Researchers study the spatial distribution of SARS-CoV-2 Omicron BA.1 variant in England

By Pooja Toshniwal PahariaReviewed by Aimee MolineuxJan 9 2023

In a recent study posted to the medRxiv* preprint server, researchers performed a genomic assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant’s BA.1 subvariant transmission in England.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Background

The swift upsurge in coronavirus disease 2019 (COVID-19) case counts due to Omicron infections in England resulted in the enforcement of COVID-19 prevention measures such as compulsory COVID-19 passes to enter particular indoor settings, facemask use, and remote working with accelerated COVID-19 vaccination for improving booster dose availability to all adult individuals. In January 2022, SARS-CoV-2 prevalence in England reduced, with fewer Omicron BA.1 subvariant infections, with a concomitant increase in Omicron BA.2 subvariant infections, replaced eventually by Omicron BA.4/5.

About the study

In the present study, researchers performed a phylodynamic analysis for analyzing BA.1 transmission dynamics in England between November 2021 and January 2022.

The team analyzed 48,615 genomes of BA.1 from samples obtained (one percent of confirmed Omicron infections) that represented 313 LTLAs (lower-tier local authorities), with anonymized epidemiological and human mobility data aggregated at a sub-city level. Statistical modelling was performed to explore the effects of altered COVID-19 prevalence on travel connectivity between main travelling hubs of England. To evaluate Omicron importation timing and subvariant transmission dynamics, phylodynamic assessments were performed for 1,15,622 genomes of Omicron BA.1 subvariant, Omicron BA.2 subvariant and other subvariants) sampled worldwide between November 8, 2021, and January 31, 2022.

Forty-two percent of genomes were subjected to sequencing analysis by the COG-UK (coronavirus disease 2019 Genomics United Kingdom) consortium. Omicron genomes, obtained globally and from England, [from GISAID (global initiative on sharing all influenza database) and COG-UK on April 9 and 12, 2022, respectively] before November 28, 2021, were analyzed. Weighted genome subsampling was performed, considering sequencing differences for COVID-19 cases at the UTLA (upper-tier local authority) level.

City-wise importation intensity estimates from the United States (US) and country-wise estimates from South Africa were derived from EII (estimated importation intensity) values based on the COVID-19 case counts per week, Omicron BA.1 prevalence per week, and incoming flight passengers travelling to the UK per month. The UKHSA (UK health security agency) VAM (variant and mutations) line list data were obtained for calculating daily counts of incoming travellers later testing Omicron-positive in Pillar 2 (community-level surveillance) of the UK COVID-19 testing programme.

The dispersal history of identified subvariants was reconstructed based on spatial phylogeographic methods. Generalized linear modelling (GLM) was performed for quantitative assessment of the role of epidemiological, mobility-associated, and demographic factors on BA.1 transmission in England and to assess their relationship with Omicron movement in LTLAs. The period before December 26, 2021, was the expansion phase, and between December 26, 2021, and end-January 2022 was the post-expansion phase.

Results

More than 6,455 independent importations of Omicron in England were observed. Commuting limitations in South Africa did not lower BA.1 importation intensity since secondary hubs became the main exporters. Most (70%) of the Omicron BA.1 genome were imported from outside England (70%), and the most initial importation event was estimated between November 5 and November 18. Between the initial importation and mid-month of December 2021, an exponential rise in the influx of regular importations followed by a plateau phase in the initial days of January 2022 was estimated.

The swift rise in importations observed despite travel restrictions for individuals travelling from South Africa was likely to be the result of an upsurge in Omicron variant infections in cities on the eastern coast of the United States in December of 2021 and more incoming US-residing individuals by air. The mean BA.1 subvariant EII weekly from US introductions was 4.0-fold higher than from South Africa during restricted travel.

The size of variant transmission was overdispersed, with the eight largest transmission lineages (>700 genomes each) accounting for >60% of Omicron genomes in England. Most of the large variant transmissions were estimated to have occurred between November 5 and 13, 2021. Importation timing was the main factor affecting the lineage transmission size. Local viral movements in Greater Manchester and Greater London comprised 60% and 90% of all movements from November to December 2021, respectively. A second phase of increased frequency of mid-to-long range (50 to 300 km) variant transmission was observed during the 2021/22 New Year period, with more outward movement occurring from the East of England, West Midlands, and East Midlands.

In addition, the more frequent inward movement was observed in North East and North West England. Human movement changes between mid-December 2021 and early January 2022 could be due to remote working, lesser socialization during Christmas and new year, and behavioural changes due to rising COVID-19 cases. Trips taken between home and hub units during the initial growth period of the epidemic reduced by 12.0% for each unit elevation in weekly COVID-19 cases among every 100 individuals at the hub that week, with a four-day lag. The team estimated 20% and 16% lesser connectivity for every unit increase in weekly COVID-19 cases per 100 individuals at the hub when the home and hub units were located within distances of 50 kilometres and 100 kilometres, respectively.

Overall, the study findings highlighted the transmission dynamics of Omicron BA.1 in England and the factors that could have affected the spatial expansion of the Omicron wave in England.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.