Covid Variant BA.4.6 outperforms dominant BA.5 across the US for the first time

Covid Variant BA.4.6 outperforms dominant BA.5 across the US region for the first time.

The CDC's weekly update of variable pedigree data today provided the most unambiguous indication yet that a new Omicron strain dubbed BA.4.6 may be able to outcompete BA.5, now dominant in the United States.

While BA.4.6 has been in the US since at least May, it remained under 2% of new serial cases through July, when it began to gradually rise, even as BA.5 continued to do the same. As of this week's CDC report, it currently stands at 7.5%. But the natural wrinkles come when the regionally varying proportions are broken down.

In the area defined primarily by California, Arizona, and Nevada, BA.4.6 lags even behind BA.4, with a share of 2.8% and 3.3%, respectively. The BA.5 in the region is 93% and is rising.

Compare that with the Nebraska, Iowa, Kansas, and Missouri areas aggregated by the Centers for Disease Control and Prevention, where the BA.4.6 rate rose to 17.2% of all new cases sequenced, and the BA.5 decreased for the first time in the past week to 78.5%. It peaked at 80% there in the first week of August and declined slightly in the following three weeks. Over the same time frame, BA.4.6 nearly doubled in those states from 8.7%.

From a single analysis of the GISAID data, the new Omicron variant has a 16% growth advantage over BA.5, which makes it all the more surprising that it has outperformed BA.5 in some US regions while making little progress in others.

The reasons for these differences in the region are not clear. Los Angeles' director of public health, Barbara Ferrer, told the Los Angeles Times last week.

"I don't know if there is something to do with the environment, the weather, or certain conditions, including the vaccination status of the population in those communities, as well as the previous infections that people had," she said. "It's hard for us to elicit all that from California here. I know we need to oversee it."

According to data cited by The Times, "BA.4.6 makes up only 1.5% of cases in Los Angeles County, a rate that remains relatively the same compared to the previous week."

GISAID data show that in many other countries where BA.4.6 made significant progress, it quickly faded in the face of another new highly mutated Omicron variant, BA.2.75. It was first serialized in May in India, where it spread rapidly.

According to the World Health Organization, "BA.2.75 has nine additional spikes in height compared to BA.2." Some of these modifications could allow the virus to bind to cells more efficiently, said Matthew Pinker, director of clinical virology at the Mayo Clinic in Rochester, Minn.

In countries such as Spain, Germany, the United Kingdom, Ireland, and Italy, where BA.4.6 initially made its way against a semi-uniform dominance by BA.5, BA.2.75 overtook both of these predecessors and became dominant.

While BA.2.75 exists in the United States, it is hardly just an image. It is not explicitly tracked on the CDC's Variable Ratio Control Panel but has been combined with parent lineage BA.2, which currently stands at 0%. Los Angeles, one of the largest counties in the country, has sequenced only four cases so far. Whether BA.2.75 makes headway here in the fall and winter.

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