morbidity and mortality following maternal SARS-CoV-2 infection in pregnancy, particularly from low-income countries and following early pregnancy infections. Large, representative studies addressing these outcomes are needed to better understand the consequences for babies born to women with SARS-CoV-2 in pregnancy. Trial registration PROSPERO ID: CRD42021249818 Strengths and limitations Inclusion of studies of both asymptomatic and symptomatic SARS-CoV-2 infections at any point in pregnancy to maximise generalisability of findings Focus on neonatal outcomes, as opposed to purely obstetric outcomes, to accurately quantify neonatal morbidity Study is limited by available data; important data gap in low-income settings

Background: People with SARS-CoV-2 infection during pregnancy are at increased risk for adverse pregnancy outcomes, such as preterm birth and stillbirth. Few studies have assessed whether the risk of adverse pregnancy and infant outcomes varies by trimester of infection. Objectives: We describe clinical characteristics (i.e., treatment among pregnant people with moderate to critical illness) and pregnancy and infant outcomes in pregnant people with laboratory-confirmed SARS-CoV-2 infection by trimester of infection. Study Design: The Surveillance for Emerging Threats to Mothers and Babies Network (SET-NET) collects longitudinal data on people with confirmed SARS-CoV-2 infection during pregnancy and their infants. This analysis included people reported to SET-NET with infection in 2020, with known timing of infection and pregnancy outcome. Outcomes are described by trimester of infection. Pregnancy outcomes examined were live birth and pregnancy loss (<20 weeks gestation and ≥20 weeks gestation). Infant outcomes included preterm birth (<37 weeks gestation), small for gestational age (SGA), birth defects, and neonatal intensive care unit (NICU) admission. Adjusted prevalence ratios (aPR) were calculated for pregnancy and selected infant outcomes by trimester of infection, controlling for age, race/ethnicity and health insurance. Among those with moderate-to-critical COVID-19 illness, demographic and clinical characteristics of pregnant people by COVID-19 specific treatment status were described. Results: : Among 44,914 people with SARS-CoV-2 infection in pregnancy, 35,200 (78.3%) people with known timing of infection and pregnancy outcome were included. There were 35,574 liveborn infants and 193 pregnancy losses (<20 weeks (n=52) and ≥20 weeks (n=141)) reported. Half (50.8%) of pregnant people had infection in the third trimester, 30.8% in the second, and 18.3% in the first. Third trimester infection was associated with a higher frequency of preterm birth compared to first or second trimester infection combined (17.8% vs. 11.8%; aPR 1.44 95% CI: 1.35-1.54). For term infants, those born to people with third trimester infection were more likely to be admitted to the NICU compared to those born to people with first or second trimester infections (6.7% vs. 4.5%, aPR 1.29, 95% CI: 1.16-1.36). Approximately five percent of infants were born SGA, with a higher frequency among infants born to people with third trimester infection (aPR 1.16, 95% CI: 1.06-1.27). Prevalence of birth defects was 553.4/10,000 live births, with no difference by trimester of infection. Of 1,732 pregnant people with moderate-to-critical illness, 24.4% (422 cases) were reported to have received any treatment, with 15.3% (265) receiving COVID-19 specific treatment. The most common COVID-19 treatments were remdesivir (57.0%), dexamethasone (45.8%), and azithromycin with hydroxychloroquine (15.4%). Conclusions: : There were no signals for increased birth defects or SGA among infants in this population relative to national baseline estimates, regardless of timing of infection. However, the prevalence of preterm birth in people with SARS-CoV-2 infection in pregnancy in our analysis was higher relative to national baseline data (10.0-10.2%), particularly among people with third trimester infection. Consequences of COVID-19 during pregnancy, including preterm birth, support recommended COVID-19 prevention strategies, including vaccination for people who are pregnant or may become pregnant. The findings in this report further highlight gaps in COVID-19 treatment for pregnant people.

During the course of the 2015-2017 outbreak of Zika virus (ZIKV) infection in the Americas, the emerging virus was recognized as a congenital infection that could damage the developing brain. As the Latin American ZIKV outbreak advanced, the scientific and public health community questioned if this newly recognized neurotropic flavivirus could affect the developing brain of infants and young children infected after birth. We report here the design, methods and rapid operationalization of a prospective natural history cohort study aimed at evaluating the potential neurological and neurodevelopmental effects of postnatal Zika virus infection in infants and young children, which had become epidemic in Central America. This study enrolled a cohort of 500 mothers and their infants, along with nearly 400 children 1.5-3.5 years of age who were born during the initial phase of the ZIKV epidemic in a rural area of Guatemala. Our solutions and lessons learned while tackling real-life challenges may serve as a guide to other researchers carrying out studies of emerging infectious diseases of public health priority in resource-constrained settings.

Background Congenital Zika virus (ZIKV) infection can result in birth defects, including malformations in the fetal brain and visual system. There are two distinct genetic lineages of ZIKV: African and Asian. Asian lineage ZIKVs have been associated with adverse pregnancy outcomes in humans; however, recent evidence from experimental models suggests that African-lineage viruses can also be vertically transmitted and cause fetal harm. Methodology/Principal Findings To evaluate the potential for vertical transmission of African-lineage ZIKV, we inoculated nine pregnant rhesus macaques ( Macaca mulatta ) subcutaneously with 44 plaque- forming units of a ZIKV strain from Senegal, (ZIKV-DAK). Dams were inoculated either at gestational day 30 or 45. Following maternal inoculation, pregnancies were surgically terminated seven or 14 days later and fetal and maternal-fetal interface tissues were collected and evaluated. Infection in the dams was evaluated via plasma viremia and neutralizing antibody titers pre- and post- ZIKV inoculation. All dams became productively infected and developed strong neutralizing antibody responses. ZIKV RNA was detected in maternal-fetal interface tissues (placenta, decidua, and fetal membranes) by RT-qPCR and in situ hybridization. In situ hybridization detected ZIKV predominantly in the decidua and revealed that the fetal membranes may play a role in ZIKV vertical transmission. Infectious ZIKV was detected in the amniotic fluid of three pregnancies and one fetus had ZIKV RNA detected in multiple tissues. No significant pathology was observed in any fetus; however, we did find an increase in the occurrence of decidual vasculitis and necrosis in ZIKV-exposed pregnancies compared to gestational-age-matched controls. Conclusions/Significance This study demonstrates that African-lineage ZIKV, like Asian-lineage ZIKV, can be vertically transmitted to the macaque fetus during pregnancy. The low inoculating dose used in this study suggests a low minimal infectious dose for rhesus macaques. Vertical transmission with a low dose in macaques further supports the high epidemic potential of African ZIKV strains. Author Summary Zika virus infection during pregnancy can result in adverse pregnancy outcomes including birth defects and miscarriage. There are two distinct genetic backgrounds of Zika virus: Asian-lineage and African-lineage. Currently, only Asian-lineage Zika virus is causally associated with adverse pregnancy outcomes in people. However, experimental studies have shown that African-lineage Zika virus can infect the fetus during pregnancy and cause adverse outcomes. Adverse pregnancy outcomes may not be associated with infection in people until there is an outbreak in a naive population. Thus, as African-lineage Zika virus continues to spread globally, the risk that it may pose to pregnant people remains a public health concern. In this study, we demonstrate that African-lineage Zika virus can be transmitted from the mother to the fetus during pregnancy. This study is significant because we used rhesus macaques, an animal that shares many key elements of Zika virus infection in pregnant people. This study is also significant because we inoculated pregnant macaques with a very small amount of virus, suggesting that fetal infection reported in previously published macaque studies is not limited to high-dose inoculation.

ABSTRACT The lack of preparedness for detecting the highly infectious SARS-CoV-2 pathogen, the pathogen responsible for the COVID-19 disease, has caused enormous harm to public health and the economy. It took ∼60 days for the first reverse transcription quantitative polymerase chain reaction (RT-qPCR) tests for SARS-CoV-2 infection developed by the United States Centers for Disease Control (CDC) to be made publicly available. It then took >270 days to deploy 800,000 of these tests at a time when the estimated actual testing needs required over 6 million tests per day. Testing was therefore limited to individuals with symptoms or in close contact with confirmed positive cases. Testing strategies deployed on a population scale at ‘Day Zero’ i.e., at the time of the first reported case, would be of significant value. Next Generation Sequencing (NGS) has such Day Zero capabilities with the potential for broad and large-scale testing. However, it has limited detection sensitivity for low copy numbers of pathogens which may be present. Here we demonstrate that by using CRISPR-Cas9 to remove abundant sequences that do not contribute to pathogen detection, NGS detection sensitivity of COVID-19 is comparable to RT-qPCR. In addition, we show that this assay can be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single workflow using existing open-source analysis pipelines. This NGS workflow is pathogen agnostic, and therefore has the potential to transform how both large-scale pandemic response and focused clinical infectious disease testing are pursued in the future. SIGNIFICANCE STATEMENT The lack of preparedness for detecting infectious pathogens has had a devastating effect on the global economy and society. Thus, a ‘Day Zero’ testing strategy, that can be deployed at the first reported case and expanded to population scale, is required. Next generation sequencing enables Day Zero capabilities but is inadequate for detecting low levels of pathogen due to abundant sequences of little biological interest. By applying the CRISPR-Cas system to remove these sequences in vitro , we show sensitivity of pathogen detection equivalent to RT-qPCR. The workflow is pathogen agnostic, and enables detection of strain types, co-infections and human host response with a single workflow and open-source analysis tools. These results highlight the potential to transform future large-scale pandemic response.

Natural hepatitis C virus (HCV) infection is restricted to humans whereas in other primates such as rhesus macaques, the virus is non-permissive. To identify human and rhesus macaque genes that differ or share the ability to inhibit HCV replication, we conducted a medium-throughput screen of lentivirus-expressed host genes that disrupt replication of HCV subgenomic replicon RNA expressing secreted Gaussia luciferase. A combined total of >800 interferon-stimulated genes (ISGs) were screened. Our findings confirmed established anti-HCV ISGs, such as IRF1, PKR and DDX60 . Novel species-specific inhibitors were also identified and independently validated. Using a cell-based system that recapitulates productive HCV infection, we identified the ‘Rho Guanine Nucleotide Exchange Factor 3’ gene ( ARHGEF3 ) from both species as a restriction factor for full-length virus replication. Mechanistically, ARHGEF3 -mediated inhibition was ablated by mutating a critical GEF active site residue and deleting the N-terminal portion of the protein. Additionally, replication of two mosquito-borne flaviviruses, yellow fever virus (YFV) and Zika virus (ZIKV), were reduced in ARHGEF3 -expressing cell lines compared to controls. In conclusion, we ascribe novel antiviral activity to the cellular gene ARHGEF3 that inhibits replication of HCV and other important human viral pathogens belonging to the Flaviviridae , and is conserved between humans and rhesus macaques.

Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID-19) outbreak. Therefore, it is necessary to better understand the evolution of coronaviruses as well as viruses in general. This study reports a comparative analysis of the amino acid usage within several key viral families and genera that are prone to triggering outbreaks, including coronavirus (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-HKU1, HCoV-OC43, HCoV-NL63, HCoV-229E), influenza A (H1N1, H3N2), flavivirus (dengue virus serotypes 1-4, Zika) and ebolavirus (Zaire, Sudan, Bundibugyo ebolavirus). Our analysis reveals that the distribution of amino acid usage in the viral genome is constrained to follow a linear order, and the distribution remains closely related to the viral species within the family or genus. This constraint can be adapted to predict viral mutations and future variants of concern. By studying previous SARS and MERS outbreaks, we have adapted this naturally occurring pattern to determine that although pangolin plays a role in the outbreak of COVID-19, it may not be the sole agent as an intermediate animal. In addition to this study, our findings contribute to the understanding of viral mutations for subsequent development of vaccines and toward developing a model to determine the source of the outbreak.

In late December 2019, the novel coronavirus (Sars-Cov-2) and the resulting disease COVID-19 were first identified in Wuhan China. The disease slipped through containment measures, with the first known case in the United States being identified on January 20th, 2020. In this paper, we utilize survey data from the Inter-university Consortium for Political and Social Research and apply several statistical and machine learning models and techniques such as Decision Trees, Multinomial Logistic Regression, Naive Bayes, k-Nearest Neighbors, Support Vector Machines, Neural Networks, Random Forests, Gradient Tree Boosting, XGBoost, CatBoost, LightGBM, Synthetic Minority Oversampling, and Chi-Squared Test to analyze the impacts the COVID-19 pandemic has had on the mental health of frontline workers in the United States. Through the interpretation of the many models applied to the mental health survey data, we have concluded that the most important factor in predicting the mental health decline of a frontline worker is the healthcare role the individual is in (Nurse, Emergency Room Staff, Surgeon, etc.), followed by the amount of sleep the individual has had in the last week, the amount of COVID-19 related news an individual has consumed on average in a day, the age of the worker, and the usage of alcohol and cannabis.

ABSTRACT We present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼ $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1×10 3 -fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

TOPLINE SUMMARY What is a Rapid Review? Our rapid reviews use a variation of the systematic review approach, abbreviating or omitting some components to generate the evidence to inform stakeholders promptly whilst maintaining attention to bias. They follow the methodological recommendations and minimum standards for conducting and reporting rapid reviews, including a structured protocol, systematic search, screening, data extraction, critical appraisal and evidence synthesis to answer a specific question and identify key research gaps. They take one to two months, depending on the breadth and complexity of the research topic/question(s), the extent of the evidence base and type of analysis required for synthesis. Background / Aim of Rapid Review The COVID-19 pandemic has led to differential economic, health and social impacts illuminating prevailing gender inequalities (WEN Wales, 2020). This rapid review investigated evidence for effectiveness of interventions to address gender inequalities across the domains of work, health, living standards, personal security, participation, and education. Key Findings Extent of the evidence base 21 studies were identified: 7 reviews, 6 commentaries and 8 primary studies Limited evidence for the effectiveness of identified innovations in minority groups A lack of evaluation data for educational interventions A lack of evidence for cost-effectiveness of the identified interventions 14 additional articles were identified in the grey literature but not used to inform findings (apart from the Education domain, where there was a lack of peer-reviewed evidence). Recency of the evidence base All studies were published in 2020-2021 Summary of findings Some evidence supported interventions/innovations related to work Permanent contracts, full-time hours, and national childcare programmes to increase income for women and thereby decrease the existing gender wage gap. More frequent use of online platforms in the presentation of professional work can reduce gender disparities due to time saved in travel away from home. Some evidence supported interventions/innovations related to health Leadership in digital health companies could benefit from women developing gender-friendly technology that meets the health needs of women. Create authentic partnerships with black women and female-led organisations to reduce maternal morbidity and mortality (Bray & McLemore, 2021). Some evidence supported interventions/innovations related to living standards including: Multi-dimensional care provided to women and their children experiencing homelessness. Limited evidence supported interventions/innovations related to personal security including: Specific training of social workers, psychologists and therapists to empower women to use coping strategies and utilise services to gain protection from abusive partners. Helplines, virtual safe spaces smart phone applications and online counselling to address issues of violence and abuse for women and girls. Very limited evidence supported interventions/innovations related to participation including: Use of online platforms to reduce gender disparities in the presentation of academic/professional work. Ensuring equal representation, including women and marginalised persons, in pandemic response and recovery planning and decision-making. Limited evidence from the grey literature described interventions/innovations related to education including: Teacher training curricula development to empower teachers to understand and challenge gender stereotypes in learning environments. Education for girls to enable participation in STEM. Policy Implications This evidence can be used to map against existing policies to identify which are supported by the evidence , which are not in current policy and could be implemented and where further research/evaluation is needed . Further research is needed to evaluate the effectiveness of educational innovations, the effectiveness of the innovations in minority groups and the social value gained from interventions to address gender inequalities. Strength of Evidence One systematic review on mobile interventions targeting common mental disorders among pregnant and postpartum women was rated as high quality (Saad et al., 2021). The overall confidence in the strength of evidence was rated as ‘low’ due to study designs . Searches did not include COVID specific resources or pre-prints. There may be additional interventions/innovations that have been implemented to reduce inequalities experienced by women and girls due to the COVID-19 pandemic but have not been evaluated or published in the literature and are therefore not included here.

First identified in 1947, Zika virus took roughly 70 years to cause a pandemic unusually associated with virus-induced brain damage in newborns. Zika virus is transmitted by mosquitoes, mainly Aedes aegypti , and secondarily, Aedes albopictus , both colonizing a large strip encompassing tropical and temperate regions. As part of the international project ZIKAlliance initiated in 2016, 50 mosquito populations from six species collected in 12 countries were experimentally infected with different Zika viruses. Here, we show that Ae. aegypti is mainly responsible for Zika virus transmission having the highest susceptibility to viral infections. Other species play a secondary role in transmission while Culex mosquitoes are largely non-susceptible. Zika strain is expected to significantly modulate transmission efficiency with African strains being more likely to cause an outbreak. As the distribution of Ae. aegypti will doubtless expand with climate change and without new marketed vaccines, all the ingredients are in place to relive a new pandemic of Zika.

Objective: To conduct a proof-of-concept study of the detection of two synthetic models of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using polarimetric imaging. Methods: Two SARS-CoV-2 models were prepared as engineered lentiviruses pseudotyped with the G protein of the vesicular stomatitis virus, and with the characteristic Spike protein of SARS-CoV-2. Samples were preparations in two biofluids (saline solution and artificial saliva), in four concentrations, and deposited as 5-μL droplets on a supporting plate. The angles of maximal degree of linear polarization (DLP) of light diffusely scattered from dry residues were determined using Mueller polarimetry of 87 samples at 405 nm and 514 nm. A polarimetric camera was used for simultaneous imaging of several samples under 380-420 nm illumination at angles similar to those of maximal DLP. A per-pixel image analysis included quantification and combination of polarization feature descriptors in other 475 samples. Results: The angles (from sample surface) of maximal DLP were 3 degrees for 405 nm and 6 degrees for 514 nm. Similar viral particles that differ only in the characteristic spike protein of the SARS-CoV-2, their corresponding negative controls, fluids, and the sample holder were discerned from polarimetric image analysis at 10-degree and 15-degree configurations. Conclusion: Polarimetric imaging in the visible spectrum has the potential for non-contact, reagent-free detection of viruses in multiple dry fluid residues simultaneously. Further analysis including real SARS-CoV-2 in human samples -- particularly, fresh saliva -- are required. Significance: Polarimetric imaging under visible light could contribute to fast, cost-effective screening of SARS-CoV-2 and other pathogens.

T follicular helper (Tfh) cells are specialized CD4 + T cells that regulate humoral immunity by providing B cell help. Tfh1 sub-population was recently identified and associated with severity in infection and autoimmune diseases. The cellular and molecular requirements to induce human Tfh1 differentiation are unknown. Our work investigated the role of human dendritic cells (DC) in promoting Tfh1 differentiation and their physiopathological implication in mycobacterium tuberculosis and mild COVID-19 infection. Activated human blood CD1c + DC were cocultured with allogeneic naive CD4 + T cells. Single-cell RNA sequencing was then used alongside protein validation to define the induced Tfh lineage. DC signature and correlation with Tfh1 cells in infected patients was established through bioinformatic analysis. Our results show that GM-CSF-activated DC drove the differentiation of Tfh1 cells, displaying typical Tfh molecular features, including 1) high levels of PD-1, CXCR5, and ICOS expression; 2) BCL6 and TBET co-expression; 3) IL-21 and IFN-γ secretion. Mechanistically, GM-CSF triggered the emergence of two distinct DC sub-populations defined by their differential expression of CD40 and ICOS-ligand (ICOS-L), and distinct phenotype, morphology, transcriptomic signature, and function. We showed that Tfh1 differentiation was efficiently and specifically induced by CD40 high ICOS-L low DC in a CD40-dependent manner. Tfh1 cells were positively associated with a CD40 high ICOS-L Low DC signature in patients with latent mycobacterium tuberculosis and mild COVID-19 infection. Our study uncovers a novel CD40-dependent human Tfh1 axis. Immunotherapy modulation of Tfh1 activity might contribute to control diseases where Tfh1 are known to play a key role, such as infections. Significance Statement Dendritic cells (DC) play a central role in triggering the adaptive immune response due to their T cell priming functions. Among different T cell subsets, it is still not clear how human type1 T follicular helper cells (Tfh1) differentiate. Tfh1 cells are implicated in several physiopathological conditions, including infections. Here we show that GM-CSF induces diversification of human DC. Only CD40 high ICOS-L Low DC were able to drive Tfh1 cell differentiation. We found that CD40 high ICOS-L Low DC signature was associated to Tfh1 cells in mycobacterium tuberculosis and COVID-19 patients. Our data reveal a previously undescribed pathway leading to human Tfh1 cell differentiation and highlight the importance of GM-CSF and CD40 as potential targets for the design of anti-infective therapies.

Despite much concerted effort to better understand SARS-CoV-2 viral infection, relatively little is known about the dynamics of early viral entry and infection in the airway. Here we analyzed a single-cell RNA sequencing dataset of early SARS-CoV-2 infection in a humanized in vitro model, to elucidate key mechanisms by which the virus triggers a cell-systems-level response in the bronchial epithelium. We find that SARS-CoV-2 virus preferentially enters the tissue via ciliated cell precursors, giving rise to a population of infected mature ciliated cells, which signal to basal cells, inducing further rapid differentiation. This feed-forward loop of infection is mitigated by further cell-cell communication, before interferon signaling begins at three days post-infection. These findings suggest hijacking by the virus of potentially beneficial tissue repair mechanisms, possibly exacerbating the outcome. This work both elucidates the interplay between barrier tissues and viral infections, and may suggest alternative therapeutic approaches targeting non- immune response mechanisms. Funding Information: This work was supported by grants from the National Institutes of Health (U54 CA209992 (NCI) to A.L.; F30HL143906 and T32GM136651 to M.S.B.R.), as well as private research gifts and an unrestricted research gift from Humacyte Inc. Conflict of Interests: L.E.N. is the CEO, founder and shareholder in Humacyte, Inc, which is a regenerative medicine company. Humacyte produces engineered blood vessels from allogeneic smooth muscle cells for vascular surgery. L.E.N.’s spouse has equity in Humacyte, and L.E.N. serves on Humacyte’s Board of Directors. L.E.N. is an inventor on patents that are licensed to Humacyte and that produce royalties for L.E.N. L.E.N. has received an unrestricted research gift to support research in her laboratory at Yale. Humacyte did not influence the conduct, description or interpretation of the findings in this report.

Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (M pro , 3CL pro ) and papain-like protease (PL pro ) are responsible for viral polyprotein cleavage – a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2 H )-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and anti-viral assays. In this study, we screened a collection of 34 ebselen and ebselen diselenide derivatives for SARS-CoV-2 PL pro and M pro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PL pro and four M pro inhibitors superior to ebselen. Independently, ebselen was shown to inhibit the N7-methyltransferase activity of SARS-CoV-2 nsp14 protein involved in viral RNA cap modification. Hence, selected compounds were also evaluated as nsp14 inhibitors. In the second part of our work, we employed 11 ebselen analogues – bis(2-carbamoylaryl)phenyl diselenides – in biological assays to evaluate their anti-SARS-CoV-2 activity in Vero E6 cells. We present their antiviral and cytoprotective activity and also low cytotoxicity. Our work shows that ebselen, its derivatives and diselenide analogues constitute a promising platform for development of new antivirals targeting the SARS-CoV-2 virus.

The expression of m6A-related gene and its significance in COVID − 19 patients are still unknown. In the present study, we used the GSE177477 dataset of Gene Expression Omnibus to extract RNA-seq data of patients with COVID-19. The expression levels of 26 m6A-related genes between COVID-19 patients and healthy people were analyzed, thereby gaining 8 different expression genes. COVID-19 patients were classified into two categories, cluster A and cluster B, based on the expression level of the differential gene, which in this study happened to be the asymptomatic and symptomatic groups. In addition, differential expression of immune cells and the correlation with m6A-related genes was also examined in COVID-19 patients. Finally, 5 m6A-related disease characteristic genes, HNRNPA2B1, FTO, YTHDC1, HNRNPC, and WTAP, were screened by random forest and support vector machine algorithm. These five genes were applied to construct a nomogram model for predicting the risk of COVID-19. The calibration curve and decision curve analysis (DCA) show that the nomogram model is effective and has high net benefit. Then clinical impact curve analysis (CICA) revealed that the high-risk patients classified by the nomogram model had a high degree of coincidence with the actual positive patients. In summary, it has been found that m6A-related genes correlate with immune cells. The nomogram model effectively predicts the risk of COVID-19. And m6A-related genes may be associated with the presence or absence of symptoms in COVID-19 patients.

Bats are important natural reservoir hosts of a diverse range of viruses that can be transmitted to humans and have been suggested that could play an important role in the Zika virus (ZIKV) transmission cycle. However, the exact role of these animals as reservoirs for Flaviviruses is still controversial. To further expand our understanding of the role of bats in the ZIKV transmission cycle in Latin America, we carried an experimental infection in wild-caught Artibeus bats and sampled several free-living neotropical bats over three countries of the region. Experimental ZIKV infection was made in free-ranging adult bats (4 females and 5 males). The most relevant gross findings were hemorrhages in the bladder, stomach and patagium. Significant histological findings included inflammatory infiltrate consisting of a predominance of neutrophils and lymphocytes, in addition to degeneration in the reproductive tract of males and females. This suggests that bat reproduction might be at some level affected by ZIKV. Leukopenia was also observed in some inoculated animals. Hemorrhages, genital alterations, and leukopenia are suggestive to be caused by ZIKV, however, since these are wild-caught bats, we can not exclude other agents. Excretion of ZIKV by qPCR was detected (low titles) in only two urine samples in two inoculated animals. All other animals and tissues tested negative. Finally, no virus-neutralizing Abs were found in any animal. To determine ZIKV infection in nature, a total of 2056 bats were blood sampled for ZIKV detection by qPCR. Most of the sampled individuals belonged to the genus Pteronotus sp. (23%), followed by the species Carollia sp. (17%); Anoura sp. (14%), and Molossus sp. (13.7 %). No sample of any tested species resulted positive to ZIKV by qPCR. These results together suggest that bats are not efficient amplifiers or reservoirs of ZIKV and may not have an important role in ZIKV transmission dynamics. Author summary In previous works made in 2008-2009, we have found the presence of antibodies against Flaviviruses and viral RNA has been detected in Neotropical chiropterans of Mexico, which led us to support the hypothesis that these animals could be reservoirs of Flaviviruses. As controversial opinions have been exposed, and based on a previous (2019) experimental ZIKV infection made in Colorado State University using adult Artibeus males from a captive colony, in this work we also experimentally infected adult Artibeus males complementarily adding females and using free-living animals instead of laboratory bats. We also monitored a diverse range of natural bat populations in Latin America for the presence of viral RNA against ZIKV in blood. A plaque reduction seroneutralization test was used for the detection of antibodies against ZIKV. Similar to the previous work, we found histopathological alteration in male testicles but also in ovaries and oviducts of females, as well as gliosis and multifocal necrosis in pyramidal neurons and Purkinge cells of inoculated animals. Only two urine samples from inoculated animals showed viral RNA. Additionally, leukopenia and lymphoid follicular splenic hyperplasia were evidenced. Differing to what was reported, no neutralizing antibodies against ZIKV were detected in any sample. Viral RNA within the blood was not present in any of the 2056 bat samples collected in French Guyana, Peru and Costa Rica and proceeding from 33 bat genera. These results together suggest that bats are not efficient amplifiers or reservoirs of ZIKV and might not have an important role on ZIKV transmission dynamics.

Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is widely used to quantify viral RNA genomes for diagnostics and research, yet conventional RT-qPCR protocols are unable to accurately distinguish between the different viral RNA species that exist during infection. Here we show that false-priming and self-priming occur during reverse transcription with several published Zika virus (ZIKV) primer sets. We developed a RT-qPCR assay using tagged primers and thermostable reverse transcriptase, which greatly reduced the occurrence of nonspecific cDNA products. Furthermore, we optimized the assay for use in multiplex qPCR which allows for simultaneous quantitative detection of positive-strand and negative-strand ZIKV RNA along with an internal control from both human and mosquito cells. Importantly, this assay is sensitive enough to study early stages of virus infection in vitro . Strikingly, using this assay, we detected ZIKV negative-strand RNA as early as 3 h post-infection in mammalian cell culture, at a time point prior to the onset of positive-strand RNA synthesis. Overall, the strand-specific RT-qPCR assay developed herein is a valuable tool to quantify ZIKV RNA and to study viral replication dynamics during infection. The application of these findings has the potential to increase accuracy of RNA detection methods for a variety of viral pathogens. Highlights Self-primed cDNA is amplified by widely-used ZIKV qPCR primer sets Use of tagged primers and thermostable RT increases strand-specificity for RT-qPCR Multiplexed qPCR allows for simultaneous quantitation of (+) and (-) strand viral RNAs, and an internal control Strand-specific RT-qPCR can detect fewer than one copy of viral RNA per cell in human and mosquito cells

The interferon-induced transmembrane (IFITM) proteins broadly inhibit the entry of diverse pathogenic viruses, including Influenza A virus (IAV), Zika virus, HIV-1, and SARS coronaviruses by inhibiting virus-cell membrane fusion. IFITM3 was previously shown to disrupt cholesterol trafficking, but the functional relationship between IFITM3 and cholesterol remains unclear. We previously showed that inhibition of IAV entry by IFITM3 is associated with its ability to promote cellular membrane rigidity, and these activities are functionally linked by a shared requirement for the amphipathic helix (AH) found in the intramembrane domain (IMD) of IFITM3. Furthermore, it has been shown that the AH of IFITM3 alters lipid membranes in vitro in a cholesterol-dependent manner. Therefore, we aimed to elucidate the relationship between IFITM3 and cholesterol in more detail. Using a fluorescence-based in vitro binding assay, we found that a peptide derived from the AH of IFITM3 directly interacted with the cholesterol analog, NBD-cholesterol, while other regions of the IFITM3 IMD did not, and native cholesterol competed with this interaction. In addition, recombinant full-length IFITM3 protein also exhibited NBD-cholesterol binding activity. Importantly, previously characterized mutations within the AH of IFITM3 that strongly inhibit antiviral function (F63Q and F67Q) disrupted AH structure in solution, inhibited cholesterol binding in vitro , and restricted bilayer insertion in silico . Our data suggest that direct interactions with cholesterol may contribute to the inhibition of membrane fusion pore formation by IFITM3. These findings may facilitate the design of therapeutic peptides for use in broad-spectrum antiviral therapy.

Since the outbreak of the new crown epidemic, it has dealt a severe blow to economies around the world. How to quickly recover the traumatized economies in the post-epidemic era is now an important task. This paper constructs a prediction model based on the data of five major epidemics similar to the current one that occurred in history. Based on the prediction model built, we make a comprehensive forecast and individual economic indicators forecast for China's economy after the current epidemic, and the forecast results show that the overall economy of the country name and import and export can basically recover to the pre-epidemic level in about one year, and the recovery time for tourism and air transportation is longer and requires a slow recovery. This result is also very much in line with China's reality. China has already gained some experience in this kind of economic recovery, and a summary of these experiences will provide inspiration to other economies .

Although ocular manifestations are commonly reported in patients with coronavirus disease 2019 (COVID-19), there is currently no consensus on ocular tropism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To investigate this, we infected K18-hACE2 mice with SARS-CoV-2 using various routes. We observed ocular manifestation and retinal inflammation with cytokine production in the eyes of intranasally (IN) infected mice. An intratracheal (IT) injection resulted in virus spread from the lungs to the brain and eyes via trigeminal and optic nerves. Ocular and neuronal invasion were confirmed by an intracerebral (IC) infection. Notably, eye-dropped (ED) virus did not infect the lungs and was undetectable with time. Using infectious SARS-CoV-2-mCherry clones, we demonstrated the ocular and neurotropic distribution of the virus in vivo by a fluorescence-imaging system. Evidence for the ocular tropic and neuroinvasive characteristics of SARS-CoV-2 was confirmed in wild-type Syrian hamsters. Our data provides further understanding of the viral transmission; SARS-CoV-2 clinical characteristics; and COVID-19 control procedures. Summary SARS-CoV-2 can spread from the respiratory tract to the brain and eyes via trigeminal and optic nerves in animal models. This ocular tropism of SARS-CoV-2 through neuronal invasion likely causes ocular manifestation and retinal inflammation. Graphical Abstract

Flavivirus Non-structural 1 (NS1) protein performs multiple functions such as host immune evasion, interaction with complement system factors, membrane rearrangement, etc. Therefore, it is highly plausible that significant structural and folding dynamics of NS1 might play a role in its multifunctionality. The dimeric structures of NS1 of multiple flaviviruses, including Zika virus (ZIKV), are available. However, its domain-wise dynamics perspective has not been explored so far. Therefore, it is of utmost importance to understand the structural conformations of NS1 and its domains in isolation, possibly highlighting the implications on the overall NS1 protein dynamics. Here, we have employed extensively long molecular dynamic (MD) simulations to understand the role of monomer, dimer, and a reductionist approach in understanding the dynamics of the three structural domains (i.e., β- roll, wing, and β-ladder) in isolation. Further, we experimentally validated our findings using CD spectroscopy and confirmed the intrinsically disordered behavior of NS1 β-roll in isolation and lipid mimetic environments. We also found that the β-ladder domain is highly flexible during long simulations. Therefore, we believe this study may have implications for significant dynamics played by NS1 protein, specifically during oligomerization of NS1. Graphical Abstract Schematic representation of the ZIKV NS1 protein and the models that we have used in this study.

Due to the recent Coronaviruse Disease 2019 (COVID-19) pandemic that occurred since early 2020, scientists have been researching for rapid and less invasive methods to detect the presence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causal agent of COVID-19. Optical spectroscopy, a method that employs the interaction of light has been previously used in detecting viruses in biological samples. It is a promising method that could also be similarly applied in detecting the presence of SARS-CoV-2 in biological samples such as nasopharyngeal swabs. Three methods of optical spectroscopy are discussed in this paper, namely ultraviolet (UV), infrared (IR) and Raman spectroscopy. UV and IR spectroscopy differs in terms of their wavelength ranges, < 400 nm and > 700 nm respectively. Meanwhile, Raman spectroscopy involves shift in wavelength due to the scattering of light. These three methods have been shown to be able to differentiate true negative, virus-free samples from true positive, virus-containing samples. UV spectroscopy is useful in determining the presence of viruses based on the 260nm/280nm absorbance ratio. However, its usefulness is limited as at sufficiently high intensities. UV radiation damages fundamental biomolecules such as proteins, lipids and nucleic acids, all of which are essential building components of viruses. Meanwhile, IR spectroscopy is becoming more widely used in studies involving the detection of viruses. Mid-infrared (MIR) spectroscopy is most commonly used among IR spectroscopy as it provides useful information directly from the spectral data. Near infrared (NIR) spectroscopy has also been used in virus-detection studies. But additional methods such as principal component analysis (PCA) and partial least squares (PLS) are required to process the raw spectral data and to identify molecules based on the spectral peaks. On the other hand, Raman spectroscopy is useful because spectral data can be analyzed directly by identifying the vibrational modes of specific molecules in virus-containing samples. Both IR and Raman spectroscopy can be applied directly with lesser manipulation of samples and without damaging the target molecules to be measured. An increasing uses of these two spectroscopy methods is foreseeable in future studies involving the detection of viruses in a wide variety of samples. Funding Information: Universiti Malaysia Sabah Research Grant [code SDK0163- 2020]. Conflict of Interests: None to declare.

ABSTRACT Zika virus (ZIKV) from Uganda (UG) expresses a phenotype related to fetal loss whereas the variant from Brazil (BR) induces microcephaly in neonates. The differential virulence has a direct relation to biomolecular mechanisms that make one strain more aggressive than the other. The non-structural protein 1 (NS1) is a key viral toxin to comprehend these viral discrepancies because of its versatility in many processes of the virus life cycle. Here, we aim to examine through coarse-grained models and molecular dynamics simulations the protein-membrane interactions for both NS1 ZIKV-UG and NS1 ZIKV-BR dimers. A first evaluation allowed us to establish that the NS1 proteins, in the membrane presence, explore new conformational spaces when compared to systems simulated without a lipid bilayer. These events derive from both differential coupling patterns and discrepant binding affinities to the membrane. The N-terminal domain, intertwined loop, and greasy finger proposed previously as binding membrane regions were also computationally confirmed by us. The anchoring sites have aromatic and ionizable residues that manage the assembly of NS1 toward the membrane, especially for the Ugandan variant. Furthermore, the protein-membrane interaction induces perturbation in the distal part related to putative epitopes. These results open up new strategies for the treatment of flaviviruses. Abstract Figure