Impact of spatiotemporal heterogeneity in COVID-19 disease surveillance on epidemiological parameters and case growth rates.

SARS-CoV-2 case data are primary sources for estimating epidemiological parameters and for modelling the dynamics of outbreaks. Understanding biases within case-based data sources used in epidemiological analyses is important as they can detract from the value of these rich datasets. This raises questions of how variations in surveillance can affect the estimation of epidemiological parameters such as the case growth rates. We use standardised line list data of COVID-19 from Argentina, Brazil, Mexico and Colombia to estimate delay distributions of symptom-onset-to-confirmation, -hospitalisation and -death as well as hospitalisation-to-death at high spatial resolutions and throughout time. Using these estimates, we model the biases introduced by the delay from symptom-onset-to-confirmation on national and state level case growth rates (rt) using an adaptation of the Richardson-Lucy deconvolution algorithm. We find significant heterogeneities in the estimation of delay distributions through time and space with delay difference of up to 19 days between epochs at the state level. Further, we find that by changing the spatial scale, estimates of case growth rate can vary by up to 0.13 d-1. Lastly, we find that states with a high variance and/or mean delay in symptom-onset-to-diagnosis also have the largest difference between the rt estimated from raw and deconvolved case counts at the state level. We highlight the importance of high-resolution case-based data in understanding biases in disease reporting and how these biases can be avoided by adjusting case numbers based on empirical delay distributions. Code and openly accessible data to reproduce analyses presented here are available.

A cocktail of human monoclonal antibodies broadly neutralizes North American rabies virus variants as a promising candidate for rabies post-exposure prophylaxis.

Human rabies remains a globally significant public health problem. Replacement of polyclonal anti-rabies immunoglobulin (RIG), a passive component of rabies post-exposure prophylaxis (PEP), with a monoclonal antibody (MAb), would eliminate the cost and availability constraints associated with RIG. Our team has developed and licensed a human monoclonal antibody RAB1 (Rabishield©), as the replacement for RIG where canine rabies is enzootic. However, for the highly diverse rabies viruses of North America, a cocktail containing two or more MAbs targeting different antigenic sites of the rabies glycoprotein should be included to ensure neutralization of all variants of the virus. In this study, two MAb cocktails, R172 (RAB1-RAB2) and R173 (RAB1-CR57), were identified and evaluated against a broad range of rabies variants from North America. R173 was found to be the most potent cocktail, as it neutralized all the tested North American RABV isolates and demonstrated broad coverage of isolates from both terrestrial and bat species. R173 could be a promising candidate as an alternative or replacement for RIG PEP in North America.

Tumor suppressor CEBPA interacts with and inhibits DNMT3A activity.

DNA methyltransferases (DNMTs) catalyze DNA methylation, and their functions in mammalian embryonic development and diseases including cancer have been extensively studied. However, regulation of DNMTs remains under study. Here, we show that CCAAT/enhancer binding protein α (CEBPA) interacts with the long splice isoform DNMT3A, but not the short isoform DNMT3A2. CEBPA, by interacting with DNMT3A N-terminus, blocks DNMT3A from accessing DNA substrate and thereby inhibits its activity. Recurrent tumor-associated CEBPA mutations, such as preleukemic CEBPAN321D mutation, which is particularly potent in causing AML with high mortality, disrupt DNMT3A association and cause aberrant DNA methylation, notably hypermethylation of PRC2 target genes. Consequently, leukemia cells with the CEBPAN321D mutation are hypersensitive to hypomethylation agents. Our results provide insights into the functional difference between DNMT3A isoforms and the regulation of de novo DNA methylation at specific loci in the genome. Our study also suggests a therapeutic strategy for the treatment of CEBPA-mutated leukemia with DNA-hypomethylating agents.

Cell-free DNA TAPS provides multimodal information for early cancer detection.

Multimodal, genome-wide characterization of epigenetic and genetic information in circulating cell-free DNA (cfDNA) could enable more sensitive early cancer detection, but it is technologically challenging. Recently, we developed TET-assisted pyridine borane sequencing (TAPS), which is a mild, bisulfite-free method for base-resolution direct DNA methylation sequencing. Here, we optimized TAPS for cfDNA (cfTAPS) to provide high-quality and high-depth whole-genome cell-free methylomes. We applied cfTAPS to 85 cfDNA samples from patients with hepatocellular carcinoma (HCC) or pancreatic ductal adenocarcinoma (PDAC) and noncancer controls. From only 10 ng of cfDNA (1 to 3 ml of plasma), we generated the most comprehensive cfDNA methylome to date. We demonstrated that cfTAPS provides multimodal information about cfDNA characteristics, including DNA methylation, tissue of origin, and DNA fragmentation. Integrated analysis of these epigenetic and genetic features enables accurate identification of early HCC and PDAC.

Pharmacokinetic Profiles of Gabapentin after Oral and Subcutaneous Administration in Black-tailed Prairie Dogs (Cynomys ludovicianus).

In veterinary and human medicine, gabapentin (a chemical analog of γ-aminobutyric acid) is commonly prescribed to treat postoperative and chronic neuropathic pain. This study explored the pharmacokinetics of oral and subcutaneous administration of gabapentin at high (80 mg/kg) and low (30 mg/kg) doses as a potential analgesic in black-tailed prairie dogs (Cynomys ludovicianus; n = 24). The doses (30 and 80 mg/kg) and half maximal effective concentration (1.4 to 16.7 ng/mL) for this study were extrapolated from pharmacokinetic efficacy studies in rats, rabbits, and cats. Gabapentin in plasma was measured by using an immunoassay, and data were evaluated using noncompartmental analysis. The peak plasma concentrations (mean ±1 SD) were 42.6 ±14.8 and 115.5 ±15.2 ng/mL, respectively, after 30 and 80 mg/kg SC and 14.5 ±3.5 and 20.7 ±6.1 ng/mL after the low and high oral dosages, respectively. All peak plasma concentrations of gabapentin occurred within 5 h of administration. Disappearance half-lives for the low and high oral doses were 7.4 ± 6.0 h and 5.0 ± 0.8 h, respectively. The results of this study demonstrate that oral administration of gabapentin at low (30 mg/kg) doses likely would achieve and maintain plasma concentrations at half maximum effective concentration for 12 h, making it a viable option for an every 12-h treatment.

Antiviral Ranpirnase TMR-001 Inhibits Rabies Virus Release and Cell-to-Cell Infection In Vitro.

Currently, no rabies virus-specific antiviral drugs are available. Ranpirnase has strong antitumor and antiviral properties associated with its ribonuclease activity. TMR-001, a proprietary bulk drug substance solution of ranpirnase, was evaluated against rabies virus in three cell types: mouse neuroblastoma, BSR (baby hamster kidney cells), and bat primary fibroblast cells. When TMR-001 was added to cell monolayers 24 h preinfection, rabies virus release was inhibited for all cell types at three time points postinfection. TMR-001 treatment simultaneous with infection and 24 h postinfection effectively inhibited rabies virus release in the supernatant and cell-to-cell spread with 50% inhibitory concentrations of 0.2-2 nM and 20-600 nM, respectively. TMR-001 was administered at 0.1 mg/kg via intraperitoneal, intramuscular, or intravenous routes to Syrian hamsters beginning 24 h before a lethal rabies virus challenge and continuing once per day for up to 10 days. TMR-001 at this dose, formulation, and route of delivery did not prevent rabies virus transit from the periphery to the central nervous system in this model (n = 32). Further aspects of local controlled delivery of other active formulations or dose concentrations of TMR-001 or ribonuclease analogues should be investigated for this class of drugs as a rabies antiviral therapeutic.

SAFETY, IMMUNOGENICITY, AND EFFICACY OF INTRAMUSCULAR AND ORAL DELIVERY OF ERA-G333 RECOMBINANT RABIES VIRUS VACCINE TO BIG BROWN BATS (EPTESICUS FUSCUS).

Attenuated strains of rabies virus (RABV) have been used for oral vaccination of wild carnivores in Europe and North America. However, some RABV vaccines caused clinical rabies in target animals. To improve the safety of attenuated RABV as an oral vaccine for field use, strategies using selection of escape mutants under monoclonal antibody neutralization pressure and reverse genetics-defined mutations have been used. We tested the safety, immunogenicity, and efficacy of one RABV construct, ERA-g333, developed with reverse genetics by intramuscular (IM) or oral (PO) routes in big brown bats (Eptesicus fuscus). Twenty-five bats received 5×106 mouse intracerebral median lethal doses (MICLD50) of ERA-g333 by IM route, 10 received 5×106 MICLD50 of ERA-g333 by PO route, and 22 bats served as unvaccinated controls. Twenty-one days after vaccination, 44 bats were infected by IM route with 102.9 MICLD50 of E. fuscus RABV. We report both the immunogenicity and efficacy of ERA-g333 delivered by the IM route; no induction of humoral immunity was detected in bats vaccinated by the PO route. Two subsets of bats vaccinated IM (n=5) and PO (n=3) were not challenged, and none developed clinical rabies from ERA-g333. Scarce reports exist on the evaluation of oral rabies vaccines in insectivorous bats, although the strategy evaluated here may be feasible for future application to these important RABV reservoirs.

Inactivated Rabies Virus-Based Ebola Vaccine Preserved by Vaporization Is Heat-Stable and Immunogenic Against Ebola and Protects Against Rabies Challenge.

BACKGROUND: Ebola virus (EBOV) is a highly lethal member of the Filoviridae family associated with human hemorrhagic disease. Despite being a sporadic disease, it caused a large outbreak in 2014-2016 in West Africa and another outbreak recently in the Democratic Republic of Congo. Several vaccine candidates are currently in preclinical and clinical studies but none are stable without cold chain storage. METHODS: We used preservation by vaporization (PBV), a novel processing technology to heat-stabilize FiloRab1 (inactivated rabies-based Ebola vaccine), a candidate Ebola vaccine, and stored the vials at temperatures ranging from 4°C to 50°C for 10 days to 12 months. We immunized Syrian hamsters with the best long-term stable FiloRab1 PBV vaccines and challenged them with rabies virus (RABV). RESULTS: Syrian hamsters immunized with FiloRab1 PBV-processed vaccines stored at temperatures of 4°C and 37°C for 6 months, and at 50°C for 2 weeks, seroconverted against both RABV-G and EBOV-GP. Notably, all of the FiloRab1 PBV vaccines proved to be 100% effective in a RABV challenge model. CONCLUSIONS: We successfully demonstrated that the FiloRab1 PBV vaccines are stable and efficacious for up to 6 months when stored at temperatures ranging from 4°C to 37°C and for up to 2 weeks at 50°C.

PREVALENCE OF ANTIBODIES TO ORTHOPOXVIRUS IN WILD CARNIVORES OF NORTHWESTERN CHIHUAHUA, MEXICO.

The distribution of orthopoxviruses (OPXVs) across the North American continent is suggested to be widespread in a wide range of mammalian hosts on the basis of serosurveillance studies. To address the question of whether carnivores in northwestern Mexico are exposed to naturally circulating OPXVs, wild carnivores were collected by live trapping within four different habitat types during fall of 2013 and spring of 2014 within the Janos Biosphere Reserve in northwestern Chihuahua, Mexico. A total of 51 blood samples was collected for testing. Anti-OPXV immunoglobulin G enzymelinked immunosorbent assay, western blot, and rapid fluorescent focus inhibition test (RFFIT) assays were conducted. About 47% (24/51) of the carnivores tested were seropositive for anti-OPXV binding antibodies and had presence of immunodominant bands indicative of OPXV infection. All samples tested were negative for rabies virus neutralizing antibodies by RFFIT, suggesting that the OPXV antibodies were due to circulating OPXV, and not from exposure to oral rabies vaccine (vacciniavectored rabies glycoprotein vaccine) bait distributed along the US-Mexico border. Our results indicated that there may be one or more endemic OPXV circulating within six species of carnivores in northwestern Mexico.

Bioprocess decision support tool for scalable manufacture of extracellular vesicles.

Newly recognized as natural nanocarriers that deliver biological information between cells, extracellular vesicles (EVs), including exosomes and microvesicles, provide unprecedented therapeutic opportunities. Large-scale and cost-effective manufacturing is imperative for EV products to meet commercial and clinical demands; successful translation requires careful decisions that minimize financial and technological risks. Here, we develop a decision support tool (DST) that computes the most cost-effective technologies for manufacturing EVs at different scales, by examining the costs of goods associated with using published protocols. The DST identifies costs of labor and consumables during EV harvest as key cost drivers, substantiating a need for larger-scale, higher-throughput, and automated technologies for harvesting EVs. Importantly, we highlight a lack of appropriate technologies for meeting clinical demands, and propose a potentially cost-effective solution. This DST can facilitate decision-making very early on in development and be used to predict, and better manage, the risk of process changes when commercializing EV products.

Revisiting rabies virus neutralizing antibodies through infecting BALB/c mice with live rabies virus.

This study investigates the production of rabies virus (RABV) neutralizing antibody after virus infection through a mouse model. The BALB/c mice from different age groups (three, five, seven week old) were intramuscularly inoculated with live rabies virus (TX coyote 323R). Without pre-exposure or post-exposure prophylaxis (PEP), we found there is a decreased fatality with increased age of animals, the mortalities are 60%, 50%, and 30%, respectively. Interestingly, through assay of rapid fluorescent focus inhibition test (RFFIT), direct fluorescent antibody (DFA) and quantitative Polymerase Chain Reaction (qPCR), the results showed that all the animals that succumbed to rabies challenge, except one, developed circulating neutralizing antibodies, and all the healthy animals, except two, did not generate virus neutralizing antibodies (VNA). Our animal study suggests that the induction of VNA was an indicator of infection progression in the central nervous system (CNS) and speculate that RABV neutralizing antibodies did not cross the blood-brain barrier of the CNS for those diseased animals. We hypothesize that early release of viral antigens from damaged nerve tissue might potentially be a benefit for survivors, and we also discuss several other aspects of the interaction of RABV and its neutralizing antibodies.

Rabies death attributed to exposure in Central America with symptom onset in a U.S. detention facility - Texas, 2013.

On June 7, 2013, a man was diagnosed in a Texas hospital with rabies. He had been detained in a U.S. detention facility during his infectious period. To identify persons exposed to rabies who might require rabies postexposure prophylaxis (PEP), CDC and the Texas Department of State Health Services (DSHS) conducted investigations at four detention facilities, one medical clinic, and two hospitals. In all, 25 of 742 persons assessed for rabies exposure were advised to receive PEP. Early diagnosis of rabies is essential for implementation of appropriate hospital infection control measures and for rapid assessment of potential contacts for PEP recommendations.

Anthropogenic roost switching and rabies virus dynamics in house-roosting big brown bats.

Big brown bats (Eptesicus fuscus) are the most commonly encountered rabid bat in North America and represent an important source of wildlife rabies epizootics. Urban and suburban colonies of E. fuscus are often evicted from their roosts in houses, with poorly understood consequences for bat dispersal, population dynamics, and rabies virus transmission. We combined radiotelemetry and mark-recapture of E. fuscus with enhanced surveillance to understand the frequency of rabies virus exposure in house-roosting bats and to assess the potential for behavioral responses of eviction to exacerbate viral transmission. Serology demonstrated the circulation of rabies virus in nearly all sites, with an overall seroprevalence of 12%, but no bats were excreting rabies virus at the time of capture. Bats that were excluded from roosts relocated to houses <1 km from the original roost. However, behavioral responses to eviction differed, with bats switching repeatedly among new roosts in 1 site, but fusing with a neighboring colony in another. These findings confirm the circulation of rabies virus in E. fuscus that live in close contact with humans and companion animals, suggest mechanisms through which anthropogenic disturbance of bats might influence pathogen transmission, and highlight simple strategies to balance conservation and public health priorities.

Response to vaccination with a commercial inactivated rabies vaccine in a captive colony of Brazilian free-tailed bats (Tadarida brasiliensis).

A captive colony of Brazilian free-tailed bats (Tadarida brasiliensis) was vaccinated with a commercial monovalent inactivated rabies virus (RABV) vaccine (RABVAC 1). Baseline rabies virus neutralizing antibodies (VNA) and the response to vaccination were measured in 50 bats. Rabies VNA was detected in the plasma of 64% (27/42) of bats that had been vaccinated 1 yr prior, but only 19% (8/42) had levels considered adequate. Rabies VNA was detected in the plasma of 63% (5/8) of bats with no record of previous vaccination, suggesting natural RABV exposure before captivity. All bats demonstrated a VNA response by 10 days postvaccination, and baseline titer significantly predicted humoral response to vaccination. No adverse reactions to vaccination or clinical signs of RABV infection were observed in the bats during a 6-mo observation period. Annual vaccination may maintain immunity against RABV infection in captive colonies of bats. Bat, rabies virus, Tadarida brasiliensis, vaccination, virus neutralizing antibodies.

Ecology of rabies virus exposure in colonies of Brazilian free-tailed bats (Tadarida brasiliensis) at natural and man-made roosts in Texas.

Previous studies have investigated rabies virus (RABV) epizootiology in Brazilian free-tailed bats (Tadarida brasiliensis) in natural cave roosts. However, little is known about geographic variation in RABV exposure, or if the use of man-made roosts by this species affects enzootic RABV infection dynamics within colonies. We sampled rabies viral neutralizing antibodies in bats at three bridge and three cave roosts at multiple time points during the reproductive season to investigate temporal and roost variation in RABV exposure. We report seropositive bats in all age and sex classes with minimal geographic variation in RABV seroprevalence among Brazilian free-tailed bat colonies in south-central Texas. While roost type was not a significant predictor of RABV seroprevalence, it was significantly associated with seasonal fluctuations, suggesting patterns of exposure that differ between roosts. Temporal patterns suggest increased RABV seroprevalence after parturition in cave colonies, potentially related to an influx of susceptible young, in contrast to more uniform seroprevalence in bridge colonies. This study highlights the importance of life history and roost ecology in understanding patterns of RABV seroprevalence in colonies of the Brazilian free-tailed bat.

Rabies virus pathogenesis in relationship to intervention with inactivated and attenuated rabies vaccines.

Despite progress in vaccine development in the past century the mechanisms behind immune responses elicited by rabies biologics or via natural infection remain largely unknown. In this study, we compared protection elicited by standard, early, or delayed prophylaxis with a reduced number of vaccine doses using inactivated and live-attenuated vaccines. Two-month-old Syrian hamsters, 4-week-old ICR mice or adult rhesus macaques were inoculated with canine rabies virus variants. Thereafter, prophylaxis was initiated 6h, 1, 2, 3, 4, 5, 6 or 7 days post-exposure (p.e.). One or several doses of inactivated (HDCV), or reverse genetically attenuated (live), or gamma-irradiated (inactivated)-ERAG333 vaccines were administered intramuscularly. The dynamics of virus spread were measured over time in the rodent models. Rabies virus reached the spinal cord at day 4 and brain at day 6 p.e. All hamsters succumbed in groups in which live ERAG333 was delayed until days 5 and 6 p.e. However, 78%, 44%, 56% and 22% of hamsters survived when one dose of live ERAG333 was administered 6h, 1, 2, 3, and 4 days p.e., respectively. Similarly, 67% survived when inactivated ERAG333 was administered at 24h p.e. All hamsters succumbed when standard prophylaxis (the Essen regimen) was delayed until days 3-6, but 67% and 33% of hamsters survived when PEP began 1 or 2 days p.e., respectively. Macaques were protected by one dose of attenuated ERAG333 at 24h p.e. The highly attenuated (live) and inactivated ERAG333 vaccines elicited potent protective immune responses, even when prophylaxis initiation was delayed. When 2-5 doses of commercial vaccine and HRIG were administered according to the Essen scheme, 89-100% of the animals survived. Reduced vaccine schedules provided efficacious intervention, regardless of the total number of vaccine doses administered.

Oral immunization of raccoons and skunks with a canine adenovirus recombinant rabies vaccine.

Oral vaccination is an important part of wildlife rabies control programs. Currently, the vaccinia-rabies glycoprotein recombinant virus is the only oral rabies vaccine licensed in the United States, and it is not effective in skunks. In the current study, captive raccoons and skunks were used to evaluate a vaccine developed by incorporating the rabies virus glycoprotein gene into a canine adenovirus serotype 2 vector (CAV2-RVG). Seven of 7 raccoons orally vaccinated with CAV2-RVG developed virus neutralizing antibodies and survived lethal challenge. Five of 5 and 6 of 6 skunks in 2 experimental groups receiving 10-fold different dilutions of CAV2-RVG developed neutralizing antibodies and survived challenge. The results of this preliminary study suggest that CAV2-RVG stimulates protective immunity against rabies in raccoons and skunks.

No adverse effects of simultaneous vaccination with the immunocontraceptive GonaCon and a commercial rabies vaccine on rabies virus neutralizing antibody production in dogs.

Parenteral vaccination campaigns are integral to the elimination of canine rabies. To maximize herd immunity in dogs, immunocontraception provided at the time of rabies vaccination should reduce fecundity and dog abundance. GonaCon has been used successfully as an immunocontraceptive in a variety of mammals, and by inference, the dog would be an ideal candidate for testing. As an initial step in evaluating a combination-vaccination program, we assessed the effects of GonaCon on rabies virus neutralizing antibody production in dogs after administration of a veterinary rabies vaccine. Eighteen feral/free ranging dogs were included in this initial study: six were given GonaCon only, six were given rabies vaccination only, and six received GonaCon and rabies vaccination. Antibody levels were evaluated over 82 days. The use of the immunocontraceptive GonaCon did not affect the ability of dogs to seroconvert in response to the rabies vaccine. Thus, GonaCon provides a potential immunocontraceptive for use in combination with rabies vaccine to increase herd immunity and address dog population over abundance to better manage rabies.

Human rabies and rabies in vampire and nonvampire bat species, Southeastern Peru, 2007.

After a human rabies outbreak in southeastern Peru, we collected bats to estimate the prevalence of rabies in various species. Among 165 bats from 6 genera and 10 species, 10.3% were antibody positive; antibody prevalence was similar in vampire and nonvampire bats. Thus, nonvampire bats may also be a source for human rabies in Peru.

Experimental rabies virus infection of big brown bats (Eptesicus fuscus).

A captive colony of adult Big Brown Bats (Eptesicus fuscus) was experimentally infected with a rabies virus (RABV) variant isolated from the salivary glands of a naturally infected Big Brown Bat and passaged once through murine neuroblastoma cell culture. Bats were divided into 11 groups, which were composed of one to three noninfected and one to three infected individuals each. Twenty of 38 animals were infected intramuscularly into both left and right masseter muscles; they received a total of 10(3.2) median mouse intracerebral lethal dose (MICLD50) of Big Brown Bat RABV variant. Experimental outcome after viral exposure was followed in the bats for 140 days postinoculation (PI). Of 20 infected bats, 16 developed clinical rabies, and the mean incubation period was 24 days (range: 13-52 days). Three infected bats never seroconverted and succumbed early to infection (13 days). Four infected bats that survived until the end of the experiment without any signs of disease maintained detectable antibody titers until the third month PI, peaking between days 13 and 43, and consequent drop-off below the threshold for detection occurred by day 140. Limited excretion of virus in saliva of infected bats during the clinical course of disease was observed in two individuals on days 13 and 15 PI (<24 hr prior to onset of clinical illness). No bat-to-bat transmission of RABV to noninfected bats was detected.