A New Variant is Outcompeting XBB.1.5

Multiple viruses are gaining in prevalence. Norovirus, Rotavirus and Coronavirus

While looking at the NY variant update that came out yesterday, I noticed XBB.1.5 lost some ground and two variants expanded. According to the update, it shows BQ.1.1 and BA.5 expanding in prevalence. XBB.1.5 is brown on the graph below. XBB.1.5 declined from 45.5% to 39.2%. BQ.1.1 went from 20.7% to 26.2%. The more impressive growth was in BA.5, increasing from 9.2% to 15.3%.

After spending most of the night researching what is going on, it looks like BA.5 has been traveling the world, learning new tricks. BA.5.2.48 was first sequenced in Guangdong, China, on October 5, 2022. That’s before XBB.1.5 was sequenced in the U.S. on October 22, 2022. It branched out within China, Hong Kong, and then England in December. We can see that BA.2.48 is the darker red in the picture below. It is dominating much of China.

The big picture view of the evolution below, shows where it is in relation to BA.2 and BA.5.

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Zooming in on the evolutionary tree a bit further, below.

Now we will zoom in to see the history of the sequences. We can see that it made its way from China into California and Washington State before the holidays.

Somewhere along the way, it acquired the N:Q241K mutation. Without knowing specifically what it does, we do know quite a bit about the N-protein.

Published on December 30, 2022, “The role of SARS-CoV-2 nucleocapsid protein in antiviral immunity and vaccine development”

This study says, “The SARS-CoV-2 N-protein plays pivotal roles in inflammation, cell death, innate antiviral immunity, and adapted antiviral immunity.” (1)

”Multiple-functional CD8+ T cell responses against SARS-CoV-2 N-protein are associated with mild disease.” How could a change in the N domain give it an advantage? The other variants crushed the antibody response, so what is the next best way to gain an advantage?

It also says, ”SARS-CoV-2 N-protein induces stronger CD8+ T cell responses in COVID-19-recovered individuals.” “Furthermore, the corresponding CD8+ T cells can be maintained for months with preserved antiviral efficacy to various SARS-CoV-2 strains” (1)

If it were to gain an advantage above that of XBB.1.5 by a mutation in the N-protein, then the most likely answer is to beat the next most common immune response. That is the T-cell response. Let’s hope I am wrong, but selective pressure tends to dictate its next move.

BA.5.2.48 likely hitched a ride over from the U.K., into New York and Chicago as well as California and Washington. This is a great example of how COVID keeps moving around the world. Once it gains an advantage anywhere on Earth, it can move in from multiple angles via international air travel. Until we figure out how to get that under control, this will likely continue at this pace for years. We are also seeing how much China has protected the world by maintaining COVID zero all this time. Unfortunately, we didn’t take advantage of it. Instead, we were the world’s super-spreaders.

On January 24th, another 622 people died. The total number of people that have died since 2020, as we go into the 4th year of this, is over 1,110,000.

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Be aware of the multiple viruses that are increasing now. Norovirus, rotavirus, and coronavirus (common cold). Co-infections with these and COVID can be more severe.

Note below, how much more prevalent the coronavirus (common cold) is this year compared to last year. A higher prevalence than last year and a month earlier than last year.