Viruses like SARS-CoV-2 keep changing their genetic makeup to escape human immune response. One of the ways they can change rapidly is 'Genetic Recombination', which happens in a person co-infected with two different SARS-CoV-2 strains simultaneously.

Researchers from the Department of Microbiology & Cell Biology, and the Centre for Infectious Diseases Research, Indian Institute of Science Bangalore, have found that recombination events had escalated during the Omicron wave, which made the virus more immune-evasive and infectious.

Genetic recombination is an essential driver of SARS-CoV-2 evolution, which requires the coinfection of a single host cell with different SARS-CoV-2 strains. The team comprising Rishad Shiraz and Shashank Tripathi found that in the event of recombination, two-parent strains can give rise to a hybrid 'Recombinant' virus, which has features of both parent strains. Researchers examined the role of recombination in the evolution of SARS-CoV-2 since the beginning of the pandemic.

“Understanding the drivers, mechanisms, and trajectories of SARS-CoV-2 evolution is crucial to plan mitigation measures, especially vaccine design. We have discovered an unprecedented escalation in the recombination of SARS-CoV-2 during the Omicron wave. The cause of this could be more co-infections and few molecular changes in viral proteins of Omicron. The effect of this was increased transmission and immune evasion by the Omicron strains,” the team informs India Science Wire.

“Understanding the drivers, mechanisms, and trajectories of SARS-CoV-2 evolution is crucial to plan mitigation measures, especially vaccine design. We have discovered an unprecedented escalation in the recombination of SARS-CoV-2 during the Omicron wave. The cause of this could be more co-infections and few molecular changes in viral proteins of Omicron. The effect of this was increased transmission and immune evasion by the Omicron strains,” the team informs India Science Wire.

“We curated SARS-CoV-2 full-length genome sequences from all the public databases, deposited from the start of the pandemic till the peak of the Omicron wave. We analysed these sequences using specialized programs to identify recombinant lineages, their parent strains, and their prevalence across time and geographical locations. We also examined the protein sequence changes accumulated through recombination, especially in the Spike of Omicron strains, which were reported to increase viral immune evasion and transmission,” researchers explain.

Enhanced recombination can increase the chances of new strains emerging, therefore, tracking such recombination through regular virus sequencing is very important.

“In humans and wild animals, continuous genomic surveillance of SARS-Cov-2 globally is crucial for understanding the SARS-CoV-2 evolutionary trajectories and pandemic preparedness,” researchers observe.

The study has been published in Journal of Medical Virology.

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