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Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) is a novel human coronavirus that was identified in 2019. SARS-CoV-2 infection results in an acute, severe respiratory disease called coronavirus disease 2019 (COVID-19). The emergence and rapid spread of SARS-CoV-2 has led to a global public health crisis, which continues to affect populations across the globe. Real time reverse transcription polymerase chain reaction (RT-PCR) is the reference standard test for COVID-19 diagnosis. Serological tests are valuable tools for serosurveillance programs and establishing correlates of protection from disease. This study evaluated the performance of one in-house enzyme linked immunosorbent assay (ELISA) utilizing the pre-fusion stabilized ectodomain of SARS-CoV-2 spike (S), two commercially available chemiluminescence assays Ortho VITROS Immunodiagnostic Products Anti-SARS-CoV-2 Total Reagent Pack and Abbott SARS-CoV-2 IgG assay and one commercially available Surrogate Virus Neutralization Test (sVNT), GenScript USA Inc., cPass SARS-CoV-2 Neutralization Antibody Detection Kit for the detection of SARS-CoV-2 specific antibodies. Using a panel of RT-PCR confirmed COVID-19 patients’ sera and a negative control group as a reference standard, all three immunoassays demonstrated high comparable positivity rates and low discordant rates. All three immunoassays were highly sensitive with estimated sensitivities ranging from 95.4%-96.6%. ROC curve analysis indicated that all three immunoassays had high diagnostic accuracies with area under the curve (AUC) values ranging from 0.9698-0.9807. High positive correlation was demonstrated among the conventional microneutralization test (MNT) titers and the sVNT inhibition percent values. Our study indicates that independent evaluations are necessary to optimize the overall utility and the interpretation of the results of serological tests. Overall, we demonstrate that all serological tests evaluated in this study are suitable for the detection of SARS-CoV-2 antibodies.

Genomic surveillance is a critical tool for tracking emerging variants of SARS-CoV-2 (the virus that causes COVID-19), which can exhibit characteristics that potentially affect public health and clinical interventions, including increased transmissibility, illness severity, and capacity for immune escape. During June 2021-January 2022, CDC expanded genomic surveillance data sources to incorporate sequence data from public repositories to produce weighted estimates of variant proportions at the jurisdiction level and refined analytic methods to enhance the timeliness and accuracy of national and regional variant proportion estimates. These changes also allowed for more comprehensive variant proportion estimation at the jurisdictional level (i.e., U.S. state, district, territory, and freely associated state). The data in this report are a summary of findings of recent proportions of circulating variants that are updated weekly on CDC's COVID Data Tracker website to enable timely public health action.

IntroductoryThe evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of many new variant lineages that have exacerbated the COVID-19 pandemic. Some of those variants were designated as variants of concern/interest (VOC/VOI) by national or international authorities based on many factors including their potential impact on vaccines. To ascertain and rank the risk of VOCs and VOIs, we analyzed their ability to escape from vaccine-induced antibodies. The variants showed differential reductions in neutralization and replication titers by post-vaccination sera. Although the Omicron variant showed the most escape from neutralization, sera collected after a third dose of vaccine (booster sera) retained moderate neutralizing activity against that variant. Therefore, vaccination remains the most effective strategy to combat the COVID-19 pandemic.

Summary Background The ongoing Ebola virus outbreak in the Ituri and North Kivu Provinces of the Democratic Republic of the Congo, which began in July, 2018, is the second largest ever recorded. Despite civil unrest, outbreak control measures and the administration of experimental therapies and a vaccine have been initiated. The aim of this study was to test the efficacy of candidate therapies and diagnostic tests with the outbreak strain Ituri Ebola virus. Lacking a virus isolate from this outbreak, a recombinant Ituri Ebola virus was compared with a similarly engineered Makona virus from the 2013–16 outbreak. Methods Using Ebola virus sequences provided by organisations in DR Congo and a reverse genetics system, we generated an authentic Ebola virus from the ongoing outbreak in Ituri and North Kivu provinces. To relate this virus to other Ebola viruses in DR Congo, we did a phylogenetic analysis of representative complete Ebola virus genome sequences from previous outbreaks. We evaluated experimental therapies being tested in clinical trials in DR Congo, including remdesivir and ZMapp monoclonal antibodies, for their ability to inhibit the growth of infectious Ituri Ebola virus in cell culture. We also tested diagnostic assays for detection of the Ituri Ebola virus sequence. Findings The phylogenetic analysis of whole-genome sequences from each Ebola virus outbreak suggests there are at least two Ebola virus strains in DR Congo, which have independently crossed into the human population. The Ituri Ebola strain initially grew slower than the Makona strain, yet reached similar mean yields of 3 × 107 50% tissue culture infectious dose by 72 h infection in Huh-7 cells. Ituri Ebola virus was similar to Makona in its susceptibility to inhibition by remdesivir and to neutralisation by monoclonal antibodies from ZMapp and other monoclonal antibodies. Remdesivir inhibited Ituri Ebola virus at a 50% effective concentration (EC50) of 12nM (with a selectivity index of 303) and Makona Ebola virus at 13nM (with a selectivity index of 279). The Zmapp monoclonal antibodies 2G4 and 4G7 neutralised Ituri Ebola virus with a mean EC50 of 0·24 μg/mL and 0·48 μg/mL, and Makona Ebola virus with a mean EC50 of 0·45 μg/mL and 0·2 μg/mL. The Xpert Ebola and US Centers for Disease Control and Prevention real-time RT-qPCR diagnostic assays detected Ituri and Makona Ebola virus sequences with similar sensitivities and efficiencies, despite primer site binding mismatches in the Ituri Ebola virus. Interpretation Our findings provide a rationale for the continued testing of investigational therapies, confirm the effectiveness of the diagnostic assays used in the region, and establish a paradigm for the use of reverse genetics to inform response activities in an outbreak. Funding US Centers for Disease Control and Prevention.

Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection, we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results, we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms present at nearly 20% in East Asian populations reduce flavivirus infection. Based on our mechanistic studies, we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication., Graphical Abstract, Hoffmann et al. determine that the transmembrane protein, TMEM41B, is required for infection by members of the Flaviviridae family of viruses. Loss of TMEM41B reduces viral RNA replication and increases innate immune activation in response to flavivirus infection. Thus, TMEM41B is a potential host target for antiviral therapeutics.

Significance Remdesivir is a nucleotide analog prodrug that has been evaluated in humans against acute Ebola virus disease; it also recently received emergency use authorization for treating COVID-19. For antiviral product development, the Food and Drug Administration recommends the characterization of in vitro selected resistant viruses to define the specific antiviral mechanism of action. This study identified a single amino acid residue in the Ebola virus polymerase that conferred low-level resistance to remdesivir. The significance of our study lies not only in characterizing this particular mutation, but also in relating it to a resistance mutation observed in a similar structural motif of coronaviruses. Our findings thereby indicate a consistent mechanism of action by remdesivir across genetically divergent RNA viruses causing diseases of high consequence in humans., Remdesivir is a broad-spectrum antiviral nucleotide prodrug that has been clinically evaluated in Ebola virus patients and recently received emergency use authorization (EUA) for treatment of COVID-19. With approvals from the Federal Select Agent Program and the Centers for Disease Control and Prevention’s Institutional Biosecurity Board, we characterized the resistance profile of remdesivir by serially passaging Ebola virus under remdesivir selection; we generated lineages with low-level reduced susceptibility to remdesivir after 35 passages. We found that a single amino acid substitution, F548S, in the Ebola virus polymerase conferred low-level reduced susceptibility to remdesivir. The F548 residue is highly conserved in filoviruses but should be subject to specific surveillance among novel filoviruses, in newly emerging variants in ongoing outbreaks, and also in Ebola virus patients undergoing remdesivir therapy. Homology modeling suggests that the Ebola virus polymerase F548 residue lies in the F-motif of the polymerase active site, a region that was previously identified as susceptible to resistance mutations in coronaviruses. Our data suggest that molecular surveillance of this region of the polymerase in remdesivir-treated COVID-19 patients is also warranted.

SARS-CoV-2 emerged in late 2019 and has since spread around the world, causing a pandemic of the respiratory disease COVID-19. Detecting antibodies against the virus is an essential tool for tracking infections and developing vaccines. Such tests, primarily utilizing the enzyme-linked immunosorbent assay (ELISA) principle, can be either qualitative (reporting positive/negative results) or quantitative (reporting a value representing the quantity of specific antibodies). Quantitation is vital for determining stability or decline of antibody titers in convalescence, efficacy of different vaccination regimens, and detection of asymptomatic infections. Quantitation typically requires two-step ELISA testing, in which samples are first screened in a qualitative assay and positive samples are subsequently analyzed as a dilution series. To overcome the throughput limitations of this approach, we developed a simpler and faster system that is highly automatable and achieves quantitation in a single-dilution screening format with sensitivity and specificity comparable to those of ELISA.

There are no approved therapies for Ebola virus infection. Here, to find potential therapeutic targets, we perform a screen for genes essential for Ebola virus (EBOV) infection. We identify GNPTAB, which encodes the α and β subunits of N-acetylglucosamine-1-phosphate transferase. We show that EBOV infection of a GNPTAB knockout cell line is impaired, and that this is reversed by reconstituting GNPTAB expression. Fibroblasts from patients with mucolipidosis II, a disorder associated with mutations in GNPTAB, are refractory to EBOV, whereas cells from their healthy parents support infection. Impaired infection correlates with loss of the expression of cathepsin B, known to be essential for EBOV entry. GNPTAB activity is dependent upon proteolytic cleavage by the SKI-1/S1P protease. Inhibiting this protease with the small-molecule PF-429242 blocks EBOV entry and infection. Disruption of GNPTAB function may represent a strategy for a host-targeted therapy for EBOV., Genetic screens are important tools to identify host factors associated with viral infections. Here, Flint et al. perform a genome-wide CRISPR screen using infectious Ebola virus (EBOV) and show that the host transferase GNPTAB is required for EBOV infection and a potential target for antiviral therapies

Crimean-Congo hemorrhagic fever virus is an important human pathogen with a wide global distribution for which no therapeutic interventions are available. CCHFV encodes a cysteine protease belonging to the ovarian tumor (OTU) family which is involved in host immune suppression. Here we demonstrate that artificially prolonged binding of the OTU to a substrate inhibits virus infection. This provides novel insights into CCHFV OTU function during the viral replicative cycle and highlights the OTU as a potential antiviral target., Crimean-Congo hemorrhagic fever virus (CCHFV) infection can result in a severe hemorrhagic syndrome for which there are no antiviral interventions available to date. Certain RNA viruses, such as CCHFV, encode cysteine proteases of the ovarian tumor (OTU) family that antagonize interferon (IFN) production by deconjugating ubiquitin (Ub). The OTU of CCHFV, a negative-strand RNA virus, is dispensable for replication of the viral genome, despite being part of the large viral RNA polymerase. Here, we show that mutations that prevent binding of the OTU to cellular ubiquitin are required for the generation of recombinant CCHFV containing a mutated catalytic cysteine. Similarly, the high-affinity binding of a synthetic ubiquitin variant (UbV-CC4) to CCHFV OTU strongly inhibits viral growth. UbV-CC4 inhibits CCHFV infection even in the absence of intact IFN signaling, suggesting that its antiviral activity is not due to blocking the OTU’s immunosuppressive function. Instead, the prolonged occupancy of the OTU with UbV-CC4 directly targets viral replication by interfering with CCHFV RNA synthesis. Together, our data provide mechanistic details supporting the development of antivirals targeting viral OTUs.

Lassa virus (LASV) and Ebola virus (EBOV) infections are important global health issues resulting in significant morbidity and mortality. While several promising drug and vaccine trials for EBOV are ongoing, options for LASV infection are currently limited to ribavirin treatment. A major factor impeding the development of antiviral compounds to treat these infections is the need to manipulate the virus under BSL-4 containment, limiting research to a few institutes worldwide. Here we describe the development of a novel LASV minigenome assay based on the ambisense LASV S segment genome, with authentic terminal untranslated regions flanking a ZsGreen (ZsG) fluorescent reporter protein and a Gaussia princeps luciferase (gLuc) reporter gene. This assay, along with a similar previously established EBOV minigenome, was optimized for high-throughput screening (HTS) of potential antiviral compounds under BSL-2 containment. In addition, we rescued a recombinant LASV expressing ZsG, which, in conjunction with a recombinant EBOV reporter virus, was used to confirm any potential antiviral hits in vitro. Combining an initial screen to identify potential antiviral compounds at BSL-2 containment before progressing to HTS with infectious virus will reduce the amount of expensive and technically challenging BSL-4 containment research. Using these assays, we identified 6-azauridine as having anti-LASV activity, and demonstrated its anti-EBOV activity in human cells. We further identified 2'-deoxy-2'-fluorocytidine as having potent anti-LASV activity, with an EC50 value 10 times lower than that of ribavirin.

During the Ebola virus outbreak of 2013-2016, the Viral Special Pathogens Branch field laboratory in Sierra Leone tested approximately 26 000 specimens between August 2014 and October 2015. Analysis of the B2M endogenous control Ct values showed its utility in monitoring specimen quality, comparing results with different specimen types, and interpretation of results. For live patients, blood is the most sensitive specimen type and oral swabs have little diagnostic utility. However, swabs are highly sensitive for diagnostic testing of corpses.

The most recent Ebola virus outbreak in West Africa, which was unprecedented in the number of cases and fatalities, geographic distribution, and number of nations affected, highlights the need for safe, effective, and readily available antiviral agents for treatment and prevention of acute Ebola virus (EBOV) disease (EVD) or sequelae. No antiviral therapeutics have yet received regulatory approval or demonstrated clinical efficacy. Here we report the discovery of a novel small molecule GS-5734, a monophosphoramidate prodrug of an adenosine analogue, with antiviral activity against EBOV. GS-5734 exhibits antiviral activity against multiple variants of EBOV and other filoviruses in cell-based assays. The pharmacologically active nucleoside triphosphate (NTP) is efficiently formed in multiple human cell types incubated with GS-5734 in vitro, and the NTP acts as an alternative substrate and RNA-chain terminator in primer-extension assays using a surrogate respiratory syncytial virus RNA polymerase. Intravenous administration of GS-5734 to nonhuman primates resulted in persistent NTP levels in peripheral blood mononuclear cells (half-life, 14 h) and distribution to sanctuary sites for viral replication including testes, eyes, and brain. In a rhesus monkey model of EVD, once-daily intravenous administration of 10 mg kg(-1) GS-5734 for 12 days resulted in profound suppression of EBOV replication and protected 100% of EBOV-infected animals against lethal disease, ameliorating clinical disease signs and pathophysiological markers, even when treatments were initiated three days after virus exposure when systemic viral RNA was detected in two out of six treated animals. These results show the first substantive post-exposure protection by a small-molecule antiviral compound against EBOV in nonhuman primates. The broad-spectrum antiviral activity of GS-5734 in vitro against other pathogenic RNA viruses, including filoviruses, arenaviruses, and coronaviruses, suggests the potential for wider medical use. GS-5734 is amenable to large-scale manufacturing, and clinical studies investigating the drug safety and pharmacokinetics are ongoing.

Odds of survival were greatest when first Ebola virus–positive blood sample collected had low viral load., To determine whether 2 readily available indicators predicted survival among patients with Ebola virus disease in Sierra Leone, we evaluated information for 216 of the 227 patients in Bo District during a 4-month period. The indicators were time from symptom onset to healthcare facility admission and quantitative real-time reverse transcription PCR cycle threshold (Ct), a surrogate for viral load, in first Ebola virus–positive blood sample tested. Of these patients, 151 were alive when detected and had reported healthcare facility admission dates and Ct values available. Time from symptom onset to healthcare facility admission was not associated with survival, but viral load in the first Ebola virus–positive blood sample was inversely associated with survival: 52 (87%) of 60 patients with a Ct of >24 survived and 20 (22%) of 91 with a Ct of

Background: The ongoing Ebola virus (EBOV) outbreak in the Ituri and North Kivu provinces of the Democratic Republic of Congo (DRC) is the second largest ever recorded. Despite civil unrest, outbreak control measures, and the administration of experimental therapies and a vaccine, have been initiated. Lacking a virus isolate from this outbreak, we rescued recombinant, infectious EBOV-Ituri virus from plasmid DNA. Methods: We report a phylogenetic analysis of EBOV-Ituri. In addition, we evaluated experimental therapeutics currently undergoing clinical trials in DRC: remdesivir (GS-5734) and ZMapp monoclonal antibodies (mAbs) to inhibit EBOVI-Ituri. We also tested diagnostic assays used in DRC for detection of the EBOV-Ituri sequence despite having mismatches in the primer binding sites. EBOV-Ituri results were compared with the 2013-2016 outbreak EBOV-Makona. Findings: Our analysis suggests there are at least 2 EBOV strains in DRC, which have independently crossed into the human population. The EBOV-Ituri strain initially grew significantly slower than EBOV-Makona from the 2013-2016 outbreak, yet reached similar titers by 72H p.i. EBOV-Ituri was similar to EBOV-Makona in its susceptibility to inhibition by remdesivir, neutralizing ZMapp, and other EBOV mAbs. The Xpert Ebola and CDC RT-qPCR diagnostic assays detected EBOV-Ituri with high sensitivity despite primer site binding mismatches. Interpretation: Our findings provide a rationale for the continued testing of investigational therapies, confirm the effectiveness of the diagnostic assay used in the region, and establish a paradigm for the use of reverse genetics-launched strains to inform response activities in an ongoing outbreak. Funding: US Centers for Disease Control and Prevention. Declaration of Interest: Danielle Porter is an employee of Gilead. Ethical Approval: Not needed.

We report here the complete genome sequences for all three segments of the New York hantavirus (New York 1). This is the first reported L segment sequence for hantaviruses maintained in Peromyscus spp. endemic to the eastern United States and Canada.

Host cell kinases are important for the replication of a number of hemorrhagic fever viruses. We tested a panel of kinase inhibitors for their ability to block the replication of multiple hemorrhagic fever viruses. OSU-03012 inhibited the replication of Lassa, Ebola, Marburg and Nipah viruses, whereas BIBX 1382 dihydrochloride inhibited Lassa, Ebola and Marburg viruses. BIBX 1382 blocked both Lassa and Ebola virus glycoprotein-dependent cell entry. These compounds may be used as tools to understand conserved virus–host interactions, and implicate host cell kinases that may be targets for broad spectrum therapeutic intervention.

In August 2014, the Viral Special Pathogens Branch of the US Centers for Disease Control and Prevention established a field laboratory in Sierra Leone in response to the ongoing Ebola virus outbreak. Through March 2015, this laboratory tested >12 000 specimens from throughout Sierra Leone. We describe the organization and procedures of the laboratory located in Bo, Sierra Leone.

No antiviral therapies are available for the tick-borne flaviviruses associated with hemorrhagic fevers: Kyasanur Forest disease virus (KFDV), both classical and the Alkhurma hemorrhagic fever virus (AHFV) subtype, and Omsk hemorrhagic fever virus (OHFV). We tested compounds reported to have antiviral activity against members of the Flaviviridae family for their ability to inhibit AHFV replication. 6-Azauridine (6-azaU), 2′-C-methylcytidine (2′-CMC), and interferon alpha 2a (IFN-α2a) inhibited the replication of AHFV and also KFDV, OHFV, and Powassan virus. The combination of IFN-α2a and 2′-CMC exerted an additive antiviral effect on AHFV, and the combination of IFN-α2a and 6-azaU was moderately synergistic. The combination of 2′-CMC and 6-azaU was complex, being strongly synergistic but with a moderate level of antagonism. The antiviral activity of 6-azaU was reduced by the addition of cytidine but not guanosine, suggesting that it acted by inhibiting pyrimidine biosynthesis. To investigate the mechanism of action of 2′-CMC, AHFV variants with reduced susceptibility to 2′-CMC were selected. We used a replicon system to assess the substitutions present in the selected AHFV population. A double NS5 mutant, S603T/C666S, and a triple mutant, S603T/C666S/M644V, were more resistant to 2′-CMC than the wild-type replicon. The S603T/C666S mutant had a reduced level of replication which was increased when M644V was also present, although the replication of this triple mutant was still below that of the wild type. The S603 and C666 residues were predicted to lie in the active site of the AHFV NS5 polymerase, implicating the catalytic center of the enzyme as the binding site for 2′-CMC.

During outbreaks of infectious diseases or in cases of severely ill patients, it is imperative to identify the causative agent. This report describes several events in which virus isolation and identification by electron microscopy were critical to initial recognition of the etiologic agent, which was further analyzed by additional laboratory diagnostic assays. Examples include severe acute respiratory syndrome coronavirus, and Nipah, lymphocytic choriomeningitis, West Nile, Cache Valley, and Heartland viruses. These cases illustrate the importance of the techniques of cell culture and electron microscopy in pathogen identification and recognition of emerging diseases.

Viruses in the Ebolavirus and Marburgvirus genera (family Filoviridae ) have been associated with large outbreaks of hemorrhagic fever in human and nonhuman primates. The first documented cases occurred in primates over 45 years ago, but the amount of virus genetic diversity detected within bat populations, which have recently been identified as potential reservoir hosts, suggests that the filoviruses are much older. Here, detailed Bayesian coalescent phylogenetic analyses are performed on 97 whole-genome sequences, 55 of which are newly reported, to comprehensively examine molecular evolutionary rates and estimate dates of common ancestry for viruses within the family Filoviridae . Molecular evolutionary rates for viruses belonging to different species range from 0.46 × 10 −4 nucleotide substitutions/site/year for Sudan ebolavirus to 8.21 × 10 −4 nucleotide substitutions/site/year for Reston ebolavirus . Most recent common ancestry can be traced back only within the last 50 years for Reston ebolavirus and Zaire ebolavirus species and suggests that viruses within these species may have undergone recent genetic bottlenecks. Viruses within Marburg marburgvirus and Sudan ebolavirus species can be traced back further and share most recent common ancestors approximately 700 and 850 years before the present, respectively. Examination of the whole family suggests that members of the Filoviridae , including the recently described Lloviu virus, shared a most recent common ancestor approximately 10,000 years ago. These data will be valuable for understanding the evolution of filoviruses in the context of natural history as new reservoir hosts are identified and, further, for determining mechanisms of emergence, pathogenicity, and the ongoing threat to public health.

Volcanic ash falls are one of the most widespread and frequent volcanic hazards, and are produced by all explosive volcanic eruptions. Ash falls are arguably the most disruptive volcanic hazard because of their ability to affect large areas and to impact a wide range of assets, even at relatively small thicknesses. From an insurance perspective, the most valuable insured assets are buildings. Ash fall vulnerability curves or functions, which relate the magnitude of ash fall to likely damage, are the most developed for buildings, although there have been important recent advances for agriculture and infrastructure. In this paper, we focus on existing vulnerability functions developed for volcanic ash fall impact on buildings, and apply them to a hypothetical building portfolio impacted by a modern-day Tambora 1815 eruption scenario. We compare and contrast the different developed functions and discuss some of the issues surrounding estimation of potential building damage following a volcanic eruption. We found substantial variability in the different vulnerability estimates, which contribute to large uncertainties when estimating potential building damage and loss. Given the lack of detailed and published studies of building damage resulting from ash fall this is not surprising, although it also appears to be the case for other natural hazards for which there are far more empirical damage data. Notwithstanding the potential limitations of some empirical data in constraining vulnerability functions, efforts are required to improve our estimates of building damage under ash fall loading through the collection of damage data, experimental testing and perhaps theoretical failure analysis. For insurance purposes, the current building typologies provided for use with vulnerability functions are too detailed to map to the relatively limited information on building types that is typically available to insurers. Thus, efforts to provide vulnerability functions that can be used where only limited information is available regarding building types would also be valuable, both for insurers and for at-risk areas that have not been subject to detailed building vulnerability surveys. Published version

GS-5734 is a monophosphate prodrug of an adenosine nucleoside analog that showed therapeutic efficacy in a non-human primate model of Ebola virus infection. It has been administered under compassionate use to two Ebola patients, both of whom survived, and is currently in Phase 2 clinical development for treatment of Ebola virus disease. Here we report the antiviral activities of GS-5734 and the parent nucleoside analog across multiple virus families, providing evidence to support new indications for this compound against human viruses of significant public health concern.

Arenaviruses are rodent-borne viruses with a bisegmented RNA genome. A genetically unique arenavirus, Lujo virus, was recently discovered as the causal agent of a nosocomial outbreak of acute febrile illness with hemorrhagic manifestations in Zambia and South Africa. The outbreak had a case fatality rate of 80%. A reverse genetics system to rescue infectious Lujo virus from cDNA was established to investigate the biological properties of this virus. Sequencing the genomic termini showed unique nucleotides at the 3′ terminus of the S segment promoter element. While developing this system, we discovered that reconstructing infectious Lujo virus using the previously reported L segment intergenic region (IGR), comprising the arenaviral transcription termination signal, yielded an attenuated Lujo virus. Resequencing revealed that the correct L segment IGR was 36 nucleotides longer, and incorporating it into the reconstructed Lujo virus restored the growth rate to that of the authentic clinical virus isolate. These additional nucleotides were predicted to more than double the free energy of the IGR main stem-loop structure. In addition, incorporating the newly determined L-IGR into a replicon reporter system enhanced the expression of a luciferase reporter L segment. Overall, these results imply that an extremely stable secondary structure within the L-IGR is critical for Lujo virus propagation and viral protein production. The technology for producing recombinant Lujo virus now provides a method to precisely investigate the molecular determinants of virulence of this newly identified pathogen.

Two men from northwestern Missouri independently presented to a medical facility with fever, fatigue, diarrhea, thrombocytopenia, and leukopenia, and both had been bitten by ticks 5 to 7 days before the onset of illness. Ehrlichia chaffeensis was suspected as the causal agent but was not found on serologic analysis, polymerase-chain-reaction (PCR) assay, or cell culture. Electron microscopy revealed viruses consistent with members of the Bunyaviridae family. Next-generation sequencing and phylogenetic analysis identified the viruses as novel members of the phlebovirus genus. Although Koch's postulates have not been completely fulfilled, we believe that this phlebovirus, which is novel in the Americas, is the cause of this clinical syndrome.

The ESA (European Space Agency) Sentinel-5 Precursor (S-5 P) is a low Earth orbit polar satellite to provide information and services on air quality, climate and the ozone layer in the timeframe 2015-2022. The S-5 P mission is part of the Global Monitoring of the Environment and Security (GMES) Space Component Programme. The payload of the mission is the TROPOspheric Monitoring Instrument (TROPOMI) that will measure key atmospheric constituents including ozone, NO2, SO2, CO, CH4, CH2O and aerosol properties. TROPOMI has heritage to both the Ozone Monitoring Instrument (OMI) as well as to the SCanning Imaging Absorption spectroMeter for Atmospheric CartograpHY (SCIAMACHY). The S-5 P will extend the data records of these missions as well as be a preparatory mission for the Sentinel-5 mission planned for 2020 onward. The mission is pre-operational and is the link between the current scientific and the operational Sentinel-4/-5 missions. This contribution describes the science and mission objectives, the mission and the instrument, and the data products. While building on a solid foundation of the heritage instruments, the S-5P/TROPOMI mission is an exciting step forward with a strong focus on the troposphere. This is achieved by a combination of a high spatial resolution and improved signal-to-noise, as well as dedicated data product development. It is anticipated that the S-5 P mission will make a large contribution to the monitoring of the global atmospheric composition, as well as to the scientific knowledge of relevant atmospheric processes. © 2012 Elsevier Inc.

The hepatitis C virus (HCV) core gene is more conserved at the nucleic acid level than is necessary to preserve the sequence of the core protein, suggesting that it contains information for additional functions. We used a battery of anticore antibodies to test the hypothesis that the core gene directs the synthesis of core protein isoforms. Infectious viruses, replicons, and RNA transcripts expressed a p8 minicore containing the C-terminal portion of the p21 core protein and lacking the N-terminal portion. An interferon resistance mutation, U271A, which creates an AUG at codon 91, upregulated p8 expression in Con1 replicons, suggesting that p8 is produced by an internal initiation event and that 91-AUG is the preferred, but not the required, initiation codon. Synthesis of p8 was independent of p21, as shown by the abundant production of p8 from transcripts containing an UAG stop codon that blocked p21 production. Three infectious viruses, JFH-1 (2a core ), J6/JFH (2a core ), and H77/JFH (1a core ), and a bicistronic construct, Bi-H77/JFH, all expressed both p8 and larger isoforms. The family of minicores ranges in size from 8 to 14 kDa. All lack the N-terminal portion of the p21 core. In conclusion, the core gene contains an internal signal that stimulates the initiation of protein synthesis at or near codon 91, leading to the production of p8. Infectious viruses of both genotype 1 and 2 HCV express a family of larger isoforms, in addition to p8. Minicores lack significant portions of the RNA binding domain of p21 core. Studies are under way to determine their functions.

The European Space Agency's Soil Moisture and Ocean Salinity satellite comprises a single payload instrument known as the Microwave Interferometric Radiometer with Aperture Synthesis (MIRAS) coupled to a PROTEUS platform. MIRAS synthesizes a large aperture from a reasonably sized 2-D array of passive microwave radiometers. By using interferometric techniques, the required coverage and spatial resolution can be achieved without the need for a large antenna. This paper describes the MIRAS instrument, its observation modes, the imaging geometry, and data products.

In the fall of 2014, an international news agency reported that patients suffering from Ebola virus disease (EVD) in Liberia were treated successfully with lamivudine, an antiviral drug used to treat human immunodeficiency virus-1 and hepatitis B virus infections. According to the report, 13 out of 15 patients treated with lamivudine survived and were declared free from Ebola virus disease. In this study, the anti-Ebola virus (EBOV) activity of lamivudine and another antiretroviral, zidovudine, were evaluated in a diverse set of cell lines against two variants of wild-type EBOV. Variable assay parameters were assessed to include different multiplicities of infection, lengths of inoculation times, and durations of dosing. At a multiplicity of infection of 1, lamivudine and zidovudine had no effect on EBOV propagation in Vero E6, Hep G2, or HeLa cells, or in primary human monocyte-derived macrophages. At a multiplicity of infection of 0.1, zidovudine demonstrated limited anti-EBOV activity in Huh 7 cells. Under certain conditions, lamivudine had low anti-EBOV activity at the maximum concentration tested (320 μM). However, lamivudine never achieved greater than 30% viral inhibition, and the activity was not consistently reproducible. Combination of lamivudine and zidovudine showed no synergistic antiviral activity. Independently, a set of in vitro experiments testing lamivudine and zidovudine for antiviral activity against an Ebola-enhanced green fluorescent protein reporter virus was performed at the Centers for Disease Control and Prevention. No antiviral activity was observed for either compound. A study evaluating the efficacy of lamivudine in a guinea pig model of EVD found no survival benefit. This lack of benefit was observed despite plasma lamivudine concentrations in guinea pig of about 4 μg/ml obtained in a separately conducted pharmacokinetics study. These studies found no evidence to support the therapeutic use of lamivudine for the treatment of EVD.

Brincidofovir (BCV) is the 3-hexadecyloxy-1-propanol (HDP) lipid conjugate of the acyclic nucleoside phosphonate cidofovir (CDV). BCV has established broad-spectrum activity against double-stranded DNA (dsDNA) viruses; however, its activity against RNA viruses has been less thoroughly evaluated. Here, we report that BCV inhibited infection of Ebola virus in multiple human cell lines. Unlike the mechanism of action for BCV against cytomegalovirus and other dsDNA viruses, phosphorylation of CDV to the diphosphate form appeared unnecessary. Instead, antiviral activity required the lipid moiety and in vitro activity against EBOV was observed for several HDP-nucleotide conjugates.

Azithromycin is a broad-spectrum macrolide antibiotic with a long half-life and excellent tissue penetration. It is primarily used for the treatment of respiratory, enteric and genitourinary infections and may be used in preference to other macrolides for some sexually transmitted and enteric infections. Azithromycin has additional immunomodulatory effects and has been used in chronic respiratory inflammatory diseases for this purpose. Potential major adverse effects include cardiovascular arrhythmias and hearing loss. Macrolide resistance is also a problem, as are interactions with commonly prescribed drugs.

In this paper, two themes are specifically targeted for developing a cost-effective option to transport methane hydrates from distant locations. Under the first theme, data are presented on crystal growth techniques, sample preparation and neutron diffraction studies of 3.5Xe · 8CCl4· 136D2O, xCH4· 8CCl4· 136D2O, xH2S · 8CS2· 136 H2O, and 20Br2· 172D2O. Under the second theme, the GTL option is selected wherein methanol is the product of choice for transport. For GTL, the processing of aqueous CH4 by steam reforming is the preferred route to synthesis gas. Subsequent conversion of synthesis gas into methanol will require the formulation of advanced catalysts.

The crystal structure of Sr(OH)2·8H2O has been determined at 20, 100 and 200 K from neutron diffraction data. The structure consists of double layers of H2O and OH− ions separated by Sr2+ along the c axis. The Sr2+ ions are eight-coordinated by water O atoms in a square antiprism configuration. Each H2O molecule is engaged in three hydrogen bonds. The OH− ions form chains of acceptor and donor bonds along the fourfold axis with O atoms engaged in four bonds with H2O molecules, such that both non-equivalent O atoms have square-pyramidal environments of five H atoms and the overall bonding configurations of distorted octahedra.

Sin Nombre virus (SNV) and Hantaan virus (HTN) infect endothelial cells and are associated with different patterns of increased vascular permeability during human disease. It is thought that such patterns of increased vascular permeability are a consequence of endothelial activation and subsequent dysfunction mediated by differential immune responses to hantavirus infection. In this study, the ability of hantavirus to directly induce activation of human lung microvascular endothelial cells (HMVEC-Ls) was examined. No virus-specific modulation in the constitutive or cytokine-induced expression of cellular adhesion molecules (CD40, CD54, CD61, CD62E, CD62P, CD106, and major histocompatibility complex classes I and II) or in cytokines and chemokines (eotaxin, tumor necrosis factor alpha, interleukin 1β [IL-1β], IL-6, IL-8, MCP-1, MIP-1α, and MIP-1β) was detected at either the protein or message level in hantavirus-infected HMVEC-Ls. Furthermore, no virus-specific enhancement of paracellular or transcellular permeability or changes in the organization and distribution of endothelial intercellular junctional proteins was observed. However, infection with either HTN or SNV resulted in detectable levels of the chemokines RANTES and IP-10 (the 10-kDa interferon-inducible protein) in HMVEC-Ls within 72 h and was associated with nuclear translocation of interferon regulatory factor 3 (IRF-3) and IRF-7. Gamma interferon (IFN-γ)-induced expression of RANTES and IP-10 could also be detected in uninfected HMVEC-Ls and was associated with nuclear translocation of IRF-1 and IRF-3. Treatment of hantavirus-infected HMVEC-Ls with IFN-γ for 24 h resulted in a synergistic enhancement in the expression of both RANTES and IP-10 and was associated with nuclear translocation of IRF-1, IRF-3, IRF-7, and NF-κB p65. These results reveal a possible mechanism by which hantavirus infection and a TH1 immune response can cooperate to synergistically enhance chemokine expression by HMVEC-Ls and trigger immune-mediated increases in vascular permeability.

The crystal structure of the AgClO4.C6H6 \pi complex, earlier determined by X-ray diffraction at room temperature, has been redetermined at 18, 78 and 158 K by neutron diffraction. Crystal data: orthorhombic, space group Cmcm, Z = 4, F(000) = 225.318 fm, T: 18, 17, 158 K; D x = 2.591 (2), 2.570 (1), 2.523 (1) g cm−1; \mu n = 0.166, 0.165, 0.162 cm−1; a = 7.913 (1), 7.973 (1), 8.100 (1), 8.336 (1) Å (at 295 K); b = 7.837 (2), 7.857 (1), 7.902 (1), 7.996 (1) Å (at 295 K); c = 11.798 (3), 11.777 (2), 11.739 (2), 11.638 (2) Å (at 295 K); wR(F 2) = 0.037, 0.035, 0.045, S = 1.18, 1.08, 1.10 for 782, 628, 800 reflections and 51 variable parameters. This study confirms the principal features reported in the X-ray investigation and reveals details of structure not observable at room temperature. Distortions of the benzene molecule from D 6h symmetry ascribed to Ag+...C6H6 interactions are small, but significant. At 18 K the two C—C bonds complexed by Ag+ are 1.405 (1) Å in length; the other four are 1.398 (1) Å. The C—H bonds are equal in length at 1.087 (2) (two) and 1.089 (1) Å (four). The H atoms nearest to Ag+ are displaced 0.064 (1) Å from the C6 plane, away from the silver. The shortest Ag+...C distance of the complex is 2.565 (1) Å. This value and bond lengths of the benzene molecule are invariant between 18 and 158 K within 2 e.s.d.'s or less. The nonequivalent bond lengths of ClO^{-}_4, 1.451 (1) (two) and 1.441 (1) Å (two) at 18 K, are foreshortened by −0.007 and −0.005 Å at 158 K by effects of thermal motion. The O—Cl—O angles, 109.08 (7), 109.98 (2) and 107.83 (8)° at 18 K, are virtually unchanged by temperature. The Ag+...ClO^{-}_4 interactions occur at Ag+...O distances of 2.785 (1) and 2.612 (1) Å (18 K), where the shorter values involve ClO^{-}_4 acting as a bidentate group. Rigid-body and riding-motion models do not adequately account for the observed temperature dependence of bond lengths in ClO^{-}_4 nor provide significant corrections to the C6H6 bond lengths at 18, 78 and 158 K beyond their uncertainty limits. A harmonic potential rationalizes the motion of Ag+ at these three temperatures.

The absolute configuration of (+)-ethanol-1-d has been determined to be R by the single-crystal neutron diffraction analysis of its (−)-camphanate ester. The absolute configuration of the (−)-camphanate group, which served as the chiral reference for the neutron study, was in turn established to be 1S,4R in an X-ray anomalous dispersion study of the complex Cu2(camphanate)4(ethanol)2. These results provide unambiguous confirmation that the optical rotation of (R)-ethanol-1-d (positive) is opposite to that of its higher homologs, (R)-propanol-1-d, (R)-butanol-1-d, and (R)-neopentanol-1-d (all negative), and demonstrates the usefulness of neutron diffraction in determining the absolute configuration of molecules possessing chiral methylene groups (i.e., molecules of the type CHDRR‘). Crystallographic details: for the neutron analysis of (+)-(R)-ethyl-1-d (−)-(1S)-camphanate: space group P21212 (orthorhombic), a = 6.422(1) A, b = 21.004(4) A, c = 9.275(2) A, V = 1251.1(7) A3, Z = 4; R(F2) = 0.083, and wR(F...

Marburg virus (MARV) and Ebola virus (EBOV), members of the family Filoviridae, represent a significant challenge to global public health. Currently, no licensed therapies exist to treat filovirus infections, which cause up to 90% mortality in human cases. To facilitate development of antivirals against these viruses, we established two distinct screening platforms based on MARV and EBOV reverse genetics systems that express secreted Gaussia luciferase (gLuc). The first platform is a mini-genome replicon to screen viral replication inhibitors using gLuc quantification in a BSL-2 setting. The second platform is complementary to the first and expresses gLuc as a reporter gene product encoded in recombinant infectious MARV and EBOV, thereby allowing for rapid quantification of viral growth during treatment with antiviral compounds. We characterized these viruses by comparing luciferase activity to virus production, and validated luciferase activity as an authentic real-time measure of viral growth. As proof of concept, we adapt both mini-genome and infectious virus platforms to high-throughput formats, and demonstrate efficacy of several antiviral compounds. We anticipate that both approaches will prove highly useful in the development of anti-filovirus therapies, as well as in basic research on the filovirus life cycle.

Crystal data: Na4Si3Al3O12Cl, cubic, space group P43n, Z = 2, F(000) = 233.06 fm, μ n = 0.06 cm−1, lattice parameter ao (Å) [T] (K) at eight temperatures: 8.882 (1) [295]; 8.902 (2) [500]; 8.912 (1) [600]; 8.923 (1) [700] 8.951 (2) [800]; 8.971(1) [900]; 8.988 (1) [1000]; 9.037 (1) [1200]. The crystal structure has been determined at six temperatures (295 ≤ T ≤ 1200 K) based on neutron diffraction data with (sin θ/λ) < 0.80 Å−1. Besides conventional parameters, the least-squares refinement model included thermal tensor parameters up to fourth-order for sodium and chlorine (295 ≤ T ≤ 1200 K) and up to third-order for oxygen (T ≥ 700 K), together with the 1:1 coupled site occupancy factors of sodium and chlorine (T = 1200 K). The indices-of-fit, wR(F 2), are in the range 0.015–0.028 with observation-to-parameter ratios from 7.0 to 8.6. Bond lengths and angles in the aluminosilicate framework have average e.s.d.'s less than 0.002 Å and 0.08°. Between 295 and 1200 K, the observed Si—O (Al—O) bond lengths differ by −0.015 Å (−0.012 Å); corrections for librating rigid SiO4 (AlO4) groups change the difference to +0.004 Å (+0.006 Å), compared with the 295 K value of 1.620 Å (1.741 Å). The unique Si—O—Al angle increases from 138.24° (295 K) to 146.87° (1200 K), while the Si and Al valence angles are virtually unchanged. Between 295 and 1200 K the [Na4Cl] clusters expand with increases in the Na—Cl bond lengths of 0.200 Å, with simultaneous increases in Na—O bond lengths of 0.145 Å and decreases in the shortest Na...O contact distances of 0.126 Å. The thermal expansion of sodalite is attributed to the increasing amplitudes of coupled translational motion of the Na+ ions and the librational motion of the [Al/ SiO4] tetrahedra, leading to the untwisting of the aluminosilicate framework. Maps of the probability density functions for Na+ and Cl− indicate ionic diffusion paths along (111) directions. There is a finite probability of finding the Na+ ion within the plane of the next-nearest O atoms, suggesting that Na+ jumps from an occupied to an unoccupied site in the next-nearest cage through the six-membered ring of [Al/SiO4] tetrahedra.