Monitoring COVID-19 Transmission Risks by Quantitative Real-Time PCR Tracing of Droplets in Hospital and Living Environments
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Abstract
Several studies evaluated the presence of SARS-CoV-2 in the environment. Saliva and nasopharyngeal droplets can land on objects and surfaces, creating fomites.
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SciScore for 10.1101/2020.08.22.20179754: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Samples were tested for SARS-CoV-2 RNA, whereas anthropic contamination was assessed searching for biological fluids of nose, mouth, gut through their microbiota traces by RT-PCR and/or NGS (Table 1). 2.2. NGSsuggested: (PM4NGS, RRID:SCR_019164)Approximately 200 μL lysozyme solution (20mg/mL Lisozima, 20 mM tris[hydroxymethyl]aminomethanehydrochloride at pH 8, 2mM ethylenediaminetetraacetic acid, and 1.2%TritonX-100; Sigma Aldrich, St Louis, USA) were added into the NAO Baskets and incubated a 37°C for 30 minutes. TritonX-100; Sigma Aldrichsuggested: NoneRaw sequence data was processed … SciScore for 10.1101/2020.08.22.20179754: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Samples were tested for SARS-CoV-2 RNA, whereas anthropic contamination was assessed searching for biological fluids of nose, mouth, gut through their microbiota traces by RT-PCR and/or NGS (Table 1). 2.2. NGSsuggested: (PM4NGS, RRID:SCR_019164)Approximately 200 μL lysozyme solution (20mg/mL Lisozima, 20 mM tris[hydroxymethyl]aminomethanehydrochloride at pH 8, 2mM ethylenediaminetetraacetic acid, and 1.2%TritonX-100; Sigma Aldrich, St Louis, USA) were added into the NAO Baskets and incubated a 37°C for 30 minutes. TritonX-100; Sigma Aldrichsuggested: NoneRaw sequence data was processed using an in-house pipeline that was built on the Galaxy platform and incorporated various software tools to evaluate the quality of the raw sequence data (FASTA/Q Information tools, Mothur). Galaxysuggested: (Galaxy, RRID:SCR_006281)Demultiplexing was performed to remove PhiX sequences and sort sequences; moreover, to minimize sequencing errors and ensure sequence quality, the reads were trimmed based on the sequence quality score using Btrim (an average quality score of 30 from the ends, and remove reads that are less any 200 bp after end-trimming) (Kong, 2011). Btrimsuggested: (Btrim, RRID:SCR_011836)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:Another limitation concerns the set of experimental conditions for RT-PCR and NGS. Primers and probes for selected bacterial genes from selected bacterial markers where chosen because of their feasibility and effectiveness, but we did not made comparisons with different sequences, indicators or reaction conditions for RT-PCR. The same concern can be raised for the NGS approach, which was adopted for the analysis of 16S rDNA amplicon sequencing, following standard protocols. A whole genome analysis would have been more informative. However, it would have also been more expensive for materials and bioinformatic analysis, being less appropriate for public health surveys on a larger scale. Finally, we used arbitrary thresholds to quantify droplets contamination based on CT values, proposing the highest sensibility for droplets detection. A lower threshold would have provided more specific data, or it could have been adapted to the different kind of transmission risks or expected hygiene levels in the different environments.
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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