SARS-CoV-2 and the COVID-19 disease: a mini review on diagnostic methods

Oliveira, Beatriz Araujo; Oliveira, Lea Campos de; Sabino, Ester Cerdeira; Okay, Thelma Suely

doi:10.1590/S1678-9946202062044

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REVIEW • Rev. Inst. Med. trop. S. Paulo 62 • 2020 • https://doi.org/10.1590/S1678-9946202062044 copy

SARS-CoV-2 and the COVID-19 disease: a mini review on diagnostic methods

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

Coronavirus disease 2019 (COVID-19) is an infectious disease initially reported in China and currently worldwide dispersed caused by a new coronavirus (SARS-CoV-2 or 2019-nCoV) affecting more than seven million people around the world causing more than 400 thousand deaths (on June 8^th, 2020). The diagnosis of COVID-19 is based on the clinical and epidemiological history of the patient. However, the gold standard for COVID-19 diagnosis is the viral detection through the amplification of nucleic acids. Although the quantitative Reverse-Transcription Polymerase Chain Reaction (RT-PCR) has been described as the gold standard for diagnosing COVID-19, there are several difficulties involving its use. Here we comment on RT-PCR and describe alternative tests developed for the diagnosis of COVID-19.

COVID-19; SARS-CoV-2; 2019-nCoV; RT-PCR; Serological methods; Immunochromatography

Institution/ country	Primer ID	Method	Findings
China’s CDC – China^29,56	ORF1ab, E and N	Three singleplex RT-PCR using fluorescent-labeled probes	Lowest detection limit of ORF1ab was 203 copies/mL Lowest detection limit of E gene was 664 copies/mL Lowest detection limit of N gene was 667 copies/mL
Institut Pasteur – France²⁹	RdRp gene/nCoV_IP2 RdRp gene/nCoV_IP4	Two singleplex RT-PCR or one multiplex RT-PCR with fluorescent-labeled probes	95% assertiveness in samples containing ~ 100 viral copies The multiplex RT-PCR detects 10 viral copies No cross-reactivity with other viruses
CDC – USA^29,57	2019-nCoV_N1 2019-nCoV_N2 2019-nCoV_N3	Three singleplex RT-PCR using fluorescent-labeled probes	95% assertiveness in samples containing 10^0,5 RNA copies/µL using automatic RNA extraction and 10⁰ RNA copies/µL using manual RNA extraction
Charité – Germany^29,58	RdRP_SARSr E_Sarbeco	Two singleplex RT-PCR, the screening made by the E gene amplification confirmed by RdRP	Lowest detection limit of RdRp and E_Sarbeco 3.8 and 5.2 copies/reaction, respectively
HKU - Hong Kong^29,59	ORF1b-nsp14 N	Two RT-PCR, firstly the N gene amplification with fluorescent-labed probe followed by confirmation by amplifying the ORF1b-nsp14 with fluorescent-labeled probe	N gene Ct values up to 35.43 were positive corresponding to 15 copies/reaction ORF1b Ct values up to 38.97 were positive corresponding to 1.5 copies/reaction
National Institute of Health – Thailand^29,59	N	Singleplex RT-PCR with fluorescent-labeled probe	N gene Ct values were positive up to 38.12, corresponding to 15 copies/reaction

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[1] Correspondence to: Beatriz Araujo Oliveira Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM 46), Av. Dr. Enéas Carvalho de Aguiar, 470, CEP 05403-000, São Paulo, SP, Brazil Tel: +55 11 30617011E-mail:Beatriz_oliveira@usp.br