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22 March 2023: XBB.1.16, the Omicron recombinant behind India’s new COVID spike

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Context: 

SARS-CoV-2 has evolved over the last three years and many waves of infection by accumulating genetic variants. A co-infection of various lineages of the virus may result in recombinations across genomes, giving birth to chimeric genomes, also known as recombinants.

Two recombinant lineages of SARS-CoV-2

  • While most recombinations do not result in live viruses, there is a small chance that recombination will result in the production of a new viral lineage with higher functional capabilities than either of the parent lineages. Because they would have the variation complement of two-parent lineages, genome sequencing and viral monitoring might effectively discover such recombinants.
  • Several recombinant SARS-CoV-2 lineages have developed during the COVID-19 epidemic.

The PANGO network:

    • It is an international team of researchers tasked with naming SARS-CoV-2 lineages and has a well-established procedure for detecting and recognizing SARS-CoV-2 recombinants.
    • The PANGO network has currently recognized almost 100 recombinant lineages, all of which begin with the letter “X,” followed by a letter denoting the sequence of findings.

World Health Organization

    • It has recognized two recombinant lineages of SARS-CoV-2 as “variants under monitoring”:
      • XBB, a recombinant of Omicron, has sublineages BA.2.10.1 and BA.2.75.
        • The WHO has declared the lineage XBB.1.5, a sublineage of the XBB discovered in New York City in October 2022, as a variant of interest (VOI).
      • XBF is a recombinant of BA.5.2.3 and BA.2.75.3 Omicron sublineages.

XBB.1.16 lineage of SARS-CoV-2

  • The XBB.1.16 virus, discovered in SARS-CoV-2 sequences from India, is a recombinant lineage of the virus and a descendant of the XBB lineage.
    • The lineage XBB.1.16 shares many mutations with the VOI XBB.1.5.
    • The XBB.1.16 lineage also contains important alterations such as E180V and T478R in the spike protein and I5T in ORF9b.
    • The lineage has so far been discovered in samples from Telangana, Maharashtra, Karnataka, Gujarat, Delhi, Puducherry, Haryana, Himachal Pradesh, and Odisha.
    • The states of Telangana, Karnataka, Gujarat, and Maharashtra have reported the most XBB.1.16 occurrences; however, this may be skewed because not all states aggressively sequence samples.
  • The initial sequence of this lineage was found in a viral genome recovered in New York in January 2023, and the lineage has been shown to be mostly circulating in India.
  • To date, the variation has been identified in at least 14 nations throughout the world.

Major concerns: 

  • Despite the low number of tests, an increase in COVID-19 cases was noticed in India in March 2023, despite the continuous increase in seasonal influenza H3N2 cases, as the total number of active COVID-19 cases across the country grew to over 6,000.
    • Although data from systematic genomic monitoring in India is scarce, XBB.1.16 now accounts for more than 30% of all sequenced genomes as of March 2023, and its fraction has been found to increase in recent weeks, becoming the dominant lineage in several states.
  • The rapidly spreading XBB.1.16 lineage is thought to be to blame for the recent increase in COVID-19 infections in India.

Significance: 

  • Tracking Omicron recombinants is critical for the early discovery of lineages that may have functional benefits over currently circulating variations, including greater transmissibility in populations that had previously been immune to the virus.

Way forward: 

  • Although vaccination and hybrid immunity remain beneficial in preventing severe COVID-19 symptoms, further study is needed to establish the effects of newly developing lineages on how the pandemic proceeds.
  • As more individuals become ill and new viral lineages develop, time-tested preventative measures such as wearing masks and being vaccinated become more crucial than ever, since the COVID-19 pandemic is far from over.

Source: The Hindu