SARS-CoV-2 N501Y variants of concern and their potential transmission by mouse
Bibliographic record
Abstract
The infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus causes pneumonia of coronavirus diseases 2019 (COVID-19) [ 1 ]. A portion of patients with COVID-19 develop severe conditions that are closely related to aberrant immunity and local inflammation [ 2 ], clinically manifested as cytokine storm, expansion of myeloid-derived suppressor cells and lymphopenia, and the like [ 3 , 4 ]. As of the end of March 2021, the pandemic of SARS-CoV-2 has resulted in more than 126.6 million of patients with COVID-19, leading to about 2.8 million deaths around the world (Fig. 1a ) [ 5 ]. Over the past year, considerable efforts had been endeavored to implant public health measures to limit the spreading of SARS-Co-V2. However, before people started to cheer the staged success in the middle of January 2021, another wave of global SARS-CoV-2 spreading is surging up shortly after the fall-off of the second wave of pandemic (Fig. 1a ). Similar to the second wave that came up with a highly transmissible variant carrying D614G mutation [ 6 ], the third wave of pandemic emerged with a number of different variants, among which three variants, B.1.1.7, B1.351, and P.1, displayed increasing transmissibility, and therefore were categorized by the world health organization (WHO) as variants of concern (VOC). By 29 March 2021, these three variants have been constituting about two-thirds of SARS-CoV-2 viruses circulating around the world (Fig. 1b ) [ 5 ]. Fig. 1: Implication of mouse-mediated transmission of SARS-CoV-2 N501Y variants in the 3rd wave pandemic. a Weekly cases of global confirmed COVID-19 by May 28, 2021. Data were retrieved from the COVID-19 Dashboard of the World Health Organization (WHO). b The proportion of different SARS-CoV-2 clades over time. The graph was made from data adopted from Nextstrain SARS-CoV-2 resources. c Schematic diagram depicts the mutations on spike proteins of three SARS-CoV-2 N501Y variants of concern. Key mutations are in black and bold. Shared mutations are shadowed. SP signal peptide, NTD N terminus domain, CTD/RBD C terminus domain/receptor-binding domain, TM transmembrane region, CT cytoplasmic terminus. d A list of SARS-CoV-2 strains, harboring mutations in the RBD region of S glycoprotein, that could effectively infect wild-type mice. e Schematic demonstration of the mouse as a transmitter of the SARS-CoV-2 N501Y variants of concern. Full size image
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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 | 0.006 | 0.009 |
| Meta-epidemiology (narrow) | 0.003 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.005 | 0.003 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.019 | 0.019 |
| Insufficient payload (model declined to judge) | 0.008 | 0.005 |
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".