Origins and evolutions of SARS-CoV-2 Alpha variant in the UK

In a recent study posted to the bioRxiv* preprint server, researchers presented the origins and evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.1.7 in the United Kingdom (UK).

The first SARS-CoV-2 variant to be designated as a variant of concern (VOC) by the World Health Organization (WHO) was the lineage B.1.1.7, later named Alpha. The Alpha variant originated in early Autumn in the UK yet was only discovered in December 2020. It quickly spread over the world, causing enormous waves of infection.

The SARS-CoV-2 Alpha variant having a long ancestral phylogenetic branch with an elevated evolutionary rate had just two sampled sequences along its ancestral branch. Despite continuous limits on social mingling across the UK and the implementation of additional restrictions, such as the national lockdown in November 2020, the Alpha-driven coronavirus disease 2019 (COVID-19) epidemic continued to spread in the UK. However, these non-pharmaceutical measures successfully lowered the spread of the SARS-CoV-2 lineages that preceded Alpha.

About the study

In the current study, the researchers analyzed the only two sampled sequences available that belong to the ancestral branch of the SARS-CoV-2 Alpha variant. The team determined which of the two sequences might be the true intermediate sequence for the Alpha variant. This shed light on knowledge regarding the order of mutational events that resulted in the emergence of Alpha. Mutational scanning was conducted via aligning the sequences against the reference SARS-CoV-2 Wuhan-Hu-1 sequence.

The team investigated alternate hypotheses, such as a chronically infected individual, a non-human animal population, or an under-sampled geographic location, to describe how Alpha gained a vast number of mutations while remaining undetected in a zone of intense genomic monitoring. Finally, the researchers analyzed and compared the mutation patterns and ancestral branches of the five SARS-CoV-2 VOCs: Omicron, Delta, Gamma, Beta, and Alpha.

Findings

The results showed that in the initial B.1.1.7 sequence sampled on September 20, 2020, the lineage differentiated from other simultaneously circulating background lineages in late April 2020 in the UK. Nevertheless, it seemed that the fast transmission of this lineage just began later in the year in the UK, with the Alpha clade's time of most recent common ancestor (TMRCA) estimated to be on September 19, 2020.

In terms of time and genetic alterations, the ancestral branch that evolved into the B.1.1.7 lineage was extremely long. There were 23 nucleotide alterations, and the majority were amino acid changes. The ancestral branch's evolutionary rate was at least 2.3 times greater than the background's rate. However, there was no proof for a faster rate of evolution inside the B.1.1.7 clade. An analysis of root-to-tip genetic distances versus genome sampling date revealed that the rates between background sequences and the B.1.1.7 clade were almost identical.

Both the sampled ancestral Alpha sequences were located on the branch resulting in the B.1.1.7 clade. In addition, they exhibited some, though not all, mutations defining Alpha. The oldest genome (CAMC-946506) was sampled on July 15, 2020, and the latest (MILK-B154B6) on October 23, 2020.

The MILK-B154B6 was confusing at many points, including position 501 in the Spike (S), with 20% of reads encoding Y, i.e., tyrosine in Alpha, and 80% encoding N, i.e., asparagine in background lineages. These equivocal sites point to either a concurrent infection of two separate virus populations or contamination in the laboratory. The coinfection was probably by a background lineage and an early sequence of Alpha.

MILK-B154B6 had the C5986T synonymous mutation, which was detected in 971 of 976 early Alpha sequences but not in any of the 1,100 background sequences analyzed in this work. It also demonstrated two additional mutations, C913T and C15279T, present in 970 and 974 of the 976 sequences in the Alpha dataset, respectively, but just once in the background dataset. These observations indicate that MILK-B154B6 cannot be considered an evolutionary intermediate of Alpha.

In contrast, the CAMC-946506 exhibited no unclear sites and four Alpha-defining mutations: 1) Q27, 2) R52I to Q27* stop codon mutation in ORF8, 3) nine base pair deletion in non-structural protein 6 (NSP6), and 4) N501Y in the S. Before September 1, 2020, 37 sequences with Q27*, five with R52I, and none with the N501Y or NSP6 deletion were sampled in the UK. These observations suggest that the CAMC-94506 might be the true intermediate sequence of Alpha.

However, it is also possible that the CAMC-94506 just harbored mutations shared by the cryptic population's common ancestor and CAMC-94506. The Alpha intermediate sequence, CAMC-94506, indicated that the nine base pair deletion in NSP6, the R52I and Q27* ORF8 mutations, and the S mutation N501Y evolved between April 24, 2020, and May 26, 2020.

The B.1.1.7's growth in England during 2020's second half was rapid relative to the background lineages existent at the time. B.1.1.7 continued to expand at 2021's start, while other lineages started to decline. The three-epoch paradigm consisting of pre-, during, and post-lockdown periods in England best suited the genomic data. B.1.1.7 had a positive and a zero growth rate during the lockdown and post-lockdown period, respectively.

In contrast, the background lineages had a robust negative growth rate during the post-lockdown period. This indicates that although the national lockdown in England during November lowered both lineages' growth rates considerably, it was not stringent enough to put B.1.1.7's growth rate beneath zero.

Before the national lockdown in November, both the B.1.1.7 and background lineages had reproduction numbers (Re) over 1. Although the lockdown pushed the background lineages' Re to approximately 1, Re of B.1.1.7 continued above 1.

The most frequent mutations among Omicron, Gamma, Beta, and Alpha were the nine base pair deletion in NSP6 and N501Y in the S. Omicron and Alpha only shared the P681H mutation in the furin cleavage site of the S. Delta did not share any mutations relative to the background lineages with Omicron and Alpha, other than P681R. Further, Omicron and Beta had the K417N mutation in the S as the only frequent mutation. It was also seen in the 'Delta plus' variant.

All VOCs except Delta had the highest prevalence of non-synonymous mutations in the S. There was no indication of a quicker rate of evolution along the ancestral branches of the Delta and variants of interest (VOIs). Delta also had fewer S mutations than the other VOCs because Delta's mutations were distributed more equally across the genome. These inferences suggest that the Delta variant emerged via a distinct mechanism relative to other VOCs.

Conclusions

The study findings demonstrate that among the only two ancestral sequences of Alpha that have been sampled to date, CAMC-94506 was most probably a true intermediate sequence for Alpha. Further, this sequence revealed the chain of mutational events that led to the SARS-CoV-2 Alpha variant evolution. The best explanation for how Alpha attained numerous mutations and existed unnoticed in an area of high genomic monitoring was through a chronically infected person.

However, the chronically infected immunocompetent host also exhibited a greater within-host rate of evolution. This inference indicates that the person does not need to be immunocompromised to harbor mutations that allow the evolution of a variant.

Additionally, Delta appeared to be an anomaly considering the absence of rapid evolutionary pace on the ancestral branch and the genomic positions of its defining mutations compared to other SARS-CoV-2 VOCs.

The present findings will be valuable for examining SARS-CoV-2 VOCs that originate in regions with less genomic sequencing or monitoring, those that do not have features such as S gene target failure (SGTF) drop-out. As novel SARS-CoV-2 variants such as Omicron continue to emerge, it is critical to look into the origins of existing variants to identify potential strategies to stop them from evolving and emerging.

*Important notice

bioRxiv 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.

Written by

Shanet Susan Alex

Shanet Susan Alex, a medical writer, based in Kerala, India, is a Doctor of Pharmacy graduate from Kerala University of Health Sciences. Her academic background is in clinical pharmacy and research, and she is passionate about medical writing. Shanet has published papers in the International Journal of Medical Science and Current Research (IJMSCR), the International Journal of Pharmacy (IJP), and the International Journal of Medical Science and Applied Research (IJMSAR). Apart from work, she enjoys listening to music and watching movies.