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

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.

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

“…Samples collected by the Microbiology Institute at Universidad San Francisco de Quito (IM-USFQ) were obtained from third-level hospitals (i.e. specialised tertiary referral hospitals) across all 24 provinces in the country without unified selection criteria ( 27 ). Samples collected by the Omics Sciences Laboratory at Universidad de Especialidades Espiritu Santo (UEES) were obtained from samples collected from the laboratory’s diagnostic service and selected at random for sequencing.…”

“…From these samples we generated 160 complete SARS-CoV-2 genomic sequences using different methodologies. IM-USFQ generated 108 whole genome sequences using Oxford Nanopore MinION sequencing and the ARTIC Network primer scheme approach as previously described ( 27 ). UEES generated 33 whole genome sequences through Illumina sequencing on a MiniSeq platform (Illumina, San Diego, CA).…”

Whole Genome Sequencing: A Powerful Tool for Understanding the Diversity of Genotypes and Phenotypes among COVID-19 Infected Patients to Help in Controlling Outbreaks

“…The sequences of the confirmed cases in Ecuador were found to have high similarity (99.68 percent) with Wuhan strain reference case (GenBank accession number MN908947). The information discussed in this section is summarized in Table 1 [68].…”

Late incidence of SARS-CoV-2 infection in a highly-endemic remote rural village. A prospective population-based cohort study

“…Atahualpa -a rural Ecuadorian village -was severely struck by this pandemic, as noticed by a sudden increase in adult mortality associated with respiratory diseases during April and May, 2020 [9], coinciding with the introduction of SARS-CoV-2 in Ecuador [10]. We then conducted a study of SARS-CoV-2 prevalence in middle-aged and older adults enrolled in the Atahualpa Project Cohort, and demonstrated that almost half of adult individuals had SARS-CoV-2 antibodies [11].…”