Molecular epidemiology of canid rabies in Sudan: evidence for a common origin of rabies with Ethiopia

Rabies is an endemic zoonosis in Sudan with the principal reservoir species being the domestic dog. A panel of rabies virus isolates from dogs in Sudan have been used to establish a molecular phylogeny based on a partial sequence of the viral nucleoprotein. These isolates were then compared to those from countries bordering Sudan in north-east Africa. The Sudanese viruses form a tight cluster of isolates with a single outlier. When compared to other African viruses, the Sudanese isolates cluster most closely with isolates from Ethiopia to the East suggesting a common origin for rabies in both countries which supports historical records of the movement of rabies into Sudan. The Sudanese group of viruses belong to the Africa 1a group of viruses that are present throughout much of north Africa.

MOLECULAR EPIDEMIOLOGY OF TERRESTRIAL RABIES IN THE FORMER SOVIET UNION

Fifty-five rabies virus isolates originating from different regions of the former Soviet Union (FSU) were compared with isolates originating from Eurasia, Africa, and North America according to complete or partial nucleoprotein (N) gene sequences. The FSU isolates formed five distinct groups. Group A represented viruses originating from the Arctic, which were similar to viruses from Alaska and Canada. Group B consisted of "Arctic-like" viruses, originating from the south of East Siberia and the Far East. Group C consisted of viruses circulating in the steppe and forest-steppe territories from the European part of Russia to Tuva and in Kazakhstan. These three phylogenetic groups were clearly different from the European cluster. Viruses of group D circulate near the western border of Russia. Their phylogenetic position is intermediate between group C and the European cluster. Group E consisted of viruses originating from the northwestern part of Russia and comprised a "northeastern Europe" group described earlier from the Baltic region. According to surveillance data, a specific host can be defined clearly only for group A (arctic fox; Alopex lagopus) and for the Far Eastern part of the group B distribution area (raccoon dog; Nyctereutes procyonoides). For other territories and rabies virus variants, the red fox (Vulpes vulpes) is the main virus reservoir. However, the steppe fox (Vulpes corsac), wolf (Canis lupus), and raccoon dog are also involved in virus circulation, depending on host population density. These molecular data, joined with surveillance information, demonstrate that the current fox rabies epizootic in the territory of the FSU developed independently of central and western Europe. No evidence of positive selection was found in the N genes of the isolates. In the glycoprotein gene, evidence of positive selection was strongly suggested in codons 156, 160, and 183. At these sites, no link between amino acid substitutions and phylogenetic placement or specific host species was detected.

Bat rabies, Texas, 1996-2000

Bats submitted to the Texas Department of Health (1996–2000) were speciated and tested for rabies virus antigen by direct immunofluorescence microscopy. Antigenic analysis of rabies virus–positive specimens was performed with monoclonal antibodies against the nucleoprotein of the virus; atypical or unexpected results were confirmed by genetic analysis of nucleoprotein sequence.

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

Historically, canine rabies in Colombia has been caused by two geographically distinct canine variants of rabies virus (RV) which between 1992 and 2002 accounted for approximately 95% of Colombian rabies cases. Genetic variant 1 (GV1) has been isolated up until 1997 in the Central Region and the Department of Arauca, and is now considered extinct through a successful vaccination program. Genetic variant 2 (GV2) has been isolated from the northern Caribbean Region and continues to circulate at present. Here we have analyzed two sets of sequence data based upon either a 147 nucleotide region of the glycoprotein (G) gene or a 258 nucleotide region that combines a fragment of the non-coding intergenic region and a fragment of the polymerase gene. Using both maximum likelihood (ML) and Markov chain Monte Carlo (MCMC) methods we have estimated the time of the most recent common ancestor (MRCA) of the two variants to be between 1983 and 1988. Reconstructions of the population history suggest that GV2 has been circulating in Colombia since the 1960s and that GV1 evolved as a separate lineage from GV2. Estimations of the effective population size at present show the GV2 outbreak to be approximately 20 times greater than that of GV1. Demographic reconstructions were unable to detect a decrease in population size concurrent with the elimination of GV1. We find a raised rate of nucleotide substitution for GV1 gene sequences when compared to that of GV2, although all estimates have wide confidence limits. We demonstrate that phylogenetic reconstructions and sequence analysis can be used to support incidence data from the field in the assessment of RV epidemiology.

Characterization of rabies virus isolates in Bolivia

In Latin America, rabies is still an important public health problem. Canine rabies, and wild animal rabies, especially transmitted by hematofagous and insectivorous bats, has become an emerging problem in the countries of this region. We received 363 samples with a laboratory-confirmed rabies diagnosis from Bolivia during l997-2001. From these, we could obtain 222 rabies virus isolates by intra-cerebral inoculation in mice. By antigenic characterization we could identify 147 isolates as variant 1, 2 isolates as variant 2, 3 isolates as variant 3, and 1 isolate as variant 5. Phylogenetic analysis of 84 isolates established that they segregated in 3 different branches, corresponding to 3 genetic variants, 78 isolates corresponding to antigenic variant 1 segregated in the same lineage as the antigenic variant 5, 2 isolates corresponding to antigenic variant 2 segregated in another lineage, and 3 isolates from antigenic variant 3 segregated in a different lineage.The genetic variant that mainly circulates in Bolivia is maintained in a cycle whose main reservoir are dogs, but it is not possible to discard the presence of other cycles, in which different species of bats or other wild mammals could be participating.

Characterization of nucleoprotein gene sequence of an Indian isolate of rabies virus

Rabies occurs in all parts of Indian sub-continent except Andaman and Nicobar and Lakshadweep group of islands. The full-length nucleoprotein (N) gene sequence of a rabies virus isolate from India is reported for the first time and the same has been compared with available N gene sequences from the database. A central domain of 230 amino acids (aa) from aa 141 to aa 370 exhibited more than 95% similarity. There were 8 amino acid positions (aa 29, 32, 38, 84, 119, 379, 438, and 439) at which substitution was unique for Indian isolates but common for laboratory strains. In antigenic epitopes, except for a single amino acid difference at the antigenic site IV, the amino acids were conserved. The Indian isolate also possessed two Bam HI sites (aa 247 and 278), while the other Asian isolates had only one site at aa 278 or were not digested with Bam HI at all. Phylogenetic analysis also demonstrated that the Indian isolate was closely related to the Sri Lankan isolate and grouped in the cluster that comprised of the isolates from other Asian countries namely China and Pakistan.

[A case of bat rabies in a cat in the province of Buenos Aires, Argentina]

In the Central Laboratory of Public Health in Buenos Aires, rabies was detected in a cat that was brought in for diagnosis by its owners. The animal, which was displaying symptoms of the furious form of the disease, had attacked three people in the rural area of Chascomús, near the Rio de la Plata. All three of the people who had been bitten received the necessary treatment. The diagnosis was made using the fluorescent antibody test and the inoculation of mice and the results were communicated to the Zoonoses Division of the Ministry of Health. The virus was then typed at the Institute Pasteur of Buenos Aires using monoclonal antibodies, where it was found to be antigenic variant 4 of serotype 1, i.e., the type of virus usually found in insectivorous bats. This area has been free of the canine variant since 1984. This is the first known case in the province of Buenos Aires of a cat becoming infected with this type of virus. It confirms that there is a link between the air and terrestrial cycles of rabies in this area.

Sequence Analysis of Rabies Virus in Humans Exhibiting Encephalitic or Paralytic Rabies

Two distinct clinical patterns, encephalitic (furious) and paralytic (dumb), have been recognized in human rabies. It has been postulated that different rabies virus variants associated with particular vectors may be responsible for these different clinical manifestations. Analysis of the glycoprotein (G), nucleoprotein (N), and phosphoprotein (P) genes of rabies viruses from 2 human cases of encephalitic rabies and from 2 human cases of paralytic rabies demonstrated only minor nucleotide differences. Deduced amino-acid patterns of the N protein were identical in both human and canine samples that came from the same geographic location, regardless of the clinical form. All differences in amino-acid patterns of the G protein were found outside the ectodomain, in either the signal peptide or the transmembrane and endodomains. None of the amino-acid differences of the P protein was within the interactive site with dynein. These findings support the concept that clinical manifestations of rabies are not explained solely by the associated rabies virus variant.

Use of discriminatory probes for strain typing of formalin-fixed, rabies virus-infected tissues by in situ hybridization

An in situ hybridization (ISH) method has been developed to overcome difficulties encountered in the viral typing of formalin-fixed rabies virus-infected brain tissue. Rabies viruses representative of all strains normally encountered in diagnostic submissions throughout Canada, including 3 strains of terrestrial hosts (arctic fox, western skunk, mid-Atlantic raccoon), 10 strains circulating in several bat reservoirs (BBCAN1 to BBCAN7, LACAN, SHCAN, and MYCAN), and the Evelyn-Rokitniki-Abelseth (ERA) strain, used as an oral vaccine for fox rabies control in Ontario, were targeted. Partial phosphoprotein gene fragments generated from reverse transcription (RT)-PCR products of specimens of each viral type were molecularly cloned and used to produce negative-sense digoxigenin-labeled RNA transcripts. Conditions permitting the use of these transcripts as strain-specific probes were optimized by blotting analyses with RT-PCR amplicons generated with representative rabies viruses and by ISH applied to mouse brains inoculated with these strains. The successful application of this methodology to two rabies virus-positive specimens that were also identified by traditional methods and the retrospective typing of two archival rabies virus-positive equine specimens is described. This technique provides a typing regimen for rabies virus isolates submitted in a form that is normally recalcitrant to alternate typing strategies.

Rabies in Wildlife in Latvia

In the Baltic States, lyssaviruses are often detected in wildlife and presumed to constitute an important public health hazard. In order to decrease rabies incidence and eradicate wildlife reservoirs, a national rabies eradication program has been in place. Since 1970 a vaccination program in dogs and cats has been executed, and in 1991 oral vaccination of foxes was started. However, due to an insufficient budget, the latter was not done regularly and nationwide before 2000. Now, the program in force consists of compulsory vaccination of all dogs and cats, and a tetracycline marker vaccine oral vaccination program of foxes in the whole country. In 2001, 151 of 285 (53%) fox jaws were tested positive for tetracycline. All animals showing rabies-like symptoms were killed and tested for rabies. In this way, 250-400 cases of rabies per year were diagnosed in wildlife. To molecularly characterize the prevalent lyssaviruses in wildlife, lyssavirus RNA of 25 recent rabies positive samples, collected in the year 1999, was amplified by RT-PCR. Direct sequencing of the RT-PCR-amplified products of the virus' nucleoprotein encoding region and subsequent sequence analyses resulted in a 99.3-100% homology between isolates and a 99.0-100% similarity with a 1995 genotype I, classical rabies virus (RABV) raccoon dog isolate from Estonia. These results confirmed that RABV is endemic in wildlife in Latvia and should be considered a serious public health threat. To successfully eradicate the wildlife reservoirs, the national rabies eradication program must be continued, and it may need to be intensified.

Discrimination between dog-related and vampire bat-related rabies viruses in Brazil by strain-specific reverse transcriptase-polymerase chain reaction and restriction fragment length polymorphism analysis

BACKGROUND

There is a geographical overlap between the two main rabies epidemiological cycles maintained by dogs and vampire bats in Latin America. The geographical and temporal coincidence of rabies outbreaks of respective origins is not unusual in rural areas of Latin America. These circumstances make it difficult to discriminate the intraspecies and interspecies transmission pathways of rabies.

OBJECTIVE

This study was conducted to develop techniques to discriminate dog-related and vampire bat-related rabies virus isolates (DRRV and VRRV, respectively) in Brazil.

STUDY DESIGN

The 1396 nucleotides of the nucleoprotein gene of a total of 27 DRRV and VRRV were sequenced. Strain-specific (SS) primers were developed based on these sequences. Forty-nine rabies virus strains isolated from animals and humans in several parts of Brazil were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) with SS primers. These rabies viruses were also amplified by RT-PCR with general rabies primers and the PCR products were cut by three restriction enzymes, Blp I, Bsu36 I and BspE I.

RESULTS

All the DRRV and VRRV were distinguished by RT-PCR with SS primers. The PCR products obtained from DRRV were cut at one site by Blp I, but not by Bsu36 I. The PCR products obtained from VRRV were cut at one or two sites by Bsu36 I, but not by Blp I. Blp I and Bsu36 I clearly discriminated DRRV and VRRV in restriction fragment length polymorphysim (RFLP) assays. The results of SS RT-PCR and RFLP were consistent.

CONCLUSION

SS RT-PCR and RFLP assays have been developed for determining the origins of rabies virus isolates in Brazil. These assays are simple and rapid, and will be useful for identifying the rabies virus reservoirs of field isolates in Brazil, especially when used together.

Effect of heterogeneity of rabies virus strain and challenge route on efficacy of inactivated rabies vaccines in mice

OBJECTIVE

To determine effect of route of challenge and strain of rabies virus on efficacy of inactivated rabies vaccines in mice.

ANIMALS

3,056 mice.

PROCEDURE

Challenge was performed with fixed and street rabies virus strains by use of footpad and intracerebral routes as well as IM injection into the hip, shoulder, neck, and masseter muscles. Intraperitoneal and IM vaccination was performed with 1 or 2 doses of 1 of 3 vaccine-strain inactivated rabies vaccines. For 2 of the vaccine strains, the vaccines were adjuvanted and nonadjuvanted.

RESULTS

Incubation periods were dependent on route, dose, and virus strain used for challenge. Use of an intramasseter challenge route with challenge virus-strain rabies virus, which more accurately models natural exposure to rabies virus, resulted in reproducible mortality rates in mice. Use of this route revealed that differences among vaccines and challenge virus strains affected mortality rate less than that observed in the National Institutes of Health potency test, even when street isolates of widely variant origin were used for challenge.

CONCLUSIONS AND CLINICAL RELEVANCE

These results, combined with earlier data, support a proposal for a new rabies potency test that more closely models current vaccine administration practices and natural infection routes.

Rabies emergence among foxes in Turkey

Sixteen rabies isolates recently collected from mainland Turkey and two isolates held within a British archive were used to form a representative cohort from a range of vectors, and were analyzed to identify potential causes for an increase of rabies within the fox (Vulpes vulpes) population in Turkey. Each isolate was characterized by sequence analysis of the nucleoprotein gene and compared phylogenetically to the cohort, to isolates from neighboring countries and to isolates from continental Europe and Russia. From this analysis the isolates could be divided into three groups associated with geographic location. This included a western group, an eastern group, and one isolate that did not group with any other Turkish isolate. This observation was also found using the heteroduplex mobility assay as an alternative method for typing rabies virus isolates. Further comparison with isolates from neighboring countries suggests that this isolate was related to viruses present in Georgia and could represent a recent import to Turkey from that country. Within the two larger groups, sequence data were obtained from both infected dogs and foxes suggesting that there has been transmission of virus between these two species. The direction of transmission could not be identified by the phylogenetic analysis, although absence of rabies within the fox population in previous years suggests that this could represent a recent spillover from the domestic dog to the fox.

Rabies among infrequently reported mammalian carnivores in the United States, 1960-2000

Most cases of rabies reported annually in the United States occur among three groups of carnivores--raccoons (Procyon lotor), skunks (Mephitis, Spilogale, and Putorius), foxes (Vulpes, Urocyon, and Alopex)--and among bats (numerous species). However, between 1960 and 2000, a total of 2,851 cases of rabies in 17 other carnivore taxa were reported to the Centers for Disease Control and Prevention, Atlanta, Georgia (USA), from 49 states, the District of Columbia, and Puerto Rico. Three species of these other carnivores (mongooses [Herpestes javanicus], coyotes [Canis latrans], and bobcats [Lynx rufus]) accounted for 92% (2,624/2,851) of the cases reported among other canivorous mammals (OCMs). Most OCMs demonstrated temporal or spatial variation in numbers of reported cases. Tests of specimens from OCMs infected in the United States identified variants of the rabies virus that corresponded with variants associated with the major terrestrial reservoirs within their respective regions of origin. Variants of the rabies virus in samples from mongooses in Puerto Rico could not be distinguished from those in samples from dogs in Puerto Rico by virus typing methods.

Immune response to Japanese rabies vaccine in domestic dogs

To evaluate the immune response induced by Japanese rabies vaccine for veterinary use as international units (IU), we measured levels of rabies antibody in serum samples from dogs by the rapid fluorescent focus inhibition test (RFFIT). In dogs immunized with a reference vaccine (potency level of 3.1 IU/ml), prepared by the same method as that used to produce commercial vaccine, and its dilutions (1 : 2 or 1 : 4), neutralizing-antibody levels increased to 1.0-2.0 IU/ml over a period of 1 month and then decreased to 0.2-1.5 IU/ml over a period of 1 year after the first vaccination and showed a remarkable increase to 12-47 IU/ml after the second vaccination. Sixty-five (74.7%) of the 87 serum samples from domestic dogs that were tested were seropositive (> or =0.1 IU/ml). However, the seropositive rate in dogs less than 1-year old at the time of vaccination was low (57.1%), and the antibody levels in these dogs were not sufficiently high for the rabies antibody titre in serum to be maintained for 1-year. Levels of rabies antibody in all serum samples were also measured by the virus neutralizing test (VNT), and a strong correlation (r > 0.95) was found between the results of the RFFIT and those of the VNT.

[Molecular epidemiology of rabies epizootics in Colombia, 1994-2002: evidence of human and canine rabies associated with chiroptera]

Three urban rabies outbreaks have been reported in Colombia during the last two decades, one of which is ongoing in the Caribbean region (northern Colombia). The earlier outbreaks occurred almost simultaneously in Arauca (eastern Colombia) and in the Central region, ending in 1997. Phylogenetic relationships among rabies viruses isolated from the three areas were based on a comparison of cDNA fragments coding for the endodomain of protein G and a fragment of L protein obtained by RT-PCR. The sequenced amplicons which included the G-L intergenic region contained 902 base pairs. Phylogenetic analysis showed three distinct groups of viruses. Colombian genetic variant I viruses were isolated only from Arauca and the Central region, but are now apparently extinct. Colombian genetic variant II viruses were isolated in the Caribbean region and are still being transmitted in that area. The third group of bat rabies variants were isolated from two insectivorous bats, three domestic dogs and a human. This associates bat rabies virus with rabies in Colombian dogs and humans, and indicates bats to be a rabies reservoir of public health significance.

Molecular epidemiology of canid rabies in Zimbabwe and South Africa

The epidemiology of rabies in southern Africa is complex, due to a large number of vector species and the presence of at least two distinct biotypes of the virus. Our objective was to contribute to the understanding of the epidemiology of rabies in the southern African subcontinent by studying the genetic relationship of 89 rabies virus isolates from this region. In this study, we have focused on an analysis of viruses that cycle in canid host species (canid biotype) throughout South Africa and Zimbabwe. By phylogenetic analysis of the cytoplasmic domain of the glycoprotein and the non-coding G-L intergenic region, all the southern African canid viruses were found to be closely related and no apparent general distinction could be made between them. Although there was a minor degree of phylogenetic branching, with certain branches associated with cycles defined by species, location and time, the phylogenetic pattern indicated that canid rabies in southern Africa is derived from a single virus lineage, which has spread opportunistically within whatever canid host population is ecologically capable of sustaining prolonged cycles. This molecular epidemiological study presents the first comprehensive comparison of rabies viruses from South Africa and Zimbabwe and has demonstrated the need for multinational approaches towards the control of this important zoonotic disease in Africa.

Investigation of a human case of rabies in the United Kingdom

In May of 2001 a Nigerian woman visiting the United Kingdom presented with fever, headache and difficulty swallowing. Within 24 h she showed a marked deterioration and died shortly afterwards. Autopsy samples from a range of tissues were analysed to confirm a clinical diagnosis of rabies. Phylogenetic analysis of the viral nucleoprotein gene confirmed that this was an infection with a genotype 1 virus (classical rabies) belonging to the Africa 2 group, which is endemic in Northern Africa. Comparison of both the nucleoprotein and glycoprotein coding sequences of this isolate with an imported case of human rabies from 1996, also from Nigeria, showed that the two viruses were 99% homologous.

Genetic and antigenic typing of rabies virus in Chile. Brief report

Forty-one isolates of rabies virus from insectivorous bats and one from a domestic cat in Chile, were characterized using eight anti-nucleoprotein monoclonal antibodies (N-Mabs) and by nucleotide sequence analysis. Thirty-two isolates were identified as antigenic variant 4 associated with Tadarida brasiliensis bats, twenty-eight were genetically associated with variant Tadarida brasiliensis and four with Lasiurus sp. bats. One isolate was identified as antigenic variant 3 associated with Desmodus rotundus bats, and by genetic analysis was identified as variant Myotis sp. bat. Eight isolates were unrelated to any antigenic variant, and they were identified as a genetic variant associated with Histiotus sp. bats. These antigenic and genetic characterizations may establish epidemiological links between rabies cases and increase the understanding of rabies epidemiology in this country.

A rapid RT-PCR method to differentiate six established genotypes of rabies and rabies-related viruses using TaqMan technology

A rapid and sensitive reverse transcriptase-polymerase chain reaction (RT-PCR) assay incorporating TaqMan probes has been developed that can distinguish among the six established rabies and rabies-related virus genotypes. TaqMan probes were designed and validated against 106 rabies and rabies-related virus isolates, one isolate of the Australian bat Lyssaviruses (genotype 7), and 18 other non-rabies viruses important in the veterinary field. The N gene was used as the target for the probes as it is well conserved and has been intensively used to genotype rabies isolates. Additionally, it was found to contain regions specific to each genotype conducive to probe design. The RT-PCR assay described amplifies a portion of the nucleoprotein gene of all 107 rabies and rabies-related viruses, but none of the other viruses tested. Inclusion of TaqMan-genotype-specific probes in the RT-PCR assay permits rapid identification of the virus present. By combining RT-PCR with TaqMan genotyping probes suspect rabies virus isolates can be identified in a single closed tube system that prevents potential PCR-product carry over contamination.

Antigenic typing of Brazilian rabies virus samples isolated from animals and humans, 1989-2000

Animal and human rabies samples isolated between 1989 and 2000 were typified by means of a monoclonal antibody panel against the viral nucleoprotein. The panel had been previously established to study the molecular epidemiology of rabies virus in the Americas. Samples were isolated in the Diagnostic Laboratory of the Pasteur Institute and in other rabies diagnostic centers in Brazil. In addition to the fixed virus samples CVS-31/96-IP, preserved in mouse brain, and PV-BHK/97, preserved in cell culture, a total of 330 rabies virus samples were isolated from dogs, cats, cattle, horses, bats, sheep, goat, swine, foxes, marmosets, coati and humans. Six antigenic variants that were compatible with the pre-established monoclonal antibodies panel were defined: numbers 2 (dog), 3 (Desmodus rotundus), 4 (Tadarida brasiliensis), 5 (vampire bat from Venezuela), 6 (Lasiurus cinereus) and Lab (reacted to all used antibodies). Six unknown profiles, not compatible with the panel, were also found. Samples isolated from insectivore bats showed the greatest variability and the most commonly isolated variant was variant-3 (Desmodus rotundus). These findings may be related to the existence of multiple independent transmission cycles, involving different bat species.

First case of human rabies in chile caused by an insectivorous bat virus variant

The first human rabies case in Chile since 1972 occurred in March 1996 in a patient without history of known exposure. Antigenic and genetic characterization of the rabies isolate indicated that its reservoir was the insectivorous bat Tadarida brasiliensis. This is the first human rabies case caused by an insectivorous bat rabies virus variant reported in Latin America.

Typing of field rabies virus strains in FR Yugoslavia by limited sequence analysis and monoclonal antibodies

A total of 32 rabies virus isolates (15 of fox, 14 of cat and 3 of dog origin) from the territory of FR Yugoslavia were collected from December 1996 till February 1998 and analyzed by limited sequencing of N gene and by indirect immunofluorescence and a panel of 20 antinucleocapsid monoclonal antibodies (MAbs). All examined strains were characterized as sylvatic fox strains. Two main genetic variants were detected, 15 isolates belonging to Group I, 14 belonging to Group II, while the remaining 3 could not be classified into any group. This classification was confirmed by MAbs. The obtained results indicate at least two independent cycles of rabies transmission, probably resulting from multiple modes of transmission to the territories now belonging to FR Yugoslavia.

Survey of bat populations from Mexico and Paraguay for rabies

A mammalian survey was conducted in Mexico (October 1994-January 1996) and in Paraguay (August 1996-March 1997); a complete specimen was collected for each bat in the survey, including primary voucher specimen, ectoparasites, karyotype, and various frozen tissues. The surveys combined provided 937 brain samples (65 bat species) for rabies diagnosis. One male Lasiurus ega, collected in Paraguay, tested positive for the rabies virus (overall prevalence rate of 0.1%). Nucleotide sequence from a 300 bp region of the rabies nucleoprotein gene was compared with sequence obtained from representative rabies virus samples in the repository at the Centers for Disease Control and Prevention (Atlanta, Georgia, USA). Rabies virus extracted from the brain material of L. ega differed by only one nucleotide from a 300 bp consensus sequence (>99% homology) derived from samples for the variant of rabies virus transmitted by Lasiurus cinereus. Lasiurus ego differed by approximately 15% for the variant transmitted by Desmodus rotundus. Phylogenetic analysis found no evidence to suggest L. ego is a reservoir for rabies antigenic variant 6. The most likely explanation for rabies in L. ega was infection following contact with a rabid L. cinereus.

Epidemiologic characteristics of rabies virus variants in dogs and cats in the United States, 1999

OBJECTIVE

To evaluate epidemiologic features of rabies virus variants in dogs and cats in the United States during 1999 and assess the role of bat-associated variants.

DESIGN

Epidemiologic survey.

SAMPLE POPULATION

Rabies viruses from 78 dogs and 230 cats.

PROCEDURE

Brain specimens from rabid dogs and cats were submitted for typing of rabies virus. Historical information, including ownership and vaccination status, was obtained for each animal. Specimens were typed by use of indirect fluorescent antibody assay or reverse transcriptase polymerase chain reaction assay and nucleotide sequence analysis.

RESULTS

Nearly all animals were infected with the predicted terrestrial rabies virus variant associated with the geographic location of the submission. A bat-associated variant of rabies virus was found in a single cat from Maryland. More than half (53%) of submitted animals were classified as owned animals, and most had no known history of vaccination. One vaccination failure was reported in a dog that did not receive a booster dose of rabies vaccine after exposure to a possibly rabid animal.

CONCLUSIONS AND CLINICAL RELEVANCE

Bat-associated rabies virus variants were not a common cause of rabies in dogs and cats during 1999. Vaccine failures were uncommon during the study period. Because most rabid dogs and cats were unvaccinated and were owned animals rather than strays, educational campaigns targeting owners may be useful.

Report of isolations of unusual lyssaviruses (rabies and Mokola virus) identified retrospectively from Zimbabwe

Rabies isolates that had been stored between 1983 and 1997 were examined with a panel of anti-lyssavirus nucleocapsid monoclonal antibodies. Out of 56 isolates from cats and various wild carnivore species, 1 isolate of Mokola virus and 5 other non-typical rabies viruses were identified. The Mokola virus isolate was diagnosed as rabies in 1993 from a cat. Genetic analysis of this isolate suggests that it falls in a distinct subgroup of the Mokola virus genotype. The 5 non-typical rabies viruses were isolated from honey badgers (Mellivora capensis), African civets (Civettictis civetta) and an unidentified mongoose (Herpestidae). These isolates are representatives of rarely-reported wildlife-associated strains of rabies, probably maintained by the slender mongoose (Galerella sanguinea). These findings indicate that both Mokola virus and the mongoose-associated variant may be more common in Zimbabwe than is apparent from routine surveillance.

Antigenic and genetic divergence of rabies viruses from bat species indigenous to Canada

Antigenic characterisation of over 350 chiropteran rabies viruses of the Americas, especially from species reported rabid in Canada, distinguished 13 viral types. In close accord with this classification, nucleotide sequencing of representative isolates, at both the N and G loci, identified four principal phylogenetic groups (I-IV), sub-groups of which circulated in particular bat species. Amongst the North American bat viruses, there was a notable division between group I specimens associated with colonial, non-migratory bats (Myotis sp. and Eptesicus fuscus) and those of group II harbored by solitary, migratory species (Lasiurus sp. and Lasionycteris noctivagans). Certain species of Myotis were clearly identified as rabies reservoirs, an observation often obscured previously by their frequent infection by viral variants of other chiroptera. An additional group (III) apparently circulates in E. fuscus, whilst viruses harbored by both insectivorous and haematophagus bats of Latin America clustered to a separate clade (group IV). Comparison of the predicted N and G proteins of these viruses with those of strains of terrestrial mammals indicated a similarity in structural organisation regardless of host species lifestyle. Finally, these sequences permitted examination of the evolutionary relationship of American bat rabies viruses within the Lyssavirus genus.

Rabies in marmosets (Callithrix jacchus), Ceará, Brazil

A new Rabies virus variant, with no close antigenic or genetic relationship to any known rabies variants found in bats or terrestrial mammals in the Americas, was identified in association with human rabies cases reported from the state of Ceará, Brazil, from 1991 to 1998. The marmoset, Callithrix jacchus acchus, was determined to be the source of exposure.

Rabies in tamarins (Callithrix jacchus) in the state of Ceará, Brazil, a distinct viral variant?

Presently, the State of Ceará reports the largest percentage of human rabies cases originated from wild animals in Brazil, transmitted by the principal simian species, the tamarin (Callithrix jacchus), found in various locations throughout the State, but concentrated along the coast. Epidemiological studies indicated that possibly the same virus caused the deaths in humans and non-human primates. This rabies virus seem to be different from all other identified so far.

Molecular methods to distinguish between classical rabies and the rabies-related European bat lyssaviruses

A rapid and sensitive reverse transcriptase-polymerase chain reaction (RT-PCR) assay for the detection of classical rabies virus (genotype 1) and the rabies related European bat lyssaviruses (EBLs) (genotypes 5 and 6) was developed. When combined with specific oligonucleotide probes and a PCR-enzyme linked immunosorbent assay (PCR-ELISA), genotype 5 and 6 viruses can be distinguished from each other and from genotype 1 viruses. Ninety-two isolates from the six established genotypes of rabies and rabies-related viruses were screened by RT-PCR and PCR-ELISA to determine the specificity of the assays. All genotype 1, 5 and 6 viruses were detected by RT-PCR while none of the genotype 2, 3 and 4 viruses were detected. All the genotype 5 and 6 viruses were detected by the two PCR-ELISA probes when used in combination while none of the genotype 1-4 viruses were detected. When used individually, the PCR-ELISA probes also distinguished between the genotype 5 and 6 viruses. This new discriminatory test should allow the rapid genotyping of all lyssaviruses likely to be encountered in Europe and as such could provide useful epidemiological information in the event of an outbreak.

A panel of monoclonal antibodies targeting the rabies virus phosphoprotein identifies a highly variable epitope of value for sensitive strain discrimination

A recombinant rabies virus phosphoprotein fusion product (GST-P) was used to generate a series of monoclonal antibodies (MAbs) with anti-P reactivity. Competitive binding assays classified 27 of these MAbs into four groups (I to IV), and 24 of them were deemed to recognize linear epitopes, as judged by their reaction in immunoblots. The linear epitope recognized in each case was mapped by using two series of N- and C-terminally deleted recombinant phosphoproteins. Assessment of the reactivities of representative MAbs to a variety of lyssavirus isolates by an indirect fluorescent antibody test indicated that group I MAbs, which recognized a highly conserved N-terminal epitope, were broadly cross-reactive with all lyssaviruses assayed, while group III MAbs, which reacted with a site overlapping that of group I MAbs, exhibited variable reactivities and group IV MAbs reacted with most isolates of genotypes 1, 6, and 7 only. In contrast, group II MAbs, which recognized an epitope located within a highly divergent central portion of the protein, were exquisitely strain specific. These anti-P MAbs are potentially useful tools for lyssavirus identification and discrimination.

Antigenic characterization of rabies virus isolates from vaccinated dogs in plateau state, Nigeria

Rabies isolates (genotype 1 lyssaviruses) from vaccinated dogs that died of rabies infection in the Plateau area of Nigeria were characterized using monoclonal antibodies (MAbs). The isolates were examined for rabies (genotype 1) and rabies-related (genotypes 2, 3 and 4) viruses by the indirect fluorescent antibody test carried out with MAb 502-2, which recognizes the nucleocapsid protein of all known lyssaviruses, and with MAb 422-5, which identifies only rabies-related viruses. All three isolates showed positive immunofluorescence with MAb 502-2 and were negative with MAb 422-5, indicating that they were all rabies (genotype 1) viruses. Characterization with a panel of 36 anti-nucleocapsid monoclonal antibodies showed that all three isolates reacted positively with 35 of the anti-nucleocapsid MAbs, including MAb 102-27 and MAb 377-7. Characterization using a panel of 44 anti-glycoprotein MAbs differentiated the isolates sharply from LEP Flury and PM vaccine viruses. The pattern of anti-glycoprotein reactivity of the isolates showed them to belong to one distinct viral subtype, except for a minor variation in one isolate that was not neutralized by MAb 1101-3. None of the three isolates was identified as the Flury low egg passage (LEP) vaccine strain used for vaccinating dogs in Nigeria. In fact, all the three isolates had the typical pattern of reactivity of isolates from unvaccinated dogs, including MASS 83, a rabies virus isolated in Nigeria and characterized at the Wister Institute before this study.

Bat rabies in urban centers in Chile

One hundred and five rabies isolates obtained from domestic animals and insectivorous bats in Chile between 1977 and 1998 were molecularly characterized by limited sequence analysis of their nucleoprotein genes. These isolates were compared with viruses isolated from known domestic and wildlife rabies reservoirs in the Americas to identify potential reservoirs of rabies in Chile. The phylogenetic analyses showed that none of the Chilean isolates segregated with viruses from the terrestrial reservoirs. No non-rabies lyssaviruses were found in this study. The Chilean samples were not related to viruses of the sylvatic cycle maintained by the common vampire bat (Desmodus rotundus) in Latin America. Five genetic variants were identified from insectivorous bats in Chile. The Brazilian free-tailed bat (Tadarida brasiliensis) was identified as the reservoir for the rabies genetic variant most frequently isolated in the country between 1977 and 1998. The close association of a group of viruses obtained from a domestic dog (Canis familiaris), Brazilian free-tailed bats, and a red bat (Lasiurus borealis) with viruses maintained by Lasiurus spp. in North America implicated species of this genus as the possible reservoirs of this particular genetic variant in Chile. Reservoirs for the other three variants remain unknown.

Molecular characterization of rabies virus isolates from Mexico: implications for transmission dynamics and human risk

Twenty-eight samples from humans and domestic and wild animals collected in Mexico between 1990 and 1995 were characterized by using anti-nucleoprotein monoclonal antibodies and limited sequence analysis of the nucleoprotein gene. The variants of rabies viruses identified in these samples were compared with other isolates from Mexico and the rest of the Americas to establish epidemiologic links between cases and outbreaks and to increase the understanding of rabies epidemiology in the Western Hemisphere. Antigenic and genetic diversity was found in all samples from dogs and dog-related cases, suggesting a long-term endemic situation with multiple, independent cycles of virus transmission. Two isolates from bobcats were antigenically and genetically homologous to the rabies variant circulating in the Arizona gray fox population, indicating a wider distribution of this variant than previously reported. Rabies isolates from skunks were unrelated to any variant analyzed in this study and represent a previously unrecognized cycle of rabies transmission in skunks in Baja California Sur. Two antigenic and genetic variants co-circulating in southern and eastern Mexico were found in viruses obtained from cases epidemiologically related to vampire bats. These results serve as a baseline for the better understanding of the molecular epidemiology of rabies in Mexico.

Ecology and evolution of rabies virus in Europe

The evolution of rabies viruses of predominantly European origin was studied by comparing nucleotide sequences of the nucleoprotein and glycoprotein genes, and by typing isolates using RFLP. Phylogenetic analysis of the gene sequence data revealed a number of distinct groups, each associated with a particular geographical area. Such a pattern suggests that rabies virus has spread westwards and southwards across Europe during this century, but that physical barriers such as the Vistula river in Poland have enabled localized evolution. During this dispersal process, two species jumps took place - one into red foxes and another into raccoon dogs, although it is unclear whether virus strains are preferentially adapted to particular animal species or whether ecological forces explain the occurrence of the phylogenetic groups.

Molecular epidemiology of rabies in Thailand

For the purpose of making clear the dynamics of rabies viruses that are prevalent among dogs in Asia, especially Thailand, nucleoprotein (N) genes of isolates derived from Thailand were partially sequenced, and a phylogenetic analysis was performed on the basis of the sequencing data. Firstly, all 27 isolates from Thailand belonged to one group that was distantly related to an isolate from China and was separated into at least six lineages. On the other hand, the isolate from Japan was related to viruses from the Arctic. Secondly, in order to analyze the diversity of the N gene more conveniently, restriction fragment length polymorphism (RFLP) analysis was performed on the N gene of 27 isolates from Thailand. The RFLP analysis could distinguish the lineages of each isolate, and the lineages of additional 34 isolates were deduced by this method. On examination of the geographical distribution of the six lineages, based on the results of phylogenetic and RFLP analyses, it was clear that infection cycles of the rabies virus in Thailand have tended to be maintained endemically.

Typing of rabies virus isolates by DNA enzyme immunoassay

BACKGROUND

Alternatives to antigenic typing are needed for epidemiologic surveys of the rabies virus associated with translocated coyotes and foxes, especially in areas where a closely related rabies virus is transmitted by striped skunks.

OBJECTIVES

We developed and evaluated two enzyme based typing methods for rabies virus. The products of a reverse transcription-polymerase chain reaction (RT/PCR) of the nucleoprotein gene were hybridized to type specific probes and detected by enzyme assay after immobilization on microtiter plates.

STUDY DESIGN

We tested RT/PCR products of 27 rabies isolates by two different DNA enzyme immunoassays (DEIA) and evaluated the quality of the results from the corresponding nucleotide sequence of the samples.

RESULTS

Using a set of two probes, one of the DEIAs correctly identified 26/27 samples as variants of rabies virus associated with either skunks, foxes, or coyotes. The identity of one fox rabies sample was unresolved by this assay. The second DEIA correctly identified 24/27 samples as variants of rabies virus associated with either skunks, foxes, or coyotes. This assay did not resolve the identity of two fox rabies samples, and misidentified one fox rabies sample as a skunk rabies sample.

CONCLUSIONS

DEIA can be used for epidemiologic studies of variants of rabies virus associated with skunks, foxes, and coyotes. Both DEIA methods were effective when typing probes recognized changes at a minimum of two nucleotide positions between variants, but only one assay method was sufficiently stringent to detect a single base pair mismatch. The inherent mutability of RNA viruses must be considered when designing and evaluating typing methods.

A nucleotide-specific polymerase chain reaction assay to differentiate rabies virus biotypes in South Africa

Antigenic and nucleotide sequence analyses have shown that two distinct biotypes of rabies virus are circulating in South Africa. One of these typically infects members of the family Canidae, while the other comprises a heterogeneous group of apparently indigenous viruses, infecting members of the Viverridae family. In recent times, it has become evident that a considerable amount of cross-infection may occur and the manifestation of viverrid rabies in non-viverrid animals in particular appears to have become more commonplace. Consequently, the need to rapidly distinguish between rabies virus biotypes has become increasingly important in efforts to monitor the epidemiology of rabies in the southern African region. In this study, a nested polymerase chain reaction (PCR) assay was developed to distinguish between these two groups of rabies viruses. Consensus oligonucleotides were used to amplify the cytoplasmic domain of the rabies virus glycoprotein and the adjacent intergenic region. The resultant amplicon was subsequently used as template in second round heminested PCR in the presence of type-specific primers, thereby successfully generating amplicons of characteristic size for each biotype.

Polymerase chain reaction protocols for rabies virus discrimination

The development of RT PCR methodology has facilitated greatly the genetic characterisation of many rabies viruses (RVs), distinct strains of which persist in certain host species reservoirs within geographically defined regions. The relative temporally conserved nature of certain regions of the RV genome, particularly the N gene, permits development of rapid molecular methods for RV typing. Two main strategies have been applied to viral discrimination: (1) restriction fragment length polymorphism (RFLP) of PCR products and (2) strain-specific PCR (SS-PCR), in which sequences of specific viral strains are amplified differentially using strain-specific primers. Both these approaches have yielded methods of value to rabies epidemiological studies and control programs in Ontario. These procedures have facilitated the identification of intra-strain variants of the arctic fox strain, the only terrestrial RV strain persisting in the area, and they allow rapid discrimination of this strain from those circulating in insectivorous bat reservoirs and from the foreign raccoon strain, which continues to spread throughout the northeastern US and threatens to enter Ontario. Such methods can be adapted readily for use in other regions harbouring multiple overlapping RV reservoirs.

Nucleoprotein gene analysis of fixed and street rabies virus variants using RT-PCR

A simple and rapid single-step reverse transcriptase-polymerase chain reaction (RT-PCR) was used to investigate the nucleoprotein (N) gene of 11 rabies viruses. A conserved set of RT-PCR primers was designed to amplify the most variable region in the N gene. N gene regions were amplified from 6 fixed laboratory viruses, 4 street viruses from dogs in Thailand, and a horse in Zambia. Sequences of the amplified products, together with the database of 91 additional sequences, were analyzed by using PILEUP program of the GCG package. The rabies viruses grouped into at least 9 distinct clusters by < 90% nucleotide similarity of the N gene region: I (4 isolates, USA), II (2 isolates, South America), III (3 isolates, Africa), IV (52 strains, Europe, Middle East, Africa and South America), V (16 isolates, North America and Arctic), VI (17 isolates, Africa), VII (1 isolate, Africa), VIII (6 isolates, Thailand and Malaysia) and IX (1 isolate, Sri Lanka). A unique group of rabies viruses from Thailand and clusters of isolates corresponding to their geographic origin also were determined. The simple and rapid single-step RT-PCR proved to be useful for identifying rabies viruses, and for grouping the viruses into clades by sequence analysis.

Rabies virus quasispecies: implications for pathogenesis

Passage of the mouse-adapted rabies virus strain CVS-24 (where CVS is challenge virus standard) in BHK cells results in the rapid selection of a dominant variant designated CVS-B2c that differs genotypically and phenotypically from the dominant variant CVS-N2c present in mouse-brain- or neuroblastoma-cell-passaged CVS-24. The glycoprotein of CVS-B2c has 10 amino acid substitutions compared with that of CVS-N2c. Because CVS-B2c can be reproducibly selected in BHK cells, it is likely to be a conserved minor subpopulation of CVS-24. CVS-N2c is more neurotropic in vitro and in vivo than CVS-B2c, which replicates more readily in nonneuronal cells in vitro and in vivo. These characteristics appear to be relevant to the pathogenicity of the two variants. CVS-N2c is more pathogenic for adult mice than CVS-B2c. In contrast, CVS-B2c is more pathogenic for neonatal mice. These differences in pathogenicity are reflected in the selection pattern when mixtures of CVS-N2c and CVS-B2c were used to infect neonatal and adult mice. Although CVS-N2c was highly selected in adult mice, no selection for either variant was seen in neonates, suggesting that certain aspects of development, such as maturation of the nervous and immune systems, may contribute to the selection process. We speculate that the existence of different variants within a rabies virus strain may facilitate the virus in overcoming barriers to its spread, both within the host and between species.

Rapid detection of rabies and rabies-related viruses by RT-PCR and enzyme-linked immunosorbent assay

A rapid detection method for the six established genotypes of rabies and rabies-related viral RNA using RT-PCR-ELISA is described. The detection of digoxigenin-labelled amplified products is performed by solution hybridization to two specific, biotin-labelled, capture probes, which are complementary to the inner region of the amplification products. The capture probe and amplified product hybrid are then immobilised on a streptavidin-coated microtitre plate, bound products are detected by an anti-DIG Fab fragment conjugated to peroxidase, and colorimetric reaction automatically measured. This method was up to 100-fold more sensitive than Southern blot hybridization, detecting 0.00002 TCID50/ml of a genotype 1, classical rabies virus strain. The complete detection methodology from RT-PCR to PCR-ELISA detection could be completed within 10 h. Using this procedure, we were 100% successful in detecting 60 isolates from a representative selection of the six established genotypes from all over the world. This test is a useful additional tool for the detection of the rabies and rabies-related viruses, which is easy to perform, rapid and highly sensitive.

Natural spillover of a distinctly Canidae-associated biotype of rabies virus into an expanded wildlife host range in southern Africa

Rabies enzootics in southern Africa are associated with two genetically distinct groups of viruses, thought to be adapted to two different sets of host species. The virus groups are referred to as the canid biotype (infecting carnivores of the family Canidae) and the viverrid biotype (infecting carnivores of the subfamily Viverrinae). Cross- or spillover infections of one biotype into the host range of the other are thought to occur from time to time. However, very little is known about this phenomenon and its role in the epidemiology of rabies in southern Africa. We have investigated spillover by monoclonal antibody and nucleic acid sequence analysis of a wide range of virus isolates. Although the inverse had been documented, this report constitutes the first evidence of spillover of canid biotype viruses into viverrid hosts. Our genetic analysis was focused specifically on the G-L intergenic region of the virus genome, thought to be a remnant or pseudogene and it was indicated that, with respect to this region of the genome, spillover does not influence the phylogeny of virus isolates.

Heminested PCR assay for detection of six genotypes of rabies and rabies-related viruses

A heminested reverse transcriptase PCR (hnRT-PCR) protocol which is rapid and sensitive for the detection of rabies virus and rabies-related viruses is described. Sixty isolates from six of the seven genotypes of rabies and rabies-related viruses were screened successfully by hnRT-PCR and Southern blot hybridization. Of the 60 isolates, 93% (56 of 60) were positive by external PCR, while all isolates were detected by heminested PCR and Southern blot hybridization. We also report on a comparison of the sensitivity of the standard fluorescent-antibody test (FAT) for rabies antigen and that of hnRT-PCR for rabies viral RNA with degraded tissue infected with a genotype 1 virus. Results indicated that FAT failed to detect viral antigen in brain tissue that was incubated at 37 degrees C for greater than 72 h, while hnRT-PCR detected viral RNA in brain tissue that was incubated at 37 degrees C for 360 h.

An outbreak of vampire bat-transmitted rabies in cattle in northeastern Mexico

An outbreak of bovine rabies occurred on a ranch when cattle were bitten by vampire bats. Microscopic lesions showed a nonsuppurative encephalitis with intracytoplasmic inclusion bodies. Immunohistochemistry demonstrated viral antigen in the brain, and monoclonal antibodies identified a serotype 1 (vampire strain) of the rabies virus.