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Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients.
Brief Bioinform ; 22(2): 1215-1224, 2021 03 22.
Article in English | MEDLINE | ID: covidwho-1343625
Semantic information from SemMedBD (by NLM)
1. Detection TREATS COVID-19
Subject
Detection
Predicate
TREATS
Object
COVID-19
2. COVID-19 PROCESS_OF Patients
Subject
COVID-19
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PROCESS_OF
Object
Patients
3. Detection TREATS Patients
Subject
Detection
Predicate
TREATS
Object
Patients
4. Detection TREATS Hypersensitivity
Subject
Detection
Predicate
TREATS
Object
Hypersensitivity
5. Binding Sites PART_OF 2019 novel coronavirus
Subject
Binding Sites
Predicate
PART_OF
Object
2019 novel coronavirus
6. Oligonucleotide Primers INTERACTS_WITH Endoribonucleases
Subject
Oligonucleotide Primers
Predicate
INTERACTS_WITH
Object
Endoribonucleases
7. Oligonucleotide Primers INTERACTS_WITH RNA
Subject
Oligonucleotide Primers
Predicate
INTERACTS_WITH
Object
RNA
8. RNA INTERACTS_WITH Endoribonucleases
Subject
RNA
Predicate
INTERACTS_WITH
Object
Endoribonucleases
9. Polymerase Chain Reaction METHOD_OF Detection
Subject
Polymerase Chain Reaction
Predicate
METHOD_OF
Object
Detection
10. RNA compared_with Endoribonucleases
Subject
RNA
Predicate
compared_with
Object
Endoribonucleases
11. Polymerase chain reaction analysis DIAGNOSES Present
Subject
Polymerase chain reaction analysis
Predicate
DIAGNOSES
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Present
12. Senility PROCESS_OF Patients
Subject
Senility
Predicate
PROCESS_OF
Object
Patients
13. Detection TREATS COVID-19
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Detection
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TREATS
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COVID-19
14. COVID-19 PROCESS_OF Patients
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COVID-19
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PROCESS_OF
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Patients
15. Detection TREATS Patients
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Detection
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TREATS
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Patients
16. Detection TREATS Hypersensitivity
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Detection
Predicate
TREATS
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Hypersensitivity
17. Binding Sites PART_OF 2019 novel coronavirus
Subject
Binding Sites
Predicate
PART_OF
Object
2019 novel coronavirus
18. Oligonucleotide Primers INTERACTS_WITH Endoribonucleases
Subject
Oligonucleotide Primers
Predicate
INTERACTS_WITH
Object
Endoribonucleases
19. Oligonucleotide Primers INTERACTS_WITH RNA
Subject
Oligonucleotide Primers
Predicate
INTERACTS_WITH
Object
RNA
20. RNA INTERACTS_WITH Endoribonucleases
Subject
RNA
Predicate
INTERACTS_WITH
Object
Endoribonucleases
21. Polymerase Chain Reaction METHOD_OF Detection
Subject
Polymerase Chain Reaction
Predicate
METHOD_OF
Object
Detection
22. RNA compared_with Endoribonucleases
Subject
RNA
Predicate
compared_with
Object
Endoribonucleases
23. Polymerase chain reaction analysis DIAGNOSES Present
Subject
Polymerase chain reaction analysis
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DIAGNOSES
Object
Present
24. Senility PROCESS_OF Patients
Subject
Senility
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PROCESS_OF
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Patients
ABSTRACT
The pandemic of coronavirus disease 2019 (COVID-19) urgently calls for more sensitive molecular diagnosis to improve sensitivity of current viral nuclear acid detection. We have developed an anchor primer (AP)-based assay to improve viral RNA stability by bioinformatics identification of RNase-binding site of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and implementing AP dually targeting the N gene of SARS-CoV-2 RNA and RNase 1, 3, 6. The arbitrarily primed polymerase chain reaction (AP-PCR) improvement of viral RNA integrity was supported by (a) the AP increased resistance of the targeted gene (N gene) of SARS-CoV-2 RNA to RNase treatment; (b) the detection of SARS-CoV-2 RNA by AP-PCR with lower cycle threshold values (-2.7 cycles) compared to two commercially available assays; (c) improvement of the viral RNA stability of the ORF gene upon targeting of the N gene and RNase. Furthermore, the improved sensitivity by AP-PCR was demonstrated by detection of SARS-CoV-2 RNA in 70-80% of sputum, nasal, pharyngeal swabs and feces and 36% (4/11) of urine of the confirmed cases (n = 252), 7% convalescent cases (n = 54) and none of 300 negative cases. Lastly, AP-PCR analysis of 306 confirmed and convalescent cases revealed prolonged presence of viral loading for >20 days after the first positive diagnosis. Thus, the AP dually targeting SARS-CoV-2 RNA and RNase improves molecular detection by preserving SARS-CoV-2 RNA integrity and reveals the prolonged viral loading associated with older age and male gender in COVID-19 patients.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Main subject: Ribonucleases / Polymerase Chain Reaction / SARS-CoV-2 / COVID-19 Type of study: Controlled clinical trial / Diagnostic study Limits: Aged / Female / Humans / Male Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Ribonucleases / Polymerase Chain Reaction / SARS-CoV-2 / COVID-19 Type of study: Controlled clinical trial / Diagnostic study Limits: Aged / Female / Humans / Male Language: English Journal: Brief Bioinform Journal subject: Biology / Medical Informatics Year: 2021 Document Type: Article