About: Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador

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About: Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador
Creator	Gutierrez, Bernardo García, María Grunauer, Michelle Reyes, Jorge Jibaja, Manuel Barragán, Verónica Cárdenas, Paúl Espinosa, Franklin Gaviria, Juan Guadalupe, Juan Ligña, Edison Mora, Francisco Márquez, Sully Prado-Vivar, Belén Rojas-Silva, Patricio Tobar, Milton Trueba, Gabriel
Source	MedRxiv; Medline; PMC
abstract	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.
has issue date	2020-06-14(xsd:dateTime)
bibo:doi	10.1101/2020.06.11.20128330
bibo:pmid	32588004
has license	cc-by-nc-nd
schema:url	https://doi.org/10.1101/2020.06.11.20128330
resource representing a document's title	Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador
has PubMed Central identifier	PMC7310664
has PubMed identifier	32588004
schema:publication	medRxiv
resource representing a document's body	covid:PMC7310664#body_text
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