A phylogenetic reconstruction of the epidemiological history of canine rabies virus variants in Colombia

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).

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).

Hospital-based, prospective, multicentre surveillance to determine the incidence of intussusception in children aged below 15 years in Germany

Background

A new vaccine against Rotavirus (RV) gastroenteritis was introduced in Germany in 2006. In 1997 the first RV vaccine was withdrawn due to an increased incidence in intussusception (IS). Thus, an accurate estimation of the incidence of IS is important for post-licensure surveillance.

Methods

IS-Data were obtained from the 'Erhebungseinheit für seltene pädiatrische Erkrankungen Deutschland' (ESPED, German surveillance unit for rare pediatric diseases) collaborations' central register where all cases of intussusception in Germany for the years 2006 and 2007 are collected (n = 1200). In order to obtain an unbiased estimate of the incidence, it is necessary to determine the population under risk out of which these cases originated, and the proportion of real cases not reported to the registry (underreporting). In order to assess underreporting, a random sample of 31 hospitals was re-assessed by an outside reviewer. The estimation of incidence was done using a single Maximum-Likelihood (ML) estimator based on data from both the registry and the sample.

Results

The uncorrected observed incidence was calculated to be 26.6/100,000 child-years for children below 1 year old, 23.8 for those below 2 years old, and 5.2 for those below 15 years old. The review revealed a mean reporting quota of about 41% and the ML approach yielded an incidence of 51.5/100,000 child-years (95%CI [41.7;61.1]) for children below 2 years of age.

Conclusions

While substantial under-reporting led to very conservative estimates of the IS incidence, the approach described here allows an accurate estimation of IS incidence including corresponding confidence bands. Therefore, ML estimation is a straightforward instrument to derive stable, unbiased estimates in epidemiological studies with incomplete data.

Genetic tracking of the raccoon variant of rabies virus in eastern North America

To gain insight into the incursion of the raccoon variant of rabies into the raccoon population in three Canadian provinces, a collection of 192 isolates of the raccoon rabies virus (RRV) strain was acquired from across its North American range and was genetically characterized. A 516-nucleotide segment of the non-coding region between the G and L protein open reading frames, corresponding to the most variable region of the rabies virus genome, was sequenced. This analysis identified 119 different sequences, and phylogenetic analysis of the dataset supports the documented history of RRV spread. Three distinct geographically restricted RRV lineages were identified. Lineage 1 was found in Florida, Alabama and Georgia and appears to form the ancestral lineage of the raccoon variant of rabies. Lineage 2, represented by just two isolates, was found only in Florida, while the third lineage appears broadly distributed throughout the rest of the eastern United States and eastern Canada. In New York State, two distinct spatially segregated variants were identified; the one occupying the western and northern portions of the state was responsible for an incursion of raccoon rabies into the Canadian province of Ontario. Isolates from New Brunswick and Quebec form distinct, separate clusters, consistent with their independent origins from neighboring areas of the United States. The data are consistent with localized northward incursion into these three separate areas with no evidence of east-west viral movement between the three Canadian provinces.

Viral phylodynamics and the search for an 'effective number of infections'

Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the ‘effective number of infections’, a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.

A history estimate and evolutionary analysis of rabies virus variants in China

To investigate the evolutionary dynamics of rabies virus (RABV) in China, we collected and sequenced 55 isolates sampled from 14 Chinese provinces over the last 40 years and performed a coalescent-based analysis of the G gene. This revealed that the RABV currently circulating in China is composed of three main groups. Bayesian coalescent analysis estimated the date of the most recent common ancestor for the current RABV Chinese strains to be 1412 (with a 95 % confidence interval of 1006-1736). The estimated mean substitution rate for the G gene sequences (3.961x10(-4) substitutions per site per year) was in accordance with previous reports for RABV.

Enzootic rabies elimination from dogs and reemergence in wild terrestrial carnivores, United States

To provide molecular and virologic evidence that domestic dog rabies is no longer enzootic to the United States and to identify putative relatives of dog-related rabies viruses (RVs) circulating in other carnivores, we studied RVs associated with recent and historic dog rabies enzootics worldwide. Molecular, phylogenetic, and epizootiologic evidence shows that domestic dog rabies is no longer enzootic to the United States. Nonetheless, our data suggest that independent rabies enzootics are now established in wild terrestrial carnivores (skunks in California and north-central United States, gray foxes in Texas and Arizona, and mongooses in Puerto Rico), as a consequence of different spillover events from long-term rabies enzootics associated with dogs. These preliminary results highlight the key role of dog RVs and human-dog demographics as operative factors for host shifts and disease reemergence into other important carnivore populations and highlight the need for the elimination of dog-related RVs worldwide.

The origin and phylogeography of dog rabies virus

Rabies is a progressively fatal and incurable viral encephalitis caused by a lyssavirus infection. Almost all of the 55 000 annual rabies deaths in humans result from infection with dog rabies viruses (RABV). Despite the importance of rabies for human health, little is known about the spread of RABV in dog populations, and patterns of biodiversity have only been studied in limited geographical space. To address these questions on a global scale, we sequenced 62 new isolates and performed an extensive comparative analysis of RABV gene sequence data, representing 192 isolates sampled from 55 countries. From this, we identified six clades of RABV in non-flying mammals, each of which has a distinct geographical distribution, most likely reflecting major physical barriers to gene flow. Indeed, a detailed analysis of phylogeographic structure revealed only limited viral movement among geographical localities. Using Bayesian coalescent methods we also reveal that the sampled lineages of canid RABV derive from a common ancestor that originated within the past 1500 years. Additionally, we found no evidence for either positive selection or widespread population bottlenecks during the global expansion of canid RABV. Overall, our study reveals that the stochastic processes of genetic drift and population subdivision are the most important factors shaping the global phylogeography of canid RABV.

Lyssaviruses: current trends

Various technological developments have revitalized the approaches employed to study the disease of rabies. In particular, reverse genetics has facilitated the generation of novel viruses used to improve our understanding of the fundamental aspects of rabies virus (RABV) biology and pathogenicity and yielded novel constructs potentially useful as vaccines against rabies and other diseases. Other techniques such as high throughput methods to examine the impact of rabies virus infection on host cell gene expression and two hybrid systems to explore detailed protein-protein interactions also contribute substantially to our understanding of virus-host interactions. This review summarizes much of the increased knowledge about rabies that has resulted from such studies but acknowledges that this is still insufficient to allow rational attempts at curing those who present with clinical disease.

Molecular epidemiology of rabies in Colombia 1994–2005 based on partial nucleoprotein gene sequences

One hundred and twenty-four rabies viruses (RABV) were isolated from humans and eight species of mammals in Colombia during 1994-2005. To determine the genetic and reservoir-associated diversity cDNA fragments encoding 88 amino acids at the carboxyl terminus of the nucleoprotein were sequenced and used in phylogenetic analyses. Eight genetic lineages (GL) were characterized. GL1, GL2 and GL3 consisted of dog-associated antigenic variant (AV) 1 RABV, isolated in the centre-east, north and southwest of Colombia, respectively. GL1 is apparently extinct in Colombia. The GL4 were AV3, AV8 and non-determined (ND) AV viruses associated with hematophagous bats. The GL5 and GL6 consisted of AV4 viruses. GL6 isolate was found associated with Tadarida brasiliensis bats. GL5 segregated independently. The GL7 and GL8 segregated independently within clades associated with colonial insectivorous and solitary bats, respectively. Both of these were represented by NDAV viruses. Viruses isolated from humans grouped within GL2, GL3 and GL4, which in turn corresponded to AV1, 3, 8 and ND. Dogs and D. rotundus are the two major rabies reservoirs and vectors in Colombia. Insectivorous bats may also be important rabies reservoirs but spillovers to other species are rare. Our data were consistent with previous studies in which partial Psi, G and L gene sequences were analyzed. Our results confirmed the existence of RABV of unclassified AV in Colombia.

Are all lyssavirus genes equal for phylogenetic analyses?

Individual lyssavirus genes were evaluated for phylogenetic studies from available full genome sequences. The full genome of the ERA rabies virus was sequenced and its accuracy was confirmed through virus recovery by reverse genetics. The full length of the ERA is 11,931 nucleotides (nt), with a leader sequence of 58 nt, the nucleoprotein (N) gene of 1350 nt, phosphoprotein (P) gene of 891 nt, matrix protein (M) gene of 606 nt, glycoprotein (G) gene of 1572 nt, RNA-dependent RNA polymerase (L) gene of 6384 nt, Psi-region (or G-L intergenic region) of 400 nt, and a trailer region of 70 nt. The five mono-cistrons are separated by intergenic regions of 2, 5, 5 and 24 nt, respectively. One obvious difference between the ERA and SAD-B19 rabies virus strains was the putative stop/polyadenylation signal of the G gene, with a poly(A(8)) tract for ERA, and a poly(A(5)) for SAD-B19. The TGpoly(A(8)) sequence tract was identified to be a leaky termination signal in the ERA strain. Through analyses of nt diversity, protein co-variations, structural and functional constraints, and reconstruction of phylogenetic trees from comprehensive datasets, we propose lyssavirus genes probably are of similar value for phylogenetic analyses.

Molecular epidemiology of rabies in Guangxi Province, south of China

BACKGROUND

Surveillance data for rabies in Guangxi Province in China showed that human rabies cases have gradually increased since 1996.

OBJECTIVE

To evaluate the epidemiology of rabies at the molecular level and provide suggestions for effective prevention of rabies in Guangxi.

STUDY DESIGN

Since 2000, 1569 brains from suspected rabid animals were collected from different areas of Guangxi. Rabies virus was isolated from 42 samples. RT-PCR was used to amplify a 455 nucleotide segment of the 3'-terminal of the N gene. The sequencing data from that segment was used for phylogenetic analysis.

RESULTS

Nucleotide homology comparisons and phylogenetic tree analysis based on this sequence indicated that all the rabies virus isolates from Guangxi belonged to genotype 1 and could be divided into four groups. Groups I, II and IV included 23, 10 and 8 isolates, respectively. These had nucleotide homologies of 97.1-100%, 98.2-100% and 99.1-99.6%, respectively. Only the GXN119 strain belonged to group III. Group I had two group-specific mutations: T90N and E110D. Group II had one group-specific mutation of T42S.

CONCLUSIONS

This study showed that rabies virus isolates from Guangxi have a close genetic relationship and topographical distribution.

Identification of novel canine rabies virus clades in the Middle East and North Africa

Four novel phylogenetic clades of canine rabies virus (RABV) variants have been identified in the Middle East and North Africa. The three novel Middle Eastern clades comprise RABV isolates from the borders between Israel and neighbouring countries. The North African clade (Africa 4) comprises four RABV isolates from Egypt and one from Israel. We characterized various RABV lineages antigenically by using a panel of monoclonal antibodies to the nucleoprotein (N) and phylogenetically by analysis of entire N gene sequences. The estimated mean substitution rate for the N gene alignment (2.7x10(-4) substitutions per site per year) is comparable with previous estimates for RABV. The application of a molecular clock indicates the emergence of current canine RABV diversity to have occurred at about the same time (approx. 1870) in the Middle East and Europe, following divergence from established lineages in Africa and Asia.

The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa

Two variants of rabies virus (RABV) currently circulate in southern Africa: canid RABV, mainly associated with dogs, jackals, and bat-eared foxes, and mongoose RABV. To investigate the evolutionary dynamics of these variants, we performed coalescent-based analyses of the G-L inter-genic region, allowing for rate variation among viral lineages through the use of a relaxed molecular clock. This revealed that mongoose RABV is evolving more slowly than canid RABV, with mean evolutionary rates of 0.826 and 1.676 x 10(-3) nucleotide substitutions per site, per year, respectively. Additionally, mongoose RABV exhibits older genetic diversity than canid RABV, with common ancestors dating to 73 and 30 years, respectively, and while mongoose RABV has experienced exponential population growth over its evolutionary history in Africa, populations of canid RABV have maintained a constant size. Hence, despite circulating in the same geographic region, these two variants of RABV exhibit striking differences in evolutionary dynamics which are likely to reflect differences in their underlying ecology.

Molecular epidemiology of rabies virus isolates in India

In India, rabies is enzootic and is a serious public health and economic problem. India has a large population of stray dogs which, together with a lack of effective control strategies, might have led to the persistence of rabies virus (RV) in the canine population. Our objective was to study the molecular epidemiology of RV isolates in India based on nucleotide sequence analysis of 29 RV isolates originating from different species of animals in four states. Here we have analyzed two sets of sequence data based upon a 132-nucleotide region of the cytoplasmic domain (CD) of the G gene (G-CD) and a 549-nucleotide region (Psi-L) that combines the noncoding G-L intergenic region (Psi) and a fragment of the polymerase gene (L). Phylogenetic analysis revealed that the RV isolates belong to genotype 1 and that they were related geographically but were not related according to host species. Five different genetic clusters distributed among three geographical regions were identified. Comparison of the deduced amino acid sequences of G-CD between RV isolates revealed three amino acid changes (amino acid 462G [aa462G], aa465H, and aa468K) that distinguished the Indian RVs from RV isolates in other parts of the world. Analysis of the data indicated that the dog rabies virus variants are the major circulating viruses in India that transmit the disease to other domestic animals and humans as well.

The evolutionary history and dynamics of bat rabies virus

Rabies virus (RABV) is endemic in terrestrial mammals throughout the world and in bats on the American continent. We performed the most extensive phylogenetic analyses of bat RABV sequences undertaken to date using a variety of genes. Our study supported previous suggestions that viral sequences are grouped according to the behaviour of the host species. However, there was more genetic and geographical diversity within each phylogenetic group than previously recognised, including evidence for new groups. Furthermore, three clades of Latin American bat RABV that were distinct from the previously identified "group IV" bat RABV clade and more closely related to North American bat RABV clades, were identified. Strikingly, phylogenetic trees for the G (glycoprotein) gene had a significantly different evolutionary history to those inferred for the N (nucleoprotein) and P (phosphoprotein) genes, and an analysis of these competing topologies revealed that it is not possible on current data to resolve whether bat RABV arose from terrestrial mammal RABV, or vice-versa. Finally, using coalescent approaches, we estimated that RABV had similar rates of population growth and nucleotide substitution (approximately 2.5-4x10(-4) substitutions per site, per year) in both bats and terrestrial mammals, despite underlying differences in epidemiology.

Phylogeography, population dynamics, and molecular evolution of European bat lyssaviruses

European bat lyssaviruses types 1 and 2 (EBLV-1 and EBLV-2) are widespread in Europe, although little is known of their evolutionary history. We undertook a comprehensive sequence analysis to infer the selection pressures, rates of nucleotide substitution, age of genetic diversity, geographical origin, and population growth rates of EBLV-1. Our study encompassed data from 12 countries collected over a time span of 35 years and focused on the glycoprotein (G) and nucleoprotein (N) genes. We show that although the two subtypes of EBLV-1--EBLV-1a and EBLV-1b--have both grown at a low exponential rate since their introduction into Europe, they have differing population structures and dispersal patterns. Furthermore, there were strong constraints against amino acid change in both EBLV-1 and EBLV-2, as reflected in a low ratio of nonsynonymous to synonymous substitutions per site, particularly in EBLV-1b. Our inferred rate of nucleotide substitution in EBLV-1, approximately 5 x 10(-5) substitutions per site per year, was also one of the lowest recorded for RNA viruses and implied that the current genetic diversity in the virus arose 500 to 750 years ago. We propose that the slow evolution of EBLVs reflects their distinctive epidemiology in bats, where they occupy a relatively stable fitness peak.

Evolutionary timescale of rabies virus adaptation to North American bats inferred from the substitution rate of the nucleoprotein gene

Throughout North America, rabies virus (RV) is endemic in bats. Distinct RV variants exist that are closely associated with infection of individual host species, such that there is little or no sustained spillover infection away from the primary host. Using Bayesian methodology, nucleotide substitution rates were estimated from alignments of partial nucleoprotein (N) gene sequences of nine distinct bat RV variants from North America. Substitution rates ranged from 2.32 x 10(-4) to 1.38 x 10(-3) substitutions per site per year. A maximum-likelihood (ML) molecular clock model was rejected for only two of the nine datasets. In addition, using sequences from bat RV variants across the Americas, the evolutionary rate for the complete N gene was estimated to be 2.32 x 10(-4). This rate was used to scale trees using Bayesian and ML methods, and the time of the most recent common ancestor for current bat RV variant diversity in the Americas was estimated to be 1660 (range 1267-1782) and 1651 (range 1254-1773), respectively. Our reconstructions suggest that RV variants currently associated with infection of bats from Latin America (Desmodus and Tadarida) share the earliest common ancestor with the progenitor RV. In addition, from the ML tree, times were estimated for the emergence of the three major lineages responsible for bat rabies cases in North America. Adaptation to infection of the colonial bat species analysed (Eptesicus fuscus, Myotis spp.) appears to have occurred much quicker than for the solitary species analysed (Lasionycteris noctivagans, Pipistrellus subflavus, Lasiurus borealis, Lasiurus cinereus), suggesting that the process of virus adaptation may be dependent on host biology.