Mutation detail:
| Mutation site | D5574Y |
| Virus | SARS-CoV-2 |
Mutation level  |
Amino acid level |
| Gene/protein/region type | ORF1ab(NSP3) |
| Gene ID | 43740578 |
| Country | USA |
| Mutation type |
nonsynonymous mutation |
| Genotype/subtype/clade | - |
| Sample |
Human |
| Variants | - |
| Viral reference sequence | NC_045512.2 |
| Drug/antibody/vaccine | - |
| Transmissibility |
- |
| Transmission mechanism | - |
| Pathogenicity |
- |
| Pathogenicity mechanism | - |
| Immune escape mutation | - |
| Immune escape mechanism | - |
| RT-PCR primers probes | - |
Protein detail:
| Protein name | ORF1ab polyprotein |
| Uniprot protein ID | P0DTC1 |
| Protein length | 7096 amino acids |
| Protein description | ORF1ab, the largest gene, contains overlapping open reading frames that encode polyproteins PP1ab and PP1a. The polyproteins are cleaved to yield 16 nonstructural proteins, NSP1-16. Production of the longer (PP1ab) or shorter protein (PP1a) depends on a -1 ribosomal frameshifting event. The proteins, based on similarity to other coronaviruses, include the papain-like proteinase protein (NSP3), 3C-like proteinase (NSP5), RNA-dependent RNA polymerase (NSP12, RdRp), helicase (NSP13, HEL), endoRNAse (NSP15), 2'-O-Ribose-Methyltransferase (NSP16) and other nonstructural proteins. SARS-CoV-2 nonstructural proteins are responsible for viral transcription, replication, proteolytic processing, suppression of host immune responses and suppression of host gene expression. The RNA-dependent RNA polymerase is a target of antiviral therapies. |
Literature information:
| Pubmed ID | 33571356 |
| Clinical information | No |
| Disease | - |
| Published year | 2021 |
| Journal | JAMA Network Open |
| Title | Emergence of a Novel SARS-CoV-2 Variant in Southern California |
| Author | Wenjuan Zhang,Brian D. Davis,Stephanie S. Chen,Jorge M. Sincuir Martinez,Jasmine T. Plummer |
| Evidence | Of 2311 samples at CSMC, 192 were selected and 185 (67 inpatient; 118 outpatient) underwent phylogenetic analysis, along with 1480 representative genomes using Nextstrain. A diverse set of lineages with 2 main clusters was identified (Figure 1). The smaller of the 2 clusters was from the 20G lineage and accounted for 22% (40 of 185) of the samples. The larger cluster (36%; 67 of 185) consisted of a novel variant descended from cluster 20C, defined by 5 mutations (ORF1a: I4205V, ORF1b: D1183Y, S: S13I; W152C; L452R) and designated CAL.20C (20C/S:452R; /B.1.429). |