Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation
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SciScore for 10.1101/2021.04.12.21255337: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Sample collection and study area: Three (3) ml viral transport medium (VTM) containing nasopharyngeal swab samples were collected in Covid-19 clinically suspected individuals (n=67) at Coronavirus Research and Identification Lab in the University of Garmian in Kalar town, Sulaymaniyah province, Kurdistan region of Iraq from June to October 2020.
Consent: Written consent forms were taken from the covid-19 suspected persons and the study was ethically approved by an ethical committee, which is adhered to WHO Guidelines on Ethical Issues in Public Health Surveillance and to the principles of the Declaration of Helsinki, at the department of biology, University of Garmian. …SciScore for 10.1101/2021.04.12.21255337: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Sample collection and study area: Three (3) ml viral transport medium (VTM) containing nasopharyngeal swab samples were collected in Covid-19 clinically suspected individuals (n=67) at Coronavirus Research and Identification Lab in the University of Garmian in Kalar town, Sulaymaniyah province, Kurdistan region of Iraq from June to October 2020.
Consent: Written consent forms were taken from the covid-19 suspected persons and the study was ethically approved by an ethical committee, which is adhered to WHO Guidelines on Ethical Issues in Public Health Surveillance and to the principles of the Declaration of Helsinki, at the department of biology, University of Garmian. 2.2. Viral RNA Extraction: Sample processing was handled according to WHO standards under biological safety Level 2 using personal protection equipment (PPE) and biological safety cabinet (Labconco, Kansas City, MO, USA).
IRB: Written consent forms were taken from the covid-19 suspected persons and the study was ethically approved by an ethical committee, which is adhered to WHO Guidelines on Ethical Issues in Public Health Surveillance and to the principles of the Declaration of Helsinki, at the department of biology, University of Garmian. 2.2. Viral RNA Extraction: Sample processing was handled according to WHO standards under biological safety Level 2 using personal protection equipment (PPE) and biological safety cabinet (Labconco, Kansas City, MO, USA).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: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:A limitation of this study was the absence of the D614 wild type subtype in the area where SARS CoV-2 has been spreading. However, in our study, three assays, as Taqman probes, ARMS, and RFLP all validated each other, in addition to the DNA sequencing data. Co-segregations of SNVs are also essential for future understanding of the roles of viral pathogenesis and host immune responses against the virus. For instance, identifications of common co-occurred mutations in SARS CoV-2 spike proteins at a particular population would overcome problems of the viral antibody resistance and host cell binding capacity of the virus. By 12 February 2021, the D614G (A23403G) is the most prevalent single nucleotide variations (SNVs) in the world that is about 439,559 sequences (95.5%). Other common mutations in the spike (S) protein, including A222V (C22227T), L81S (C21614T), and S477N (G22992A), are co-occurred with D614G in 100,401 sequences (21.8%), 45,943 sequences (10%) and 23,426 sequences (5.1%), respectively (Covid19 CG data: https://covidcg.org/?tab=group). Moreover, a UK variant, N501Y, has been emerged since October 2020 and currently spreading in the country (Leung et al., 2021) and has become public threat in more than 30 countries (WHO, 2020). Therefore, future work should concentrate on these four mutations to see whether their co-occurrences with D614G are associated with disease severity, infectivity, transmissions, and antibody sensitivity. Moreover, mutations play roles in z...
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.
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