Over the previous three years and a number of waves of an infection, SARS-CoV-2 continues to evolve by accumulating genetic variations. Uncommonly, a co-infection of a number of lineages of the virus might lead to recombinations between genomes which may give rise to chimeric genomes, in any other case referred to as recombinants.
While most recombinations could not give rise to viable viruses, there’s a uncommon risk that recombination might lead to the creation of a new lineage of the virus with higher purposeful capabilities than both of the mother or father lineages. Genome sequencing and surveillance of viruses might effectively establish such recombinants, as they’d have the variant complement of two-parent lineages.
Several recombinant lineages of SARS-CoV-2 have emerged throughout the course of the COVID-19 pandemic. The PANGO community, a global consortium of researchers for naming SARS-CoV-2 lineages, has a longtime system for figuring out and designating recombinants of SARS-CoV-2. Currently, near 100 recombinant lineages have been designated by the PANGO community, all of which start with the letter ‘X’, adopted by a letter to indicate the order of their detection.
Two recombinant lineages of SARS-CoV-2 are presently 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 recognized in New York City in October 2022, is presently designated as a Variant of Interest (VOI) by the WHO. Tracking Omicron recombinants is vital for the early detection of lineages which will have purposeful benefits over presently circulating variants comparable to elevated 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 lineage of the virus and is a descendent of the XBB lineage. The earliest sequence of this lineage belongs to a viral genome remoted in New York in January 2023 and the lineage has been seen to be circulating predominantly in India.
A major variety of the genomes from exterior India, comparable to in the U.S. and Singapore, have been linked to worldwide journey, largely from India. The variant has so far been detected in no less than 14 nations throughout the world.
The lineage XBB.1.16 has quite a few mutations in frequent with the VOI XBB.1.5. Additional key mutations together with E180V and T478R in the Spike protein and I5T in ORF9b are current in the XBB.1.16 lineage.
In distinction, the XBB.1.5 has the mutation T478K in the Spike space. T478R is related to immune escape, or the skill of the virus to evade antibodies raised from earlier infections or vaccines. The ORF9b I5T mutation can be present in the lineage XBB.1.9 and has been broadly believed to lend a development benefit to the virus.
Preliminary knowledge additionally counsel that XBB.1.16 has the next development benefit over presently circulating SARS-CoV-2 lineages, together with the XBB.1.5 lineage.
Why is XBB.1.16 inflicting considerations in India?
Amid the ongoing improve in the variety of seasonal Influenza H3N2 circumstances, an uptick in COVID-19 circumstances is being seen in India in March 2023, regardless of the low variety of exams, as the complete variety of energetic COVID-19 circumstances throughout the nation elevated to over 6,000.
The fast-spreading XBB.1.16 lineage is believed to be chargeable for the current spike in COVID-19 circumstances in India.
Although knowledge from systematic genomic surveillance in India is proscribed, XBB.1.16 as we speak accounts for greater than 30% of all the sequenced genomes in March 2023, and its proportion has been seen to be rising in the previous few weeks, to turn into the main lineage in some states.
To date, the lineage has been present 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 variety of XBB.1.16 circumstances, however with the caveat that this could possibly be biased as not all states proactively sequence samples.
The earliest genomes of XBB.1.16 obtainable from India and deposited in GISAID, a worldwide database for pathogen sequences, have been from early February 2023, from Karnataka and Maharashtra.
Based on preliminary knowledge, there is no such thing as a proof to counsel that infections with the XBB.1.16 lineage differ in scientific severity from these attributable to different Omicron lineages, though the increased development benefit additionally probably the increased immune escape might result in the next danger of reinfection with XBB.1.16 in comparison with different circulating Omicron lineages.
Protecting the susceptible via time-tested means might subsequently considerably blunt the rise in infections. It will subsequently be essential to watch the prevalence of XBB.1.16 and the scientific correlates in the coming days if circumstances proceed to extend.
In abstract
Genomic surveillance of SARS-CoV-2 has repeatedly confirmed to be important for the early detection and monitoring of new viral lineages together with recombinants. Although vaccination and hybrid immunity in opposition to the illness stay efficient in defending in opposition to extreme COVID-19 signs, additional analysis is important to find out the affect of newly evolving lineages on how the pandemic progresses.
As individuals proceed to get contaminated and new lineages of the virus proceed to emerge, time-tested preventive measures comparable to carrying masks and getting vaccinated, when you have not obtained the scheduled doses are extra vital than ever, since the COVID-19 pandemic is much from over.
Bani Jolly and Vinod Scaria are researchers at the CSIRs Institute of Genomics and Integrative Biology in Delhi. All opinions expressed are private.
