SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

Abstract

Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.

Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during Large Nationwide Outbreak of COVID-19, Vietnam, 2021

“…Although our estimated evolutionary rate was AY.57-lineage specific, the result was within the range of previously estimated values for the Delta variant more broadly ( 10 ; N. Benazi, Institut Pasteur of Algeria, and S. Bounab, University of M’sila, pers. comm., email, 2023 Mar 1).…”

“…Viral movement between provinces was not apparent. During the study period, nearly 200 sublineages of the Delta variant were documented worldwide ( 9 ), and in other countries, such as the United Kingdom and the United States, where use of nonpharmaceutical measures was relaxed, viral dispersal across the localities was more apparent ( 10 , 11 ). The rigorous containment approach applied in Vietnam in 2021, with limited domestic travels and tight border controls, was probably the key factor determining the localization of a single AY.57 lineage in Vietnam and its limited dispersal across the country.…”

Investigating the cause of a 2021 winter wave of COVID-19 in a border region in Eastern Germany: a mixed-methods study, August to November 2021

“…The AY.43 lineage had been detected in multiple European countries since early 2021. AY.4 was distributed worldwide, and also frequently detected in Europe, especially in UK, since April 2021 20 . In Saxony, these several lineages were not frequently detected until late June 2021.…”

“…With available meta data, we performed more detailed analysis of the AY.122 clusters in both Saxony, Germany, and in Ustecky Kraj, Czech Republic. The samples in one community transmission cluster are often geographically clustered at the early stages of the cluster development 20,21 . Consistent with that, we observed clear geographic clustering in both two AY.122 clusters.…”

Gonadal androgens are associated with decreased type I interferon production by plasmacytoid dendritic cells and increased IgG titres to BNT162b2 following co-vaccination with live attenuated influenza vaccine in adolescents

“…The main limitation of this study is that the number of adolescents studied was lower than planned due to reduced recruitment resulting from contact isolation during the SARS-CoV-2 Delta wave in autumn 2021 ( 58 ). This precluded stratification of the phenotypic data by LAIV co-vaccination and natural SARS-CoV-2 infection status, limited LASSO analyses in the number of concurrently analysed covariates, and precluded LASSO analysis of IgG titres in the absence of natural SARS-CoV-2 infection.…”