#16,573
As I mentioned last week - which was the first week that the CDC's Nowcast began tracking the BA.2 Omicron subvariant - the first few weeks tracking new variants are always chaotic, and we'd likely see several weeks of `adjustments' made to previous week's estimates.
This morning the CDC has updated their Nowcast - and not only have they revised the past few week's numbers - they have further divided their Omicron tracking into 3 subvariants (B.1.1.529, BA.1.1 & BA.2).
The newcomer is BA.1.1, a further subvariant of BA.1, and the surprise here is that according to this report, it currently comprises more than 73% of the current cases in the United States. While differential information on BA.1.1 is limited, here is what the WHO said in their last weekly epidemiological update.
The spread and prevalence of the Omicron variant
Since the designation of B.1.1.529 as a VOC on 26 November 2021, several lineages have been identified. These include Pango lineages BA.1, BA.1.1, BA.2 and BA.3, which are all being monitored by WHO under the umbrella of ‘Omicron’. BA.2 shares many mutations with BA.1, but also has a number of differences, including in the Spike protein – critically, it does not carry the Spike 69-70 deletion associated with S-gene target failure, used as a proxy for detecting BA.1, BA.1.1, B.1.1.529 and BA.3. BA.1.1 carries an additional R346K mutation, which is suspected to provide additional immune escape potential.
Most of the current evidence describing the phenotypic characteristics of the Omicron variant is based on the BA.1 Pango lineage. However, a relative increase in the BA.2 lineage has been observed in multiple countries and investigations into the characteristics of BA.2, including its transmissibility, immune escape properties and virulence, need to be prioritized independently (and comparatively) to BA.1 (WHO Tracking SARS-CoV-2 variants website).
As the following WHO chart indicates, BA.1.1 has been making up a sizable chunk of Omicron sequences deposited at GISAID over the past month.
The other big news is that last week's estimate of 3.6% of cases coming from BA.2 has been cut by more than half, to 1.6%. This week it has increased to 3.9%, showing it is slowly gaining ground.
Since these Nowcast numbers are likely subject to further fine tuning, it may take a couple of more weeks before we can confirm any trends, but with B.1.1529 in apparent retreat, it is looking like a contest between BA.2 and BA.1.1.
While we don't have a lot of data on either of these emerging variants, for now at least, we aren't seeing any signs of increased severity, or hospitalizations, around the nation. And that is good news.
If nothing else, this latest report shows that COVID variants are still battling for supremacy, and that additional `players' will likely emerge in the weeks and months ahead.
