Comparison between RT-qPCR for SARS-CoV-2 and expanded triage in sputum of symptomatic and asymptomatic COVID-19 subjects in Ecuador

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Background

The quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) effectively detects the SARS-COV-2 virus. SARS-CoV-2 Nevertheless, some critical gaps remain in the identification and monitoring of asymptomatic people.

Methods

This retrospective study included 733 asymptomatic and symptomatic COVID-19 subjects, who were submitted to the RT-qPCR test. The objective was to assess the efficacy of an expanded triage of subjects undergoing the RT-qPCR test for SARS-COV-2 to identify the largest possible number of COVID-19 cases in a hospital setting in Ecuador. SARS-CoV-2 Firstly, the sensitivity and specificity as well as the predictive values of an expanded triage method were calculated. In addition, the Kappa coefficient was also determined to assess the concordance between laboratory test results and the expanded triage.

Results

Of a total of 733 sputum samples; 229 were RT-qPCR-positive (31.2%) and mortality rate reached 1.2%. Overall sensitivity and specificity were 86.0% (95% confidence interval: 81.0–90.0%) and 37.0% (95% confidence interval: 32.0–41.0%) respectively, with a diagnostic accuracy of 52.0% and a Kappa coefficient of 0.73. An association between the positivity of the test and its performance before 10 days was found.

Conclusions

The clinical sensitivity for COVID-19 detection was within acceptable standards, but the specificity still fell below the values of reference. The lack of symptoms did not always mean to have a negative SARS-COV-2 RT-qPCR test. The expanded triage identified a still unnoticed percentage of asymptomatic subjects showing positive results for the SARS-COV-2 RT-qPCR test. The study also revealed a significant relationship between the number of RT-qPCR-positive cases and the performance of the molecular diagnosis within the first 10 days of COVID-19 in the symptomatic group .

Related collections

Most cited references 13

Record: found
Abstract: found
Article: found

Is Open Access

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Victor M Corman, Olfert Landt, Marco Kaiser … (2020)

Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.

0 comments Cited 3490 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

Interrater reliability: the kappa statistic

Mary L McHugh (2012)

The kappa statistic is frequently used to test interrater reliability. The importance of rater reliability lies in the fact that it represents the extent to which the data collected in the study are correct representations of the variables measured. Measurement of the extent to which data collectors (raters) assign the same score to the same variable is called interrater reliability. While there have been a variety of methods to measure interrater reliability, traditionally it was measured as percent agreement, calculated as the number of agreement scores divided by the total number of scores. In 1960, Jacob Cohen critiqued use of percent agreement due to its inability to account for chance agreement. He introduced the Cohen’s kappa, developed to account for the possibility that raters actually guess on at least some variables due to uncertainty. Like most correlation statistics, the kappa can range from −1 to +1. While the kappa is one of the most commonly used statistics to test interrater reliability, it has limitations. Judgments about what level of kappa should be acceptable for health research are questioned. Cohen’s suggested interpretation may be too lenient for health related studies because it implies that a score as low as 0.41 might be acceptable. Kappa and percent agreement are compared, and levels for both kappa and percent agreement that should be demanded in healthcare studies are suggested.

0 comments Cited 2946 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Diagnosis of the Coronavirus disease (COVID-19): rRT-PCR or CT?

Chunqin Long, Huaxiang Xu, Qinglin Shen … (2020)

Highlights • The COVID-19 outbreak highlights the need for early diagnosis, isolation and treatment • The sensitivity of the CT was 97.2%, while the sensitivity of initial rRT-PCR was 83.3%. • Patients with typical CT findings but negative rRT-PCR results should be isolated.

0 comments Cited 409 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Ariel Torres: ariton74@gmail.com

Martha Fors: martha.fors@udla.edu.ec

Tamaris Rivero: tamarisrivero@yahoo.com

Karina Pantoja: karis_eliz@hotmail.com

Santiago Ballaz: sballazg@gmail.com

Journal

Journal ID (nlm-ta): BMC Infect Dis

Journal ID (iso-abbrev): BMC Infect Dis

Title: BMC Infectious Diseases

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2334

Publication date (Electronic): 12 June 2021

Publication date PMC-release: 12 June 2021

Publication date Collection: 2021

Volume: 21

Electronic Location Identifier: 558

Affiliations

[1 ]Medicina General Integral, Máster en Enfermedades Infecciosas, Hospital Gineco-obstétrico Nueva Aurora Luz Elena Arismendi, Quito, Ecuador

[2 ]GRID grid.442184.f, ISNI 0000 0004 0424 2170, Escuela de Medicina, Facultad de Ciencias de la Salud, Redondel del Ciclista, Antigua Via a Nayón, , Universidad de las Américas, ; 170125 Quito, Ecuador

[3 ]Medicina General Integral, Hospital General Santo Domingo de los Tsáchilas, Santo Domingo, Ecuador

[4 ]Enfermería, Hospital General Santo Domingo de los Tsáchilas, Santo Domingo, Ecuador

[5 ]GRID grid.472632.6, ISNI 0000 0004 4652 2912, Escuela de Ciencias Biológicas e Ingeniería, , Universidad Yachay Tech, ; Hacienda San José s/n, San Miguel de Urcuquí, Ibarra, Ecuador

[6 ]GRID grid.442156.0, ISNI 0000 0000 9557 7590, Facultad de Ciencias Médicas Enrique Ortega Moreira, , Universidad Espíritu Santo, ; Samborondón, Ecuador

Article

Publisher ID: 6272

DOI: 10.1186/s12879-021-06272-8

PMC ID: 8195713

PubMed ID: 34118895

SO-VID: a50ff8a0-db1a-4158-9e57-7e90f5443909

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.