Indian Institute of Science (IISc) researchers, who are part of a multi-institutional team probing the cause of the outbreak of the Lumpy Skin Disease Virus (LSDV) which resulted in the death of about one lakh cows, have found two distinct LSDV variants circulating in India.
To investigate the current outbreak, the team collected skin nodules, blood, and nasal swabs from infected cattle in various States, including Gujarat, Maharashtra, Rajasthan, and Karnataka, in collaboration with veterinary institutes. They performed advanced whole-genome sequencing of DNA extracted from 22 samples.
According to IISc, their genomic analysis revealed two distinct LSDV variants circulating in India, one with a low number of genetic variations and another with a high number of genetic variations.
Similarities between strains
The sequence with fewer variations was genetically similar to the 2019 Ranchi and 2020 Hyderabad strains that were sequenced previously. The samples with high variations turned out to be similar to LSDV strains from an outbreak in Russia in 2015.
Ankeet Kumar, PhD. student at IISc and co-lead author of the study published in BMC Genomics, said that there are no previous reports of such highly varied LSDV strains in India. “Viruses that have DNA as the genetic material – like LSDV – are generally more stable than RNA viruses. Therefore, finding so many genetic variations was quite surprising, and could explain the severity of the disease,” he said.
Huge genetic variations
The team found a large number of genetic variations – over 1,800. These include deletions and insertions in various genes, single-letter changes in DNA (called SNPs), and genetic variations in regions between genes. Importantly, they found a large number of genetic variations in viral genes critical for binding to host cells, evading immune response, and replicating efficiently. This likely enhanced the virus’s ability to cause disease.
“Cattle developed more severe symptoms in areas where we found highly diverse strains. This suggests that the genetic variations could elevate virulence,” said Kumar.
LSDV was first found in Zambia in 1931 and remained confined to the Sub-African region until 1989, after which it started spreading to the Middle East, Russia, and other southeast European nations, before spreading to South Asia.
There have been two major outbreaks of this disease in India, the first in 2019 and a more severe outbreak in 2022.
