Enhanced rapid commercial DNA extraction kit for the molecular detection of severe acute respiratory syndrome coronavirus 2: Easy adaptation to current protocols

Pessoa-e-Silva, Rômulo; Oliveira, Priscilla Stela Santana de; Gonçalves, Sayonara Maria Calado; Guarines, Klarissa Miranda; Carvalho, Lidiane Vasconcelos do Nascimento; Correia, Maria Andreza Bezerra; Rosa, Michelle Melgarejo da; Rêgo, Moacyr Jesus Barreto de Melo; Pitta, Maira Galdino da Rocha; Pereira, Michelly Cristiny

doi:10.1590/0037-8682-0270-2021

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Revista da Sociedade Brasileira de Medicina Tropical

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Short Communication • Rev. Soc. Bras. Med. Trop. 54 • 2021 • https://doi.org/10.1590/0037-8682-0270-2021 copy

Enhanced rapid commercial DNA extraction kit for the molecular detection of severe acute respiratory syndrome coronavirus 2: Easy adaptation to current protocols

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

INTRODUCTION

Herein, the authors describe a simple enhancement to a commercial rapid DNA extraction kit based on simple viral lysis for detecting COVID-19 via RT-qPCR.

METHODS

After testing several different modifications, the adapted protocol with the best results in preliminary experiments was statistically evaluated in comparison with an automated robotic protocol.

RESULTS

Processing and testing of 119 nasopharyngeal samples ultimately yielded near-perfect agreement with the automated protocol (κ = 0.981 [95% confidence interval 0.943-1.000]).

CONCLUSIONS

The low cost and rapidity of the enhanced protocol makes it suitable for adoption in laboratories diagnosing COVID-19, especially those with high demand for examinations.

Keywords:
COVID-19; SARS-CoV-2; Rapid extraction protocol; RT-qPCR

Sample	Automated RNA			Rapid extraction -			Rapid extraction (dilution of the
(nº)	extraction			manufacturer’s			extracted sample: 160 µL of
	procedure			protocol			RNase free water)
	N1	N2	RP	N1	N2	RP	N1	N2	RP
1	17.91	18.22	25.11	21.95	25.77	31.59	22.02	25.65	29.25
2	16.67	16.46	24.52	20.26	23.40	30.46	22.50	25.38	32.94
3	25.53	27.26	24.04	30.93	35.36	28.36	32.42	36.27	31.26
4 (late Ct)	32.37	34.36	25.58	(-)	(-)	31.82	(-)	(-)	32.95
5	19.68	19.95	25.11	24.32	28.04	30.18	26.47	29.83	32.75
6	20.22	20.76	27.28	24.22	23.67	31.14	26.91	26.50	34.2
7 (late Ct)	36.77	34.42	26.85	(-)	(-)	32.00	(-)	(-)	35.95
8 (late Ct)	35.63	39.82	25.33	(-)	(-)	28.57	(-)	(-)	32.01
Mean Ct value	25.59	26.40	25.47	24.33	27.24	30.51	26.06	28.72	32.66

		Automated extraction procedure (Robotic extraction)
		Positive	Negative	Total
Adapted rapid DNA extraction protocol (20/80)	Positive	41	0	41
Adapted rapid DNA extraction protocol (20/80)	Negative	1	67	68
Total		42	67	109
Kappa		0.981 (very good)
SE		0.019
CI (95%)		0.943 - 1.000

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[1] Corresponding author: Michelly Cristiny Pereira. e-mail:michelly.pereira@ufpe.br