Everything You Need To Know About Omicron Recombinant, XBB.1.16, Behind India's Latest COVID Spike

Over the past three years and multiple waves of infection, SARS-CoV-2 has continued to evolve by accumulating genetic variations. Uncommonly, a co-infection of multiple virus lineages 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 creating a new virus lineage with better functional capabilities than either of the parent lineages. Genome sequencing and surveillance of viruses could efficiently identify such recombinants, as they would have the variant complement of two-parent lineages.

Several recombinant lineages of SARS-CoV-2 have emerged during the course of the COVID-19 pandemic. The PANGO network, an international consortium of researchers for naming SARS-CoV-2 lineages, has an established system for identifying and designating recombinants of SARS-CoV-2. Currently, close to 100 recombinant lineages have been designated by the PANGO network, all of which begin with the letter ¡®X¡¯, followed by a letter to denote the order of their detection.

Two recombinant lineages of SARS-CoV-2 are currently designated as ¡®Variants Under Monitoring¡¯ 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. Tracking Omicron recombinants is vital for the early detection of lineages that may have functional advantages over currently circulating variants, such as increased transmissibility in populations with prior immunity to the virus.

What Is The XBB.1.16 Lineage Of Sars-CoV-2?

First detected in SARS-CoV-2 sequences from India, the XBB.1.16 is a recombinant virus lineage and a descendent of the XBB lineage. The earliest sequence of this lineage belongs to a viral genome isolated in New York in January 2023, and the lineage has been seen to be circulating predominantly in India.

Many genomes from outside India, such as in the U.S. and Singapore, have been linked to 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 several 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 the Spike area. T478R is associated with immune escape, or the ability of the virus to evade antibodies raised 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.

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Why Is XBB.1.16 Causing Concerns In India?

Amid the ongoing increase in the number of seasonal Influenza H3N2 cases, an uptick in COVID-19 cases is being seen in India in March 2023, despite the low number of tests, as the total number of active COVID-19 cases across the country 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 March 2023, and its proportion has been seen to be increasing in the past few weeks to become the major lineage in some states.

To date, the lineage has been found 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 highest number of XBB.1.16 cases, but with the caveat that this could be biased as not all states proactively sequence samples.

In Summary

As people continue to get infected and new lineages of the virus continue to emerge, time-tested preventive measures such as wearing masks and getting vaccinated if you have not received the scheduled doses are more critical than ever since the COVID-19 pandemic is far from over.

• Several recombinant lineages of SARS-CoV-2 have emerged during the course of the COVID-19 pandemic.
• First detected in SARS-CoV-2 sequences from India, the XBB.1.16 is a recombinant virus lineage and a descendent of the XBB lineage.
• The fast-spreading XBB.1.16 lineage is believed to be responsible for the recent spike in COVID-19 cases in India.