Amplicon-based nanopore minion sequencing of patients with COVID-19 omicron variant from India
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
SARS-CoV-2 infection has been playing havoc with emerging omicron variants of concern (VoC). Here, we report sequencing of the omicron variant in 13 patients from India using Oxford Nanopore Technology (ONT) Minion, wherein a rapid amplicon based sequence analysis was performed to assess and compare with existing 34 mutations in spike glycoprotein. We highlight and discuss the nature of these mutations that are unique and common to other populations. This is perhaps the first report on omicron variants from India using a long read sequencing chemistry.
Article activity feed
-
SciScore for 10.1101/2021.12.27.21268364: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Informed consent was judiciously taken before the sample was sequenced. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
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: We detected the following sentences addressing limitations in the study:The limitation of our study is that although the adopted ARCTIC protocol allowed the confirmation of SARS-CoV-2 infections, given the urgent need for rapid identification and traceability of …
SciScore for 10.1101/2021.12.27.21268364: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Informed consent was judiciously taken before the sample was sequenced. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
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: We detected the following sentences addressing limitations in the study:The limitation of our study is that although the adopted ARCTIC protocol allowed the confirmation of SARS-CoV-2 infections, given the urgent need for rapid identification and traceability of omicron variants, an indefatigable checking the antibody titer against deleterious mutations and subsequent single cell genomic assay would have been a better proposition (Kannan et al. 2022). Furthermore, the difference in viral loads among samples will possibly affect the stability of average depth and genome-wide coverage with increase in whole-genome mapping. In summary, our study has demonstrated the utility of nanopore sequencing for SARS-CoV-2 genomes from clinical specimens. We firmly hope that prompt diagnosis and rapid whole-genome analysis would allow a decisive response to the SARS-CoV-2 outbreak that will bring disease control and prevention efforts.
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.
-
