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

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. Here 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. From 9 to 27 September 2021 (round 14) and 19 October to 5 November 2021 (round 15), all lineages sequenced within REACT-1 were Delta or a Delta sub-lineage with 44 unique lineages identified. The proportion of the original Delta variant (B.1.617.2) was found to be increasing between September and November 2021, which may reflect an increasing number of sub-lineages which have yet to be identified. The proportion of B.1.617.2 was greatest in London, which was further identified as a region with an increased level of genetic diversity. The Delta sub-lineage AY.4.2 was found to be robustly increasing in proportion, with a reproduction number 15% (8%, 23%) greater than its parent and most prevalent lineage, AY.4. 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. Though no difference in the viral load based on cycle threshold (Ct) values was identified, a lower proportion of those infected with AY.4.2 had symptoms for which testing is usually recommend (loss or change of sense of taste, loss or change of sense of smell, new persistent cough, fever), compared to AY.4 (p = 0.026). The evolutionary rate of SARS-CoV-2, as measured by the mutation rate, was found to be slowing down during the study period, with AY.4.2 further found to have a reduced mutation rate relative to AY.4. 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 a Large Nationwide Outbreak in Vietnam, 2021

“…Viruses of the Delta variant have been divided into over 240 sublineages [35]. Of these, AY.57 lineage is characterized by the presence of signature mutations in ORF1a (P380S, P1640L, A3209V, V3718A, and T3750I), and in spike protein (A222V).…”

“…Notably, in other countries, such as the UK and the US, where travel restriction and border control were less stringent as compared to those applied in Vietnam, viral dispersal across the localities was more apparent [36, 37]. Additionally, during the study period, 198 and 195 sublineages of the Delta variant were documented in the UK and the US, respectively [35]. In contrast, the 2021 outbreak in Vietnam was almost entirely confined to the AY.57 lineage, likely via a single introduction as suggested by the tight cluster of the Vietnamese AY.57 lineage on the NextClade-based global phylogenetic tree.…”

Tracing the trajectories of SARS-CoV-2 variants of concern between December 2020 and September 2021 in the Canary Islands (Spain)

“…We attribute this not only to the intrinsically higher transmissibility of the Delta variant compared to the previously circulating VOCs (Campbell et al ., 2021) but also to the concurrent lifting of COVID-19 restrictions in the archipelago and nationwide. Since August 2021, we observed the emergence of diverse Delta sub-lineages (AY.4 and AY.12), similar to what occurred worldwide throughout the summer (Angeletti et al ., 2021; Eales et al ., 2021).…”

“…While Alpha spread ubiquitously across the archipelago early after its first appearance in the island of Tenerife, Beta and Gamma variants were observed only in some of the islands and not in others. Beta was observed in the archipelago from late January up to August 2021, and its spatial distribution was mainly circumscribed to the islands of Gran Canaria and Tenerife, even though it was already present in several European countries by mid-January (O’Toole et al ., 2021), representing up to 20% and 8% of cases in Austria and France, respectively, at that moment (Hodcroft, 2021). Cases associated with the Gamma variant were also relatively few, with a small cluster of cases observed in Tenerife in late January 2021, followed by isolated cases in the other islands.…”

“…In the final analysis, the sequences having a genome coverage less than 70% of the entire SARS-CoV-2 sequence and having a QC classified as “bad” by Nextclade software were excluded. Pangolin v3.1.1 (O’Toole et al ., 2021) was used for the classification of the consensus sequences. Microbetrace v0.8.2 (E.…”