literature

SARS_CoV_2 mutation literature information.

SARS-CoV-2 genomic variations associated with mortality rate of COVID-19.

PMID: 32699345 2020 Journal of human genetics

Result: Comparing the mutations among the three clusters, the average frequency of an L variant of an ORF1ab P4715L in the countries classified as the cluster 1 was 14.7%, which is significantly lower than 81.3% and 73.2%, respectively, in the countries classified as the clusters 2 and 3 (P = 1.3 x 10-6 and P = 2.5 x 10-5, respectively; Supplementary.

Result: We finally searched peptide epitopes with a high binding affinity to HLA molecules, which we previously reported, involving the two SARS-CoV-2 mutations, ORF1ab P4715L and S D614G, to investigate the association with host immune responses.

Result: We found that several epitopes, which include the position of ORF1ab P4715L<

SARS-CoV-2 Genomes From Oklahoma, United States.

PMID: 33613621 2020 Frontiers in genetics

Abstract: Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K, and G204R in N gene were identified in the genomes sequenced in this study.

Introduction: P4715L in ORF1ab is believed to play a major role in interaction with other proteins that regulate RNA dependent RNA polymerase.

Introduction: SNPs in the genome that result in commonly reported non-synonymous mutations such as P4715L in ORF1ab, D614G in S g

Variant analysis of SARS-CoV-2 genomes.

PMID: 32742035 2020 Bulletin of the World Health Organization

Abstract: The most common variants were the synonymous 3037C > T (6334 samples), P4715L in the open reading frame 1ab (6319 samples) and D614G in the spike protein (6294 samples).

Result: Most samples in the D614G clade also display the non-coding variant 241C > T, the synonymous variant 3037C > T and ORF1ab

Discussion: Almost all strains with D614G mutation also have a mutation in the protein responsible for replication (ORF1ab P4715L; RdRp P323L), which might affect replication speed of the virus.

SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.

PMID: 32543353 2020 Emerging microbes & infections

Result: In addition to the signature mutation S-D614G annotated by GISAID in clade III, all the Taiwanese genomes shared two ORF1ab mutations C2772T and C14144T (P4715L) (Figure 3E).

Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide.

PMID: 32820179 2020 Scientific reports

Introduction: For example, most strains of the D614G clade also harbor a mutation (P4715L) in orf1ab and a subclade processes three nucleotide changes in the nucleoprotein (N) gene (GGG to AAC; G204R), which plays diverse roles in virion assembly as well as genome transcription and translation.

A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants.

PMID: 32868447 2020 Proc Natl Acad Sci U S A

Result: Across the genome, there were, on average, 4.05 nucleotide mutations per individual genome when compared to the consensus, with only P4715L and D614G found in >50% of sequences.

Result: Since the beginning of the pandemic, two mutations across the genome have become consensus: P4715L in ORF1ab (nucleotide 14,143, C to T) and D614G in S (nucleotide 23,403, A to G).

Figure: (B) Phylogenetic tree reconstructed from all of the ORFs showing the linkage between D614G in S and P4715L in ORF1ab.

SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution.

PMID: 32869023 2020 bioRxiv

Result: Four genetically linked mutations previously described as the globally dominant haplotype in April 2020 were found in the majority of our consensus sequences: C241T (100%; 5'UTR region), C3037T (98.6%; silent mutation), C14408T (100%; resulting in P4715L/P323L amino acid change in ORF1ab) and A23403G (100%; resulting in D614G amino acid change in S).

BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission.

PMID: 32904401 2020 Sustainable cities and society

Table: P4715L

A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual.

PMID: 32967693 2020 Journal of translational medicine

Result: Alignment analyses showed that, with respect to the Wuhan-Hu-1 Reference Genome NC_045512.2, SARS-CoV-UNIBS-2 AP66 consensus sequence displayed 6 nucleotide substitutions (C241T; C3037T; C14408T; T21784G; C21846T; A23403G) leading to 4 non-synonymous changes (ORF1ab polypeptide: P4715L; S protein: N74K, T95I, D614G).

Result: Less pathogenic GZ69 consensus sequence differed from Wuhan-Hu-1 isolate in 11 nucleotide positions (C241T; C2939T; C3037T

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.

PMID: 33024961 2020 Research square

Result: Spike D614G was nearly always co-inherited with Pol P4715L (also radical and altering a perfectly-conserved residue in a highly-conserved context, but potentially-deleterious given Pol's slow evolution and less-likely-to-be-adaptive function), nsp3 nucleotide change C3037T (repeatedly-observed synonymous change, outside synonymously-constrained elements, likely-neutral), and nucleotide change C241T (perfectly-conserved, non-coding, in a loop of six unpaired bases in the conserved 5'UTR SL5B secondary structure 25 nucleotides upstream of ORF1ab).

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