Genome Mapping of Chandipura Virus: Key Findings and Implications

Genome Mapping of Chandipura Virus: Key Findings and Implications

Sub : Sci

Sec :  Biotech

Why this is in News?

The Gujarat Biotechnology Research Centre (GBRC) in Gandhinagar has successfully published the fully mapped genome of the Chandipura vesiculovirus (CHPV). This virus was responsible for causing approximately one-third of the encephalitis (brain swelling) cases reported in Gujarat during the outbreak in July-August. The genome mapping provides crucial insights into the virus and its behavior, contributing significantly to the study of CHPV.

What is Chandipura Vesiculovirus (CHPV)?

Symptoms: CHPV primarily causes encephalitis, fever, headaches, convulsions, coma, and can even lead to death within a few days of symptom onset.

Target Population: The virus most severely affects children below the age of 15.

Transmission Vectors: It is transmitted through sandflies, ticks, and the Aedes aegypti mosquito, which also spreads dengue and chikungunya. In the recent outbreak, sandflies were identified as the primary vector.

Fatality Rate: CHPV has a high mortality rate, with some outbreaks witnessing mortality as high as 75%. For example, during India’s worst outbreak in 2003, 322 children died in Andhra Pradesh and Gujarat. The fatality rate for this year’s outbreak is about 45%, as of August 16.

CHPV is a virus of the Rhabdoviridae family.

Other members such as the lyssavirus that causes rabies.

There is no specific antiretroviral therapy or vaccine available for treatment.

Disease progression can be as rapid as a patient reporting high fever in the morning, and their kidneys or liver being affected by the evening. This makes it harder to manage the symptoms.

Rhabdoviridae family:

CHPV is a member of the Rhabdoviridae family and is known to cause sporadic cases and outbreaks of AES in western, central and southern parts of India, especially during the monsoon season.

Rhabdoviridae virus: Rhabdoviridaeis a family of negative-strand RNA virus.

Vertebrates (including mammals, humans), invertebrates, plants, fungi and protozoans serve as natural.

Diseases associated with member viruses include rabies encephalitis caused by the rabies virus, and flu-like symptoms in humans.

The individual virus particles (virions) of rhabdoviruses are composed of RNA, protein, carbohydrate and lipid. 

How is it transmitted?

The virus resides in the salivary gland of these insects, and can be transmitted to humans or other vertebrates like domestic animals through bites.

The infection caused by the virus can then reach the central nervous system which can lead to encephalitis — inflammation of the active tissues of the brain.

Symptoms of CHPV infection: Initially with flu-like symptoms, acute onset of fever, body ache, headache

It may then progress to altered sensorium or seizures and

Other symptoms such as respiratory distress, bleeding tendencies, or anaemia.

The infection often progresses rapidly after encephalitis, which may then lead to mortality within 24-48 hours of hospitalisation.

 What is Genome Mapping?

Genome mapping is the process of determining the specific locations of genes on an organism’s chromosomes.

Significance: For deadly viruses like CHPV, genome mapping can provide essential information about the virus’s origin, mutations, and its evolutionary behavior. This knowledge is instrumental in developing testing kits, vaccines, and therapeutics.

GBRC Genome Mapping

Minimal Mutation Since 2003-04: The virus has not evolved much since the 2003-04 and 2012 outbreaks. Four significant mutations were detected in the glycoprotein gene when compared to the 2003-04 sample. Glycoproteins are responsible for binding the virus to human cell receptors and triggering immune responses.

Comparison with Covid-19 Mutations: While CHPV had only one significant mutation in its glycoprotein gene from 2012, Covid-19 variants showed 20 to 30 mutations every few months. This indicates that CHPV has not undergone rapid mutations to escape immunity.

Types of Genome Mapping:

Genetic Mapping (Linkage Mapping): Determines the relative position of genes based on genetic linkage and recombination frequencies.

Useful for locating genes associated with specific traits or diseases.

Physical Mapping: Identifies the physical distances between genes or markers on a chromosome, measured in base pairs.

Techniques include Restriction Mapping, Fluorescence In Situ Hybridization (FISH), and DNA sequencing.

Techniques of Genome Mapping:

Genetic Mapping Techniques:

• Linkage Analysis: Determines the likelihood that two genes or markers are inherited together based on their recombination frequency.
• Cross-Breeding (Pedigree Analysis): Observes gene inheritance patterns across generations to map gene locations.

Physical Mapping Techniques:

• Restriction Mapping: Uses restriction enzymes to cut DNA at specific sites, then measures the length of fragments to determine distances between markers.
• Fluorescence In Situ Hybridization (FISH): Involves labelling DNA probes with fluorescent dyes to locate specific genes on chromosomes.
• Contig Mapping: Assembles overlapping DNA fragments (contigs) to map a larger sequence.
• Sequencing: Modern techniques like Next-Generation Sequencing (NGS) provide high-resolution physical maps by reading DNA sequences directly.

Cycle Threshold (Ct) Value: In an RT-PCR test, the Ct value indicates the number of times genetic material in a sample needs to be amplified to detect the pathogen.

Higher Ct Value: Means lower viral load in the sample.

Lower Ct Value: Suggests a higher concentration of the virus in the sample.

Findings: The Ct values for CHPV samples were high, meaning the viral load in patients was low. Despite this, the virus caused severe symptoms in infected individuals.

Glycoprotein Gene:

The glycoprotein gene in the Chandipura vesiculovirus (CHPV) encodes for glycoproteins, which are essential proteins found on the virus’s surface. These proteins play a crucial role in:

Virus Attachment and Entry: Glycoproteins enable the virus to bind to human cell receptors, facilitating entry into the host cell and initiating infection.

Immune Response: They trigger an immune response in the host, making them a primary target for vaccine development.

Mutation in CHPV: In the Chandipura virus, four significant mutations in the glycoprotein gene were observed compared to the 2003-04 strain. These mutations affect how the virus binds to human cells but have not led to significant immune escape, unlike faster-mutating viruses like Covid-19.

The genome mapping of the Chandipura vesiculovirus by GBRC provides valuable insights into the virus’s behavior and its limited mutation since past outbreaks. The findings emphasize the need for continued research and development of vaccines and therapeutics for CHPV, especially given its high mortality rate and severe impact on children.