Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV‑2 Viral Antigen and to Study Host Response

SARS-CoV-2 infection has become a
major public health burden and
affects many organs including lungs, kidneys, the liver, and the brain.
Although the virus is readily detected and diagnosed using nasopharyngeal
swabs by reverse transcriptase polymerase chain reaction (RT-PCR),
detection of its presence in body fluids is fraught with difficulties.
A number of published studies have failed to detect viral RNA by RT-PCR
methods in urine. Although microbial identification in clinical microbiology
using mass spectrometry is undertaken after culture, here we undertook
a mass spectrometry-based approach that employed an enrichment step
to capture and detect SARS-CoV-2 nucleocapsid protein directly from
urine of COVID-19 patients without any culture. We detected SARS-CoV-2
nucleocapsid protein-derived peptides from 13 out of 39 urine samples.
Further, a subset of COVID-19 positive and COVID-19 negative urine
samples validated by mass spectrometry were used for the quantitative
proteomics analysis. Proteins with increased abundance in urine of
SARS-CoV-2 positive individuals were enriched in the acute phase response,
regulation of complement system, and immune response. Notably, a number
of renal proteins such as podocin (NPHS2), an amino acid transporter
(SLC36A2), and sodium/glucose cotransporter 5 (SLC5A10), which are
intimately involved in normal kidney function, were decreased in the
urine of COVID-19 patients. Overall, the detection of viral antigens
in urine using mass spectrometry and alterations of the urinary proteome
could provide insights into understanding the pathogenesis of COVID-19.