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Authors: Ong et al., Link to paper:

Journal/ Pre-Print: Cell host and Microbe

NB: Supplemental data not yet available online, so couldn’t be evaluated in this review!

Key Words: Case study, Whole blood transcriptomics, Cytokine Expression, IL-1 Pathway


1. Repeated blood sampling of the same moderate-severe Covid-19 patient showed that expression of a cluster of pro-inflammatory genes peaked 1 day later than clinical symptoms.

2. Repeated oropharyngeal swabs of 3 patients showed that they remained positive for SARS-CoV2 RNA (RT-PCR) for up to 29 days after onset of symptoms, and up to 10 days after symptoms resolved.

3. mRNA levels of IL-1A & IL-1B in blood exceeded HC levels only in the severe patient (1 out of 3) and only during the 3-day peak of clinical symptoms. IL-1 receptor mRNA was increased for longer and also in one of the mild cases. The authors propose repurposing of IL1 antagonists canakinumab & anakinra to prevent respiratory dysfunction in COVID-19 patients.


This study performed repeated whole blood RNA analysis using the nCounter Human Immunology V2 panel for three Covid-19 patients, one moderate-severe patient and two mild cases. Each patient was sampled 4 or 9 times over 4-15 days, and samples were analysed to describe the time course of Covid-19. Cytokines such as IL2, IL6, TNF and IFNA1/13 were reported to be “expressed within the range of healthy controls or were induced only after respiratory function nadir”, but the data nor statistical testing are shown. Conclusions are largely anecdotal, undermined by low power and poorly matched controls. Raw data and normalized counts are available online at Array Express, which could be a valuable resource upon further investigation.


Understand the immune response to SARS-CoV2/COVID19

IL1 pathway cytokines are upregulated prior to most severe respiratory symptoms and therefore could be used as a correlate to disease severity. Proposal for repurposing of IL1 antagonists canakinumab & anakinra to prevent respiratory dysfunction in COVID-19 patients.

Clinical symptoms and pathogenesis of SARS-Cov2/COVID19:

For the moderate-severe patient, it was attempted to link the transcriptomics results to clinical symptoms (only supplemental O2 quantity, O2 saturation, and heart rate).

Treatment of SARS-CoV2/COVID19 positive individuals:

The moderate-severe patient was treated with lopinavir/ritonavir and there was no impact noted on pro-inflammatory gene expression, T cell responses or viral clearance (but control group is lacking).

Develop diagnostic tools for SARS-CoV2/COVID19

Study promotes use of the NanoStrings nCounter platform for rapid transcriptomic analysis for a pre-defined panel of pro-inflammatory cytokines in whole blood. Platform reported to use minimal amounts of blood (within ethical guidelines) and does not require extensive manipulation or use of a Cat.3 Lab.


· Patient Case study


Novelty: No solid conclusions due to low number of patients and lack of statistical testing, but this study may hint towards IL-1 having a bigger role in pathogenesis than other cytokines.

Standing in the field: > The fact that the peak in a cluster of pro-inflammatory genes came 1 day later than clinical symptoms is contradictory to the proposed role of a cytokine storm in Covid-19 pathogenesis. However, before/during the peak in symptoms the expression of those genes is still higher than mild cases or HC. Also, the identity of the genes in this cluster is not given so difficult to appreciate the results.

> The reduction in CD4 & CD8 mRNA in the blood of the moderate-severe patient fits with other reports of lymphopenia in Covid-19.

Appropriate statistics: No statistical comparison was made in this study (possibly because of lack of power), making it difficult to judge the merit of the results.

Viral model used: SARS-CoV2

Translatability: > Difficult, because transcriptomics were not confirmed by protein level measurements nor by differential cell counts in blood, and because only 3 patients were described.

> Wider use for technology (NanoStrings nCounter platform) may prove interesting

Main limitations: > No statistical comparison was made in this study, making it difficult to judge the merit of the results.

> Not matched controls (study 100% male, HC 70% female)

> Only 3 patients, although repeated sampling. Focus on N=1 severe-moderate case, results could easily be anomalous.

> The authors don’t acknowledge that shifts in whole blood RNA levels can simply be explained by shift in relative numbers of different cell types (lymphocytes, monocytes, granulocytes).

> Transcriptomics results not confirmed at protein level.

> Oropharyngeal swabs were tested for viral RNA not for infectious particles.