Over the past three years, SARS-CoV-2 has continued to evolve by accumulating genetic variations. A co-infection of multiple lineages of the virus could result in recombinations between genomes that can give rise to chimeric genomes or recombinants. While most recombinations may not give rise to viable viruses, a rare possibility exists where recombination could result in the creation of a new lineage of the virus with better functional capabilities than either of the parent lineages.
Genomic 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 has an established system for identifying and designating recombinants of SARS-CoV-2, and currently, close to 100 recombinant lineages have been designated. Two recombinant lineages of SARS-CoV-2, XBB, and XBF, are currently designated as ‘Variants Under Monitoring’ by the World Health Organization. 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.
XBB.1.16, a recombinant lineage of the virus, is a descendant of the XBB lineage first detected in SARS-CoV-2 sequences from India. The fast-spreading XBB.1.16 lineage is believed to be responsible for the recent spike in COVID-19 cases in India. The lineage has been found in samples from Telangana, Maharashtra, Karnataka, Gujarat, Delhi, Puducherry, Haryana, Himachal Pradesh, and Odisha. To date, the lineage has been detected in at least 14 countries across the world. Preliminary data suggest that XBB.1.16 has a higher growth advantage over currently circulating SARS-CoV-2 lineages, including the XBB.1.5 lineage.
Protecting the vulnerable through time-tested means could significantly blunt the rise in infections. It will be crucial to monitor the prevalence of XBB.1.16 and the clinical correlates in the coming days if cases continue to increase. 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 important than ever, since the COVID-19 pandemic is far from over.
Key Takeaways in a Nutshell – Health Newstrack
– SARS-CoV-2 continues to evolve and accumulate genetic variations through multiple waves of infection, and co-infection of multiple lineages could result in recombinants or chimeric genomes.
– The XBB.1.16 lineage of SARS-CoV-2 is a recombinant lineage and is believed to be responsible for the recent spike in COVID-19 cases in India. It has a higher growth advantage and possibly higher immune escape than other circulating Omicron lineages.
– Genomic surveillance of SARS-CoV-2 is essential for the early detection and tracking of new viral lineages including recombinants, and time-tested preventive measures such as wearing masks and getting vaccinated remain important.