Molecular epidemiology of rabies virus circulating in domestic animals in India

A prospective study on safety and clinical efficacy of rabies biologicals in paediatric patients with category III animal exposure

Purpose

Rabies remains a significant public health concern worldwide, particularly among paediatric populations who are vulnerable to animal exposures. This prospective study aimed to assess the safety and clinical efficacy of rabies biologicals in pediatric patients following category III animal exposures.

Materials and Methods

A prospective study was undertaken enrolling 289 pediatric patients fulfilling eligibility criteria who presented with category III animal exposures at the anti-rabies clinic of Kempegowda Institute of Medical Sciences Hospital and Research Centre, Bangalore. All the subjects received rabies biologicals as per National Centre for Disease Control guidelines. The details pertaining to socio-demographic profile, biting animal, characteristics of wound, and details of post-exposure prophylaxis (PEP) provided were recorded. All the study subjects were followed up for immediate and delayed adverse events (AEs). Subsequently, all were followed up for 6 months to demonstrate the clinical efficacy of PEP.

Results

The mean age of study subjects was 9.4 years, and most of them (43%) were going to school. Dog was the predominant biting animal (96.6%) with most bites being abrasions (45%), mainly on the lower limbs (42%). Single rabies monoclonal antibody was the most commonly administered passive immunization (67%), and purified Vero cell rabies vaccine was the predominant vaccine (65%). AEs following PEP were primarily local, predominantly pain (13.2%), and there were no systemic events. All the subjects were alive and healthy at the end of 6 months following PEP.

Conclusion

This study contributes valuable insights into the safety and clinical efficacy of rabies biologicals in a pediatric cohort following category III animal exposures, supporting the continued use of these biologicals in pediatric patients.

Ante-mortem and Post-mortem Diagnosis Modalities and Phylogenetic Analysis of Rabies Virus in Domestic and Wild Animals of Gujarat, India

In the present study, total of 32 ante-mortem (AM) samples (saliva = 18 and corneal smears = 14) from six animal species (cattle = 5; camel = 1; goat = 1; horse = 1; buffalo = 4; dog = 6) and 28 post-mortem (PM) samples of domestic (cattle = 6; camel = 1; goat = 1; buffalo = 5; dog = 7) and wild animals (lion = 4, mongoose = 2; bear = 1; leopard = 1) were examined for rabies diagnosis in Gujarat, India. Direct fluorescent antibody test (dFAT) and reverse transcriptase polymerase chain reaction (RT-PCR) were applied on AM samples, whereas along with dFAT and RT-PCR, histopathological examination, immunohistochemistry (IHC) and real time PCR (qPCR) were used for PM diagnosis. Nucleotide sequencing of full nucleoprotein (N) and glycoprotein (G) genes were carried out upon representative amplicons. In AM examination, 7/18 saliva and 5/14 corneal impressions samples were found positive in dFAT and 8/18 saliva samples were found positive in RT-PCR. In PM examination, 14/28 samples showed positive results in dFAT and IHC with unusual large fluorescent foci in two samples. In histopathology, 11/28 samples showed appreciable lesion and Negri bodies were visible in 6 samples, only. Out of 23 brain samples examined. 12 samples were found positive in N gene RT-PCR and qPCR, and 10 samples in G gene RT-PCR. Phylogenetic analysis of N gene revealed that test isolates (except sample ID: lion-1; lion, Gir) form a close group with sequence ID, KM099393.1 (Mongoose, Hyderabad) and KF660246.1 (Water Buffalo, Hyderabad) which was far from some south Indian and Sri Lankan isolates but similar to Indian isolates from rest of India and neighboring countries. In G gene analysis, the test isolates form a close group with sequence ID, KP019943.1.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01126-0.

Large-scale phylogenetic analysis reveals genetic diversity and geographic distribution of rabies virus in South-East and South Asia

South-East Asia (SEA) and South Asia (SA) are two important geographic regions with the most severe enzootic rabies in the world. In these regions, phylogenetic analysis of rabies virus (RABV) has been conducted only at a country level; the results obtained from different countries are scattered and unequal, with a non-uniform system to name RABV genotypes. Therefore, it is difficult to undertake origin-tracking and compare inter-country RABV evolution and transmission. To avoid the confusion in understanding and to generate a panoramic picture of RABV genetic diversity, distribution, and transmission in SEA and SA, the present study conducted a systematic phylogenetic analysis by combining all sequences representing 2368 RABV strains submitted to GenBank by 14 rabies endemic SEA and SA countries. The results showed that RABVs circulating in two regions were classified into four major clades and many subclades: the Asia clade is circulating only in SEA, the Indian subcontinent, and Arctic-like clades only in SA, while the Cosmopolitan clade has been detected in both regions. The results also showed a wide range of hosts were infected by divergent RABV subclades, with dogs being the major transmission source. However, wildlife rabies was also found to be an important issue with 6 wild carnivore species identified as potential sources of spillover risk for sylvatic rabies to humans, domestic animals, and other wild animals. Current findings indicate that the two regions have separate virus clades circulating thus indicating the absence of cross-transmission between the regions. The study emphasizes the importance of phylogenetic analysis in the regions using uniform genotyping and naming systems for rabies surveillance, to coordinate actions of member countries to eliminate dog-mediated human rabies by 2030.

Effect of inhibition of Toll-like receptor 3 signaling on pathogenesis of rabies virus in mouse model

Rabies is a zoonotic viral disease with inevitably fatal outcome. Toll-like receptor 3 (TLR3) could sense dsRNA viral infections, and implicated in pathogenesis of rabies and Negri bodies (NBs) formation. Present study was undertaken to elucidate the role of TLR3 in pathogenesis, NBs formation, and therapeutic potential of blocking TLR3/dsRNA interaction in rabies infection. Young Swiss albino mice were infected with 100 LD₅₀ of street rabies virus (SRABV) intracerebrally (i/c) on day 0 and treated with 30 μg of CU CPT 4a (selective TLR3 inhibitor) i/c on 0, 3 and 5 days post-infection (DPI). Three mice each were sacrificed at 1, 3, 5, 7, 9, 11, and 13 DPI to study sequential pathological consequences through histopathology, Seller's staining, immunofluorescence, immunohistochemistry, TUNEL assay, flow cytometry, and viral and cytokine genes quantification by real-time PCR. CU CPT 4a inhibited TLR3 expression resulted in delayed development and decreased intensity of clinical signs and pathological lesions, low viral load, significantly reduced NBs formation, and increased survival time in SRABV-infected mice. These parameters suggested that TLR3 did influence the SRABV replication and NBs formation. Inhibition of TLR3 led to decreased expression of pro-inflammatory cytokines and interferons indicated an anti-inflammatory effect of CU CPT 4a during SRABV infection. Further, TLR3-inhibited group revealed normal CD4⁺/CD8⁺ T-cells ratio with less TUNEL-positive apoptotic cells indicated that immune cell kinetics are not affected during TLR3-inhibition. SRABV-infected and mock-treated mice were developed severe clinical signs and histopathological lesions, more NBs formation, high viral load, increased pro-inflammatory cytokines expression in brain, which were correlated with higher expression levels of TLR3. In conclusion, these data suggested that TLR3/dsRNA signaling pathway could play critical role in pathogenesis of SRABV infection in vivo and opens up new avenues of therapeutics.

The Comparison of Full G and N Gene Sequences From Turkish Rabies Virus Field Strains

The rabies infection is a zoonotic viral disease in humans and is spread by both wild and domestic carnivores. This study aimed to molecularly characterize the field strains of the rabies virus circulating in Turkey between 2013 and 2020. Brain samples obtained from 16 infected animals (8 cattle, one donkey, three foxes, three dogs, and one marten) were tested. Full nucleoprotein (N) and glycoprotein (G) gene sequences were used to determine the genetic and antigenic characteristics of the rabies virus field strains. The phylogenetic analyses revealed that the 16 field strains identified in Turkey belonged to the Cosmopolitan lineage.

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.

Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION

As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination. Sequencing can provide critical information to inform control and vaccination strategies by identifying genetically distinct virus variants that may have different host reservoir species or geographic distributions. However, many rabies testing laboratories lack the resources or expertise for sequencing, especially in remote or rural areas where human rabies deaths are highest. We developed a low-cost, high throughput rabies virus sequencing method using the Oxford Nanopore MinION portable sequencer. A total of 259 sequences were generated from diverse rabies virus isolates in public health laboratories lacking rabies virus sequencing capacity in Guatemala, India, Kenya, and Vietnam. Phylogenetic analysis provided valuable insight into rabies virus diversity and distribution in these countries and identified a new rabies virus lineage in Kenya, the first published canine rabies virus sequence from Guatemala, evidence of rabies spread across an international border in Vietnam, and importation of a rabid dog into a state working to become rabies-free in India. Taken together, our evaluation highlights the MinION's potential for low-cost, high volume sequencing of pathogens in locations with limited resources.

Molecular epidemiological analysis of wild animal rabies isolates from India

Aim

This study was conducted to know the genetic variability of rabies viruses (RVs) from wild animals in India.

Materials and Methods

A total of 20 rabies suspected brain samples of wild animals from different states of India were included in the study. The samples were subjected for direct fluorescent antibody test (dFAT), reverse transcription polymerase chain reaction (RT-PCR), and quantitative reverse transcriptase real-time PCR (RT-qPCR). The phylogenetic analysis of partial nucleoprotein gene sequences was performed.

Results

Of 20 samples, 11, 10, and 12 cases were found positive by dFAT, RT-PCR, and RT-qPCR, respectively. Phylogenetic analysis showed that all Indian wild RVs isolates belonged to classical genotype 1 of Lyssavirus and were closely related to Arctic/Arctic-like single cluster indicating the possibility of a spillover of rabies among different species.

Conclusion

The results indicated the circulation of similar RVs in sylvatic and urban cycles in India. However, understanding the role of wild animals as reservoir host needs to be studied in India.