[Molecule character of rabies virus in 3 counties in Hunan China]

OBJECTIVE

To study the rabies molecular biology features in animals between high incidence area of rabies and no rabies cases area in Hunan.

METHODS

detect saliva of dogs and brains of dogs and cats by direct immunofluorescence assay, review positive samples by RT-PCR, sequencing extract RNA virus for genetic analysis.

RESULTS

12 were detected rabies virus antigen and positive nucleoside acid in 82 dogs from Wugang city also 1 in 17 from Dongkou county; the positive rate: Wugang 14.63 percent, Dongkou 5.88 percent. No rabies virus was detected in 67 samples of dog brains from Fenghuang County. Also none in 28 samples of cat brains. Amplificating N gene of rabies virus from positive samples of dog brain's tissue (No Wg13, Dk13) by RT-PCR, it shows that homology of nucleoside acid between two strain of virus is 99.4 percent; also 99.1 percent of amino acid. The homology of nucleoside acid (amonio acid) among Wg13 stain and Chinese strain CTN and aG strain is 89.4 percent (98.2 percent) and 86.1 percent (95.1 percent); The homology of nucleoside acid (amonio acid) among Dk13 stain Chinese strain CTN and aG strain is 89.1 percent (98.0 percent), 86.1 percent (94.9 percent).Compare with isolated rabies virus from abroad, the homology between two strains and Indonesia is 92.8 percent and 93.2 percent, the most similar of them. The strains isolated from other countries including Japan, Sri Lanka and India are relatively lower; The sequence of gene Wg13 and Dk13 were taken replacement of amino acid.

CONCLUSION

Two strains are belong to type I rabies virus, comparing its N gene with current using vaccine strains, both are in same group, and homology are relatively higher.

[An epidemiological study of rabies virus in domestic dogs, cats and wildlife and the immunogenicity study for rabies vaccines derived from different cell cultured virus strains]

For epidemiological investigation of the rabies virus carrier rates of domestic dogs, cats and wild animals like rodent animals and bats,three kinds of regions where rabies had higher incidence (Hunan and Guizhou Provinces), lower incidence (Jiangsu Province, Wuhan City) and provisionally rabies-free (Shenyang City) were selected. Then the antigenic types, the genovariation of the isolaled viruses and the currently vaccine matching of the virus strains were analyzed. The results showed that in China the principal host of rabies is dog,the total virus carrier rate of the captured dogs was 2.56%, and the highest positive isolation rate was 20.0% in some monitoring site. However,there was no evidence about the rabies virus carrier rate in rodent animals,bats or other wild animals. The rabies vaccines which prepared from aG and CTN strains have already been produced successfully in China. The research showed that the nucleotide sequences of the newly isolated viruses were more similar with the glycoprotein gene of CTN strain. In order to evaluate the safety and the efficacy of the vaccines currently used, two groups (50 people each) were injected with vaccine of aG strain and CTN strain respectively in five surveillance points. The neutralizing antibody tested were 0.49 IU/mL-0.52 IU/mL and 6.7 IU/mL-7.53 IU/mL after the 7 and the 14 days of vaccine injection respectively. In addition, the rates of antibody positive seroconversion were 45.1%-47.9% and 100% respectively, and there was no moderate or severe adverse reactions observed. These data showed the vaccines have satisfactory effect on safety and protection.

Molecular epidemiology identifies only a single rabies virus variant circulating in complex carnivore communities of the Serengeti

Understanding the transmission dynamics of generalist pathogens that infect multiple host species is essential for their effective control. Only by identifying those host populations that are critical to the permanent maintenance of the pathogen, as opposed to populations in which outbreaks are the result of 'spillover' infections, can control measures be appropriately directed. Rabies virus is capable of infecting a wide range of host species, but in many ecosystems, particular variants circulate among only a limited range of potential host populations. The Serengeti ecosystem (in northwestern Tanzania) supports a complex community of wild carnivores that are threatened by generalist pathogens that also circulate in domestic dog populations surrounding the park boundaries. While the combined assemblage of host species appears capable of permanently maintaining rabies in the ecosystem, little is known about the patterns of circulation within and between these host populations. Here we use molecular phylogenetics to test whether distinct virus-host associations occur in this species-rich carnivore community. Our analysis identifies a single major variant belonging to the group of southern Africa canid-associated viruses (Africa 1b) to be circulating within this ecosystem, and no evidence for species-specific grouping. A statistical parsimony analysis of nucleoprotein and glycoprotein gene sequence data is consistent with both within- and between-species transmission events. While likely differential sampling effort between host species precludes a definitive inference, the results are most consistent with dogs comprising the reservoir of rabies and emphasize the importance of applying control efforts in dog populations.

Phylogenetic Comparison of Rabies Viruses from Disease Outbreaks on the Svalbard Islands

Periodic wildlife rabies epizootics occur in Arctic regions. The original sources of these outbreaks are rarely identified. In 1980, a wildlife epizootic of rabies occurred on the previously rabies-free Svalbard Islands, Norway. After this outbreak of rabies in the arctic fox population (Alopex lagopus), only single cases have been reported from the Islands over the following two decades. Phylogenetic characterization of four viruses isolated from infected arctic foxes from Svalbard from three different time periods suggest that the source of these epizootics could have been migration of this species from the Russian mainland. Arctic fox migration has likely contributed to the establishment of another zoonotic disease, Echinococcus multilocularis, on Svalbard in recent years.

Genetic diversity of bat rabies viruses in Brazil

Thirty-three Brazilian bat rabies viruses (RVs) were studied by sequence analysis and were compared against sequences of bat-related RVs from other regions of the Americas. Phylogenetic analysis revealed that bat-related RVs formed several monophyletic lineages and that these were associated with bat species. Brazilian bat RVs were found to include nine major lineages, one of which grouped with RVs isolated from Lasiurus spp. from different regions of the Americas. These results suggest that there is considerable diversity among Brazilian bat RV variants and that some of these RV variants may be associated with bats from other countries.

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.

Genetic heterogeneity of Russian, Estonian and Finnish field rabies viruses

Thirty-five field rabies virus strains were collected in recent years in different regions of the Russian Federation in order to characterize their genetic heterogeneity and to study their molecular epidemiology. In addition to the Russian viruses, seven archive samples from Estonia and Finland and two Russian vaccine strains were also included in the study. The viruses collected were subjected to two different reverse transcription-polymerase chain reaction tests, the amplicons were sequenced and the sequences were analysed phylogenetically. Among the field viruses studied, two main phylogenetic groups were found and designated as Pan-Eurasian and Caucasian according to their geographic origin. The Pan-Eurasian group, comprising some reference viruses from Europe, was further divided into four subgroups. All of the vaccine strains were clearly different from the field strains. No recombination between the field and vaccine virus strains was observed. The data obtained here show the critical role of geographical isolation and limitation for the genetic clustering and evolution of the rabies virus and also help in predicting its distribution from rabies-affected areas to rabies-free areas.

An outbreak of pig rabies in Hunan province, China

The first dog-associated outbreak of rabies in swine in China (Hunan province) has been diagnosed and the related virus isolated. Sequence analysis showed that the pig isolate was a genotype 1 rabies virus with a very high nucleotide identity to local dog isolates.

A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus

Emerging pathogens potentially undergo rapid evolution while expanding in population size and geographic range during the course of invasion, yet it is generally difficult to demonstrate how these processes interact. Our analysis of a 30-yr data set covering a large-scale rabies virus outbreak among North American raccoons reveals the long lasting effect of the initial infection wave in determining how viral populations are genetically structured in space. We further find that coalescent-based estimates derived from the genetic data yielded an amazingly accurate reconstruction of the known spatial and demographic dynamics of the virus over time. Our study demonstrates the combined evolutionary and population dynamic processes characterizing the spread of pathogen after its introduction into a fully susceptible host population. Furthermore, the results provide important insights regarding the spatial scale of rabies persistence and validate the use of coalescent approaches for uncovering even relatively complex population histories. Such approaches will be of increasing relevance for understanding the epidemiology of emerging zoonotic diseases in a landscape context.

Rabies virus maintained by dogs in humans and terrestrial wildlife, Ceará State, Brazil

Rabies viruses circulating in Ceará, Brazil, were identified by molecular analysis to be related to variants maintained by dogs, bats, and other wildlife. Most of these viruses are associated with human rabies cases. We document the emergence of a rabies virus variant responsible for an independent epidemic cycle in the crab-eating fox (Cerdocyon thous).

Emerging epidemic dog rabies in coastal South Africa: a molecular epidemiological analysis

Towards understanding the molecular epidemiology of a severe dog rabies epidemic in the KwaZulu Natal province of South Africa, we analyzed a variable 592 nucleotide genome sequence domain of 170 rabies viruses from KwaZulu Natal and surrounding regions. Viruses from the KwaZulu Natal and Eastern Cape provinces belonged to a unique lineage, circulating as two independent and expanding epidemiological cycles. The first presented as closely related dog cycles along the eastern coastal regions of the two provinces, while the second, in northern KwaZulu Natal, has entered into at least one wildlife reservoir, the black backed jackal. We underline the success and opportunism of rabies in southern Africa, in a likely reflection of the emergence and radiation of rabies in new host species and locales throughout the larger continent as a whole.

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.

Genetic divergence of rabies viruses from bat species of Colorado, USA

Molecular epidemiological studies have linked many cryptic human rabies cases in the United States with exposure to rabies virus (RV) variants associated with insectivorous bats. In Colorado, bats accounted for 98% of all reported animal rabies cases between 1977 and 1996. The genetic divergence of RV was investigated in bat and terrestrial animal specimens that were submitted for rabies diagnosis to the Colorado Department of Public Health and Environment (CDPHE), Colorado, USA. RV isolates from animal specimens across the United States were also included in the analysis. Phylogenetic analyses were performed on partial nucleoprotein (N) gene sequences, which revealed seven principal clades. RV associated with the colonial big brown bat, Eptesicus fuscus, an bats of the genus Myotis were found to segregate into two distinct clades (I and IV). Clade I was harbored by E. fuscus and Myotis species, but was also identified in terrestrial animals such as domestic cats and striped skunks (Mephitis mephitis). Clade IV was divided into subclades IVA, IVB, and IVC; IVA was identified in E. fuscus, and Myotis species bats, and also in a fox; subclades IVB and IVC circulated predominantly in E. fuscus. Clade II was formed by big free-tailed bat (Nyctinomops macrotis) and striped skunk (Mephitis mephitis) samples. Clade III included RVs that are maintained by generally solitary, migratory bats such as the silver-haired bat (Lasionycteris noctivagans) and bats of the genus Lasiurus. Big brown bats were found to harbor this RV variant. None of the Colorado specimens segregated with clades V and VII that harbor RVs associated with terrestrial animals. Different species of bats had the same RV variant, indicating active inter-species rabies transmission. In Colorado, animal rabies occurs principally in bats, and the identification of bat RVs in cat, gray fox Urocyon cinereoargenteus), and striped skunks demonstrated the importance of rabies spillover from bats to domestic and terrestrial wildlife species.

Effects of aerosolized rabies virus exposure on bats and mice

Between 1956 and 1977, 4 human cases of rabies virus infection were attributed to aerosolized rabies virus; however, little work has been done to address this topic since the late 1960s. Employing modern nebulization equipment coupled with serologic, cell culture, and molecular technology, we have continued the investigation into aerosolized rabies virus as a potential route of transmission. Laboratory mice and 2 species of bats were exposed, through aerosol, to 3 variants of rabies virus. All bats survived exposure to aerosolized rabies virus and produced rabies neutralizing antibody. Several mice died of rabies as a result of aerosol exposure. Antibody response was followed for 6 months before animals were given an intramuscular challenge of rabies virus. Poor protection from challenge was afforded in bats, despite the presence of neutralizing antibodies.

[Analyses on the isolation and characterization of canine rabies virus isolates in Henan]

OBJECTIVE

To analyze the genetic characteristics of two rabies virus isolates from Henan province and to compare their relations hip with known rabies virus isolates and vaccine strains.

METHODS

Rabies viral antigens were detected in 100 canine brains by immunofluorescence assay method. Rabies virus was isolated through inoculating the suspensions of positive brains into suckling mice. N gene and G were amplified by RT-PCR and sequenced. Phylogenetic trees were constructed for the analysis on genetic characteristics of rabies virus.

RESULTS

Two rabies virus strains were isolated (Henan Hb1 and Henan Sq1). Data from sequential comparison revealed that the nucleotide and amino acid identities of N and G gene between the two isolates were 99.3% and 98.9%, and 98.7% and 98.4% respectively. The two isolates were more closely related to CTN, with the homogeny of N gene and G gene as 89.1% and 85.6%-85.7% at the nucleotide level, but 97.6%-98.0% and 92.3% at the amino acid level respectively, than to other vaccine strains. When comparing with other known viruses including Chinese isolates, the two stains shared closer identity with the isolates from Indonesia, and the rates of homogeny of N and G gene were 92.1%-93.2% and 91.9%-92.1% at the nucleotide level, 97.5%-98.6% and 96.0%-96.2% at the amino acid level, respectively. Data from the deduced amino acid sequences revealed that some amino acid residues including the residues in the N and G antigenic sites were substituted in the two isolates. Furthermore, phylogenetic analysis showed that the two isolates were also more closely related to the strains from Indonesia and vaccine strain CTN than to any other known street viruses and vaccine strains.

CONCLUSION

Both Henan Hbl and Henan Sql belonged to genotype 1. However, the N and G gene diverged from known street viruses and vaccine strains at either nucleotide level or amino acid level.

A simple sandwich ELISA (WELYSSA) for the detection of lyssavirus nucleocapsid in rabies suspected specimens using mouse monoclonal antibodies

Monoclonal antibody (MAb)-based capture enzyme-linked immunosorbent assays (ELISA) were developed for the diagnosis of rabies-suspect specimens. A combination of four mouse monoclonal antibodies directed against the rabies virus nucleocapsid was selected and used for the detection. The test was optimized and standardized so that maximum concordance could be maintained with the standard procedures of rabies diagnosis recommended by the WHO expert committee. Using prototype viruses from the different genotypes of lyssavirus and from various geographic origins and phylogenetic lineages, this paper presents a reliable, rapid and transferable diagnostic method, named WELYSSA that readily permits the detection of lyssaviruses belonging to the 7 genotypes of lyssavirus circulating in Europe, Africa, Asia and Oceania. The threshold of detection of lyssavirus nucleocapsids is low (0.8 ng/ml). With a panel of 1030 specimens received for rabies diagnostic testing, this test was found to be highly specific (0.999) and sensitive (0.970) when compared to other recommended rabies diagnostic methods.

A molecular epidemiological study targeting the glycoprotein gene of rabies virus isolates from China

A group of 31 rabies viruses (RABVs), recovered primarily from dogs, one deer and one human case, were collected from various areas in China between 1989 and 2006. Complete G gene sequences determined for these isolates indicated identities of nucleotide and amino acid sequences of >or=87% and 93.8%, respectively. Phylogenetic analysis of these and some additional Chinese isolates clearly supported the placement of all Chinese viruses in Lyssavirus genotype 1 and divided all Chinese isolates between four distinct groups (I-IV). Several variants identified within the most commonly encountered group I were distributed according to their geographical origins. A comparison of representative Chinese viruses with other isolates retrieved world-wide indicated a close evolutionary relationship between China group I and II viruses and those of Indonesia while China group III viruses formed an outlying branch to variants from Malaysia and Thailand. China group IV viruses were closely related to several vaccine strains. The predicted glycoprotein sequences of these RABVs variants are presented and discussed with respect to the utility of the anti-rabies biologicals currently employed in China.

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.

Molecular epidemiology of rabies virus strains isolated from wild canids in Northeastern Brazil

Rabies in wild canids in Northeastern Brazil is frequent and has been reported for some time, with episodes of rabies transmission from these animals to humans also reported. In this study, we analyzed the antigenic and genetic profiles of the rabies virus nucleoprotein gene, isolated from 20 samples taken from domestic animals and wild canids located in the Northeastern region of Brazil. All viruses isolated from domestic animals (dogs and cats) belonged to the antigenic variant 2 (AgV2). Among the wild animal samples, only four were AgV2, and nine showed a divergent antigenic profile. Phylogenetic analysis revealed two Brazilian clusters. Cluster 1 (Brazilian domestic carnivore-related strains) showed two subclusters, called 1A and 1B, and cluster 2 (Brazilian wild canid-related strains) also showed two subclusters, called 2A and 2B. The majority of the samples with divergent antigenic strains segregated into subcluster 2A. The intracluster identity of cluster 1 was 95.6% and that of cluster 2, 92.4%. When clusters 1 and 2 were compared, an identity of 88.6% was found. The genetic analysis of wild canid samples performed in this study indicates that there are two distinct rabies cycles among canids in Brazil, one represented by domestic canids and the other by wild canids. This study shows that the virus samples isolated in Northeastern Brazil are region and species-specific.

The histopathogenesis of paralytic rabies in six-week-old C57BL/6J mice following inoculation of the CVS-11 strain into the right triceps surae muscle

A fatal encephalomyelitis was developed after intracerebral and hind limb inoculation of in 6-week-old C57BL/6J mice by the inoculation of fixed rabies virus (CVS-11 strain), intracerebrally and into hind. After the intracerebral inoculation, virus antigens were detected in the cerebral cortex and hippocampus at 2 days postinoculation (PI), and later spread centrifugally to thalamus, brain stem, cerebellum, spinal cord and spinal ganglia. At 4 days PI, severe apoptosis and DNA fragmentation were observed in the hippocampus and cerebral cortex. All mice infected intracerebrally were dead without limb paralysis at from 10 to 11 days PI. In contrast, mice infected with virus intramuscularly were persistently observed virus antigens in the myocytes at the site of inoculation from 2 days PI. At 4 days PI, the antigens were demonstrated in the spinal dorsal root ganglia, spinal cord and muscle spindles without their detection in the cerebrum and hippocampus. There were no apoptosis in the spinal cord and dorsal root ganglia, however hind limb paralysis was found in all infected mice. Hind limb paralysis was progressed to quadriparalysis, and mice were dead from 11 to 13 days PI. From 4 days PI, necrosis of neuron was observed in the the spinal and dorsal ganglia with infiltration of lymphocyte. This study suggested that the necrosis of spinal neurons was more important to cause the paralysis of hind limb rather than the severe cerebral infection and apoptosis in C57BL/6J mice infected with CVS-11 strain. The virus primarily replicated in the muscles was ascended the spinal cord via afferent fibers and retrogradely invaded the cerebrum, and with subsequent spread to muscle spindles.

A new phylogenetic lineage of Rabies virus associated with western pipistrelle bats (Pipistrellus hesperus)

Bats represent the major source of human rabies cases in the New World. In the USA, most cases are associated with species that are not commonly found or reported rabid. To understand better the epidemiology and public health significance of potentially important bat species, a molecular study was performed on samples collected from naturally infected rabid western pipistrelle (Pipistrellus hesperus), eastern pipistrelle (Pipistrellus subflavus) and silver-haired bats (Lasionycteris noctivagans) from different regions of their geographical distribution in the USA. A 264 bp fragment at the 5′ end of the N gene coding region was sequenced and analysed in comparison with rabies virus variants circulating within other North American mammals. Phylogenetic analysis demonstrated that P. hesperus bats maintain a unique rabies virus variant. Preliminary data also suggest that P. subflavus and Lasionycteris noctivagans may harbour two different rabies virus variants (Ps and Ln) that are likely to be maintained independently by each bat species, which recently appear to have emerged as major vectors of human disease.

Bat-transmitted human rabies outbreaks, Brazilian Amazon

We describe 2 bat-transmitted outbreaks in remote, rural areas of Portel and Viseu Municipalities, Pará State, northern Brazil. Central nervous system specimens were taken after patients' deaths and underwent immunofluorescent assay and histopathologic examination for rabies antigens; also, specimens were injected intracerebrally into suckling mice in an attempt to isolate the virus. Strains obtained were antigenically and genetically characterized. Twenty-one persons died due to paralytic rabies in the 2 municipalities. Ten rabies virus strains were isolated from human specimens; 2 other cases were diagnosed by histopathologic examination. Isolates were antigenically characterized as Desmodus rotundus variant 3 (AgV3). DNA sequencing of 6 strains showed that they were genetically close to D. rotundus-related strains isolated in Brazil. The genetic results were similar to those obtained by using monoclonal antibodies and support the conclusion that the isolates studied belong to the same rabies cycle, the virus variants found in the vampire bat D. rotundus.

Molecular diversity of rabies viruses associated with bats in Mexico and other countries of the Americas

Bat rabies and its transmission to humans and other species in Mexico were investigated. Eighty-nine samples obtained from rabid livestock, cats, dogs, and humans in Mexico were studied by antigenic typing and partial sequence analysis. Samples were further compared with enzootic rabies associated with different species of bats in the Americas. Patterns of nucleotide variation allowed the definition of at least 20 monophyletic clusters associated with 9 or more different bat species. Several lineages associated with distinctive antigenic patterns were found in rabies viruses related to rabies in vampire bats in Mexico. Vampire bat rabies virus lineages associated with antigenic variant 3 are widely spread from Mexico to South America, suggesting these lineages as the most likely ancestors of vampire bat rabies and the ones that have been moved by vampire bat populations throughout the Americas. Rabies viruses related to Lasiurus cinereus, Histiotus montanus, and some other not yet identified species of the genus Lasiurus were found circulating in Mexico. Long-range dissemination patterns of rabies are not necessarily associated with migratory bat species, as in the case of rabies in Desmodus rotundus and Histiotus montanus. Human rabies was associated with vampire bat transmission in most cases, and in one case, rabies transmission from free-tailed bats was inferred. The occurrence of rabies spillover from bats to domestic animals was also demonstrated. Genetic typing of rabies viruses allowed us to distinguish trends of disease dissemination and to address, in a preliminary fashion, aspects of the complex evolution of rabies viruses in different host-reservoir species.

Molecular epidemiology of rabies from Maranhão and surrounding states in the northeastern region of Brazil

Although many outbreaks of rabies have been reported in northern Brazil, few epidemiological studies of these outbreaks have been undertaken. In this study, molecular epidemiological analyses were performed using 41 rabies virus samples isolated in the Maranhão (MA), Pará (PA), and Tocantins (TO) states of northeastern Brazil. A 599-bp region of the glycoprotein (G) gene was first amplified from each sample by RT-PCR, then sequenced and subjected to phylogenetic analysis. A phylogenetic tree divided the 41 isolates into two clades: Clade I was associated with terrestrial carnivores and Clade II was associated with vampire bats. The Clade I isolates were further sub-divided into two groups. The first group was closer to carnivore isolates that predominate in central Brazil, whereas the second group more closely resembled wild fox isolates from the northeastern coastal state of Paraíba (PB). MA isolates of Clade II formed an entirely separate group. These results demonstrate that bat- and dog-transmitted rabies occur in northwestern Brazil.

A molecular epidemiological study of rabies in Cuba

To investigate the emergence and current situation of terrestrial rabies in Cuba, a collection of rabies virus specimens was employed for genetic characterization. These data supported the monophyletic nature of all terrestrial rabies viruses presently circulating in Cuba but additionally delineated several distinct variants exhibiting limited spatial distribution which may reflect the history of rabies spread on the island. The strain of rabies currently circulating in Cuba, which emerged on the island in the early 20th century, has very close evolutionary ties to the Mexican dog type and is a member of the cosmopolitan lineage widely distributed during the colonial period. The Cuban rabies viruses, which circulate predominantly within the mongoose population, are phylogenetically distant from viruses circulating in mongooses in other parts of the world. These studies illustrate, at a global level, the adaptation of multiple strains of rabies to mongoose species which should be regarded as important wildlife hosts for rabies re-emergence. Given the recent emergence of human cases due to bat contact in Cuba, this study also included a single insectivorous bat specimen which was found to most closely resemble the rabies viruses known to circulate in Mexican vampire bats.

A molecular epidemiological analysis of the incursion of the raccoon strain of rabies virus into Canada

Three physically separate incursions of the raccoon strain of rabies have entered Canada, two into eastern Ontario in 1999 and one into New Brunswick in 2000. The course of these epizootics is described. Phylogenetic analysis of the index cases from these two provinces with raccoon rabies viruses representative of this strain in the United States supported the independence of these incursions into Canada via cross-border transmission from the United States. Genetic characterization of 190 isolates from these two Canadian provinces over a 550-bp region of the variable central portion of the viral P gene distinguished 14 variants in Ontario and five in New Brunswick although in both regions the variant represented by the initial case was most commonly encountered. The quasi-species nature of the Ontario virus was analysed using isolates taken at different times during the main outbreak to examine whether viral variation was increasing with time as well as changing in nature. These data provide a framework for study of future incursions of this rabies strain into Canada.

Molecular epidemiological study of Arctic rabies virus isolates from Greenland and comparison with isolates from throughout the Arctic and Baltic regions

We report a molecular epidemiological study of rabies in Arctic countries by comparing a panel of novel Greenland isolates to a larger cohort of viral sequences from both Arctic and Baltic regions. Rabies virus isolates originating from wildlife (Arctic/red foxes, raccoon-dogs and reindeer), from domestic animals (dogs/cats) and from two human cases were investigated. The resulting 400 bp N-gene sequences were compared with isolates representing neighbouring Arctic or Baltic countries from North America, the former Soviet Union and Europe. Phylogenetic analysis demonstrated similarities between sequences from the Arctic and Arctic-like viruses, which were distinct from rabies isolates originating in the Baltic region of Europe, the Steppes in Russia and from North America. The Arctic-like group consist of isolates from India, Pakistan, southeast Siberia and Japan. The Arctic group was differentiated into two lineages, Arctic 1 and Arctic 2, with good bootstrap support. Arctic 1 is mainly comprised of Canadian isolates with a single fox isolate from Maine in the USA. Arctic 2 was further divided into sub-lineages: 2a/2b. Arctic 2a comprises isolates from the Arctic regions of Yakutia in northeast Siberia and Alaska. Arctic 2b isolates represent a biotype, which is dispersed throughout the Arctic region. The broad distribution of rabies in the Arctic regions including Greenland, Canada and Alaska provides evidence for the movement of rabies across borders.

Antigenic and genetic characterization of rabies viruses isolated from domestic and wild animals of Brazil identifies the hoary fox as a rabies reservoir

Fifty Brazilian rabies viruses, collected from many different animal species and several regions of the country, were characterized by partial sequencing of the central, variable region of the P gene, a locus useful for sensitive molecular epidemiological studies. Phylogenetic analysis of the sequences, which included comparison with other rabies strains recovered from throughout the Americas, identified three main groups of Brazilian viruses, arbitrarily designated BRL-1 to BRL-3. BRL-1 was found in terrestrial carnivores and clusters with other American strains of the cosmopolitan lineage. BRL-2 comprised two distinct isolates, recovered from two species of non-haematophagous bats, that had evolutionary links to insectivorous-bat-derived strains of North America. BRL-3 consisted of isolates from vampire bats and from livestock species probably infected via contact with vampire bats. The terrestrial group was further subdivided into three subtypes: BRL-1a was associated exclusively with dogs and cats, while BRL-1b and BRL-1c were found exclusively in hoary foxes. These observations strongly support the role of the Brazilian hoary fox as a rabies reservoir. Screening of representative Brazilian rabies viruses against a collection of anti-rabies monoclonal antibodies (mAbs) identified a small panel of mAbs that could be used to discriminate between all Brazilian subgroups as defined by genetic classification in this study.

A molecular epidemiological study of rabies epizootics in kudu (Tragelaphus strepsiceros) in Namibia

BACKGROUND

A panel of 37 rabies virus isolates were collected and studied, originating mainly from the northern and central regions of Namibia, between 1980 and 2003.

RESULTS

These virus isolates demonstrated a high degree of genetic similarity with respect to a 400 bp region of the nucleoprotein gene, with the virus isolates originating from kudu antelope (n = 10) sharing 97.2-100% similarity with jackal isolates, and 97-100% similarity with those isolated from domestic dogs. Phylogenetic analysis suggested that these viruses were all of the canid rabies biotype of southern Africa. The viruses from kudu were closely associated with jackal isolates (n = 6), bat-eared fox isolates (n = 2) and domestic dog isolates (n = 2) at the genetic level and identical at the amino acid level, irrespective of the year of isolation.

CONCLUSION

These data suggest that jackal and kudu may form part of the same epidemiological cycle of rabies in Namibian wildlife, and might demonstrate the close-relationship between rabies virus strains that circulate within Namibia and those that circulate between Namibia and its neighbouring countries such as Botswana and South Africa.

Genetic and phylogenetic characterization of rabies virus isolates from wildlife and livestock in Paraiba, Brazil

Thirty-four rabies virus (RV) isolates from foxes (8), insectivore bats (9), cattle (14), sheep (1), a goat (1) and a donkey (1) from Paraiba state, northeastern Brazil, were genetically characterized. Sequences of 890 nts of nucleoprotein (N) genes of these isolates were analyzed and compared with those of other Brazilian isolates characterized earlier. Phylogenetic analysis revealed three genetical lineages of RV co-existing in this region. Each lineage was found to be associated with particular host species and to circulate independently of each other. The first lineage was found in foxes (Dusicyon sp.) and could be discriminated from domestic carnivore isolates from Sao Paulo, Goias and Minas Gerais in the southern and central Brazil. The second lineage was associated with insectivorous bats (Molossus spp.) and differed from vampire bat-associated RV isolates. The third lineage was found in livestock and clustered with vampire bat-associated RV isolates from Sao Paulo, Tocantins, Goias and Matto Grosso. These results indicate that RV of these genetic lineages are cocirculating in the Paraiba state and that livestock in this region are infected with vampire bat-associated RV, suggesting that the vampire bat is the main reservoir of livestock rabies in this region.

Persistence of genetic variants of the arctic fox strain of Rabies virus in southern Ontario

Genetic-variant analysis of rabies viruses provides the most sensitive epidemiologic tool for following the spread and persistence of these viruses in their wildlife hosts. Since its introduction by a southern epizootic movement that began in the far north, the arctic fox (AFX) strain of Rabies virus has been enzootic in Ontario for almost 50 y. Prior genetic studies identified 4 principal genetic variants (ONT.T1 to ONT.T4) that were localized to different regions of the province; furthermore, these viruses could be distinguished from the variant circulating in northern regions of Quebec, Newfoundland, and arctic zones, ARC.T5. Despite an intensive provincial control program undertaken over the last decade that involved aerial distribution of baits laden with rabies vaccine to combat fox rabies throughout the enzootic zone of Ontario, pockets of rabies activity persist. Re-evaluation of the genetic characteristics of the viral variants circulating in these areas of persistence has been undertaken. These data demonstrate that the recent outbreaks are, with 1 exception, due to persistence of the regional variant first identified in the area in the early 1990s. In contrast, the disease in the Georgian Bay area is a consequence of the incursion of a variant previously found further south. An outbreak that occurred in northern Ontario north and west of North Bay and in the neighboring border areas of Quebec in 2000-2001 was due to renewed incursion of the ARC.T5 variant from more northerly areas.

Complex genetic structure of the rabies virus in Bangkok and its surrounding provinces, Thailand: implications for canine rabies control

Dog vaccination and population management have been suggested as priorities in attempts at disease control in canine rabies-endemic countries. Budget limitations and the complexity of social, cultural and religious variables have complicated progress in the developing world. In Bangkok, Thailand, an intensive canine vaccination and sterilization programme has been in place since November 2002. Our objective was to determine if the rabies virus could be mapped according to its genetic variations and geographical location on the small localized scale of Bangkok and its surrounding provinces. Phylogenetic characterization of 69 samples from Bangkok and five neighbouring and two remote provinces, by limited sequence analysis of the rabies virus nucleoprotein gene, distinguished six different clades. Rabies viruses of four clades were intermixed in Bangkok and in the surrounding highly populated regions whereas the other two clades were confined to rural and less populated provinces. Such a complex pattern of gene flow, particularly in Bangkok, may affect the outcome of canine control programmes.

Detection of multiple strains of rabies virus RNA using primers designed to target Mexican vampire bat variants

A reverse transcription-polymerase chain reaction (RT-PCR), that uses primers specifically designed to amplify a portion of the N gene of vampire bat strains of rabies that circulate in Mexico, but also recognizing most of the rabies variants circulating in endemic areas, was established. This standardized PCR assay was able to detect viral RNA in tenfold serial dilutions up to a 10(7) dilution using stock virus at an original titre of 10(7.5) LD50. The assay was highly specific for rabies virus. Forty different rabies isolates recovered from different species and geographical regions in the country were diagnosed as positive and negative by the fluorescent antibody test (FAT). These same samples were re-examined by both PCR and the mouse inoculation test (MIT). Compared with MIT the PCR exhibited an epidemiological sensitivity of 86% and a specificity of 91% while its positive predictive value was 96%.

Importation of canid rabies in a horse relocated from Zimbabwe to South Africa : research communication

In July 2003 a 2-year-old Thoroughbred colt was imported from Harare, Zimbabwe to the Ashburton Training Centre, Pietermaritzburg, South Africa. Five months after importation, the colt presented with clinical signs suggestive of rabies: it was uncoordinated, showed muscle tremors and was biting at itself. Brain tissue was submitted for analysis and the clinical diagnosis was confirmed by the fluorescent antibody test and reverse-transcription polymerase chain reaction (RT-PCR). Phylogenetic analysis of the nucleotide sequence of the cytoplasmic domain of the glycoprotein and the G-L intergenic region of the rabies virus confirmed it to be an infection with a canid rabies virus, originating from an area in Zimbabwe endemic for the domestic dog (Canis familiaris) and side-striped jackal (Canis adustus) rabies.

Genetic characterization of rabies virus isolates in Korea

In investigation of the genetic characteristics of rabies viruses in Korea, the nucleotide and deduced amino acid sequences of the nucleoprotein (N) gene were determined in four Korean rabies virus strains obtained from dogs and raccoons, and were compared with published sequences for non-Korean rabies viruses. Three Korean rabies virus isolates had identical nucleotide sequences, and the fourth differed at only one nucleotide position. The Korean virus isolates had 84.5-92.0% nucleotide sequence similarity and 94.0-99.2% amino acid sequence similarity with non-Korean rabies virus isolates. In a phylogenetic tree based on partial nucleotide sequences of the N gene, the Korean rabies viruses formed a single cluster closely related to Arctic rabies viruses (FXCAN, 9141RUS, and 94260NEP). However, they were divergent from other Asian rabies viruses (94256SRL, 8677MAL, ChiNo.7, Phil 12301, and Mdn1278).

Development of a real-time, TaqMan reverse transcription-PCR assay for detection and differentiation of lyssavirus genotypes 1, 5, and 6

Several reverse transcription-PCR (RT-PCR) methods have been reported for the detection of rabies and rabies-related viruses. These methods invariably involve multiple transfers of nucleic acids between different tubes, with the risk of contamination leading to the production of false-positive results. Here we describe a single, closed-tube, nonnested RT-PCR with TaqMan technology that distinguishes between classical rabies virus (genotype 1) and European bat lyssaviruses 1 and 2 (genotypes 5 and 6) in real time. The TaqMan assay is rapid, sensitive, and specific and allows for the genotyping of unknown isolates concomitant with the RT-PCR. The assay can be applied quantitatively and the use of an internal control enables the quality of the isolated template to be assessed. Despite sequence heterogeneity in the N gene between the different genotypes, a universal forward and reverse primer set has been designed, allowing for the simplification of previously described assays. We propose that within a geographically constrained area, this assay will be a useful tool for the detection and differentiation of members of the Lyssavirus genus.

Rapid discrimination of rabies viruses isolated from various host species in Brazil by multiplex reverse transcription-polymerase chain reaction

Rabies is carried mainly by mammalian carnivores and vampire bats in Latin America. However, rabies virus (RV) has been isolated in recent years from not only vampire bats in rural areas but also from several non-vampire bat species in urban areas, respectively. Therefore, rapid molecular screening is necessary for efficient epidemiology of these RVs. In this study, we investigated the usefulness of multiplex reverse transcription-polymerase chain reaction (RT-PCR) for determining the origins of 54 RV isolates from various host species in Brazil. And to evaluate the multiplex RT-PCR as a potential diagnostic tool, we investigated the sensitivity of this method. In addition, we compared the results with a phylogenetic tree developed from sequences of the RV glycoprotein (G protein) gene. Multiplex RT-PCR products showed five different sizes of products, whereas the phylogenic tree showed six groups. Of these six groups, four corresponded with the four sizes of the multiplex RT-PCR products. The other two groups showed correspondance with another one size of the multiplex RT-PCR products, indicating that multiplex RT-PCR results reflected the lineage of the 54 isolates. This study also showed that this method can detect trace amounts of RNA. In conclusion, this multiplex RT-PCR method allows the rapid, specific, and simultaneous detection of RVs isolated from various host species in Brazil.

Mongoose rabies in southern Africa: a re-evaluation based on molecular epidemiology

Relative to the developed world, rabies has been poorly studied in the vast African continent. The southern African countries of Zimbabwe and South Africa, however, are known to sustain a great diversity of lyssaviruses, with large biological variations amongst genotype 1 (rabies viruses) at present more apparent here than elsewhere on the continent. One recognized biotype of rabies virus in the subcontinent appears to be specifically adapted to a variety of mongooses, belonging to the Viverrinae subfamily (family Herpestidae) and are commonly referred to as viverrid viruses, although the term mongoose rabies would be more correct, considering the taxonomic status of the host species involved. It was our objective to study the genetic relationships of 77 rabies virus isolates of this mongoose biotype, isolated in South Africa and Zimbabwe, towards elucidation of the molecular epidemiology of this interesting group of African viruses. In our study of a 592 nucleotide sequence encompassing the cytoplasmic domain of the glycoprotein and the G-L intergenic region of the viral genomes, we provide the first comprehensive data on the molecular epidemiology of these viruses and indicate a history of extended evolutionary adaptation in this geographical domain. The molecular epidemiological observations reported here are highly unlikely to be limited to the small geographical areas of South Africa and Zimbabwe and illustrate the need for lyssavirus surveillance in the rest of sub-Saharan Africa and throughout the entire continent.

Molecular epizootiology of rabies associated with terrestrial carnivores in Mexico

Epizootiological patterns of rabies are described, using antigenic and genetic analysis of samples obtained from infected domestic and wild mammals in 20 Mexican states during 1976-2002. Two independent origins are suggested for rabies in Mexican carnivores. One group shares ancestry with canine rabies, while the other group appears to share a common origin with bat rabies in North America. More than 12 sublineages were found in rabid dog populations, suggesting at least six major spatio-temporal foci. Coyote rabies was found as independent enzootic foci that probably emerged via spillover from dog rabies, translocated from major foci in the southcentral and western regions of Mexico. One focus of gray fox rabies was widely distributed in northwestern Mexico, overlapping with a focus in the same species in the southwestern United States. A skunk rabies focus distributed in the northcentral Mexican states appears to share a common origin with bat rabies foci in North America, and is a close relative of southcentral skunk and raccoon rabies in the United States. Two other skunk foci share a common ancestor with canine rabies and were distributed in northwest Mexico and Yucatan.

Transmission dynamics of rabies virus in Thailand: implications for disease control

Background

In Thailand, rabies remains a neglected disease with authorities continuing to rely on human death statistics while ignoring the financial burden resulting from an enormous increase in post-exposure prophylaxis. Past attempts to conduct a mass dog vaccination and sterilization program have been limited to Bangkok city and have not been successful. We have used molecular epidemiology to define geographic localization of rabies virus phylogroups and their pattern of spread in Thailand.

Methods

We analyzed 239 nucleoprotein gene sequences from animal and human brain samples collected from all over Thailand between 1998 and 2002. We then reconstructed a phylogenetic tree correlating these data with geographical information.

Results

All sequences formed a monophyletic tree of 2 distinct phylogroups, TH1 and TH2. Three subgroups were identified in the TH1 subgroup and were distributed in the middle region of the country. Eight subgroups of TH2 viruses were identified widely distributed throughout the country overlapping the TH1 territory. There was a correlation between human-dependent transportation routes and the distribution of virus.

Conclusion

Inter-regional migration paths of the viruses might be correlated with translocation of dogs associated with humans. Interconnecting factors between human socioeconomic and population density might determine the transmission dynamics of virus in a rural-to-urban polarity. The presence of 2 or more rabies virus groups in a location might be indicative of a gene flow, reflecting a translocation of dogs within such region and adjacent areas. Different approaches may be required for rabies control based on the homo- or heterogeneity of the virus. Areas containing homogeneous virus populations should be targeted first. Control of dog movement associated with humans is essential.

Studies on antigenic and genomic properties of Brazilian rabies virus isolates

Despite the recognized stability of rabies virus, differences among isolates from different species have been found. This work was carried out with the aim to identify antigenic and genomic differences in Brazilian rabies virus isolates and to verify whether such alterations would bear any relationship with the different hosts for the virus in nature. For that, 79 Brazilian rabies viruses isolated from different host species and from distinct regions within Brazil were submitted to antigenic characterization with a panel of 11 monoclonal antibodies (Mabs) directed to lyssavirus antigens and to genomic analyses by the reverse transcriptase-polymerase chain reaction (RT-PCR) amplification of the N gene followed by restriction endonuclease analysis (REA). In addition, the nucleotide sequences of part of the N gene (225 bp) of seven isolates, taken as representative of the majority of the viruses under study, were determined. The analyses with the Mabs and RT-PCR/REA allowed the identification of two major groups of variants, the first formed by most isolates of cattle and bats and the second formed by viruses of dog origin. Partial sequencing of the N gene confirmed the similarity among isolates from cattle origin and those of vampire bats. However, viruses from non-haematophagous bats exhibited consistent differences from those of vampire bat isolates. Such findings suggest that the variants have evolved fairly stable modifications, which are not altered after passage in a dead-end host of a distinct species. No association could be established between antigenic or genomic alterations and geographic distribution of the isolates, which suggests that evolution of the virus has been directed to adaptation to the host species.

Spatial dynamics and molecular ecology of North American rabies

Rabies, caused by a single-stranded RNA virus, is arguably the most important viral zoonotic disease worldwide. Although endemic throughout many regions for millennia, rabies is also undergoing epidemic expansion, often quite rapid, among wildlife populations across regions of Europe and North America. A current rabies epizootic in North America is largely attributable to the accidental introduction of a particularly well-adapted virus variant into a naive raccoon population along the Virginia/West Virginia border in the mid-1970s. We have used the extant database on the spatial and temporal occurrence of rabid raccoons across the eastern United States to construct predictive models of disease spread and have tied patterns of emergence to local environmental variables, genetic heterogeneity, and host specificity. Rabies will continue to be a remarkable model system for exploring basic issues in the temporal and spatial dynamics of expanding infectious diseases and examining ties between disease population ecology and evolutionary genetics at both micro- and macro-evolutionary time scales.

Antigenic and molecular characterization of rabies virus in Argentina

The nucleoprotein genes of 54 human, domestic and wild animals rabies isolates obtained in Argentina between 1995 and 2002 were characterized using monoclonal antibodies and partial gene sequence analysis. The antigenic and genetic diversities of rabies virus in samples from bat and bat-related cases were studied, leading to the identification of five distinct genetic variants. Rabies viruses isolated from vampire bat related cases were very similar to each other, showing 98.9% overall similarity. Specific antigenic variants (AgV) were detected associated with different insectivorous bats species, in samples from Tadarida brasiliensis and Eumops patagonicus bats. In contrast, isolates from Myotis sp. and Histiotus sp. bats could not be matched to any antigenic type. Additionally, bat rabies cases were also detected in southern provinces previously considered rabies-free. Finally, two independent antigenic and genetic variants co-circulating in northern Argentina were found in isolates obtained from dogs and dog-related cases, suggesting two independent cycles of virus transmission. This is the first national coordinated study of antigenic as well as molecular epidemiology of rabies in Argentina. The information presented here will improve our knowledge about rabies epidemiology and therefore, will assist preventing fatal human cases.

Detection and characterization of rabies virus in Southern Brazil by PCR amplification and sequencing of the nucleoprotein gene

Due to the medical and socio-economical importance of both human and animal rabies infection, several studies have suggested the use of molecular techniques such as RT-PCR and DNA sequencing for diagnosis and phylogenetic studies of the rabies virus. Considering the conservancy of the nucleoprotein (N) gene of the virus, we herein describe a RT-PCR assay for rabies diagnosis and characterization. A total of 75 samples obtained from a variety of animal species in the state of Santa Catarina (SC), Southern Brazil, were comparatively studied by fluorescence antibody test (FAT), mouse inoculation test (MIT), cell infection assay and RT-PCR, which revealed itself to be as sensitive as FAT and MIT and less time-consuming than MIT. Direct sequencing of the 5' end of the N gene allowed the clustering of the SC samples with samples from the vampire bat-related or sylvatic cycle through comparative sequence analysis.