Result: The p.Glin57His substitution in open reading frame 3a (ORF3a) and the p.Leu84Ser substitution in open reading frame 8 (ORF8) was found in 33 (12%) and 32 (11%) SARS-COV-2 samples, respectively.
SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation.
PMID: 33905892
2021
Infection, genetics and evolution
Abstract: The prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere.
Discussion: L84S, one out of the two variants that define the clade S (GISAID classification), has been reported mainly for Asian countries, with a lower freque
Discussion: Altogether, the variant calling analysis reveals that the patterns found in Costa Rica, with 283 distinct mutations, are similar to those observed worldwide (such as D614G in the Spike and L84S in the ORF8), except for the T1117I in the Spike.
A Founder Effect Led Early SARS-CoV-2 Transmission in Spain.
Abstract: Most sequences from Spain were distributed in clades characterized by a D614G substitution in the S gene (20A, 20B, and 20C) and an L84S substitution in ORF8 (19B) with 163 and 118 sequences, respectively, with the remaining sequences branching in 19A.
Introduction: According to Nextstrain, almost all sequences in clade 19B are characterized by the presence of L84S in ORF8 (GISAID clade S), whereas the clades that emerged in 2020 (20A, 20B, and 20C) are characterized by D614G in the S protein (GISAID clade G).
Result: Approximately 40% of all genome sequences from Spain harbored the L84S substitution in
Result: Consistent with the mutational analysis of our internal data set (Figure 2), the phylogenetic analysis of the publicly available Uruguayan sequences reveals a predominance of clades S and G (G, GH, and GR), the former occupying most of the upper half of the maximum-likelihood tree (Figure S5A) and the right half of the haplotype network (Figure S5B), the latter the respective opposite halves, highlighted by green and red arrows for spike D614G and ORF8 L84S key mutations, respectively.
Result: In March and early April, ORF8 mutation L84S and the associated C8782 T SNP were most abundant (>1/3 of sequences) (Figure 2A, C, Figures S2 and S3).
Discussion: According to the CoV-GLUE databas
Engineering a Reliable and Convenient SARS-CoV-2 Replicon System for Analysis of Viral RNA Synthesis and Screening of Antiviral Inhibitors.
Abstract: L84S is by far the most predominant mutation, followed by S24L that appeared first in USA.
Abstract: Genetic diversity analysis showed two main regions that harbor L84S and S24L.
Abstract: Phylogenetic analysis of ORF8 variants revealed the appearance of small clades with that of L84S being closer to bats.
Introduction: Single Nucleotide Variations (SNVs) in ORF8 at 28144T>C (251T>C, L84S) characterize the SARS-CoV-2 S clade, leading to divergence of phylogenetic group.
Result: 74 different double co-mutations were also observed, with L84S
A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity.
PMID: 33524589
2021
Clinical microbiology and infection
Method: With reference to GISAID, variants were assigned to four lineages: L (reference sequence, nucleotide T28144, ORF8 amino acid L84), S (nt T28144C, ORF8 aa L84S), V (nt G26144T, ORF3a aa G251V) and G* (nt A23403G, S gene aa D614G).
SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions.
PMID: 33556558
2021
Infection, genetics and evolution
Result: Among these sites, a subset of 11 early high-frequency sites (of which 8 were coding [ORF8 -L84S, ORF1a - V378I, ORF1a - L3606F, ORF1a - A3220V, ORF3a - G251V, ORF1a - L3606F, S - D614G, ORF1b - P314L]) enabled defining the phylogenetic clade structure of the viral sequences.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Microbial genomics
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