Phylogenetic analysis of rabies virus isolated from canids in North and Northeast Brazil

Fifty Years of the National Rabies Control Program in Brazil under the One Health Perspective

In 1973, the National Rabies Program was created in Brazil through an agreement between the Ministry of Health and Agriculture. Since its beginning, it developed integrated action through access to free post-exposure prophylaxis (PEP) for people at risk, dog vaccination campaigns, a joint surveillance system, and awareness. This study aims to describe human rabies in Brazil under the One Health perspective in recent decades, including achievements in the control of dog-mediated cases and challenges in human cases transmitted by wild animals. This paper also explores possible drivers of human rabies in the Northeast Region with half of the cases. The first part of this study was descriptive, presenting data and examples by periods. Statistical analysis was performed in the last period (2010-2022) to explore possible drivers. Dog-mediated human cases decreased from 147 to 0, and dog cases decreased from 4500 to 7. A major challenge is now human cases transmitted by wild animals (bats, non-human primates, and wild canids). Most current human cases occur in municipalities with a tropical and subtropical moist broadleaf forest biome and a Gini index higher than 0.5. In the multivariable analysis, an association with temperature was estimated (OR = 1.739; CI95% = 1.181-2.744), and primary healthcare coverage (OR = 0.947; CI95% = 0.915-0.987) was identified as a protector. It is possible to significantly reduce the number of dog-mediated human rabies cases through the efforts presented. However, Brazil has wildlife variants of the rabies virus circulating. The association of human cases with higher temperatures in the Northeast is a concern with climate change. To reduce human cases transmitted by wild animals, it is important to continue distributing free PEP, especially in remote at-risk areas in the Amazon Region, and to increase awareness.

Evolution and divergence of the genetic lineage Desmodus rotundus/Artibeus lituratus of rabies virus in São Paulo State

The last record of a rabies case caused by the dog-specific rabies virus (RABV) lineage in dogs or cats in São Paulo State was in 1998. From 2002 to 2021, 57 cases of rabies in these animals were reported, and the vast majority (51) were genetically characterized as belonging to the Desmodus rotundus/Artibeus lituratus RABV lineage. However, it is not currently possible to infer which of these bats is the source of infection by genome sequencing of RABV isolates. The aims of this study were (a) to characterize the Desmodus rotundus/Artibeus lituratus lineage to determine the relationships between the RABV lineages and each reservoir, (b) to assess the phylogeny and common ancestors of the RABV lineages found in D. rotundus and A. lituratus, and (c) to further understand the epidemiology and control of rabies. In this study, we genetically analyzed 70 RABV isolates from São Paulo State that were received by the Virology Laboratory of the Pasteur Institute of São Paulo between 2006 and 2015. Of these isolates, 33 were associated with the hematophagous bat D. rotundus and 37 with the fruit bat A. lituratus. A genomic approach using phylogenetic analysis and nucleotide sequence comparisons demonstrated that these isolates belonged to the same genetic lineage of RABV. We also found that, in São Paulo State, the D. rotundus/A. lituratus lineage could be subdivided into at least four phylogenetic sublineages: two associated with D. rotundus and two with A. lituratus. These results are of importance for the epidemiological surveillance of rabies in São Paulo.

A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles

The rabies virus (RABV) is characterized by a history dominated by host shifts within and among bats and carnivores. One of the main outcomes of long-term RABV maintenance in dogs was the establishment of variants in a wide variety of mesocarnivores. In this study, we present the most comprehensive phylogenetic and phylogeographic analysis, contributing to a better understanding of the origins, diversification, and the role of different host species in the evolution and diffusion of a dog-related variant endemic of South America. A total of 237 complete Nucleoprotein gene sequences were studied, corresponding to wild and domestic species, performing selection analyses, ancestral states reconstructions, and recombination analyses. This variant originated in Brazil and disseminated through Argentina and Paraguay, where a previously unknown lineage was found. A single host shift was identified in the phylogeny, from dog to the crab-eating fox (Cerdocyon thous) in the Northeast of Brazil. Although this process occurred in a background of purifying selection, there is evidence of adaptive evolution -or selection of sub-consensus sequences- in internal branches after the host shift. The interaction of domestic and wild cycles persisted after host switching, as revealed by spillover and putative recombination events.

Molecular characterisation of rabies virus detected in livestock animals in the southern part of Egypt during 2018 and 2019

Brain samples were collected from 33 animals of different species, including buffalo, cattle, dog, donkey, fox and wolf, that had been suspected to be infected by rabies virus (RABV) in different geographical regions of Aswan and Luxor governorates in Egypt. The samples were submitted for histopathological examination and the presence of the nucleic acid and antigens of RABV was tested by RT-PCR and indirect fluorescent antibody technique (IFAT), respectively. Sixteen samples were found positive by all the three examinations. Three samples were selected for further study from animals in which the highest virus loads were detected. The partial sequence of the RABV N gene was determined and analysed from the samples of a buffalo, a cow and a donkey. The viruses in the samples were found to share 95-98% and 95-97% nucleotide and amino acid sequence identities, respectively. In comparison to reference sequences, a few amino acid substitutions occurred in the N protein antigenic sites I and IV in the immunodominant epitopes of the viruses detected in the cow and the donkey but not in the one from the buffalo. The phylogenetic analysis revealed that the RABVs sequenced from the samples belonged to genotype 1, Africa-4 clade, and formed two distinct sub-clades within the Egyptian clade. These findings indicate the circulation of RABV among livestock animals in the southern part of Egypt and raise public health concerns. The amino acid changes detected in this work may contribute to the antigenic diversification of RABVs.

Development of biotinylated polyclonal anti-ribonucleoprotein IgG for detection of rabies virus antigen by direct rapid immunohistochemical test

The direct rapid immunohistochemical test (dRIT) has been recommended for laboratorial diagnosis of rabies, especially in developing countries. The absence of commercial primary antibodies, however, still represents a major limitation to its wider use in testing. We describe here the development of a biotinylated polyclonal antibody against Rabies lyssavirus (RABV) ribonucleoprotein (RNP) and its use as a primary reagent in dRIT. Anti-RNP polyclonal horse IgG was purified by ionic exchange chromatography followed by immunoaffinity column chromatography, and its affinity, diagnostic sensitivity, and specificity were evaluated. CNS samples (120) of suspected rabies cases in different animal species were tested by dRIT, with the positive (n = 14) and negative (n = 106) results confirmed by direct fluorescence antibody testing (dFAT). Comparing the results of dRIT and dFAT, we found that the biotinylated anti-RNP IgG delivered 100% diagnostic specificity and sensibility for rabies diagnosis. Our findings show that the biotinylated anti-RNP polyclonal IgG can be produced with the quality required for application in dRIT. This work represents an important step in efforts to diagnose rabies in developing countries.

Nyctinomops laticaudatus bat-associated Rabies virus causes disease with a shorter clinical period and has lower pathogenic potential than strains isolated from wild canids

Rabies is a lethal viral disease that can affect a wide range of mammals. Currently, Rabies virus (RABV) in some European and American countries is maintained primarily in wild species. The regulation of viral replication is one of the critical mechanisms involved in RABV pathogenesis. However, the relationship between replication and the pathogenesis of RABV isolated from wild animals remains poorly understood. In the present study, we evaluated the pathogenicity of the street viruses Nyctinomops laticaudatus bat-associated RABV (NYBRV) and Cerdocyon thous canid-associated RABV (CECRV). Infection of mice with NYBRV led to 33% mortality with rapid disease evolution and marked histopathological changes in the CNS. In contrast, infection with CECRV led to 67% mortality and caused mild neuropathological lesions. The proportion of RABV antigen was significantly higher in the cytoplasm of neuronal cells of the cerebral cortex and in the meninges of mice infected with CECRV and NYBRV, respectively. Moreover, the replication rate of NYBRV was significantly higher (p < 0.001) than that of CECRV in neuroblastoma cells. However, CECRV replicated to a significantly higher titer in epithelial cells. Our results indicate that NYBRV infection results in rapid disease progression accompanied by frequent and intense histopathological alterations in the CNS in mice, and in a high replication rate in neuroblastoma cells. Although, CECRV is more pathogenic in mice, it caused milder histopathological changes in the CNS and replicated more efficiently in epithelial cells. Our data point to a correlation between clinical aspects of disease and the replication of RABV in different cell lines.

VALORES HEMATOLÓGICOS DE LOBINHOS (Cerdocyon thous) DO PANTANAL, MATO GROSSO DO SUL, BRASIL NATURALMENTE INFECTADOS E NÃO INFECTADOS POR Trypanosoma cruzi e T. evansi

Resumo O objetivo do trabalho foi avaliar a influência do sexo, da sazonalidade e de infecções por Trypanosoma cruzi e Trypanosoma evansi nos valores hematológicos de lobinhos (Cerdocyon thous) que habitam o Pantanal Sul-Mato-Grossense. Entre novembro de 2015 e outubro de 2016, foram amostrados 48 lobinhos. Os valores hematológicos mensurados foram as contagens de eritrócitos e leucócitos, volume globular e volume corpuscular médio. Consideramos como parasitados os animais positivos para T.cruzi e T. evansi em qualquer um dos testes diagnósticos utilizados. Observamos que sete (14.5%) lobinhos encontraram-se parasitados somente por T.cruzi, sete por T. evansi, e nove (19%) estavam coinfectados. Os animais parasitados por T.cruzi mostraram um aumento significativo das contagens de leucócitos (14.7 x 103) em relação aos animais não parasitados (10.4 x 103), parasitados por T. evansi (12.4 x 103) e coinfectados (12.9 x 103). Observamos diferença significativa em relação aos valores médios de eritrócitos e volume corpuscular médio entre os períodos de cheia e seca: 2.6 x 106 e 165, e 3.4 x 106 e 132, respectivamente. Todos apresentaram macrocitose não confirmada morfologicamente.

Isolation of Clostridium perfringens and C. difficile in crab-eating fox ( Cerdocyon thous - Linnaeus 1776) from Northeastern Brazil

ABSTRACT The aim of the present study was to isolate Clostridium perfringens and C. difficile in crab-eating fox (Cerdocyon thous) from Northeastern Brazil. Stool samples of 18 captive crab-eating foxes from four states of Northeastern Brazil (Alagoas, Bahia, Paraíba e Pernambuco) were collected and subjected to C. perfringens and C. difficile isolation. Suggestive colonies of C. perfringens were then analyzed for genes encoding the major C. perfringens toxins (alpha, beta, epsilon and iota), beta-2 toxin (cpb2), enterotoxin (cpe), and NetB- (netB) and NetF- (netF) encoding genes. C. difficile strains were analyzed by multiplex-PCR for a housekeeping gene (tpi), toxins A (tcdA) and B (tcdB) and a binary toxin gene (cdtB). Unthawed aliquots of stool samples positive for toxigenic C. difficile were subjected to a commercial ELISA to evaluate the presence of A/B toxins. Clostridium perfringens (type A) was isolated from five (27%) samples, and only one sample was positive for beta-2 enconding gene (cpb2). Two (11%) stool samples were positive for C. difficile, but negative for A/B toxins. These two wild canids were also positive for C. perfringens type A. This is the first report of C. difficile in crab-eating fox.

A rabies virus vampire bat variant shows increased neuroinvasiveness in mice when compared to a carnivore variant

Rabies is one of the most important zoonotic diseases and is caused by several rabies virus (RABV) variants. These variants can exhibit differences in neurovirulence, and few studies have attempted to evaluate the neuroinvasiveness of variants derived from vampire bats and wild carnivores. The aim of this study was to evaluate the neuropathogenesis of infection with two Brazilian RABV street variants (variant 3 and crab-eating fox) in mice. BALB/c mice were inoculated with RABV through the footpad, with the 50% mouse lethal dose (LD₅₀) determined by intracranial inoculation. The morbidity of rabies in mice infected with variant 3 and the crab-eating fox strain was 100% and 50%, respectively, with an incubation period of 7 and 6 days post-inoculation (dpi), respectively. The clinical disease in mice was similar with both strains, and it was characterized initially by weight loss, ruffled fur, hunched posture, and hind limb paralysis progressing to quadriplegia and recumbency at 9 to 12 dpi. Histological lesions within the central nervous system (CNS) characterized by nonsuppurative encephalomyelitis with neuronal degeneration and necrosis were observed in mice infected with variant 3 and those infected with the crab-eating fox variant. However, lesions and the presence of RABV antigen, were more widespread within the CNS of variant-3-infected mice, whereas in crab-eating fox-variant-infected mice, RABV antigens were more restricted to caudal areas of the CNS, such as the spinal cord and brainstem. In conclusion, the results shown here demonstrate that the RABV vampire bat strain (variant 3) has a higher potential for neuroinvasiveness than the carnivore variant.