SARS-CoV-2 diagnostic diary: from rumors to the first case. Early reports of molecular tests from the military research and diagnostic institute of Rio de Janeiro

Corona virus disease (COVID-19) presents a serious threat to global health. A historical timeline of early molecular diagnostics from government alert (January 22) (D) was presented. After in silico analysis, Brazilian Army Institute of Biology (IBEx-RJ) tested samples in house using real-time reverse transcriptase polymerase chain reaction (RT-PCR) (fast mode) based on Centers for Disease Control and Prevention (CDC) recommendations. First cases from Brazil, Rio de Janeiro, IBEx, and diagnosis team were reported in D36, D44, D66, and D74 respectively. Therefore, after 1300 tests, we recommend N1/N2 primer sets (CDC) for preliminary and Charité protocol confirmation in case of positive results. Moreover, every professional should be tested before starting work, in addition to weekly tests for everyone involved.

key words:
coronavirus; SARS-CoV-2; RT-PCR; global pandemic; COVID-19

Authorship

Marcio da Costa Cipitelli

Instituto de Biologia do Exército, Laboratório de Biologia Molecular, Rio de Janeiro, RJ, BrasilInstituto de Biologia do ExércitoBrazilRio de Janeiro, RJ, BrazilInstituto de Biologia do Exército, Laboratório de Biologia Molecular, Rio de Janeiro, RJ, Brasil

Elizabeth Valentin

Instituto de Biologia do Exército, Laboratório de Biodefesa, Rio de Janeiro, RJ, BrasilInstituto de Biologia do ExércitoBrazilRio de Janeiro, RJ, BrazilInstituto de Biologia do Exército, Laboratório de Biodefesa, Rio de Janeiro, RJ, Brasil

Nadia Vaez Gonçalves da Cruz

Tatiana LS Nogueira

Instituto de Biologia do Exército, Laboratório de Genética, Rio de Janeiro, RJ, BrasilInstituto de Biologia do ExércitoBrazilRio de Janeiro, RJ, BrazilInstituto de Biologia do Exército, Laboratório de Genética, Rio de Janeiro, RJ, Brasil

Elaine Cristina Amaro de Melo

Rebeca Araujo da Silva

Marcelo M Serra

André L Meriano

Alberto ML Colares

Marcos Dornelas-Ribeiro

Caleb GM Santos ⁺+ Corresponding author: calebguedes@gmail.com

https://orcid.org/0000-0002-2700-0049

+ Corresponding author: calebguedes@gmail.com

MD-R and CGMS contributed equally to this work.

MD-R and CGMS - Conceptualisation; MCC , NVGC, TLSN, EV, EA and CGMS - formal analysis; MD-R, CGMS, MMS, ALM and AMLC - funding acquisition; RS, EA, EV and CGMS - investigation; CGMS - methodology; MCC , NVGC, TLSN, EV, MD-R, MMS, ALM and AMLC - project administration; MMS, ALM, AMLC, EA and MD-R - resources; RS and CGMS - software; NVGC, TLSN and MD-R - supervision; MCC and CGMS - writing-original draft; MCC and CGMS -writing-review and editing. The authors declare no conflicts of interest, financial or otherwise.

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables

Figures (4)
Tables (2)

Thumbnail

Fig. 1:
preliminary phylogenetic tree of simple reference genomes from important coronavirus subtypes. Highlighted, the sequence name referring to SARS-Cov-2 in January 22.

Thumbnail

Fig. 2:
21VIR panel pathogens detectable in our laboratory.

Thumbnail

Fig. 3:
(A) diagnosed cases of 129 tests of 21VIR related to SARS-CoV-2 results. (B) Proportion of respiratory virus detected and codetected in our investigation. RV: rhinovirus: EV: enterovirus; FLUA: influenza A; H1N1: influenza A (swine); HadV: adenovirus; Cor229: coronavirus subtype 229; HKU: coronavirus subtype HKU1; HMPV A/B: metapneumovirus subtypes A or B; HPIV2: parainfluenza 2; Mpneu: Micoplasma pneumoniae (bacteria)*; HpeV: parecovirus; SARS-CoV2: coronavirus COVID-19.

Thumbnail

Fig. 4:
(A) timeline of new cases diagnosed and negative results by our Institute. (B) Timeline of new cases diagnosed and deaths obtained from Brazilian Health Ministery.

Thumbnail

TABLE I
Primers suggested by Centers for Disease Control and Prevention (CDC) previously

Thumbnail

TABLE II
Cycle conditions for SARS-Cov-2 real-time reverse transcriptase polymerase chain reaction (RT-PCR) detection based in Centers for Disease Control and Prevention (CDC) primers

Fig. 1: preliminary phylogenetic tree of simple reference genomes from important coronavirus subtypes. Highlighted, the sequence name referring to SARS-Cov-2 in January 22.

Fig. 2: 21VIR panel pathogens detectable in our laboratory.

Fig. 3: (A) diagnosed cases of 129 tests of 21VIR related to SARS-CoV-2 results. (B) Proportion of respiratory virus detected and codetected in our investigation. RV: rhinovirus: EV: enterovirus; FLUA: influenza A; H1N1: influenza A (swine); HadV: adenovirus; Cor229: coronavirus subtype 229; HKU: coronavirus subtype HKU1; HMPV A/B: metapneumovirus subtypes A or B; HPIV2: parainfluenza 2; Mpneu: Micoplasma pneumoniae (bacteria)*; HpeV: parecovirus; SARS-CoV2: coronavirus COVID-19.

Fig. 4: (A) timeline of new cases diagnosed and negative results by our Institute. (B) Timeline of new cases diagnosed and deaths obtained from Brazilian Health Ministery.

TABLE I Primers suggested by Centers for Disease Control and Prevention (CDC) previously

Name	Sequence	Conc
2019-nCoV_N1 Forward Primer	5’-GAC CCC AAA ATC AGC GAA AT-3’	20 μM
2019-nCoV_N1 Reverse Primer	5’-TCT GGT TAC TGC CAG TTG AAT CTG-3’	20 μM
2019-nCoV_N1 Probe	5’-FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1-3’	5 μM
2019-nCoV_N2 Forward Primer	5’-TTA CAA ACA TTG GCC GCA AA-3’	20 μM
2019-nCoV_N2 Reverse Primer	5’-GCG CGA CAT TCC GAA GAA-3’	20 μM
2019-nCoV_N2 Probe	5’-FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1-3’	5 μM
2019-nCoV_N3 Forward Primer	5’-GGG AGC CTT GAA TAC ACC AAA A-3’	20 μM
2019-nCoV_N3 Reverse Primer	5’-TGT AGC ACG ATT GCA GCA TTG-3’	20 μM
2019-nCoV_N3 Probe	5’-FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1-3’	5 μM

TABLE II Cycle conditions for SARS-Cov-2 real-time reverse transcriptase polymerase chain reaction (RT-PCR) detection based in Centers for Disease Control and Prevention (CDC) primers

Steps	Cycles	Temperature	Time
Reverse transcription	1	45ºC	5 min
Reverse transcriptase inactivation and DNA Polymerase activation	1	95ºC	2 min
Denaturation	40	95ºC	3 sec
Annealing and extension	40	60ºC	30 sec

How to cite

copy

Instituto Oswaldo Cruz, Ministério da Saúde Av. Brasil, 4365 - Pavilhão Mourisco, Manguinhos, 21040-900 Rio de Janeiro RJ Brazil, Tel.: (55 21) 2562-1222, Fax: (55 21) 2562 1220 - Rio de Janeiro - RJ - Brazil
E-mail: memorias@fiocruz.br

Acompanhe os números deste periódico no seu leitor de RSS

Versão para download de PDF

PDF

Inglês

Versões e tradução automática

Versão original do texto

English

Tradução automática

Google Translator
Microsoft Translator

Como citar

RIS

BIBTEX

Outros formatos de citação e exportação:

SciELO - Scientific Electronic Library Online
Rua Dr. Diogo de Faria, 1087 – 9º andar – Vila Clementino 04037-003 São Paulo/SP - Brasil
E-mail: scielo@scielo.org

Leia a Declaração de Acesso Aberto

Métricas

SARS-CoV-2 diagnostic diary: from rumors to the first case. Early reports of molecular tests from the military research and diagnostic institute of Rio de Janeiro

PlumX

Mensagem

[1] + Corresponding author: calebguedes@gmail.com