Discussion: Although Delta shows compromised sensitivity to some RBD and NTD neutralizing antibodies with up to 8-fold reduced sensitivity in vitro to vaccine-induced antibodies compared to D614G viruses (including infectious virus assays), neutralization escape is substantially lower in magnitude as compared to Beta, Gamma, and Mu.
SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection.
Abstract: Neutralization capacity of the D614G virus was much higher in infected and vaccinated versus vaccinated only participants but both groups had 22-fold Omicron escape from vaccine elicited neutralization.
Abstract: We isolated and sequence confirmed live Omicron virus from an infected person in South Africa and compared plasma neutralization of this virus relative to an ancestral SARS-CoV-2 strain with the D614G mutation, observing that Omicron still required ACE2 to infect.
Method: P2 stock was sequenced and confirmed Omicron with the following substitutions: E:T9I,M:D3G,M:Q19E,M:A63T,N:P13L,N: PMID: 34910734
2021
PloS one
Abstract: The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein.
Result: The D614G in spike protein and P323L in non-structural protein 12 (NSP12) were the most prevalent (95.2%) mutations in minks.
Discussion: D614G mutation is a very common variant in human populations worldwide.
Discussion: Another commonest mutation was D614G in mink found in almost 95% of minks.
Introduction: In December 2020, the variant B.1.351 was first detected in South Africa, with mutations such as K417N, E484K, N501Y, D614G, and A701V.
Introduction: In this regard, the variant B.1.1.7 was first identified in the United Kingdom, which contains E484K, N501Y, D614G, and P681H mutations in Spike glycoprotein.
Introduction: On the other hand, the variant B.1.617.2 was first identified in India with L452R, T478K, D614G, and P681R mutations in Spike glycopr
Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant.
Result: Additionally, in March when the D614G mutation became predominant in Japan, there was an increase of cough searches much greater than the increase of searches of fever that continued in April (Fig 4F).
Result: Because we observed that symptom order changes by viral variant between the initial outbreak in China and the subsequent outbreak in the USA and in Japan and studies link the D614G mutation with changes in disease pathology, we hypothesized that these changes in likely symptom order are not due to comorbidities of the patients.
Result: Furthermore, the magnitudes of these changes indicate that more people were searching these terms in March 2020 than the previous year, as the number of D614G patients increased throughout Japan.
Result: Given the evidence that the D614G variant affects symptom order, we tested the effect of
Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.
Discussion: Although hydrogen bonding with Y453 is possible in both H34 rotamers (Figures S4K-S4P), the dominant rotamer positioning of H34 in the D614G + N501Y + E484K-ACE2 complex enables it to participate in additional favourable intermolecular interactions with Y453 (hydrogen bond + OH/pi) and L455 (CH/pi), yielding estimated interaction energies of -10.29 and -2.75 kcal/mol, respectively.
Discussion: The combination of enhanced intermolecular interactions due to the concomitant repositioning of H34 and Q493 in the D614G + N501Y + E484K-ACE2 complex provides structural rationale for the increased ACE2 binding affinity relative to the D614G + N501Y spike.
Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China.
Abstract: After March 11, 2020, the Chinese domestic clade was naturally divided into the imported SARS-CoV-2 D614G mutant strain and evolutionarily-related similar sequences and that of sequences collected in the original Wuhan area.
Abstract: As expected, the identified sequence was closely related to the evolution of the SARS-CoV-2 D614G mutant strain circulating in Spain.
Abstract: In this study, we conducted transcriptome sequencing on respiratory throat swabs from the subject and found that the dominant SARS-CoV-2 sequence (Gene Bank ID: MW301121) was a spike protein D614G mutant strain, which is currently popular throughout world.
Figure: Phylogenetic tree of the SARS-CoV-2 spike protein sequence with the D614G mutation collected in Spain before March 11, 2020.
Heterologous prime-boost immunizations with chimpanzee adenoviral vectors elicit potent and protective immunity against SARS-CoV-2 infection.
Method: pS-B.1.1.7 and pS-B.1.351 plasmids were constructed with mutant S genes expressing the spike protein of the B.1.1.7 variant (GenBank: QQH18545.1, containing the H69, V70, and Y145 deletions and N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H mutations) and B.1.351 variant (GenBank: QRI43207.1, containing the L242, A243, and L244 deletions and L18F, D80A, D215G, S305T, K417N, E484K, N501Y, D614G
Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants.
Introduction: The Alpha (B.1.1.7) variant encodes an S protein with nine mutations (del 69-70, Del 144, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H), of which N501Y is in the receptor-binding domain (RBD).
Introduction: The Beta (B.1.351) variant encodes an S protein with nine mutations (L18F, D80A, D215G, Del 241-243, K417N, E484K, N501Y, D614G and
Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization.
Abstract: Omicron was 41-84-fold less sensitive to neutralization than D614G and 5.3-7.4-fold less sensitive than Beta when assayed with serum samples obtained 4 weeks after 2 standard inoculations with 100 mug mRNA-1273.
Abstract: To assess the potential risk of this variant to existing vaccines, serum samples from mRNA-1273 vaccine recipients were tested for neutralizing activity against Omicron and compared to neutralization titers against D614G and Beta in live virus and pseudovirus assays.
Introduction: A post-boost improvement in neutralization also was seen for Beta (3.4- and 2.6-fold less susceptible, respectively, than D614G).
Introduction: A second subset of COVE samples having moderate titers against D614G was pre-selected to avoid potential bias of high titer sera.
Introduction: Alpha and Delta were modest neutraliz
SARS_CoV_2 mutation literature information.
PMID: 
2021
medRxiv
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