Since the start of the COVID19 pandemic, arising from SARS-CoV-2 viral infection, approximately 13000 patients have been admitted to critical care in the United Kingdom, the majority have required advanced respiratory support1.

Samples for SARS-CoV-2 detection can be obtained from the upper (nasopharyngeal/oropharyngeal swabs) or lower respiratory tract (sputum/endotracheal aspirate/broncho-alveolar lavage (BAL))2. Viral ribonucleic acid (RNA) is detected using reverse transcriptase polymerase chain reaction (RT-PCR). The Cycle threshold (Ct) has a simple negative linear correlation with the logarithm of the number of gene copies in the original sample and thus can be used to provide a semi-quantitative estimate of the viral RNA in a specimen3.

It has been suggested that SARS-CoV-2 is predominantly shed from upper respiratory tract, distinguishing it from SARS-CoV-1, where replication occurs mainly in the lower respiratory tract.4-6 A recent multi-site viral detection study5 indicated higher nasopharyngeal (NP) viral loads in some patients early in the course of disease, although they generally detected viral RNA in sputum for longer. However, this study5 was conducted on patients with mild disease, and it is unclear whether the results pertain to critically ill patients.

Our objective was to evaluate SARS-CoV-2 RNA loads between paired NP and deep lung (endotracheal aspirate or BAL) samples from critically ill patients.