Rabies surveillance in the United States during 2014

Monroe, Benjamin; Yager, Pamela A.; Blanton, Jesse D.; Birhane, Meseret; Wadhwa, Ashutosh; Orciari, Lillian A.; Petersen, Brett W.; Wallace, Ryan M.

doi:10.2460/javma.248.7.777

Cited by 65 publications

(57 citation statements)

References 19 publications

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“…By contrast, our model results in the growth rate being a-priori constant, so that the clear decline in growth rate started in the mid-1990s is likely to have continued to the point that the growth rate became negative and Ne declined. Our result is in good agreement with CDC surveillance that shows a clear decline in rabid raccoons after the peak in the mid-1990s (Monroe et al 2016).…”

Section: Resultssupporting

confidence: 91%

Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

Volz

Didelot

2017

Preprint

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Non-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stationary stochastic processes which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a non-parametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data is sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of β-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://mrc-ide.github.io/skygrowth/.

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Section: Resultssupporting

confidence: 91%

Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

Volz

Didelot

2017

Preprint

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“…Each year, rabies surveillance in the United States involves testing over 100,000 suspected rabid animal samples, of which over 6,000 rabid animals were diagnosed in 2014 [34]. The inherent high throughput nature of the LN34 assay has the potential to improve the speed of testing and reduce the workload for diagnostic laboratories.…”

Section: Discussionmentioning

confidence: 99%

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses

et al. 2017

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Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N) coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high throughput capability and its simplicity of use, which can be quickly adapted in a laboratory to enhance the capacity of rabies molecular diagnostics. The LN34 assay provides an alternative approach for rabies diagnostics, especially in rural areas and rabies endemic regions that lack the conditions and broad experience required to run the standard DFA assay.

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“…26 To work, IBCM programmes rely on timely reporting of dog bites and a skilled workforce to assess animals, collect samples, and make timely diagnoses. Furthermore, bite victims must adhere to treatment recommendations.…”

Section: Discussionmentioning

confidence: 99%

Effect of counselling on health-care-seeking behaviours and rabies vaccination adherence after dog bites in Haiti, 2014–15: a retrospective follow-up survey

Etheart

Kligerman

Augustin

et al. 2017

The Lancet Global Health

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Summary Background Haiti has an integrated bite case management (IBCM) programme to counsel animal-bite victims on the risk of rabies and appropriate treatment, as well as the Haiti Animal Rabies Surveillance Program (HARSP) to examine the animals. We assessed the usefulness of the IBCM programme to promote best practices for rabies prophylaxis after exposure in a low-income rabies-endemic setting. Methods We did a retrospective follow-up survey of randomly selected bite victims who were counselled by Haiti's IBCM programme between May 15, 2014, and Sept 15, 2015. We classified participants by HARSP decisions of confirmed, probable, suspected, or non-rabies exposures. We compared health-care outcomes in people who sought medical care before IBCM counselling with those in people who sought care after counselling. We used decision trees to estimate the probability of actions taken in the health-care system, and thereby human deaths. Findings During the study period, 1478 dog bites were reported to HARSP for assessment. 37 (3%) were confirmed exposures, 76 (5%) probable exposures, 189 (13%) suspected exposures, and 1176 (80%) non-rabies exposures. 115 of these cases were followed up in the survey. IBCM counselling was associated with a 1.2 times increase in frequency of bite victims seeking medical care and of 2.4 times increase in vaccination uptake. We estimated that there would be four human rabies deaths among the 1478 people assessed by IBCM during the survey period, and 11 in the absence of this programme, which would equate to a 65% decrease in rabies deaths. Among three people dead at the time of the follow-up survey, one was deemed to be due to rabies after a probable rabies exposure. Interpretation Adherence to medical providers' recommendations might be improved through counselling provided by IBCM programmes.

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Rabies surveillance in the United States during 2014

Cited by 65 publications

References 19 publications

Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses

Effect of counselling on health-care-seeking behaviours and rabies vaccination adherence after dog bites in Haiti, 2014–15: a retrospective follow-up survey

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