Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Abstract

Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (i) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (ii) interactions of Spike with ACE2 receptors, and (iii) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron over all previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected.

Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.1.529 (Omicron)

“…In late November 2021, a distinct SARS-CoV-2 variant emerged (B.1.529) that had an unusual cluster of mutations, especially in the spike gene (5, 6). There was an unprecedented and rapidly disseminated series of studies on this variant, which was subsequently named “Omicron” by the World Health Organization.…”

Independent acquisition of short insertions at the RIR1 site in the spike N-terminal domain of the SARS-CoV-2 BA.2 lineage

“…Some of the mutations shared by BA.1 and BA.2, if taken individually, would have been predicted to significantly decrease viral fitness. Nevertheless, they are thought to cooperatively interact by positive epistasis, mitigating the negative fitness costs associated with their presence and possibly altering some biological properties of the spike protein (Martin et al, 2022b). Insertion XLI (i.e.…”

Binding and neutralizing abilities of antibodies towards SARS-CoV-2 S2 domain

“… 36 Compared with SARS-CoV-2 WT, Omicron has 53 more mutations, of which 34 mutations occurred in the S protein region, 13 mutations cluster within three functionally important regions of the S-gene seem cooperatively interact to mitigate their individual fitness costs and adaptively alter the function of SARS-CoV-2 S protein. 37 A recent study confirmed that Omicron S protein binds more strongly to hACE2 than other variants, and it mediates enhanced entry into cells expressing several different animal ACE2s, including various domestic avian species, horseshoe bats and mice, suggesting it has an increased propensity for reverse zoonosis and is more likely to establish an animal reservoir of SARS-CoV-2 than previous variants. 38 Another study also found that the N501Y and Q498 R in Omicron could enable the variant to bind rat ACE2 with increased affinity to almost 20-fold, which would be expected to drive increased human-to-human and cross-species transmission.…”