E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces.
Introduction: The Beta variant has non-synonymous spike mutations such as LAL 242-244 deletion, D80A, D215G, E484K, N501Y, A701V, L18F, R246I, K417N, and D614G.
The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia.
Discussion: Although not associated with worse disease severity, the S_D614G change has been implicated in enhanced transmission and higher viral loads .
Discussion: For Delta variants, we observed 12 key amino acid changes in spike protein that were mostly similar to other studies, including S_T19R, S_T95I, S_G142D, S_E156-, S_F157-, S_R158G, S_K417N, S_L452R, S_T478K, S_D614G, S_P681R, and S_D950N .
Discussion: On the other hand, substitutions in the region encoding the spike protein in Indonesian lineages mainly consisted of thr
SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study.
Result: 21 (75%) of 28 patients with a titre of 1/10 to 1/20 (p=0 047), 21 (49%) of 43 patients with a titre of 1/20 to 1/32 (p<0 0001), and five (11%) of 44 patients with a titre of 1/32 or more (p=0 0001) lost neutralising activity to the D614G variant at 12 months.
Result: By contrast, only 68 (48%) had neutralising antibodies against D614G, 32 (23%) had neutralising antibodies against the beta variant, and 69 (49%) had neutralising antibody responses against the delta variant (all p<0 0001; figure 4A ).
Result: Moreover, the neutralising antibody titres against the D614G and delta variants were similar (p=0 42), and both were higher than those against the beta variant (p=0 036 for D614G vs beta and p=0 0019 for delta vs beta; figure 4A).
Result: The D614G (p=0 36) and beta (p=0 82) variants escape
AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2.
Method: SARS-CoV-2-pseudotyped lentiviruses were prepared by co-transfecting the HEK 293T cell line with either the SARS-CoV-2 original spike (D614G) or the SARS-CoV-2 beta or delta spike plasmids in conjunction with a firefly luciferase encoding pNL4 lentivirus backbone plasmid.
Method: The RBD proteins were derived from the original D614G strain and the four variants of concern, namely alpha, beta, gamma, and delta.
Method: The SARS-CoV-2 original (D614G) spike and RBD proteins were expressed in human embryonic kidney (HEK) 293F suspension cells by transfecting the cells with the spike plasmid.
Figure: D Magnitude of neutralisation activity against the beta, <
High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations.
PMID: 35349821
2022
Biochemical and biophysical research communications
Introduction: reported the detection of D614G (nucleotide mutation: A23403G) and L452R (nucleotide mutation: T22917G) variations in the SARS-CoV-2 spike protein by post-PCR HRM analysis, respectively.
Discussion: In the case of detection for the D614G variation (mutation A23403G) reported by Gazali et al., the difference in the Tm value was 0.23 C.
Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2.
Introduction: As vaccine development was initiated almost immediately after the pandemic started, current major vaccines, including BNT162b2, mRNA1273 and ChAdOx1-S, are all based on the original strain without D614G.
Introduction: One of the salient mutations, spike-D614G, appeared in January 2020 and soon became ubiquitously dominant by April.
Differential neutralizing antibody responses elicited by CoronaVac and BNT162b2 against SARS-CoV-2 Lambda in Chile.
Abstract: Compared with the ancestral virus, neutralization against D614G, Alpha, Gamma, Lambda and Delta variants was reduced by between 0.93- and 4.22-fold for CoronaVac, 1.04- and 2.38-fold for BNT162b2, and 1.26- and 2.67-fold for convalescent plasma.
Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant.
Abstract: Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and PMID: 35396511
2022
Nature communications
Method: A subset of eleven of these samples were used to test neutralization activity against Delta (N = 11) and C.1.2 (N = 11) using the pseudovirus neutralization assay and ADCC (N = 9) activity against D614G and C.1.2.
Method: ChAdOx1 nCOV-19 (AZD1222) Vaccinees: samples from donors vaccinated with the ChAdOx1 nCOV-19 (AZD1222) vaccine were previously assessed for neutralization activity against the D614G (N = 11) and Beta variants (N = 11).
Method: HEK293T cells were transfected with 5 mug of SARS-CoV-2 wild-type variant spike (D614G), Beta, Delta or C.1.2 spike plasmids using PEI-MAX 40,000 (Polysciences) and incubated for 2 days at 37C.
Method: Janssen/Johnson and Johnson (Ad26.COV2.S) Vaccinees: samples from healthy donors vaccinated with the Janssen/Johnson and
Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020.
Abstract: In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the w
Result: Seventeen amino acid substitutions were present in more than 10% of the Italian isolates but only one of them was in the spike protein (D614G).
Result: the analyses showed that B.1 probably originated in China and spread to several European countries reaching Italy several times, forming a large cluster which included initially 59 (around the first week of March) and finally 198 genomes, and 6 further independent introductions mainly corresponding to a group of genomes characterized only by the substitution D614G but lacking other substitutions, in particular the P314L in the RdRp identifying the clade 20A (lineage B.1, clade 19A).
SARS_CoV_2 mutation literature information.
PMID: 
2022
PeerJ
Browser Board
Co-occurred Entities
Filtrator
ViMRT