No major change in genetic makeup, no ‘selection pressure to escape immunity’

A major finding was that the virus had not changed much since the 2003-04 outbreak. “The CHPV virus isolated now from patients in Gujarat has differences only in the glycoproteins as compared to the 2003-04 virus isolates. The virus remains similar to the 2012 sample, which means that the virus did not require to evolve significantly over the last 12 years,” the GBRC report stated. When compared to the 2003-04 sample, there were four significant mutations in the glycoprotein gene — one of the five types of proteins that make the structure of the virus. That said, the glycoprotein gene is the most important one for the virus, with it being responsible for binding to human cell receptors and eliciting an immune response — just like the spike protein for Sars-CoV-2. Significantly, there was only one amino acid change in glycoprotein-B between 2012 and 2024, the researchers found. For comparison, new variants and sub-variants of Covid-19 detected every few months would have 20 or 30 mutations compared to their predecessor. “The current virus is highly similar to the isolate from 2012, with just a single amino acid substitution, suggesting that the virus has not been under selection pressure to escape immunity,” the report says. This is possibly because a significant proportion of the population did not develop antibodies against Chandipura, unlike say a fast-spreading virus like Covid-19, which by now has infected a majority of the global population. The other selection pressure comes from antibodies developed against a vaccine. CHPV does not yet have a vaccine, unlike Covid-19. Researchers said that it is difficult to assess the level of antibodies against CHPV in the population due to the absence of seroprevalence studies.

Low viral load, but nonetheless deadly

The Cycle Threshold (or Ct value) for the samples tested was high, a major clinical finding according to the researchers. In an RT-PCR test, the Ct value is the number of times the genetic material of the sample has to be amplified in order to detect the pathogen. A high Ct value implies that the viral load — the amount of virus in the sample — is quite low. “The Ct value of most of the patients was high. This means that the viral load was very less. But even this was enough to cause severe symptoms,” the researchers said. This value could not compared with previous outbreaks due to unavailability of data.

Not imported from abroad

When the researchers traced the genome sequence on the 27-strain family tree of the virus, they found it to be related to the virus isolated during previous outbreaks in India. The researchers said that even with the variations, the virus isolated during the current outbreak still closely resembled those isolated during 2003-04 and 2007 outbreaks. The current isolate is very different from strains isolated from Europe and Africa. “This means that the virus that infected patients in this outbreak was the one circulating in India and was not imported from other countries,” a health department official said.

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This is an archive article published on September 4, 2024

Genome mapping of Chandipura virus: what researchers found

The Chandipura virus has not evolved much since the 2003, when India saw its deadliest ever outbreak. Here are 3 key findings of the genome mapping.

The virus is spread by sand flies and other insects. (European Centre for Disease Prevention and Control)

The Gujarat Biotechnology Research Centre (GBRC) in Gandhinagar has published the only fully mapped genome of the Chandipura Vesiculovirus (CHPV) — the viral infection that caused at least a third of the encephalitis or brain swelling cases in Gujarat during the outbreak in July-August.

What is Chandipura?

Chandipura is a viral infection that can lead to outbreaks of Acute Encephalitis Syndrome (AES) or brain swelling. It is known to cause fever, headache, and encephalitis leading to convulsions, coma, and death, usually within a few days of the symptoms showing up. The disease’s rapid progression is one of its defining features.

Children who tested positive and died of Chandipura during this year’s outbreak reported high grade fever, severe rashes from sandfly bites, convulsions, brain swelling, liver problems, and multi-organ failure usually within 72 hours of symptoms showing up.

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In Explained | What is the Chandipura virus?

First isolated in Maharashtra in 1965, the Chandipura virus most severely affects children below the age of 15. It can be transmitted by sandflies, ticks, as well as the Aedes aegypti mosquitoe which also transmits infections such as dengue and chikungunya. Sandflies were responsible for spreading the virus during the current outbreak, researchers found.

With no specific treatment, mortality due to the virus can be as high as 56 to 75 per cent, as seen in Andhra Pradesh and Gujarat in 2003 during India’s worst ever Chandipura outbreak that killed 322 children. The case fatality ratio stood at about 45 per cent during the current outbreak, according to data till August 16.

What is genome mapping? Why is it important?

In simple words, genome mapping refers to the process of determining the location of genes on an organism’s chromosomes. Scientists at the GBRC undertook this process to better understand the virus which was afflicting so many children in the state.

Genome mapping provides important clues on where a virus comes from, how it is changing, and whether it has any mutations that are likely to make it more transmissible or deadly. Sequencing viral genomes helps researchers keep an eye on viruses that may lead to outbreaks in the future.

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What did researchers at the GBRC find?

The genome mapping yielded a few important findings.

01
No major change in genetic makeup, no ‘selection pressure to escape immunity’
A major finding was that the virus had not changed much since the 2003-04 outbreak. “The CHPV virus isolated now from patients in Gujarat has differences only in the glycoproteins as compared to the 2003-04 virus isolates. The virus remains similar to the 2012 sample, which means that the virus did not require to evolve significantly over the last 12 years,” the GBRC report stated.

When compared to the 2003-04 sample, there were four significant mutations in the glycoprotein gene — one of the five types of proteins that make the structure of the virus. That said, the glycoprotein gene is the most important one for the virus, with it being responsible for binding to human cell receptors and eliciting an immune response — just like the spike protein for Sars-CoV-2.

Significantly, there was only one amino acid change in glycoprotein-B between 2012 and 2024, the researchers found. For comparison, new variants and sub-variants of Covid-19 detected every few months would have 20 or 30 mutations compared to their predecessor.

“The current virus is highly similar to the isolate from 2012, with just a single amino acid substitution, suggesting that the virus has not been under selection pressure to escape immunity,” the report says.

This is possibly because a significant proportion of the population did not develop antibodies against Chandipura, unlike say a fast-spreading virus like Covid-19, which by now has infected a majority of the global population. The other selection pressure comes from antibodies developed against a vaccine. CHPV does not yet have a vaccine, unlike Covid-19.

Researchers said that it is difficult to assess the level of antibodies against CHPV in the population due to the absence of seroprevalence studies.
02
Low viral load, but nonetheless deadly
The Cycle Threshold (or Ct value) for the samples tested was high, a major clinical finding according to the researchers.

In an RT-PCR test, the Ct value is the number of times the genetic material of the sample has to be amplified in order to detect the pathogen. A high Ct value implies that the viral load — the amount of virus in the sample — is quite low.

“The Ct value of most of the patients was high. This means that the viral load was very less. But even this was enough to cause severe symptoms,” the researchers said. This value could not compared with previous outbreaks due to unavailability of data.
03
Not imported from abroad
When the researchers traced the genome sequence on the 27-strain family tree of the virus, they found it to be related to the virus isolated during previous outbreaks in India.

The researchers said that even with the variations, the virus isolated during the current outbreak still closely resembled those isolated during 2003-04 and 2007 outbreaks. The current isolate is very different from strains isolated from Europe and Africa.

“This means that the virus that infected patients in this outbreak was the one circulating in India and was not imported from other countries,” a health department official said.