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Cedro-Tanda A, Gómez-Romero L, de Anda-Jauregui G, Garnica-López D, Alfaro-Mora Y, Sánchez-Xochipa S, García-García EF, Mendoza-Vargas A, Frías-Jiménez EJ, Moreno B, Campos-Romero A, Moreno-Camacho JL, Alcantar-Fernández J, Ortíz-Ramírez J, Benitez-González M, Trejo-González R, Aguirre-Chavarría D, Núñez-Martínez ME, Uribe-Figueroa L, Angulo O, Ruiz R, Hidalgo-Miranda A, Herrera LA. Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Viruses 2022; 14:545. [PMID: 35336952 PMCID: PMC8950183 DOI: 10.3390/v14030545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
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.
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Affiliation(s)
- Alberto Cedro-Tanda
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Guillermo de Anda-Jauregui
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
- 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
| | - Dora Garnica-López
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Yair Alfaro-Mora
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Sonia Sánchez-Xochipa
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Eulices F. García-García
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Alfredo Mendoza-Vargas
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Emmanuel J. Frías-Jiménez
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Bernardo Moreno
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, Culiacan 80000, Mexico; (A.C.-R.); (J.A.-F.)
| | | | | | - Jesús Ortíz-Ramírez
- Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico; (J.O.-R.); (M.B.-G.)
| | - Mariana Benitez-González
- Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico; (J.O.-R.); (M.B.-G.)
| | - Roxana Trejo-González
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Daniel Aguirre-Chavarría
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Marcela E. Núñez-Martínez
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Laura Uribe-Figueroa
- Laboratorio Arion Genética, Margaritas 440-Bis, Hacienda de Guadalupe Chimalistac, Chimalistac, Álvaro Obregón, Mexico City 01050, Mexico;
| | - Ofelia Angulo
- Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Rosaura Ruiz
- Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Luis A. Herrera
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
- 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
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