SARS-CoV-2 Omicron Variant Genomic Sequences and Their Epidemiological Correlates Regarding the End of the Pandemic: In Silico Analysis
Bibliographic record
Abstract
BACKGROUND A newly emerged SARS-CoV-2 variant B.1.1.529 worried the health policy makers worldwide due to a large number of mutations in its genomic sequence, especially in the spike protein region. World Health Organization (WHO) designated it as a global variant of concern (VOC) and was named 'Omicron.' Following Omicron's emergence, a surge in new COVID-19 cases was reported globally, primarily in South Africa (SA). OBJECTIVE We aimed to understand whether the Omicron had an epidemiological advantage over existing variants. METHODS We performed an in silico analysis of the complete genomic sequences of Omicron available on GISAID to analyze the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period of 01 Oct-29 Nov 2021) with the matched epidemiological data (new COVID-19 cases and deaths) from SA. RESULTS Compared to the current list of global VOCs/VOIs (as per WHO), Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with the Alpha variant for the complete sequence and RBM. The mutations were found primarily condensed in the spike region (28-48) of the virus. Further, the mutational analysis showed enrichment for the mutations decreasing ACE2-binding affinity and RBD protein expression, in contrast, increasing the propensity of immune escape. An inverse correlation of Omicron with Delta variant was noted (r=-0.99, p< .001, 95% CI: -0.99 to -0.97) in the sequences reported from SA post-emergence of the new variant, later showing a decrease. There was a steep rise in the new COVID-19 cases in parallel with the increase in the proportion of Omicron since the first case (74-100%). In contrary, the incidences of new deaths was not increased (r=-0.04, p>0.05, 95% CI =-0.52 to 0.58). CONCLUSIONS In silico analysis of the viral genomic sequences suggest that the Omicron variant has more remarkable immune escape ability than the existing VOCs/VOIs, including Delta, but lesser virulence/lethality than other reported variants. The higher power for immune escape for Omicron was a likely reason for the surge in COVID-19 cases and soon becoming a globally dominant strain. They were more infectious but less lethal than the existing variants, hence outpaced them, thus scripting the pandemic's downfall.
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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 | 0.002 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.003 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".