HOW ARE VARIANTS CREATED

• SARS-CoV-2, the virus that causes COVID-19, is an RNA virus which evolves by accumulating genetic errors in its genome, produced when the virus infects a person and makes copies of itself inside the host’s cells.
• Also called mutations, errors are by-product of replication of SARS-CoV-2 inside the cell and may be carried forward as the virus continues to infect people
• When viruses having a specific set of errors or mutations infect a number of people, this forms a cluster of infections descending from a common parental virus genome and is known as a lineage or a variant of the virus
• The PANGO network, an open global consortium of researchers from across the world, provides a system for naming different lineages of SARS-CoV-2

WHAT IS A RECOMBINANT VARIANT

Process through which a virus increases its genetic diversity

Recombination

• Occurs when, in extremely rare situations, two different lineages of the virus co-infect the same cell in the host and exchange fragments of their individual genomes which generates a descendent variant having mutations that occurred in both the original lineages of the virus
• Happens in a variety of other viruses, including those that cause influenza, as well as other coronaviruses
• Occur typically in situations where two or more lineages of SARS-CoV-2 may be co-circulating in a certain region during the same time period

ARE RECOMBINANT VARIANTS MORE DEADLY?

There is little evidence to suggest that recombinant lineages have a varied clinical outcome compared to the currently dominant Omicron variant, although preliminary data from the U.K. health security agency suggests a transmission advantage over the Omicron variant. It is certain at this point in time that more data will be needed to ascertain the impact of these lineages on the epidemiology of COVID-19

WHAT ARE THE METHODS THROUGH WHICH RECOMBINANTS ARE IDENTIFIED

• Identifying and tracking recombinant lineages for SARS-CoV-2 is a challenging task. This would require specialised tools and the availability of primary (or raw) data for genome sequences as similar variant combinations could also arise from inadvertent errors in sequencing or analysis as well as contamination of sequencing experiments.
• A cluster of recombinant genomes can be designated a lineage name by the PANGO network if it can be confirmed that samples in the cluster have a common origin and descend from two individual lineages of SARS-CoV-2. Additionally, there should be at least 5 genomes in the public domain belonging to the cluster, indicating an ongoing transmission of the lineage
• Furthermore, screening the sequencing data of these samples should show no signs of contamination and meet the definition of a recombinant.

WAY FORWARD

• Since re-combinations are extremely rare occurrences, it is unclear how and why the viruses recombine
• It is, therefore, important to track recombination of SARS-CoV-2 lineages because it may lead to the generation of a viral lineage that is better at infecting people or transmitting from host to host
• Regardless of the consequences that recombination events may have on the evolution of the virus, monitoring circulating SARS-CoV-2 genomes for evidence of recombination will not only help gain a better understanding of the ongoing evolution of SARS-CoV-2 but will also be able to give one a heads up, if a more “concerning” variant of the virus were to emerge.