Genome Mapping of Chandipura Virus

Why in the News?

The Gujarat Biotechnology Research Centre (GBRC) in Gandhinagar has released the first complete genome map of the Chandipura Vesiculovirus (CHPV). This virus, which causes encephalitis or brain swelling, was behind a significant number of cases during the Gujarat outbreak in July-August.

What’s in Today’s Article?

• Genome Mapping
• Chandipura
• Key Findings of the Study
• India’s Genome Mapping

Genome mapping

About

• Genome mapping is the process of identifying the locations of genes and significant sequences within a genome.
• It offers valuable insights into a virus’s origin, how it is evolving, and whether it has mutations that could increase its transmissibility or severity.

What is a gene?

A gene is a segment of DNA that carries the instructions for producing proteins or functional RNA molecules. Genes are the fundamental units of heredity, inherited from parents and arranged on chromosomes within the cell nucleus.

There are two types of genome maps:

• Genetic maps, which display the relative positions of genes based on recombination frequency.
• Physical maps, which depict the exact positions of genes based on DNA base pairs.

Significance

• Understanding Genetic Disorders: Genome mapping aids in identifying genes linked to genetic diseases, enabling early diagnosis, targeted treatments, and genetic counselling.
• Personalized Medicine: It allows for the development of personalized treatment plans based on an individual’s genetic profile, enhancing the effectiveness of therapies.
• Agriculture: In crops and livestock, genome mapping helps identify desirable traits, supporting breeding programs aimed at improving yield, disease resistance, and quality.
• Vaccine and Drug Development: Mapping the genomes of pathogens, such as viruses, is crucial for developing effective vaccines and drugs, as demonstrated in the battle against infectious diseases like COVID-19 and CHPV.
• Evolutionary Studies: Genome maps offer insights into evolutionary relationships between species by comparing genetic sequences across different organisms.

Challenges

• Complexity of Genomes: Larger genomes, like those of plants and animals, are highly complex and contain repetitive sequences, making precise mapping a challenging task.
• Ethical Concerns: Genome mapping raises privacy and ethical issues, particularly regarding the use and access to genetic information.
• Cost and Resources: Despite decreased costs, genome mapping, especially for large-scale projects, still demands substantial financial investment and technological resources.
• Data Interpretation: After mapping, understanding the significance of various genes and sequences remains difficult due to limited knowledge of their functions.

Chandipura Vesiculovirus

• About:Chandipura is a viral infection that can cause outbreaks of Acute Encephalitis Syndrome (AES), also known as brain swelling.

Symptoms include fever, headache, and encephalitis, which can lead to convulsions, coma, and death, typically within a few days of onset.

Family and Vectors

• CHPV is a member of the Rhabdoviridae family, which includes viruses such as the lyssavirus (rabies).
• It is transmitted by various sandfly species, including Phlebotomine sandflies and Phlebotomus papatasi, as well as Aedes aegypti mosquitoes (which also spread dengue).
• The virus resides in the salivary glands of these insects and is transmitted to humans or other vertebrates through their bites.

Transmission and Progression of Infection

• After transmission, CHPV can spread to the central nervous system, causing encephalitis (brain inflammation).
• Initial symptoms include flu-like signs such as fever, body aches, and headaches, which can progress to altered mental status, seizures, and encephalitis.
• Additional symptoms may involve respiratory distress, bleeding tendencies, or anemia.
• The infection often advances swiftly, with death occurring within 24-48 hours of hospitalization.

Most Affected Population

• The virus primarily impacts children under the age of 15.
• Infections are often seasonal, with outbreaks commonly occurring during times of increased sandfly populations, especially during monsoon seasons.

Historical Outbreaks and Endemic Regions

• CHPV was first identified in 1965 during an investigation into dengue and chikungunya in Maharashtra.
• Major outbreaks occurred in 2003-2004 in Maharashtra, northern Gujarat, and Andhra Pradesh, leading to over 300 deaths among children.
  • During the 2004 outbreak in Gujarat, the case fatality rate (CFR) reached 78%, while Andhra Pradesh reported a CFR of 55% in 2003.
• The infection remains endemic in central India, where the vector population is denser.
• Outbreaks are most frequently reported in rural, tribal, and peripheral areas.

 Key Findings from GBRC’s Genome Mapping of CHPV

• No Major Change in Genetic Makeup

  • The CHPV strain from the recent Gujarat outbreak is nearly identical to the 2012 strain, with only a single amino acid mutation in the glycoprotein-B gene.
  • This gene is essential for the virus’s ability to bind to human cell receptors and provoke an immune response.
  • Unlike COVID-19, CHPV has not undergone significant changes, likely due to limited population-wide antibody development and the lack of a vaccine.

• Low Viral Load but Severe Impact

  • Although RT-PCR tests showed a high Cycle Threshold (Ct) value, indicating a low viral load, the virus still caused severe symptoms.

• Indigenous Virus, Not Imported

  • Genome sequencing confirmed that the current virus strain is closely related to those from previous outbreaks in India during 2003-04 and 2007.
  • The virus is not imported from abroad and differs from strains found in Europe and Africa, confirming its circulation within India.

INDIA’s GENOME PROJECT :

India’s Genome Project is a government-funded initiative aimed at sequencing the genomes of over a thousand individuals from diverse ethnic backgrounds to create a comprehensive genome database for the country. The Genome India Project, a collaboration involving 20 institutions including the Indian Institute of Science and several IITs, is set to advance efficiencies in medicine, agriculture, and life sciences.

Significance and Potential Benefits of Human Genome Sequencing:

• Healthcare: The diverse genome samples from participants will enhance personalized medicine by predicting diseases and tailoring treatments based on individual genetic profiles. Since diseases often result from the interaction between genes and the environment, and these interactions vary across populations, this approach is particularly valuable.
• Determining Gene-Disease Links: Sequencing the human genome helps establish connections between genetic variations and diseases. For example, mapping genetic predispositions to conditions like cardiovascular disease in South Asians could lead to more targeted public health interventions.
• Better Understanding of Diseases Like Cancer: Genome sequencing can provide insights into how genetics influence cancer, allowing a shift from viewing it as an organ-specific disease to understanding it from a genetic perspective. This can improve treatment strategies and drug development.
• Drug Efficacy: Sequencing can reveal how genetic variations affect drug efficacy and potential adverse effects. This is crucial for developing medications that are effective for the Indian population, as drugs developed elsewhere may not always be suitable or effective.
• Agricultural Applications: The project will enhance India’s scientific capabilities by enabling genome mapping of crops. This will help in understanding the genetic basis of crop susceptibility to diseases and pests, potentially leading to genetically engineered solutions that reduce reliance on chemicals.
• Evolutionary Studies: The project will also contribute to global scientific knowledge by providing data on the spread and migration of various life forms in the Old World, thus offering a deeper understanding of human evolution.

Way Forward:

• Training: Expanding the training of clinicians in gene data interpretation and increasing the number of laboratories involved in sequencing is crucial. More physicians need to be trained in medical genetics to facilitate quicker and more efficient analyses.
• Data Security: Given the sensitive nature of genomic data, it is essential to minimize the risk of data breaches and maintain public trust in institutions managing such data. Implementing blockchain technology could offer a practical solution to ensure the security and integrity of genomic information.
• Effective Policy: Developing a comprehensive and effective policy to govern the use of genomic information is necessary, with a strong focus on protecting the privacy of research participants. Implementing ‘dynamic consent,’ where individuals can register and continuously provide consent for their participation in research, could be a viable approach.
• Collaborative Effort: A coordinated effort is needed to balance the sharing of genomic data with individual privacy. Establishing a transparent framework that clearly defines the purpose of data collection and the duration for which it will be stored is important.

Genome sequencing holds the promise of improving our understanding of the human body and advancing treatments for previously untreatable diseases. Although there are challenges, they can be addressed and resolved with careful planning and implementation.

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