Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City.

Autor: Cedro-Tanda A; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Gómez-Romero L; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., de Anda-Jauregui G; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico.; Researchers for Mexico (Previously Cátedras CONACYT para Jóvenes Investigadores), Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Mexico City 03940, Mexico.; Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Circuito Centro Cultural S/N, Cd. Universitaria, Delegación Coyoacán, Mexico City 04510, Mexico., Garnica-López D; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Alfaro-Mora Y; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Sánchez-Xochipa S; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., García-García EF; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Mendoza-Vargas A; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Frías-Jiménez EJ; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Moreno B; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Campos-Romero A; Innovation and Research Department, Salud Digna, Culiacan 80000, Mexico., Moreno-Camacho JL; Clinical Laboratory Division, Salud Digna, Culiacan 80000, Mexico., Alcantar-Fernández J; Innovation and Research Department, Salud Digna, Culiacan 80000, Mexico., Ortíz-Ramírez J; Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico., Benitez-González M; Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico., Trejo-González R; Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico., Aguirre-Chavarría D; Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico., Núñez-Martínez ME; Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico., Uribe-Figueroa L; Laboratorio Arion Genética, Margaritas 440-Bis, Hacienda de Guadalupe Chimalistac, Chimalistac, Álvaro Obregón, Mexico City 01050, Mexico., Angulo O; Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico., Ruiz R; Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico., Hidalgo-Miranda A; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico., Herrera LA; Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico.; Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico.
Jazyk: angličtina
Zdroj: Viruses [Viruses] 2022 Mar 06; Vol. 14 (3). Date of Electronic Publication: 2022 Mar 06.
DOI: 10.3390/v14030545
Abstrakt: Omicron is the most mutated SARS-CoV-2 variant-a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found 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. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance 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, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy.
Databáze: MEDLINE
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