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Whole Genome Sequencing for Rapid Characterization of Rabies Virus Using Nanopore Technology

Genomic data can be used to track the transmission and geographic spread of infectious diseases. However, the sequencing capacity required for genomic ...

Ahmadu Bello University

A canine rabies virus (RABV) was isolated from a trade dog in Nigeria. Its entire genome was sequenced and found to be closely related to canine RABVs circulating in Africa. Sequence comparison indicates that the virus is closely related to the Africa 2 RABV lineage. The virus is now termed DRV-NG11.

Complete genome sequence of a street rabies virus isolated from a dog in Nigeria.

There is a great need for a chemical method of tissue preservation that would allow sample storage for extended periods at room temperature. This study aimed at retrieving and detecting rabies virus antigen by direct fluorescent antibody test (DFAT) in formalin-fixed dog brain tissues. Forty fresh dog brain specimens were collected as paired samples from rabies suspected cases that were received for postmortem detection of rabies in the Central Diagnostic Laboratory, National Veterinary Research Institute, Vom. One portion of each paired sample was prepared for fresh fluorescent antibody testing and the other portion was prepared for epitope retrieval and florescent antibody testing following fixation in 10% neutral buffered formalin. DFAT on formalin-fixed tissue exhibited a sensitivity of 100% in comparison to DFAT on fresh-tissue. No false positive result was obtained in formalin-fixed DFAT procedure, demonstrating 100% specificity. There was no apparent difference in the intensity of fluorescence in DFAT on fresh sample and formalin-fixed DFAT following heat induced epitope retrieval (concordance = 98%; 95% C.I. 0.9660 to 0.9903). The strength of agreement between DFAT on formalin-fixed and DFAT on fresh tissue was very good (Cohen's kappa coefficient value= 1.000; 95% C.I. 1.000-1.000). This study provides new information on the retrieval of rabies antigen by heat induced epitope retrieval for DFAT on formalinized tissues. Formalin could therefore, be used henceforth to fix tissues of rabies suspected cases for routine diagnosis, transportation or archival purposes. The heat induced epitope retrieval can be routinely used to retrieve rabies virus antigen for DFAT in cases where only formalin-fixed tissues are available or when preservation by freezing is difficult.

Heat induced epitope retrieval for rabies virus detection by direct fluorescent antibody test in formalin-fixed dog brain tissues.

Twice a year in southwestern Nigeria, during a traditional bat festival, community participants enter designated caves to capture bats, which are then consumed for food or traded. We investigated the presence of Bartonella species in Egyptian fruit bats (Rousettus aegyptiacus) and bat flies (Eucampsipoda africana) from these caves and assessed whether Bartonella infections had occurred in persons from the surrounding communities. Our results indicate that these bats and flies harbor Bartonella strains, which multilocus sequence typing indicated probably represent a novel Bartonella species, proposed as Bartonella rousetti. In serum from 8 of 204 persons, we detected antibodies to B. rousetti without cross-reactivity to other Bartonella species. This work suggests that bat-associated Bartonella strains might be capable of infecting humans.

Human Exposure to Novel Bartonella Species from Contact with Fruit Bats.

As feared and deadly human diseases globally, Rabies virus contrived mechanisms to escape early immune recognition via suppression of the interferon response. This study, preliminarily investigated whether Rabies virus employs epigenetic mechanism for the suppression of the interferon using the Challenge virus standard (CVS) strain and Nigerian street Rabies virus (SRV) strain. Mice were challenged with Rabies virus (RABV) infection, and presence of RABV antigen was assessed by direct fluorescent antibody test (DFAT). A real time quantitative Polymerase chain reaction (qRT-PCR) was used to measure the expression of type II interferon gamma (IFNG) and methylation specific quantitative PCR for methylation analysis of 1FNG promoter region. Accordingly, DNA methyltransferase (DNMT) and histone acetyltransferase (HAT) enzymes activities were determined. RABV antigen was detected in all infected samples. A statistically significant increase (p < 0.05) in mRNA level of IFNG was observed at the onset of the disease and a decrease as the disease progressed. An increase in methylation in the test groups from the control group was observed, with a fluctuation in methylation as the disease progressed. DNMT and HAT activities also agree with methylation as there was an observed increase activity in test group compared with control group. Similar fluctuation pattern was observed in both CVS and SRV groups as the disease progressed with HAT, being the most active proportionally. This study suggests that epigenetic modification via DNA methylation and histone acetylation may have played a role in the expression of type II interferon gamma in Rabies virus infection. Graphical abstract.

Induction of Rabies Virus Infection in Mice Brain may Up and Down Regulate Type II Interferon gamma via epigenetic modifications.

Rabies is one of the most dreadful diseases and a major viral zoonosis which has been shown to cause an almost 100% fatality rate in infected victims. It is characterized by acute progressive encephalitis in mammals. This study determined the genotypic characteristics of rabies virus in dogs slaughtered for human consumption based on sequence of a fragment of nucleoprotein gene. Brain tissues were collected from 50 dogs slaughtered in Billiri and Kaltungo Local Government Areas of Gombe State, Nigeria. Direct fluorescent antibody test (DFAT) was used to screen for the presence of rabies virus antigen. Viral RNA isolated from DFAT positive brain tissues were subjected to the reverse transcription polymerase chain reaction (RT-PCR) followed by sequencing of the amplicons. Maximum Likelihood (ML) was used to construct a phylogenetic tree for sequences obtained with 1000 bootstrap replicates. The DFAT detected rabies antigen in 3 (6%) of the 50 dog brain tissues, from which 1 (2%) was positive by RT-PCR. ML phylogeny approach of the nucleotide sequences inferred members as originating lyssavirus genus and dog species. Essentially, MK234794 in this study displayed 99.3% sequence similarity with other related rabies viruses in the Africa 2 cluster (Nigeria, Cameroon, Chad and Niger). Interestingly, MK234794 showed no cluster relation with the Africa 1a, 1b, 3 and Africa 4 clades, respectively. This indicates there is in-country and trans-boundary circulation of the rabies viruses with no co-circulation between the Africa lineages, especially as dogs are continuously being traded due to consumption of dog meat in West Africa. This finding has given additional insight into the molecular epidemiology of rabies virus in Nigeria, therefore providing more baseline information for future design of rabies control programs in the country.

Molecular study of rabies virus in slaughtered dogs in Billiri and Kaltungo local government areas of Gombe state, Nigeria.

Using questionnaires and serologic testing, we evaluated bat and lyssavirus exposure among persons in an area of Nigeria that celebrates a bat festival. Bats from festival caves underwent serologic testing for phylogroup II lyssaviruses (Lagos bat virus, Shimoni bat virus, Mokola virus). The enrolled households consisted of 2,112 persons, among whom 213 (10%) were reported to have ever had bat contact (having touched a bat, having been bitten by a bat, or having been scratched by a bat) and 52 (2%) to have ever been bitten by a bat. Of 203 participants with bat contact, 3 (1%) had received rabies vaccination. No participant had neutralizing antibodies to phylogroup II lyssaviruses, but >50% of bats had neutralizing antibodies to these lyssaviruses. Even though we found no evidence of phylogroup II lyssavirus exposure among humans, persons interacting with bats in the area could benefit from practicing bat-related health precautions.

Bat and Lyssavirus Exposure among Humans in Area that Celebrates Bat Festival, Nigeria, 2010 and 2013.

Rabies virus infection is an endemic disease which remains central to public health issues. The presence of epigenetics associated with the over-expression of  in mice brain infected with rabies virus was investigated for the first time. A significant increase ( < 0.05) in mRNA level of  as the disease progressed was observed. The percentage of methylated region was significantly ( < 0.05) higher in infected tissues relative to uninfected. DNA methyltransferase (DNMT) and histone acetylase (HAT) activities were also significantly ( < 0.05) higher in most infected brain tissues. HAT had a relatively higher proportion than DNMT when compared to the normal. Paradoxically, it can be inferred that the rabies virus uses epigenetic mechanisms as a means of manipulating host genes, as there was an increase in global DNMT and HAT activities with concomitant increase in  promoter methylation and expression.

Rabies virus infection in mice up-regulates  via epigenetic modifications.

Bats are often consumed by some ethnic groups in Nigeria despite association of bats with many important emerging viruses. More than 300 bats representing eight species were captured during 2010-2011 in eight locations of northern Nigeria. Available fecal swabs (n = 95) were screened for the presence of arenaviruses, CoVs, paramyxoviruses (PMVs), reoviruses, rhabdoviruses, and influenza viruses using generic reverse transcription-polymerase chain reaction assays. Here, we document the detection of CoVs, PMVs, reoviruses, and rotaviruses (RVs) in Nigerian bats. The Nigerian bat CoVs are grouped within other bat SARS-CoV-like viruses identified from Ghana in a sister clade next to the human SARS-CoV clade. The phylogenetic analysis indicated a broad range of RVs present in Nigerian bats, some cluster with human RVs and some represent novel species. Our study adds that continuing global surveillance for viruses in bats to understand their origin, adaptation, and evolution is important to prevent and control future zoonotic disease outbreaks.

Identification of Coronaviruses, Paramyxoviruses, Reoviruses, and Rotaviruses among Bats in Nigeria.

Infection with the deadly rabies virus (RABV) leads to alteration of cellular gene expression. The RABV, similar to other neurodegenerative diseases may be implicated in neuronal death due to an imbalance in Ca homeostasis. Parvalbumin (PV) and Secretagogin (Scgn), two members of the Calcium-Binding Proteins (CBPs) are useful neuronal markers responsible for calcium regulation and buffering with possible protective roles against infections. This study investigated whether infection with rabies virus causes variance in expression levels of PV and Scgn using the Challenge virus standard (CVS) and Nigerian Street Rabies virus (SRV) strains. Forty-eight, 4-week-old BALB/c mice strains were divided into two test groups and challenged with Rabies virus (RABV) infection and one control group. The presence of RABV antigen was verified by direct fluorescent antibody test (DFAT) and real-time quantitative PCR (qRT-PCR) was used to assess PV and Scgn gene expression. Infection with both virus strains resulted in significant (p < 0.05) increases in expression during early infection. Mid-infection phase caused reduced expression for both genes. However, as infection progressed to the terminal phase, a lower increase in expression was measured. Gene expression and viral load correlation indicated no positive relationship. Neurons with these CBPs may have a greater capacity to buffer calcium and be more resistant to degenerative changes caused by RABV. This implies that, when PV and Scgn expression levels are kept adequately high, the integrity of neurons may be maintained and degeneration caused by RABV infection may be prevented or stopped, hence, these are possible constituents of effective rabies therapy.

Rabies virus infection is associated with alterations in the expression of parvalbumin and secretagogin in mice brain.

Rabies virus (RABV) infection leads to a fatal neurological outcome in humans and animals and is associated with major alterations in cellular gene expression. In this study, we describe the effects of RABV infection on the mRNA expression levels of two genes, encoding the Ca-binding proteins (Ca-BPs) calbindin D-28K (Calb1) and calretinin (Calb2), in the brains of BALB/c mice. Sixty 4-week-old mice were divided into two test groups and one control group. Mice were inoculated intramuscularly with either a street rabies virus (SRV) strain or a challenge virus standard (CVS-11) strain and sacrificed at 3-day intervals up to day 18 postinfection. A direct fluorescent antibody test (DFAT) was used to verify the presence of RABV antigen in brain tissues, and real-time quantitative PCR (RT-PCR) was used to assess gene expression. Infection with both RABV strains resulted in significant (p < 0.05) increases in Calb1 and Calb2 expression in the test animals when compared with the controls at various time points in the study. Correlation analysis indicated very weak insignificant (p > 0.05) negative and positive relationships, respectively, between Calb1 expression (r = -0.04) and Calb2 expression (r = 0.08) with viral load (CVS-11 strain). Insignificant (p > 0.05) relationships were also observed Calb1 expression (r = -0.28) and Calb2 expression (r = 0.06) and viral load for the SRV strain.The observed alterations in Calb1 and Calb2 expression in this study indicate possible impairments in neuronal Ca buffering and Ca homeostasis as a result of RABV infection and, consequently, possible involvement of calbindin-D28K and calretinin in the neuropathogenesis of rabies.

Article	Year
Complete genome sequence of a street rabies virus isolated from a dog in Nigeria. Genome announcements\| PubMed ID: 23469344	2013
Heat induced epitope retrieval for rabies virus detection by direct fluorescent antibody test in formalin-fixed dog brain tissues. Open veterinary journal\| PubMed ID: 30237978	2018
Human Exposure to Novel Bartonella Species from Contact with Fruit Bats. Emerging infectious diseases\| PubMed ID: 30457529	2018
Induction of Rabies Virus Infection in Mice Brain may Up and Down Regulate Type II Interferon gamma via epigenetic modifications. Metabolic brain disease\| PubMed ID: 32172520	2020
Molecular study of rabies virus in slaughtered dogs in Billiri and Kaltungo local government areas of Gombe state, Nigeria. Acta tropica\| PubMed ID: 32243880	2020
Bat and Lyssavirus Exposure among Humans in Area that Celebrates Bat Festival, Nigeria, 2010 and 2013. Emerging infectious diseases\| PubMed ID: 32568051	2020
Rabies virus infection in mice up-regulates via epigenetic modifications. Virusdisease\| PubMed ID: 32904877	2020
Identification of Coronaviruses, Paramyxoviruses, Reoviruses, and Rotaviruses among Bats in Nigeria. The American journal of tropical medicine and hygiene\| PubMed ID: 33534762	2021
Rabies virus infection is associated with alterations in the expression of parvalbumin and secretagogin in mice brain. Metabolic brain disease\| PubMed ID: 33783673	2021
Rabies virus infection is associated with variations in calbindin D-28K and calretinin mRNA expression levels in mouse brain tissue. Archives of virology\| PubMed ID: 37069450	2023

Grace S. N. Kia

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