Author(s):
Lesbon, Jéssika Cristina Chagas ; Poleti, Mirele Daiana ; de Mattos Oliveira, Elisângela Chicaroni ; Patané, José Salvatore Leister ; Clemente, Luan Gaspar ; Viala, Vincent Louis ; Ribeiro, Gabriela ; Giovanetti, Marta ; de Alcantara, Luiz Carlos Junior ; de Lima, Loyze Paola Oliveira ; Martins, Antonio Jorge ; Barros, Claudia Renata Dos Santos ; Marqueze, Elaine Cristina ; Bernardino, Jardelina de Souza Todão ; Moretti, Debora Botequio ; Brassaloti, Ricardo Augusto ; Cassano, Raquel de Lello Rocha Campos ; Mariani, Pilar Drummond Sampaio Correa ; Slavov, Svetoslav Nanev ; Dos Santos, Rafael Bezerra ; Rodrigues, Evandra Strazza ; Santos, Elaine Vieira ; Borges, Josiane Serrano ; de La Roque, Debora Glenda Lima ; Kitajima, Joao Paulo ; Santos, Bibiana ; Assato, Patricia Akemi [UNESP] ; da Costa, Felipe Allan da Silva [UNESP] ; Banho, Cecilia Artico ; Sacchetto, Livia ; Moraes, Marilia Mazzi ; Palmieri, Melissa ; da Silva, Fabiana Erica Vilanova ; Grotto, Rejane Maria Tommasini [UNESP] ; Souza-Neto, Jayme A. [UNESP] ; Nogueira, Mauricio Lacerda ; Coutinho, Luiz Lehman ; Calado, Rodrigo Tocantins ; Neto, Raul Machado ; Covas, Dimas Tadeu ; Kashima, Simone ; Elias, Maria Carolina ; Sampaio, Sandra Coccuzzo ; Fukumasu, Heidge
Date: 2022
Persistent ID: http://hdl.handle.net/11449/231570
Origin: Oasisbr
Subject(s): COVID-19; GeneFinder; Mutation; N gene; RT-PCR
Description
Made available in DSpace on 2022-04-29T08:46:11Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-12-01
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.
Laboratory of Comparative and Translational Oncology Department of Veterinary Medicine School of Animal Science and Food Engineering University of Sao Paulo
Butantan Institute São Paulo
Functional Genomic Center Department of Animal Science Luiz de Queiroz School of Agriculture University of Sao Paulo
Fundação Oswaldo Cruz FIOCRUZ
Institute of Biological Sciences Federal University of Minas Gerais, Minas Gerais
NGS Soluções Genômicas
Blood Center of Ribeirão Preto Ribeirão Preto Medical School University of São Paulo
Mendelics Genomic Analysis São Paulo
School of Agricultural Sciences São Paulo State University
Laboratório de Pesquisas em Virologia Departamento de Doenças Dermatológicas Infecciosas e Parasitárias Faculdade de Medicina de São José do Rio Preto
Coordenação de Vigilância em Saúde–Secretaria Municipal da Saúde São Paulo
Laboratory Assistance Coordination of Primary Care Municipal Health Department São Paulo
School of Agricultural Sciences São Paulo State University
CAPES: 001
FAPESP: 2013/08135-2
FAPESP: 2020/05367-3
FAPESP: 2020/10127-1
CNPq: 401119/2020-3
