The study of mutations and phylogenetics of the SARS-CoV-2 spike gene in population from Tehran province
Bibliographic record
Abstract
In December 2019, an outbreak of pneumonia of unknown etiology was reported in Wuhan, China. The virus, known as SARS-CoV-2, is contagious and infects the lower respiratory tract. Since various coherent research needs to be conducted in Iran to detect mutations in the SARS-CoV-2 S gene, the present study was conducted to determine the sequence, mutation pattern, and phylogenetic evaluation of this gene. To this end, 120 positive samples were included in the study to evaluate the complete S gene sequence by Reverse transcriptase-PCR.Subsequent to the sequencing process, the gene assembly, blasting, mutation analysis, and phylogenetic analysis were performed using MEGA-X.A total of 161 mutations were observed in the S gene sequences of Iran. The results of the phylogenetic tree showed that all the S gene sequences of Iranian samples were divergent from the Wuhan strain and had the most similarity to it and also alpha variants. 161 nonsynonymous variations were found along the complete coding S gene with a high frequency of A262T, D614G, and P863H, which were embedded in HVR1, HVR2, and HVR3, respectively. The majority of highly variable fragments have been identified in the loop secondary structure of protein. In the present study, the predominant variants (predominantly alpha variants) and mutations were observed to be in parallel with the evolution of the virus and its fitness. A comprehensive overview of the genetic mutation of the first three waves of SARS-CoV-2 in Iran was provided, which could be used to make significant decisions and take effective measures in future pandemics to develop vaccines, kits and effective therapeutics.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".