SARS-CoV-2 awakens ancient retroviral genes and the expression of proinflammatory HERV-W envelope protein in COVID-19 patients

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1. Version published to 10.1016/j.isci.2023.106604

   May 1, 2023
2. 

   Version published to 10.1101/2022.01.18.21266111v2 on medRxiv

   Jan 21, 2022
3. 

   ScreenIT

   Jan 20, 2022

   SciScore for 10.1101/2022.01.18.21266111: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: PBMC and plasma of 27 (Lyon_2 cohort) and 20 (Lyon_3 cohort) SARS-CoV-2-positive individuals were obtained from the biobank of “Hospices Civils de Lyon” under conditions approved by the ethical committee (CRB, hôpital de la Croix-Rousse, Lyon France) (clinical data are provided in Supplementary Tables S2 and S3). IACUC: The nasal/brain tissues sampling was performed via nasal cavity such as presented in Figure 8A (Ethical committee approval and legal authorization: Autorización para realizar estudios postmortem INER-SAM-01, Secretaria de Salud, Mexico)
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line …

   SciScore for 10.1101/2022.01.18.21266111: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: PBMC and plasma of 27 (Lyon_2 cohort) and 20 (Lyon_3 cohort) SARS-CoV-2-positive individuals were obtained from the biobank of “Hospices Civils de Lyon” under conditions approved by the ethical committee (CRB, hôpital de la Croix-Rousse, Lyon France) (clinical data are provided in Supplementary Tables S2 and S3). IACUC: The nasal/brain tissues sampling was performed via nasal cavity such as presented in Figure 8A (Ethical committee approval and legal authorization: Autorización para realizar estudios postmortem INER-SAM-01, Secretaria de Salud, Mexico)
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: Vero E6 cells were grown in DMEM Glutamax (Thermo) supplemented with 10% fetal bovine serum (FBS), glutamine and antibiotics (100 U/mL of penicillin and 100 µg/mL of streptomycin) in 5% CO2 incubators at 37°C and were tested negative for mycoplasma spp.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Saturation was performed using 2.5% horse serum, 0.2% Tween20, 1 X PBS, during 30 minutes at room temperature before incubation with a mix of primary antibodies during 1 hour or overnight: 3 µg/mL of anti-HERV-W ENV (GeNeuro, GN_mAb_Env01	anti-HERV-W ENV suggested: None
   , murine antibody) or 10 µg/mL anti-HERV-K ENV (GeNeuro, GN_mAb_Env-K01, murine antibody), together with either anti-N SARS-CoV-2 diluted 1/500 (SinoBiological, 40143-T62, rabbit antibody) or anti-S SARS-CoV-2 diluted 1/500 (SinoBiological, 40590-T62, rabbit antibody).	anti-HERV-K ENV suggested: None anti-N suggested: None anti-S suggested: (LSBio (LifeSpan Cat# LS-C91688-500, RRID:AB_10635347)
   After three washes in PBS 1X, cells were incubated during 1 hour with secondary antibodies mix containing 1µg/mL goat anti-mouse Alexa Fluor 488 (ThermoFisher Scientific, A11029), 1 µg/mL donkey anti-rabbit Alexa Fluor 647 (ThermoFisher Scientific, A31573) and DAPI 1/2000 (Sigma, D9542) diluted in the previously described saturation buffer.	anti-mouse suggested: (Molecular Probes Cat# A-11029, RRID:AB_138404) anti-rabbit suggested: (Molecular Probes Cat# A-31573, RRID:AB_2536183)
   The following primary antibodies were used: anti-HERV-W ENV mAb GN_mAb_ENV01 (-W01) (20 µg/mL) and anti-HERV-K ENV mAb GN_mAb_ENV-K01 (30 µg/mL) (antibodies description in Table 1B).	anti-HERV-W suggested: None -W01 suggested: (George Fu Gao; Chinese Academy of Sciences; Beijing; China Cat# Z3L1, RRID:AB_2725798) anti-HERV-K suggested: None
   PBMC were incubated with FcR Blocking Reagent according to manufacturer’s protocol (Miltenyi Biotec, 130-113-199) and stained with CD3-PE (BD Biosciences, 552127), CD14-PerCP (BioLegend, 301848), CD19-APC-H7 (BD Biosciences, 560252) and 10 µg/mL GN_mAb_ENV01-biotin (GeNeuro, murine antibody).	CD14-PerCP suggested: (Miltenyi Biotec Cat# 130-094-969, RRID:AB_10830714) GN_mAb_ENV01-biotin suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Vero E6 cells were grown in DMEM Glutamax (Thermo) supplemented with 10% fetal bovine serum (FBS), glutamine and antibiotics (100 U/mL of penicillin and 100 µg/mL of streptomycin) in 5% CO2 incubators at 37°C and were tested negative for mycoplasma spp.	Vero E6 suggested: RRID:CVCL_XD71)
   The housekeeping gene beta-2 microglobulin (B2M) was used to normalize the results in PBMC experiments whereas glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used in Vero cells experiments.	Vero suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
   Software and Algorithms
   Sentences	Resources
   Wes device was associated with Compass software for device settings and raw data recording (ProteinSimple/Biotechne).	Compass suggested: (COMPASS, RRID:SCR_015874)
   Pictures were acquired on NIKON Eclipse TS2R microscope and analyzed on ImageJ software.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   Stained cells were acquired on a BD LSR Fortessa, fluorochrome emissions from the pool of antibodies were compensated using OneComp Beads (Invitrogen, 01-1111-42) and data analyzed with FlowJo software (v.10).	FlowJo suggested: (FlowJo, RRID:SCR_008520)

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04480307	Active, not recruiting	Clinical Trial Assessing Temelimab Following Rituximab Treat…

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   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 51, 44, 45 and 46. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a protocol registration statement.

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   Results from scite Reference Check: We found no unreliable references.

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4. 

   Version published to 10.1101/2022.01.18.21266111v1 on medRxiv

   Jan 18, 2022