Mutations in the SARS-CoV-2 Spike Protein

The spike (S) protein of the virus mediates receptor binding and membrane fusion. The sequence specificity also defines the range of the hosts and the specificity of the virus. Also, the S protein is the target for a variety of neutralizing antibodies and vaccine design.

Gene recombination or mutations of the receptor-binding domain (RBD) appears to allow transmission between different hosts. Some of these mutations can lead to a higher mortality rate of the infected hosts. Some observed mutations are in the reference sequence for the spike protein. Korber et al. developed a analysis pipeline to track mutations in the SARS-CoV-2 spike protein. However, the clinical evidence of all these mutations still needs to be verified.

Schematic of the coronavirus spike (S) protein domain structure

The location of receptor-binding subunit S1, the membrane-fusion subunit S2, the transmembrane anchor (TM), the intercellular tail (IC) are indicated. The location of the S1 N-terminal domain (S1-NTD), the S1 C-terminal domain (S1-CTD), the fusion peptide (FP), and the heptade repeat regions N and C (HR-N and HR-C) are indicated as well.

The following image shows the annotated sequence for SARS-CoV-2 spike protein mutations from the coronavirus associated with COVID-19 originating in Wuhan of Hubei province in China. Source: ORIGIN   YP_009724390, 1273 a, surface glycoprotein [Severe acute respiratory syndrome coronavirus 2].

A new SARS-CoV-2 virus emerged in the UK containing a noval set of spike mutations named B.1.1.7. This new virus strain appears to be more infectious.

The potential biological effects of these mutations are:

(i)  Mutation N501Y is part of six key contact residues within the receptor-binding domain (RBD) thought to increase binding
     affinity to human and murine receptor protein ACE2.

(ii)  The spike deletion 69-70del may help the virus to evade the human immune response.

(iii)  Mutation P681H is close to the furin cleavage site.

Other identified mutations in B.1.1.7 spike protein are: A570D, T716I, S982A, D1118H.

Wibmer et al., and others, recently, January 2021, described the emergence of a new SARS-CoV-2 lineage in South Africa, 501Y.V2. 

Nine changes in the spike protein were found. One cluster in the N-terminal domian (NTD) includes four substitutions and a deletion (L18F, D80A, D215G, Δ242-244, and R246I). Another cluster contained three substitutions in RBD (K417N, E484K, and N501Y). The 501Y change has been associated with increased transmissibility, rather than immune pressure. The accumulation of these mutations may possibley allow the virus to escape from neutralization by earleir aquired antibodies. Mutations in the same regions have also been described in a new variant, which has recently emerged independently in Brazil. 

Omicron Variant B.1.1.529 

More recently, on November 24, 2021, a new SARS-CoV-2 variant, B.1.1.529 was identifed in South Africa. This variant is called the Omicron variant. The spike protein of this variant has at least 30 amino acid substitutions, three small deletions, and one small insertion. Fifteen (15) of the 30 amino acid substituions are located in the receptor binding domain.

Key Amino Acid Substitutions in Spike Protein:

A67V, del69-70, T95I, del142-144, Y145D, del211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

     N-term.  S1

   1 MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS S1

     ---------- -------F-- ---------- ---------- ---------- ---------- 
                   SA501Y.V2 L18F

  61 NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV
     --------|| ---------Y ---------- -------F-- ---------- ----------
     ---------- ---------A[SA 501Y.V2 D80A]----- ---------- ---------- 

          B.1.1.7 Del S:D80Y               S:S98F
     ------V-|| ---------- ---------- ----I----- ---------- ----------
  Omicron B.1.1.529 Deletion

 121 NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE

     ---------- ---------- ---|------ ---------- ---------- ----------
                      B.1.1.7 Deletion
     ---------- ---------- -|||D----- ---------- ---------- ----------
                 Omicron B.1.1.529 Deletion

 181 GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT
     ---------- ---------- ---------- ----G----- -V-------- ----------
                                  SA501Y.V2 D215G 20A.EU1

     ---------- ---------- ---------- |--------- ---------- ----------
                                         EPE insertion 214

 241 LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK
     ---------- ---------- ---------- ---------- ---------- ----------
     -[.]-I----
     DELETION[SA501Y.V2 242-244; R246I]
       
 301 CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN RBD

     ---------- ---------- ---------- ------SL-- IL-S---S-- -S-D----N-
     ---------- ---------- ---------- --------D- ---------- ----------

 361 CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD

     ------F--S -T----LN-- ---LA----- --P-I----- ----VQ-IE- ---R--N---
     ---------- -S-----R-- ---------- ---------- ---------- ---E------
     ---------- ---------- ---------- ---------- ---------- ---A---N--
                                                         [SA501Y.V2 K417N] 

     ---------- L-P-F----- ---------- ---------- ---------- ------N---

 421 YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC
     ---------- ----SR--KK ---RFV---- -RF--L-R-- ---------- QV---SNIS-
                                                                20A.EU2
     ---------- ---------- -----S---- -----E-Q-- ---------- ------R---
     ---------- ---------- ---------- ---------- ---------- ------I---
     ---------- ---------K -----S---- ---------- ---------- ------NK-- 

 481 NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN
     DSA-SS---S ---P----R- Y-F-C--H-A PA-------- ---------- ----------
     --IK------ ---------- Y--------S RS-------- ---------- ----------
[SA501Y.V2 E484K]        B.1.1.7[SA501Y.V2 N501Y]
     ---A------ --R--S-R-- Y---H----- ---------- ---------- ---------- 
              Region of transmissibility ?

Figure 1: Location of observed mutations for SARS-CoV-2 lineage, South Africa, 501Y.V2 are shown in yellow in the trimeric S protein structure published by Deng et al. in 2020 (PDB ID 7CAI). Residues shown in different colors depict glycosylation sites. 



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