COVID-19 Diagnosed by Next Generation Sequencing (Explify)

In Brief
Explify® Respiratory pathogen detection identified SARS-CoV-2 in an elderly patient presenting with fall-related trauma, lung opacities, and hypoxia.

Case Vignette
An elderly man presented at a California emergency room with trauma-related injuries, including subdural hematoma and a radial fracture, suffered from a fall at his home. Pulse-oximetry indicated hypoxia. A chest CT scan revealed lung opacities with a ground-glass appearance. He was intubated for hypoxic respiratory failure and admitted to the ICU. A tracheal aspirate was sent for directed RT-PCR and to IDbyDNA for Explify Respiratory pathogen detection, which returned a strong positive result for SARS-CoV-2. 100% genome coverage was obtained with shotgun sequencing. Comparison with other sequences in public databases revealed the virus was most closely related to Clade G viruses with close similarities to other strains circulating in the United States. Unfortunately, the patient did not survive.

Screen shot of coverage and depth obtained by Explify. Median depth calculated at 20,060.

Unrooted neighbor-joining tree of representative SARS-CoV-2 genomes in the public domain with patient’s strain noted by an asterisk*.

Representative axial cut lung windowing of patient’s admission chest CT showing diffuse ground glass opacities.