End-point RT-PCR based on a conservation landscape for SARS-COV-2 detection
Por:
Cruz-Rangel, Armando, Gomez-Romero, Laura, Cisneros-Villanueva, Mireya, de Anda Jauregui, G., Luna-Pineda, Victor, Cedro-Tanda, Alberto, Campos-Romero, Abraham, Mendoza-Vargas, Alfredo, Reyes-Grajeda, J. P., Hidalgo-Miranda, Alfredo, Herrera, Luis A., Vadillo-Ortega, Felipe
Publicada:
19 mar 2022
Categoría:
Multidisciplinary
Resumen:
End-point RT-PCR is a suitable alternative diagnostic technique since it
is cheaper than RT-qPCR tests and can be implemented on a massive scale
in low- and middle-income countries. In this work, a bioinformatic
approach to guide the design of PCR primers was developed, and an
alternative diagnostic test based on end-point PCR was designed.
End-point PCR primers were designed through conservation analysis based
on kmer frequency in SARS-CoV-2 and human respiratory pathogen genomes.
Highly conserved regions were identified for primer design, and the
resulting PCR primers were used to amplify 871 nasopharyngeal human
samples with a previous RT-qPCR based SARS-CoV-2 diagnosis. The
diagnostic test showed high accuracy in identifying SARS-CoV-2-positive
samples including B.1.1.7, P.1, B.1.427/B.1.429 and B.1.617.2/ AY
samples with a detection limit of 7.2 viral copies/mu L. In addition,
this test could discern SARS-CoV-2 infection from other viral infections
with COVID-19-like symptomatology. The designed end-point PCR diagnostic
test to detect SARS-CoV-2 is a suitable alternative to RT-qPCR. Since
the proposed bioinformatic approach can be easily applied in thousands
of viral genomes and over highly divergent strains, it can be used as a
PCR design tool as new SARS-CoV-2 variants emerge. Therefore, this
end-point PCR test could be employed in epidemiological surveillance to
detect new SARS-CoV-2 variants as they emerge and propagate.
Filiaciones:
Cruz-Rangel, Armando:
Biochemistry of Chronic Diseases Laboratory, National Institute of Genomic MedicineMexico City, Mexico
Gomez-Romero, Laura:
Computational Genomics Department, National Institute of Genomic MedicineMexico City, Mexico
Cisneros-Villanueva, Mireya:
Cancer Genomics Laboratory, National Institute of Genomic MedicineMexico City, Mexico
de Anda Jauregui, G.:
Computational Genomics Department, National Institute of Genomic MedicineMexico City, Mexico
Cátedras CONACYT Program for Young Researchers, National Council for Science and Technology, CONACYTMéxico City, Mexico
Center for Complexity Sciences (C3), National Autonomous University of MexicoMexico City, Mexico
Luna-Pineda, Victor:
Research Unit in Immunology and Proteomics, COVID-19 Research Laboratory, Children's Hospital of Mexico "Federico Gómez"Mexico City, Mexico
Cedro-Tanda, Alberto:
National Institute of Genomic Medicine, Periférico Sur 4809, Tlalpan, Mexico City 14610, Mexico
Campos-Romero, Abraham:
Innovation and Research Department, Culiacan, Sinaloa, Mexico
Mendoza-Vargas, Alfredo:
Sequencing Unit, National Institute of Genomic MedicineMexico City, Mexico
Reyes-Grajeda, J. P.:
Biochemistry of Chronic Diseases Laboratory, National Institute of Genomic MedicineMexico City, Mexico
Hidalgo-Miranda, Alfredo:
Cancer Genomics Laboratory, National Institute of Genomic MedicineMexico City, Mexico
Herrera, Luis A.:
National Institute of Genomic Medicine, Periférico Sur 4809, Tlalpan, Mexico City 14610, Mexico
Biomedical Research Unit in Cancer, National Institute of CancerologyMexico City, Mexico
Institute of Biomedical Research, National Autonomous University of MexicoMexico City, Mexico
Vadillo-Ortega, Felipe:
Unidad de Vinculación de la Facultad de Medicina, Periférico Sur 4809, Tlalpan, Mexico City 14610, Mexico
gold, Green Published, Gold, Green
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