No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
-
SciScore for 10.1101/2021.05.28.446065: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Further ethics approvals were provided by the Mater Health Services Human Research Ethics Committee (Reference: HREC-15-MHS-52) and the University of Queensland Medical Research Review Committee (Reference: Sex as a biological variable Hepatocellular carcinoma patient samples: Liver tumour and non-tumour tissue were previously obtained from a HBV-positive patient (HCC32, male, 73yrs) who underwent surgical resection at the Centre Hepatobiliaire, Paul-Brousse Hospital, and made available for research purposes with approval from the French Institute of Medical Research and Health (Reference: 11-047). Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line … SciScore for 10.1101/2021.05.28.446065: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Further ethics approvals were provided by the Mater Health Services Human Research Ethics Committee (Reference: HREC-15-MHS-52) and the University of Queensland Medical Research Review Committee (Reference: Sex as a biological variable Hepatocellular carcinoma patient samples: Liver tumour and non-tumour tissue were previously obtained from a HBV-positive patient (HCC32, male, 73yrs) who underwent surgical resection at the Centre Hepatobiliaire, Paul-Brousse Hospital, and made available for research purposes with approval from the French Institute of Medical Research and Health (Reference: 11-047). Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: Viral titration was determined by immuno-plaque assay (iPA), as previously described54. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources SARS-CoV-2 infection of HEK293T cells: HEK293T cells and African green monkey kidney cells (Vero E6) were maintained in standard Dulbecco’s Modified Eagle Medium (DMEM). Vero E6suggested: RRID:CVCL_XD71)HEK293T viral infection was undertaken as follows: 3×106 HEK293T cells were seeded onto 6-well plates pre-coated with polylysine one day before infection. HEK293Tsuggested: NoneSoftware and Algorithms Sentences Resources 350-500ng of each prepared library was sequenced separately on one PromethION (Oxford Nanopore Technologies) flow cell (FLO-PRO002, R9.4.1 chemistry) (Supplementary Table 1). PromethIONsuggested: (PromethION, RRID:SCR_017987)Sequencing data were deposited in the Sequence Read Archive (SRA) under project PRJEB44816. Sequence Read Archivesuggested: (DDBJ Sequence Read Archive, RRID:SCR_001370)ONT bioinformatic analyses: To call non-reference insertions with TLDR23, ONT reads generated here, by Zhang et al.29, and by our previous ONT study of human tissues23 (Supplementary Table 1) were aligned to the human reference genome build hg38 using minimap255 version 2.17 (index parameter: -x map-ont; alignment parameters: -ax map-ont -L -t 32) and samtools56 version 1.12. samtools56suggested: Nonefa were counted with samtools idxstats. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)PCR primers for the HBV insertion 3’ junction (Fig. 2b and Supplementary Table 2) were designed with Primer3 using the reference genome and closest match HBV sequence (Genbank accession AB602818) as inputs. Primer3suggested: (Primer3, RRID:SCR_003139)Results from OddPub: Thank you for sharing your code and data.
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.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
-