| Autor: |
Muñoz-Valle JF; Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico., Venancio-Landeros AA; Translational Institute of Genomic Singularity (ITRASIG), Irapuato 36615, Mexico., Sánchez-Sánchez R; Molecular Design Department, Genes2Life (Grupo T), Irapuato 36615, Mexico., Reyes-Díaz K; Research and Development Department, Genes2Life (Grupo T), Irapuato 36615, Mexico., Galindo-Ornelas B; Research and Development Department, Genes2Life (Grupo T), Irapuato 36615, Mexico., Hérnandez-Monjaraz WS; Research and Development Department, Genes2Life (Grupo T), Irapuato 36615, Mexico., García-Ríos A; Research and Development Department, Genes2Life (Grupo T), Irapuato 36615, Mexico., García-Ortega LF; Department of Genetic Engineering, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), Irapuato 36824, Mexico., Hernández-Bello J; Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico., Peña-Rodríguez M; Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico., Vega-Magaña N; Institute for Research in Biomedical Sciences (IICB), University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico.; Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico., Delaye L; Department of Genetic Engineering, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), Irapuato 36824, Mexico., Díaz-Sánchez M; Research and Development Department, Genes2Life (Grupo T), Irapuato 36615, Mexico., García-González OP; Translational Institute of Genomic Singularity (ITRASIG), Irapuato 36615, Mexico. |
| Abstrakt: |
SARS-CoV-2 variants surveillance is a worldwide task that has been approached with techniques such as Next Generation Sequencing (NGS); however, this technology is not widely available in developing countries because of the lack of equipment and limited funding in science. An option is to deploy a RT-qPCR screening test which aids in the analysis of a higher number of samples, in a shorter time and at a lower cost. In this study, variants present in samples positive for SARS-CoV-2 were identified with a RT-qPCR mutation screening kit and were later confirmed by NGS. A sample with an abnormal result was found with the screening test, suggesting the simultaneous presence of two viral populations with different mutations. The DRAGEN Lineage analysis identified the Delta variant, but there was no information about the other three mutations previously detected. When the sequenced data was deeply analyzed, there were reads with differential mutation patterns, that could be identified and classified in terms of relative abundance, whereas only the dominant population was reported by DRAGEN software. Since most of the software developed to analyze SARS-CoV-2 sequences was aimed at obtaining the consensus sequence quickly, the information about viral populations within a sample is scarce. Here, we present a faster and deeper SARS-CoV-2 surveillance method, from RT-qPCR screening to NGS analysis. |
