Post-peak dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022
File(s)
Working paper
Author(s)
Type
Working Paper
Abstract
Background: Rapid transmission of the SARS-CoV-2 Omicron variant has led to the highest
ever recorded case incidence levels in many countries around the world.
Methods: The REal-time Assessment of Community Transmission-1 (REACT-1) study has
been characterising the transmission of the SARS-CoV-2 virus using RT-PCR test results from
self-administered throat and nose swabs from randomly-selected participants in England at
ages 5 years and over, approximately monthly since May 2020. Round 17 data were collected
between 5 and 20 January 2022 and provide data on the temporal, socio-demographic and
geographical spread of the virus, viral loads and viral genome sequence data for positive
swabs.
Results: From 102,174 valid tests in round 17, weighted prevalence of swab positivity was
4.41% (95% credible interval [CrI], 4.25% to 4.56%), which is over three-fold higher than in
December 2021 in England. Of 3,028 sequenced positive swabs, 2,393 lineages were
determined and 2,374 (99.2%) were Omicron including 19 (0.80% of all Omicron lineages)
cases of BA.2 sub-lineage and one BA.3 (0.04% of all Omicron) detected on 17 January 2022,
and only 19 (0.79%) were Delta. The growth of the BA.2 Omicron sub-lineage against BA.1
and its sub-lineage BA.1.1 indicated a daily growth rate advantage of 0.14 (95% CrI, 0.03,
0.28) for BA.2, which corresponds to an additive R advantage of 0.46 (95% CrI, 0.10, 0.92).
Within round 17, prevalence was decreasing overall (R=0.95, 95% CrI, 0.93, 0.97) but
increasing in children aged 5 to 17 years (R=1.13, 95% CrI, 1.09, 1.18). Those 75 years and
older had a swab-positivity prevalence of 2.46% (95% CI, 2.16%, 2.80%) reflecting a high
level of infection among a highly vulnerable group. Among the 3,613 swab-positive
individuals reporting whether or not they had had previous infection, 2,334 (64.6%)
reported previous confirmed COVID-19. Of these, 64.4% reported a positive test from 1 to
30 days before their swab date. Risks of infection were increased among essential/key
workers (other than healthcare or care home workers) with mutually adjusted Odds Ratio
(OR) of 1.15 (95% CI, 1.05, 1.26), people living in large compared to single-person
households (6+ household size OR 1.73; 95% CI, 1.44, 2.08), those living in urban vs rural
areas (OR 1.24, 95% CI, 1.13, 1.35) and those living in the most vs least deprived areas (OR
1.34, 95% CI, 1.20, 1.49).
Conclusions: We observed unprecedented levels of infection with SARS-CoV-2 in England in
January 2022, an almost complete replacement of Delta by Omicron, and evidence for a
growth advantage for BA.2 compared to BA.1. The increase in the prevalence of infection
with Omicron among children (aged 5 to 17 years) during January 2022 could pose a risk to
adults, despite the current trend for prevalence in adults to decline. (Funded by the
Department of Health and Social Care in England.)
ever recorded case incidence levels in many countries around the world.
Methods: The REal-time Assessment of Community Transmission-1 (REACT-1) study has
been characterising the transmission of the SARS-CoV-2 virus using RT-PCR test results from
self-administered throat and nose swabs from randomly-selected participants in England at
ages 5 years and over, approximately monthly since May 2020. Round 17 data were collected
between 5 and 20 January 2022 and provide data on the temporal, socio-demographic and
geographical spread of the virus, viral loads and viral genome sequence data for positive
swabs.
Results: From 102,174 valid tests in round 17, weighted prevalence of swab positivity was
4.41% (95% credible interval [CrI], 4.25% to 4.56%), which is over three-fold higher than in
December 2021 in England. Of 3,028 sequenced positive swabs, 2,393 lineages were
determined and 2,374 (99.2%) were Omicron including 19 (0.80% of all Omicron lineages)
cases of BA.2 sub-lineage and one BA.3 (0.04% of all Omicron) detected on 17 January 2022,
and only 19 (0.79%) were Delta. The growth of the BA.2 Omicron sub-lineage against BA.1
and its sub-lineage BA.1.1 indicated a daily growth rate advantage of 0.14 (95% CrI, 0.03,
0.28) for BA.2, which corresponds to an additive R advantage of 0.46 (95% CrI, 0.10, 0.92).
Within round 17, prevalence was decreasing overall (R=0.95, 95% CrI, 0.93, 0.97) but
increasing in children aged 5 to 17 years (R=1.13, 95% CrI, 1.09, 1.18). Those 75 years and
older had a swab-positivity prevalence of 2.46% (95% CI, 2.16%, 2.80%) reflecting a high
level of infection among a highly vulnerable group. Among the 3,613 swab-positive
individuals reporting whether or not they had had previous infection, 2,334 (64.6%)
reported previous confirmed COVID-19. Of these, 64.4% reported a positive test from 1 to
30 days before their swab date. Risks of infection were increased among essential/key
workers (other than healthcare or care home workers) with mutually adjusted Odds Ratio
(OR) of 1.15 (95% CI, 1.05, 1.26), people living in large compared to single-person
households (6+ household size OR 1.73; 95% CI, 1.44, 2.08), those living in urban vs rural
areas (OR 1.24, 95% CI, 1.13, 1.35) and those living in the most vs least deprived areas (OR
1.34, 95% CI, 1.20, 1.49).
Conclusions: We observed unprecedented levels of infection with SARS-CoV-2 in England in
January 2022, an almost complete replacement of Delta by Omicron, and evidence for a
growth advantage for BA.2 compared to BA.1. The increase in the prevalence of infection
with Omicron among children (aged 5 to 17 years) during January 2022 could pose a risk to
adults, despite the current trend for prevalence in adults to decline. (Funded by the
Department of Health and Social Care in England.)
Date Issued
2022-01-26
Citation
2022
Copyright Statement
© 2022 The Author(s).
Subjects
SARS-CoV-2 coronavirus research
Notes
Embargoed until 00.01 Wednesday 25 January
Publication Status
Published