#17,091
Just over two weeks ago (Oct 14th) the CDC added two new Omicron subvariants to their weekly COVID NOWCAST - BQ.1 and BQ.1.1 - estimating them each to have just over a 5% share of cases in the U.S.
In yesterday's report, the CDC now estimates - that combined - these new variants now account for over 27% of current cases. Based on their increased prevalence over the past 3 reports, they appear to be doubling every 10 days or so.
Last weekend the ECDC warned that BQ.1 (and its subvariants) were likely to become dominant in the EU/EEA sometime in November.
Complicating matters, another subvariant - XBB - is making inroads across India and parts of Asia - and while it has yet to be reported in the CDC's Nowcast - has shown up in Europe, and could eventually challenge BQ.1/BQ.1.1 for dominance.
In yesterday's WHO: TAG-VE Statement on Omicron Sublineages BQ.1 and XBB, we looked at the WHO's expert committee's assessment of these two variants, which focused on their immune escape advantage; their ability to evade existing immunity gained from vaccination, previous infection, or both.
While concerning, at this point - based on very limited data - we have seen no indication that these variants produce any greater severity of illness than BA.5.
Yesterday the UK's Health Security Agency (UKHSA) added the XBB and BQ.1 subvariants to their official watch list (see below) - and while stopping short of designating them VOCs (Variants of Concern) - devoted much of their latest Technical Briefing (#47) to these recent arrivals.
First the UKHSA announcement, followed by some excerpts from the update technical briefing.UKHSA designates 2 new COVID-19 variants
The UK Health Security Agency (UKHSA) has published its latest COVID-19 variant technical briefing. It contains epidemiological data and updated analysis of COVID-19 variants currently circulating in the UK.
A number of Omicron variants are currently circulating in England, many of which have acquired mutations which may produce a degree of immune escape. Omicron sublineages BQ.1 and XBB have been given UKHSA variant designations to facilitate continued studies. Neither have currently been designated as variants of concern.
BQ.1 (V-22OCT-01) is a BA.5 sub-lineage which has been designated on the basis of rapid growth. So far, there have been 717 V-22OCT-01 sequences uploaded from the UK to the international GISAID database.
XBB (V-22OCT-02) is a recombinant lineage derived from 2 previous Omicron sublineages. Currently there are 18 UK samples in GISAID, out of a global total of 1,086; 639 samples have been uploaded from Singapore, and it is thought that XBB may be a factor in the recent spike in cases there.
Neutralisation studies are currently being undertaken at the University of Oxford. Overall, data shows significant reductions in neutralisation against several of the newly emergent variants (BA.2.75.2, BA.2.3.20 and BJ.1), compared to BA.2, BA.4 and the dominant BA.5. This suggests that, as immunity begins to wane, these newly emerging BA.2 variants may fuel future waves of SARS-CoV-2 infection.
Dr Meera Chand, Director of Clinical and Emerging Infection at UKHSA, said:
It is not unexpected to see new variants of SARS-CoV-2 emerge. Neither BQ.1 nor XBB have been designated as variants of concern and UKHSA is monitoring the situation closely, as always.Vaccination remains our best defence against future COVID-19 waves, so it is still as important as ever that people come take up all the doses for which they are eligible as soon as possible.
Some excerpts from the 32-page PDF Technical Briefing #47 follow:
Part 2. Horizon scanning: newly designatedvariants
2.1 Newly escalated variant: V-22OCT-02 (XBB recombinant)
XBB was first raised as a signal on 11 October 2022 as part of horizon scanning. This recombinant lineage is composed of 2 BA.2 parent lineages BJ.1 and BM.1.1.1, with an approximate break point between spike mutations G446S and N460K. This recombinant is characterised by the acquisition of E: T11A, Spike: V83A, H146Q, Q183E, F486S, F490S. Spike mutations inherited from BJ.1 are G339H, R346T, V445P, G446S and from BM.1.1.1 are N460K, F486V, F490S, and R493Q. XBB contains more RBD mutations at antigenic sites than any other widespread circulating variant and, according to Cao and others, is less well neutralised than either BQ.1.1 or BA.2.75.2.
From 16 October 2022 to 24 October 2022, there have been 1,104 XBB samples uploaded to GISAID from 28 countries, across 5 continents (Figure 9). Currently, the majority of samples uploaded from GISAID are from Singapore (639, 58%). Eighteen English samples have been uploaded to GISAID.
2.2 Newly escalated variant: V-22OCT-01 (BQ.1)
BQ.1 (B.1.1.529.5.3.1.1.1.1.1) was first raised as a signal in monitoring on 12 September 2022 as part of horizon scanning. This BA.5 sub-lineage has acquired spike mutations L452R, N460K, and K444T. The affinity impact of N460K is reported to be significant (Saito and others 2022, Cao and others 2022). Additionally, the BQ.1.1 sub-lineage has acquired the spike mutation R346T, a site which has been associated with a recent influx of convergent mutations and appears to infer a notable growth advantage. This sub-lineage is captured as part of UKHSA V-22OCT-01 lineage definition.
From 4 July 2022 to 24 October 2022 there have been a total of 3,207 BQ.1 samples uploaded to GISAID from 48 distinct countries, across 6 continents (Figure 10). Since it was first allocated a Pangolin lineage, BQ.1 GISAID uploads have increased by more than 75% each week. BQ.1 is most commonly uploaded from the USA (1,060) and the UK (717).
A further 3,004 BQ.1.1 samples have been uploaded to GISAID since 21 June 2022, spanning 35 countries and 6 continents. Since BQ.1.1 was first raised as a distinct signal on 20 September 2022, the total number of GISAID uploads have increased by more than 90% each week.
Additionally, 317 BQ.1.2 (Spike I666V) samples have been uploaded to GISAID with collection dates starting from 18 July 2022; 143 BQ.1.3 (Spike E619Q) samples have been uploaded with collection dates starting from 22 August 2022; and 34 BQ.1.4 (Spike R190T) samples have been uploaded to GISAID with collection dates starting from 11 July 2022.
New Omicron variants continue to spawn with mind-numbing regularity, and while we've been lucky not to see a more severe subvariant emerge, there are no guarantees that can't happen in the future.
As tired as we may be of dealing with this virus, it isn't showing any signs of being tired of us.
