Deep RNA Sequencing of Intensive Care Unit Patients with COVID-19

Background: COVID-19 has impacted millions of patients across the world. Molecular testing occurring now identifies the presence of the virus at the sampling site: nasopharynx, nares, or oral cavity. RNA sequencing has the potential to establish both the presence of the virus and define the host’s response in COVID-19. Methods: Single center, prospective study of patients with COVID-19 admitted to the intensive care unit to investigate the potential of deep RNA sequencing (>100 million reads) of peripheral blood with computational biology analysis to assist the clinician in caring for these patients. All patients had positive SARS-CoV-2 PCR from the nasopharynx. Clinical data was prospectively collected. Findings: We enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. Entropy calculated from alternative RNA splicing and transcription start/end predicted mortality in these patients. Interpretation: Current upper respiratory tract testing for COVID-19 only determines if the virus is present. Deep RNA sequencing with appropriate computational biology may provide important prognostic information and point to therapeutic foci to be precisely targeted in future studies. Funding: This study was supported by funding from the US National Institutes of Health: P20 GM103652 (SFM, WGF, EOH, AA), T32 HL134625 (AMF, EOH), R01 GM 127472 (WGF), P20 GM121344 (GJN), R01 HL147525 (JSR), R01 HL141268 (CEV), R35 GM118097 (AA).Declaration of Interests: None.Ethics Approval Statement: All participants, or their appropriate surrogate, provided informed consent as approved by the Institutional Review Board (Approval #: 411616).