ABSTRACT COVID-19 caused by SARS-CoV-2 has been spreading worldwide. To date, several vaccine candidates moved into EUA or CA applications. Although DNA vaccine is on phase III clinical trial, it is a promised technology platform with many advantages. Here, we showed that the pGX9501 DNA vaccine encoded the spike full-length protein-induced strong humoral and cellular immune responses in mice with higher neutralizing antibodies, blocking the hACE2-RBD binding against live virus infection in vitro. Importantly, higher levels of IFN-γ expression in CD8+ and CD4+ T cell and specific cytotoxic lymphocyte (CTL) killings effect were also observed in the pGX9501-immunized group. It provided subsequent protection against virus challenges in the hACE2 transgenic mouse model. Overall, pGX9501 was a promising DNA vaccine candidate against COVID-19, inducing strong humoral immunity and cellular immunity that contributed to the vaccine’s protective effects.

Background: The COVID-19 pandemic had raised a severe health concern across the globe, as most countries are fighting with the second wave of SARS-CoV-2 infection. Although several vaccines had cleared the clinical trials and are being administered in different countries, the degree of protection varies due to the emergence of novel viral strains. Moreover, no antiviral drug against SARS-CoV-2 was reported to date. Recently published reports on statin therapy on COVID-19 patients indicated that statin therapy is associated with a better clinical outcome and a significant reduction in mortality risk.MethodsBlind docking of the critical structural and functional proteins of SARS-CoV-2 like RNA-dependent RNA polymerase, M-protease of 3-CL-Pro, Helicase, and the Spike proteins ( wild type and mutants) with the statin molecules were performed using the Schrodinger docking tool. Prevalent mutations in the spike protein were determined by analyzing the SARS-CoV-2 genome sequences deposited in GISAID, using the NextAlign aligner tool. Wild type and mutant spike proteins were modeled using the Swiss Model server and subjected to energy minimization via YASARA server. The percentage of the allowed region was determined by the Ramachandran plot. The MD simulation studies of free protein templates and protein-ligand complex were performed using NAMD (Nanoscale Molecular Dynamics) program; v 2.8.ResultsWe observed that fluvastatin and pitavastatin showed fair binding affinities to RNA polymerase, 3-CL-Pro, and spike-double mutant with similar docking scores. But of all the target proteins, fluvastatin showed the strongest binding affinity to the helicase with the glide score, emodel score, and glide energy values of -11.333, -66.511 and -58.72 (kcal/mol), respectively. Pitavastatin having similar chemical properties like fluvastatin (logP and pKa values) exhibited strong biding affinities to RdRp, 3-CL-Pro, and S-double mutant. Additionally, molecular dynamics simulation confirmed the formation of a stable drug-protein complex. ConclusionThus our study shows that of all the statins, fluvastatin can bind to multiple target proteins of SARS-CoV-2, including the spike-mutant proteins. This property might contribute to the potent antiviral efficacy of this drug.

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) issued a significant and urgent threat to global health. The exact animal origin of SARS-CoV-2 remains obscure and understanding its host range is vital for preventing interspecies transmission. Previously, we have assessed the target cell profiles of SARS-CoV-2 in pets, livestock, poultry and wild animals. Herein, we expand this investigation to a wider range of animal species and viruses to provide a comprehensive source for large-scale screening of potential virus hosts. Single cell atlas for several mammalian species (alpaca, hamster, hedgehog, chinchilla etc.), as well as comparative atlas for lung, brain and peripheral blood mononuclear cells (PBMC) for various lineages of animals were constructed, from which we systemically analyzed the virus entry factors for 113 viruses over 20 species from mammalians, birds, reptiles, amphibians and invertebrates. Conserved cellular connectomes and regulomes were also identified, revealing the fundamental cell-cell and gene-gene cross-talks between these species. Overall, our study could help identify the potential host range and tissue tropism of SARS-CoV-2 and a diverse set of viruses and reveal the host-virus co-evolution footprints.

Aedes aegypti mosquito has spread throughout the tropical and subtropical world and is currently the primary species responsible for transmitting dengue, urban yellow fever, Chikungunya, and Zika virus. This study aimed to investigate the inter- and intrapopulational genetic variability of Aedes aegypti through mitochondrial DNA, COI, ND4, and ND5 molecular markers in four municipalities in Mato Grosso. We used the Geneious software to build dendrograms for differentiating populations from each municipality. The interpopulational genetic distance obtained from sequence analysis showed a difference within populations through groups' formation in the ordering. Besides, we identified a difference in the interindividual genetic distance values, notably for the ND5 gene from the populations captured in the four municipalities. We recorded the smallest interindividual genetic distance within populations for populations from Chapada dos Guimarães. Extrinsic factors, including breeding habitat removal, can contribute to decreasing variability. Consequently, the dendrogram showed some similarities. Ovitrap monitoring, vector elimination, and genetic flow investigation stimulate actions to prevent transmitted diseases and support essential effective measures to control and fight Ae. aegypti .

Timely, accurate, and comparative data on human mobility is of paramount importance for epidemic preparedness and response, but generally not available or easily accessible. Mobile phone metadata, typically in the form of Call Detail Records (CDRs), represents a powerful source of information on human movements at an unprecedented scale. In this work, we investigate the potential benefits of harnessing aggregated CDR-derived mobility to predict the 2015-2016 Zika virus (ZIKV) outbreak in Colombia, when compared to other traditional data sources. To simulate the spread of ZIKV at sub-national level in Colombia, we employ a stochastic metapopulation epidemic model for vector-borne disease. Our model integrates detailed data on the key drivers of ZIKV spread, including the spatial heterogeneity of the mosquito abundance, and the exposure of the population to the virus due to environmental and socio-economic factors. Given the same modelling settings (i.e. initial conditions and epidemiological parameters), we perform in-silico simulations for each mobility network and assess their ability in reproducing the local outbreak as reported by the official surveillance data. We assess the performance of our epidemic modelling approach in capturing the ZIKV outbreak both nationally and sub-nationally. Our model estimates are strongly correlated with the surveillance data at the country level (Pearson’s r =0.92 for the CDR-informed network). Moreover, we found strong performance of the model estimates generated by the CDR-informed mobility network in reproducing the local outbreak observed at the sub-national level. Compared to the CDR-informed network, the performance of the other mobility networks is either comparatively similar or substantially lower, with no added value in predicting the local epidemic. This suggests that mobile phone data capture a better picture of human mobility patterns. This work contributes to the ongoing discussion on the value of aggregated mobility estimates from CDRs data that, with appropriate data protection and privacy safeguards, can be used for social impact applications and humanitarian action.

Background: The global spread of the novel coronavirus 2019 (COVID-19) has been sudden shock to the world and resulted in many questions that remain unanswered. Limited data has been published in low-middle-income country settings (LMICS) Objectives: To describe the clinical characteristics and outcome of mothers and neonates delivered from COVID-19 positive mothers, and to identify the incidence of COVID-19 positive neonates. Methods: A prospective, descriptive study, from 1 August 2020 to 31 March 2021 conducted at a tertiary hospital, in JohannesburgAll neonates born to mothers that were COVID-19 positive and that required admission to the neonatal unit were included. Informed consent was obtained from mothers prior to enrolment. Results: A total of 111 COVID-19 positive pregnant women delivered neonates at the tertiary hospital. In this study, only 28 of the 111 (25%) neonates born to COVID-19 positive mothers were admitted. The majority of the COVID-19 pregnant mothers were asymptomatic or had mild symptomatic disease (80%). Two (2/111 (2%) mothers required ICU admission and three (3/111 (3%) of them demised. In relation to neonatal outcomes, the majority of the neonates were delivered at a gestational age of 35 weeks with a birth weight of 2400 grams .The most common symptom was respiratory distress (89 %). The one (3%) neonate that tested positive for COVID-19 was born moderately preterm with a low birth weight and respiratory distress syndrome. Two (2/28 (7%) neonates demised, however the cause of death was not related to COVID-19. All the remaining (26/28 (93%) neonates were discharged and were well on follow up. Conclusion: Our study has shown that the risk of neonatal transmission from pregnant COVID-19 mothers is relatively low, and the majority of neonatal disease ranged from asymptomatic to mildly symptomatic disease. Further research efforts are essential to improve neonatal care in LMICS.

Background: Viral infections such as measles virus (MV), herpes virus, and human immunodeficiency virus (HIV) can lead to transient or permanent neurological or psychiatric dysfunction. However, respiratory system affecting viruses have appeared as an unbeatable challenge to the modern world. They include the human respiratory syncytial virus (hRSV), the influenza virus (IV), and the coronavirus (CoV). They cause acute respiratory infections mainly children under 5 years old and also the elderly. The most frequent clinical manifestations are febrile or afebrile seizures, status epilepticus, encephalopathies, and encephalitis. Objective: The objective of this review is to assess the effect of COVID-19 on our mood and thinking during this pandemic. Method: We reviewed the literature using different databases e.g., Google Scholar, PubMed, and Science direct etc. Results: Viral Infections badly affect the nervous system functions and ultimate can lead to the onset of neurological and psychological illnesses. Conclusion: COVID-19 is somehow causing depression, anxiety, panic attacks, and stress. As a consequence, social distancing has increased that has ultimately modified our thinking style, mood and has lead to the psychological, emotional and behavioral changes. Review Criteria We reviewed the literature using different databases e.g., Google Scholar, PubMed, etc. from 1997 to 2021 without language limitations. Message for the clinic It is clear that COVID-19 causes cardiac, respiratory, renal, and gastrointestinal dysfunctions and has also a direct effect on brain functioning resulting in psychological and behavioral changes. Along with other dysfunctions, it has severely affected the living style of people and brought depression, anxiety, panic attacks, loneliness, and self-deprecation. It is highly recommended that while treating such patients, all these aspects should be kept in mind. Hence, not only medication can ameliorate the side impacts of this infection but counseling is another tool to bring positive impact in those respondents.

Neuropsychiatric manifestations are common in both acute and post-acute phase of SARS-CoV-2 infection, but the mechanism of these effects is unknown. Here, we derive human brain organoids with innately developing microglia to investigate the cellular responses to SARS-CoV-2 infection on a single cell level. We find evidence of limited tropism to SARS-CoV-2 and observe extensive neuronal cell death that also include non-infected cells. Single cell transcriptome profiling reveals distinct responses in microglia and astrocytes that share features with cellular states observed in neurodegenerative diseases, includes upregulation of genes with relevance for synaptic stripping, and suggests altered blood brain barrier integrity. Across all cell types, we observe a global translational shut-down as well as altered carbohydrate metabolism and cellular respiration. Together, our findings provide insights into cellular responses of the resident brain immune cells to SARS-CoV-2 and pinpoint mechanisms that may be of relevance for the neuropathological changes observed in COVID-19 patients.

Background: Research has been an essential part of the COVID-19 pandemic response, including in Latin American (LA) countries. However, implementing research in emergency settings poses the challenge of producing valuable knowledge rapidly while upholding research ethical standards. Research ethics committees (RECs) therefore must conduct timely and rigorous ethics reviews and oversight of COVID-19 research. In the LA region, there is limited knowledge on how countries have responded to this need. To address this gap, the objective of our project is to explore if LA countries developed policies to streamline ethics review and oversight of research in response to the pandemic while ensuring its adherence to ethical standards, and to analyze to what extent these governance frameworks are in accordance with international guidance. Methods: We conducted a descriptive and exploratory study assessing the COVID-19 research ethics governance frameworks of 19 LA countries, considering 4 dimensions based on international COVID-19 ethics guidance documents: (i) ethics review organizational model adopted, (ii) measures to coordinate between RECs and other research stakeholders, (iii) operational guidance for RECs, and (iv) key ethical issues for review and oversight of COVID-19 research. Results: 10 out of 19 LA countries have some policy to streamline ethics review of COVID-19 research. Of these countries only 6 issued comprehensive documents following international guidance that contemplated strategies with recommendations for concrete actions for a timely and rigorous review. Conclusion: LA countries adopted partial strategies and operational guidance that may demonstrate a lack of a comprehensive view of research ethics for the review and oversight of COVID-19 research. Continuing efforts should be directed to strengthen LA countries' research capacity to respond timely and ethically to future health emergencies. Past lessons and the ones from this pandemic should be the basis to develop international standards and operational guidelines for ethics review and oversight of any research for public health emergencies of international concern.

Infection with Zika virus (ZIKV), a member of the Flavivirus genus of the Flaviviridae family, typically results in mild self-limited illness, but severe neurological disease occurs in a limited subset of patients. In contrast, serious outcomes commonly occur in pregnancy that affect the developing fetus, including microcephaly and other major birth defects. The genetic similarity of ZIKV to other widespread flaviviruses, such as dengue virus (DENV), presents a challenge to the development of specific ZIKV diagnostic assays. Nonstructural protein 1 (NS1) is established for use in immunodiagnostic assays for flaviviruses. To address the cross-reactivity of ZIKV NS1 with proteins from other flaviviruses we used site-directed mutagenesis to modified putative epitopes. Goat polyclonal antibodies to variant ZIKV NS1 were affinity-purified to remove antibodies binding to the closely related NS1 protein of DENV. An antigen-capture ELISA configured with the affinity-purified polyclonal antibody showed a linear dynamic range between approximately 500 to 30 ng/mL, with a limit of detection of between 1.95 and 7.8 ng/mL. NS1 proteins from DENV, yellow fever virus, St. Louis encephalitis virus and West Nile virus showed significantly reduced reactivity in the ZIKV antigen-capture ELISA. Refinement of approaches similar to those employed here could lead to development of ZIKV-specific immunoassays suitable for use in areas where infections with related flaviviruses are common.

In examining how badly the United States bungled its COVID-19 pandemic response, it is worth going back to the commemorations of the 100th anniversary of the 1918 flu pandemic. Author after author cautioned that the next pandemic would overwhelm the United States health system and that the demand for hospital beds, treatments, and medical staff would quickly outstrip supply. These prescient predictions from just two years ago. Why, when the risks were so obvious and so clearly understood, were they ignored? In answering that question there is blame enough to go around. The American public increasingly refused vaccines for communicable diseases, resisted spending for health research, and elected anti-science candidates. Those elected officials in turn failed to take obvious steps to ward off an entirely foreseeable disaster. Some of these developments are new(ish), relating to the specifics of the current political climate. Yet what is most striking is how readily official responses fell into virtually the same patterns that stymied effective pandemic response in 1918, and how structural racism predicted which communities would be hardest hit and least served by government responses. Instead of learning from the mistakes of the 1918 pandemic we have largely repeated them. This paper traces some of the threads of complacency, hubris, isolationism, and distrust that got in the way both times, and draws some broader lessons we must learn about American political culture before the pandemic next time.

Arthropod-borne viral (arboviral) pathogens comprise a significant global disease burden, and outbreaks are expected to increase as vectors expand. Surveillance and mitigation of arboviruses like Zika virus (ZIKV) require accurate estimates of transmissibility by vector mosquitoes. While numerous laboratory vector competence experiments show that Aedes spp . mosquitoes are competent ZIKV vectors, differences in experimental protocols prevent direct comparisons of relative transmissibility across studies. An understudied factor complicating these comparisons is differential environmental microbiota exposures, where most vector competence studies use mosquitoes reared in laboratory tap water, which does not represent the microbial complexity of environmental water where wild larvae develop. We simulated natural larval development by rearing Californian Aedes aegypti with microbes obtained from cemetery headstone water, a common larval habitat in California, compared to conventional laboratory tap water. Ae. aegypti larvae reared in environmental cemetery water pupated 3 days faster and at higher rates. Female adult mosquitoes reared in environmental water were less competent vectors of ZIKV compared to laboratory water-reared Ae. aegypti , as evidenced by significantly reduced infection and transmission rates for two 2015 ZIKV strains and in two Ae. aegypti colonies from California. Microbiome comparisons of laboratory- and environment-water reared mosquitoes as well as their rearing water showed significantly higher bacterial diversity in environment water; despite this pattern, corresponding differences in diversity were not consistently detected in adult mosquitoes reared in different water sources. We also detected more significant associations between the microbial composition of adult mosquitoes and whether they ingested a bloodmeal than larval water type. Together, these results highlight the role of transient microbes in the larval environment in modulating vector competence. Laboratory vector competence likely overestimates true transmissibility of arboviruses like ZIKV when conventional laboratory water is used for rearing. Importance We observed that Ae. aegypti mosquitoes reared in water from cemetery headstones instead of the laboratory tap exhibited a reduced capacity to become infected with and transmit Zika virus. Water from the environment contained more bacterial species than tap water, but these bacteria were not consistently detected in adult mosquitoes. Our results suggest that rearing mosquito larvae in water collected from local environments as opposed to laboratory tap water, as is conventional, provides a more realistic assessment of vector competence since it better recapitulates the natural environment in which larvae develop. Given that laboratory vector competence is used to define the species to target for control, use of environmental water to rear larvae could better approximate the microbial exposures of wild mosquitoes, lessening the potential for overestimating transmission risk.

Abstract Background: Although the number of Zika virus (ZIKV) cases has substantially declined in Latin America and the Caribbean since the 2015-2016 outbreaks, the cohort of children born at that time and affected by congenital zika syndrome (CZS) are now around 4-5 years old and experiencing an ongoing impact on their health and development. Gaps in our understanding remain regarding the outcomes of ZIKV exposure in utero and congenital infection and the consequences of congenital zika syndrome (CZS) for health throughout childhood. Methods: The ZIKAction Paediatric Registry is an international multi-centre registry of infants and children with documented ZIKV exposure in utero (i.e. born to mother with confirmed infection in pregnancy) and/or with confirmed or suspected congenital ZIKV infection. Clinical teams at participating sites in Argentina, Brazil and Jamaica conduct retrospective case note reviews of children eligible for inclusion in the Registry and enter pseudonymised data into a central Registry database, with additional data collected prospectively on routine follow-up at some sites. Data collected will include sociodemographic, maternal and pregnancy information, delivery information and newborn assessment, paediatric clinical assessments (physical, neurological, developmental, ophthalmological, audiological), and laboratory results conducted as part of local standard of care. The ZIKAction Paediatric Registry network will conduct pooled analyses to address questions relating to characteristics, health and neurodevelopmental outcomes of this population. The Registry is embedded within a larger programme of research studies conducted by ZIKAction. Discussion: As the health outcomes of children affected by ZIKV continue to unfold, this paediatric registry will provide comprehensive data on their clinical and neurodevelopmental outcomes, growth and management, as well as on later sequelae. This will inform their support and care and provide potential insights on pathogenesis of the disease, of importance to currently affected families and for the response to possible future outbreaks. It will highlight the service needs of the affected populations in Latin America and the Caribbean and allow the identification of potential participants for future studies.

ABSTRACT Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly emerging virus responsible for the ongoing Covid-19 pandemic with no known effective prophylaxis. We investigated whether hydroxychloroquine(HCQ) could prevent SARS CoV-2 in healthcare workers(HCW) at high-risk of exposure. Method This voluntary observational study for the prevention and treatment of COVID-19 was conducted at a tertiary care center, from 12 th June to 12th October 2020(total 16 weeks). All consented asymptomatic HCW’s of CIMS hospital were administered 400 mg HCQ twice a day on day one followed by 400 mg once weekly to be taken with meals up to 16 weeks. Data collected included OPD registration, risk assessment, medical and family history (related to COVID), physical examination and vitals, pulse oximetry, ECG (pre and post HCQ), drug adherence, side effects, adverse drug reactions. Result The study enrolled 927 full-time, hospital-based HCWs ((including doctors, nurses, paramedical, lab technicians, sanitary workers and others), of whom 731(78.85%) initially started HCQ while 196 (21.14%) did not volunteer. The median age and weight of the study population was 27.5 years and 69.5 kg respectively. No major associated co-morbidities were present in these HCW’s. There was an increased trend towards non adherence to HCQ with each proceeding week more so after week 11. Of the 731 HCW’s taking HCQ a total of 167(22.8%) tested COVID positive at different intervals of time as against 30 HCW (15.3%) out of 196 not taking HCQ. The rate of COVID-19 positive was statistically significantly higher in the HCW’s taking HCQ (p=0.0220; 95% CI: 1.14% to 12.94%), as compared to those not on HCQ. Thus HCQ was not prophylactically effective against COVID 19 infection. No participants in this study experienced grade 3 or 4 adverse events. No significant difference in the median of ECG changes in QTc between pre and post HCQ administration of 46 HCW’s was observed. Conclusions This clinical study did not detect a reduction in SARS CoV-2 transmission with prophylactic administration of 400 mg/HCQ in HCW’s. All participants who did contract SARSCoV-2 were either asymptomatic or had mild disease courses with full recoveries. All adverse events were self-limiting and no serious cardiovascular events were reported with use of HCQ. In the absence of robust data, it seems premature to recommend HCQ as a prophylactic panacea for COVID-19.

Wastewater surveillance of SARS-CoV-2 has shown to be a valuable source of information regarding SARS-CoV-2 transmission and COVID-19 cases. Though the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens surveilled through wastewater. The aim of this study is to identify what infectious diseases have been previously studied via wastewater surveillance prior to the COVID-19 Pandemic and identify common characteristics between the studies, as well as identify current gaps in knowledge. Peer-reviewed articles published as of August 1, 2020 that examined wastewater for communicable and infectious human pathogens on 2 or more occasions were included in the study. Excluded from this list were all reviews and methods papers, single collection studies, and non-human pathogens. Infectious diseases and pathogens were identified in studies of wastewater surveillance, as well as themes of how wastewater surveillance and other measures of disease transmission were linked. This review did not include any numerical data from individual studies and thus no statistical analysis was done. 1005 articles were identified but only 100 were included in this review after applying the inclusion criteria. These studies came from 38 countries with concentration in certain countries including Italy, Israel, Brazil, Japan, and China. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and non-polio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did compare wastewater surveillance to other measures of disease transmission the value observed was dependent upon pathogen and varied by study. Wastewater surveillance has historically been used to assess water-borne and fecal-orally transmitted pathogens causing diarrheal disease. However, numerous other types of pathogens have been surveilled using wastewater and wastewater surveillance should be considered as a potential tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.

Zika virus (ZIKV) is a mosquito-borne flavivirus, and its infection may cause severe neurodegenerative diseases. The outbreak of ZIKV in 2015 in South American has caused severe human congenital and neurologic disorders. Thus, it is vitally important to figure out inner mechanism of ZIKV infection. Here, our data suggested that the ubiquitin-specific peptidase 38 (USP38) played an important role in host resistance to ZIKV infection, during which ZIKV infection did not affect USP38 expression. Mechanistically, USP38 bound to ZIKV envelope (E) protein through its C-terminal domain and attenuated its K48-linked and K63-linked polyubiquitination, thereby repressed the infection of ZIKV. In addition, we found that the deubiquitinase activity of USP38 was essential to inhibit ZIKV infection, and the mutant that lacked the deubiquitinase activity of USP38 lost ability to inhibit the infection. In conclusion, we found a novel host protein USP38 against ZIKV infection, and this may represent a potential therapeutic target for the treatment and prevention of ZIKV infection.

The 3C-like protease (3CLpro) of SARS-CoV-2 is an attractive drug target for developing antivirals against SARS-CoV-2. A few small molecule inhibitors of 3CLpro are in clinical trials for COVID-19 treatments and more inhibitors are being developed. One limiting factor for 3CLpro inhibitors development is that the cellular activities of such inhibitors have to be evaluated in a Biosafety Level 3 (BSL-3) or BSL-4 laboratory. Here, we design genetically encoded biosensors that can be used in BSL-2 laboratories to set up cell-based assays for 3CLpro inhibitor discovery. The biosensors were constructed by linking a green fluorescent protein (GFP2) to the N-terminus and a Renilla luciferase (RLuc8) to the C-terminus of SARS-CoV-2 3CLpro, with the linkers derived from the cleavage sequences of 3CLpro. After over-expression of the biosensors in HEK293 cells, 3CLpro can be released from GFP2 and RLuc by self-cleavage, resulting in a decrease of the bioluminescence resonance energy transfer (BRET) signal. Using one of these biosensors, pBRET-10, we evaluated the cellular activities of several 3CLpro inhibitors. These inhibitors restored the BRET signal by blocking the proteolysis of pBRET-10, and their relative activities measured using pBRET-10 were consistent with their anti-SARS-CoV-2 activities reported previously. We conclude that the biosensor pBRET-10 is a useful tool for SARS-CoV-2 3CLpro inhibitor discovery. Furthermore, our strategy can be used to design biosensors for other viral proteases that share the same activation mechanism as 3CLpro, such as HIV protease PR and HCV protease NS3. Highlights Sensitive cell-based biosensors for 3CLpro inhibitor discovery in BSL-2 laboratories. The BRET-based self-cleaving biosensors mimic the in vivo autoproteolytic activation of 3CLpro. Similar biosensors can be designed for other self-cleaving proteases, such as HIV protease PR and HCV protease NS3.

The use of social media data, like Twitter, for biomedical research has been gradually increasing over the years. With the COVID-19 pandemic, researchers have turned to more nontraditional sources of clinical data to characterize the disease in near real-time, study the societal implications of interventions, as well as the sequelae that recovered COVID-19 cases present (Long-COVID). However, manually curated social media datasets are difficult to come by due to the expensive costs of manual annotation and the efforts needed to identify the correct texts. When datasets are available, they are usually very small and their annotations do not generalize well over time or to larger sets of documents. As part of the 2021 Biomedical Linked Annotation Hackathon, we release our dataset of over 120 million automatically annotated tweets for biomedical research purposes. Incorporating best practices, we identify tweets with potentially high clinical relevance. We evaluated our work by comparing several SpaCy-based annotation frameworks against a manually annotated gold-standard dataset. Selecting the best method to use for automatic annotation, we then annotated 120 million tweets and released them publicly for future downstream usage within the biomedical domain.

ABSTRACT Accurate tracing of epidemic spread over space enables effective control measures. We examined three metrics of infection and disease in a pediatric cohort (N ≈ 3,000) over two chikungunya and one Zika epidemic, and in a household cohort (N=1,793) over one COVID-19 epidemic in Managua, Nicaragua. We compared spatial incidence rates (cases/total population), infection risks (infections/total population), and disease risks (cases/infected population). We used generalized additive and mixed-effects models, Kulldorf’s spatial scan statistic, and intracluster correlation coefficients. Across different analyses and all epidemics, incidence rates considerably underestimated infection and disease risks, producing large and spatially non-uniform biases distinct from biases due to incomplete case ascertainment. Infection and disease risks exhibited distinct spatial patterns, and incidence clusters inconsistently identified areas of either risk. While incidence rates are commonly used to infer infection and disease risk in a population, we find that this can induce substantial biases and adversely impact policies to control epidemics. Article summary line Inferring measures of spatial risk from case-only data can substantially bias estimates, thereby weakening and potentially misdirecting measures needed to control an epidemic.

Motivation The assembly of contiguous sequence from metagenomic samples presents a particular challenge, due to the presence of multiple species, often closely related, at varying levels of abundance. Capturing diversity within species, for example viral haplotypes, or bacterial strain-level diversity, is even more challenging. Results We present MetaCortex, a metagenome assembler that captures intra-species diversity by searching for signatures of local variation along assembled sequences in the underlying assembly graph and outputting these sequences in sequence graph format. We show that MetaCortex produces accurate assemblies with higher genome coverage and contiguity than other popular metagenomic assemblers on mock viral communities with high levels of strain level diversity, and on simulated communities containing simulated strains. Availability and Implementation Source code is freely available to download from https://github.com/SR-Martin/metacortex , is implemented in C and supported on MacOS and Linux. Contact richard.leggett@earlham.ac.uk Supplementary information Supplementary materials are available at the journal’s website. All assemblies, simulated reads, and simulated genomes used in this paper have been deposited online on Zenodo and can be found at DOI 10.5281/zenodo.6616437.

Diseases caused by Dengue (DENV) and Zika (ZIKV) viruses cause significant mortality and illness globally. Due to the high sequence similarity of the viral proteins and the purported cross-reactive immune responses against the viruses, we envisioned a common multi-epitope vaccine (MEV) against both viruses by adopting a novel approach of identifying “immunogenic hotspots”. These stretches of the structural and non-structural proteins are enriched with MHC class I and class II supertype-restricted T cell epitopes, and B cell epitopes, in addition to being highly conserved between different DENV serotypes and ZIKV. Such an approach ensures inclusion of multiple overlapping T and B cell epitopes common to both viruses, and also warrants high population coverage. Importantly, epitopes known to cause antibody-dependent-enhancement of infection have been excluded. These immunogenic hotspots have then been stitched together with linkers in-silico along with an adjuvant, CTxB to develop the MEV candidate. Four structural models of the MEV were selected on the basis of conformational preservation of CTxB, and their biophysical parameters, which also conserved the immunogenicity of the multiple epitopes. Importantly, each of the MEV candidates were found to interact with TLR4-MD2 complex by molecular docking studies, indicative of their ability to induce TLR-mediated immune responses.

The first reports of COVID-19 cases were traced in Wuhan City, China, in late December 2019, post which, the deadly virus rapidly registered itself into the category of pandemics. It has continued to upend lives across the world ever since. “Lockdowns” have ensued, aimed at saving lives by putting the virus on leash, and preventing health systems from being overrun. Such quarantine measures have led to economic depression, leaving millions jobless, befalling deplorably the more vulnerable sections of society, women and girls being the primary unseen targets globally. The socio-economic downturns of the pandemic, such as closure of work places, child day-care facilities, schools, decrease in cross-country migration, and so on, have impacted women across different strata. In this article, we have attempted to collect and collate information related to the impact of the COVID-19 pandemic on women and girls in South Asia. Owing to unavailability of sufficient research literature on the gendered aspect of COVID-19 in South Asia, we present excerpts and case studies from various local sources like newspapers, blogs, online archives, press releases, journal articles, and some statistics of gendered impact of COVID-19 from well-respected sources. Through this article we aim to illuminate the reader about the plight of women in such a distressful time, a matter particularly less-focused on by the governments in South Asia, at the same time highlight the importance of addressing the alarming issue of staggering gender imbalance in bringing our world back to an equilibrium and achieving the Sustainable Development Goals (SDGs).

The COVID-19 pandemic raises serious questions about the operation of international agreements for accessing and sharing viruses potentially delaying emergency responses. The access and benefit-sharing (ABS) frameworks under the United Nations’ Convention on Biological Diversity and its Nagoya Protocol apply to the collection and use of the COVID-19 pathogen SARS-CoV-2. These frameworks aim to ensure countries of origin reap some of the benefits from the use of their resources. Using real-world examples, we demonstrate conceptual and definitional ambiguities relating to “country of origin” that make not only operationalising the ABS scheme for biodiversity conservation and sustainable use objectives difficult but may also undermine public health emergency responses. Understanding how COVID-19 fits (or does not fit) within ABS laws is a valuable exercise for international policymakers trying to determine how best to operationalise pathogen ABS, an issue currently under examination at the World Health Organization and critical to responding to pandemics.

Increasing evidence of new-onset diabetes during the COVID19 pandemic indicates that the SARS-CoV2 virus may drive beta-cell dysfunction leading to diabetes, but it is unclear if it is a primary or secondary effect. Here, we present evidence of SARS-CoV-2 infection of pancreatic beta cells in vivo using a robust and reproducible non-human primates model of mild to moderate COVID19 pathogenesis. Pancreas from SARS-CoV-2 infected subjects were positive for the SARS-CoV2 spike protein by immunohistochemistry and structures indicative of viral replication were evident by electron microscopy. Total beta cell area was decreased in SARS-CoV-2-infected pancreas, attributable to beta cell atrophy. Beta cell granularity was decreased. These histologic phenotypes persisted beyond the duration of the clinical disease course. Detailed electron microscopy of SARS-CoV-2 infected beta-cells revealed ultrastructural hallmarks of beta cell stress that are seen in islets of patients with Type 2 diabetes, including disrupted mitochondria and dilated endoplasmic reticulum. To assess the metabolic status of beta cells from SARS-CoV-2-infected subjects, we used fluorescence life-time imaging to measure the ratio of free and bound NADH as a surrogate of glycolytic and oxidative metabolism. We report an increase in free NADH levels, suggesting that beta cells from SARS-CoV-2-infected subjects adopt a more glycolytic metabolic profile. Taken together, we conclude that SARS-CoV-2 infection induces beta cell stress that may compromise beta-cell function beyond the duration of the disease course. This raises the possibility that the beta cell stress and injury may have clinical implications of the long-term future health of patients that have recovered from COVID19.

Establishment of the interferon (IFN)-mediated antiviral state provides a crucial initial line of defense against viral infection. Numerous genes that contribute to this antiviral state remain to be identified. Using a loss-of-function strategy, we screened an original library of 1156 siRNAs targeting 386 individual curated human genes in stimulated microglial cells infected with Zika virus (ZIKV), an emerging RNA virus that belongs to the flavivirus genus. The screen recovered twenty-one potential host proteins that modulate ZIKV replication in an IFN-dependent manner, including the previously known IFITM3 and LY6E. Further characterization contributed to delineate the spectrum of action of these genes towards other pathogenic RNA viruses, including Hepatitis C virus and SARS-CoV-2. Our data revealed that APOL3 acts as a proviral factor for ZIKV and several other related and unrelated RNA viruses. In addition, we showed that MTA2, a chromatin remodeling factor, possesses potent flavivirus-specific antiviral functions. Our work identified previously unrecognized genes that modulate the replication of RNA viruses in an IFN-dependent way, opening new perspectives to target weakness points in the life cycle of these viruses.