Molecular characterization of cryptically circulating rabies virus from ferret badgers, Taiwan

Detection of Rabies Virus in a Yellow-throated Marten (Martes flavigula chrysospila) in Taiwan

In June 2021, a yellow-throated marten (Martes flavigula chrysospila) submitted for postmortem examination was diagnosed as rabid through laboratory testing. The rabies virus detected was closest phylogenetically to viruses of ferret badgers (Melogale moschata subaurantiaca) in Taiwan, indicating spillover infection from the primary reservoir in this area, the ferret badger.

Contrasting patterns in the early stage of SARS-CoV-2 evolution between humans and minks

One of the unique features of SARS-CoV-2 is its apparent neutral evolution during the early pandemic (before February 2020). This contrasts with the preceding SARS-CoV epidemics, where viruses evolved adaptively. SARS-CoV-2 may exhibit a unique or adaptive feature which deviates from other coronaviruses. Alternatively, the virus may have been cryptically circulating in humans for a sufficient time to have acquired adaptive changes before the onset of the current pandemic. To test the scenarios above, we analyzed the SARS-CoV-2 sequences from minks (Neovision vision) and parental humans. In the early phase of the mink epidemic (April to May 2020), nonsynonymous to synonymous mutation ratio per site in the spike protein is 2.93, indicating a selection process favoring adaptive amino acid changes. Mutations in the spike protein were concentrated within its receptor binding domain and receptor binding motif. An excess of high frequency derived variants produced by genetic hitchhiking was found during the middle (June to July 2020) and late phase I (August to September 2020) of the mink epidemic. In contrast, the site frequency spectra of early SARS-CoV-2 in humans only show an excess of low frequency mutations, consistent with the recent outbreak of the virus. Strong positive selection in the mink SARS-CoV-2 implies the virus may not be pre-adapted to a wide range of hosts and illustrates how a virus evolves to establish a continuous infection in a new host. Therefore, the lack of positive selection signal during the early pandemic in humans deserves further investigation.

Novel Bat Lyssaviruses Identified by Nationwide Passive Surveillance in Taiwan, 2018–2021

Bat lyssaviruses were identified in Taiwan’s bat population during 2016–2017. The lyssavirus surveillance system was continuously conducted to understand the epidemiology. Through this system, the found dead bats were collected for lyssavirus detection by direct fluorescent antibody test and reverse transcription polymerase chain reaction. Three bats were identified as positive during 2018–2021. A novel lyssavirus, designated as Taiwan bat lyssavirus 2, was detected in a Nyctalus plancyi velutinus. This lyssavirus had less than 80% nucleotide identity in the nucleoprotein (N) gene with other lyssavirus species, forming a separate branch in the phylogenetic analysis. The other two cases were identified in Pipistrellus abramus (Japanese pipistrelles); they were identified to be similar to the former lyssavirus identified in 2016–2017, which was renominated as Taiwan bat lyssavirus 1 (TWBLV-1) in this study. Even though one of the TWBLV-1 isolates showed high genetic diversity in the N gene compared with other TWBLV-1 isolates, it may be a TWBLV-1 variant but not a new species based on its high amino acid identities in the nucleoprotein, same host species, and same geographic location as the other TWBLV-1.

Genetic Diversity, Evolutionary Dynamics, and Pathogenicity of Ferret Badger Rabies Virus Variants in Mainland China, 2008–2018

In contrast to dog-associated human rabies cases decline year by year due to the rabies vaccination coverage rates increase in China, ferret badger (FB, Melogale moschata)-associated human rabies cases emerged in the 1990s, and are now an increasingly recognized problem in southeast China. To investigate epidemiology, temporal evolution dynamics, transmission characterization, and pathogenicity of FB-associated rabies viruses (RABVs), from 2008 to 2018, we collected 3,622 FB brain samples in Jiangxi and Zhejiang Province, and detected 112 RABV isolates. Four FB-related lineages were identified by phylogenetic analysis (lineages A–D), the estimated Times to Most Recent Common Ancestor were 1941, 1990, 1937, and 1997 for lineages A–D, respectively. Furthermore, although no FB-associated human rabies case has been reported there apart from Wuyuan area, FB-RABV isolates are mainly distributed in Jiangxi Province. Pathogenicity of FB-RABVs was assessed using peripheral inoculation in mice and in beagles with masseter muscles, mortality-rates ranging from 20 to 100% in mice and 0 to 20% in beagles in the groups infected with the various isolates. Screening of sera from humans with FB bites and no post-exposure prophylaxis to rabies revealed that five of nine were positive for neutralizing antibodies of RABV. All the results above indicated that FB-RABV variants caused a lesser pathogenicity in mice, beagles, and even humans. Vaccination in mice suggests that inactivated vaccine or recombinant subunit vaccine products can be used to control FB-associated rabies, however, oral vaccines for stray dogs and wildlife need to be developed and licensed in China urgently.

The Comparison of Full G and N Gene Sequences From Turkish Rabies Virus Field Strains

The rabies infection is a zoonotic viral disease in humans and is spread by both wild and domestic carnivores. This study aimed to molecularly characterize the field strains of the rabies virus circulating in Turkey between 2013 and 2020. Brain samples obtained from 16 infected animals (8 cattle, one donkey, three foxes, three dogs, and one marten) were tested. Full nucleoprotein (N) and glycoprotein (G) gene sequences were used to determine the genetic and antigenic characteristics of the rabies virus field strains. The phylogenetic analyses revealed that the 16 field strains identified in Turkey belonged to the Cosmopolitan lineage.

Knowledge, attitudes, practices (KAP) and control of rabies among community households and health practitioners at the human-wildlife interface in Limpopo National Park, Massingir District, Mozambique

Background

Rabies is a viral zoonotic disease that kills more than 26,000 people each year in Africa. In Mozambique, poverty and inadequate surveillance result in gross underreporting and ineffective control of the disease in animals and people. Little is known of the role of human attitudes and behaviour in prevention or control of rabies, thus this study was undertaken to assess the knowledge, attitudes and practices amongst selected households and health practitioners in one affected area, the Limpopo National Park (LNP), Massingir district.

Methodology

A cross-sectional study was conducted among 233 households in eight villages in LNP and among 42 health practitioners from eight health facilities in Massingir district between 2016 and 2018. Consenting household representatives aged 18 years or over were purposively selected. A KAP survey was administered to obtain information on dog ownership and knowledge of rabies, host species affected, modes of transmission, symptoms, recommended treatment and preventive methods.

Similar to household study participants, health practitioners were purposively selected and completed the questionnaire during the investigators’ visit. The questionnaire sought information on knowledge of rabies, management of bite wounds, vaccination sites and schedules of pre- and post-exposure prophylaxis. Descriptive and inferential data analyses were performed using SPSS software version 18.0.

Results

Approximately twenty per cent (18.9%; 95% CI: 14.3–24.3) and 13.3% (95% CI: 9.4–18.1) of households had good knowledge and practices of rabies, respectively. For health practitioners, only 16.7% (95% CI: 7.5–31.9) had good knowledge, whilst 33.3% (95% CI: 20.0–49.7) adopted adequate attitudes/practices towards the disease.

Conclusions/Significance

In conclusion, both households and health practitioners displayed poor levels of knowledge and adopted bad attitudes and practices towards rabies. The former, had more gaps in their attitudes and practices towards the disease. Village location and education level (P < .05) and similarly, sex and occupation, were found to be statistically associated with good knowledge of rabies among households as compared to HPs. Overall, a lack of community-based education and professional retraining courses contribute significantly to poor awareness of rabies in the LNP of Mozambique. Enhancing public health knowledge should consequently reduce dog-mediated human rabies deaths in this country.

In Mozambique, rabies is maintained primarily by the domestic dog, the principal vector and host species responsible for the majority of human cases dating back to the early 1900s. Control of animal rabies has historically been undertaken by government veterinary authorities, with limited involvement of the health and environment sectors. In the Massingir District in general, and in Limpopo National Park (LNP) in particular, parenteral dog rabies mass-vaccination campaigns and the provision of post-exposure prophylaxis are inconsistent. Limited resources for dog vaccination campaigns, insufficient veterinary field staff, inefficient disease notification procedures and inadequate training of health practitioners constraint effective rabies control across the country. Awareness of good practices regarding management of bite wounds among local community members and health practitioners is crucial to reducing rabies deaths. The results obtained in this study will inform government policy on practical interventions in the control of dog and human rabies.

Epidemiology of Animal Rabies - China, 2010-2020

Introduction

Rabies is a fatal zoonotic infectious disease that poses a serious threat to public health in China. Since 2005, a National Animal Rabies Surveillance System has been operating to understand the rabies situation in animals in China with a view to control and eventually eliminate dog-mediated human rabies.

Methods

From 2010, the brain tissues of dogs, livestock, and wild animals showing rabies-like clinical signs were collected and tested by the National Reference Laboratory (NRL) for Animal Rabies to analyze the epidemiological characteristics of rabies, including animal species, geographic distribution, and transmission sources. Over the same period, clinically suspected animal rabies cases were collected by Animal Disease Control Centers through the National Animal Disease Monitoring Information Platform (NADMIP) and then reported in the Veterinary Bulletin.

Results

During 2010-2020, 170 of 212 suspected animal rabies cases were submitted to and confirmed by NRL as rabies virus-positive. Of these confirmed cases dogs, especially free-roaming and ownerless dogs in rural areas, were major transmission hosts (71/170). A total of 51 infected dogs attacked humans with 45 biting more than one person. The dog cases were reported all year round, but with significantly more in spring and summer. The majority of livestock rabies cases (70/80) being caused by rabid wild foxes in Xinjiang and Inner Mongolia revealed that foxes play a pivotal role in animal rabies epizootics in the north and northwest of the country.

Conclusion

Dogs were the main transmission sources of rabies in China, and along with the recent increase of rabies in foxes and other wildlife, presented an increasing threat to livestock and public health.

Use of partial N-gene sequences as a tool to monitor progress on rabies control and elimination efforts in Ethiopia

Ethiopia is one of the African countries most affected by rabies. A coarse catalog of rabies viruses (RABV) was created as a benchmark to assess the impact of control and elimination activities. We evaluated a 726 bp amplicon at the end of the N-gene to infer viral lineages in circulation using maximum likelihood and Bayesian methods for phylogenetic reconstruction. We sequenced 228 brain samples from wild and domestic animals collected in five Ethiopian regions during 2010-2017. Results identified co-circulating RABV lineages that are causing recurrent spillover infections into wildlife and domestic animals. We found no evidence of importation of RABVs from other African countries or vaccine-induced cases in the area studied. A divergent RABV lineage might be involved in an independent rabies cycle in jackals. This investigation provides a feasible approach to assess rabies control and elimination efforts in resource-limited countries.

Neglected challenges in the control of animal rabies in China

Complex rabies transmission dynamics, including in dogs, wildlife livestock, and human-acquired rabies, can be observed in China. A temporary decrease in human rabies deaths with a simultaneous increase in animal rabies transmission is a typical example of "sectoral management separation" but not of the recommended "one-health" concept. In contrast to reliance on mass dog vaccination, reliance on postexposure prophylaxis to reduce human rabies burden is costly and ineffective in the prevention of rabies transmission from dogs to humans and other susceptible animal species. To answer the WHO call for the "elimination of dog-mediated human rabies by 2030," China faces the challenge of a lack of a strong political commitment and a workable plan and must act now before the rabies transmission dynamics become increasingly complicated by spreading to other species, such as ferret badgers in the Southeast and raccoon dogs and foxes in the North.

Animal Rabies Surveillance, China, 2004-2018

Rabies is a severe zoonotic disease in China, but the circulation and distribution of rabies virus (RABV) within animal reservoirs is not well understood. We report the results of 15 years of surveillance of the first Chinese Rabies Surveillance Plan in animal populations, in which animal brain tissues collected during 2004–2018 were tested for RABV and phylogenetic and spatial–temporal evolutionary analyses performed using obtained RABV sequences. The results have provided the most comprehensive dataset to date on the infected animal species, geographic distribution, transmission sources, and genetic diversity of RABVs in China. In particular, the transboundary transmission of emerging RABV subclades between China and neighboring countries was confirmed. The study highlights the importance of continuous animal rabies surveillance in monitoring the transmission dynamics, and provides updated information for improving current control and prevention strategies at the source.

Canine Parvovirus Infections in Taiwanese Pangolins (Manis pentadactyla pentadactyla)

Canine parvovirus type 2 (CPV-2) is among the most important and highly contagious pathogens that cause enteric or systemic infections in domestic and nondomestic carnivores. However, the spillover of CPV-2 to noncarnivores is rarely mentioned. Taiwanese pangolins (Manis pentadactyla pentadactyla) are threatened due to habitat fragmentation and prevalent animal trafficking. Interactions between Taiwanese pangolins, humans, and domestic animals have become more frequent in recent years. However, information about the susceptibility of pangolins to common infectious agents of domestic animals has been lacking. From October 2017 to June 2019, 4 pangolins that were rescued and treated in wildlife rescue centers in central and northern Taiwan presented with gastrointestinal signs. Gross and histopathological examination revealed the main pathologic changes to be necrotic enteritis with involvement of the crypts in all intestinal segments in 2 pangolins. By immunohistochemistry for CPV-2, there was positive labeling of cryptal epithelium throughout the intestine, and immunolabeling was also present in epidermal cells adjacent to a surgical amputation site, and in mononuclear cells in lymphoid tissue. The other 2 pangolins had mild enteritis without crypt involvement, and no immunolabeling was detected. The nucleic acid sequences of polymerase chain reaction (PCR) amplicons from these 4 pangolins were identical to a Chinese CPV-2c strain from domestic dogs. Quantitative PCR revealed a higher ratio of CPV-2 nucleic acid to internal control gene in the 2 pangolins with severe intestinal lesions and positive immunoreactivity. Herein, we present evidence of CPV-2 infections in pangolins.

Ferret badger rabies in Zhejiang, Jiangxi and Taiwan, China

Ferret badger (FB, Melogale moschata) rabies is an increasing public health threat to humans, with FBs being a major reservoir and vector of rabies in China. Based on 152 published nucleotide sequences of the FB rabies virus (RABV) nucleoprotein, phylogenetic analysis revealed them to be clustered into six FB-related lineages, FB-I to FB-VI. The genetic features of members of lineage FB-VI suggest that cross-species transmission occurs between FBs and dogs. Here, we describe the phylogenetic relationships between FB-RABVs, their geographic segregation, and their evolutionary dynamics in epizootic regions.

Encephalomyocarditis virus is potentially derived from eastern bent-wing bats living in East Asian countries

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EMCV genome was widely found in fecal guanos in Taiwanese, Korean, and Japanese caves.

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Miniopterus fuliginosus is the main source of the fecal guano.

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It is possible that Miniopterus fuliginosus is one of the natural hosts of EMCV in East Asia.

Bats are reservoir hosts of many zoonotic viruses and identification of viruses that they carry is important. This study aimed to use high throughput screening to identify the viruses in fecal guano of Taiwanese insectivorous bats caves in order to obtain more information on bat-derived pathogenic viruses in East Asia. Guano samples were collected from two caves in Taiwan, pooled, and then subjected to Multiplex PCR-based next generation sequencing for viral identification. Subsequently, encephalomyocarditis virus (EMCV) sequence was detected and confirmed by reverse transcription PCR. EMCV is considered as rodent virus and thus, animal species identification through cytochrome oxidase I (COI) barcoding was further done to identify the viral source. Finally, determination of distribution and verification of the presence of EMCV in guano obtained from Japanese and South Korean caves was also done. We concluded that the guano collected was not contaminated with the excrement of rodents which were reported and presumed to live in Taiwan. Also, EMCV genome fragments were found in guanos of Japanese and South Korean caves. It is possible that the eastern bent-wing bat (Miniopterus fuliginosus) is one of the natural hosts of EMCV in East Asia.

A systematic review of spatial decision support systems in public health informatics supporting the identification of high risk areas for zoonotic disease outbreaks

BACKGROUND

Zoonotic diseases account for a substantial portion of infectious disease outbreaks and burden on public health programs to maintain surveillance and preventative measures. Taking advantage of new modeling approaches and data sources have become necessary in an interconnected global community. To facilitate data collection, analysis, and decision-making, the number of spatial decision support systems reported in the last 10 years has increased. This systematic review aims to describe characteristics of spatial decision support systems developed to assist public health officials in the management of zoonotic disease outbreaks.

METHODS

A systematic search of the Google Scholar database was undertaken for published articles written between 2008 and 2018, with no language restriction. A manual search of titles and abstracts using Boolean logic and keyword search terms was undertaken using predefined inclusion and exclusion criteria. Data extraction included items such as spatial database management, visualizations, and report generation.

RESULTS

For this review we screened 34 full text articles. Design and reporting quality were assessed, resulting in a final set of 12 articles which were evaluated on proposed interventions and identifying characteristics were described. Multisource data integration, and user centered design were inconsistently applied, though indicated diverse utilization of modeling techniques.

CONCLUSIONS

The characteristics, data sources, development and modeling techniques implemented in the design of recent SDSS that target zoonotic disease outbreak were described. There are still many challenges to address during the design process to effectively utilize the value of emerging data sources and modeling methods. In the future, development should adhere to comparable standards for functionality and system development such as user input for system requirements, and flexible interfaces to visualize data that exist on different scales. PROSPERO registration number: CRD42018110466.

Development of a quantitative real-time RT-PCR assay for detecting Taiwan ferret badger rabies virus in ear tissue of ferret badgers and mice

In 2013, the first case of Taiwan ferret badger rabies virus (RABV-TWFB) infection was reported in Formosan ferret badgers, and two genetic groups of the virus were distinguished through phylogenetic analysis. To detect RABV-TWFB using a sensitive nucleic acid-based method, a quantitative real-time reverse transcription polymerase chain reaction targeting the conserved region of both genetic groups of RABV-TWFB was developed. This method had a limit of detection (LOD) of 40 RNA copies/reaction and detected viral RNA in brain and ear tissue specimens of infected and dead Formosan ferret badgers and mice with 100% sensitivity and specificity. The mean viral RNA load detected in the ear tissue specimens of ferret badgers ranged from 3.89 × 10⁸ to 9.73 × 10⁸ RNA copies/g-organ, which was 111-fold to 2,220-fold lower than the concentration detected in the brain specimens, but 2,000-fold to 5,000-fold higher than the LOD of the assay. This highly sensitive technique does not require facilities or instruments complying with strict biosafety criteria. Furthermore, it is efficient, safe, and labor-saving as only ear specimens need be sampled. Therefore, it is a promising technique for epidemiological screening of Taiwan ferret badger rabies.

Human Exposure to Ferret Badger Rabies in Taiwan

On 17 July 2013, Taiwan confirmed multiple cases of the rabies virus (RABV) in the wild Taiwan Ferret badger (TFB) (Melogale moschata) member of the family Mustelidae. This study aims at investigating the risk factors for human exposure to rabid TFBs. Statistical inference based on Pearson correlation showed that there was a strong positive correlation between the total number of positive TFB rabies cases and the number of rabid TFBs involved with human activities in 81 enzootic townships (r = 0.91; p < 0.001). A logistic regression analysis indicated that the risk probability of a human being bitten by rabid TFBs was significantly higher when there were no dogs around (35.55% versus 6.17% (indoors, n = 171, p = 0.0001), and 52.00% versus 5.26% (outdoors, n = 44, p = 0.021)), and whether or not there was a dog around was the only crucial covariate that was statistically significantly related to the risk of a human being bitten. In conclusion, this study showed the value of having vaccinated pets as a deterrent to TFB encounters and as a buffer to prevent human exposure to rabid TFBs. The presence of unvaccinated pets could become a significant risk factor in the longer term if rabies isn’t controlled in TFBs because of the spillover between the sylvatic and urban cycles of rabies. Consequently, raising dogs, as well as keeping rabies vaccinations up-to-date for them, can be considered an effective preventive strategy to reduce the risk for human exposure to rabid TFBs.

Epidemiological and Genetic Characteristics of Rabies Virus Transmitted Through Organ Transplantation

In January 2016, two patients died of rabies after receiving kidney transplants from a common organ donor at a hospital in Changsha, Hunan, China. The medical records, epidemiological data of the organ donor, two kidney and a liver recipients were reviewed. Intravitam saliva samples of the two kidney recipients were tested for rabies virus (RABV) using real-time RT-PCR, and the nucleoprotein (N) gene was amplified and sequenced by Sanger sequencing. Whole genome sequences were analyzed using next-generation sequencing. The N genes of the two kidney recipients showed 100% nucleic acid identity. Phylogenetic analysis of the complete genome, N and glycoprotein (G) genes indicated that the RABV was homologous with dog isolates from the Hunan province and belong to the China I lineage, which is widespread in China. The organ donor was a 22-month-old boy who died from unknown acute progressive encephalitis. After undergoing sub-hypothermia hibernation therapy, rabies-associated symptoms were atypical, and rabies was neglected because serum RABV-specific antibodies were negative. An unknown wound on the forehead of the donor was found 2 months before the onset of symptoms. Based on the clinical, epidemiological, and molecular findings, we speculated that the RABV initially originated in the donor from a dog bite, and was then transmitted to the recipients by organ transplantation. An uncertain exposure history and misdiagnosis played important roles in the spread of the RABV. Rabies should be considered in patients with acute progressive encephalitis of unexplained etiology, especially in potential organ donors.

The spread and evolution of rabies virus: conquering new frontiers

Rabies is a lethal zoonotic disease that is caused by lyssaviruses, most often rabies virus. Despite control efforts, sporadic outbreaks in wildlife populations are largely unpredictable, underscoring our incomplete knowledge of what governs viral transmission and spread in reservoir hosts. Furthermore, the evolutionary history of rabies virus and related lyssaviruses remains largely unclear. Robust surveillance efforts combined with diagnostics and disease modelling are now providing insights into the epidemiology and evolution of rabies virus. The immune status of the host, the nature of exposure and strain differences all clearly influence infection and transmission dynamics. In this Review, we focus on rabies virus infections in the wildlife and synthesize current knowledge in the rapidly advancing fields of rabies virus epidemiology and evolution, and advocate for multidisciplinary approaches to advance our understanding of this disease.

Initial pen and field assessment of baits to use in oral rabies vaccination of Formosan ferret-badgers in response to the re-emergence of rabies in Taiwan

Background

Taiwan had been considered rabies free since 1961, until a newly established wildlife disease surveillance program identified rabies virus transmission within the Formosan ferret-badger (Melogale moschata subaurantiaca) in 2013. Ferret-badgers occur throughout southern China and Southeast Asia, but their ecological niche is not well described.

Methodology/Principle findings

As an initial feasibility assessment for potential rabies control measures, field camera trapping and pen assessment of 6 oral rabies vaccine (ORV) baits were conducted in Taiwan in 2013. 46 camera nights were recorded; 6 Formosan ferret-badgers and 14 non-target mammals were sighted. No baits were consumed by ferret-badgers and 8 were consumed by non-target mammals. Penned ferret-badgers ingested 5 of the 18 offered baits. When pen and field trials were combined, and analyzed for palatability, ferret-badgers consumed 1 of 9 marshmallow baits (11.1%), 1 of 21 fishmeal baits (4.8%), 0 of 3 liver baits, and 3 of 3 fruit-flavored baits. It took an average of 261 minutes before ferret-badgers made oral contact with the non-fruit flavored baits, and 34 minutes for first contact with the fruit-based bait. Overall, ferret-badgers sought out the fruit baits 8 times faster, spent a greater proportion of time eating fruit baits, and were 7.5 times more likely to have ruptured the vaccine container of the fruit-based bait.

Conclusions/Significance

Ferret-badgers are now recognized as rabies reservoir species in China and Taiwan, through two independent ‘dog to ferret-badger’ host-shift events. Species of ferret-badgers can be found throughout Indochina, where they may be an unrecognized rabies reservoir. Findings from this initial study underscore the need for further captive and field investigations of fruit-based attractants or baits developed for small meso-carnivores. Non-target mammals’ competition for baits, ants, bait design, and dense tropical landscape represent potential challenges to effective ORV programs that will need to be considered in future studies.

Rabies

Rabies is a life-threatening neglected tropical disease: tens of thousands of cases are reported annually in endemic countries (mainly in Africa and Asia), although the actual numbers are most likely underestimated. Rabies is a zoonotic disease that is caused by infection with viruses of the Lyssavirus genus, which are transmitted via the saliva of an infected animal. Dogs are the most important reservoir for rabies viruses, and dog bites account for >99% of human cases. The virus first infects peripheral motor neurons, and symptoms occur after the virus reaches the central nervous system. Once clinical disease develops, it is almost certainly fatal. Primary prevention involves dog vaccination campaigns to reduce the virus reservoir. If exposure occurs, timely post-exposure prophylaxis can prevent the progression to clinical disease and involves appropriate wound care, the administration of rabies immunoglobulin and vaccination. A multifaceted approach for human rabies eradication that involves government support, disease awareness, vaccination of at-risk human populations and, most importantly, dog rabies control is necessary to achieve the WHO goal of reducing the number of cases of dog-mediated human rabies to zero by 2030.

A 3-year surveillance on causes of death or reasons for euthanasia of domesticated dogs in Taiwan

Over the last 2 decades, there has been growing interest in research on the mortality of domesticated pets. These studies relied on an effective data-collecting system. During 2012-2014, a real-time reporting system was designed for mortality data in owned dogs and cats. The present retrospective study aimed to report on the causes of death (CODs) or reasons for euthanasia (RFEs) in domesticated dogs in Taiwan, and to investigate CODs/RFEs segregated by demographic variables. Data from 2306 domesticated dogs were acquired during the 3-year period in the present study. The median age at death of the study population was 10.2 years (median interquartile range 7.0-14.0; range 0.0-25.0). Crossbred, female, and neutered dogs showed greater ages at death than other groups. The most common COD/RFE was neoplasia, followed by multiple organ involvement (MOI) and cardiovascular diseases. Segregated by cut-off ages, the most common COD/RFE was infection among dogs younger than 3 years or 1year, and neoplasia among dogs at or older than 3 years or 1year of age; the most common COD/RFE was neoplasia among dogs younger than median age, and MOI among dogs at or older than median age. Segregated by geographic variables, the ranking and frequency of CODs/RFEs displayed different patterns between the capital city/non-capital areas, and among areas stratified by human population densities. The study provides various insights into age at death and CODs/RFEs in owned-dog population in Taiwan, and provides new directions for future research.

The history of rabies in the Western Hemisphere

Before the introduction of control programs in the 20th century, rabies in domestic dogs occurred throughout the Western Hemisphere. However, historical records and phylogenetic analysis of multiple virus isolates indicate that, before the arrival of the first European colonizers, rabies virus was likely present only in bats and skunks. Canine rabies was either rare or absent among domestic dogs of Native Americans, and first arrived when many new dog breeds were imported during the period of European colonization. The introduction of the cosmopolitan dog rabies lyssavirus variant and the marked expansion of the dog population provided ideal conditions for the flourishing of enzootic canine rabies. The shift of dog-maintained viruses into gray foxes, coyotes, skunks and other wild mesocarnivores throughout the Americas and to mongooses in the Caribbean has augmented the risk of human rabies exposures and has complicated control efforts. At the same time, the continued presence of bat rabies poses novel challenges in the absolute elimination of canine and human rabies. This article compiles existing historical and phylogenetic evidence of the origins and subsequent dynamics of rabies in the Western Hemisphere, from the era preceding the arrival of the first European colonizers through the present day. A companion article reviews the current status of canine rabies control throughout the Western Hemisphere and steps that will be required to achieve and maintain its complete elimination (Velasco-Villa et al., 2017).

Predicting spatial spread of rabies in skunk populations using surveillance data reported by the public

Background

Prevention and control of wildlife disease invasions relies on the ability to predict spatio-temporal dynamics and understand the role of factors driving spread rates, such as seasonality and transmission distance. Passive disease surveillance (i.e., case reports by public) is a common method of monitoring emergence of wildlife diseases, but can be challenging to interpret due to spatial biases and limitations in data quantity and quality.

Methodology/Principal findings

We obtained passive rabies surveillance data from dead striped skunks (Mephitis mephitis) in an epizootic in northern Colorado, USA. We developed a dynamic patch-occupancy model which predicts spatio-temporal spreading while accounting for heterogeneous sampling. We estimated the distance travelled per transmission event, direction of invasion, rate of spatial spread, and effects of infection density and season. We also estimated mean transmission distance and rates of spatial spread using a phylogeographic approach on a subsample of viral sequences from the same epizootic. Both the occupancy and phylogeographic approaches predicted similar rates of spatio-temporal spread. Estimated mean transmission distances were 2.3 km (95% Highest Posterior Density (HPD₉₅): 0.02, 11.9; phylogeographic) and 3.9 km (95% credible intervals (CI₉₅): 1.4, 11.3; occupancy). Estimated rates of spatial spread in km/year were: 29.8 (HPD₉₅: 20.8, 39.8; phylogeographic, branch velocity, homogenous model), 22.6 (HPD₉₅: 15.3, 29.7; phylogeographic, diffusion rate, homogenous model) and 21.1 (CI₉₅: 16.7, 25.5; occupancy). Initial colonization probability was twice as high in spring relative to fall.

Conclusions/Significance

Skunk-to-skunk transmission was primarily local (< 4 km) suggesting that if interventions were needed, they could be applied at the wave front. Slower viral invasions of skunk rabies in western USA compared to a similar epizootic in raccoons in the eastern USA implies host species or landscape factors underlie the dynamics of rabies invasions. Our framework provides a straightforward method for estimating rates of spatial spread of wildlife diseases.

Rabies is a deadly zoonotic infection with a global distribution. In 2012, an epizootic of skunk rabies established in northern Colorado, USA and spread rapidly through three counties. The epizootic was documented through reports of dead skunks by the public. We examined the reports to determine how rapidly rabies was moving and which factors could explain the patterns of spread. We compared these estimates of spatial movement of rabies to those obtained from analyzing rabies genetic sequences that we obtained from some of the dead skunks reported by the public. By both methods, we found the virus was moving south at a little over 20 km/year and that most transmission between skunks occurred at short distances (< 4 km). Rabies was most likely to spread to new areas during the first half of the year, when skunk populations were producing new offspring. Our genetic model suggested that roads and rivers in the study landscape did not affect movement speed of rabies. We developed a framework that used the spatial data in the public reports to predict where and when skunk rabies would occur next. This framework could be used on public health surveillance data for other diseases or countries.

Indigenous Wildlife Rabies in Taiwan: Ferret Badgers, a Long Term Terrestrial Reservoir

The emerging disease of rabies was confirmed in Taiwan ferret badgers (FBs) and reported to the World Organization for Animal Health (OIE) on July 17, 2013. The spread of wildlife rabies can be related to neighborhood countries in Asia. The phylogenetic analysis was conducted by maximum likelihood (ML) methods and the Bayesian coalescent approach based on the glycoprotein (G) and nucleoprotein (N) genes. The phylogeographic and spatial temporal dynamics of viral transmission were determined by using SPREAD, QGIS. Therefore, the origin and the change with time of the viruses can be identified. Results showed the rabies virus of FB strains in Taiwan is a unique clade among other strains in Asia. According to the phylogeographic coalescent tree, three major genotypes of the FB rabies virus have circulated in three different geographical areas in Taiwan. Two genotypes have distributed into central and southern Taiwan between two ecological river barriers. The third genotype has been limited in southeastern Taiwan by the natural mountain barrier. The diversity of FB rabies viruses indicates that the biological profile of FBs could vary in different geographical areas in Taiwan. An enhanced surveillance system needs to be established near the currently identified natural barriers for early warnings of the rabies virus outbreak in Taiwan.

The history of rabies in the Western Hemisphere

Before the introduction of control programs in the 20th century, rabies in domestic dogs occurred throughout the Western Hemisphere. However, historical records and phylogenetic analysis of multiple virus isolates indicate that, before the arrival of the first European colonizers, rabies virus was likely present only in bats and skunks. Canine rabies was either rare or absent among domestic dogs of Native Americans, and first arrived when many new dog breeds were imported during the period of European colonization. The introduction of the cosmopolitan dog rabies lyssavirus variant and the marked expansion of the dog population provided ideal conditions for the flourishing of enzootic canine rabies. The shift of dog-maintained viruses into gray foxes, coyotes, skunks and other wild mesocarnivores throughout the Americas and to mongooses in the Caribbean has augmented the risk of human rabies exposures and has complicated control efforts. At the same time, the continued presence of bat rabies poses novel challenges in the absolute elimination of canine and human rabies. This article compiles existing historical and phylogenetic evidence of the origins and subsequent dynamics of rabies in the Western Hemisphere, from the era preceding the arrival of the first European colonizers through the present day. A companion article reviews the current status of canine rabies control throughout the Western Hemisphere and steps that will be required to achieve and maintain its complete elimination (Velasco-Villa et al., 2017).

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15^th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics.

Zoonoses account for most recently emerged infectious diseases of humans, although little is known about the evolutionary mechanisms involved in cross-species virus transmission. Understanding the evolutionary patterns and processes that underpin such cross-species transmission is of importance for predicting the spread of zoonotic infections, and hence to their ultimate control. We present a large-scale and detailed reconstruction of the evolutionary history of rabies virus (RABV) in domestic and wildlife animal species. RABV is of particular interest as it is capable of infecting many mammals but, paradoxically, is only maintained in distinct epidemiological cycles associated with animal species from the orders Carnivora and Chiroptera. We show that bat-related RABV and dog-related RABV have experienced very different evolutionary dynamics, and that host jumps are sometimes characterized by significant increases in evolutionary rate. Among Carnivora, the association between RABV and particular host species most likely arose from a combination of the historical human-mediated spread of the virus and jumps into new primary host species. In addition, we show that changes in host species are associated with multiple evolutionary pathways including the occurrence of host-specific parallel evolution. Overall, our data indicate that the establishment of dog-related RABV in new carnivore hosts may only require subtle adaptive evolution.

Spatial Temporal Dynamics and Molecular Evolution of Re-Emerging Rabies Virus in Taiwan

Taiwan has been recognized by the World Organization for Animal Health as rabies-free since 1961. Surprisingly, rabies virus (RABV) was identified in a dead Formosan ferret badger in July 2013. Later, more infected ferret badgers were reported from different geographic regions of Taiwan. In order to know its evolutionary history and spatial temporal dynamics of this virus, phylogeny was reconstructed by maximum likelihood and Bayesian methods based on the full-length of glycoprotein (G), matrix protein (M), and nucleoprotein (N) genes. The evolutionary rates and phylogeographic were determined using Beast and SPREAD software. Phylogenetic trees showed a monophyletic group containing all of RABV isolates from Taiwan and it further separated into three sub-groups. The estimated nucleotide substitution rates of G, M, and N genes were between 2.49 × 10⁻⁴–4.75 × 10⁻⁴ substitutions/site/year, and the mean ratio of dN/dS was significantly low. The time of the most recent common ancestor was estimated around 75, 89, and 170 years, respectively. Phylogeographic analysis suggested the origin of the epidemic could be in Eastern Taiwan, then the Formosan ferret badger moved across the Central Range of Taiwan to western regions and separated into two branches. In this study, we illustrated the evolution history and phylogeographic of RABV in Formosan ferret badgers.

PATHOLOGY AND MOLECULAR DETECTION OF RABIES VIRUS IN FERRET BADGERS ASSOCIATED WITH A RABIES OUTBREAK IN TAIWAN

Until Rabies virus (RABV) infection in Taiwan ferret badgers (TWFB; Melogale moschata subaurantiaca) was diagnosed in mid-June 2013, Taiwan had been considered rabies free for >50 yr. Although rabies has also been reported in ferret badgers in China, the pathologic changes and distribution of viral antigens of ferret badger-associated rabies have not been described. We performed a comprehensive pathologic study and molecular detection of rabies virus in three necropsied rabid TWFBs and evaluated archival paraffin-embedded tissue blocks of six other TWFBs necropsied during 2004 and 2012. As in other RABV-infected species, the characteristic pathologic changes in TWFBs were nonsuppurative meningoencephalomyelitis, ganglionitis, and the formation of typical intracytoplasmic Negri bodies, with the brain stem most affected. There was also variable spongiform degeneration, primarily in the perikaryon of neurons and neuropil, in the cerebral cortex, thalamus, and brain stem. In nonnervous system tissues, representative lesions included adrenal necrosis and lymphocytic interstitial sialadenitis. Immunohistochemical staining and fluorescent antibody test demonstrated viral antigens in the perikaryon of the neurons and axonal or dendritic processes throughout the nervous tissue and in the macrophages in various tissues. Similar to raccoons (Procyon lotor) and skunks (Mephitidae), the nervous tissue of rabid TWFBs displayed widely dispersed lesions, RABV antigens, and large numbers of Negri bodies. We traced the earliest rabid TWFB case back to 2004.

Government Response to the Discovery of a Rabies Virus Reservoir Species on a Previously Designated Rabies-Free Island, Taiwan, 1999-2014

Taiwan had been considered rabies free since 1961. In 2013, Taiwan confirmed the detection of rabies virus in wild Taiwan ferret-badgers. Up to December 2014, there have been 423 rabies-confirmed ferret-badgers and three cases of spillover infection into non-reservoir hosts. Genetic analysis indicates that TFBV is distinct from all other known rabies virus variants. To date, ferret-badger rabies is known to occur only in China and Taiwan. The temporal dynamics of rabid ferret-badgers in Taiwan suggests that the epizootic appears to have subsided to enzootic levels as of December 2014. According to the current epidemiologic data, there is only one TFBV strain in Taiwan. TFBV is still sequestered to the mountainous regions. Humans are at risk mainly through exposure to the virus from infected domestic meso-carnivores, mainly dogs and cats. Dogs and cats should be vaccinated to establish an immunological barrier to stop the spread of the disease from mountainous regions to domestic meso-carnivores.

Emergence of a sylvatic enzootic formosan ferret badger-associated rabies in Taiwan and the geographical separation of two phylogenetic groups of rabies viruses

Taiwan had been declared rabies-free in humans and domestic animals for five decades until July 2013, when surprisingly, three Formosan ferret badgers (FB) were diagnosed with rabies. Since then, a variety of wild carnivores and other wildlife species have been found dead, neurologically ill, or exhibiting aggressive behaviors around the island. To determine the affected animal species, geographic areas, and environments, animal bodies were examined for rabies by direct fluorescent antibody test (FAT). The viral genomes from the brains of selected rabid animals were sequenced for the phylogeny of rabies viruses (RABV). Out of a total of 1016 wild carnivores, 276/831 (33.2%) Formosan FBs were FAT positive, with occasional biting incidents in 1 dog and suspected spillover in 1 house shrew. All other animals tested, including dogs, cats, bats, mice, house shrews, and squirrels, were rabies-negative. The rabies was badger-associated and confined to nine counties/cities in sylvatic environments. Phylogeny of nucleoprotein and glycoprotein genes from 59 Formosan FB-associated RABV revealed them to be clustered in two distinct groups, TWI and TWII, consistent with the geographic segregation into western and eastern Taiwan provided by the Central Mountain Range and into northern rabies-free and central-southern rabies-affected regions by a river bisecting western Taiwan. The unique features of geographic and genetic segregation, sylvatic enzooticity, and FB-association of RABV suggest a logical strategy for the control of rabies in this nation.

Rabies Virus Infection in Ferret Badgers (Melogale moschata subaurantiaca) in Taiwan: A Retrospective Study

Fifteen ferret badgers (Melogale moschata subaurantiaca), collected 2010-13 and stored frozen, were submitted for rabies diagnosis by direct fluorescent antibody test and reverse transcription PCR. We detected seven positive animal samples, including some from 2010, which indicated that the ferret badger population in Taiwan had been affected by rabies prior to 2010.

Public Health Responses to Reemergence of Animal Rabies, Taiwan, July 16-December 28, 2013

Taiwan had been free of indigenous human and animal rabies case since canine rabies was eliminated in 1961. In July 2013, rabies was confirmed among three wild ferret-badgers, prompting public health response to prevent human rabies cases. This descriptive study reports the immediate response to the reemergence of rabies in Taiwan. Response included enhanced surveillance for human rabies cases by testing stored cerebrospinal fluids (CSF) from patients with encephalitides of unknown cause by RT-PCR, prioritizing vaccine use for postexposure prophylaxis (PEP) during periods of vaccine shortage and subsequent expansion of PEP, surveillance of animal bites using information obtained from vaccine application, roll out of preexposure prophylaxis (PrEP) with vaccine stock restoration, surveillance for adverse events following immunization (AEFI), and ensuring surge capacity to respond to general public inquiries by phone and training for healthcare professionals. Enhanced surveillance for human rabies found no cases after testing 205 stored CSF specimens collected during January 2010-July 2013. During July 16 to December 28, 2013, we received 8,241 rabies PEP application; 6,634 (80.5%) were consistent with recommendations. Among the 6,501 persons who received at least one dose of rabies vaccine postexposure, 4,953 (76.2%) persons who were bitten by dogs; only 59 (0.9%) persons were bitten by ferret-badgers. During the study period, 6,247 persons received preexposure prophylaxis. There were 23 reports of AEFI; but no anaphylaxis, Guillain-Barré syndrome, or acute disseminated encephalomyelitis were found. During the study period, there were 40,312 calls to the Taiwan Centers for Disease Control hotline, of which, 8,692 (22%) were related to rabies. Recent identification of rabies among ferret-badgers in a previously rabies-free country prompted rapid response. To date, no human rabies has been identified. Continued multifaceted surveillance and interministerial collaboration are crucial to achieve the goal of rabies-free status in Taiwan.