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http://conacyt.repositorioinstitucional.mx/jspui/handle/1000/7851| Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City | |
| Alberto Cedro-Tanda Laura Gómez-Romero Guillermo de Anda Jáuregui DORA GARNICA LÓPEZ YAIR ALFARO MORA SONIA SÁNCHEZ XOCHIPA FREDERIK EULICES GARCIA GARCIA ALFREDO MENDOZA VARGAS JESUS EMMANUEL FRIAS JIMENEZ BERNARDO MORENO QUIROGA ABRAHAM CAMPOS ROMERO Jonathan Alcántar Fernández JOSÉ LUIS MORENO CAMACHO JESUS ORTIZ RAMIREZ MARIANA BENITEZ GONZALEZ Roxana Trejo Gonzalez DANIEL AGUIRRE CHAVARRIA MARCELA NÚÑEZ MARTÍNEZ LAURA URIBE FIGUEROA JESUS OFELIA ANGULO GUERRERO ROSAURA RUIZ GUTIERREZ ALFREDO HIDALGO MIRANDA LUIS ALONSO HERRERA MONTALVO | |
| Acceso Abierto | |
| Atribución-NoComercial-SinDerivadas | |
| https://doi.org/10.1101/2022.02.06.22270482 | |
| Background Omicron is the most mutated SARS-CoV-2 variant that has emerged, resulting in viral phenotype alterations, which can affect transmissibility, disease severity, and immune evasiveness. Genomic surveillance of a highly transmissible variant is important in cities with millions of inhabitants and an economic center such as Mexico City. In this work, we describe the early effects of the Omicron variant in Mexico City, exploring its genomic profile and clinical description. Methodology We sequenced SARS-CoV-2-positive samples in November and December 2021 and we using the public database GISAID. Haplotype and phylogenetic analyses were performed to genomically characterize Omicron. We used the Mexican federal database toexplore the association with clinical information such as symptoms and vaccination status. Findings The first case of Omicron was detected on November 16, 2022, and until December 31, 2021, we observed an increase from 88% in sequenced samples. Nineteen nonsynonymous mutations were found in the Omicron RBD, and we further explored the R346K substitution, which was prevalent in 42% of the samples and associated with immune escape by monoclonal antibodies. In the phylogenetic analysis, we found that there were several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. The haplotype analysis allowed us to observe that there was no association between haplotype and vaccination status. Of the patients with clinical data, 66% were vaccinated, none of the reported comorbidities were associated with Omicron, the presence of odynophagia and absence of dysgeusia were significant predictor symptoms for Omicron, and the Ct value on RT–qPCR was lower in Omicron. Conclusions Genomic surveillance in highly populated and fast-moving urban regions such as Mexico City is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, to detect patterns that can inform public health decisions. It is also necessary to continue sequencing to detect the spread of any mutation that may affect the therapeutic efficacy or guide it. | |
| Medrxiv | |
| 07-02-2022 | |
| Preimpreso | |
| medrxiv.org/ | |
| Inglés | |
| VIRUS RESPIRATORIOS | |
| Aparece en las colecciones: | Artículos científicos |
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