Skip to main content
SearchLogin or Signup

Review 2: "Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19"

This preprint uses single cell RNA-seq (scRNA-seq) to reconstruct nasopharyngeal tissue reorganization in COVID-19 patients. Reviewers deemed the manuscript's main claims well-substantiated, carefully qualified, and significantly novel.

Published onApr 09, 2021
Review 2: "Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19"
1 of 2
key-enterThis Pub is a Review of
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Description

ABSTRACTInfection with SARS-CoV-2, the virus that causes COVID-19, can lead to severe lower respiratory illness including pneumonia and acute respiratory distress syndrome, which can result in profound morbidity and mortality. However, many infected individuals are either asymptomatic or have isolated upper respiratory symptoms, which suggests that the upper airways represent the initial site of viral infection, and that some individuals are able to largely constrain viral pathology to the nasal and oropharyngeal tissues. Which cell types in the human nasopharynx are the primary targets of SARS-CoV-2 infection, and how infection influences the cellular organization of the respiratory epithelium remains incompletely understood. Here, we present nasopharyngeal samples from a cohort of 35 individuals with COVID-19, representing a wide spectrum of disease states from ambulatory to critically ill, as well as 23 healthy and intubated patients without COVID-19. Using standard nasopharyngeal swabs, we collected viable cells and performed single-cell RNA-sequencing (scRNA-seq), simultaneously profiling both host and viral RNA. We find that following infection with SARS-CoV-2, the upper respiratory epithelium undergoes massive reorganization: secretory cells diversify and expand, and mature epithelial cells are preferentially lost. Further, we observe evidence for deuterosomal cell and immature ciliated cell expansion, potentially representing active repopulation of lost ciliated cells through coupled secretory cell differentiation. Epithelial cells from participants with mild/moderate COVID-19 show extensive induction of genes associated with anti-viral and type I interferon responses. In contrast, cells from participants with severe lower respiratory symptoms appear globally muted in their anti-viral capacity, despite substantially higher local inflammatory myeloid populations and equivalent nasal viral loads. This suggests an essential role for intrinsic, local epithelial immunity in curbing and constraining viral-induced pathology. Using a custom computational pipeline, we characterized cell-associated SARS-CoV-2 RNA and identified rare cells with RNA intermediates strongly suggestive of active replication. Both within and across individuals, we find remarkable diversity and heterogeneity among SARS-CoV-2 RNA+ host cells, including developing/immature and interferon-responsive ciliated cells, KRT13+ “hillock”-like cells, and unique subsets of secretory, goblet, and squamous cells. Finally, SARS-CoV-2 RNA+ cells, as compared to uninfected bystanders, are enriched for genes involved in susceptibility (e.g., CTSL, TMPRSS2) or response (e.g., MX1, IFITM3, EIF2AK2) to infection. Together, this work defines both protective and detrimental host responses to SARS-CoV-2, determines the direct viral targets of infection, and suggests that failed anti-viral epithelial immunity in the nasal mucosa may underlie the progression to severe COVID-19.

RR:C19 Evidence Scale rating by reviewer:

  • Strong. The main study claims are very well-justified by the data and analytic methods used. There is little room for doubt that the study produced has very similar results and conclusions as compared with the hypothetical ideal study. The study’s main claims should be considered conclusive and actionable without reservation.

***************************************

Review:

Ziegler and collaborators use single-cell genomic data from patients under different classes of COVID-19 progression and controls to investigate which cell types in the human nasopharynx are the primary targets of SARS-CoV-2 infection, and how the coronavirus infection influences the cellular organization of the respiratory epithelium. This is a phenomenon that remains incompletely understood and the authors made an exceptional effort to understand it and identify some of the changes in cell organization in human nasopharynx undergoing different infection states or disease outcomes. Overall, I think this research is strong, and the authors make a careful discussion of their experimental design and its caveats. Claims are very well-supported by the data and methods used. Decision-makers should consider the claims in this study actionable without reservation based on the methods and data. Moreover, I don’t have significant concerns regarding the implementation of the Seurat and other computational tools for computing RNA Velocity and Pseudotime.  In particular, I am very impressed by this manuscript, it is well written and the statistical analysis are sound. Finally, the authors unlock insights that will help to identify what cells and what novel candidate genes would help to predict the severity outcome of the disease. Some highlights of this work are: 1) Massive reorganization of the nasopharyngeal tissue or upper respiratory epithelium. 2) Cells from patients with mild/moderate COVID-19 show induction of genes associated with anti-viral and type I interferon responses, while this response is muted in severe cases. 3) Extraordinary diversity and heterogeneity among SARS-CoV-2 RNA+ host cells. 4) SARS-CoV-2 RNA+ host cells also exhibit an enrichment of genes involved in susceptibility (e.g., CTSL, TMPRSS2) or response (e.g., MX1, IFITM3, EIF2AK2) to infection. The authors also report the upregulation of alarmins S100A8/S100A9 (i.e., calprotectin) among severe and moderate/mild cases relative to controls.

The manuscript confirms previous work of the current understanding of the effect of SARS-CoV-2 infection on interferon genes. Indeed, the evidence that has been provided will improve the understanding of COVID-19 and the degree of novelty is highly significant.

The authors make an excellent job at keeping up with current literature and their remarks and findings are clearly explained and of interest to broader audiences. However, the title as it reads seems a bit misleading and should include elements of the single-cell approach used. I almost reject reviewing it just by the title, but then I got very excited with the abstract.

The authors made clear statements of where the data and scripts will be deposited, and the methods section has clear statements of inclusivity and ethics.

I highly recommend (accept) this article for publication and just recommend tuning the title to make it more specific.

Comments
0
comment

No comments here