Molecular double-check strategy for the identification and characterization of European Lyssaviruses

Detection and Serological Evidence of European Bat Lyssavirus 1 in Belgian Bats between 2016 and 2018

Lyssaviruses are neurotropic viruses capable of inducing fatal encephalitis. While rabies virus has been successfully eradicated in Belgium, the prevalence of other lyssaviruses remains uncertain. In this study, we conducted a survey on live animals and passive surveillance to investigate the presence of lyssaviruses in Belgium. In 2018, a total of 113 saliva samples and 87 blood samples were collected from bats. Saliva was subjected to RT-qPCR to identify lyssavirus infections. Additionally, an adapted lyssavirus neutralisation assay was set up for the detection of antibodies neutralising EBLV-1 in blood samples. Furthermore, we examined 124 brain tissue samples obtained from deceased bats during passive surveillance between 2016 and 2018. All saliva samples tested negative for lyssaviruses. Analysis of the blood samples uncovered the presence of lyssavirus-neutralising antibodies in five bat species and 32% of samples with a wide range depending on bat species, suggesting past exposure to a lyssavirus. Notably, EBLV-1 was detected in brain tissue samples from two Eptesicus serotinus specimens collected in 2016 near Bertrix and 2017 near Étalle, confirming for the first time the presence of EBLV-1 in Belgium and raising awareness of the potential risks associated with this species of bats as reservoirs of the virus.

Lack of detection of SARS-CoV-2 in wildlife from Kerala, India in 2020-21

Spillover of SARS-CoV-2 into a variety of wild and domestic animals has been an ongoing feature of the human pandemic. The establishment of a new reservoir in white-tailed deer in North America and increasing divergence of the viruses circulating in them from those circulating in the human population has highlighted the ongoing risk this poses for global health. Some parts of the world have seen more intensive monitoring of wildlife species for SARS-CoV-2 and related coronaviruses but there are still very large gaps in geographical and species-specific information. This paper reports negative results for SARS-CoV-2 PCR based testing using a pan coronavirus end point RDRP PCR and a Sarbecovirus specific E gene qPCR on lung and or gut tissue from wildlife from the Indian State of Kerala. These animals included: 121 Rhinolophus rouxii (Rufous Horsehoe Bat), six Rhinolophus bedommei (Lesser Woolly Horseshoe Bat), 15 Rossettus leschenaultii (Fulvous Fruit Bat), 47 Macaca radiata (Bonnet macaques), 35 Paradoxurus hermaphroditus (Common Palm Civet), five Viverricula indica (Small Indian Civet), four Herpestes edwardsii (Common Mongoose), ten Panthera tigris (Bengal Tiger), eight Panthera pardus fusca (Indian Leopard), four Prionailurus bengalensis (Leopard cats), two Felis chaus (Jungle cats), two Cuon alpinus (Wild dogs) and one Melursus ursinus (sloth bear).

Lack of detection of SARS-CoV-2 in British wildlife 2020-21 and first description of a stoat (Mustela erminea) Minacovirus

Repeat spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into new hosts has highlighted the critical role of cross-species transmission of coronaviruses and establishment of new reservoirs of virus in pandemic and epizootic spread of coronaviruses. Species particularly susceptible to SARS-CoV-2 spillover include Mustelidae (mink, ferrets and related animals), cricetid rodents (hamsters and related animals), felids (domestic cats and related animals) and white-tailed deer. These predispositions led us to screen British wildlife with sarbecovirus-specific quantitative PCR and pan coronavirus PCR assays for SARS-CoV-2 using samples collected during the human pandemic to establish if widespread spillover was occurring. Fourteen wildlife species (n=402) were tested, including: two red foxes (Vulpes vulpes), 101 badgers (Meles meles), two wild American mink (Neogale vison), 41 pine marten (Martes martes), two weasels (Mustela nivalis), seven stoats (Mustela erminea), 108 water voles (Arvicola amphibius), 39 bank voles (Myodes glareolous), 10 field voles (Microtus agrestis), 15 wood mice (Apodemus sylvaticus), one common shrew (Sorex aranaeus), two pygmy shrews (Sorex minutus), two hedgehogs (Erinaceus europaeus) and 75 Eurasian otters (Lutra lutra). No cases of SARS-CoV-2 were detected in any animals, but a novel minacovirus related to mink and ferret alphacoronaviruses was detected in stoats recently introduced to the Orkney Islands. This group of viruses is of interest due to pathogenicity in ferrets. The impact of this virus on the health of stoat populations remains to be established.

Metagenomic Sequencing of Lloviu Virus from Dead Schreiber's Bats in Bosnia and Herzegovina

Bats are a natural host for a number of viruses, many of which are zoonotic and thus present a threat to human health. RNA viruses of the family Filoviridae, many of which cause disease in humans, have been associated with specific bat hosts. Lloviu virus is a Filovirus which has been connected to mass mortality events in Miniopterus schreibersii colonies in Spain and Hungary, and some studies have indicated its immense zoonotic potential. A die-off has been recorded among Miniopterus schreibersii in eastern Bosnia and Herzegovina for the first time, prompting the investigation to determine the causative agent. Bat carcasses were collected and subjected to pathological examination, after which the lung samples with notable histopathological changes, lung samples with no changes and guano were analyzed using metagenomic sequencing and RT-PCR. A partial Lloviu virus genome was sequenced from lung samples with histopathological changes and found to be closely related to Hungarian and Italian virus sequences. Further accumulation of mutations on the GP gene, coding the glycoprotein responsible for cell tropism and host preference, enhances the need for further characterization and monitoring of this virus to prevent spillover events and protect human health.

Comparison of Pan-Lyssavirus RT-PCRs and Development of an Improved Protocol for Surveillance of Non-RABV Lyssaviruses

Rabies is a zoonotic and fatal encephalitis caused by members of the Lyssavirus genus. Among them, the most relevant species is Lyssavirus rabies, which is estimated to cause 60,000 human and most mammal rabies deaths annually worldwide. Nevertheless, all lyssaviruses can invariably cause rabies, and therefore their impact on animal and public health should not be neglected. For accurate and reliable surveillance, diagnosis should rely on broad-spectrum tests able to detect all known lyssaviruses, including the most divergent ones. In the present study, we evaluated four different pan-lyssavirus protocols widely used at an international level, including two real-time RT-PCR assays (namely LN34 and JW12/N165-146), a hemi-nested RT-PCR and a one-step RT-PCR. Additionally, an improved version of the LN34 assay ((n) LN34) was developed to increase primer–template complementarity with respect to all lyssavirus species. All protocols were evaluated in silico, and their performance was compared in vitro employing 18 lyssavirus RNAs (encompassing 15 species). The (n) LN34 assay showed enhanced sensitivity in detecting most lyssavirus species, with limits of detection ranging from 10 to 100 RNA copies/µL depending on the strain, while retaining high sensitivity against Lyssavirus rabies. The development of this protocol represents a step forward towards improved surveillance of the entire Lyssavirus genus.

Rustrela virus infection - An emerging neuropathogen of red-necked wallabies (Macropus rufogriseus)

The rustrela virus (RusV) was recently described as a novel pathogen in a circumscribed area of northern Germany close to the Baltic Sea. Up to now, the virus has been detected in cases of fatal non-suppurative meningoencephalitis in zoo animals of different species and a single wild carnivore as well as in apparently healthy yellow-necked field mice (Apodemus flavicollis). Data regarding the background of this previously undiscovered pathogen, including clinical presentation of the disease, host range and distribution of the virus, are still limited. Here, three euthanized red-necked wallabies (Macropus rufogriseus) from zoos of different areas in northeastern Germany were submitted for necropsy after presenting with apathy and therapeutically unresponsive neurological signs. A moderate to severe, non-suppurative meningoencephalitis was diagnosed in all three cases. RusV was consistently detected via RT-qPCR and RNA in situ hybridization in the brains of all wallabies. Other commonly known neuropathogens could not be detected.

Comparative pathogenesis of different phylogroup I bat lyssaviruses in a standardized mouse model

A plethora of bat-associated lyssaviruses potentially capable of causing the fatal disease rabies are known today. Transmitted via infectious saliva, occasionally-reported spillover infections from bats to other mammals demonstrate the permeability of the species-barrier and highlight the zoonotic potential of bat-related lyssaviruses. However, it is still unknown whether and, if so, to what extent, viruses from different lyssavirus species vary in their pathogenic potential. In order to characterize and systematically compare a broader group of lyssavirus isolates for their viral replication kinetics, pathogenicity, and virus release through saliva-associated virus shedding, we used a mouse infection model comprising a low (10² TCID₅₀) and a high (10⁵ TCID₅₀) inoculation dose as well as three different inoculation routes (intramuscular, intranasal, intracranial). Clinical signs, incubation periods, and survival were investigated. Based on the latter two parameters, a novel pathogenicity matrix was introduced to classify lyssavirus isolates. Using a total of 13 isolates from ten different virus species, this pathogenicity index varied within and between virus species. Interestingly, Irkut virus (IRKV) and Bokeloh bat lyssavirus (BBLV) obtained higher pathogenicity scores (1.14 for IRKV and 1.06 for BBLV) compared to rabies virus (RABV) isolates ranging between 0.19 and 0.85. Also, clinical signs differed significantly between RABV and other bat lyssaviruses. Altogether, our findings suggest a high diversity among lyssavirus isolates concerning survival, incubation period, and clinical signs. Virus shedding significantly differed between RABVs and other lyssaviruses. Our results demonstrated that active shedding of infectious virus was exclusively associated with two RABV isolates (92% for RABV-DogA and 67% for RABV-Insectbat), thus providing a potential explanation as to why sustained spillovers are solely attributed to RABVs. Interestingly, 3D imaging of a selected panel of brain samples from bat-associated lyssaviruses demonstrated a significantly increased percentage of infected astrocytes in mice inoculated with IRKV (10.03%; SD±7.39) compared to RABV-Vampbat (2.23%; SD±2.4), and BBLV (0.78%; SD±1.51), while only individual infected cells were identified in mice infected with Duvenhage virus (DUVV). These results corroborate previous studies on RABV that suggest a role of astrocyte infection in the pathogenicity of lyssaviruses.

Globally, there are at present 17 different officially recognized lyssavirus species posing a potential threat for human and animal health. Bats have been identified as carriers for the vast majority of those zoonotic viruses, which cause the fatal disease rabies and are transmitted through infectious saliva. The occurrence of sporadic spillover events where lyssaviruses are spread from bats to other mammalian species highlights the importance of studying pathogenicity and virus shedding in regard to a potentially sustained onward cross-species transmission. Therefore, as part of this study, we compared 13 different isolates from ten lyssavirus species in a standardized mouse infection model, focusing on clinical signs, incubation periods, and survival. Based on the latter two, a novel pathogenicity index to classify different lyssavirus species was established. This pathogenicity index varied within and between different lyssavirus species and revealed a higher ranking of other bat-related lyssaviruses in comparison to the tested Rabies virus (RABV) isolates. Altogether, our results demonstrate a high diversity among the investigated isolates concerning pathogenicity and clinical picture. Furthermore, we comparatively analyzed virus shedding via saliva and while there was no indication towards a reduced pathogenicity of bat-associated lyssaviruses as opposed to RABV, shedding was increased in RABV isolates. Additionally, we investigated neuronal cell tropism and revealed that bat lyssaviruses are not only capable of infecting neurons but also astrocytes.

A New Molecular Detection System for Canine Distemper Virus Based on a Double-Check Strategy

Due to changing distemper issues worldwide and to inadequate results of an inter-laboratory study in Germany, it seems sensible to adapt and optimize the diagnostic methods for the detection of the canine distemper virus (CDV) to the new genetic diversity of virus strains. The goal of the project was the development, establishment and validation of two independent one-step reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) methods for the safe detection of CDV in domestic and wild animals. For this purpose, an existing CDV-RT-qPCR was decisively adapted and, in addition, a completely new system was developed. Both CDV-RT-qPCR systems are characterized by a very high, comparable analytical and diagnostic sensitivity and specificity and can be mutually combined with inhibition or extraction controls. The reduction in the master mix used allows for the parallel implementation of both CDV-RT-qPCR systems without significant cost increases. For validation of the new CDV-RT-qPCR duplex assays, a panel comprising 378 samples derived from Germany, several European countries and one African country were tested. A sensitivity of 98.9% and a specificity of 100% were computed for the new assays, thus being a reliable molecular diagnostic tool for the detection of CDV in domestic and wild animals.

Retrospective Enhanced Bat Lyssavirus Surveillance in Germany between 2018-2020

Lyssaviruses are the causative agents for rabies, a zoonotic and fatal disease. Bats are the ancestral reservoir host for lyssaviruses, and at least three different lyssaviruses have been found in bats from Germany. Across Europe, novel lyssaviruses were identified in bats recently and occasional spillover infections in other mammals and human cases highlight their public health relevance. Here, we report the results from an enhanced passive bat rabies surveillance that encompasses samples without human contact that would not be tested under routine conditions. To this end, 1236 bat brain samples obtained between 2018 and 2020 were screened for lyssaviruses via several RT-qPCR assays. European bat lyssavirus type 1 (EBLV-1) was dominant, with 15 positives exclusively found in serotine bats (Eptesicus serotinus) from northern Germany. Additionally, when an archived set of bat samples that had tested negative for rabies by the FAT were screened in the process of assay validation, four samples tested EBLV-1 positive, including two detected in Pipistrellus pipistrellus. Subsequent phylogenetic analysis of 17 full genomes assigned all except one of these viruses to the A1 cluster of the EBLV-1a sub-lineage. Furthermore, we report here another Bokeloh bat lyssavirus (BBLV) infection in a Natterer's bat (Myotis nattereri) found in Lower Saxony, the tenth reported case of this novel bat lyssavirus.

Multi-annual performance evaluation of laboratories in post-mortem diagnosis of animal rabies: Which techniques lead to the most reliable results in practice?

Rabies diagnosis proficiency tests on animal specimens using four techniques (FAT, RTCIT, conventional RT-PCR and real-time RT-PCR) were organised over 10 years (2009–2019). Seventy-three laboratories, of which 59% were from Europe, took part. As the panels were prepared with experimentally-infected samples, the error rate of laboratories on positive and negative samples was accurately estimated. Based on fitted values produced by mixed modelling including the variable “laboratory” as a random variable to take into account the longitudinal design of our dataset, the technique that provided the most concordant results was conventional RT-PCR (99.3%; 95% CI 99.0–99.6), closely followed by FAT (99.1%; 95% CI 98.7–99.4), real-time RT-PCR (98.7%; 95% CI 98.1–99.3) and then RTCIT (96.8%; 95% CI 95.8–97.7). We also found that conventional RT-PCR provided a better diagnostic sensitivity level (99.3% ±4.4%) than FAT (98.7% ±1.6%), real-time RT-PCR (97.9% ±0.8%) and RTCIT (95.3% ±5.1%). Regarding diagnostic specificity, RTCIT was the most specific technique (96.4% ±3.9%) followed closely by FAT (95.6% ±3.8%), real-time RT-PCR (95.0% ±1.8%) and conventional RT-PCR (92.9% ±0.5%). Due to multiple testing of the samples with different techniques, the overall diagnostic conclusion was also evaluated, and found to reach an inter-laboratory concordance level of 99.3%. The concordance for diagnostic sensitivity was 99.6% ±2.0% and for diagnostic specificity, 98.0% ±8.5%. Molecular biology techniques were, however, found to be less specific than expected. The potential reasons for such findings are discussed herein. The regular organisation of performance tests has contributed to an increase in the performance of participating laboratories over time, demonstrating the benefits of such testing. Maintaining a high-quality rabies diagnosis capability on a global scale is key to achieving the goal of eliminating dog-mediated human rabies deaths. The regular organisation of exercises on each continent using selected local strains to be tested according to the local epidemiological situation is one factor that could help increase reliable diagnosis worldwide. Rabies diagnosis capabilities could indeed be enhanced by providing adequate and sustainable proficiency testing on a large scale and in the long term

This study shares the rabies diagnosis proficiency test results of 73 laboratories on animal specimens using four techniques (FAT, RTCIT, conventional RT-PCR and real-time RT-PCR) organised over a 10-year period. This long-term exercise allowed us to compute accurate sensitivity and specificity values for the rabies diagnosis test for a large panel of laboratories. Conventional RT-PCR provided a better diagnostic sensitivity level than FAT, real-time RT-PCR and RTCIT. Regarding diagnostic specificity, RTCIT was the most specific technique followed closely by FAT, real-time RT-PCR and conventional RT-PCR. The specificity of molecular biology techniques was found to be lower than expected. The potential reasons for such findings are discussed herein. The regular organisation of performance tests has contributed to an increase in the performance of participating laboratories over time, demonstrating the likely benefits of such testing.

Neuroglia infection by rabies virus after anterograde virus spread in peripheral neurons

The highly neurotropic rabies virus (RABV) enters peripheral neurons at axon termini and requires long distance axonal transport and trans-synaptic spread between neurons for the infection of the central nervous system (CNS). Recent 3D imaging of field RABV-infected brains revealed a remarkably high proportion of infected astroglia, indicating that highly virulent field viruses are able to suppress astrocyte-mediated innate immune responses and virus elimination pathways. While fundamental for CNS invasion, in vivo field RABV spread and tropism in peripheral tissues is understudied. Here, we used three-dimensional light sheet and confocal laser scanning microscopy to investigate the in vivo distribution patterns of a field RABV clone in cleared high-volume tissue samples after infection via a natural (intramuscular; hind leg) and an artificial (intracranial) inoculation route. Immunostaining of virus and host markers provided a comprehensive overview of RABV infection in the CNS and peripheral nerves after centripetal and centrifugal virus spread. Importantly, we identified non-neuronal, axon-ensheathing neuroglia (Schwann cells, SCs) in peripheral nerves of the hind leg and facial regions as a target cell population of field RABV. This suggests that virus release from axons and infected SCs is part of the RABV in vivo cycle and may affect RABV-related demyelination of peripheral neurons and local innate immune responses. Detection of RABV in axon-surrounding myelinating SCs after i.c. infection further provided evidence for anterograde spread of RABV, highlighting that RABV axonal transport and spread of infectious virus in peripheral nerves is not exclusively retrograde. Our data support a new model in which, comparable to CNS neuroglia, SC infection in peripheral nerves suppresses glia-mediated innate immunity and delays antiviral host responses required for successful transport from the peripheral infection sites to the brain.

Armoured exogenous internal control for real-time PCR diagnosis of avian influenza

An exogenous "armoured" PCR internal control (IC) short RNA was analyzed in conjunction with real-time RT-PCR method for diagnosis of avian influenza. The resistance to nucleases and increased physical stability of the IC was ensured using branched polyethyleneimine (PEI) which was in complex with IC-RNA. The option to add the IC directly to pathological material suspensions allows measurement of the nucleic acids extraction efficiency. Stability of armoured RNA-IC during storage and tissue suspension preparation was shown. The advantage of exogenous "armoured" IC was demonstrated in the experiment with AIV genome detection by qPCR in samples from different species of wild birds. The exogenous IC gave reproducible homogeneous Ct values in all tests.

Evaluation of six TaqMan RT-rtPCR kits on two thermocyclers for the reliable detection of rabies virus RNA

Rabies is diagnosed postmortem in animals, based on tests prescribed by the World Organization for Animal Health (OIE), such as the fluorescent antibody test, the direct rapid immunohistochemistry test, or pan-lyssavirus PCR assays. Several reverse-transcription real-time PCR (RT-rtPCR) methods have been developed and validated for rapid and accurate detection of lyssaviruses. We evaluated the performance of 6 TaqMan RT-rtPCR kits using different commercial master mixes and 2 real-time thermocyclers. Changing the master mix overall did not influence the TaqMan RT-rtPCR performance, regardless of the thermocycler used. The limits of detection at the 95% confidence level were 18.1-25.8 copies/µL for the Rotor-Gene Q MDx thermocycler and 16.7-21.5 for the Mx3005P thermocycler. Excellent repeatability was demonstrated for rabies virus (RABV) RNA samples of 100, 50, and 25 copies/µL regardless of the thermocycler used. RABV field samples ( n = 35) isolated worldwide gave positive results using the most efficient of the 6 kits tested, with a copy number of 6.03 × 10² to 6.78 × 10⁷ RNA copies per reaction. The TaqMan RT-rtPCR assay provides sensitive and rapid amplification of RABV RNA.

Development of molecular confirmation tools for swift and easy rabies diagnostics

BACKGROUND

As rabies still represents a major public threat with tens of thousands of deaths per year, particularly in developing countries, adequate surveillance based on rapid and reliable rabies diagnosis for both humans and animals is essential. Rabies diagnosis relies on highly sensitive and specific laboratory tests for detection of viral antigens. Among those tests, at present the immunofluorescence antibody test is the "gold standard test" for rabies diagnosis, followed by virus isolation in either mice or cell culture. Because of the advantages of molecular assays in terms of sensitivity and applicability their approval as confirmatory diagnostic test by international organizations (OIE, WHO) is envisaged. Therefore, the objective was to develop and validate novel molecular assays and RNA extraction methods for rabies that reduce the turnaround time but remain highly sensitive and specific.

METHODS

Here, novel assays, i.e. HighSpeed RT-qPCR and isothermal recombinase polymerase amplification (RPA) were designed and tested. Furthermore, three magnetic bead-based rapid extraction methods for manual or automated extraction were validated and combined with the new downstream assays.

RESULTS

While the conventional column based RNA extraction method showed the highest intra-run variations, all magnetic bead-based rapid extraction methods delivered nearly comparable sensitivity and efficiency of RNA recovery. All newly developed molecular tests were able to detect different rabies virus strains in a markedly reduced timeframe in comparison to the standard diagnostic assays. The observed detection limit for the HighSpeed RT-qPCR was 10 genome copies per reaction, and 1000 genome copies per reaction for the RPA assay.

CONCLUSION

Magnetic bead-based rapid RNA extraction methods are highly sensitive and show a high level of reproducibility and therefore, are particularly suitable for molecular diagnostic assays including rabies. In addition, with a detection limit of 10 genome copies per reaction, the HighSpeed RT-qPCR is suitable for rapid ante mortem rabies diagnosis in humans as well as confirmatory test in integrated bite management and subsequent post-exposure prophylaxis.

Development and validation of sensitive real-time RT-PCR assay for broad detection of rabies virus

Rabies virus (RABV) remains one of the most important global zoonotic pathogens. RABV causes rabies, an acute encephalomyelitis associated with a high rate of mortality in humans and animals and affecting different parts of the world, particularly in Asia and Africa. Confirmation of rabies diagnosis relies on laboratory diagnosis, in which molecular techniques such as detection of viral RNA by reverse transcription polymerase chain reaction (RT-PCR) are increasingly being used. In this study, two real-time quantitative RT-PCR assays were developed for large-spectrum detection of RABV, with a focus on African isolates. The primer and probe sets were targeted highly conserved regions of the nucleoprotein (N) and polymerase (L) genes. The results indicated the absence of non-specific amplification and cross-reaction with a range of other viruses belonging to the same taxonomic family, i.e. Rhabdoviridae, as well as negative brain tissues from various host species. Analytical sensitivity ranged between 100 to 10 standard RNA copies detected per reaction for N-gene and L-gene assays, respectively. Effective detection and high sensitivity of these assays on African isolates showed that they can be successfully applied in general research and used in diagnostic process and epizootic surveillance in Africa using a double-check strategy.

The Recently Discovered Bokeloh Bat Lyssavirus: Insights Into Its Genetic Heterogeneity and Spatial Distribution in Europe and the Population Genetics of Its Primary Host

In 2010, a novel lyssavirus named Bokeloh bat lyssavirus (BBLV) was isolated from a Natterer's bat (Myotis nattereri) in Germany. Two further viruses were isolated in the same country and in France in recent years, all from the same bat species and all found in moribund or dead bats. Here we report the description and the full-length genome sequence of five additional BBLV isolates from Germany (n=4) and France (n=1). Interestingly, all of them were isolated from the Natterer's bat, except one from Germany, which was found in a common Pipistrelle bat (Pipistrellus pipistrellus), a widespread and abundant bat species in Europe. The latter represents the first case of transmission of BBLV to another bat species. Phylogenetic analysis clearly demonstrated the presence of two different lineages among this lyssavirus species: lineages A and B. The spatial distribution of these two lineages remains puzzling, as both of them comprised isolates from France and Germany; although clustering of isolates was observed on a regional scale, especially in Germany. Phylogenetic analysis based on the mitochondrial cytochrome b (CYTB) gene from positive Natterer's bat did not suggest a circulation of the respective BBLV sublineages in specific Natterer's bat subspecies, as all of them were shown to belong to the M. nattereri sensu stricto clade/subspecies and were closely related (German and French positive bats). At the bat host level, we demonstrated that the distribution of BBLV at the late stage of the disease seems large and massive, as viral RNA was detected in many different organs.

Dual Combined Real-Time Reverse Transcription Polymerase Chain Reaction Assay for the Diagnosis of Lyssavirus Infection

The definitive diagnosis of lyssavirus infection (including rabies) in animals and humans is based on laboratory confirmation. The reference techniques for post-mortem rabies diagnosis are still based on direct immunofluorescence and virus isolation, but molecular techniques, such as polymerase chain reaction (PCR) based methods, are increasingly being used and now constitute the principal tools for diagnosing rabies in humans and for epidemiological analyses. However, it remains a key challenge to obtain relevant specificity and sensitivity with these techniques while ensuring that the genetic diversity of lyssaviruses does not compromise detection. We developed a dual combined real-time reverse transcription polymerase chain reaction (combo RT-qPCR) method for pan-lyssavirus detection. This method is based on two complementary technologies: a probe-based (TaqMan) RT-qPCR for detecting the RABV species (pan-RABV RT-qPCR) and a second reaction using an intercalating dye (SYBR Green) to detect other lyssavirus species (pan-lyssa RT-qPCR). The performance parameters of this combined assay were evaluated with a large panel of primary animal samples covering almost all the genetic variability encountered at the viral species level, and they extended to almost all lyssavirus species characterized to date. This method was also evaluated for the diagnosis of human rabies on 211 biological samples (positive n = 76 and negative n = 135) including saliva, skin and brain biopsies. It detected all 41 human cases of rabies tested and confirmed the sensitivity and the interest of skin biopsy (91.5%) and saliva (54%) samples for intra-vitam diagnosis of human rabies. Finally, this method was successfully implemented in two rabies reference laboratories in enzootic countries (Cambodia and Morocco). This combined RT-qPCR method constitutes a relevant, useful, validated tool for the diagnosis of rabies in both humans and animals, and represents a promising tool for lyssavirus surveillance.

Evaluation of Six Commercially Available Rapid Immunochromatographic Tests for the Diagnosis of Rabies in Brain Material

Rabies is a neglected zoonotic disease that causes an estimated 60,000 human deaths annually. The main burden lies on developing countries in Asia and Africa, where surveillance and disease detection is hampered by absence of adequate laboratory facilities and/or the difficulties of submitting samples from remote areas to laboratories. Under these conditions, easy-to-use tests such as immunochromatographic assays, i.e. lateral flow devices (LFD), may increase surveillance and improve control efforts. Several LFDs for rabies diagnosis are available but, except for one, there are no data regarding their performance. Therefore, we compared six commercially available LFDs for diagnostic and analytical sensitivity, as well as their specificity and their diagnostic agreement with standard rabies diagnostic techniques using different sample sets, including experimentally infected animals and several sets of field samples. Using field samples the sensitivities ranged between 0% up to 100% depending on the LFD and the samples, while for experimentally infected animals the maximum sensitivity was 32%. Positive results in LFD could be further validated using RT-qPCR and sequencing. In summary, in our study none of the tests investigated proved to be satisfactory, although the results somewhat contradict previous studies, indicating batch to batch variation. The high number of false negative results reiterates the necessity to perform a proper test validation before being marketed and used in the field. In this respect, marketing authorization and batch release control could secure a sufficient quality for these alternative tests, which could then fulfil their potential.

Despite being preventable with adequate biologicals, rabies still causes an estimated 60,000 human deaths annually. The main burden lies on developing countries in Asia and Africa, where dog rabies surveillance is hampered by laboratory confirmation of disease due to a number of reasons, including laboratory infrastructure and logistics. Lateral flow devices (LFD) may increase surveillance and improve control efforts. Several LFDs for rabies diagnosis are available but, except for one, there are no data available regarding their performance. Therefore, we compared six commercially available LFDs for diagnostic and analytical sensitivity. With sensitivities ranging from 0% up to 100% depending on the LFD and the samples, none of the tests investigated proved to be satisfactory, and the results somewhat contradict previous studies, indicating batch to batch variation. The high number of false negative results reiterates the necessity to perform a proper test validation before being marketed and used in the field. Only when sufficient quality is assured for these alternative tests, then they can fulfil their potential. In this respect, we demonstrated that positive results in LFD can be further validated and characterized using RT-qPCR and sequencing.

Tick infestation in birds and prevalence of pathogens in ticks collected from different places in Germany

The importance of ticks and tick-borne pathogens for human and animal health has been increasing over the past decades. For their transportation and dissemination, birds may play a more important role than wingless hosts. In this study, tick infestation of birds in Germany was examined. Eight hundred ninety-two captured birds were infested with ticks and belonged to 48 different species, of which blackbirds (Turdus merula) and song thrushes (Turdus philomelos) were most strongly infested. Ground feeders were more strongly infested than non-ground feeders, sedentary birds more strongly than migratory birds, and short-distance migratory birds more strongly than long-distance migratory birds. Mean tick infestation per bird ranged between 2 (long-distance migratory bird) and 4.7 (sedentary bird), in some single cases up to 55 ticks per bird were found. With the exception of three nymphs of Haemaphysalis spp., all ticks belonged to Ixodes spp., the most frequently detected tick species was Ixodes ricinus. Birds were mostly infested by nymphs (65.1 %), followed by larvae (32.96 %). Additionally, ticks collected from birds were examined for several pathogens: Tick-borne encephalitis virus (TBEV) and Sindbisvirus with real-time RT-PCR, Flaviviruses, Simbuviruses and Lyssaviruses with broad-range standard RT-PCR-assays, and Borrelia spp. with a Pan-Borrelia real-time PCR. Interestingly, no viral pathogens could be detected, but Borrelia spp. positive ticks were collected from 76 birds. Borrelia (B.) garinii, B. valaisiaina, B. burgdorferi s.s. and B. afzelii were determined. The screening of ticks and birds for viral pathogens with broad range PCR-assays was tested and the use as an “early warning system” is discussed.

Successful Generation of Human Induced Pluripotent Stem Cell Lines from Blood Samples Held at Room Temperature for up to 48 hr

The collection sites of human primary tissue samples and the receiving laboratories, where the human induced pluripotent stem cells (hIPSCs) are derived, are often not on the same site. Thus, the stability of samples prior to derivation constrains the distance between the collection site and the receiving laboratory. To investigate sample stability, we collected blood and held it at room temperature for 5, 24, or 48 hr before isolating peripheral blood mononuclear cells (PBMCs) and reprogramming into IPSCs. Additionally, PBMC samples at 5- and 48-hr time points were frozen in liquid nitrogen for 4 months and reprogrammed into IPSCs. hIPSC lines derived from all time points were pluripotent, displayed no marked difference in chromosomal aberration rates, and differentiated into three germ layers. Reprogramming efficiency at 24- and 48-hr time points was 3- and 10-fold lower, respectively, than at 5 hr; the freeze-thaw process of PBMCs resulted in no obvious change in reprogramming efficiency.

Lagos bat virus transmission in an Eidolon helvum bat colony, Ghana

A brain sample of a straw-coloured fruit bat (Eidolon helvum) from Ghana without evident signs of disease tested positive by generic Lyssavirus RT-PCR and direct antigen staining. Sequence analysis confirmed the presence of a Lagos bat virus belonging to phylogenetic lineage A. Virus neutralization tests using the isolate with sera from the same group of bats yielded neutralizing antibodies in 74% of 567 animals. No cross-neutralization was observed against a different Lagos bat virus (lineage B).

Why we can prevent, control and possibly treat – but will not eradicate – rabies

ABSTRACT 

Rabies is an acute, progressive viral encephalitis. Despite historical recognition, millions still remain exposed annually. Most fatalities are of children, although this zoonosis is a vaccine-preventable disease. All developed countries interrupted canine transmission and increasingly, Asian and African communities recognize what Latin Americans demonstrated – dog rabies can be eliminated – by mass application of veterinary vaccines. Realistically, rabies is not a candidate for eradication. Management is lacking for major reservoirs, such as bats. Increasing pre-exposure immunization of individuals at risk, simplification of postexposure schedules, enhancing vaccine delivery by alternative routes, development of less expensive biologics and antiviral drugs, may lessen its impact if applied strategically in a One Health context.

Cross-platform evaluation of commercial real-time SYBR green RT-PCR kits for sensitive and rapid detection of European bat Lyssavirus type 1

This study evaluates the performance of five two-step SYBR Green RT-qPCR kits and five one-step SYBR Green qRT-PCR kits using real-time PCR assays. Two real-time thermocyclers showing different throughput capacities were used. The analysed performance evaluation criteria included the generation of standard curve, reaction efficiency, analytical sensitivity, intra- and interassay repeatability as well as the costs and the practicability of kits, and thermocycling times. We found that the optimised one-step PCR assays had a higher detection sensitivity than the optimised two-step assays regardless of the machine used, while no difference was detected in reaction efficiency, R (2) values, and intra- and interreproducibility between the two methods. The limit of detection at the 95% confidence level varied between 15 to 981 copies/µL and 41 to 171 for one-step kits and two-step kits, respectively. Of the ten kits tested, the most efficient kit was the Quantitect SYBR Green qRT-PCR with a limit of detection at 95% of confidence of 20 and 22 copies/µL on the thermocyclers Rotor gene Q MDx and MX3005P, respectively. The study demonstrated the pivotal influence of the thermocycler on PCR performance for the detection of rabies RNA, as well as that of the master mixes.

Identification of rhabdoviral sequences in oropharyngeal swabs from German and Danish bats

Background

In the frame of active lyssavirus surveillance in bats, oropharyngeal swabs from German (N = 2297) and Danish (N = 134) insectivorous bats were investigated using a newly developed generic pan-lyssavirus real-time reverse transcriptase PCR (RT-qPCR).

Findings

In total, 15 RT-qPCR positive swabs were detected. Remarkably, sequencing of positive samples did not confirm the presence of bat associated lyssaviruses but revealed nine distinct novel rhabdovirus-related sequences.

Conclusions

Several novel rhabdovirus-related sequences were detected both in German and Danish insectivorous bats. The results also prove that the novel generic pan-lyssavirus RT-qPCR offers a very broad detection range that allows the collection of further valuable data concerning the broad and complex diversity within the family Rhabdoviridae.