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Optimizing SARS-CoV-2 Molecular Diagnostic Using N Gene Target

25 Pages Posted: 3 Dec 2020

See all articles by Raphael Contelli Klein

Raphael Contelli Klein

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores

Mary Hellen Fabres-Klein

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores

Larissa Gomes Barbosa

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores

Lívia Vasconcelos Gonzaga Knnup

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores

Larissa Paola Rodrigues Venâncio

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores

Jonilson Berlink Lima

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores

Théo Araújo-Santos

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores

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Abstract

Background: Molecular diagnosis of SARS-CoV-2 is a huge challenge to many countries around the world. The cost of tests to check infected people is inaccessible since specialized teams and equipment are not disposable in remote locations. Herein, we compared the fitness of two primers sets to the SARS-CoV-2 N gene in the molecular diagnosis of COVID-19.

Methods: The 1029 patient samples were tested to presense/abscence molecular test using in house US CDC protocol. We compared the fitness of two primers sets to two different regions of N gene targets.

Findings: Both targets, N1 and N2 displayed similar fitness during testing with no differences between Ct or measurable viral genome copies.  In addition, we verified security ranges Cts related to positive diagnostic with Ct above 35 value failuring in 66,6% after retesting of samples.

Interpretation: Our data suggest that it is secure to use just one primer set to the N gene to identify SARS-CoV-2 in samples and the labs should be careful to set positive samples in high Ct values using high cutoffs.

Funding: Associação Baiana de Produtores de Algodão (ABAPA); Associação Baiana de Agricultores Irrigantes da Bahia (AIBA); Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB) (Grant Number: #1381/2020); FINEP (Grant Number: # 0418000600); CNPq; CAPES, MEC, MCTIC.

Declaration of Interests: None to declare.

Ethics Approval Statement: The Research Ethics Committee of UFOB approved this study in 2020 (license number: 30629520.6.0000.0008). All clinical investigations were conducted according to the Declaration of Helsinki.

Keywords: Diagnostic, SARS-CoV-2, COVID-19, N gene, Reinfection

Suggested Citation

Klein, Raphael Contelli and Fabres-Klein, Mary Hellen and Barbosa, Larissa Gomes and Knnup, Lívia Vasconcelos Gonzaga and Venâncio, Larissa Paola Rodrigues and Lima, Jonilson Berlink and Araújo-Santos, Théo, Optimizing SARS-CoV-2 Molecular Diagnostic Using N Gene Target. THELANCETID-D-20-06152, Available at SSRN: https://ssrn.com/abstract=3727304 or http://dx.doi.org/10.2139/ssrn.3727304

Raphael Contelli Klein

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores ( email )

892, Morada Nobre II
Bahia, 47810-059
Brazil

Mary Hellen Fabres-Klein

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores ( email )

Larissa Gomes Barbosa

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores ( email )

Lívia Vasconcelos Gonzaga Knnup

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores ( email )

Larissa Paola Rodrigues Venâncio

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores ( email )

Jonilson Berlink Lima

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores ( email )

892, Morada Nobre II
Bahia, 47810-059
Brazil

Théo Araújo-Santos (Contact Author)

Federal University of Western Bahia (UFOB) - Universidade Federal do Oeste da Bahia (UFOB) - Laboratory of Infectious Agents and Vectors - Laboratório de Agentes Infecciosos e Vetores ( email )

892, Morada Nobre II
Bahia, 47810-059
Brazil