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Covid-19 diagnosis by combining RT-PCR and pseudo-convolutional machines to characterize virus sequences.
Gomes, Juliana Carneiro; Masood, Aras Ismael; Silva, Leandro Honorato de S; da Cruz Ferreira, Janderson Romário B; Freire Júnior, Agostinho Antônio; Rocha, Allana Laís Dos Santos; de Oliveira, Letícia Castro Portela; da Silva, Nathália Regina Cauás; Fernandes, Bruno José Torres; Dos Santos, Wellington Pinheiro.
  • Gomes JC; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
  • Masood AI; Information Technology Department, Technical College of Informatics, Sulaimani Polytechnic University, Sulaymaniyah, Iraq.
  • Silva LHS; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
  • da Cruz Ferreira JRB; Instituto Federal de Educação, Ciência e Tecnologia da Paraíba, Campus Cajazeiras, IFPB, Cajazeiras, Brazil.
  • Freire Júnior AA; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
  • Rocha ALDS; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
  • de Oliveira LCP; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
  • da Silva NRC; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
  • Fernandes BJT; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
  • Dos Santos WP; Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
Sci Rep ; 11(1): 11545, 2021 06 02.
Article in English | MEDLINE | ID: covidwho-1253983
ABSTRACT
The Covid-19 pandemic, a disease transmitted by the SARS-CoV-2 virus, has already caused the infection of more than 120 million people, of which 70 million have been recovered, while 3 million people have died. The high speed of infection has led to the rapid depletion of public health resources in most countries. RT-PCR is Covid-19's reference diagnostic method. In this work we propose a new technique for representing DNA sequences they are divided into smaller sequences with overlap in a pseudo-convolutional approach and represented by co-occurrence matrices. This technique eliminates multiple sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database 347,363 virus DNA sequences from 24 virus families and SARS-CoV-2. When comparing SARS-CoV-2 with virus families with similar symptoms, we obtained [Formula see text] for sensitivity and [Formula see text] for specificity with MLP classifier and 30% overlap. When SARS-CoV-2 is compared to other coronaviruses and healthy human DNA sequences, we obtained [Formula see text] for sensitivity and [Formula see text] for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify DNA sequences for SARS-CoV-2 with greater specificity and sensitivity.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Computational Biology / Reverse Transcriptase Polymerase Chain Reaction / COVID-19 Nucleic Acid Testing / SARS-CoV-2 Type of study: Diagnostic study Limits: Humans Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-90766-7

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Computational Biology / Reverse Transcriptase Polymerase Chain Reaction / COVID-19 Nucleic Acid Testing / SARS-CoV-2 Type of study: Diagnostic study Limits: Humans Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-90766-7