First 6 complete SARS-COV-2 genome sequencies by NGS in El Salvador

Abstract

Introduction. This work describes the first complete SARS-CoV-2 genome sequencies from samples of Salvadorean patients. Objective. To report the first six complete SARS-CoV-2 genome sequencies of six indigenous cases of COVID-19 detected in El Salvador, from nasopharyngeal discharge samples. Methodology. An NGS next generation sequencing was performed from indigenous samples in the Illumina platform. Results. The phylogenetic analysis showed that these isolated belong to the clade 20C secondary of 20A, which have in common the S:D614G variant; the D614G mutation of the spike glycoprotein was found in the six sequencies of the SARS-CoV-2 genome. Using the GISAID platform, the sequencies were found to belong to the clade GH lineage pangolin  B.1.2 y B.1.370, both present in the United States. Conclusion. This is the first report of complete SARS-CoV-2 genome sequencies in El Salvador, and it identifies the predominant variant in Central and North America.