Result: All the missed mutations were due to a lack of coverage (<10 reads) and were grouped on the same amplicon NC_045512.2:22903-23122 (missing mutations: N440K, S477N, T478K, E484K, N501Y, A522S).
Result: For example, a variant harboring mutations S477N and D614G was identified as belonging to lineage B.1.160.
Result: Taken together, the most frequently missed mutations were G142D (n = 11), E156G, 157del, 158del (n = 6), N501Y (n = 6), S477N (n = 5), T95I
SARS-CoV-2 Omicron neutralization by therapeutic antibodies, convalescent sera, and post-mRNA vaccine booster.
Introduction: The predominant strain of Omicron has mutations in the spike gene encoding 15 amino acid changes in the receptor binding domain (RBD) of the spike surface protein (G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, and Y505H).
Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India.
Result: We also identified 8 substitution mutants in the SARS-CoV-2, K417N, G446V, L452R, S477N, T478K, E484Q, F490S, and A522V in the RNA binding domain (RBD) of S1 subunit of Spike protein.
Table: S477N
Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka.
Result: Of these, five (S477N, E484K, E484Q, S494L, S494P) were found in viruses circulating in Bengaluru, and the amino acid replacement V483A was from an imported case.
Discussion: All nine amino acid changes, namely N440K, S477N, V483A, E484K/Q, F490S, S494L/P, N501Y are associated with immune escape.
SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia.
Result: None of the 41 rare receptor binding variants described in GISAID-including the two most common, S477N and N439K -were observed in the Malaysian sequences.
Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants.
PMID: 33380328
2020
Journal of translational medicine
Result: Next, there are a few variants with a frequency of 2-7% that are slowly rising in the viral populations, namely S477N, Q613H and A222V.
Result: The S477N has been firstly identified in Colombia and is harbored in more than 60% of the isolates sequenced
Result: The geographical distribution shows how the S477N variant is strongly rooted in Australia, and the N439K is associated with clusters starting from the United Kingdom (Scotland).
Result: The overall Epitope score, that takes into account a variable amino acid window surrounding the mutation, is slightly increased, from 0.535/0.516 in the WT sequence to 0.561 and 0.548 for S477N and N439K, respectively (Additional file 1: Table S5).
SARS_CoV_2 mutation literature information.
PMID: 
2021
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