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The COVID-19 pandemic has demonstrated the need for real-time, open-access epidemiological information to inform public health decision-making and outbreak control efforts. In Canada, authority for healthcare delivery primarily lies at the provincial and territorial level; however, at the outset of the pandemic no definitive pan-Canadian COVID-19 datasets were available. The COVID-19 Canada Open Data Working Group was created to fill this crucial data gap. As a team of volunteer contributors, we collect daily COVID-19 data from a variety of governmental and non-governmental sources and curate a line-list of cases and mortality for all provinces and territories of Canada, including information on location, age, sex, travel history, and exposure, where available. We also curate time series of COVID-19 recoveries, testing, and vaccine doses administered and distributed. Data are recorded systematically at a fine sub-national scale, which can be used to support robust understanding of COVID-19 hotspots. We continue to maintain this dataset, and an accompanying online dashboard, to provide a reliable pan-Canadian COVID-19 resource to researchers, journalists, and the general public., Measurement(s) COVID-19 Cases • COVID-19 Mortalities • COVID-19 vaccination Technology Type(s) digital curation Sample Characteristic - Organism Homo sapiens Sample Characteristic - Location Canada Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14331311

We aerosolized severe acute respiratory syndrome coronavirus 2 and determined that its dynamic aerosol efficiency surpassed those of severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome. Although we performed experiment only once across several laboratories, our findings suggest retained infectivity and virion integrity for up to 16 hours in respirable-sized aerosols.

Most H1 influenza A viruses (IAVs) of swine are derived from past human viruses. As human population immunity against these IAVs gradually decreases, the risk of reintroduction to humans increases. We examined 549 serum samples from persons 0-97 years of age collected in Belgium during 2017-2018 for hemagglutination inhibiting and virus neutralizing antibodies against 7 major H1 swine IAV (swIAV) clades and 3 human progenitor IAVs. Seroprevalence (titers >= 40) rates were >= 50% for classical swine and European human-like swIAVs, >= 24% for North American human-like delta 1a and Asian avian-like swIAVs, and

While evidence exists supporting the potential for aerosol transmission of SARS-CoV-2, the infectious dose by inhalation remains unknown. In the present study, the probability of infection following inhalation of SARS-CoV-2 was dose-dependent in a nonhuman primate model of inhalational COVID-19. The median infectious dose, assessed by seroconversion, was 52 TCID50 (95% CI: 23–363 TCID50), and was significantly lower than the median dose for fever (256 TCID50, 95% CI: 102–603 TCID50), resulting in a group of animals that developed an immune response post-exposure but did not develop fever or other clinical signs of infection. In a subset of these animals, virus was detected in nasopharyngeal and/or oropharyngeal swabs, suggesting that infected animals without signs of disease are able to shed virus and may be infectious, which is consistent with reports of asymptomatic spread in human cases of COVID-19. These results suggest that differences in exposure dose may be a factor influencing disease presentation in humans, and reinforce the importance of public health measures that limit exposure dose, such as social distancing, masking, and increased ventilation. The dose-response data provided by this study are important to inform disease transmission and hazard modeling, and, ultimately, mitigation strategies. Additionally, these data will be useful to inform dose selection in future studies examining the efficacy of therapeutics and vaccines against inhalational COVID-19, and as a baseline in healthy, young adult animals for assessment of the importance of other factors, such as age, comorbidities, and viral variant, on the infectious dose and disease presentation., Author summary SARS-CoV-2 infection and subsequent disease presentation are dependent on exposure dose in a nonhuman primate model of inhalational COVID-19.

Multi-drug resistant (MDR) Acinetobacter baumannii (Ab) and Acinetobacter spp. present monumental global health challenges. These organisms represent model Gram-negative pathogens with known antibiotic resistance and biofilm-forming properties. Herein, a novel, nontoxic biocide, AB569, consisting of acidified nitrite (A-NO2-) and ethylenediaminetetraacetic acid (EDTA), demonstrated bactericidal activity against all Ab and Acinetobacter spp. strains, respectively. Average fractional inhibitory concentrations (FICs) of 0.25 mM EDTA plus 4 mM A-NO2- were observed across several clinical reference and multiple combat wound isolates from the Iraq/Afghanistan wars. Importantly, toxicity testing on human dermal fibroblasts (HDFa) revealed an upper toxicity limit of 3 mM EDTA plus 64 mM A-NO2-, and thus are in the therapeutic range for effective Ab and Acinetobacter spp. treatment. Following treatment of Ab strain ATCC 19606 with AB569, quantitative PCR analysis of selected genes products to be responsive to AB569 revealed up-regulation of iron regulated genes involved in siderophore production, siderophore biosynthesis non-ribosomal peptide synthetase module (SBNRPSM), and siderophore biosynthesis protein monooxygenase (SBPM) when compared to untreated organisms. Taken together, treating Ab infections with AB569 at inhibitory concentrations reveals the potential clinical application of preventing Ab from gaining an early growth advantage during infection followed by extensive bactericidal activity upon subsequent exposures.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing a high-mortality global pandemic. The clinical spectrum of disease caused by this virus is broad, ranging from asymptomatic infection to organ failure and death. Risk stratification of individuals with coronavirus disease 2019 (COVID-19) is desirable for management, and prioritization for trial enrollment. We developed a prediction rule for COVID-19 mortality in a population-based cohort in Ontario, Canada. Methods Data from Ontario’s provincial iPHIS system were extracted for the period from January 23 to May 15, 2020. Logistic regression–based prediction rules and a rule derived using a Cox proportional hazards model were developed and validated using split-halves validation. Sensitivity analyses were performed, with varying approaches to missing data. Results Of 21 922 COVID-19 cases, 1734 with complete data were included in the derivation set; 1796 were included in the validation set. Age and comorbidities (notably diabetes, renal disease, and immune compromise) were strong predictors of mortality. Four point-based prediction rules were derived (base case, smoking excluded, long-term care excluded, and Cox model–based). All displayed excellent discrimination (area under the curve for all rules > 0.92) and calibration (P > .50 by Hosmer-Lemeshow test) in the derivation set. All performed well in the validation set and were robust to varying approaches to replacement of missing variables. Conclusions We used a public health case management data system to build and validate 4 accurate, well-calibrated, robust clinical prediction rules for COVID-19 mortality in Ontario, Canada. While these rules need external validation, they may be useful tools for management, risk stratification, and clinical trials.

Youth living with HIV (YLWH; aged 16–24) are at elevated risk of alcohol and drug use. Studies in older populations have identified patterns or profiles of multiple substance use differentially associated with mental health and anti-retroviral therapy (ART) adherence. No studies of YLWH have yet examined such patterns. A sample of 179 YLWH, reporting ART non-adherence and alcohol use, were recruited at five Adolescent Trials Network clinics in urban areas of the US between November 2014 and August 2017. Participants completed the Alcohol Smoking and Substance Involvement Screening Test (ASSIST) to assess substance use involvement scores, and the Brief Symptom Inventory. Latent Profile Analysis identified three substance use patterns: minimal illicit drug use (15.1%), cannabis only (56.4%), and global polysubstance use (28.5%). Global polysubstance users experienced more mental health problems compared to the minimal illicit drug use group. The co-occurrence of drug use with alcohol was common among these YLWH – all of whom reported ART adherence problems – indicating the importance of interventions capable of addressing multiple substance use rather than alcohol alone.

Vaccines are urgently needed to combat the global coronavirus disease 2019 (COVID-19) pandemic, and testing of candidate vaccines in an appropriate non-human primate (NHP) model is a critical step in the process. Infection of African green monkeys (AGM) with a low passage human isolate of SARS-CoV-2 by aerosol or mucosal exposure resulted in mild clinical infection with a transient decrease in lung tidal volume. Imaging with human clinical-grade 18F-fluoro-2-deoxy-D-glucose positron emission tomography (18F-FDG PET) co-registered with computed tomography (CT) revealed pulmonary lesions at 4 days post-infection (dpi) that resolved over time. Infectious virus was shed from both respiratory and gastrointestinal (GI) tracts in all animals in a biphasic manner, first between 2–7 dpi followed by a recrudescence at 14–21 dpi. Viral RNA (vRNA) was found throughout both respiratory and gastrointestinal systems at necropsy with higher levels of vRNA found within the GI tract tissues. All animals seroconverted simultaneously for IgM and IgG, which has also been documented in human COVID-19 cases. Young AGM represent an species to study mild/subclinical COVID-19 disease and with possible insights into live virus shedding. Future vaccine evaluation can be performed in AGM with correlates of efficacy being lung lesions by PET/CT, virus shedding, and tissue viral load., Author summary SARS-CoV-2 infection can result in asymptomatic, mild or severe disease in humans. Vaccines against SARS-CoV-2 are paramount for combating COVID-19 disease and curtailing the pandemic. Large animal models are critical for early vaccine testing before human clinical trials. Here, we found that infection of African green monkeys (AGM) with SARS-CoV-2 resulted in mild disease yet lesions were detectable by PET/CT imaging of the lungs. Shedding of infectious virus from both respiratory and gastrointestinal tracts was also documented. This study provides a detailed account of the pathogenesis of a low-passage SARS-CoV-2 isolate in the AGM model and suggests that AGM can be used for preclinical evaluation of candidate vaccines and therapeutic interventions.

Methicillin-resistant Staphylococcus aureus (MRSA) has proven to be an imminent threat to public health, intensifying the need for novel therapeutics. Previous evidence suggests that cannabinoids harbour potent antibacterial activity. In this study, a group of previously inaccessible phytocannabinoids and synthetic analogues were examined for potential antibacterial activity. The minimum inhibitory concentrations and dynamics of bacterial inhibition, determined through resazurin reduction and time-kill assays, revealed the potent antibacterial activity of the phytocannabinoids against gram-positive antibiotic-resistant bacterial species, including MRSA. One phytocannabinoid, cannabichromenic acid (CBCA), demonstrated faster and more potent bactericidal activity than vancomycin, the currently recommended antibiotic for the treatment of MRSA infections. Such bactericidal activity was sustained against low-and high-dose inoculums as well as exponential- and stationary-phase MRSA cells. Further, mammalian cell viability was maintained in the presence of CBCA. Finally, microscopic evaluation suggests that CBCA may function through the degradation of the bacterial lipid membrane and alteration of the bacterial nucleoid. The results of the current study provide encouraging evidence that cannabinoids may serve as a previously unrecognised resource for the generation of novel antibiotics active against MRSA.

The poxvirus, myxoma virus (MYXV) has shown efficacy as an oncolytic virus (OV) in some cancer models. However, MYXV replication within murine cancer models and spontaneous canine sarcomas is short-lived. In mice, successful treatment of tumors requires frequent injections with MYXV. We hypothesize that treatment of cancer with a recombinant MYXV that promotes apoptosis could improve the efficacy of MYXV. The orfC gene of walleye dermal sarcoma virus (WDSV), which induces apoptosis, was recombined into the MYXV genome (MYXVorfC). A marked increase in apoptosis was observed in cells infected with MYXVorfC. To ensure that expression of WDSV orfC by MYXV does not potentiate the pathogenesis of MYXV, we evaluated the effects of MYXVorfC inoculation in the only known host of MYXV, New Zealand white rabbits. Virus dissemination in rabbit tissues was similar for MYXVorfC and MYXV. Virus titers recovered from tissues were lower in MYXVorfC-infected rabbits as compared to MYXV-infected rabbits. Importantly, rabbits infected with MYXVorfC had a delayed onset of clinical signs and a longer median survival time than rabbits infected with MYXV. This study indicates that MYXVorfC is attenuated and suggests that MYXVorfC will be safe to use as an OV therapy in future studies.

Streptococcus suis is a swine pathogen that is capable of causing severe outbreaks of disease in the nursery. Demographic parameters such as host recruitment rates can have profound effects on the transmission dynamics of infectious diseases and, thus, are critically important in high-turnover populations such as farmed swine. However, knowledge concerning the implications that such parameters have on S. suis disease control remains unknown. A stochastic mathematical model incorporating sub-clinically infected pigs was developed to capture the effects of changes in host recruitment rate on disease incidence. Compared to our base model scenario, our results show that monthly introduction of pigs into the nursery (instead of weekly introduction) reduced cumulative cases of S. suis by up to 59%, while increasing disease-removal rates alone averted up to 64% of cases. Sensitivity analysis demonstrated that the course of infection in sub-clinically infected pigs was highly influential and generated significant variability in the model outcomes. Our model findings suggest that modifications to host recruitment rates could be leveraged as a tool for S. suis disease control, however improving our understanding of additional factors that influence the risk of transmission would improve the precision of the model estimates.

Primary central nervous system lymphoma is notoriously challenging to diagnose in immunocompetent patients as it is an uncommon diagnosis. We present a case of synchronous diagnosis with tuberculosis. A 60-year-old woman presented with cognitive difficulties, memory loss, social withdrawal, unintentional weight loss, and night sweats, the work-up of which ultimately identified multiple brain lesions and mediastinal adenopathy. Brain biopsy showed lymphohistiocytic infiltrate, while mediastinal node histopathology showed necrotizing granulomas, and cultures grew Mycobacterium tuberculosis. The patient was initiated on anti-tuberculosis therapy. However, follow-up brain MRI demonstrated disease progression, prompting repeat brain biopsy, which in turn confirmed the diagnosis of diffuse large B-cell lymphoma. Although unrelated synchronous diagnoses are rare, the potential for clinically significant confounding is considerable-particularly where disease markers may overlap, as is often the case with infectious, inflammatory, and neoplastic processes. The present case illustrates the importance of diligence in ruling out competing diagnosis, and timely action when an anticipated finding or response-to-treatment is not observed.

Background Identification of factors associated with antifungal utilization in neonatal, pediatric, and adult patient groups is needed to guide antifungal stewardship initiatives in academic medical centers. Methods For this hospital-level analysis, we analyzed antifungal use in hospitals across the United States of America, excluding centers only providing care for hematology/oncology patients. Analysis of variance was used to compare antifungal use between patient groups. Three multivariable linear regression models were used to determine independent factors associated with antifungal use in the neonatal, pediatric, and adult patient groups. Results For the neonatal, pediatric, and adult patient groups, 54, 44, and 60 hospitals were included, respectively. Total antifungal use was significantly lower in the neonatal patient group (14 days of therapy (DOT)/1000 patient days (PDs) versus 76 in pediatrics and 74 in adults, p

Background Six amino acid positions (145, 155, 156, 158, 159, and 189, referred to as the antigenic motif; H3 numbering) in the globular head region of hemagglutinin (HA1 domain) play an important role in defining the antigenic phenotype of swine Clade IV (C-IV) H3N2 IAV, containing an H3 from a late 1990s human-to-swine introduction. We hypothesized that antigenicity of a swine C-IV H3 virus could be inferred based upon the antigenic motif if it matched a previously characterized antigen with the same motif. An increasing number of C-IV H3 genes encoding antigenic motifs that had not been previously characterized were observed in the U.S. pig population between 2012 and 2016. Objectives A broad panel of contemporary H3 viruses with uncharacterized antigenic motifs was selected across multiple clades within C-IV to assess the impact of HA1 genetic diversity on the antigenic phenotype. Methods Hemagglutination inhibition (HI) assays were performed with isolates selected based on antigenic motif, tested against a panel of swine antisera, and visualized by antigenic cartography. Results A previously uncharacterized motif with low but sustained circulation in the swine population demonstrated a distinct phenotype from those previously characterized. Antigenic variation increased for viruses with similar antigenic motifs, likely due to amino acid substitutions outside the motif. Conclusions Although antigenic motifs were largely associated with antigenic distances, substantial diversity among co-circulating viruses poses a significant challenge for effective vaccine development. Continued surveillance and antigenic characterization of circulating strains is critical for improving vaccine efforts to control C-IV H3 IAV in U.S. swine.

A canine influenza A(H3N2) virus emerged in the United States in February-March 2015, causing respiratory disease in dogs. The virus had previously been circulating among dogs in Asia, where it originated through the transfer of an avian-origin influenza virus around 2005 and continues to circulate. Sequence analysis suggests the US outbreak was initiated by a single introduction, in Chicago, of an H3N2 canine influenza virus circulating among dogs in South Korea in 2015. Despite local control measures, the virus has continued circulating among dogs in and around Chicago and has spread to several other areas of the country, particularly Georgia and North Carolina, although these secondary outbreaks appear to have ended within a few months. Some genetic variation has accumulated among the US viruses, with the appearance of regional-temporal lineages. The potential for interspecies transmission and zoonotic events involving this newly emerged influenza A virus is currently unknown.

Background In the fall of 2014, highly pathogenic avian influenza (HPAI) subtype H5N8 clade 2.3.4.4 was introduced into North America by migrating waterfowl from Asia where, through reassortment, novel HPAI H5N2 and H5N1 viruses emerged. Objectives Assess the susceptibility of pigs to HPAI H5N1, H5N2, and H5N8 clade 2.3.3.3 from North America. Methods Pigs and trachea explants were inoculated with a representative panel of H5NX clade 2.3.4.4 HPAI viruses from North America. Nasal swabs, BALF, and sera were collected to assess replication and transmission in challenged and direct contact pigs by RRT-PCR, virus isolation, hemagglutination inhibition, and ELISA. Results Limited virus replication was restricted to the lower respiratory tract of challenged pigs, though absent in the nasal passages and trachea cultures, as determined by RRT-PCR in all samples. Seroconversion of inoculated pigs was detected by NP ELISA but was not reliably detected by antigen-specific hemagglutination inhibition. Boost with adjuvanted virus was required for the production of neutralizing antibodies to assess cross-reactivity between wild-type avian strains. All RRT-PCR and serology tests were negative for contact animals indicating a failure of transmission from primary inoculated pigs. Conclusions H5NX clade 2.3.4.4 strains can replicate in the lower respiratory tract of swine upon high titer inoculation, though appear to be incapable of replication in swine nasal epithelium in vivo or ex vivo in trachea explants in culture. Infected pigs did not produce high levels of serum antibodies following infection. Collectively, our data show HPAI H5NX clade 2.3.4.4 viruses to be poorly adapted for replication and transmission in swine.

While acknowledging the great achievements in getting 23 million people living with HIV to access antiretroviral treatment (ART) globally, there is still more to do in order to close the HIV treatment gap between the paediatric and adult ART programmes, with only 54% of children accessing ART compared to 62% of adults. Furthermore, while tremendous global gains have been made in preventing perinatal and postnatal HIV acquisition, HIV-exposed and uninfected children are still not achieving early childhood developmental outcomes comparable to HIV-unexposed children. In this article, we present highlights from two pre-conference meetings (11th International Workshop on HIV Pediatrics and 5th Workshop on Children and Adolescents HIV Exposed and Uninfected) and the International Aids Society (IAS) meeting held in Mexico in July 2019.

Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic disease transmitted from dromedary camels to people, which can result in outbreaks with human-to-human transmission. Because it is a subclinical infection in camels, epidemiological measures other than prevalence are challenging to assess. This study estimated the force of infection (FOI) of MERS-CoV in camel populations from age-stratified serological data. A cross-sectional study of MERS-CoV was conducted in Kenya from July 2016 to July 2017. Seroprevalence was stratified into four age groups: 3 years old. Age-independent and age-dependent linear and quadratic generalised linear models were used to estimate FOI in pastoral and ranching camel herds. Models were compared based on computed AIC values. Among pastoral herds, the age-dependent quadratic FOI was the best fit model, while the age-independent FOI was the best fit for the ranching herd data. FOI provides an indirect estimate of infection risk, which is especially valuable where direct estimates of incidence and other measures of infection are challenging to obtain. The FOIs estimated in this study provide important insight about MERS-CoV dynamics in the reservoir species, and contribute to our understanding of the zoonotic risks of this important public health threat.

While extensive research efforts have decreased human immunodeficiency virus (HIV) transmissions and mortalities, new challenges have arisen in the fight to eradicate HIV. Drug resistance to antiretroviral therapy threatens infected individuals, while the prevalence of heterosexual transmission creates an urgent need for therapies effective in the female reproductive tract (FRT) mucosa. We screened a library of 2095 small molecule compounds comprising a unique chemical space, purchased from Asinex Corporation, for antiviral activity against human immunodeficiency virus type 1 (HIV-1) strain BaL and identified several molecular representatives of a unique class of HIV-1 inhibitors, which we termed &ldquo, Avirulins.&rdquo, We determined that Avirulins were active against clinical isolates of HIV-1 from genetically variant subtypes, several of which have reduced sensitivity to other antivirals. Avirulins displayed specific dose-dependent inhibition of the HIV-1 drug target, reverse transcriptase (RT). Avirulins were effective against several nucleoside RT-inhibitor resistant strains of HIV-1, as well as one nonnucleoside RT-inhibitor resistant strain containing a 106A mutation, suggesting a noncompetitive mechanism of action. Drugs, which are damaging to the FRT, can increase the risk of HIV-1 transmission. We therefore explored the cytotoxicity of Avirulins against epithelial cells derived from the FRT and found no significant toxicity, even at the highest concentrations tested. Importantly, Avirulin antiviral activity was not diminished in human cervico&ndash, vaginal fluid, suggesting retained potency in the milieu of the FRT. Based on these promising results, Avirulins should be valuable chemical scaffolds for development into next-generation treatments and preventatives that target HIV-1.

Background Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic in dromedary camels in the Arabian Peninsula, and zoonotic transmission to people is a sporadic event. In the absence of epidemiological data on the reservoir species, patterns of zoonotic transmission have largely been approximated from primary human cases. This study aimed to identify meteorological factors that may increase the risk of primary MERS infections in humans. Methods A case-crossover design was used to identify associations between primary MERS cases and preceding weather conditions within the 2-week incubation period in Saudi Arabia using univariable conditional logistic regression. Cases with symptom onset between January 2015 – December 2017 were obtained from a publicly available line list of human MERS cases maintained by the World Health Organization. The complete case dataset (N = 1191) was reduced to approximate the cases most likely to represent spillover transmission from camels (N = 446). Data from meteorological stations closest to the largest city in each province were used to calculate the daily mean, minimum, and maximum temperature (οC), relative humidity (%), wind speed (m/s), and visibility (m). Weather variables were categorized according to strata; temperature and humidity into tertiles, and visibility and wind speed into halves. Results Lowest temperature (Odds Ratio = 1.27; 95% Confidence Interval = 1.04–1.56) and humidity (OR = 1.35; 95% CI = 1.10–1.65) were associated with increased cases 8–10 days later. High visibility was associated with an increased number of cases 7 days later (OR = 1.26; 95% CI = 1.01–1.57), while wind speed also showed statistically significant associations with cases 5–6 days later. Conclusions Results suggest that primary MERS human cases in Saudi Arabia are more likely to occur when conditions are relatively cold and dry. This is similar to seasonal patterns that have been described for other respiratory diseases in temperate climates. It was hypothesized that low visibility would be positively associated with primary cases of MERS, however the opposite relationship was seen. This may reflect behavioural changes in different weather conditions. This analysis provides key initial evidence of an environmental component contributing to the development of primary MERS-CoV infections.

Arenaviruses are a significant cause of hemorrhagic fever, an often-fatal disease for which there is no approved antiviral therapy. Lassa fever in particular generates high morbidity and mortality in West Africa, where the disease is endemic, and a recent outbreak in Nigeria was larger and more geographically diverse than usual. We are developing LHF-535, a small-molecule viral entry inhibitor that targets the arenavirus envelope glycoprotein, as a therapeutic candidate for Lassa fever and other hemorrhagic fevers of arenavirus origin. Using a lentiviral pseudotype infectivity assay, we determined that LHF-535 had sub-nanomolar potency against the viral envelope glycoproteins from all Lassa virus lineages, with the exception of the glycoprotein from the LP strain from lineage I, which was 100-fold less sensitive than that of other strains. This reduced sensitivity was mediated by a unique amino acid substitution, V434I, in the transmembrane domain of the envelope glycoprotein GP2 subunit. This position corresponds to the attenuation determinant of Candid#1, a live-attenuated Junín virus vaccine strain used to prevent Argentine hemorrhagic fever. Using a virus-yield reduction assay, we determined that LHF-535 potently inhibited Junín virus, but not Candid#1, and the Candid#1 attenuation determinant, F427I, regulated this difference in sensitivity. We also demonstrated that a daily oral dose of LHF-535 at 10 mg/kg protected mice from a lethal dose of Tacaribe virus. Serial passage of Tacaribe virus in LHF-535-treated Vero cells yielded viruses that were resistant to LHF-535, and the majority of drug-resistant viruses exhibited attenuated pathogenesis. These findings provide a framework for the clinical development of LHF-535 as a broad-spectrum inhibitor of arenavirus entry and provide an important context for monitoring the emergence of drug-resistant viruses., Author summary Lassa fever is a viral hemorrhagic fever disease that is transmitted to humans primarily through contact with the urine or feces of infected rodents. The disease is endemic in West Africa, and an unusually large outbreak occurred in Nigeria in early 2018. The case fatality rate was 25% among confirmed cases, underscoring the need for an effective antiviral therapy. Here, we evaluated the small-molecule drug LHF-535, which targets the arenavirus envelope glycoprotein, for broad-spectrum activity against Lassa viruses of different lineages and related arenaviruses that cause hemorrhagic fever diseases in South America. We also selected for LHF-535-resistant viruses and characterized their genotype and phenotype. Using a combination of surrogate systems and wild-type viruses, we determined that all tested Lassa virus strains and New World hemorrhagic fever arenaviruses were sensitive to LHF-535. Sensitivity to the drug was modulated by specific amino acid changes in the viral envelope glycoprotein, and the majority of emerging drug-resistant viruses were attenuated for virulence. Similarly, the live-attenuated vaccine strain for Argentine hemorrhagic fever was also resistant to LHF-535. These findings indicate that LHF-535 targets a viral virulence determinant, the mutation of which may result in the emergence of drug-resistant viruses, but with reduced capacity for virulence.

Background There are many emerging diagnostic technologies that provide rapid identification (ID) and antimicrobial susceptibility testing (AST) of blood cultures after initial microbial growth is detected. The clinical utility of having these results sooner than standard of care (SOC) ID/AST testing is less clear; one potential advantage would be shorter hospital admissions for those patients with less severe infections whose discharge planning is delayed while waiting for ID/AST results. Methods The Accelerate Pheno™ rapid ID/AST system (AP) was implemented in the clinical microbiology lab at two hospitals within our academic hospital system to run in parallel with our SOC ID/AST diagnostics for all blood cultures with Gram-negative rod (GNR) bacterial growth on initial Gram stain. Results of both diagnostic assays were uploaded to the medical record when available; our antimicrobial stewardship (AS) team discussed the AP results with clinical care teams during working hours. Length of stay (LOS) data was compared between a cohort with GNR bacteremia before and after the implementation of AP testing with AS review. Results There were 207 patients with GNR bacteremia admitted to the hospital during the first six months after implementation of AP testing with AS review (12/2019 – 05/2020). A historical cohort of 96 patients with GNR bacteremia (admitted 01/2018 – 08/2018) with SOC testing without AS review was used for comparison. Median LOS was 5.28 and 5.84 days for the AP and SOC cohorts, respectively; the distribution in the two groups differed significantly (Mann-Whitney U = 8728.5, p = 0.0446). There was also an increase in the percent of admissions shorter than 2 days between the AP and SOC cohorts (12.5% v. 5.2%, p = 0.024) [Figure1]. Figure 1 Conclusion The use of a rapid ID/AST diagnostic technology with AS review may lead to shorter hospitalizations in select patient populations. Disclosures Kimberle Chapin, MD, genmark (Scientific Research Study Investigator)

Background Antimicrobial stewardship metrics that provide actionable guidance are needed to support efforts to improve hospital use of antibiotics. Antibiotics such as vancomycin and piperacillin/tazobactam are common empiric agents used frequently when the infectious process remains unknown. Thus short, incomplete courses of therapy are used more frequently for such agents. We aimed to evaluate the variability in short courses of vancomycin and piperacillin/tazobactam use across U.S. hospitals. Methods We performed a cross-sectional study among U.S. hospitals that contributed inpatient pharmacy data to the Vizient clinical database in 2016. We identified vancomycin and piperacillin-tazobactam courses initiated within the 48 hours of admission, measured as days of therapy received. We calculated the percent of patients that received 1, 2, 3, 4 or >4 days of therapy at each facility to describe short course empiric therapy use. To describe the variability across facilities, we then assessed the median, interquartile range (IQR), and total range of that percentage. Results We identified 145 hospitals representing approximately 3.7 million patient encounters for inclusion in this study. Within 48 hours of admission, 13.9% of encounters received vancomycin, 7.7% piperacillin/tazobactam, and 4.6% received both. The figure demonstrates the variability in the frequency of short course antibiotic use across hospitals; boxes indicate the IQR with the transecting line representing the median and whiskers representing the full range. The proportion of patients that received one day of therapy varied most across hospitals, with vancomycin ranging from 0–100%. In contrast, the frequency of patients that received greater than four days of therapy varied considerably less across hospitals; 0–33% for vancomycin. Conclusion The variability in use of short course empiric therapies suggests that use for non-infectious processes or infections not appropriately treated by these agents varies greatly across facilities. Measuring short course use for common empiric agents may serve as an important antimicrobial stewardship metric. Such a metric could inform antimicrobial stewardship efforts to reduce unnecessary initiation of empiric antimicrobial therapy. Disclosures All Authors: No reported disclosures

Lawrence Mbuagbaw,1–3 Amy L Slogrove,4,5 Jacqueline Sas,6 John Lengwe Kunda,7 Frederick Morfaw,8 Jackson K Mukonzo,9 Wei Cao,10–12 Gisele Ngomba-Kadima,13 Moleen Zunza,14,15 Pierre Ongolo-Zogo,3 Philip N Nana,8 Anne Cockcroft,16,17 Neil Andersson,16,18,19 Nelson Sewankambo,9 Mark F Cotton,4 Taisheng Li,12 Taryn Young,14 Joel Singer,5,6 Jean-Pierre Routy,6,10,11,20 Colin JD Ross,21 Kyaw Thin,22 Lehana Thabane,1,2,6,23–25 Aslam H Anis5,6 1Department of Health Research Methods, Evidence and Impact, McMaster University, 2Biostatistics Unit, Father Sean O’Sullivan Research Centre, St Joseph’s Healthcare Hamilton, Hamilton, ON, Canada; 3Centre for Development of Best Practices in Health, Yaoundé Central Hospital, Yaoundé, Cameroon; 4Department of Paediatrics and Child Health, Family Clinical Research Unit (FAM-CRU), Stellenbosch University, Tygerberg, South Africa; 5UBC School of Population and Public Health, Vancouver, BC, 6CIHR Canadian HIV Trials Network, UBC, Canada; 7Community Information and Epidemiological Technologies (CIET), Lusaka, Zambia; 8Department of Obstetrics and Gynaecology, Faculty of Medicines and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon; 9School of Biomedical Sciences, College of Health Sciences, University of Makerere, Kampala, Uganda; 10Chronic Viral Illness Service, McGill University Health Centre, 11Research Institute of the McGill University Health Centre, Montreal, QC, Canada; 12Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China; 13Queen Mamahato Memorial Hospital, Maseru, Lesotho; 14Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa; 15Research Institute, McGill University Health Centre, Montreal, QC, Canada; 16Community Information and Epidemiological Technologies (CIET) Trust Botswana, Gaborone, Botswana; 17Community Information and Epidemiological Technologies – Participatory Research at McGill (CIET-PRAM), Department of Family Medicine, McGill University, 18Centro de Investigación de Enfermedades Tropicales, Universidad Autónoma de Guerrero, Chilpancingo, Mexico; 19Department of Family Medicine, McGill University, Montreal, Canada; 20Division of Hematology, McGill University Health Centre, Montreal, QC, Canada; 21Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada; 22Research Coordination Unit, Ministry of Health and Social Welfare, Maseru, Lesotho; 23Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, ON, Canada; 24Centre for Evaluation of Medicine, St Joseph’s Healthcare—Hamilton, ON, Canada; 25Population Health Research Institute, Hamilton Health Sciences, Hamilton, ON, Canada Abstract: As a response to the human immunodeficiency virus (HIV) epidemic and part of ­Canadian Institutes for Health Research’s mandate to support international health research capacity building, the Canadian Institutes for Health Research Canadian HIV Trial Network (CTN) developed an international postdoctoral fellowship award under the CTN’s Postdoctoral Fellowship Awards Program to support and train young HIV researchers in resource-limited settings. Since 2010, the fellowship has been awarded to eight fellows in Cameroon, China, Lesotho, South Africa, Uganda and Zambia. These fellows have conducted research on a wide variety of topics and have built a strong network of collaboration and scientific productivity, with 40 peer-reviewed publications produced by six fellows during their fellowships. They delivered two workshops at international conferences and have continued to secure funding for their research, using the fellowship as a stepping stone. The CTN has been successful in building local HIV research capacity and forming a strong network of like-minded junior low- and middle-income country researchers with high levels of research productivity. They have developed into mentors, supervisors and faculty members, who, in turn, build local capacity. The sustainability of this international fellowship award relies on the recognition of its strengths and the involvement of other stakeholders for additional resources. Keywords: CTN, postdoctoral fellowship, capacity building, clinical trials, networking

Many oncolytic viruses that are efficacious in murine cancer models are ineffective in humans. The outcomes of oncolytic virus treatment in dogs with spontaneous tumors may better predict human cancer response and improve treatment options for dogs with cancer. The objectives of this study were to evaluate the safety of treatment with myxoma virus lacking the serp2 gene (MYXV&Delta, serp2) and determine its immunogenicity in dogs. To achieve these objectives, dogs with spontaneous soft tissue sarcomas were treated with MYXV&Delta, serp2 intratumorally (n = 5) or post-operatively (n = 5). In dogs treated intratumorally, clinical scores were recorded and tumor biopsies and swabs (from the mouth and virus injection site) were analyzed for viral DNA at multiple time-points. In all dogs, blood, urine, and feces were frequently collected to evaluate organ function, virus distribution, and immune response. No detrimental effects of MYXV&Delta, serp2 treatment were observed in any canine cancer patients. No clinically significant changes in complete blood profiles, serum chemistry analyses, or urinalyses were measured. Viral DNA was isolated from one tumor swab, but viral dissemination was not observed. Anti-MYXV antibodies were occasionally detected. These findings provide needed safety information to advance clinical trials using MYXV&Delta, serp2 to treat patients with cancer.

Expedited partner therapy (EPT) is an effective strategy for partner management of sexually transmitted infections. Some states, including Wisconsin, allow EPT prescriptions to be filled without a patient name. This study determined the refusal rates of nameless EPT prescriptions in Milwaukee pharmacies.In this cross-sectional study, 3 trained research assistants of different age, sex, and race posed as "patients" and visited 50 pharmacy locations from one pharmacy chain in Milwaukee County, WI, to fill nameless EPT prescriptions. A χ test was used to compare demographics of patients, pharmacists, and pharmacies. Multiple logistic regression was used to identify factors associated with prescription refusal.Twenty-nine (58%) of 50 nameless EPT prescriptions were refused. Univariate analysis showed that prescriptions were more likely to be refused if the pharmacy was in the suburbs (77%) compared with Milwaukee city (43%; P = 0.01), if the pharmacist was older than the patient (82%) compared with being younger (46%) or within the same age group (33%; P = 0.01 for both), and if the patient was white (78%) compared with nonwhite (47%; P = 0.03). Multivariable regression revealed significantly higher refusals for pharmacies located in the suburbs compared with the city (odds ratio, 5.3; 95% confidence interval, 1.4-20.3; P = 0.03) and in patients who were white compared with nonwhite (odds ratio: 4.8; 95% confidence interval, 1.2-19.8; P = 0.01).More than half of nameless EPT prescriptions were refused in Milwaukee county pharmacies, more frequently at suburban pharmacies and for white patients. Increased pharmacist education regarding EPT is essential to help combat the sexually transmitted infection crisis.

Infection with the larval stage of the cestode, Echinococcus granulosus sensu lato (s.l.), causes hydatid disease (hydatidosis) in a range of hosts, including macropods and other marsupials, cattle, and humans. Wild macropods are an important sylvatic reservoir for the life cycle of E. granulosus (s.l.) in Australia, and so provide a conduit for transmission of hydatid disease to domestic animals and humans. Two Lumholtz’s tree-kangaroos (Dendrolagus lumholtzi) from the Atherton Tablelands of Far North Queensland were recently found to have hydatid cysts in both liver and lung tissues. Tree-kangaroos may travel across the ground between patches of forest but are primarily arboreal leaf-eating macropods. The finding of hydatid cysts in an arboreal folivore may indicate that the area has a high level of contamination with eggs of E. granulosus (s.l.). This finding may be of significance to human health as well as indicating the need for further investigation into the prevalence of hydatid disease in domestic stock, wildlife and humans living in this rapidly urbanizing region.

The equine herpesvirus type 1 (EHV-1) ORF1 and ORF71 genes have immune modulatory effects in vitro. Experimental infection of horses using virus mutants with multiple deletions including ORF1 and ORF71 showed promise as vaccine candidates against EHV-1. Here, the combined effects of ORF1 and ORF71 deletions from the neuropathogenic EHV-1 strain Ab4 on clinical disease and host immune response were further explored. Three groups of EHV-1 naive horses were experimentally infected with the ORF1/71 gene deletion mutant (Ab4ΔORF1/71), the parent Ab4 strain, or remained uninfected. In comparison to Ab4, horses infected with Ab4ΔORF1/71 did not show the initial high fever peak characteristic of EHV-1 infection. Ab4ΔORF1/71 infection had reduced nasal shedding (1/5 vs. 5/5) and, simultaneously, decreased intranasal interferon (IFN)-α, interleukin (IL)-10 and soluble CD14 secretion. However, Ab4 and Ab4ΔORF1/71 infection resulted in comparable viremia, suggesting these genes do not regulate the infection of the mononuclear cells and subsequent viremia. Intranasal and serum anti-EHV-1 antibodies to Ab4ΔORF1/71 developed slightly slower than those to Ab4. However, beyond day 12 post infection (d12pi) serum antibodies in both virus-infected groups were similar and remained increased until the end of the study (d114pi). EHV-1 immunoglobulin (Ig) G isotype responses were dominated by short-lasting IgG1 and long-lasting IgG4/7 antibodies. The IgG4/7 response closely resembled the total EHV-1 specific antibody response. Ex vivo re-stimulation of PBMC with Ab4 resulted in IFN-γ and IL-10 secretion by cells from both infected groups within two weeks pi. Flow cytometric analysis showed that IFN-γ producing EHV-1-specific T-cells were mainly CD8+/IFN-γ+ and detectable from d32pi on. Peripheral blood IFN-γ+ T-cell percentages were similar in both infected groups, albeit at low frequency (~0.1%). In summary, the Ab4ΔORF1/71 gene deletion mutant is less virulent but induced antibody responses and cellular immunity similar to the parent Ab4 strain.

Recent avian and swine-origin influenza virus outbreaks illustrate the ongoing threat of influenza pandemics. We investigated immunogenicity and protective efficacy of a multi-antigen (MA) universal influenza DNA vaccine consisting of HA, M2, and NP antigens in cynomolgus macaques. Following challenge with a heterologous pandemic H1N1 strain, vaccinated animals exhibited significantly lower viral loads and more rapid viral clearance when compared to unvaccinated controls. The MA DNA vaccine induced robust serum and mucosal antibody responses but these high antibody titers were not broadly neutralizing. In contrast, the vaccine induced broadly-reactive NP specific T cell responses that cross-reacted with the challenge virus and inversely correlated with lower viral loads and inflammation. These results demonstrate that a MA DNA vaccine that induces strong cross-reactive T cell responses can, independent of neutralizing antibody, mediate significant cross-protection in a nonhuman primate model and further supports development as an effective approach to induce broad protection against circulating and emerging influenza strains.

Background Gram-negative bacterial infections are associated with high mortality in immunocompromised hosts, and the presence of drug resistance further increases mortality. Antibiotic consumption is a key outcome measure for Antimicrobial Stewardship Programs. Proper utilization of antibiotics can help limit the development of antimicrobial resistance. Resistance in Gram-negative organisms such as Pseudomonas, Enterobacter, and Acinetobacter is a major issue given the paucity of new drugs in the antibiotic pipeline for these organisms. A novel relative carbapenem consumption metric (the Proportion of Carbapenem Consumption, or PoCC) was recently described in US academic medical centers. The PoCC is calculated as follows: PoCC = [(meropenem Days of therapy(DOT)/1,000 patient-days (PDs))/(meropenem DOT/1,000 PDs + cefepime DOT/1,000 PDs + piperacillin–tazobactam DOT/1,000 PDs)]. The regional mean PoCC for the South Atlantic region has previously been approximated at 17%. Methods We examined the PoCC for the Bone Marrow Transplant (BMT) and dedicated Hematology/Oncology (H/O) inpatient wards at an academic medical center from August 2012 to June 2017. Results Table 1: Average Use of Antibiotics Expressed in DOT/1,000 PDs. Ward Piperacillin– Tazobactam Cefepime Meropenem Total PoCC Hematology/oncology 105.1 134.4 76.6 316.1 0.24 Bone marrow transplant 34.3 201.0 127.4 362.7 0.35 National meansa 76.2 60.2 30.7 b 0.18 aAs described by Markley et al. Infect Control Hosp Epidemiol 2018;39:229–232. bData unavailable. Conclusion This is the first description of the PoCC metric for dedicated Hematology/Oncology and Bone Marrow Transplant wards. When compared with national and regional mean PoCC scores for academic medical centers, the PoCC for these units was higher. More research is needed to determine the optimal PoCC scores for these types of units. The PoCC can contextualize relative carbapenem use and may be a useful antibiotic consumption metric. However, it does not provide data on absolute consumption. Further studies are needed to determine the best use of the PoCC metric by Antimicrobial Stewardship Programs for Hematology/Oncology and Bone Marrow Transplant wards. Disclosures All authors: No reported disclosures.

Background Antibiotic use metrics are utilized by antimicrobial stewardship programs to benchmark performance against peer institutions and inform stewardship efforts. Benchmarking requires risk adjustment for patient- and facility-level factors so that remaining differences are attributable only to prescribing practices. Antibiotics for the treatment of methicillin-resistant Staphylococcus aureus (MRSA) are one of the most frequently used drug classes. Our objective was to identify predictors of anti-MRSA antibiotic use in a nationwide network of hospitals. Methods We used data from inpatient encounters at facilities participating in the Vizient data repository between January 1, 2016 and December 31, 2016. The outcome, anti-MRSA antibiotic use, was calculated as days of therapy per patient-days present for each encounter. We constructed a multivariable negative binomial regression model and assessed the following predictors for inclusion: age, sex, race, ethnicity, diagnosis related groups (DRGs), ICU days, admit month, facility bed size, facility teaching status, and region. A clinical framework was used to categorize DRGs based on risk of anti-MRSA antibiotic use. A backwards stepwise approach was used to identify the final model. We evaluated predictor effect size and significance, and assessed model fit using a deviance-based pseudo-R2. Results One hundred forty-five facilities representing 3,608,711 encounters met inclusion criteria. All predictors considered in our model were significant. Predictors with the greatest magnitude of association included DRG categories and patient age. The DRG categories with the strongest associations were DRGs for infections likely due to Staphylococcus aureus (RR = 1.66, P < 0.0001) or for diagnoses likely to receive long-term MRSA coverage (RR = 1.49, P < 0.0001). The age group with the strongest association was age 2–10 years (RR = 1.64; P < 0.001). The deviance-based pseudo-R2 of the final model was 0.19, indicating good model fit. Conclusion DRGs and patient-level characteristics can be utilized to account for variability in anti-MRSA antibiotic use beyond what is explained through facility-level characteristics. Incorporation of the significant predictors identified in this study may aid in more meaningful interhospital comparisons of anti-MRSA antibiotic use in both adults and pediatrics. Disclosures J. C. McGregor, Merck: Grant Investigator, Research grant.

The objective of this study was to develop a discrete event agent-based stochastic model to explore the likelihood of the occurrence of porcine reproductive and respiratory syndrome (PRRS) outbreaks in swine herds with different PRRS control measures in place. The control measures evaluated included vaccination with a modified-live attenuated vaccine and live-virus inoculation of gilts, and both were compared to a baseline scenario where no control measures were in place. A typical North American 1,000-sow farrow-to-wean swine herd was used as a model, with production and disease parameters estimated from the literature and expert opinion. The model constructed herein was not only able to capture individual animal heterogeneity in immunity to and shedding of the PRRS virus, but also the dynamic animal flow and contact structure typical in such herds under field conditions. The model outcomes included maximum number of females infected per simulation, and time at which that happened and the incidence of infected weaned piglets during the first year of challenge-virus introduction. Results showed that the baseline scenario produced a larger percentage of simulations resulting in outbreaks compared to the control scenarios, and interestingly some of the outbreaks occurred over long periods after virus introduction. The live-virus inoculation scenario showed promising results, with fewer simulations resulting in outbreaks than the other scenarios, but the negative impacts of maintaining a PRRS-positive population should be considered. Finally, under the assumptions of the current model, neither of the control strategies prevented the infection from spreading to the piglet population, which highlights the importance of maintaining internal biosecurity practices at the farrowing room level.

Background Swine influenza A virus (IAV) reassortment with 2009 H1N1 pandemic (H1N1pdm09) virus has been documented, and new genotypes and subclusters of H3N2 have since expanded in the US swine population. An H3N2 variant (H3N2v) virus with the H1N1pdm09 matrix gene and the remaining genes of swine triple reassortant H3N2 caused outbreaks at agricultural fairs in 2011–2012. Methods To assess commercial swine IAV vaccines' efficacy against H3N2 viruses, including those similar to H3N2v, antisera to three vaccines were tested by hemagglutinin inhibition (HI) assay against contemporary H3N2. Vaccine 1, with high HI cross-reactivity, was further investigated for efficacy against H3N2 virus infection in pigs with or without maternally derived antibodies (MDA). In addition, efficacy of a vaccine derived from whole inactivated virus (WIV) was compared with live attenuated influenza virus (LAIV) against H3N2. Results Hemagglutinin inhibition cross-reactivity demonstrated that contemporary swine H3N2 viruses have drifted from viruses in current swine IAV vaccines. The vaccine with the highest level of HI cross-reactivity significantly protected pigs without MDA. However, the presence of MDA at vaccination blocked vaccine efficacy. The performance of WIV and LAIV was comparable in the absence of MDA. Conclusions Swine IAV in the United States is complex and dynamic. Vaccination to minimize virus shedding can help limit transmission of virus among pigs and people. However, vaccines must be updated. A critical review of the use of WIV in sows is required in the context of the current IAV ecology and vaccine application in pigs with MDA.

Background The antibiotic timeout (ATO) is a stewardship tool that protocolizes review of objective clinical data after a predefined period of time and encourages antimicrobial regimen re-assessment. Methods Vizient member hospitals were utilized to recruit a variety of acute healthcare institutions, including institutions with and without an ATO process. Participating institutions submitted de-identified patient-level antibiotic therapy courses from a single day within a 5-week window to create a snapshot of overall antibiotic utilization. Therapy courses were evaluated on metrics including the prevalence of anti-pseudomonal agents, agents active against methicillin-resistant Staphylococcus aureus (MRSA), and oral (vs. intravenous) antibiotics. The outcome measures included: percent changes in prevalence of courses with antipseudomonal and anti-MRSA agents after day 3, and percent change in antibiotics ordered for oral administration after day 3. These outcome measures were compared between ATO institutions and non-ATO institutions. Results A total of 6,184 antibiotic therapy courses were collected from 61 participating institutions (17 ATO institutions; 44 non-ATO institutions). Of 71 institutions that completed enrollment survey, 10 did not complete submission of therapy course data. Antibiotic courses prescribed for prophylaxis (n = 975) and courses that extended beyond 7 days (n = 1,192) were excluded from analysis, resulting in an analysis group that included 4,017 therapy courses (1,396 from ATO institutions vs. 2,621 from non-ATO institutions). The prevalence of patients receiving anti-pseudomonal agents increased after day 3 by 3.03% (P = 0.28) at ATO institutions and decreased 0.45% (P = 0.84) at non-ATO institutions. The prevalence of patients receiving anti-MRSA agents decreased after day 3 by 2.16% (P = 0.41) at ATO institutions and decreased 5.05% (P = 0.005) at non-ATO institutions. Oral antibiotic use increased after day 3 by 3.09% (P = 0.08) at ATO institutions while use at non-ATO institutions increased 7.99% (P = 0.0001). Conclusion Antibiotic therapy course data collected across multiple sites provided no evidence for improved antimicrobial utilization among institutions that have implemented an antibiotic timeout compared with institutions without a timeout. Disclosures All authors: No reported disclosures.

Background Development of antiviral drugs that have broad-spectrum activity against a number of viral infections would be of significant benefit. Due to the evolution of resistance to currently licensed antiviral drugs, development of novel anti-influenza drugs is in progress, including Favipiravir (T-705), which is currently in human clinical trials. T-705 displays broad-spectrum in vitro activity against a number of viruses, including Rift Valley Fever virus (RVFV). RVF is an important neglected tropical disease that causes human, agricultural, and economic losses in endemic regions. RVF has the capacity to emerge in new locations and also presents a potential bioterrorism threat. In the current study, the in vivo efficacy of T-705 was evaluated in Wistar-Furth rats infected with the virulent ZH501 strain of RVFV by the aerosol route. Methodology/Principal Findings Wistar-Furth rats are highly susceptible to a rapidly lethal disease after parenteral or inhalational exposure to the pathogenic ZH501 strain of RVFV. In the current study, two experiments were performed: a dose-determination study and a delayed-treatment study. In both experiments, all untreated control rats succumbed to disease. Out of 72 total rats infected with RVFV and treated with T-705, only 6 succumbed to disease. The remaining 66 rats (92%) survived lethal infection with no significant weight loss or fever. The 6 treated rats that succumbed survived significantly longer before succumbing to encephalitic disease. Conclusions/Significance Currently, there are no licensed antiviral drugs for treating RVF. Here, T-705 showed remarkable efficacy in a highly lethal rat model of Rift Valley Fever, even when given up to 48 hours post-infection. This is the first study to show protection of rats infected with the pathogenic ZH501 strain of RVFV. Our data suggest that T-705 has potential to be a broad-spectrum antiviral drug., Author Summary Broad-spectrum antiviral drugs are preferred because they have the capacity to treat a range of viral illnesses rather than just one. Food and Drug Administration (FDA) approval of antiviral drugs to treat neglected tropical diseases is difficult to obtain due to ethical and logistical considerations when conducting human clinical trials. Rift Valley Fever (RVF) is an endemic tropical disease that causes human morbidity and mortality, as well as economic damage to the livestock industry. There are no licensed antiviral drugs to treat RVF. In this study, we found that a novel anti-influenza drug, Favipiravir (T-705), is able to prevent lethal RVF in rats, and therefore shows promise as a broad-spectrum antiviral treatment.

Ethambutol (EMB) resistance can evolve through a multistep process, and mutations in the ubiA ( Rv3806c ) gene appear to be responsible for high-level EMB resistance in Mycobacterium tuberculosis . We evaluated the prevalence of ubiA and embB ( Rv3795 ) mutations in EMB-resistant strains originating from Africa and South Korea. No differences in embB mutation frequencies were observed between strains from both origins. However, ubiA mutations were present in 45.5% ± 6.5% of the African EMB-resistant isolates but in only 9.5% ± 1.5% of the South Korean EMB-resistant isolates. The ubiA mutations associated with EMB resistance were localized to regions encoding the transmembrane domains of the protein, whereas the embB mutations were localized to regions encoding the extramembrane domains. Larger studies are needed to investigate the causes of increased ubiA mutations as a pathway to high-level EMB resistance in African countries, such as extended EMB usage during tuberculosis treatment.

Multiple genetically and antigenically distinct hemagglutinin genes of the H1 and H3 influenza A virus (IAV) subtypes co-circulate in North American swine. This diversity has evolved by repeated transmission of IAVs from humans to swine and subsequent antigenic drift in swine. To understand the evolutionary dynamics of these diverse HA lineages in North American swine, we undertook a phylogenetic analysis of 1576 H1 and 607 H3 HA gene segments, as well as 834 N1 and 1293 N2 NA gene segments, and 2126 M gene segments. These data revealed yearly co-circulation of H1N1, H1N2, and H3N2 viruses, with three HA clades representing the majority of the HA sequences: of the H1 viruses, 42% were classified as H1δ1 and 40.6% were classified as H1γ; and of the H3 viruses 53% were classified as cluster IV-A H3N2. We detected a genetically distinct minor clade consisting of 37 H1 viruses isolated between 2003 and 2013, which we classified as H1γ-2. We estimated that this clade circulated in swine since approximately 1995, but it was not detected in swine until 2003. Though this clade only represents 1.07% of swine H1 sequences reported over the past 10 years, hemagglutination inhibition (HI) assays demonstrated that representatives of this clade of viruses are antigenically distinct, and, when measured using antigenic cartography, were as many as 7 antigenic units from other H1γ viruses. Therefore vaccines against the contemporary H1γ viruses are not likely to cross-protect against γ-2 viruses. The long-term circulation of these γ-2 viruses suggests that minor populations of viruses may be underreported in the national dataset given the long branch lengths and gaps in detections. The identification of these γ-2 viruses demonstrates the need for robust surveillance to capture the full diversity IAVs in swine in the USA and the importance of antigenic drift in the diversification and emergence of new antigenic variants in swine, which complicates vaccine design.

Leprosy is a curable neglected disease of humans caused by Mycobacterium leprae that affects the skin and peripheral nerves and manifests clinically in various forms ranging from self-resolving, tuberculoid leprosy to lepromatous leprosy having significant pathology with ensuing disfiguration disability and social stigma. Despite the global success of multi-drug therapy (MDT), incidences of clinical leprosy have been observed in individuals with no apparent exposure to other cases, suggestive of possible non-human sources of the bacteria. In this study we show that common free-living amoebae (FLA) can phagocytose M. leprae, and allow the bacillus to remain viable for up to 8 months within amoebic cysts. Viable bacilli were extracted from separate encysted cocultures comprising three common Acanthamoeba spp.: A. lenticulata, A. castellanii, and A. polyphaga and two strains of Hartmannella vermiformis. Trophozoites of these common FLA take up M. leprae by phagocytosis. M. leprae from infected trophozoites induced to encyst for long-term storage of the bacilli emerged viable by assessment of membrane integrity. The majority (80%) of mice that were injected with bacilli extracted from 35 day cocultures of encysted/excysted A. castellanii and A. polyphaga showed lesion development that was similar to mice challenged with fresh M. leprae from passage mice albeit at a slower initial rate. Mice challenged with coculture-extracted bacilli showed evidence of acid-fast bacteria and positive PCR signal for M. leprae. These data support the conclusion that M. leprae can remain viable long-term in environmentally ubiquitous FLA and retain virulence as assessed in the nu/nu mouse model. Additionally, this work supports the idea that M. leprae might be sustained in the environment between hosts in FLA and such residence in FLA may provide a macrophage-like niche contributing to the higher-than-expected rate of leprosy transmission despite a significant decrease in human reservoirs due to MDT., Author Summary Leprosy is a progressive disease of the skin and nervous system caused by the bacillus, Mycobacterium leprae. Implementation of multiple drug therapy (MDT) for leprosy has significantly reduced the global cases of leprosy. Currently, only a few endemic countries remain where relatively high number of cases persists. Despite global reduction of leprosy and the concomitant decrease in human reservoirs, leprosy transmission and incidence have not declined as expected, suggesting a possible extra-human or environmental source of the bacilli. In the current study, we demonstrate that M. leprae can survive long-term within cysts of common environmental free-living amoebae. M. leprae residing in amoebal cysts for over 30 days remain fully capable of transferring disease to mouse footpads and retain viability phenotypes after several months residence within amoebal cysts. It is hypothesized that these protozoa provide an intracellular refuge for M. leprae in environments for which they would otherwise seem ill suited. Traits allowing bacilli to survive in macrophages may likely be acquired via an evolutionary response against predation by amoebae. The results from this work suggest alternative non-human reservoirs for M. leprae exist fostering further study to determine the role of amoebae in the transmission of this Mycobacterium to humans.

Background The Centers for Disease Control and Prevention National Healthcare Safety Network (NHSN) provides hospitals a mechanism to report antibiotic use (AU) data to benchmark against peer institutions and direct antibiotic stewardship efforts. Differences in patient populations need to be adjusted for to ensure unbiased comparisons across hospitals. Our objective was to identify predictors of total AU across a nationwide network of hospitals. Methods Data from 126 academic hospitals were extracted from the Vizient Clinical Data Base Resource Manager for adult inpatients (age ≥ 18 years) in 2015. AU was expressed as total antibiotic days of therapy/patient-days. We constructed a negative binomial regression model to explore potential predictors of AU including age, race, sex, case mix index, hospital bed size, length of stay, geographic region, transfer cases, service line, and illness severity. A backwards stepwise approach based on likelihood ratio test was used to identify significant (P < 0.05) predictors and construct the final, parsimonious model. We calculated dispersion-based R2 to assess the percent variability explained by the full and final models. Results A total of 3,076,394 total admissions, representing 17,544,763 patient days, were included. Factors identified as significant predictors in the final model are shown in the Table. The percent variance explained by the full and final models was 90.3% and 89.6%, respectively. Table: Independent predictors of total facility antibiotic use per patient days Relative Risk 95% Confidence Interval Case Mix Index 1.36 1.16, 1.60 Region West Ref – Midwest 1.05 0.92, 1.20 Northeast 0.92 0.81, 1.04 South 1.07 0.94, 1.23 Transfer cases 0.31 0.15, 0.63 Surgery service line 0.45 0.25, 0.81 Major illness severity 3.24 1.04, 10.09 Conclusion The current NHSN AU risk adjustment metric, the standardized antimicrobial administration ratio (SAAR), has been developed separately for different antibiotic groupings and adjusts for a limited set of facility characteristics. Further work is needed to assess if the independent predictors identified in this model can improve upon the performance of existing SAAR metrics and aid in directing stewardship strategies. Disclosures All authors: No reported disclosures.

Background: Increases in the abundance and distribution of ticks and tick borne disease (TBD) within Europe have been reported extensively over the last 10-20 years. Changes in climate, habitat management, economic patterns and changes in the abundance of hosts, particularly deer, may all have influenced this change to varying extents. Increasing abundances of tick populations in urban and peri-urban environments, such as parks, are of particular concern. In these sites, suitable habitat, wildlife hosts, tick populations, people and their pets may be brought into close proximity and hence may provide foci for tick infestation and, ultimately, disease transmission.Methods: The distribution and abundance of ticks were examined in an intensively used, peri-urban park. First the seasonal and spatial distribution and abundance of ticks in various habitat types were quantified by blanket dragging. Then the pattern of pet dog movement in the park was mapped by attaching GPS recorders to the collars of dogs brought to the park for exercise, allowing their walking routes to be tracked. Information about the dog, its park use and its history of tick attachment were obtained from the dog-owners.Results: Ticks were found predominantly in woodland, woodland edge and deer park areas and were least abundant in mown grassland. Tick infestation of dogs was a relatively frequent occurrence with, on average, one case of tick attachment reported per year for a dog walked once per week, but for some dogs walked daily, infestation 4-5 times per week was reported. All dogs appeared to be at equal risk, regardless of walk route or duration and infestation was primarily influenced by the frequency of exposure.Conclusions: In peri-urban green spaces, tick-biting risk for dogs may be high and here was shown to be related primarily to exposure frequency. While tick-biting is of direct veterinary importance for dogs, dogs also represent useful sentinels for human tick-exposure.

Fusion inhibitors are a class of antiretroviral drugs used to prevent entry of HIV into host cells. Many of the fusion inhibitors being developed, including the drug enfuvirtide, are peptides designed to competitively inhibit the viral fusion protein gp41. With the emergence of drug resistance, there is an increased need for effective and unique alternatives within this class of antivirals. One such alternative is a class of cyclic, cationic, antimicrobial peptides known as θ-defensins, which are produced by many non-human primates and exhibit broad-spectrum antiviral and antibacterial activity. Currently, the θ-defensin analog RC-101 is being developed as a microbicide due to its specific antiviral activity, lack of toxicity to cells and tissues, and safety in animals. Understanding potential RC-101 resistance, and how resistance to other fusion inhibitors affects RC-101 susceptibility, is critical for future development. In previous studies, we identified a mutant, R5-tropic virus that had evolved partial resistance to RC-101 during in vitro selection. Here, we report that a secondary mutation in gp41 was found to restore replicative fitness, membrane fusion, and the rate of viral entry, which were compromised by an initial mutation providing partial RC-101 resistance. Interestingly, we show that RC-101 is effective against two enfuvirtide-resistant mutants, demonstrating the clinical importance of RC-101 as a unique fusion inhibitor. These findings both expand our understanding of HIV drug-resistance to diverse peptide fusion inhibitors and emphasize the significance of compensatory gp41 mutations.

BACKGROUNDThe Canadian National Antiviral Stockpile (NAS) contains treatment for 17.5% of Canadians. This assumes no concurrent intervention strategies and no wastage due to non-influenza respiratory infections. A dynamic model can provide a mechanism to consider complex scenarios to support decisions regarding the optimal NAS size under uncertainty.METHODSWe developed a dynamic model for pandemic influenza in Canada that is structured by age and risk to calculate the demand for antivirals to treat persons with pandemic influenza under a wide-range of scenarios that incorporated transmission dynamics, disease severity, and intervention strategies. The anticipated per capita number of acute respiratory infections due to viruses other than influenza was estimated for the full pandemic period from surveys based on criteria to identify potential respiratory infections.RESULTSOur results demonstrate that up to two thirds of the population could develop respiratory symptoms as a result of infection with a pandemic strain. In the case of perfect antiviral allocation, up to 39.8% of the population could request antiviral treatment. As transmission dynamics, severity and timing of the emergence of a novel influenza strain are unknown, the sensitivity analysis produced considerable variation in potential demand (median: 11%, IQR: 2-21%). If the next pandemic strain emerges in late spring or summer and a vaccine is available before the anticipated fall wave, the median prediction was reduced to 6% and IQR to 0.7-14%. Under the strategy of offering empirical treatment to all patients with influenza like symptoms who present for care, demand could increase to between 65 and 144%.CONCLUSIONSThe demand for antivirals during a pandemic is uncertain. Unless an accurate, timely and cost-effective test is available to identify influenza cases, demand for antivirals from persons infected with other respiratory viruses will be substantial and have a significant impact on the NAS.

After witnessing an episode of poor injection safety in large numbers of children in a rural under-resourced hospital in Uganda, we briefly review our own experience and that of others in investigating HIV infection in children considered unlikely to be through commonly identified routes such as vertical transmission, sexual abuse or blood transfusion. In the majority of cases, parents are HIV uninfected. The cumulative experience suggests that the problem is real, but with relatively low frequency. Vertical transmission is the major route for HIV to children. However, factors such as poor injection safety, undocumented surrogate breast feeding, an HIV-infected adult feeding premasticated food to a weaning toddler, poor hygienic practice in the home and using unsterilised equipment for minor surgical or traditional procedures are of cumulative concern.

Humans infected with Rift Valley Fever virus (RVFV) generally recover after a febrile illness; however, a proportion of patients progress to a more severe clinical outcome such as hemorrhagic fever or meningoencephalitis. RVFV is naturally transmitted to livestock and humans by mosquito bites, but it is also infectious through inhalational exposure, making it a potential bioterror weapon. To better understand the disease caused by inhalation of RVFV, Wistar-Furth, ACI, or Lewis rats were exposed to experimental aerosols containing virulent RVFV. Wistar-Furth rats developed a rapidly progressing lethal hepatic disease after inhalational exposure; ACI rats were 100-fold less susceptible and developed fatal encephalitis after infection. Lewis rats, which do not succumb to parenteral inoculation with RVFV, developed fatal encephalitis after aerosol infection. RVFV was found in the liver, lung, spleen, heart, kidney and brain of Wistar Furth rats that succumbed after aerosol exposure. In contrast, RVFV was found only in the brains of ACI or Lewis rats that succumbed after aerosol exposure. Lewis rats that survived s.c. infection were not protected against subsequent re-challenge by aerosol exposure to the homologous virus. This is the first side-by-side comparison of the lethality and pathogenesis of RVFV in 3 rat strains after aerosol exposure and the first step towards developing a rodent model suitable for use under the FDA Animal Rule to test potential vaccines and therapeutics for aerosol exposure to RVFV.

Influenza A viruses cause acute respiratory disease in swine. Viruses with H1 hemagglutinin genes from the human seasonal lineage (-cluster) have been isolated from North American swine since 2003. The objective of this work was to study the pathogenesis and transmission of -cluster H1 influenza viruses in swine, comparing three isolates from different phylogenetic subclusters, geographic locations, and years of isolation. Two isolates from the 2 subcluster, A/sw/MN/07002083/07 H1N1 (MN07) and A/sw/IL/00685/05 H1N1 (IL05), and A/sw/TX/01976/08 H1N2 (TX08) from the 1 sub-cluster were evaluated. All isolates caused disease and were transmitted to contact pigs. Respiratory disease was apparent in pigs infected with MN07 and IL05 viruses; however, clinical signs and lung lesions were reduced in severity as compared to TX08. On day 5 following infection MN07-infected pigs had lower virus titers than the TX08 pigs, suggesting that although this H1N1 was successfully transmitted, it may not replicate as efficiently in the upper or lower respiratory tract. MN07 and IL05 H1N1 induced higher serum antibody titers than TX08. Greater serological cross-reactivity was observed for viruses from the same HA phylogenetic sub-cluster; however, antigenic differences between the sub-clusters may have implications for disease control strategies for pigs.

HIV-exposed uninfected (HEU) infants have higher infectious morbidity than HIV-unexposed uninfected (HUU) infants. We present the clinical outcomes from a pilot cohort study of 27 HEU and 28 HUU infants. In the absence of infant malnutrition or advanced maternal HIV, HEU infants experienced a 2.74 (0.85–8.78) times greater risk of hospitalization in the first year.

Background HIV exposed seronegative (HESN) women represent the population most in need of a prophylactic antiviral strategy. Mucosal cationic polypeptides can potentially be regulated for this purpose and we here aimed to determine their endogenous expression and HIV neutralizing activity in genital secretions of women at risk of HIV infection. Methodology/Principal Findings Cervicovaginal secretions (CVS) of Kenyan women in HIV-serodiscordant relationships (HESN, n = 164; HIV seropositive, n = 60) and low-risk controls (n = 72) were assessed for the cationic polypeptides HNP1–3, LL-37 and SLPI by ELISA and for HIV neutralizing activity by a PBMC-based assay using an HIV primary isolate. Median levels of HNP1–3 and LL-37 in CVS were similar across study groups. Neither HSV-2 serostatus, nor presence of bacterial vaginosis, correlated with levels of HNP1–3 or LL-37 in the HESN women. However, an association with their partner's viral load was observed. High viral load (>10,000 HIV RNA copies/ml plasma) correlated with higher levels of HNP1–3 and LL-37 (p = 0.04 and 0.03, respectively). SLPI was most abundant in the low-risk group and did not correlate with male partner's viral load in the HESN women. HIV neutralizing activity was found in CVS of all study groups. In experimental studies, selective depletion of cationic polypeptides from CVS rendered the remaining CVS fraction non-neutralizing, whereas the cationic polypeptide fraction retained the activity. Furthermore, recombinant HNP1–3 and LL-37 could induce neutralizing activity when added to CVS lacking intrinsic activity. Conclusions/Significance These findings show that CVS from HESN, low-risk, and HIV seropositive women contain HIV neutralizing activity. Although several innate immune proteins, including HNP1–3 and LL-37, contribute to this activity these molecules can also have inflammatory properties. This balance is influenced by hormonal and environmental factors and in the present HIV serodiscordant couple cohort study we show that a partner's viral load is associated with levels of such molecules.

Many pathogenic bacteria, fungi, and protozoa achieve chronic infection through an immune evasion strategy known as antigenic variation. In the human malaria parasite Plasmodium falciparum, this involves transcriptional switching among members of the var gene family, causing parasites with different antigenic and phenotypic characteristics to appear at different times within a population. Here we use a genome-wide approach to explore this process in vitro within a set of cloned parasite populations. Our analyses reveal a non-random, highly structured switch pathway where an initially dominant transcript switches via a set of switch-intermediates either to a new dominant transcript, or back to the original. We show that this specific pathway can arise through an evolutionary conflict in which the pathogen has to optimise between safeguarding its limited antigenic repertoire and remaining capable of establishing infections in non-naïve individuals. Our results thus demonstrate a crucial role for structured switching during the early phases of infections and provide a unifying theory of antigenic variation in P. falciparum malaria as a balanced process of parasite-intrinsic switching and immune-mediated selection., Author Summary The malaria parasite Plasmodium falciparum avoids recognition and clearance by the immune system by sequentially switching between members of the var multi-gene family which encode the immunodominant surface proteins PfEMP1. However, some mechanism must exist to prevent rapid exposure of the pathogen's entire antigenic repertoire as this would quickly terminate the infection. It has previously been shown that the immune system can play an important role in orchestrating the sequential display of variants once an infection is established; however this does not explain how repertoire exhaustion is avoided in the initial phases of infection before an immune response has been established. Here we show that P. falciparum has evolved a highly structured switching pattern to prevent repertoire exhaustion in the early stages of infection without compromising the ability to establish new infections among partially immune individuals.