Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Replication in an Immunocompromised Patient

Article activity feed

1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.09.20.20196899: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All experiments using SARS-CoV-2 were performed at the University of Michigan under Biosafety Level 3 (BSL3) protocols in compliance with containment procedures in laboratories approved for use by the University of Michigan Institutional Biosafety Committee (IBC) and Environment, Health & Safety (EHS). IRB: This study and the use of residual specimens from patients with COVID-19 have been approved by the University of Michigan Institutional Review Board (IRB).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   T…

   SciScore for 10.1101/2020.09.20.20196899: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All experiments using SARS-CoV-2 were performed at the University of Michigan under Biosafety Level 3 (BSL3) protocols in compliance with containment procedures in laboratories approved for use by the University of Michigan Institutional Biosafety Committee (IBC) and Environment, Health & Safety (EHS). IRB: This study and the use of residual specimens from patients with COVID-19 have been approved by the University of Michigan Institutional Review Board (IRB).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   To detect viral-infected cells, anti-nucleocapsid protein (anti-N) SARS-CoV-2 antibody (Antibodies Online, Cat# ABIN6952432) was used as a primary antibody with an overnight staining at 4°C followed by staining with secondary antibody Alexa-647 (goat anti-mouse, Thermo Fisher,	anti-nucleocapsid protein (anti-N) SARS-CoV-2 suggested: None anti-mouse suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The SARS-CoV-2 WA1 strain was obtained from BEI Resources and was propagated in Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Huh-7 cells infected with SARS-CoV-2 WA1 at a multiplicity of infection (MOI) of 0.2 were used as positive control of infection.	Huh-7 suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336)
   Software and Algorithms
   Sentences	Resources
   Sequencing libraries were prepared using the NEBNext Ultra II kit and sequenced on an Illumina MiSeq with 2×250bp reads, V2 chemistry.	MiSeq suggested: (A5-miseq, RRID:SCR_012148)
   Reads were aligned to the Wuhan-1 reference (GenBank: MN908947.3) with BWA-MEM version 0.7.15.	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)
   Sequencing adaptors were removed and the ARTIC primer were trimmed with iVar version 1.2.1.	iVar suggested: None
   We determined the consensus sequences with samtools (version 1.5) mpileup and iVar consensus, excluding bases with a quality score below 20.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Whole genome consensus sequences were aligned to the Wuhan-Hu-1 reference with MUSCLE (version 3.8.31) and the phylogeny constructed with IQ-TREE using a GTR model and 1000 ultrafast bootstrap replicates.	MUSCLE suggested: (MUSCLE, RRID:SCR_011812) IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   To determine the frequency of case patient mutations in the larger global dataset of SARS-CoV-2, we downloaded all sequences >27000 bases in length from GISAID and aligned them with MAFFT within the nextstrain environment (Supplemental Table 3).	MAFFT suggested: (MAFFT, RRID:SCR_011811)

   ---

   Results from OddPub: Thank you for sharing your code and data.

   ---

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

   A major limitation of our study is that it describes a single individual whose clinical course may not be broadly generalizable to other immunocompromised population. Nevertheless, we expect that additional cases such as the one described above will continue to elucidate important aspects of SARS-CoV-2 pathogenesis, evolution, and immunity.

   ---

   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.

   ---

   Read the original source
2. Version published to 10.1093/infdis/jiaa666

   Oct 22, 2020
3. 

   Version published to 10.1101/2020.09.20.20196899v1 on medRxiv

   Sep 22, 2020