| Autor: |
Márquez S; Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología., Prado-Vivar B; Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología.; Universidad San Francisco de Quito, Centro de Bioinformática., Guadalupe JJ; Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal., Gutierrez B; Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnología Vegetal.; Departament of Zoology, University of Oxford., Jibaja M; Unidad de Cuidados Intensivos, Hospital Eugenio Espejo, Quito., Tobar M; Unidad de Cuidados Intensivos, Hospital Eugenio Espejo, Quito., Mora F; Hospital General Sur de Quito, IESS., Gaviria J; Hospital General Sur de Quito, IESS., García M; Hospital General Sur de Quito, IESS., Espinosa F; Hospital General Sur de Quito, IESS., Ligña E; Hospital General Sur de Quito, IESS., Reyes J; Hospital General Sur de Quito, IESS.; Universidad Central del Ecuador, Facultad Ciencias Químicas., Barragán V; Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología., Rojas-Silva P; Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología., Trueba G; Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología., Grunauer M; Universidad San Francisco de Quito, Escuela de Medicina, COCSA.; Unidad de Cuidados Intensivos, Hospital de los Valles, Quito., Cárdenas P; Universidad San Francisco de Quito, COCIBA, Instituto de Microbiología.; Universidad San Francisco de Quito, Centro de Bioinformática. |
| Abstrakt: |
SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus and Chlamydia spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador. |
