• Genetic mutations are the drivers of evolution of organisms.
  • Not all mutations are functional. However, the ones with a functional advantage tend to emerge over time than those without.
  • However, viruses rarely could evolve by exchanging large fragments of the genome called recombination.
  • Recombination events are rare and occur when two viruses or lineages co-infect a cell. Recombinations result in viruses that have a mixed genome, each part of the mix derived from the parent genomes which recombined.
  • While most recombinations result in a dysfunctional genome, in rare occurrences, they can bring together the best of two viruses with significant functional advantages resulting in their emergence. Such recombinations are well studied for a number of viruses, including influenza.

Recombinant lineages

  • SARS-CoV-2 also has the potential to recombine, and a number of recombinant lineages have been observed during the pandemic.
  • The PANGO network, an open and global consortium of researchers, provides a system for naming different lineages of SARS-CoV-2 and as of date, 49 recombinant lineages of SARS-CoV-2 have been detected and assigned a lineage name.
  • Recombinant lineage names start with the letter ‘X’, followed by letters that indicate the order of their detection. XA, a recombinant lineage between B.1.1.7 (Alpha) and B.1.177 lineages of the virus, was the first recombinant lineage of SARS-CoV-2 and was detected in the United Kingdom in early 2021.
  • Subsequently, recombinant lineages were also detected and designated, including lineage XB, which was detected in the United States, and lineage XC which was detected in Japan and is a recombinant of B.1.1.7 (Alpha) and the AY.29 sublineage of Delta.
  • It is important to track SARS-CoV-2 recombinant lineages as they could lead to the emergence of a lineage that is better than either of the parent lineages at infecting hosts or the ability to evade immunity elicited by vaccines.
  • Genomic surveillance for monitoring the emergence and prevalence of lineages is thus central to monitoring variants.

What is XBB lineage 

  • While Europe and North America are currently seeing an emergence of Omicron variants, especially BQ.1 and its sublineages, a recombinant lineage XBB has been emerging in Asia.
  • This lineage comes out of recombination of two Omicron sublineages BJ.1 and BA.2.75. Early data (yet to be peer-reviewed) suggest that this variant can evade a wide range of monoclonal antibodies as well as protection acquired through vaccination with or without previous infections, including with Omicron.
  • While more research will be needed to conclusively assess the growth advantage of XBB lineage, initial data suggest that the lineage may potentially outcompete previously circulating Omicron sublineages.
  • While the XBB lineage is present in multiple countries including India, XBB has been significantly emerging concurrently with a surge in COVID-19 infections in Singapore.
  • While Singapore detected its earliest XBB variant in September 2022, XBB and its sublineages account for over 50% of the genomes from Singapore in recent weeks.
  • While health authorities in Singapore suggest that severe clinical outcomes are not very likely due to XBB, the hospitalisations have increased.
  • It is probably too early to assess the clinical severity at this point.
  • The earliest genome sequence of XBB in global database was from Kolkata in August 2022. With a total of 94 genomes, India has the highest number of XBB genomes to date.
  • These genomes have been deposited from multiple States including Maharashtra, Gujarat, Tamil Nadu, and Karnataka; a majority of them are from Tamil Nadu.
  • Unlike the observations in Singapore, the increasing prevalence of XBB across India has not been associated with a spike in infections yet.
  • Monitoring the prevalence of XBB and its sublineages as well as the number of infections in the country will therefore be essential in the days ahead.
  • Apart from the recombinant variant XBB, other sub-lineages of Omicron have been emerging across the world. 

Key to detection

  • Genomic surveillance provides the key to detecting and monitoring emerging lineages including recombinant lineages of SARS-CoV-2.
  • While it is reassuring that vaccination continues to be effective in preventing severe outcomes of COVID-19, additional research efforts will be required to answer pressing questions regarding how these emerging lineages will impact the trajectory of the pandemic.
  • These trying times also calls for wider use of time-tested and effective methods like masks, ventilation, and avoidance of crowding to prevent infections, for the COVID-19 pandemic is still not over.


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