Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico
Por:
Taboada, Blanca, Vazquez-Perez, Joel Armando, Munoz-Medina, Jose Esteban, Ramos-Cervantes, Pilar, Escalera-Zamudio, Marina, Boukadida, Celia, Sanchez-Flores, Alejandro, ISA, PAVEL, Mendieta-Condado, Edgar, Martinez-Orozco, Jose A., Becerril-Vargas, Eduardo, Salas-Hernandez, Jorge, Grande, Ricardo, Gonzalez-Torres, Carolina, Gaytan-Cervantes, Francisco Javier, Vazquez, Gloria, Pulido, Francisco, Araiza-Rodriguez, Adnan, Garces-Ayala, Fabiola, Gonzalez-Bonilla, Cesar Raul, Grajales-Muniz, Concepcion, Borja-Aburto, Victor Hugo, Barrera-Badillo, Gisela, LOPEZ, SUSANA, Hernandez-Rivas, Lucia, Perez-Padilla, Rogelio, Lopez-Martinez, Irma, avila-Rios, Santiago, Ruiz-Palacios, Guillermo, Ramirez-Gonzalez, Jose Ernesto, Arias, Carlos F.
Publicada:
1 sep 2020
Resumen:
The coronavirus disease 2019 (COVID-19) pandemic has affected most
countries in the world. Studying the evolution and transmission patterns
in different countries is crucial to enabling implementation of
effective strategies for disease control and prevention. In this work,
we present the full genome sequence for 17 SARS-CoV-2 isolates
corresponding to the earliest sampled cases in Mexico. Global and local
phylogenomics, coupled with mutational analysis, consistently revealed
that these viral sequences are distributed within 2 known lineages,
severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage
A/G, containing mostly sequences from North America, and lineage B/S,
containing mainly sequences from Europe. Based on the exposure history
of the cases and on the phylogenomic analysis, we characterized 14
independent introduction events. Additionally, three cases with no
travel history were identified. We found evidence that two of these
cases represented local transmission cases occurring in Mexico during
mid-March 2020, denoting the earliest events described for the country.
Within this local transmission cluster, we also identified an H49Y amino
acid change in the Spike protein. This mutation represents a homoplasy
occurring independently through time and space and may function as a
molecular marker to follow any further spread of these viral variants
throughout the country. Our results provide a general picture of the
SARS-CoV-2 variants introduced at the beginning of the outbreak in
Mexico, setting the foundation for future surveillance efforts.
IMPORTANCE Understanding the introduction, spread, and establishment of
SARS-CoV-2 within distinct human populations as well as the evolution of
the pandemics is crucial to implement effective control strategies. In
this work, we report that the initial virus strains introduced in Mexico
came from Europe and the United States and that the virus was
circulating locally in the country as early as mid-March. We also found
evidence for early local transmission of strains with a H49Y mutation in
the Spike protein, which could be further used as a molecular marker to
follow viral spread within the country and the region.
Filiaciones:
Taboada, Blanca:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Genet Desarrollo & Fisiol Mol, Cuernavaca, Morelos, Mexico
Vazquez-Perez, Joel Armando:
Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Mexico City, DF, Mexico
Munoz-Medina, Jose Esteban:
Inst Mexicano Seguro Social, Div Labs Vigilancia & Invest Epidemiol, Mexico City, DF, Mexico
Ramos-Cervantes, Pilar:
Inst Nacl Ciencias Med & Nutr Salvador Zubiran, Mexico City, DF, Mexico
Escalera-Zamudio, Marina:
Univ Oxford, Dept Zool, Oxford, England
Boukadida, Celia:
Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Ctr Invest Enfermedades Infecciosas, Mexico City, DF, Mexico
Sanchez-Flores, Alejandro:
Univ Nacl Autonoma Mexico, Unidad Univ Secuenciac Masiva & Bioinformat, Inst Biotecnol, Cuernavaca, Morelos, Mexico
ISA, PAVEL:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Genet Desarrollo & Fisiol Mol, Cuernavaca, Morelos, Mexico
Mendieta-Condado, Edgar:
Inst Diagnost & Referencia Epidemiol, Direcc Gen Epidemiol, Mexico City, DF, Mexico
Martinez-Orozco, Jose A.:
Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Mexico City, DF, Mexico
Becerril-Vargas, Eduardo:
Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Mexico City, DF, Mexico
Salas-Hernandez, Jorge:
Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Mexico City, DF, Mexico
Grande, Ricardo:
Univ Nacl Autonoma Mexico, Unidad Univ Secuenciac Masiva & Bioinformat, Inst Biotecnol, Cuernavaca, Morelos, Mexico
Gonzalez-Torres, Carolina:
Inst Mexicano Seguro Social, Div Desarrollo Invest, Mexico City, DF, Mexico
Gaytan-Cervantes, Francisco Javier:
Inst Mexicano Seguro Social, Div Desarrollo Invest, Mexico City, DF, Mexico
Vazquez, Gloria:
Univ Nacl Autonoma Mexico, Unidad Univ Secuenciac Masiva & Bioinformat, Inst Biotecnol, Cuernavaca, Morelos, Mexico
Pulido, Francisco:
Univ Nacl Autonoma Mexico, Unidad Univ Secuenciac Masiva & Bioinformat, Inst Biotecnol, Cuernavaca, Morelos, Mexico
Araiza-Rodriguez, Adnan:
Inst Diagnost & Referencia Epidemiol, Direcc Gen Epidemiol, Mexico City, DF, Mexico
Garces-Ayala, Fabiola:
Inst Diagnost & Referencia Epidemiol, Direcc Gen Epidemiol, Mexico City, DF, Mexico
Gonzalez-Bonilla, Cesar Raul:
Inst Mexicano Seguro Social, Coordinac Invest Salud, Mexico City, DF, Mexico
Grajales-Muniz, Concepcion:
Inst Mexicano Seguro Social, Coordinac Control Tecn Insumos, Mexico City, DF, Mexico
Borja-Aburto, Victor Hugo:
Inst Mexicano Seguro Social, Direcc Prestac Med, Mexico City, DF, Mexico
Barrera-Badillo, Gisela:
Inst Diagnost & Referencia Epidemiol, Direcc Gen Epidemiol, Mexico City, DF, Mexico
LOPEZ, SUSANA:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Genet Desarrollo & Fisiol Mol, Cuernavaca, Morelos, Mexico
Hernandez-Rivas, Lucia:
Inst Diagnost & Referencia Epidemiol, Direcc Gen Epidemiol, Mexico City, DF, Mexico
Perez-Padilla, Rogelio:
Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Mexico City, DF, Mexico
Lopez-Martinez, Irma:
Inst Diagnost & Referencia Epidemiol, Direcc Gen Epidemiol, Mexico City, DF, Mexico
avila-Rios, Santiago:
Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Ctr Invest Enfermedades Infecciosas, Mexico City, DF, Mexico
Ruiz-Palacios, Guillermo:
Inst Nacl Ciencias Med & Nutr Salvador Zubiran, Mexico City, DF, Mexico
Ramirez-Gonzalez, Jose Ernesto:
Inst Diagnost & Referencia Epidemiol, Direcc Gen Epidemiol, Mexico City, DF, Mexico
Arias, Carlos F.:
Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Genet Desarrollo & Fisiol Mol, Cuernavaca, Morelos, Mexico
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