Spread of SARS-CoV-2 in the Icelandic Population
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SciScore for 10.1101/2020.03.26.20044446: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study was approved by the National Bioethics Committee of Iceland Randomization Amplified samples (20-500 ng) were randomly sheared using focused acoustics in 96-well AFA-TUBE-TPX plates (Covaris Inc.) on the Covaris LE220plus instrument with the following settings: Sample volume, 50 µL; temperature, 10 °C; peak incident power, 200W; duty factor, 25%; cycles per burst, 50; time, 350 sec Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources SEQUENCING DATA ANALYSIS: Amplicon sequences were aligned to the reference genome of the SARS-CoV-2 (NC_045512.2)2 using bwa … SciScore for 10.1101/2020.03.26.20044446: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study was approved by the National Bioethics Committee of Iceland Randomization Amplified samples (20-500 ng) were randomly sheared using focused acoustics in 96-well AFA-TUBE-TPX plates (Covaris Inc.) on the Covaris LE220plus instrument with the following settings: Sample volume, 50 µL; temperature, 10 °C; peak incident power, 200W; duty factor, 25%; cycles per burst, 50; time, 350 sec Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources SEQUENCING DATA ANALYSIS: Amplicon sequences were aligned to the reference genome of the SARS-CoV-2 (NC_045512.2)2 using bwa mem14, possible PCR duplicates were marked with markduplicates from Picard tools15 and reads with less than 50 bases aligned were omitted from the alignment. Picardsuggested: (Picard, RRID:SCR_006525)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:There are weaknesses in the design of this screening: the sample is not random as all residents of Iceland were invited to participate and those concerned about potential infection are more likely to participate than others. We asked people with symptoms of COVID-19 not to participate but to seek help in the healthcare system. However, close to half of participants reported symptoms, most commonly a rhinorrhea and coughing. The healthcare system began testing of individuals considered to be at risk of infection on January 31 2020 and tested 65 before the first infected was identified on February 28. By March 22, 4,511 had been tested and 528 (11.6%) were positive. Hence those at high risk of infection were eleven times more likely to test positively. We show here that young children and females are less likely to test positive for SARS-CoV-2 than adults and males, respectively. Others have shown that children and females are less likely to develop severe disease than adults and males, respectively7,8. These results are consistent and suggest that children and females are less vulnerable to SARS-CoV-2. To further our understanding of the spread of the virus and to determine how the virus mutates as it spreads, we sequenced the virus from 357 individuals who had tested positive before March 19. The haplotype composition of the viruses from individuals identified through the population screening was different from those tested in the early targeted testing; more had the A1a hapl...
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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