Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection

Article activity feed

1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.07.30.20165241: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Autopsy consent was per clinical care as directed by the patient or health care proxy.
   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

   Experimental Models: Cell Lines
   Sentences	Resources
   We performed immunohistochemistry (IHC) for CD3, CD8, CD20, CD163, CD123, IDO1, PD-L1, Napsin A, keratin and SARS-CoV N protein on an immunohistochemical platform.	PD-L1 suggested: ATCC Cat# CRL-1882, RRID:CVCL_G248)
   Software and Algorithms
   Sentences	Resources
   For RNA expression analysis, the initial quality control of sequencing data was carried out using …

   SciScore for 10.1101/2020.07.30.20165241: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Autopsy consent was per clinical care as directed by the patient or health care proxy.
   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

   Experimental Models: Cell Lines
   Sentences	Resources
   We performed immunohistochemistry (IHC) for CD3, CD8, CD20, CD163, CD123, IDO1, PD-L1, Napsin A, keratin and SARS-CoV N protein on an immunohistochemical platform.	PD-L1 suggested: ATCC Cat# CRL-1882, RRID:CVCL_G248)
   Software and Algorithms
   Sentences	Resources
   For RNA expression analysis, the initial quality control of sequencing data was carried out using the tool FASTQC and alignment of sequencing reads to the reference genome was carried out using STAR aligner, version 2.729.	FASTQC suggested: (FastQC, RRID:SCR_014583)
   A new index for STAR aligner was created using this new annotation.	STAR suggested: (STAR, RRID:SCR_015899)
   Post alignment using this new annotation, the duplicate reads were marked using PICARD and removed using SAMtools.	PICARD suggested: (Picard, RRID:SCR_006525) SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)
   The resulting BAM files were used to quantify the read counts per gene using HTSeq-count program.	HTSeq-count suggested: (htseq-count, RRID:SCR_011867)
   The DESeq2 package30 was used for differential expression analysis between samples.	DESeq2 suggested: (DESeq, RRID:SCR_000154)

   ---

   Results from OddPub: Thank you for sharing your data.

   ---

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

   The RNA-ISH and qRT-PCR assay could potentially be performed as complementary diagnostics on bronchoalveolar lavage samples to distinguish the two phases of the disease as well as discriminate active infection from asymptomatic carrier with another pulmonary process.However, one notable caveat is the heterogeneity in viral load, necessitating that multiple lobes must be sampled. In summary, detailed molecular analysis of multiple lung lobes from patients with severe COVID-19 infection highlights two phases in patients who succumb to the disease. While anti-viral agents are likely to be most beneficial earlier in the disease, the timing and type of immune modulation, activating or inhibiting, must be carefully considered given the heterogeneous immune responses observed in these patients. Our findings highlight the importance in serially assessing tissue pulmonary SARS-CoV-2 RNA levels and the immune response as well as attempt to identify corresponding surrogate markers in the blood, although the heterogeneity in the viral load and immune response across the lobes of the lung may prove a challenge.Additional mechanistic and biomarker driven studies of SARS-CoV-2 are needed to optimize patient selection and the timing of treatment administration to address this inherent spectrum of COVID-19 presentation. The current work provides the foundation to evaluate a larger series of autopsies characterizing the spatiotemporal relationship of viral load and host microenvironment respon...

   ---

   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 10.1038/s41467-020-20139-7

   Dec 9, 2020
3. 

   Version published to 10.1101/2020.07.30.20165241v1 on medRxiv

   Aug 2, 2020