Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients

Singh, N. K.; Srivastava, S.; Zaveri, L.; Bingi, T. C.; Mesipogu, R.; Kumar, S.; Gaur, N.; Hajirnis, N.; Maccha, P.; Shambhavi, S.; Khan, S.; Soujanya, M.; Nagabandi, T.; Mishra, R. K.; Tallapaka, K. B.; Sowpati, D. T.

doi:10.1101/2021.05.13.443721

bioRxiv · 10.1101/2021.05.13.443721

Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients

Singh, N. K.·Srivastava, S.·Zaveri, L.·Bingi, T. C.·Mesipogu, R.·Kumar, S.·Gaur, N.·Hajirnis, N.·Maccha, P.·Shambhavi, S.·Khan, S.·Soujanya, M.·Nagabandi, T.·Mishra, R. K.·Tallapaka, K. B.·Sowpati, D. T.

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Abstract

BackgroundOne of the most perplexing aspects of infection with the SARS-CoV-2 virus has been the variable response elicited in its human hosts. Investigating the transcriptional changes in individuals affected by COVID-19 can help understand and predict the degree of illness and guide clinical outcomes in diverse backgrounds. MethodsAnalysis of host transcriptome variations via RNA sequencing from naso/oropharyngeal swabs of COVID-19 patients. ResultsWe report strong upregulation of the innate immune response, especially type I interferon pathway, upon SARS-CoV-2 infection. Upregulated genes were subjected to a comparative meta-analysis using global datasets to identify a common network of interferon stimulated and viral response genes that mediate the host response and resolution of infection. A large proportion of mis-regulated genes showed a reduction in expression level, suggesting an overall decrease in host mRNA production. Significantly downregulated genes included those encoding olfactory, taste and neuro-sensory receptors. Many pro-inflammatory markers and cytokines were also downregulated or remained unchanged in the COVID-19 patients. Finally, a large number of non-coding RNAs were identified as down-regulated, with a few of the lncRNAs associated with functional roles in directing the response to viral infection. ConclusionsSARS-CoV-2 infection results in the robust activation of the bodys innate immunity. Reduction of gene expression is well correlated with the clinical manifestations and symptoms of COVID-19 such as the loss of smell and taste, and myocardial and neurological complications. This study provides a critical dataset of genes that will enhance our understanding of the nature and prognosis of COVID-19.

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Singh, N. K., Srivastava, S., Zaveri, L., Bingi, T. C., Mesipogu, R., Kumar, S., Gaur, N., Hajirnis, N., Maccha, P., Shambhavi, S., Khan, S., Soujanya, M., Nagabandi, T., Mishra, R. K., Tallapaka, K. B., Sowpati, D. T.. 2021-05-15. Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients. https://doi.org/10.1101/2021.05.13.443721

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