An in vitro and in vivo approach for the isolation of Omicron variant from human clinical specimens
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Abstract
Due to failure of virus isolation of Omicron variant in Vero CCL-81 from the clinical specimen’s of COVID-19 cases, we infected Syrian hamsters and then passage into Vero CCL-81 cells. The Omicron sequences were studied to assess if hamster could incorporate any mutation to changes its susceptibility. L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene and absence of V17I mutation in E gene was observed in sequences of hamster passage unlike human clinical specimen and Vero CCL-81 passages. No change was observed in the furin cleavage site in any of the specimen sequence which suggests usefulness of these isolates in future studies.
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SciScore for 10.1101/2022.01.02.474750: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources NT scrapings and lung tissues (20% suspension) were prepared in sterile Minimum Essential Medium (MEM; Gibco, USA) using a homogenizer and were screened using rRT-PCR.7 SARS-CoV-2 positive NT and lung homogenized suspension of hamsters (P1 and P2) were further inoculated onto Vero CCL-81 cells. Vero CCL-81suggested: NoneSoftware and Algorithms Sentences Resources The cells were examined microscopically for cellular morphological changes following inoculation.5 … SciScore for 10.1101/2022.01.02.474750: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources NT scrapings and lung tissues (20% suspension) were prepared in sterile Minimum Essential Medium (MEM; Gibco, USA) using a homogenizer and were screened using rRT-PCR.7 SARS-CoV-2 positive NT and lung homogenized suspension of hamsters (P1 and P2) were further inoculated onto Vero CCL-81 cells. Vero CCL-81suggested: NoneSoftware and Algorithms Sentences Resources The cells were examined microscopically for cellular morphological changes following inoculation.5 Simultaneously, the Next-generation sequencing for clinical specimens, hamster specimens and virus isolate was performed on the Illumina MiniSeq Machine. MiniSeqsuggested: NoneA phylogenetic tree was generated using the MEGA software version 7. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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: Please consider improving the rainbow (“jet”) colormap(s) used on page 14. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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.
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