Prevalence of Pangolin lineages in UK with sequence data
#16,601
Although we continue to get conflicting reports regarding the threat posed by Omicron BA.2 (see here, here, and here), the one thing they all seem to agree on is that it is gaining ground on the other Omicron sublineages (B.1.1.529, BA.1, BA.1.1, BA.3), and appears destined to overtake and probably supplant them.
Despite some animal studies in Japan suggesting BA.2 produces more severe illness in immunologically naive hamsters - in highly vaccinated countries like Denmark and the UK - they have not reported increased hospitalizations or deaths.
Whether those trends will hold across less-vaccinated populations remains to be seen.
Today the UK's Health Security Agency has published their bi-weekly technical report, and a new Risk Assessment, on BA.2. Buried within we find that the BA.2 variant now likely accounts for more than 50% of new cases in the UK, a significant jump in just over 2 weeks.
SARS-CoV-2 variants of concern andvariants under investigation in England
Technical briefing 37 25
February 2022
VUI-22JAN-01 (BA.2)
BA.2 does not usually contain the spike gene deletion at position 69-70 and is S-gene target positive (SGTP) on diagnostic assays with targets in this area. SGTP is now a reasonable proxy for BA.2, which accounts for 97.2% of sequenced SGTP cases. The proportion of SGTP cases has increased: the overall proportion of SGTP amongst cases tested by the relevant assay in England on 20 February 2022 is 52.3% compared to 18.7% on 6 February 2022.
There is geographical variation with the highest proportion of SGTP in London (63%) and the lowest in the North East region (33%). The proportion of BA.2 in sequenced data in the 7 days starting 13 February was 30.5%. This is compatible with the known lag in sequence data compared to test data.
Growth rate
BA.2 has demonstrated an increased growth rate compared to BA.1 in all regions of England. The growth rate estimated with data up to 21 February 2022 is 0.83 per week, compared to 1.03 using data up until 7 February 2022. Growth rates can be overestimates early in the emergence of a variant, and the growth advantage remains substantial.
Hospitalisation
Preliminary analysis finds no evidence of a greater risk of hospitalisation following infection with BA.2 compared to BA.1. These are early estimates which may change as data accrue.
Vaccine effectiveness
A test negative case control analysis continues to indicate no evidence of reduced vaccine effectiveness against symptomatic disease with BA.2 compared to BA.1. Two weeks after a booster dose vaccine effectiveness against symptomatic disease with the BA.2 variant was 67%. Further details of the BA.2 vaccine effectiveness analyses are available in the weekly vaccine surveillance report.
Reports from Variant Technical Group Members
Oxford University reported that in laboratory assessment, ACE2 binding was increased for the BA.2 receptor binding domain compared to the BA.1 receptor binding domain. Imperial College London reported that in preliminary experiments hamsters infected with BA.2 showed mild disease, similar to those infected with BA.1. Hamsters previously infected with BA.1 were reinfected upon exposure by co-housing to Delta-infected animals but were not reinfected upon exposure to BA.2 infected animals.
