The introduction of fox rabies into Italy (2008-2011) was due to two viral genetic groups with distinct phylogeographic patterns

On the Use of Phylogeographic Inference to Infer the Dispersal History of Rabies Virus: A Review Study

Rabies is a neglected zoonotic disease which is caused by negative strand RNA-viruses belonging to the genus Lyssavirus. Within this genus, rabies viruses circulate in a diverse set of mammalian reservoir hosts, is present worldwide, and is almost always fatal in non-vaccinated humans. Approximately 59,000 people are still estimated to die from rabies each year, leading to a global initiative to work towards the goal of zero human deaths from dog-mediated rabies by 2030, requiring scientific efforts from different research fields. The past decade has seen a much increased use of phylogeographic and phylodynamic analyses to study the evolution and spread of rabies virus. We here review published studies in these research areas, making a distinction between the geographic resolution associated with the available sequence data. We pay special attention to environmental factors that these studies found to be relevant to the spread of rabies virus. Importantly, we highlight a knowledge gap in terms of applying these methods when all required data were available but not fully exploited. We conclude with an overview of recent methodological developments that have yet to be applied in phylogeographic and phylodynamic analyses of rabies virus.

Current Status of Rabies and Its Eradication in Eastern and Southeastern Europe

The objective of this paper is to provide an overview of the current status of rabies in Europe, with special emphasis on Croatia and Southeast and East Europe. Due to the systematic implementation of a rabies eradication program by oral vaccination of wild animals, by the end of the 20th century, most West and Central European countries were rabies-free. The EU goal was to eradicate rabies in wildlife and domestic animals by 2020. No matter how achievable the goal seemed to be, the disease is still present in the eastern part of the EU, as was notified in 2020 by two member states—Poland and Romania. Croatia has been rabies-free for the last seven years but given that it borders a non-EU country in which a case of rabies was confirmed in 2020, it will continue to contribute to the maintenance of the rabies-free region. A rabies-free EU can only be achieved by continuous oral vaccination, coordination and a regional approach. The prevention of reintroductions from bordering countries in which rabies has not been eradicated yet, and the support for the eradication efforts made by these countries, are goals still pending.

Two waves of canine distemper virus showing different spatio-temporal dynamics in Alpine wildlife (2006-2018)

Canine distemper virus (CDV) represents an important threat for both wild and domestic carnivores. Since 2006, the North-Eastern regions in Italy have been experiencing severe and widespread recurring outbreaks of CDV affecting the wild carnivore population. In this study we performed an extensive phylogeographic analysis of CDV strains belonging to the Wildlife-Europe genetic group identified between 2006 and 2018 in Veneto, Trentino Alto Adige and Friuli Venezia Giulia regions. Our analysis revealed that viruses from the first (2006-2009) and the second (2011-2018) epidemic wave cluster separately, suggesting the introduction of two distinct genetic variants. These two events were characterized by different diffusion rates and spatial distribution, thus suggesting the existence of a connection between infection spread and host population dynamics. We also report the first spillover event of this strain to a non-vaccinated dog in a rural area of Friuli Venezia Giulia. The increasing prevalence of the infection in wildlife population, the broad host range of CDV circulating in the Alpine wildlife and the first reported transmission of a wild-adapted strain to a domestic dog in this region raise concerns over the vulnerability of wildlife species and the exposure of our pets to new threatening strains. Understanding the dynamic of CDV epidemics will also improve preparedness for re-emerging diseases affecting carnivore species.

Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran

Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Here, we performed phylogeographic inference and applied different post hoc approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran, which have remained largely unknown. We first analysed the association between environmental factors and variations in dispersal velocity among lineages. Second, we present, test and apply a new approach to study the link between environmental conditions and the dispersal direction of lineages. The statistical performance (power of detection, false-positive rate) of this new method was assessed using simulations. We performed phylogeographic analyses of RABV genomes, allowing us to describe the large diversity of RABV in Iran and to confirm the cocirculation of several clades in the country. Overall, we estimate a relatively high lineage dispersal velocity, similar to previous estimates for dog rabies virus spread in northern Africa. Finally, we highlight a tendency for RABV lineages to spread in accessible areas associated with high human population density. Our analytical workflow illustrates how phylogeographic approaches can be used to investigate the impact of environmental factors on several aspects of viral dispersal dynamics.

Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics

Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics

Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evolutionary-epidemiological study of the spatial dynamics of rabies virus (RABV) epidemics in different hosts and habitats. We compiled RABV data sets from skunk, raccoon, bat and domestic dog populations in order to investigate the viral diffusivity of different RABV epidemics, and to detect and compare the environmental factors that impact the velocity of viral spread in continuous spatial landscapes. We build on a recently developed statistical framework that uses spatially- and temporally-referenced phylogenies. We estimate several spatial statistics of virus spread, which reveal a higher diffusivity of RABV in domestic dogs compared with RABV in other mammals. This finding is explained by subsequent analyses of environmental heterogeneity, which indicate that factors relating to human geography play a significant role in RABV dispersion in domestic dogs. More generally, our results suggest that human-related factors are important worldwide in explaining RABV dispersion in terrestrial host species. Our study shows that phylogenetically informed viral movements can be used to elucidate the factors that impact virus dispersal, opening new opportunities for a better understanding of the impact of host species and environmental conditions on the spatial dynamics of rapidly evolving populations.

Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host

Host shift events play an important role in epizootics as adaptation to new hosts can profoundly affect the spread of the disease and the measures needed to control it. During the late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virus (RABV) within the fox population. We used Bayesian inferences to investigate whole genome sequences from fox and dog brain tissues from Turkey to demonstrate that the epizootic occurred in 1997 (±1 year). Furthermore, these data indicated that the epizootic was most likely due to a host shift from locally infected domestic dogs, rather than an incursion of a novel fox or dog RABV. No evidence was observed for genetic adaptation to foxes at consensus sequence level and dN/dS analysis suggested purifying selection. Therefore, the deep sequence data were analysed to investigate the sub-viral population during a host shift event. Viral heterogeneity was measured in all RABV samples; viruses from the early period after the host shift exhibited greater sequence variation in comparison to those from the later stage, and to those not involved in the host shift event, possibly indicating a role in establishing transmission within a new host. The transient increase in variation observed in the new host species may represent virus replication within a new environment, perhaps due to increased replication within the CNS, resulting in a larger population of viruses, or due to the lack of host constraints present in the new host reservoir.

Resurgence of rabies in Hungary during 2013-2014: An attempt to track the origin of identified strains

In 2013-2014, accumulation of rabies episodes raised concerns regarding ongoing elimination programme in Hungary. Nearly four dozen cases were identified over a 13-month period in the central region of the country far behind the immunization zones. Although the outbreak was successfully controlled, the origin of disease remained unknown. In this study, we sequenced the partial N and G genes from 47 Hungarian rabies virus (RV) strains isolated from the 2013-2014 outbreak. Sequencing and phylogenetic analysis of the N and G genes showed that the Hungarian RV isolates share high nucleotide similarity among each other (up to 100%). When analysing the N gene, comparable sequence similarity was seen between the outbreak strains and some historic Romanian RV strains. Unfortunately, in the lack of available sequence data from the Romanian RV strains, the genetic relationship within the G gene could not be determined. Phylogenetic analysis of Hungarian RV isolates detected in the past revealed that multiple independent RV lineages circulated in our country over the past 25 years. The parental strain of the 2013-2014 outbreak may have been imported independently perhaps from east through transborder movement of a reservoir animal. Next to the introduction, this imported RV strain seems to have spread clonally in the affected area. Our findings indicate that despite effective control measures that, overall, minimized the incidence of rabies over the past decade, field and laboratory monitoring needs to be continued to make rabies elimination programme in Hungary successful.

2008-2011 sylvatic rabies epidemic in Italy: challenges and experiences

After more than 10 years of absence, in 2008 rabies re-emerged and spread in wild foxes in north-eastern Italy. In order to control the infection and to minimize the risk of human exposure, three oral foxes vaccination campaigns were first carried out by manual distribution of baits between January and September 2009, followed by four emergency oral rabies vaccination (ORV) campaigns by aerial distribution in the affected regions starting in December 2009. Ordinary aerial ORV campaigns followed in spring and fall 2011 and 2012, although no cases were reported after February 2011. In our paper, we describe the main characteristics of the rabies epidemic that occurred in north-eastern Italy in 2008-2011, with particular focus on the innovative systems that were implemented to manage and evaluate the efficacy of the aerial ORV. The Italian experience in containing and eliminating rabies in less than 3 years may provide information and suggestions for countries affected by rabies, and sharing a similar geomorphological conformation as Italy.

Sylvatic rabies epidemic in Italy: implementation of a data management system to assess the level of application of preventive dog vaccination

After 20 years of absence, rabies re-emerged in wild animals in north-eastern Italy in October 2008. Besides measures undertaken to fight the spread of infection in wildlife, vaccination against rabies was made compulsory for dogs living in the risk area. In the last 15 years, the veterinary authorities have focused on implementing computerized data collection systems in animal health, to serve as working tools for epidemiological surveillance activities and emergencies management. The prerequisite for implementing any data collection system is knowledge of the animal population. This also applies to the Canine Registry Data Bank, in which data on dogs and their movements, together with personal data on each owner and keeper, have been stored since 2003. The management information system has been updated and specific functions have been integrated in order to support the activity of both the veterinary services and the veterinary practitioners involved in the dog vaccination program. Vaccination became voluntary in February 2013. This paper describes implementation of the software and organization of data gathering, highlighting the benefits of computerized data compared to previously used paper-based data collection systems. The new functions, designed to centralize collection of uniform, updated vaccination data, have led to more efficient organization and better control of the vaccination plan. Automated information processing allowed vaccination operations to be supervised, incurred costs to be calculated, and vaccination coverage of the dog population to be monitored during the 3 years of compulsory vaccination.

Rabies and canine distemper virus epidemics in the red fox population of northern Italy (2006-2010)

Since 2006 the red fox (Vulpes vulpes) population in north-eastern Italy has experienced an epidemic of canine distemper virus (CDV). Additionally, in 2008, after a thirteen-year absence from Italy, fox rabies was re-introduced in the Udine province at the national border with Slovenia. Disease intervention strategies are being developed and implemented to control rabies in this area and minimise risk to human health. Here we present empirical data and the epidemiological picture relating to these epidemics in the period 2006–2010. Of important significance for epidemiological studies of wild animals, basic mathematical models are developed to exploit information collected from the surveillance program on dead and/or living animals in order to assess the incidence of infection. These models are also used to estimate the rate of transmission of both diseases and the rate of vaccination, while correcting for a bias in early collection of CDV samples. We found that the rate of rabies transmission was roughly twice that of CDV, with an estimated effective contact between infected and susceptible fox leading to a new infection occurring once every 3 days for rabies, and once a week for CDV. We also inferred that during the early stage of the CDV epidemic, a bias in the monitoring protocol resulted in a positive sample being almost 10 times more likely to be collected than a negative sample. We estimated the rate of intake of oral vaccine at 0.006 per day, allowing us to estimate that roughly 68% of the foxes would be immunised. This was confirmed by field observations. Finally we discuss the implications for the eco-epidemiological dynamics of both epidemics in relation to control measures.