Rapid identification of the raccoon rabies virus variant using a real-time reverse-transcriptase polymerase chain reaction.

The raccoon-associated variant of rabies virus (RRV) is enzootic throughout the eastern seaboard of the United States with frequent incursions into Canada. Many wildlife management agencies are actively engaged in control programmes targeting elimination of this disease and rapid identification of raccoon rabies cases is crucial to the success of these operations. This report documents the development of a reverse transcriptase real-time PCR (RT-qPCR) that specifically identifies this rabies virus variant (RRV RT-qPCR) and which can be readily multiplexed with a generic rabies virus RT-qPCR for use as a typing tool. Using a large collection of rabies virus samples representative of the variants circulating around the world, but with a focus on those occurring in the Americas, the RRV RT-qPCR was 100% sensitive and 99.31% specific. To further apply these assays for diagnostic purposes, addition of an RT-qPCR targeting the host ß-actin mRNA, which serves as an internal amplification control, in a triplex format was shown to yield highly comparable results using a subset of our viral collection. Use of these assays for early and accurate identification of this viral variant will help to optimize the utilization of resources required for control of this disease.

A real-time PCR regimen for testing environmental samples for Salmonella enterica subsp. enterica serovars of concern to the poultry industry, with special focus on Salmonella Enteritidis.

A real-time PCR (qPCR) regimen, using up to six genetic targets, was developed to rapidly detect Salmonella and in particular identify Salmonella Enteritidis. The test regimen was first evaluated using a reference culture collection of Salmonella to confirm the appropriateness of the selected targets, which included up to three genetic markers for discrimination of Salmonella Enteritidis from other Salmonella serovars commonly found in poultry facilities. The qPCR procedure was then compared with culture methods used to detect Salmonella using a collection of enrichment broths previously generated from 239 environmental samples collected from a large number of hatchery facilities across Canada over several years. The qPCR regimen facilitated specific detection of Salmonella Enteritidis, and on a sample basis, it showed excellent agreement with the culture methods. Moreover, in many cases, qPCR detected Salmonella earlier in the culture process than did the culture method. Application of this method will significantly shorten test times and allow more timely identification of infected poultry premises, thereby improving present programmes aimed at controlling Salmonella Enteritidis at the environmental source.

Geography but not alternative host species explain the spread of raccoon rabies virus in Vermont.

In North America, the raccoon-associated variant of rabies virus (RRV) is of special concern, given its relatively rapid spread throughout the eastern USA and its potential public health impact due to high raccoon host densities in urban areas. Northward expansion of this epizootic included an outbreak in the Canadian province of Quebec in 2006-2009 due to trans-border spread from the State of Vermont. To inform a more proactive approach to future control efforts, this study uses phylogenetic analyses to explore the role of geography and alternative carnivore hosts in the dynamics of RRV spread within Vermont. Specifically, we sought to examine whether striped skunks, a species frequently infected by RRV, could be part of the maintenance host community. Whole genome sequencing of 160 RRV samples from Vermont and neighbouring US states were used for fine-scale phylogeographic analyses. Results, together with the complete surveillance record of raccoon rabies since its entry into Vermont in 1994, document incursions by two distinct viral lineages and identify topographical features of the landscape which have significantly influenced viral spread, resulting in a complex distribution pattern of viral variants throughout the state. Results of phylogenetic cluster analysis and discrete state reconstruction contained some evidence of skunk-to-skunk and skunk-to-raccoon transmission but overall failed to support a role for skunks as alternative maintenance hosts.

Genomic sequencing, evolution and molecular epidemiology of rabies virus.

Advances in sequencing techniques, improved computational methods of sequence interrogation and more accurate collection of epidemiological data through Global Positioning System (GPS) technology are improving our ability to monitor rabies outbreaks and better understand the processes that affect viral spread, evolution and host restriction. Whole-genome sequencing of rabies viruses (RABVs), using a range of different methodological approaches, is becoming more widespread and permits evolutionary and epidemiological studies at an unprecedented rate. Such studies are yielding insights into the fundamental processes of viral evolution, including molecular mechanisms of host adaptation and viral emergence in novel hosts. In addition, sequence data are revealing the importance of both landscape features and anthropomorphic activities as drivers of rabies spread; knowledge that is crucial for disease control efforts. This review summarises the state of the RABV genomics field and suggests how the above-mentioned approaches can be used to further understand and develop intervention strategies for rabies in the future.

Les avancées enregistrées dans les techniques de séquençage, l'amélioration des logiciels d'interrogation des banques de séquences et la collecte plus précise de données épidémiologiques grâce aux systèmes de géolocalisation par satellite (GPS) renforcent nos capacités de surveillance des foyers de rage et nous aident à mieux comprendre les processus qui influent sur la propagation du virus, sur son évolution et sur les contraintes liées aux hôtes. Le séquençage du génome entier des virus de la rage au moyen d'approches méthodologiques diverses se généralise de plus en plus, permettant d'étudier à un rythme jamais atteint auparavant l'évolution et l'épidémiologie de ces virus. Ces études apportent de nouveaux éclairages sur les processus fondamentaux de l'évolution des virus, y compris les mécanismes moléculaires sous-jacents à l'adaptation des hôtes et à l'émergence virale chez de nouveaux hôtes. En outre, les données de séquençage mettent en lumière le rôle de l'environnement et des activités humaines sur la propagation de la rage, rôle dont la connaissance est déterminante pour lutter efficacement contre la maladie. Les auteurs font le point sur l'état des connaissances dans le domaine de la génomique des virus de la rage et proposent quelques pistes afin d'utiliser ces approches pour approfondir et développer davantage les futures stratégies d'intervention contre la rage.

Gracias al progreso de las técnicas de secuenciación, a la mejora de los métodos informáticos para estudiar las secuencias y a una obtención más exacta de datos epidemiológicos mediante la tecnología del sistema de posicionamiento mundial (GPS), hoy estamos en mejores condiciones para seguir de cerca los brotes de rabia y conocer más a fondo los procesos que inciden en la propagación y evolución del virus y en los factores de restricción de los anfitriones. La secuenciación del genoma entero de virus rábicos con muy diversos enfoques metodológicos, cada vez más extendida, permite hoy realizar estudios evolutivos y epidemiológicos a un ritmo sin precedentes. Estos estudios están arrojando luz sobre los procesos fundamentales de la evolución vírica, incluidos los mecanismos moleculares de la adaptación al anfitrión y la aparición del virus en nuevos anfitriones. Además, los datos de secuenciación están revelando la importancia de las características del paisaje y de las actividades antrópicas como factores de propagación de la rabia, un conocimiento crucial para la labor de lucha contra la enfermedad. Los autores resumen la situación de la genómica aplicada a los virus rábicos y explican cómo utilizar estos métodos para entender mejor la enfermedad y perfeccionar las estrategias de intervención contra ella en el futuro.

Raccoon rabies outbreak in Hamilton, Ontario: A progress report.

BACKGROUND: Raccoon rabies is caused by a variant of the rabies virus found in raccoons but transmissible to other mammalian species, including humans. The disease of rabies caused by raccoon variant rabies virus is indistinguishable from rabies caused by other rabies virus variants. OBJECTIVE: This paper describes the raccoon rabies outbreak in Ontario (identified in December 2015) and the control measures undertaken to curb the spread of the epizootic using the One Health approach. INVESTIGATION AND RESULTS: Representatives from local, provincial and federal agencies collectively activated a raccoon rabies response that involved policy updates, enhanced surveillance, a public education campaign and mass vaccination of wildlife and domestic animals. Between December 2015 and June 2017, 338 animals tested positive for raccoon rabies in Ontario. While the majority of the cases were raccoons, there was significant spillover into striped skunks, as well as other species including two cats, a fox and a llama. Viral genome sequencing determined that this epizootic was likely caused by long-distance translocation from the United States. CONCLUSION: This outbreak of raccoon rabies is by far the largest to have occurred in Canada and the first raccoon rabies outbreak documented in a densely populated urban area. This is also the first time this rabies virus variant has been identified in a domestic animal in Canada. A collaborative approach involving numerous stakeholders in the public and private sectors has been instrumental in addressing this epizootic. Though case incidence appears to be declining, several years will likely be required to reach elimination. Continued collaboration between these agencies is necessary to achieve this goal.

Transmission of bovine viral diarrhea virus (BVDV) via in vitro-fertilized embryos to recipients, but not to their offspring.

The objective was to assess the potential of Day-7, IVP zona pellucida-intact blastocysts to transmit bovine viral diarrhea virus (BVDV) to embryo recipients. Embryos were exposed (1h) to two non-cytopathic (NCP) biotypes, either NY-1 (type 1) or two concentrations of PA-131 (type 2), washed 10 times, and transferred into recipients (two embryos/recipient) free of BVDV and its antibody. Six (30.0%) of the 20 pregnancies were lost after 30 d following transfer of the embryos exposed to the type 1 strain; none of the recipients or their 18 full term offspring seroconverted. Conversely, following exposure to the type 2 strain, 16 (51.6%) of the 31 pregnancies were lost >30 d after embryo transfer. Furthermore, 18 (51.4%) of 35 recipients receiving embryos exposed to type 2 seroconverted; 11 of those were pregnant at 30 d, but only 2 went to full term and gave birth to noninfected (seronegative) calves. Virus isolation tests were performed on single, virus-exposed, washed embryos (not transferred); 3 of 12 (25%) and 17 of 61 (28%) exposed to type 1 and type 2, respectively, were positive for live BVDV. Embryos exposed to type 2 virus had from 0 to 34 viral copies. In conclusion, a large proportion of recipients that received embryos exposed to BVDV, especially those exposed to a high concentration of type 2 virus, became infected after ET, and their pregnancies failed. However, term pregnancies resulted in calves free of both virus and antibody. Therefore, additional disinfection procedures are recommended prior to transferring potentially infected IVP embryos.

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.

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.

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%.

Molecular and antigenic characterization of rabies viruses from Iran identifies variants with distinct epidemiological origins.

A molecular epidemiological study of 48 recent rabies isolates recovered from cases reported throughout Iran identified three distinct viral variants, the evolutionary origins of which were identified by phylogenetic comparison with rabies viruses originating from Europe and Asia. Members of group 1 (15 isolates) were recovered from the northern half of the country only, while those of group 2 (31 isolates) were widely dispersed; both groups clustered within the widely disseminated cosmopolitan lineage. The two isolates of group 3 were detected in the northeastern tip of the country only and belonged to the Arctic strain. Rapid variant discrimination tools, employing restriction fragment length polymorphisms applied to amplified fragments of the viral genome, were devised whilst antigenic characterization of representative viruses identified a small panel of monoclonal antibodies that were also discriminatory. The future application of such methods should provide valuable epidemiological information on rabies incidence in Iran.

Adherence of bovine viral diarrhea virus to bovine oocytes and embryos with a hardened zona pellucida cultured in vitro.

The purpose of this study was to investigate the adherence of bovine viral diarrhea virus (BVDV) to bovine mature, or immature, cumulus-free oocytes and to in vitro fertilized embryos, maintained in vitro in a ligated bovine oviduct to allow for the hardening of the zona pellucida. Incubation of the oocytes and embryos in the oviduct for 5 h caused hardening of the zona pellucida as measured by resistance to pronase digestion (which increased from approximately 3 min to 7 h; P > 0.001). However, there was no difference between the number of infected oocytes and embryos (n = 965 in 193 samples) following experimental exposure to BVDV regardless of whether or not they were previously incubated in the oviduct (P > 0.05). It was concluded that the modification of the proteolytic resistance properties of the zona pellucida during in vitro oviductal incubation did not influence the adherence of BVDV to zona pellucida of oocytes or in vitro fertilized embryos.

Lyssavirus P gene characterisation provides insights into the phylogeny of the genus and identifies structural similarities and diversity within the encoded phosphoprotein.

A comprehensive phylogenetic analysis of the Lyssavirus genus, employing P gene sequences from 128 isolates recovered globally, is presented. While confirming prior suggestions of the genetic distinctness of the Australian bat lyssaviruses, these data also revealed a clear division within the rabies virus clade (Genotype 1) between globally distributed viruses circulating predominantly in canid species (subgroup 1-1), and American strains harbored by both chiropteran and terrestrial hosts (subgroup 1-2). Nucleotide substitution patterns within the P locus suggested differential selection operating along the length of the open reading frame (ORF) between rabies viruses of these two subgroups. Comparison of the deduced primary sequences of the encoded phosphoproteins of all isolates provided insights into the product's structural organization. Two conserved (CD1,2) and two variable (VD1,2) domains were evident; high variation in the VD2 region was reflected by differences in hydropathic profiles. Only two of five serine residues reported to function as phosphate acceptors in the P protein of the rabies challenge virus standard (CVS) strain were absolutely conserved; similarly, out of four internal methionines reported to direct internal translation initiation of the CVS strain to produce N-terminally truncated P proteins, only Met(20) was universally retained. In contrast, two sequence motifs, one believed to confer binding to the cytoplasmic dynein light chain LC8, and a lysine-rich sequence probably contributing to N protein binding, were conserved throughout the genus. Most rabies viruses of the carnivora (1-1) contain a potential C ORF in alternate frame to that of P, a feature limited or absent in most other isolates of the genus, an observation interpreted with consideration to the predicted course of lyssavirus evolution.

Experimental collection and transfer of embryos from bovine immunodeficiency virus (BIV) infected cattle.

Three experiments were conducted to determine whether the lentivirus, bovine immunodeficiency virus (BIV) is likely to be transmitted via embryo transfer. In the first experiment, embryos collected from BIV-negative heifers were exposed in vitro to BIV for 24 h, washed and then tested for the presence of the provirus. In the second experiment, embryos obtained from BIV-negative heifers were transferred to the uterine horns of BIV-infected heifers; 24 h later these embryos were recovered and tested for the presence of BIV. In the third experiment, embryos were collected from heifers experimentally infected with BIV and then transferred to BIV-negative recipients. In all three experiments, (BIV) proviral DNA was not detected by PCR in association with any oocytes, embryos, follicular fluid, oviductal or uterine washes. Twelve single embryos collected from BIV experimentally infected donors were transferred to BIV-negative recipients resulting in the birth of 7 calves all of which were also negative for BIV; the recipients remained BIV-negative throughout the experiment. In conclusion, this study demonstrates that it is possible to produce transferrable stage embryos from donors infected with BIV and that such embryos are unlikely to transmit this agent either to the recipients or the resulting offspring.

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.

Bovine immunodeficiency virus in relation to embryos fertilized in vitro.

The association of bovine immunodeficiency virus (BIV) with embryos derived by in vitro fertilization from oocytes of experimentally infected heifers or oocytes/embryos exposed to the virus in vitro was investigated. Using a nested-PCR assay, proviral DNA of BIV was not detected in follicular fluid or in embryos derived from BIV-infected donors. In vitro exposure of oocytes to BIV during maturation or insemination with BIV-infected semen resulted in zona pellucida-intact embryos testing negative for BIV provirus. However, exposure of zona pellucida-free day-7 embryos to the virus resulted in a positive BIV assay for 28% of the batches of embryos, suggesting that the zona pellucida has a role in protecting against BIV infection. The presence of BIV in the IVF system had no apparent effect on the development of bovine embryos to the blastocyst stage.

Viral contamination of embryos cryopreserved in liquid nitrogen.

Despite the worldwide application of embryo-freezing technology as the means of preserving germplasm of mammalian species, there is no information available on the possible transmission of infectious agents to cryopreserved embryos via contaminated liquid nitrogen (LN). Recently, it has been reported that new methods of cryopreservation which employ ultrarapid freezing or vitrification require direct contact between the freezing medium containing oocytes or embryos and liquid phase nitrogen (LPN). As models for human and animal viral pathogens three bovine viruses, bovine viral diarrhea virus (BVDV), bovine herpesvirus-1 (BHV), and bovine immunodeficiency virus (BIV), were employed to study the potential for their transmission by experimentally contaminated LN to embryos frozen and stored in open freezing containers. Bovine embryos in a mixture of 20% ethylene glycol, 20% ME(2)SO, and 0.6% sucrose were vitrified in either unsealed standard 0.25 ml or modified open pulled straws or in plastic cryovials and then plunged into contaminated LPN. After 3-5 weeks of storage in LN, embryos were thawed and sequentially washed and only those with intact ZP were pooled together and tested in batches of three for viral contamination. From this pool of 83 batches, 13 of 61 (21.3%) batches exposed to BVDV and BHV-1 tested positive for viral association while all 22 batches exposed to BIV in unsealed containers tested negative. All control embryos vitrified in sealed cryovials and straws were free from viral contamination.

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.

Relationship between egg size and subgroup J avian leukosis virus in eggs from broiler breeders.

Hatching eggs from three broiler breeder flocks that had experienced losses from myeloid leukosis were tested for infection with avian leukosis virus of subgroup J (ALV-J). Sufficient eggs were positive in two flocks to relate infection to egg weight. Allantoic fluid, embryonic tissue and yolk were collected after 18 days of incubation. The albumen and allantoic fluid were tested by enzyme-linked immunosorbent assay (ELISA) for group-specific (gs) antigen and all specimens were inoculated onto cell cultures to test for virus by immunofluorescence assay. Virus detected was identified as ALV-J by polymerase chain reaction techniques. The percentage of eggs that tested positive for gs antigen and virus was higher in those that weighed under 60 g than in heavier eggs (P < 0.01). In one flock, antibody to ALV-J was detected by ELISA in yolk from 14 and 43% of the eggs that tested positive or negative for virus, respectively. Testing the same eggs for antigen, virus and antibody should be useful for establishing the status of infection of the hens.