Expression of Concern: Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalization and zoonosis in pandemics
Bibliographic record
Abstract
An Expression of Concern onAnalysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics,By Colson P, Fournier P-E, Chaudet H, Delerce J, Giraud-Gatineau A, Houhamdi L, Andrieu C, Brechard L, Bedotto M, Prudent E, Gazin C, Beye M, Burel E, Dudouet P, Tissot-Dupont H, Gautret P, Lagier J-C, Million M, Brouqui P, Parola P, Fenollar F, Drancourt M, La Scola B, Levasseur A and Raoult D (2022) Analysis of SARSCoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics. Front. Microbiol. 12:786233. doi: 10.3389/fmicb.2021.786233Following publication, it was brought to our attention that the ethical approval for this study referred to the same ethics approval number 2020-016-03 that had been used across a series of unrelated published studies (1–10). Additionally, an issue around the potential need for approval from a Comité de Protection de Personnes was raised and remains unresolved.An investigation conducted by the Comité d'éthique at Aix-Marseille Université confirmed that this study is retrospective and did not require approval from a Comité de Protection de Personnes. The institution stated that the quoted ethics approval 2020-016-03 is a generic opinion concerning the study of genetic diversity and evolution of SARS-COV-2 which is valid for any study on this topic.Frontiers has not received the necessary documentation to confirm these statements.1. Dao TL, Hoang VT, Nguyen NN, Delerce J, Chaudet H, Levasseur A, et al. Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Clin Microbiol Infect. 2021 Oct 1;27(10):1516.e1-1516.e6. 2. Hoang VT, Colson P, Levasseur A, Delerce J, Lagier JC, Parola P, et al. Clinical outcomes in patients infected with different SARS-CoV-2 variants at one hospital during three phases of the COVID-19 epidemic in Marseille, France. Infect Genet Evol. 2021 Nov 1;95:105092. 3. Gautret P, Houhamdi L, Nguyen NN, Hoang VT, Giraud-Gatineau A, Raoult D. Does SARS-CoV-2 reinfection depend on virus variant? Clin Microbiol Infect. 2021 Sep 1;27(9):1374–5. 4. Hoang VT, Assoumani L, Delerce J, Houhamdi L, Bedotto M, Lagier JC, et al. Introduction of the SARS-CoV2 Beta variant from Comoros into the Marseille geographical area. Travel Med Infect Dis. 2022 Mar 1;46:102277. 5. Colson P, Fantini J, Yahi N, Delerce J, Levasseur A, Fournier PE, et al. Limited spread of a rare spike E484Kharboring SARS-CoV-2 in Marseille, France. Arch Virol. 2022 Feb 1;167(2):583–9. 6. Colson P, Delerce J, Burel E, Beye M, Fournier PE, Levasseur A, et al. Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Virus Genes. 2022 Feb 1;58(1):53–8. 7. Colson P, Delerce J, Pontarotti P, Devaux C, La Scola B, Fantini J, et al. Resistance-associated mutations to the anti-SARS-CoV-2 agent nirmatrelvir: Selection not induction. J Med Virol. 2024;96(2):e29462. 8. Colson P, Chaudet H, Delerce J, Pontarotti P, Levasseur A, Fantini J, et al. Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic. J Infect. 2024 May 1;88(5):106150. 9. La Scola B, Lavrard P, Fournier PE, Colson P, Lacoste A, Raoult D. SARS-CoV-2 variant from India to Marseille: The still active role of ports in the introduction of epidemics. Travel Med Infect Dis. 2021 Jul 1;42:102085. 10. Colson P, Levasseur A, Delerce J, Pinault L, Dudouet P, Devaux C, et al. Spreading of a new SARS
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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 | 0.014 | 0.026 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.003 | 0.001 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.005 | 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".