The biological and clinical significance of emerging SARS-CoV-2 variants

Abstract

The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.

Fig. 1. SARS-CoV-2 variants: evolution and constituent mutations.

a | Phylogenetic tree based on subsampling of globally circulating sequences created by NextStrain (CC BY 4.0). The tree shows that nearly all variants of concern (VOCs; Alpha, Beta, Gamma and Delta) and variants of interest (VOIs; Kappa, Epsilon, Eta, Theta, Iota and Lambda) emerged independently beginning in late 2020. b | The most common mutations present in multiple VOCs and VOIs. Numeric column headers indicate spike protein positions except for two non-spike mutations in the nsp6 and nucleocapsid (N) genes. The second row indicates the residue found in the reference sequence. Spike protein residues are mapped to their associated domain within the spike protein, as shown in various shades of grey above the table. Deletions are indicated 'del'. Several additional mutations in other viral proteins also appear to have arisen more than once, including orf3a:Q57H and nsp2:T85I. NTD, amino-terminal domain; PANGO, Phylogenetic Assignment of Named Global Outbreak; RBD, receptor-binding domain; RBM, receptor-binding motif; SD, subdomain; S1/S2, junction between the exposed S1 attachment domain and the partially buried S2 fusion domain; WHO, World Health Organization.

Fig. 2. Genetic variability of the SARS spike proteins.

Position-specific sequence variability and median domain-specific pairwise distances among SARS-related coronaviruses. Results were derived from an alignment of 24 representative sarbecovirus spike sequences having a nucleotide genetic distance (TN93 model) of ≥0.01. Position-specific entropy is superimposed for one of three monomers on a surface representation of trimeric SARS-CoV-2 spike (Protein Databank (PDB) code: 6XR8), with white indicating conserved residues and the shade of red indicating the extent of sequence variability. Two 90^o rotated side views (left and middle panels) and one top view (right panel) of the spike trimer are shown. The median pairwise distance among SARS-related coronaviruses is greatest for the S1 amino-terminal domain (NTD) and receptor-binding domain (RBD). Within the RBD, the median pairwise distance is greater for the receptor-binding motif (RBM) than for the core region. CTD, carboxy-terminal domain; S1, exposed attachment domain; S2, partially buried fusion domain.

Fig. 3. SARS-CoV-2 spike-targeted antibody classifications.

Classification of monoclonal antibodies (mAbs) targeting the SARS-CoV-2 spike receptor-binding domain (RBD) epitopes. For the two classes of mAbs binding the receptor-binding motif (RBM), 90^o rotated side views and one top view of a surface RBD representation are shown (parts a,b). For the two classes of RBD core-binding mAbs, just the 90^o rotated side views are shown (parts c,d). Each image derived from coordinates of the Protein Databank (PDB) structure 6M0J. Bold highlighted mAbs are in phase III clinical trials (as of July 2021). Blue intensity is proportional to the number of mAbs binding to the underlying amino acid residues. RBM refers to the region of the RBD containing the angiotensin-converting enzyme 2 (ACE2)-binding residues. RBM class 1 mAbs (part a) bind the RBD only in its up position, whereas RBM class 2 mAbs (part b) can bind the RBD in its up or down position. A third RBM mAb class binds to a quaternary epitope comprising more than one RBD but is not shown as it would require the trimeric spike. Epitopes for amino-terminal domain-binding mAbs are not shown.

Fig. 4. Locations and prevalence of key SARS-CoV-2 spike mutations.

a | Sites of 16 key S1 (exposed attachment domain) mutations on the SARS-CoV-2 spike trimer, including 9 in the receptor-binding domain (RBD; green), four in the amino-terminal domain (NTD; cyan) and three in the carboxy-terminal domain (CTD; purple). Spike trimer figure derived from a cryo-electron microscopy structure (Protein Databank (PDB) code 7BNN). S2 (partially buried fusion domain) shown in dark grey. Six of the RBD mutations (K417N/T, L452R, T478K, E484K and N501Y) are present in one or more of the World Health Organization (WHO) variants of concern (VOCs): Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). NTD mutations include three deletions and L18F, mutations present in two or more VOCs. CTD mutations include D614G, which became the consensus amino acid at this position prior to the emergence of the VOCs, and P681H and P681R, which are present in Alpha and Delta VOCs, respectively. b | Other than D614G, which has a prevalence close to 100%, the most prevalent mutations as of June 2021 are those present in Alpha (Δ69/70, Δ144, N501Y and P681H) and Delta (L452R, T478K, and P681R) VOCs. Prevalence data obtained from outbreak.info.

Fig. 5. Effects of SARS-CoV-2 spike variants on susceptibility to neutralization.

Fold-reduced susceptibility of the four variants of concern (VOCs; Alpha, Beta, Gamma and Delta) and three common spike receptor-binding domain (RBD) mutations (N501Y, E484K and L452R) to in vitro neutralization by plasma from previously infected persons (part a) and from persons vaccinated with the Pfizer/BioNTech BNT162b2 (part b), Moderna mRNA-1273 (part c), AstraZeneca AZD1222 (part d), Janssen Ad26.COV2.S (part e), Novavax NVX-CoV2373 (part f), Bharat Biotech BBV152 (part g) and Sinovac CoronaVac (part h) vaccines. y axes indicate number of plasma units tested. Colour scheme indicates fold reduction in neutralization. Only those data from plasma samples from persons receiving a full immunization schedule were included. Data obtained from https://covdb.stanford.edu/search-drdb/ on 1 July 2021. In some plots, distributions are approximate as they include results reported only in aggregate as a mean fold reduction in susceptibility.