Genomic analysis of early SARS-CoV-2 strains introduced in Mexico
Joel Armando Vazquez-Perez,
José Esteban Muñoz Medina,
Pilar Ramos Cervantes,
Edgar Mendieta Condado,
José Arturo Martínez-Orozco,
Francisco Javier Gaytán-Cervantes,
Adnan Araiza Rodríguez,
Fabiola Garcés Ayala,
Cesar Raúl González Bonilla,
Concepción Grajales Muñiz,
Víctor Hugo Borja Aburto,
Gisela Barrera Badillo,
Lucía Hernández Rivas,
Irma López Martínez,
José Ernesto Ramírez-González,
Carlos F Arias
Posted 30 May 2020
bioRxiv DOI: 10.1101/2020.05.27.120402
Posted 30 May 2020
The COVID-19 pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to implement 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, the SARS-CoV-2 lineage A/G, containing mostly sequences from North America, and the lineage B/S containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized fourteen independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represent local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described in the country. Within this Mexican cluster, we also identified an H49Y amino acid change in the spike protein. This mutation is a homoplasy occurring independently through time and space, and may function as a molecular marker to follow on any further spread of these viral variants throughout the country. Our results depict the general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.
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