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Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV-2 Viral Antigen and to Study Host Response.
Chavan, Sandip; Mangalaparthi, Kiran K; Singh, Smrita; Renuse, Santosh; Vanderboom, Patrick M; Madugundu, Anil Kumar; Budhraja, Rohit; McAulay, Kathrine; Grys, Thomas E; Rule, Andrew D; Alexander, Mariam P; O'Horo, John C; Badley, Andrew D; Pandey, Akhilesh.
  • Chavan S; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • Mangalaparthi KK; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • Singh S; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • Renuse S; Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.
  • Vanderboom PM; Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
  • Madugundu AK; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India.
  • Budhraja R; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • McAulay K; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • Grys TE; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • Rule AD; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • Alexander MP; Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
  • O'Horo JC; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States.
  • Badley AD; Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, Arizona 85054, United States.
  • Pandey A; Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, Arizona 85054, United States.
J Proteome Res ; 20(7): 3404-3413, 2021 07 02.
Article in English | MEDLINE | ID: covidwho-1253877
Semantic information from SemMedBD (by NLM)
1. Antigens PART_OF 2019 novel coronavirus
Subject
Antigens
Predicate
PART_OF
Object
2019 novel coronavirus
2. COVID-19 PROCESS_OF Patients
Subject
COVID-19
Predicate
PROCESS_OF
Object
Patients
3. Patients LOCATION_OF Urine
Subject
Patients
Predicate
LOCATION_OF
Object
Urine
4. Nasal Swab (procedure) DIAGNOSES Present
Subject
Nasal Swab (procedure)
Predicate
DIAGNOSES
Object
Present
5. Nasal Swab (procedure) DIAGNOSES Virus
Subject
Nasal Swab (procedure)
Predicate
DIAGNOSES
Object
Virus
6. Measles Virus Nucleoprotein PART_OF 2019 novel coronavirus
Subject
Measles Virus Nucleoprotein
Predicate
PART_OF
Object
2019 novel coronavirus
7. Urine LOCATION_OF Measles Virus Nucleoprotein
Subject
Urine
Predicate
LOCATION_OF
Object
Measles Virus Nucleoprotein
8. Microorganism LOCATION_OF Measles Virus Nucleoprotein
Subject
Microorganism
Predicate
LOCATION_OF
Object
Measles Virus Nucleoprotein
9. Urine PART_OF Patients
Subject
Urine
Predicate
PART_OF
Object
Patients
10. Measles Virus Nucleoprotein CONVERTS_TO Peptides
Subject
Measles Virus Nucleoprotein
Predicate
CONVERTS_TO
Object
Peptides
11. Urine PART_OF Persons
Subject
Urine
Predicate
PART_OF
Object
Persons
12. Proteins AUGMENTS Acute-Phase Reaction
Subject
Proteins
Predicate
AUGMENTS
Object
Acute-Phase Reaction
13. Proteins INTERACTS_WITH Complement System Proteins
Subject
Proteins
Predicate
INTERACTS_WITH
Object
Complement System Proteins
14. Urine LOCATION_OF Proteins
Subject
Urine
Predicate
LOCATION_OF
Object
Proteins
15. Urine LOCATION_OF SLC5A10 gene|SLC5A10
Subject
Urine
Predicate
LOCATION_OF
Object
SLC5A10 gene|SLC5A10
16. SLC5A10 gene|SLC5A10 AFFECTS Normal renal function
Subject
SLC5A10 gene|SLC5A10
Predicate
AFFECTS
Object
Normal renal function
17. Antigens PART_OF 2019 novel coronavirus
Subject
Antigens
Predicate
PART_OF
Object
2019 novel coronavirus
18. COVID-19 PROCESS_OF Patients
Subject
COVID-19
Predicate
PROCESS_OF
Object
Patients
19. Patients LOCATION_OF Urine
Subject
Patients
Predicate
LOCATION_OF
Object
Urine
20. Nasal Swab (procedure) DIAGNOSES Present
Subject
Nasal Swab (procedure)
Predicate
DIAGNOSES
Object
Present
21. Nasal Swab (procedure) DIAGNOSES Virus
Subject
Nasal Swab (procedure)
Predicate
DIAGNOSES
Object
Virus
22. Measles Virus Nucleoprotein PART_OF 2019 novel coronavirus
Subject
Measles Virus Nucleoprotein
Predicate
PART_OF
Object
2019 novel coronavirus
23. Urine LOCATION_OF Measles Virus Nucleoprotein
Subject
Urine
Predicate
LOCATION_OF
Object
Measles Virus Nucleoprotein
24. Microorganism LOCATION_OF Measles Virus Nucleoprotein
Subject
Microorganism
Predicate
LOCATION_OF
Object
Measles Virus Nucleoprotein
25. Urine PART_OF Patients
Subject
Urine
Predicate
PART_OF
Object
Patients
26. Measles Virus Nucleoprotein CONVERTS_TO Peptides
Subject
Measles Virus Nucleoprotein
Predicate
CONVERTS_TO
Object
Peptides
27. Urine PART_OF Persons
Subject
Urine
Predicate
PART_OF
Object
Persons
28. Proteins AUGMENTS Acute-Phase Reaction
Subject
Proteins
Predicate
AUGMENTS
Object
Acute-Phase Reaction
29. Proteins INTERACTS_WITH Complement System Proteins
Subject
Proteins
Predicate
INTERACTS_WITH
Object
Complement System Proteins
30. Urine LOCATION_OF Proteins
Subject
Urine
Predicate
LOCATION_OF
Object
Proteins
31. Urine LOCATION_OF SLC5A10 gene|SLC5A10
Subject
Urine
Predicate
LOCATION_OF
Object
SLC5A10 gene|SLC5A10
32. SLC5A10 gene|SLC5A10 AFFECTS Normal renal function
Subject
SLC5A10 gene|SLC5A10
Predicate
AFFECTS
Object
Normal renal function
ABSTRACT
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.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Body Fluids / COVID-19 Type of study: Diagnostic study Limits: Humans Language: English Journal: J Proteome Res Journal subject: Biochemistry Year: 2021 Document Type: Article Affiliation country: Acs.jproteome.1c00391

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Body Fluids / COVID-19 Type of study: Diagnostic study Limits: Humans Language: English Journal: J Proteome Res Journal subject: Biochemistry Year: 2021 Document Type: Article Affiliation country: Acs.jproteome.1c00391