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

Molecular basis of two broad-spectrum antibodies neutralizing rabies virus and other phylogroup-I lyssaviruses by blocking structural transition between the pleckstrin-homology and fusion domains in the glycoprotein

Rabies virus (RABV), the prototype species of the Lyssavirus genus, causes the lethal disease of rabies. Rabies can be efficiently prevented with post-exposure prophylaxis. The RABV glycoprotein (RABV-G) is an essential factor mediating virus entry and the major target of neutralizing antibodies. Here, we report the crystal structures of two neutralizing monoclonal antibodies (NM57 and SOJB) in complex with RABV-G. The two antibodies recognize highly overlapped epitopes involving both the pleckstrin-homology domain (PHD) and the junction between PHD and the fusion domain (FD). Our pseudovirus neutralization assay further shows that both antibodies could neutralize a majority of the lyssaviruses in phylogroup-I. Via sequence comparison and structural characterization, we identify two residues located at positions 226 and 231 in PHD, as key determinants for antibody recognition, which is further corroborated by mutagenesis analyses. Finally, detailed structural analyses reveal that NM57 and SOJB would lock the PHD/FD local structure in the pre-fusion-like state, thereby inhibiting viral infection by blocking structural transitions of RABV-G essential for membrane fusion. Taken together, these results provide a mechanistic glimpse into the molecular basis for broad neutralization of phylogroup-I lyssaviruses by NM57 and SOJB, which should be able to facilitate the development of monoclonal antibodies and vaccines.

Immunological findings of West Caucasian bat virus in an accidental host

The Lyssavirus genus includes seventeen viral species able to cause rabies, an acute and almost invariably fatal encephalomyelitis of mammals. Rabies virus (RABV), which represents the type species of the genus, is a multi-host pathogen that over the years has undergone multiple events of host-switching, thus occupying several geographical and ecological niches. In contrast, non-RABV lyssaviruses are mainly confined within a single natural host with rare spillover events. In this scenario, unveiling the mechanisms underlying the host immune response against a virus is crucial to understand the dynamics of infection and to predict the probability of colonization/adaptation to a new target species. Presently, the host response to lyssaviruses has only been partially explored, with the majority of data extrapolated from RABV infection. West Caucasian bat virus (WCBV), a divergent lyssavirus, has recently been associated with a spillover event to a domestic cat, raising concern about the risks to public health due to the circulation of the virus in its natural host. Through this study we have investigated the immune response determined by the WCBV versus two widely known lyssaviruses. We selected the Syrian hamster as representative of an accidental host, and chose the intramuscular route in order to mimic the natural infection. In hamsters, WCBV was highly pathogenic, determining 100% lethality and mild encephalitis. In comparison with Duvenhage virus (DUVV) and RABV, we found that WCBV displayed an intermediate ability to promote cellular antiviral response, produce pro-inflammatory cytokines, and recruit and activate lymphocytes in the hamsters' central nervous system.

IMPORTANCE

Although all lyssaviruses cause fatal encephalomyelitis in mammals, they display a different host tropism and pathogenicity, with the ecology of Rabies virus (RABV) continually evolving and adapting to new host species. In 2020, West Caucasian bat virus (WCBV) was identified as the causative agent of rabies in a domestic cat in Italy. This event raised concerns about its public health consequences, due to the absence of biologicals against the infection. Our study investigates the host immune response triggered by WCBV in comparison with a pathogenic strain of RABV and the low pathogenic Duvenhage lyssavirus (DUVV), as a proxy to understand the mechanisms leading to lyssavirus spillover and pathogenicity. We overall confirm that previous evidence indicating an inverse relationship between lyssavirus pathogenicity and immune response is applicable for WCBV as well. Importantly, this work represents the first transcriptomic analysis of the WCBV interaction in the central nervous system with an accidental host.

European distribution and intramuscular pathogenicity of divergent lyssaviruses West Caucasian bat virus and Lleida bat lyssavirus

Among lyssaviruses, West Caucasian bat virus (WCBV) and Lleida bat lyssavirus (LLEBV) raise concern as their divergence from rabies virus leads to the inefficacy of available prophylactic agents. Both viruses were described in the bat Miniopterus schreibersii. We investigated the European distribution of WCBV and LLEBV by screening sera from Miniopterus schreibersii across eight countries, finding widespread serological evidence and positivity up to 70%. We evaluated the intramuscular lethality of wild type isolates in Syrian hamsters. WCBV induced 100% lethality and a clinical disease compatible with furious rabies. All animals infected with LLEBV remained healthy for 40 days, despite one individual testing positive in the brain. We confirmed LLEBV's intramuscular a-pathogenicity using mice. Infected hamsters developed antibodies by day seven, regardless the virus and the clinical outcome. This study highlights the widespread circulation of WCBV and LLEBV in Europe and suggests differences in neuro-invasiveness and/or pathogenesis that are crucial for risk assessment.

Typing Arctic and Africa-2 clades of rabies virus using clade-defining single nucleotide polymorphisms

Rabies is a deadly neurotropic, zoonotic disease with a mortality rate of 100% after symptoms appear. Rabies virus (RABV) is the primary cause of rabies disease in humans, and it mainly spreads via dog bites in developing countries. Over the course of RABV evolution, multiple RABV variants, called clades, have emerged. However, our understanding of these clades is limited, as the only method to identify a clade is sequencing, followed by phylogeny. In this study, we have developed a rapid, PCR-based method for typing two RABV clades. We utilised highly conserved amino acid changes specific to the Arctic and Africa-2 clades of the rabies virus (RABV). A single nucleotide substitution from adenine to thymine at position 178 within the nucleoprotein gene was found to be clade-specific in the Arctic clade. Similarly, adenine at position 638 is a distinctive marker for the Africa-2 clade. The assay demonstrated high specificity and offers the added benefit of PCR-based amplification, enabling virus detection even when viral titers are low. The assay can identify the Arctic clade and Africa-2 clade without sequencing and is highly specific and sensitive. Furthermore, this method can be adapted to detect other RABV clades and a wide range of viruses.

Rabies in Cats-An Emerging Public Health Issue

Human rabies cases today are predominantly associated with infection from rabid domestic dogs. Unlike dogs, a common global reservoir species that perpetuates rabies viruses (RABV) within their populations, domestic cats are much less frequently reported or vaccinated. Epidemiologically, cats are important vectors of lyssaviruses but are not viral reservoirs. Typically, cats are incidental hosts only, infected with the predominant lyssavirus in their geographic locale. Human cases associated with rabid cats have occurred in Africa, Asia, Europe and throughout the Americas. As adept, solitary hunters, wild and domestic felids are at risk of lyssavirus infection based upon interactions with infected prey, such as bats, or from transmission by other mesocarnivores, such as rabid dogs, foxes, jackals, raccoons, and skunks. Current veterinary vaccines provide safe and effective immunity in cats against phylogroup I lyssaviruses, such as RABV, but not against divergent lyssaviruses in phylogroups II-IV. With the focus upon the global elimination of canine rabies, the emergence of rabies in cats represents a concerning trend. Clearly, education about the occurrence of rabies in cats needs to be improved, as well as the routine vaccination of cats to reduce the associated risks to public health, agriculture, and conservation biology from a One Health perspective.

Structural Determination of the Australian Bat Lyssavirus Nucleoprotein and Phosphoprotein Complex

Australian bat lyssavirus (ABLV) shows similar clinical symptoms as rabies, but there are currently no protein structures available for ABLV proteins. In lyssaviruses, the interaction between nucleoprotein (N) and phosphoprotein (N) in the absence of RNA generates a complex (N0P) that is crucial for viral assembly, and understanding the interface between these two proteins has the potential to provide insight into a key feature: the viral lifecycle. In this study, we used recombinant chimeric protein expression and X-ray crystallography to determine the structure of ABLV nucleoprotein bound to residues 1-40 of its phosphoprotein chaperone. Comparison of our results with the recently generated structure of RABV CVS-11 N0P demonstrated a highly conserved interface in this complex. Because the N0P interface is conserved in the lyssaviruses of phylogroup I, it is an attractive therapeutic target for multiple rabies-causing viral species.

Evaluation of Taxonomic Characteristics of Matlo and Phala Bat Rabies-Related Lyssaviruses Identified in South Africa

We report the genetic characterization of two potentially novel rabies-related lyssaviruses identified from bats in Limpopo province, South Africa. Matlo bat lyssavirus (MBLV) was identified in two Miniopterus natalensis (Natal long-fingered) bats in 2015 and 2016, and Phala bat lyssavirus (PBLV) was identified in a Nycticeinops schlieffeni (Schlieffen's) bat in 2021. The distribution of both of these bat species is largely confined to parts of Africa, with limited reports from the Arabian Peninsula. MBLV and PBLV were demonstrated to group with the unassigned and phylogroup I lyssaviruses, respectively. MBLV was most closely related to Lyssavirus caucasicus (WCBV), whereas PBLV was most closely related to Lyssavirus formosa (TWBLV-1) and Taiwan bat lyssavirus 2 (TWBLV-2), based on analysis of the N and G genes, the concatenated N + P + M + G + L coding sequence, and the complete genome sequence. Based on our analysis, MBLV and WCBV appeared to constitute a phylogroup separate from Lyssavirus lleida (LLEBV) and Lyssavirus ikoma (IKOV). Analysis of the antigenic sites suggests that PBLV will likely be serologically distinguishable from established lyssaviruses in virus-neutralization tests, whereas MBLV appeared to be antigenically highly similar to WCBV. Taken together, the findings suggested that, while PBLV is likely a new lyssavirus species, MBLV is likely related to WCBV.

Tissue optical clearing and 3D imaging of virus infections

Imaging pathogens within 3D environment of biological tissues provides spatial information about their localization and interactions with the host. Technological advances in fluorescence microscopy and 3D image analysis now permit visualization and quantification of pathogens directly in large tissue volumes and in great detail. In recent years large volume imaging became an important tool in virology research helping to understand the properties of viruses and the host response to infection. In this chapter we give a review of fluorescence microscopy modalities and tissue optical clearing methods used for large volume tissue imaging. A summary of recent applications for virus research is provided with particular emphasis on studies using light sheet fluorescence microscopy. We describe the challenges and approaches for volumetric image analysis. Practical examples of volumetric imaging implemented in virology laboratories and addressing specialized research questions, such as virus tropism and immune host response are described. We conclude with an overview of the emerging technologies and their potential for virus research.

From Field Tests to Molecular Tools-Evaluating Diagnostic Tests to Improve Rabies Surveillance in Namibia

Rabies is endemic in Namibia and is present both in wildlife carnivores and domestic free-roaming dogs. The disease thus represents a challenge for public human and veterinary disease control. Namibia has implemented a national strategic plan to control rabies and the country's activities are supported by international organizations. To this end, rabies diagnosis at the Central Veterinary Laboratory (CVL) was improved in the frame of a World Organization for Animal Health (WOAH) laboratory twinning program: from practical sampling techniques and the use of lateral flow devices to a novel universal and discriminatory quantitative real-time Reverse transcription polymerase chain reaction (RT-qPCR), which easily identify dog-associated rabies viruses. The procedures applied and the results can be used as a template to improve rabies laboratory diagnosis.

Glu333 in rabies virus glycoprotein is involved in virus attenuation through astrocyte infection and interferon responses

The amino acid residue at position 333 of the rabies virus (RABV) glycoprotein (G333) is a major determinant of RABV pathogenicity. Virulent RABV strains possess Arg₃₃₃, whereas the attenuated strain HEP-Flury (HEP) possesses Glu₃₃₃. To investigate the potential attenuation mechanism dependent on a single amino acid at G333, comparative analysis was performed between HEP and HEP³³³R mutant with Arg₃₃₃. We examined their respective tropism for astrocytes and the subsequent immune responses in astrocytes. Virus replication and subsequent interferon (IFN) responses in astrocytes infected with HEP were increased compared with HEP³³³R both in vitro and in vivo. Furthermore, involvement of IFN in the avirulency of HEP was demonstrated in IFN-receptor knockout mice. These results indicate that Glu₃₃₃ contributes to RABV attenuation by determining the ability of the virus to infect astrocytes and stimulate subsequent IFN responses.

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Glu₃₃₃ in G protein is responsible for astrocyte infection with RABV HEP strain

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Arg₃₃₃ mutation in G protein decreases astrocyte tropism of RABV HEP

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RABV HEP evokes higher IFN responses in astrocytes than HEP with Arg₃₃₃ mutation

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Glu₃₃₃-dependent astrocyte infection is involved in the attenuation of RABV HEP