What are recombinants?

  • Co-infection of multiple lineages of a virus could result in recombinations between genomes which can give rise to chimeric genomes, otherwise called recombinants.
  • While most recombinations may not give rise to viable viruses, there is a rare possibility that recombination could result in the creation of a new lineage of the virus with better functional capabilities than either of the parent lineages.
  • Several recombinant lineages of SARS-CoV-2 have emerged during the course of the COVID-19 pandemic.
  • Two such recombinant lineages are currently designated as Variants Under Monitoring (VUM) by the World Health Organization — XBB, a recombinant of
  • Omicron sublineages BA.2.10.1 and BA.2.75, and
  • XBF, a recombinant of BA.5.2.3 and BA.2.75.3 Omicron sublineages. The lineage XBB.1.5, a sublineage of the XBB, first identified in New York City in October 2022, is currently designated as a Variant of Interest (VOI) by the WHO.

What is the XBB.1.16 lineage?

  • First detected in SARS-CoV-2 sequences from India, the XBB.1.16 is a recombinant lineage of the virus and is a descendent of the XBB lineage.
  • The lineage has been circulating predominantly in India. A significantly large number of the genomes from outside India, such as in the U.S. and Singapore, have been linked with international travel, mostly from India.
  • The variant has to date been detected in at least 14 countries across the world. The lineage XBB.1.16 has a number of mutations in common with the VOI XBB.1.5. Additional key mutations including E180V and T478R in the Spike protein and I5T in ORF9b are present in the XBB.1.16 lineage.
  • In contrast, the XBB.1.5 has the mutation T478K in Spike. T478R is associated with immune escape, or the ability of the virus to evade antibodies generated from previous infections or vaccines.
  • The ORF9b I5T mutation is also found in the lineage XBB.1.9 and has been widely believed to lend a growth advantage to the virus. Preliminary data also suggest that XBB.1.16 has a higher growth advantage over currently circulating SARS-CoV-2 lineages, including the XBB.1.5 lineage.

Why is XBB.1.16 a cause for concern?

  • Amid the ongoing increase in the number of seasonal influenza H3N2 cases, an uptick in COVID-19 cases is also being seen in India in the month of March, despite the low number of testing.
  • The total number of active COVID-19 cases across the country has increased to over 6,000. The fast-spreading XBB.1.16 lineage is believed to be responsible for the recent spike in COVID-19 cases in India.
  • Although data from systematic genomic surveillance in India is limited, XBB.1.16 today accounts for more than 30% of all the sequenced genomes in the month of March 2023, and its proportion has been seen to be increasing in the past few weeks. The States of Telangana, Karnataka, Gujarat and Maharashtra have reported the highest number of XBB.1.16 cases.
  • However, this could be biased as not all States proactively sequence their samples. Based on preliminary data, there is no evidence to suggest that
  • infections with the XBB.1.16 lineage differ in clinical severity from those caused by other Omicron lineages although the higher growth advantage and immune escape could lead to a higher risk of reinfection with XBB.1.16 compared to other circulating Omicron lineages.
  • Protecting the vulnerable through time-tested means could therefore significantly blunt the rise in infections.


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