Tracking SARS-CoV-2 Omicron variant XBB1.16

Reviewed by Emily Henderson, B.Sc.Apr 28 2023

The World Health Organization recently named the SARS-CoV-2 Omicron variant XBB1.16 a variant of interest to encourage tracking of this genetic variant of the pandemic coronavirus.

The variant was originally detected in January 2023 in India. The rise in cases of COVID-19 in that country at that time made health offices suspect that it might be a more infectious form of the Omicron XBB strains.

From national genetic surveillance, XBB1.16 is now causing about 12% of COVID-19 cases in the United States. If indeed this strain is more transmissible, that proportion would grow over time, said Dr. Pavitra Roychoudhury, acting instructor, Division of Virology, Department of Laboratory Medicine and Pathology at the University of Washington School of Medicine in Seattle.

In the Washington state area, XBB1.16 is causing about 10% of current COVID-19 cases. It was first detected in the Seattle area in February through  the Centers for Disease Control and Prevention's airport surveillance program.

The Virology Lab at UW Medicine had its first detection of the XBB1.16 strain in a sample it received in early March 2023.

With the closure of several COVID testing sites during the winding down of the COVID-19 Public Health Emergency and the reliance of many symptomatic people on home testing, there has been a decline in PCR laboratory testing for the COVID virus. This is affecting surveillance at a fine-grade level, due to the reduction in PCR test samples.  

Although the national pandemic public health emergency is expected to expire May 11, 2023, the SARS-CoV-2 virus will remain a public health priority as the country transitions out of the emergency phase.

"As long as samples keep coming in, we at the UW Medicine virology lab will continue to conduct genomic sequencing for viral surveillance for as long as we can," said Roychoudhury, who works on COVID virus genetic tracking.

She added that at this point it is too early to tell if the XBB.1.16 strain is better at evading immunity from prior infections or vaccinations. The hypothesis is that this strain might have a combination of mutations that make it more transmissible, but Roychoudhury said that scientists do not yet have the details to confirm that. It is also not known at this time if this strain will  replace other strains that are currently circulating, or if a different variant may take off  as had happened with some prior waves of variants.  

The symptoms of COVID-19 from the XBB1.16 are like other current strains - cough, fever, general malaise. Some reports from India suggest that pink eye is seen more often with this variant of the  virus. Pink eye is an inflammation that causes redness, itchiness, and tearing or a crusty discharge.

A bit of promising news is the overall decline in COVID-19 cases in the United States as we approach the late spring and early summer seasons. Wastewater monitoring indicates a reduction in the presence of the SARS-CoV-2 coronavirus in all four U.S. regions contributing to the national data.

However, Roychoudhury added, coronavirus trackers cannot foresee what could happen in the fall when conditions, such as more people gathering indoors, once again support coronavirus transmission. "Fortunately, we have built the infrastructure and capacity to respond quickly to any future surges."