Etsin netistä lähteitä tälle varianttitiedolle,koska en satu löytämään omista muistiinpanoistani. Kolumbian sars-2 variantissa on esiintynyt tätäkin jo, joten kyse ei ole aivan uudesta mutaatiosta. Otan sitaatteja netistä. Sitä on esiintynyt Pango-linjassa B.1.621 (mu) ja tämä on ollut jo aikaa VOI-listallakin. Omikron omaa ainakin 3 mu-variantin s-mutaatiota ja jos ilmenee otsikon mutaatio R346K, niin 4 mu-spike- mutaatiota.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8364171/Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity has the potential to impact the virus transmissibility and the escape from natural infection- or vaccine-elicited neutralizing antibodies. Here, representative samples from circulating SARS-CoV-2 in Colombia between January and April 2021, were processed for genome sequencing and lineage determination following the nanopore amplicon ARTIC network protocol and PANGOLIN pipeline. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. The rapid increase in frequency and fixation in a relatively short time in Magdalena, Atlantico, Bolivar, Bogotá D.C, and Santander that were near the theoretical herd immunity suggests an epidemiologic impact. Further studies will be required to assess the biological and epidemiologic roles of the substitution pattern found in the B.1.621 lineage.
Nucleotide and amino acid substitution pattern of B.1.621.
| Genomics coordinate with respect to the reference genome (NC_045512.2) | Amino acid change | Region/Protein |
|---|---|---|
| ORF1ab: | ||
| A3428G | T1055A | Non-structural protein 3 |
| C4878T | T1538I | Non-structural protein 3 |
| A11451G | Q3729R | Non-structural protein 6 |
| C14408T | P4715L | RNA-dependent RNA polymerase |
| C17491T | P5743S | Helicase domain |
| ORF3a: | ||
| G25563T | Q57H | accessory protein ORF3a |
| deletion: 26158–26,162 (4 nucleotides) | V256- | accessory protein ORF3a |
| frameshift | N257X | accessory protein ORF3a |
| ORF8: | ||
| A27924C | T11K | ORF8 immunoglobulin (Ig) domain protein and related proteins |
| C28005T | P38S | ORF8 immunoglobulin (Ig) domain protein and related proteins |
| C28093T | S67F | ORF8 immunoglobulin (Ig) domain protein and related proteins |
| Spike: | ||
| C21846T | T95I | N-terminal domain of S1 subunit |
| T21992A, A21993C | Y144T | N-terminal domain of S1 subunit |
| A21996C, C21997T | Y145S | N-terminal domain of S1 subunit |
| 21,998:AAC | ins146N | N-terminal domain of S1 subunit |
| G22599A | R346K | receptor binding domain |
| G23012A | E484K | receptor binding domain |
| A23063T | N501Y | receptor binding domain |
| C23604A | P681H | S1/S2 cleavage region |
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