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SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro

Name: Kaimen Rigor review — SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro
Item: SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro
Rating: 57
Author: Alpha1

Jiang H, Mei YF.

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Kaimen Rigor review — 1.75★ (Critical), 0 critical, 5 high issues for “SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro”

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This rigor review was examined and confirmed by Alpha1 Editorial · August 5, 2026

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SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro

Jiang H, Mei YF.

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DOI

10.3390/v13102056

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Kaimen Rigor reviewed

Rigor-Reviewed Manuscript

SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro

Jiang H, Mei YF.

Paper source

SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro

Read full text (PMC)Journal

Embed this Rigor badge

Links back to this Kaimen Rigor review.

Alpha1 Editorial

This rigor review was examined and confirmed by Alpha1 Editorial · August 5, 2026

Kaimen Rigor review

Kaimen Rigor reviewed

1.75 / 5

Critical — serious problems across many checks

Interventional Study

Critical

High-priority

How this rating was calculated▸

Started at 5★ — deductions

IntegrityIntegrity concern ×2−1★
ClaimsOverstated claim−0.5★
ReportingStudy design not met−0.5★
ReportingKey resources not met−0.5★
ReportingData & code availability not met−0.5★
ReportingStatistical analysis partially met−0.25★

Model-reported confidence: moderateReviewer agreement: lowEngine: 7.15.0Source: full text

Not verified in this report

Statistics were not checked: no recomputable values were found in this text — no test statistic reported with its degrees of freedom, no effect estimate printed with both a 95% CI and a p-value, and no percentage printed with both its count and its denominator.

Biggest issues

01Study design lacks key rigor safeguards
highDisclosurereviewer-assessedFull detail
The study lacks adequate reporting of randomization, blinding (except for scoring), power analysis, inclusion/exclusion criteria, outlier handling, and independent replication, while only reporting replicate distinction and controls adequately.
“All scoring was performed under blinded conditions.”
Methods
02Key resources not identified
highDisclosurereviewer-assessedFull detail
Key resources are inadequately identified: antibodies are listed with catalog numbers but without RRIDs or validation data, cell lines are not authenticated, mycoplasma testing is not reported, and software versions are incomplete.
“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”
Methods
03Data and code not shared
highDisclosurereviewer-assessedFull detail
The data availability statement is vague (data available in the main text and supplementary), and no raw data are deposited in a public repository. Custom code is not shared.
“The data presented in this study are available in the main text and .”
Data availability
04Conclusion reaches beyond the evidence
mediumOverreachreviewer-assessedFull detail
Full-length spike-based vaccines may have side effects by inhibiting adaptive immunity.
“our findings also imply a potential side effect of the full–length spike–based vaccine”
Discussion

Findings by category

101ArithmeticNumerical inconsistencies 202OverreachOverstated conclusions 03AuthenticityNone found 404DisclosureReporting gaps 05AvailabilityNone found 06Copyedit8 minor suggestions

This Kaimen Rigor review uses Kaimen Rigor reviewers trained on a curated corpus of high-fidelity and retracted papers, with expert supervision and curation. It can still make mistakes; verify each finding against the source before relying on it.

The paper has a well-articulated premise, detailed methods, appropriate controls and independent biological replicates, and transparent funding/COI disclosure — the strengths of this in vitro study. Its main weaknesses are a truncated data-availability statement with no repository, under-reported study-design elements (power analysis, blinding outside IF scoring, outlier handling, independent replication), missing cell-line authentication/mycoplasma statements, threshold-only p-values with no verifiable recomputation, and one overstated vaccine-related implication.

Synthesis of three independent reviewer runs of the same model (sampling stability, not corroboration by different systems), plus a copyedit pass and verification components: 29 references checked (0 retracted, 0 not found in registry), 0 statistics recomputed (all p-values threshold-only), 1 reproducibility link live, no preregistration. Reviewers diverged on study design (fail vs warn), biological variables (pass vs N/A), key resources (pass/warn/fail), and statistics (warn vs fail); each divergence was resolved at the sub-criterion level and both positions are preserved in the dimension details.

Numerical inconsistencies

1 finding · worst low

Values that contradict each other or are impossible for the stated sample: recomputed p-values and test statistics, GRIM/GRIMMER checks on summary numbers, percentages against their own counts, totals against their parts, and estimates against their own confidence intervals.

Internal contradictions in the reported numbersAssessed

Overstated conclusions

2 findings · worst medium

Conclusions that reach past what the paper's own results support — including a significance claim that no longer holds when the statistic is recomputed, and efficacy resting on an unvalidated surrogate endpoint.

Conclusions overstated beyond the evidenceAssessed
Conclusions only partially backed by the presented evidenceAssessed

11 major claims checked against the paper's own evidence: 1 not fully backed by the presented evidence (unsupported or overstated).

Data authenticity concerns

None found

An adversarial read for patterns associated with data that may not be genuine: results that look too clean, implausibly large effects, duplicated data or images, and methods that do not match the results reported.

Checked — nothing surfaced.

Reporting gaps

4 findings · worst high

Required detail the manuscript never states — study design, biological variables, ethics approval and consent, key resources, statistical reporting, data and code availability, and overall transparency.

Data and code not sharedAssessed
Key resources not identifiedAssessed
Statistical reporting gaps (tests, assumptions, effect sizes)Assessed
Study design lacks key rigor safeguardsAssessed

Eight Dimensions3 pass · 1 warn · 3 fail

The introduction cites clinical studies showing delayed adaptive immunity in COVID-19 and the interdependence of immune and DNA repair systems. The study objective to investigate whether SARS-CoV-2 proteins hijack the DNA repair system logically follows from the cited evidence. However, the paper does not explicitly discuss how it addresses limitations of prior work, such as the lack of mechanistic studies.

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedNOT REPORTED

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

Prior work establishing the premise is cited, and a logical rationale links the premise to the study objectives. The paper does not address limitations of prior research, but this is a secondary criterion.

Evidence

“Recent clinical studies have shown that SARS–CoV–2 infection extraordinarily affects lymphocyte number and function [,,,].”

Introduction ¶1

“Therefore, we aimed to investigate whether SARS–CoV–2 proteins hijack the DNA damage repair system, thereby affecting adaptive immunity in vitro.”

Introduction

absence[Introduction]

No discussion of limitations of prior research.

PASSReviewer 2· 90% conf

The paper establishes a clear scientific premise by citing prior work on SARS-CoV-2 effects on adaptive immunity and the link between DNA repair and V(D)J recombination, and provides a logical rationale for the hypothesis.

Evidence

paraphrase[Introduction, paragraph 1]

“Recent clinical studies have shown that SARS-CoV-2 infection extraordinarily affects lymphocyte number and function”

“As two critical host surveillance systems, the immune and DNA repair systems are the primary systems that higher organisms rely on for defense against diverse threats and tissue homeostasis.”

Introduction ¶2

absence[Introduction]

No discussion of limitations of prior research is found.

PASSReviewer 3· 85% conf

The paper establishes a clear scientific premise by citing prior work on SARS-CoV-2 effects on adaptive immunity and the role of DNA repair in V(D)J recombination, and provides a logical rationale for the study.

Evidence

paraphrase[Introduction, paragraph 1]

“Recent clinical studies have shown that SARS-CoV-2 infection extraordinarily affects lymphocyte number and function [,,,]. Compared with mild and moderate survivors, patients with severe COVID-19 manifest a significantly lower number of total T cells, helper T cells, and suppressor T cells [,]. Additionally, COVID-19 delays IgG and IgM levels after symptom onset [,,].”

paraphrase[Introduction, paragraph 2]

“As two critical host surveillance systems, the immune and DNA repair systems are the primary systems that higher organisms rely on for defense against diverse threats and tissue homeostasis. Emerging evidence indicates that these two systems are interdependent, especially during lymphocyte development and maturation []. As one of the major double-strand DNA break (DSB) repair pathways, non-homologous end joining (NHEJ) repair plays a critical role in lymphocyte-specific recombination-activating gene endonuclease (RAG) –mediated V(D)J recombination.”

paraphrase[Introduction, paragraph 2]

“Therefore, we aimed to investigate whether SARS-CoV-2 proteins hijack the DNA damage repair system, thereby affecting adaptive immunity in vitro.”

The paper does not describe randomization of samples or blinding for most assays, lacks a priori power analysis, does not define inclusion/exclusion criteria or outlier handling, and does not report independent replication. Biological replicates are distinguished ('independently collected or prepared samples') and controls (empty vector) are used, but these are insufficient to meet the threshold for pass.

Sub-criteria

controlsADEQUATE

power analysisNOT REPORTED

blinding levelsINADEQUATE

outlier handlingNOT REPORTED

randomization unitNOT REPORTED

inclusion exclusionNOT REPORTED

randomization methodNOT REPORTED

replicate distinctionADEQUATE

independent replicationNOT REPORTED

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 70% conf

The study lacks many design elements expected for a preclinical study, including randomization, blinding (except for scoring), power analysis, inclusion/exclusion criteria, outlier handling, and independent replication. Only replicate distinction and controls are adequately reported.

Evidence

“All scoring was performed under blinded conditions.”

Methods

“All experiments were repeated at least three times using independently collected or prepared samples.”

Methods

paraphrase[Materials and Methods, 2.4 HR and NHEJ Reporter Assays]

“Empty vector (E.V) is used as a control, and DNA damage is induced by γ-irradiation, doxorubicin, or H2O2.”

WARNReviewer 2· 70% conf

The study design has several methodological gaps: randomization is not applicable, blinding is only partially reported for scoring, no power analysis, no outlier handling, and no independent replication. However, controls are adequate and biological replicates are distinguished.

Evidence

“All scoring was performed under blinded conditions.”

Section 2.7 (Immunofluorescence)

“All experiments were repeated at least three times using independently collected or prepared samples.”

Statistical analysis

“Effect of empty vector (E.V) and SARS–CoV–2 proteins on NHEJ DNA repair.”

Figure 1

FAILReviewer 3· 90% conf

The study lacks adequate reporting of randomization, blinding (except for scoring), power analysis, inclusion/exclusion criteria, outlier handling, and independent replication, while only reporting replicate distinction and controls adequately.

Evidence

“All scoring was performed under blinded conditions.”

Methods

“All experiments were repeated at least three times using independently collected or prepared samples.”

Methods

paraphrase[Results, Figure 1 legend]

“Figure 1C and 1E compare empty vector (E.V) with SARS-CoV-2 proteins.”

The paper specifies HEK293T and HEK293 cells from ATCC and describes culture conditions (DMEM, 5% CO2, 37°C, FCS, antibiotics). Sex of the cell line is not reported, but this is not typically considered critical for cell line studies. Other variables like age and weight are not applicable.

Sub-criteria

demographicsN/A

sex reportedN/A

sex justifiedN/A

age weight healthN/A

housing conditionsADEQUATE

species strain sourceADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 80% conf

The cell line source and culture conditions are adequately reported. Sex of the cell line is not reported, but this is not a standard requirement for in vitro studies. Age/weight/health are not applicable.

Evidence

paraphrase[Materials and Methods, 2.3 Cells and Cell Culture]

“HEK293T and HEK293 cells obtained from the American Type Culture Collection (ATCC) were cultured under 5% CO2 at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM, high glucose, GlutaMAX) (Life Technologies, Carlsbad, CA, USA) containing 10% ( v / v ) fetal calf serum (FCS, Gibco), 1% ( v / v ) penicillin (100 IU/mL), and streptomycin (100 μg/mL).”

N/AReviewer 2· 95% conf

The study uses only established human cell lines (HEK293T and HEK293), so biological variables such as sex, age, weight, housing, and demographics are not applicable. The species and source are reported.

Evidence

“HEK293T and HEK293 cells obtained from the American Type Culture Collection (ATCC)”

Section 2.3 (Cells and Cell Culture)

PASSReviewer 3· 90% conf

The paper reports the cell line source and culture conditions adequately, which are the key biological variables for an in vitro study.

Evidence

paraphrase[Methods, section 2.3]

“HEK293T and HEK293 cells obtained from the American Type Culture Collection (ATCC) were cultured under 5% CO2 at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM, high glucose, GlutaMAX) (Life Technologies, Carlsbad, CA, USA) containing 10% (v/v) fetal calf serum (FCS, Gibco), 1% (v/v) penicillin (100 IU/mL), and streptomycin (100 μg/mL).”

The paper states that the study does not involve humans or animals, and the cell lines are commercially available. Therefore, no ethics approval is needed.

Sub-criteria

iacuc statementN/A

informed consentN/A

irb ethics statementN/A

regulatory complianceN/A

Per reviewer (3) — the votes behind the verdict

N/AReviewer 1· 95% conf

The study uses only commercial cell lines and does not involve human subjects, animals, or non-public subject-level data, so ethical approvals are not applicable.

Evidence

“Not applicable, because of this study not involving humans or animals.”

Institutional Review Board Statement

N/AReviewer 2· 95% conf

The study involves only immortalized cell lines and no human participants, animals, or non-public subject data, so ethics approval is not required. The authors correctly state 'Not applicable'.

Evidence

“Not applicable, because of this study not involving humans or animals.”

Institutional Review Board Statement

N/AReviewer 3· 100% conf

The study uses established cell lines and does not involve human subjects or animals, so ethical approvals are not required.

Evidence

“Institutional Review Board Statement Not applicable, because of this study not involving humans or animals. Informed Consent Statement Not applicable, because of this study not involving humans.”

Institutional Review Board Statement

Antibodies are identified with vendor and catalog numbers but lack RRIDs, clone information, and validation data. Cell line authentication and mycoplasma testing are not reported. Software (GraphPad 8) is named but without version for Fiji. Plasmids are well-identified with Addgene numbers.

Sub-criteria

mycoplasma testingNOT REPORTED

reagents identifiedADEQUATE

organisms identifiedN/A

antibodies identifiedINADEQUATE

cell line authenticationNOT REPORTED

software tools identifiedINADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 85% conf

Antibodies and reagents are well-identified with vendor and catalog numbers. Cell line authentication and mycoplasma testing are not reported. Software tools are identified.

Evidence

“Antibodies against His tag (Cat #12698), H2A (Cat #12349), H2A.X (Cat #7631), γ–H2A.X (Cat #2577), Ku80 (Cat # 2753), and Rad51(Cat #8875) were purchased from Cell Signaling Technology (Danvers, MA, USA).”

Methods

“pHPRT–DRGFP and pCBASceI were kindly gifted by Maria Jasin (Addgene plasmids #26476 and #26477) []. pimEJ5GFP was a gift from Jeremy Stark (Addgene plasmid #44026) [].”

Methods

paraphrase[Materials and Methods, 2.9 Statistical Analysis and 2.6 Comet Assay]

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8. ... and quantified using the Fiji software”

WARNReviewer 2· 80% conf

Antibodies and reagents are well-identified with catalog numbers, and plasmids have Addgene identifiers. However, cell line authentication (e.g., STR profiling) and mycoplasma testing are not reported, and software versions are partially missing.

Evidence

“Antibodies against His tag (Cat #12698), H2A (Cat #12349), H2A.X (Cat #7631), γ–H2A.X (Cat #2577), Ku80 (Cat # 2753), and Rad51(Cat #8875) were purchased from Cell Signaling Technology”

Section 2.1 (Antibodies and Reagents)

“pHPRT–DRGFP and pCBASceI were kindly gifted by Maria Jasin (Addgene plasmids #26476 and #26477)”

Section 2.2 (Plasmids)

absence[Section 2.3 (Cells and Cell Culture)]

Mycoplasma testing is not reported.

FAILReviewer 3· 85% conf

Key resources are inadequately identified: antibodies are listed with catalog numbers but without RRIDs or validation data, cell lines are not authenticated, mycoplasma testing is not reported, and software versions are incomplete.

Evidence

paraphrase[Methods, section 2.1]

“Antibodies against His tag (Cat #12698), H2A (Cat #12349), H2A.X (Cat #7631), γ-H2A.X (Cat #2577), Ku80 (Cat # 2753), and Rad51(Cat #8875) were purchased from Cell Signaling Technology (Danvers, MA, USA).”

paraphrase[Methods, section 2.2]

“pHPRT-DRGFP and pCBASceI were kindly gifted by Maria Jasin (Addgene plasmids #26476 and #26477) []. pimEJ5GFP was a gift from Jeremy Stark (Addgene plasmid #44026) [].”

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Methods

The paper uses Student's t-test and ANOVA with Tukey's post-hoc, but reports p-values only as thresholds (e.g., p < 0.01). No effect sizes with confidence intervals are provided. Assumptions of normality and equal variance are not mentioned. Figures show bar plots with error bars but no individual data points. Statistical software (GraphPad 8) is identified.

Sub-criteria

tests namedADEQUATE

exact p valuesINADEQUATE

effect sizes ciNOT REPORTED

data presentationINADEQUATE

software identifiedADEQUATE

assumptions verifiedNOT REPORTED

mathematical plausibilityN/A

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

Statistical tests are named, but exact p-values are not reported (only thresholds), effect sizes with confidence intervals are absent, and test assumptions are not verified. Individual data points are not shown in figures.

Evidence

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Methods

“*** p < 0.001, **** p < 0.0001.”

Figure legends throughout

paraphrase[Figure 1-4 legends]

“Graphs are shown as bar plots with mean ± SD or SEM, without individual data points.”

WARNReviewer 2· 75% conf

Statistical tests are named and software is identified, but assumptions are not verified, p-values are reported as thresholds (not exact), effect sizes with confidence intervals are absent, and individual data points are not shown in bar graphs.

Evidence

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Statistical analysis

“** p < 0.01, *** p < 0.001, **** p < 0.0001”

Figure 1

absence[Figures 1-4]

Individual data points are not shown in bar graphs.

FAILReviewer 3· 85% conf

Statistical tests are named and software is identified, but assumptions are not verified, p-values are reported as thresholds, effect sizes with confidence intervals are not provided, and data are presented as bar graphs without individual data points.

Evidence

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Methods

“** p < 0.01, *** p < 0.001, **** p < 0.0001.”

Figure 1

paraphrase[Figure 1 legend]

“The values represent the mean ± SD from three independent experiments.”

The paper states 'The data presented in this study are available in the main text and supplementary materials', which is not a concrete data availability statement. No repository deposit, accession numbers, or code sharing are provided. For a study generating experimental data, this is a significant transparency gap.

Sub-criteria

code sharingN/A

accession numbersN/A

repository depositNOT REPORTED

data availability statementINADEQUATE

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 90% conf

The data availability statement is vague (data available in the main text and supplementary), and no raw data are deposited in a public repository. Custom code is not shared.

Evidence

“The data presented in this study are available in the main text and .”

Data availability

WARNReviewer 2· 90% conf

A data availability statement is present but vague, stating data are available in the main text and supplementary materials without a repository or persistent identifier. No code is shared, which is typical for this type of study.

Evidence

“The data presented in this study are available in the main text and .”

Data availability

FAILReviewer 3· 80% conf

The data availability statement is vague, stating data are available in the main text and supplementary materials, with no repository deposit or code sharing.

Evidence

“Data Availability Statement The data presented in this study are available in the main text and .”

Data availability

Methods are sufficiently detailed for replication. Limitations are discussed (in vitro system, lack of in vivo evidence). Conclusions are proportional to the in vitro data. Funding sources and conflicts of interest are declared. However, no reporting guideline (e.g., ARRIVE) is referenced.

Sub-criteria

funding coiADEQUATE

trial registrationN/A

reporting guidelineNOT REPORTED

methods completenessADEQUATE

all outcomes reportedADEQUATE

limitations discussedADEQUATE

conclusions proportionalADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 85% conf

Methods are detailed, outcomes are reported transparently, limitations are discussed, conclusions are proportional, and funding/COI are disclosed. No reporting guideline is referenced, but this is not a critical omission.

Evidence

paraphrase[Materials and Methods, sections 2.1-2.9]

“All experimental procedures, including transfection, reporter assays, immunofluorescence, and comet assays, are described in detail.”

“Although no evidence has been published that SARS–CoV–2 can infect thymocytes or bone marrow lymphoid cells, our in vitro V(D)J reporter assay shows that the spike protein intensely impeded V(D)J recombination.”

Discussion ¶1

paraphrase[Funding and Conflicts of Interest sections]

“This work was supported by Umeå University... The authors have declared that no competing interests exist.”

PASSReviewer 2· 85% conf

The study reports methods in sufficient detail, all outcomes are presented, limitations are discussed, conclusions are proportional, and funding/conflicts are disclosed. However, no reporting guideline is referenced.

Evidence

paraphrase[Section 2 (Materials and Methods)]

“Briefly, 0.5 × 10^6 HEK293T stable reporter cells were seeded in 6–well plates and transfected with 2 μg I–SceI expression plasmid (pCBASceI) together with SARS–CoV–2 proteins expression plasmids.”

Discussion

“The authors have declared that no competing interests exist.”

Funding

PASSReviewer 3· 90% conf

The paper reports methods in detail, discusses limitations, draws proportional conclusions, and provides funding and conflict of interest statements, but does not reference a reporting guideline.

Evidence

paraphrase[Methods sections 2.1-2.9]

“The methods describe cell culture, transfections, reporter assays, comet assay, immunofluorescence, and V(D)J recombination assay in sufficient detail.”

paraphrase[Discussion, paragraph 1]

“Although no evidence has been published that SARS-CoV-2 can infect thymocytes or bone marrow lymphoid cells, our in vitro V(D)J reporter assay shows that the spike protein intensely impeded V(D)J recombination.”

paraphrase[Funding and Conflicts of Interest sections]

“Funding This work was supported by Umeå University, Medical Faculty’s Planning grants for COVID-19 (research project number: 3453 16032 to Y.F.M.); the Lion’s Cancer Research Foundation at Umeå University (grants: LP 17-2153, AMP 19-982, and LP 20-2256 to Y.F.M.), and the base unit’s ALF funds for research at academic healthcare units and university healthcare units in the northern healthcare region (ALF-Basenheten: 2019, 2020, 2021 to Y.F.M.). Conflicts of Interest The authors have declared that no competing interests exist.”

Broken references and links

None found

References checked against Crossref, OpenAlex and Retraction Watch for retractions and resolvability, plus declared data and code links probed for whether they resolve to content matching the paper.

Checked — nothing surfaced.

Checked 29 references by DOI: 28 verified — 1 no DOI (shown, not verified).

1 data/code link checked; 1 live.

Copyediting

8 minor

Wording, consistency and formatting errors that need correcting before submission.

No major wording or formatting errors. 8 minor suggestions below.

8 copyedit issues flagged: mostly consistency, clarity, typo.

Kaimen Rigor Action ItemsFinal pass before journal submission

As published, the study is methodologically plausible and largely reproducible from the methods text, but readers should weigh the non-functional data-availability statement (no repository), the unreported cell-line authentication/mycoplasma status, and the fact that no reported statistic could be machine-verified. The Discussion's spike-vaccine side-effect claim and the comet-assay cell-count inconsistency ('20 fields × ~100 cells' vs 'n > 200 comets') are the most concrete points warranting a correction or author response; independent replication or formal data deposition would materially increase confidence in the findings.

1.
HIGHdata code
Complete the truncated Data Availability statement ('...available in the main text and .') and deposit the underlying flow-cytometry, comet-assay image, and reporter-assay data in a public repository (e.g., Figshare, Zenodo) with a DOI, naming the supplementary file format.
A data-driven paper whose only data-access statement is a broken sentence and which provides no repository is a concrete transparency defect that undermines reproducibility.
2.
HIGHreporting
Temper the Discussion claim that 'full-length spike-based vaccines may have side effects by inhibiting adaptive immunity' by explicitly stating that this is an untested extrapolation from in vitro data and that no in vivo vaccine evidence was produced.
The independent claim audit rated this statement as overstated; over-claiming beyond the in vitro evidence is the most likely reviewer objection.
3.
HIGHstatistics
Replace threshold-only p-values ('** p < 0.01', '**** p < 0.0001') with exact p-values and add effect sizes with 95% confidence intervals for the main spike-vs-E.V comparisons in the Figure 1–4 legends and Results text.
Threshold-only p-values are imprecise reporting that cannot be verified or reproduced by readers, and no effect sizes/CIs are provided anywhere.
4.
HIGHrigor
Add a statement in Materials and Methods 2.3 on cell-line authentication (STR profiling) and mycoplasma testing — or state explicitly that neither was performed — together with the reason.
Cell-line identity and mycoplasma status are standard key-resource reporting items; their absence was flagged by all three reviewers.
5.
HIGHstatistics
Report whether normality and equal-variance assumptions were checked for the t-tests/ANOVA in Methods 2.9, and state the fallback (Welch's t-test, non-parametric tests) if assumptions were violated.
Assumptions are never verified despite parametric tests being used, which is a statistical-transparency gap.
6.
MEDIUMrigor
Reconcile the comet-assay quantification inconsistency: Methods 2.6 states '20 fields with approximately 100 cells' (~2000 cells/sample) while the text reports 'n > 200 comets' — correct the numbers so they are consistent.
An unresolvable internal contradiction about the analyzed sample size is the kind of detail an informed reader will doubt.
7.
MEDIUMrigor
Add a sample-size justification (a priori power analysis based on expected effect sizes) for the reporter assays and V(D)J assay, or explicitly label the experiments as exploratory in Methods 2.9.
No power analysis is reported, which limits the strength of the negative and positive claims.
8.
MEDIUMrigor
Describe blinding for assays other than immunofluorescence scoring (e.g., flow-cytometry quantification) and state pre-specified inclusion/exclusion criteria and outlier-handling rules in the Methods.
Only IF scoring is reported as blinded, and no data-handling rules are given, which is the dominant study-design gap.
9.
MEDIUMcopyedit
Repair the empty parenthetical 'and ()' figure reference in Results 3.1 and replace the '[,,,]' / '[,]' bracket citation placeholders in the Introduction with the actual reference numbers.
Empty citation placeholders and an empty parenthetical are production errors that break traceability of the cited evidence.
10.
MEDIUMcopyedit
Correct the contradictory significance notation in the Figure 1 and Figure 2 legends: 'NS (Not Significant): * p > 0.05' should read 'NS: p > 0.05' with no asterisk.
Using an asterisk for a non-significant result is misleading and was flagged both by copyedit and the integrity check.
11.
LOWcopyedit
Standardize formatting: use 'H2O2' with subscript consistently in the Figure 2 legend, lowercase 'Spike' in the title to match the body text, and fix the comma splice in Results 3.1 ('...in the nucleus, and nucleoproteins...' → '...in the nucleus, while nucleoproteins...').
Minor consistency issues that a professional copyedit would catch and that reduce polish.
12.
LOWdata code
Add RRIDs or clone information and working dilutions for the antibodies in Methods 2.1, and specify the Fiji version used in Methods 2.6.
Completes the key-resource identification so other labs can reproduce the antibody conditions exactly.
13.
LOWreporting
State whether any data points were excluded and the rationale if so, and reference an applicable reporting guideline (e.g., ARRIVE or a cell-line reporting checklist) in the Methods.
Closes the remaining transparency gaps flagged by reviewers; no guideline is currently cited.

Full text (24,793 chars)Analyzed: Aug 5, 2026

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SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro

Jiang H, Mei YF.

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DOI

10.3390/v13102056

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Issued Aug 5, 2026Engine 7.15.0

Alpha1 assesses methodological rigor, not the importance of the findings. See how we calibrate →

Kaimen Rigor review

Kaimen Rigor reviewed

1.75 / 5

Critical — serious problems across many checks

Interventional Study

Critical

High-priority

How this rating was calculated▸

Started at 5★ — deductions

IntegrityIntegrity concern ×2−1★
ClaimsOverstated claim−0.5★
ReportingStudy design not met−0.5★
ReportingKey resources not met−0.5★
ReportingData & code availability not met−0.5★
ReportingStatistical analysis partially met−0.25★

Model-reported confidence: moderateReviewer agreement: lowEngine: 7.15.0Source: full text

Not verified in this report

Statistics were not checked: no recomputable values were found in this text — no test statistic reported with its degrees of freedom, no effect estimate printed with both a 95% CI and a p-value, and no percentage printed with both its count and its denominator.

Biggest issues

01Study design lacks key rigor safeguards
highDisclosurereviewer-assessedFull detail
The study lacks adequate reporting of randomization, blinding (except for scoring), power analysis, inclusion/exclusion criteria, outlier handling, and independent replication, while only reporting replicate distinction and controls adequately.
“All scoring was performed under blinded conditions.”
Methods
02Key resources not identified
highDisclosurereviewer-assessedFull detail
Key resources are inadequately identified: antibodies are listed with catalog numbers but without RRIDs or validation data, cell lines are not authenticated, mycoplasma testing is not reported, and software versions are incomplete.
“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”
Methods
03Data and code not shared
highDisclosurereviewer-assessedFull detail
The data availability statement is vague (data available in the main text and supplementary), and no raw data are deposited in a public repository. Custom code is not shared.
“The data presented in this study are available in the main text and .”
Data availability
04Conclusion reaches beyond the evidence
mediumOverreachreviewer-assessedFull detail
Full-length spike-based vaccines may have side effects by inhibiting adaptive immunity.
“our findings also imply a potential side effect of the full–length spike–based vaccine”
Discussion

Findings by category

101ArithmeticNumerical inconsistencies 202OverreachOverstated conclusions 03AuthenticityNone found 404DisclosureReporting gaps 05AvailabilityNone found 06Copyedit8 minor suggestions

Numerical inconsistencies

1 finding · worst low

Internal contradictions in the reported numbersAssessed

Overstated conclusions

2 findings · worst medium

Conclusions overstated beyond the evidenceAssessed
Conclusions only partially backed by the presented evidenceAssessed

11 major claims checked against the paper's own evidence: 1 not fully backed by the presented evidence (unsupported or overstated).

Data authenticity concerns

None found

Checked — nothing surfaced.

Reporting gaps

4 findings · worst high

Data and code not sharedAssessed
Key resources not identifiedAssessed
Statistical reporting gaps (tests, assumptions, effect sizes)Assessed
Study design lacks key rigor safeguardsAssessed

Eight Dimensions3 pass · 1 warn · 3 fail

Sub-criteria

prior work citedADEQUATE

premise rationaleADEQUATE

limitations addressedNOT REPORTED

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 90% conf

Evidence

“Recent clinical studies have shown that SARS–CoV–2 infection extraordinarily affects lymphocyte number and function [,,,].”

Introduction ¶1

“Therefore, we aimed to investigate whether SARS–CoV–2 proteins hijack the DNA damage repair system, thereby affecting adaptive immunity in vitro.”

Introduction

absence[Introduction]

No discussion of limitations of prior research.

PASSReviewer 2· 90% conf

Evidence

paraphrase[Introduction, paragraph 1]

“Recent clinical studies have shown that SARS-CoV-2 infection extraordinarily affects lymphocyte number and function”

“As two critical host surveillance systems, the immune and DNA repair systems are the primary systems that higher organisms rely on for defense against diverse threats and tissue homeostasis.”

Introduction ¶2

absence[Introduction]

No discussion of limitations of prior research is found.

PASSReviewer 3· 85% conf

Evidence

paraphrase[Introduction, paragraph 1]

paraphrase[Introduction, paragraph 2]

“Therefore, we aimed to investigate whether SARS-CoV-2 proteins hijack the DNA damage repair system, thereby affecting adaptive immunity in vitro.”

Sub-criteria

controlsADEQUATE

power analysisNOT REPORTED

blinding levelsINADEQUATE

outlier handlingNOT REPORTED

randomization unitNOT REPORTED

inclusion exclusionNOT REPORTED

randomization methodNOT REPORTED

replicate distinctionADEQUATE

independent replicationNOT REPORTED

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 70% conf

Evidence

“All scoring was performed under blinded conditions.”

Methods

“All experiments were repeated at least three times using independently collected or prepared samples.”

Methods

paraphrase[Materials and Methods, 2.4 HR and NHEJ Reporter Assays]

“Empty vector (E.V) is used as a control, and DNA damage is induced by γ-irradiation, doxorubicin, or H2O2.”

WARNReviewer 2· 70% conf

Evidence

“All scoring was performed under blinded conditions.”

Section 2.7 (Immunofluorescence)

“All experiments were repeated at least three times using independently collected or prepared samples.”

Statistical analysis

“Effect of empty vector (E.V) and SARS–CoV–2 proteins on NHEJ DNA repair.”

Figure 1

FAILReviewer 3· 90% conf

Evidence

“All scoring was performed under blinded conditions.”

Methods

“All experiments were repeated at least three times using independently collected or prepared samples.”

Methods

paraphrase[Results, Figure 1 legend]

“Figure 1C and 1E compare empty vector (E.V) with SARS-CoV-2 proteins.”

Sub-criteria

demographicsN/A

sex reportedN/A

sex justifiedN/A

age weight healthN/A

housing conditionsADEQUATE

species strain sourceADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 80% conf

Evidence

paraphrase[Materials and Methods, 2.3 Cells and Cell Culture]

N/AReviewer 2· 95% conf

Evidence

“HEK293T and HEK293 cells obtained from the American Type Culture Collection (ATCC)”

Section 2.3 (Cells and Cell Culture)

PASSReviewer 3· 90% conf

The paper reports the cell line source and culture conditions adequately, which are the key biological variables for an in vitro study.

Evidence

paraphrase[Methods, section 2.3]

“HEK293T and HEK293 cells obtained from the American Type Culture Collection (ATCC) were cultured under 5% CO2 at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM, high glucose, GlutaMAX) (Life Technologies, Carlsbad, CA, USA) containing 10% (v/v) fetal calf serum (FCS, Gibco), 1% (v/v) penicillin (100 IU/mL), and streptomycin (100 μg/mL).”

The paper states that the study does not involve humans or animals, and the cell lines are commercially available. Therefore, no ethics approval is needed.

Sub-criteria

iacuc statementN/A

informed consentN/A

irb ethics statementN/A

regulatory complianceN/A

Per reviewer (3) — the votes behind the verdict

N/AReviewer 1· 95% conf

The study uses only commercial cell lines and does not involve human subjects, animals, or non-public subject-level data, so ethical approvals are not applicable.

Evidence

“Not applicable, because of this study not involving humans or animals.”

Institutional Review Board Statement

N/AReviewer 2· 95% conf

The study involves only immortalized cell lines and no human participants, animals, or non-public subject data, so ethics approval is not required. The authors correctly state 'Not applicable'.

Evidence

“Not applicable, because of this study not involving humans or animals.”

Institutional Review Board Statement

N/AReviewer 3· 100% conf

The study uses established cell lines and does not involve human subjects or animals, so ethical approvals are not required.

Evidence

Institutional Review Board Statement

Sub-criteria

mycoplasma testingNOT REPORTED

reagents identifiedADEQUATE

organisms identifiedN/A

antibodies identifiedINADEQUATE

cell line authenticationNOT REPORTED

software tools identifiedINADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 85% conf

Antibodies and reagents are well-identified with vendor and catalog numbers. Cell line authentication and mycoplasma testing are not reported. Software tools are identified.

Evidence

Methods

“pHPRT–DRGFP and pCBASceI were kindly gifted by Maria Jasin (Addgene plasmids #26476 and #26477) []. pimEJ5GFP was a gift from Jeremy Stark (Addgene plasmid #44026) [].”

Methods

paraphrase[Materials and Methods, 2.9 Statistical Analysis and 2.6 Comet Assay]

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8. ... and quantified using the Fiji software”

WARNReviewer 2· 80% conf

Evidence

“Antibodies against His tag (Cat #12698), H2A (Cat #12349), H2A.X (Cat #7631), γ–H2A.X (Cat #2577), Ku80 (Cat # 2753), and Rad51(Cat #8875) were purchased from Cell Signaling Technology”

Section 2.1 (Antibodies and Reagents)

“pHPRT–DRGFP and pCBASceI were kindly gifted by Maria Jasin (Addgene plasmids #26476 and #26477)”

Section 2.2 (Plasmids)

absence[Section 2.3 (Cells and Cell Culture)]

Mycoplasma testing is not reported.

FAILReviewer 3· 85% conf

Evidence

paraphrase[Methods, section 2.1]

paraphrase[Methods, section 2.2]

“pHPRT-DRGFP and pCBASceI were kindly gifted by Maria Jasin (Addgene plasmids #26476 and #26477) []. pimEJ5GFP was a gift from Jeremy Stark (Addgene plasmid #44026) [].”

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Methods

Sub-criteria

tests namedADEQUATE

exact p valuesINADEQUATE

effect sizes ciNOT REPORTED

data presentationINADEQUATE

software identifiedADEQUATE

assumptions verifiedNOT REPORTED

mathematical plausibilityN/A

Per reviewer (3) — the votes behind the verdict

WARNReviewer 1· 80% conf

Evidence

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Methods

“*** p < 0.001, **** p < 0.0001.”

Figure legends throughout

paraphrase[Figure 1-4 legends]

“Graphs are shown as bar plots with mean ± SD or SEM, without individual data points.”

WARNReviewer 2· 75% conf

Evidence

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Statistical analysis

“** p < 0.01, *** p < 0.001, **** p < 0.0001”

Figure 1

absence[Figures 1-4]

Individual data points are not shown in bar graphs.

FAILReviewer 3· 85% conf

Evidence

“Data were analyzed by Student’s t test or ANOVA followed by Tukey’s multiple-comparison tests using GraphPad 8.”

Methods

“** p < 0.01, *** p < 0.001, **** p < 0.0001.”

Figure 1

paraphrase[Figure 1 legend]

“The values represent the mean ± SD from three independent experiments.”

Sub-criteria

code sharingN/A

accession numbersN/A

repository depositNOT REPORTED

data availability statementINADEQUATE

Per reviewer (3) — the votes behind the verdict

FAILReviewer 1· 90% conf

The data availability statement is vague (data available in the main text and supplementary), and no raw data are deposited in a public repository. Custom code is not shared.

Evidence

“The data presented in this study are available in the main text and .”

Data availability

WARNReviewer 2· 90% conf

Evidence

“The data presented in this study are available in the main text and .”

Data availability

FAILReviewer 3· 80% conf

The data availability statement is vague, stating data are available in the main text and supplementary materials, with no repository deposit or code sharing.

Evidence

“Data Availability Statement The data presented in this study are available in the main text and .”

Data availability

Sub-criteria

funding coiADEQUATE

trial registrationN/A

reporting guidelineNOT REPORTED

methods completenessADEQUATE

all outcomes reportedADEQUATE

limitations discussedADEQUATE

conclusions proportionalADEQUATE

Per reviewer (3) — the votes behind the verdict

PASSReviewer 1· 85% conf

Evidence

paraphrase[Materials and Methods, sections 2.1-2.9]

“All experimental procedures, including transfection, reporter assays, immunofluorescence, and comet assays, are described in detail.”

Discussion ¶1

paraphrase[Funding and Conflicts of Interest sections]

“This work was supported by Umeå University... The authors have declared that no competing interests exist.”

PASSReviewer 2· 85% conf

Evidence

paraphrase[Section 2 (Materials and Methods)]

Discussion

“The authors have declared that no competing interests exist.”

Funding

PASSReviewer 3· 90% conf

The paper reports methods in detail, discusses limitations, draws proportional conclusions, and provides funding and conflict of interest statements, but does not reference a reporting guideline.

Evidence

paraphrase[Methods sections 2.1-2.9]

“The methods describe cell culture, transfections, reporter assays, comet assay, immunofluorescence, and V(D)J recombination assay in sufficient detail.”

paraphrase[Discussion, paragraph 1]

paraphrase[Funding and Conflicts of Interest sections]

Broken references and links

None found

References checked against Crossref, OpenAlex and Retraction Watch for retractions and resolvability, plus declared data and code links probed for whether they resolve to content matching the paper.

Checked — nothing surfaced.

Checked 29 references by DOI: 28 verified — 1 no DOI (shown, not verified).

1 data/code link checked; 1 live.

Copyediting

8 minor

Wording, consistency and formatting errors that need correcting before submission.

No major wording or formatting errors. 8 minor suggestions below.

8 copyedit issues flagged: mostly consistency, clarity, typo.

Kaimen Rigor Action ItemsFinal pass before journal submission

1.
HIGHdata code
Complete the truncated Data Availability statement ('...available in the main text and .') and deposit the underlying flow-cytometry, comet-assay image, and reporter-assay data in a public repository (e.g., Figshare, Zenodo) with a DOI, naming the supplementary file format.
A data-driven paper whose only data-access statement is a broken sentence and which provides no repository is a concrete transparency defect that undermines reproducibility.
2.
HIGHreporting
Temper the Discussion claim that 'full-length spike-based vaccines may have side effects by inhibiting adaptive immunity' by explicitly stating that this is an untested extrapolation from in vitro data and that no in vivo vaccine evidence was produced.
The independent claim audit rated this statement as overstated; over-claiming beyond the in vitro evidence is the most likely reviewer objection.
3.
HIGHstatistics
Replace threshold-only p-values ('** p < 0.01', '**** p < 0.0001') with exact p-values and add effect sizes with 95% confidence intervals for the main spike-vs-E.V comparisons in the Figure 1–4 legends and Results text.
Threshold-only p-values are imprecise reporting that cannot be verified or reproduced by readers, and no effect sizes/CIs are provided anywhere.
4.
HIGHrigor
Add a statement in Materials and Methods 2.3 on cell-line authentication (STR profiling) and mycoplasma testing — or state explicitly that neither was performed — together with the reason.
Cell-line identity and mycoplasma status are standard key-resource reporting items; their absence was flagged by all three reviewers.
5.
HIGHstatistics
Report whether normality and equal-variance assumptions were checked for the t-tests/ANOVA in Methods 2.9, and state the fallback (Welch's t-test, non-parametric tests) if assumptions were violated.
Assumptions are never verified despite parametric tests being used, which is a statistical-transparency gap.
6.
MEDIUMrigor
Reconcile the comet-assay quantification inconsistency: Methods 2.6 states '20 fields with approximately 100 cells' (~2000 cells/sample) while the text reports 'n > 200 comets' — correct the numbers so they are consistent.
An unresolvable internal contradiction about the analyzed sample size is the kind of detail an informed reader will doubt.
7.
MEDIUMrigor
Add a sample-size justification (a priori power analysis based on expected effect sizes) for the reporter assays and V(D)J assay, or explicitly label the experiments as exploratory in Methods 2.9.
No power analysis is reported, which limits the strength of the negative and positive claims.
8.
MEDIUMrigor
Describe blinding for assays other than immunofluorescence scoring (e.g., flow-cytometry quantification) and state pre-specified inclusion/exclusion criteria and outlier-handling rules in the Methods.
Only IF scoring is reported as blinded, and no data-handling rules are given, which is the dominant study-design gap.
9.
MEDIUMcopyedit
Repair the empty parenthetical 'and ()' figure reference in Results 3.1 and replace the '[,,,]' / '[,]' bracket citation placeholders in the Introduction with the actual reference numbers.
Empty citation placeholders and an empty parenthetical are production errors that break traceability of the cited evidence.
10.
MEDIUMcopyedit
Correct the contradictory significance notation in the Figure 1 and Figure 2 legends: 'NS (Not Significant): * p > 0.05' should read 'NS: p > 0.05' with no asterisk.
Using an asterisk for a non-significant result is misleading and was flagged both by copyedit and the integrity check.
11.
LOWcopyedit
Standardize formatting: use 'H2O2' with subscript consistently in the Figure 2 legend, lowercase 'Spike' in the title to match the body text, and fix the comma splice in Results 3.1 ('...in the nucleus, and nucleoproteins...' → '...in the nucleus, while nucleoproteins...').
Minor consistency issues that a professional copyedit would catch and that reduce polish.
12.
LOWdata code
Add RRIDs or clone information and working dilutions for the antibodies in Methods 2.1, and specify the Fiji version used in Methods 2.6.
Completes the key-resource identification so other labs can reproduce the antibody conditions exactly.
13.
LOWreporting
State whether any data points were excluded and the rationale if so, and reference an applicable reporting guideline (e.g., ARRIVE or a cell-line reporting checklist) in the Methods.
Closes the remaining transparency gaps flagged by reviewers; no guideline is currently cited.

Full text (24,793 chars)Analyzed: Aug 5, 2026