A rare case of false‐negative: Limitations of nucleic acid amplification tests in diagnosing tuberculous peritonitis in peritoneal dialysis patients

Nephrology ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 653-654
Author(s):  
Wai Lun Will Pak ◽  
Ka Lok Chan ◽  
Zi Chan ◽  
Wai Ping Law ◽  
Yick Hei Wong ◽  
...  
Keyword(s):  
Peritoneal Dialysis ◽  
Nucleic Acid ◽  
Rare Case ◽  
False Negative ◽  
Tuberculous Peritonitis ◽  
Nucleic Acid Amplification ◽  
Dialysis Patients ◽  
Nucleic Acid Amplification Tests

scholarly journals Genomic Variations in SARS-CoV-2 Strains at the Target Sequences of Nucleic Acid Amplification Tests

2021 ◽  
Author(s):  
Canhui Cao ◽  
Ruidi Yu ◽  
Shaoqing Zeng ◽  
Dan Liu ◽  
Wenjian Gong ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
False Negative ◽  
False Negative Rate ◽  
Nucleic Acid Amplification ◽  
Whole Genome Sequencing Data ◽  
Target Sequence ◽  
Nucleic Acid Amplification Tests ◽  
Probe Target ◽  
Genomic Variations ◽  
Target Sequences

IntroductionNucleic acid amplification is the main method used to detect infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the false-negative rate of nucleic acid tests cannot be ignored.Material and methodsHerein, we demonstrated genomic variations at the target sequences for the tests and the geographical distribution of the variations across countries by analyzing the whole-genome sequencing data of SARS-CoV-2 strains from the 2019 Novel Coronavirus Resource (2019nCoVR) database.ResultsAmong the 21 pairs of primer sequences in regions ORF1ab, S, E, and N, the total length of primer and probe target sequences was 938bp, with 131(13.97%) variant loci in 2415 (38.96%) isolates. Primer targets in the N region contained the most variations that were distributed among the most isolates, and the E region contained the least. Single nucleotide polymorphisms were the most frequent variation, with C to T transitions being detected in the most variant loci. G to A transitions and G to C transversions were the most common and had the highest isolate density. Genomic variations at the three mutation sites N: 28881, N: 28882, and N: 28883 were the most commonly detected, including in 608 SARS-CoV-2 strains from 33 countries, especially in the United Kingdom, Portugal, and Belgium.ConclusionsOur work comprehensively analyzed genomic variations on the target sequences of the nucleic acid amplification tests, offering evidence to optimize primer and probe target sequence selection, thereby improving the performance of the SARS-CoV-2 diagnostic test.

scholarly journals Genomic Variations in SARS-CoV-2 Strains at the Target Sequences of Nucleic Acid Amplification Tests

2020 ◽  
Author(s):  
Canhui Cao ◽  
Ruidi Yu ◽  
Shaoqing Zeng ◽  
Dan Liu ◽  
Wenjian Gong ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
False Negative ◽  
False Negative Rate ◽  
Nucleic Acid Amplification ◽  
Whole Genome Sequencing Data ◽  
Target Sequence ◽  
Nucleic Acid Amplification Tests ◽  
Probe Target ◽  
Genomic Variations ◽  
Target Sequences

Abstract Background Nucleic acid amplification is the main method used to detect infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the false-negative rate of nucleic acid tests cannot be ignored. Methods Herein, we demonstrated genomic variations at the target sequences for the tests and the geographical distribution of the variations across countries by analyzing the whole-genome sequencing data of SARS-CoV-2 strains from the 2019 Novel Coronavirus Resource (2019nCoVR) database. Results Among the 21 pairs of primer sequences in regions ORF1ab, S, E, and N, the total length of primer and probe target sequences was 938 bp, with 131(13.97%) variant loci in 2415 (38.96%) isolates. Primer targets in the N region contained the most variations that were distributed among the most isolates, and the E region contained the least. Single nucleotide polymorphisms were the most frequent variation, with C to T transitions being detected in the most variant loci. G to A transitions and G to C transversions were the most common and had the highest isolate density. Genomic variations at the three mutation sites N: 28881, N: 28882, and N: 28883 were the most commonly detected, including in 608 SARS-CoV-2 strains from 33 countries, especially in the United Kingdom, Portugal, and Belgium. Conclusions Our work comprehensively analyzed genomic variations on the target sequences of the nucleic acid amplification tests, offering evidence to optimize primer and probe target sequence selection, thereby improving the performance of the SARS-CoV-2 diagnostic test.

scholarly journals Genomic Variations in SARS-CoV-2 Strains at the Target Sequences of Nucleic Acid Amplification Tests

2020 ◽  
Author(s):  
Canhui Cao ◽  
Ruidi Yu ◽  
Shaoqing Zeng ◽  
Dan Liu ◽  
Wenjian Gong ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
False Negative ◽  
False Negative Rate ◽  
Nucleic Acid Amplification ◽  
Whole Genome Sequencing Data ◽  
Target Sequence ◽  
Nucleic Acid Amplification Tests ◽  
Probe Target ◽  
Genomic Variations ◽  
Target Sequences

Abstract Background: Nucleic acid amplification is the main method used to detect infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the false-negative rate of nucleic acid tests cannot be ignored. Methods: Herein, we demonstrated genomic variations at the target sequences for the tests and the geographical distribution of the variations across countries by analyzing the whole-genome sequencing data of SARS-CoV-2 strains from the 2019 Novel Coronavirus Resource (2019nCoVR) database. Results: Among the 21 pairs of primer sequences in regions ORF1ab, S, E, and N, the total length of primer and probe target sequences was 938bp, with 131(13.97%) variant loci in 2415 (38.96%) isolates. Primer targets in the N region contained the most variations that were distributed among the most isolates, and the E region contained the least. Single nucleotide polymorphisms were the most frequent variation, with C to T transitions being detected in the most variant loci. G to A transitions and G to C transversions were the most common and had the highest isolate density. Genomic variations at the three mutation sites N: 28881, N: 28882, and N: 28883 were the most commonly detected, including in 608 SARS-CoV-2 strains from 33 countries, especially in the United Kingdom, Portugal, and Belgium. Conclusions: Our work comprehensively analyzed genomic variations on the target sequences of the nucleic acid amplification tests, offering evidence to optimize primer and probe target sequence selection, thereby improving the performance of the SARS-CoV-2 diagnostic test.

scholarly journals Is it time to move to nucleic acid amplification tests screening for pharyngeal and rectal gonorrhoea in men who have sex with men to improve gonorrhoea control?

Sexual Health ◽  
2011 ◽  
Vol 8 (1) ◽  
pp. 9 ◽  
Author(s):  
Christopher K. Fairley ◽  
Marcus Y. Chen ◽  
Catriona S. Bradshaw ◽  
Sepehr N. Tabrizi
Keyword(s):  
Nucleic Acid ◽  
Antimicrobial Resistance ◽  
Sexual Health ◽  
Nucleic Acid Amplification ◽  
Nucleic Acid Amplification Tests ◽  
Health Clinics ◽  
Sex With Men ◽  
Sexual Health Clinics

The use of nucleic acid amplification tests (NAAT), as well as or in preference to culture for non-genital sites is now recommended both in Australia and overseas because of their greater sensitivity and improved specificity. A survey of 22 Australian sexual health clinics who each year test over 14 500 men who have sex with men (MSM) show that culture remains the predominate method for detecting gonorrhoea at pharyngeal (64%) and rectal (73%) sites. This editorial discusses the potential disadvantages of using culture over NAAT in relation to optimal gonorrhoea control among MSM and advocates that significantly improved control would be achieved by moving to NAAT with the proviso that culture samples are taken wherever possible on NAAT-positive samples and from clients with urethritis to ensure continued surveillance for antimicrobial resistance.

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