New coronavirus mutant strain--part one

mutation of the new coronavirus (SARS-CoV-2) is the way the virus has evolved. On the premise of not destroying the key biochemical phenotype of the SARS-CoV-2, the antibody target site is used to fix the mutation and trigger the epitope drift to avoid the recognition of the relevant antibody. At present, there are thousands of new coronavirus mutants, the main epidemic mutations are alpha, beta, & delta; etc.

B .1.1.7 mutant strain, also known as 20I/501Y.V1 or VOC 202012/01, was first discovered in Britain in December 2020, and cases of B .1.1.7 lineage were subsequently reported in the United States, Canada, Japan and other countries. B .1.1.7 The mutant strain increased its binding affinity to human ACE2 receptor by 1000 times, and its infectious capacity was 1.7 times that of the original strain.

The B .1.1.7 lineage obtained 17 mutation sites at one time on the basis of the D614G mutation, and the S protein contained 9 mutation sites: 1) amino acid deletions at positions 69-70 and Y144 located in the S1 N-terminal domain (NTD); 2) N501Y mutation located in the receptor binding domain (RBD); 3) A570D, D614G, P681H located in the S1 C- terminal domain; 4) T716I,S982A,D1118H on S2.

Key Mutation Sites on SARS-CoV-2 Function

1.69-70del

The mutation is characterized by H69 and V70 deletions in the N-terminal domain (NTD) of the new crown. A single H69/V70 deletion is not common and is often accompanied by RBD mutations. In addition to the B .1.1.7 virus strain (N501Y +69-70del), the Danish mink mutant strain (N439K + Y453F +69-70del) also showed this trend. H69/V70 deletion causes the surrounding I68, S71, G72, T73, N74 and G75 to move inward to form a protruding ring and close to the binding epitope of NTD. Studies have shown that H69/V70 deletion in NTD can evade the way of NTD-specific binding neutralizing antibodies, which is conducive to the immune response of the virus to escape from the host, but it is not clear that immune escape is caused by NTD conformation caused by H69/V70 deletion.

2.D614G

mutation D614G mutation is more infectious and is currently the main form of the new crown mutant strain. The D614G mutation increases the furin protease cleavage efficiency at the S1/S2 junction. When the D mutation is G, the hydrogen bond formed by the D614 residue and the T859 residue on the S2 region of the adjacent original polymer disappears, which improves the cleavage efficiency of Furin protease, makes S1 protein easier to fall off from the S2 protein-viral membrane fusion body, and promotes the process of viral membrane fusion, suggesting that the D614G mutation has stronger or faster infectivity to host cells. At the same time, D614G will also change the conformation of RBD protein to better coordinate with ACE2. In the D614 strain, the 53% RBD polymer is totally enclosed, the 47% is single open, and the 40% RBD is in an "upward" state. In G614 strain, 5% is totally enclosed, 36% is single open, 39% is double open, 20% is triple open, and the 82% RBD is in an "upward" state. This higher RBD state "upward" tendency and the more open RBD polymer structure make the D614G mutation easier to bind to ACE2.

3.N501Y

N501 amino acid is one of the key contact residues of the new coronavirus RBD protein and is directly involved in the binding of RBD and ACE2, while the N501Y mutation enhances the binding affinity of RBD and ACE2. N501 is a hydrophilic residue. When the virus binds to ACE2, N501 is close to the Y41 hydrophobic benzene ring and K353 hydrophobic alkane chain of ACE2. However, when N501 mutates to hydrophobic residue Y, Y501 can better coordination with Y41 and K353 in ACE2 through hydrophobic interaction, improve the interaction conformation of RBD and ACE2, and increase the binding affinity by about 0.81kcal/mol, at the same time, the new coronavirus strain that did not infect mice acquired the ability to infect. The N501Y mutation has little effect on the binding efficacy of neutralizing antibodies targeting the neutralizing epitope of RBD. Studies have found that after the N501 strain binds to the neutralizing antibody to VH-Fc ab8 (the molecule fuses to express the variable heavy chain region VH and the Fc fragment of human IgG1), the S protein presents two conformations, namely, two RBD molecules are in the "up" position and Only one RBD molecule is in the "up" position. The S protein of the N501Y mutant strain shows a single conformation: the two RBD molecules are in the "upward" position. Each RBD molecule will be bound to VH-Fc ab8. The presence of mutation will not change the interaction between RBD and neutralizing antibody, and there is no immune escape phenomenon.

The B .1.1.7 mutant strain showed enhanced affinity with ACE2 and enhanced virus infection ability, but the study found that the serum of the mRNA new crown vaccine BNT162b2 vaccinated had little effect on the S protein neutralization activity of the B .1.1.7 strain. It is speculated that the B .1.1.7 mutant strain will not Affect the existing vaccine and neutralizing antibody research.

The mutant strain B .1.351 appeared in August 2020. As of the end of December 2020, the proportion of infections caused by B .1.351 in South Africa has exceeded 80%. Researchers analyzed 190 sample sequences in South Africa, and the results showed that compared with the main lineages B .1.1.54, B .1.1.56 and C.1 of the first wave of South Africa, B .1.351 had nucleotide substitutions and amino acid changes in the entire genome and spinous process region. The largest number, showing obvious hypermutation.

B .1.351 has 10 mutation points on spinous process protein (S):

a) L18F, D80A, D215G, L242_244del (or L242H), R246I located in S1 N terminal domain (NTD);

B) K417N, E484K, N501Y located on the receptor binding domain (RBD);

c) D614G in the terminal domain of S1 C;

d) A701V on S2.

Protein Sequence Position Corresponding to Amino Acid Changes in Spine Region of Genome B .1.351

Note: The length of the black line in the figure indicates the number of genomes containing specific mutations.

data show that RBD is the neutralizing active target of 90% in SARS-CoV-2 immune serum. Mutations in RBD may affect the neutralization efficiency of neutralizing antibodies (NAbs). Mutations in N501Y, E484K and K417N will affect the neutralization of the two types of NAbs. The first class of NAbs is encoded by a VH3-53 gene fragment centered on the spinous process residue K417, which blocks hACE2, binds only to "up" RBD, and crosslinks adjacent RBD within a single trimer. The second class of NAbs binds to the spike residue E484, blocks hACE2, binds to "up" and "down" RBD, and contacts adjacent RBD. K417N/N501Y mutation will eliminate the key role of NAbs of the first type, which may lead to immune escape at this site. E484 is a dominant neutralizing epitope. E484K mutation can effectively avoid the second type of neutralizing antibody in SARS-CoV-2. E484K mutation has been proved to be resistant to NAbs and convalescent serum. (Jiangsu East Anti-RBD E484K Protein Raw Material, Cat.No.A00114)

In January 2021, Japan discovered that four tourists entering Japan from Brazil were infected with a mutant new coronavirus, which was not exactly the same as the mutant new coronavirus found in the United Kingdom and South Africa. Brazilian and British researchers speculate that these four people may be infected with the P.1 variant new coronavirus. On January 14, 2021, Brazilian media reported that Brazilian and British researchers found a new variant of the new coronavirus called P.1 while analyzing samples of the new coronavirus collected from the Brazilian state of Amazonas. Of the 31 new coronavirus positive samples collected in Manaus, the capital of Amazonas, from December 15 to 23, 2020, 13 detected mutant new coronavirus P.1.

Gamma strain has 10 mutations (L18F, T20N, P26S, D138Y, R190S, H655Y, T1027IV1176, K417T, E484K and N501Y), and three mutations (L18F, K417T, E484K) are located in RBD region, similar to Beta strain. Importantly, this variant may reduce the neutralization effect of monoclonal antibody therapy, convalescent serum and post-inoculation serum.

References:

[1] Yurkovetskiy L , Wang X , Pascal K E , et al. Structuraland Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant[J]. SSRNElectronic Journal, 2020.

[2] The New SARS-CoV-2 Strain Shows a Stronger BindingAffinity to ACE2 Due to N501Y Mutation.

[3] Molecular Mechanism of the N501Y Mutation for EnhancedBinding between SARS-CoV-2's Spike Protein and Human ACE2 Receptor.

[4] Cryo-EM Structure of the N501Y SARS-CoV-2 Spike Proteinin Complex with a Potent Neutralizing Antibody.

[5] Jun Lan, Jiwan Ge, Jinfang et al. Structure of theSARS-CoV-2 spikereceptor-binding domain bound to the ACE2receptor [J]. Nature,2020

[6] Starr TN, Greaney AJ, Hilton SK, et al. Deep MutationalScanning of SARS-CoV-2Receptor Binding Domain Reveals Constraints on Foldingand ACE2 Binding[J]. Cell, 2020

[7] Wang Y, Liu M, Gao J. Enhanced receptor binding ofSARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions[J]. Proc Natl Acad Sci USA,2020

[8] H Tegally,E Wilkinson,M Giovanetti, et al. Emergence and rapid spread of a new severeacute respiratory syndrome-relatedcoronavirus 2 (SARS-CoV-2) lineage withmultiple spike mutations in South Africa[J]. medRxiv, 2020

[9] CO Barnes,CA Jette,ME Abernathy, et al.SARS-CoV-2 neutralizing antibodystructuresinform therapeutic strategies[J]. Nature, 2020

[10]Constantinos Kurt Wibmer,FrancesAyres,Tandile Hermanus, et al. SARS-CoV-2 501Y.V2escapes neutralization by South African COVID-19 donor plasma [J]. BioRxiv,2021.

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