Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – A high risk community-hospital interface

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1. Version published to 10.1016/j.jinf.2021.04.020

   Jul 1, 2021
2. 

   ScreenIT

   Mar 28, 2021

   SciScore for 10.1101/2021.03.24.21253587: (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
   For nanopore reads the ARTIC-nCov-2019 bioinformatics protocol was used, reads were size filtered, demultiplexed, trimmed with Porechop (https://github.com/rrwick/Porechop) and mapped against the reference strain Wuhan-Hu-1 (GenBank accession number MN908947), followed by clipping of primer regions.	Porechop suggested: (Porechop, RRID:SCR_016967)
   Variants were called using Nanopolish 0.11.3 (https://github.com/jts/nanopolish).	https://github.com/jts/nanopolish suggested: (Nanopolish, RRID:SCR_016157)
   For Illumina, reads were trimmed with trim_galore …

   SciScore for 10.1101/2021.03.24.21253587: (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
   For nanopore reads the ARTIC-nCov-2019 bioinformatics protocol was used, reads were size filtered, demultiplexed, trimmed with Porechop (https://github.com/rrwick/Porechop) and mapped against the reference strain Wuhan-Hu-1 (GenBank accession number MN908947), followed by clipping of primer regions.	Porechop suggested: (Porechop, RRID:SCR_016967)
   Variants were called using Nanopolish 0.11.3 (https://github.com/jts/nanopolish).	https://github.com/jts/nanopolish suggested: (Nanopolish, RRID:SCR_016157)
   For Illumina, reads were trimmed with trim_galore (bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped with BWA20 to the Wuhan-Hu-1 reference sequence, followed by primer trimming and consensus calling with iVar.	BWA20 suggested: None
   All consensus genomes are available from the GISAID database (https://www.gisaid.org), the COG-UK consortium website (https://www.cogconsortium.uk/data/) and BAM files from the European Nucleotide Archive’s Sequence Read Archive service, BioProject PRJEB37886 (https://www.ebi.ac.uk/ena/data/view/PRJEB37886).	BioProject suggested: (NCBI BioProject, RRID:SCR_004801)
   All full genomes of SARS-CoV-2 from Scotland sequenced as part of the COG-UK consortium were included and aligned using MAFFT v7.310 and with the HKY+I+G4 nucleotide substitution model determined by modeltest.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The SRT algorithm was coded in R version 3.6.0, using the ape v5.3 package for calculation of pairwise SNP differences and PostcodesioR v0.1.1 and gmt v2.0-1 packages to calculate distances between postcodes.	PostcodesioR suggested: None

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   A limitation of the study is the sequences available for analysis; accurate estimation of the likely source of infection depends on having sufficient sequences available from the community of affected patients and of cases from the hospital setting. Here, we obtained sequences from two-thirds of the lab-detected SARS-CoV-2 cases from RDU1-RDU5, and 44% for RDU6. We also compared data from the RDUs with 944 other cases in the community, 700 inpatients and 546 samples taken from patients presenting in emergency departments in the same health boards as provide care for dialysis patients. Additionally, COVID-19 is asymptomatic in up to 20% of patients, which may have reduced the number of infections captured.26 Further, early in the pandemic, HCWs were ineligible for testing. Frequent, regular testing of all HCWs and all patients, regardless of symptoms is warranted. There is also mounting evidence that HCWs have a higher seroprevalence for SARS-CoV-2 antibodies than the general population, with a high proportion being asymptomatic.27,28 The low substitution rate of SARS-CoV-2 limits the granularity of outbreak analysis; as demonstrated in this study, indistinguishable sequences may not be part of a transmission cluster if there is widespread circulation in the patients’ home communities. To address this limitation, we employed the SRT, which combines sequence data with both temporal and geographic data to improve estimates of within-unit and within-hospital versus community tran...

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04405934	Not yet recruiting	COG-UK Project Hospital-Onset COVID-19 Infections Study

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. 

   Version published to 10.1101/2021.03.24.21253587 on medRxiv

   Mar 26, 2021