Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.
Abstract: 151 (97%) of 156 had the Asp614Gly mutation in the spike protein.
Result: 151 (97%) of 156 samples contained the Asp614Gly mutation.
Result: We established the distribution and frequency of the Asp614Gly variant in SARS-CoV-2 genomes from Zimbabwe.
Discussion: The spike protein is thought to be important for entry of the virus into host cells and Asp614Gly has been implicated in increased cell entry.
Discussion: There has been considerable interest in the emergence of a variant lineage of SARS-CoV-2 with a non-synonymous mutation resulting in substitution of 614Gly in which a glycine residue was replaced by an aspartate residue at position 614 (Asp614Gly) of the spike protein.
Result: Consistent with the global trend, a high frequency of the viruses (140, 93.33%) harbored the D614G amino acid change (conferred by a SNP at nucleotide 23403) in the spike protein.
High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses.
Abstract: The clade for pangolin lineage B that conta
Result: Through our Nextstrain thread, it was observed that the clade for pangolin lineage B contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF 3a, and S84L in ORF8 covarying with the D614G spike protein mutation, which were found to be the most prevalent in the early phase of the pandemic in the state of Georgia.
Discussion: Through our Nextstrain thread, we found that the clade for pangolin lineage B that contains certain distant variants covarying with the D614G spike protein mutation had become increasingly prevalent at the early phase of the pandemic in the state of Georgia.
SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers.
Result: hCoV-19/Finland/FinD796H/2021 had a very uncommon combination of the S protein mutations, as only 0,04% (535/1204022) of complete genome sequences deposited to Gisaid at 23.4.2021 had a similar combination (S:T95I, S: 144del, S:E484K, S:D614G, S:P681H, and S:D796D&H).
Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach.
Result: A proportion of 99% of those novel variants contained the S-D614G mutation together with another 7 +- 5 amino acid variations within the S protein.
Result: A total of 139 unique S protein variants of beta (B.1.351) were clustered, with the majority carrying 7 consensus amino acid variations (D80A, D215G, K417N, E484K, N501Y, D614G, and A701V) and 1 deletion (amino acid 242).
Result: Among the amino acid mutations found in circulating SARS-CoV-2 variants, E484Q/K, P681H/R/L/S, PMID: 34702899
2021
Scientific reports
Introduction: Brufsky hypothesized that the higher number of deaths on the East coast of the United States compared to the West coast could be due to the higher prevalence of the D614G amino acid substitution on the East coast.
Introduction: In China, four early samples carried the D614G amino acid substitution.
Introduction: In Europe the first German sample from January 28th carried the A-to-G mutation at nucleotide position 23403 (D614G) mutation and the C-to-T mutation at position 3037, but not the mutation at position 14408.
Introduction: One sample from January 24th 2020 had only the A23403G (D614G) but not the C3037T and C14408T mutations which
Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle.
Result: At 1:10 serum dilution, the infectivity of both SC2-Wuhan pseudovirus and SC2 D614G mutant variant diminished to 38% +- 22% and 38% +- 5%, respectively, whereas for SC2-beta mutant variant, the infectivity dropped to only 67% +- 7%.
Result: The IC50 infectivity inhibition concentrations were determined to be 1:83.8, 1:47.5, and 1:150 serum dilutions for SC2-Wuhan, SC2-beta mutant, and SC2-D614G mutant variants, respectively (Figure S1).
Result: These trends were consistent across all three strains of pseudoviruses engineered for different variants of SC2 S proteins (i.e., SC2-Wuhan, SC2-beta mutant, and SC2-
Figure: The relative inhibition in infectivity was performed against lentiviral particles engineered with (e) S protein SC2-Wuhan, (f) SC2-beta mutant, and (g) SC2-D614G mutant variants.
Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity.
PMID: 34722330
2021
Frontiers in cellular and infection microbiology
Abstract: Here, with a vesicular stomatitis virus (VSV)-based pseudotype system, we demonstrated that the pseudovirus bearing N501Y.V2 S protein has higher infection efficiency than pseudovirus with wildtype (WT) and D614G S protein.
Abstract: However, the pseudovirus bearing N501Y.V1 or N501Y.V2 S protein has similar sensitivity to inhibitors of protease and endocytosis with WT and D614G
Method: Pseudovirions incorporated with S protein of SARS, SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 lineages were diluted with DMEM and incubated in a 37 C or 42 C water bath.
UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates.
Discussion: A recent study examining SARS-CoV-2 variants in the rhesus macaque model showed no difference in viral replication nor disease between the D614G and B.1.1.7 variants.
Discussion: B.1.1.7 replicated at higher levels in the respiratory tract resulting in lesions that were both more numerous and severe than seen for D614G infected animals.
Discussion: Consistent with higher levels of viral replication in the URT, shedding of SARS-CoV-2 RNA in both the nose and oropharyngeal cavity was also higher in B.1.1.7 infected animals suggestive of potentially enhanced transmissibility of the B.1.1.7 (Alpha) over the D614G progenitor variant (Figure 1).
Discussion: Following infection with either variant, animals in both groups exhibited minor differences in disease progression but overall disease signs were similar with mild re
Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations.
Result: All viruses contained the D614G variant, except one isolate.
Result: Besides the D614G mutation, the most common mutation in the S protein was L5F (18.8%), V213A (18.8%), and S689R (8.3%) (Table 3).
Discussion: A large-scale analysis of the COVID-19 Genomics UK consortium demonstrated that although D614G mutation is associated with higher viral loads, it is not associated with clinical severity and fatality of COVID-19 patients.
Discussion: All our samples, except one, contained the D614G variant.
Discussion: Indeed, almost all viruses circulating globally consist of the
SARS_CoV_2 mutation literature information.
PMID: 
2021
The Lancet. Global health
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