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dc.creatorMolina Mora, José Arturo
dc.creatorCordero Laurent, Estela
dc.creatorGodínez Rojas, Adriana
dc.creatorCalderón Osorno, Melany
dc.creatorBrenes Porras, Hebleen
dc.creatorSoto Garita, Claudio
dc.creatorPérez Corrales, Cristian
dc.creatorDrexler, Jan Felix
dc.creatorMoreira Soto, Andrés
dc.creatorCorrales Aguilar, Eugenia
dc.creatorDuarte Martínez, Francisco
dc.date.accessioned2022-03-01T19:28:35Z
dc.date.available2022-03-01T19:28:35Z
dc.date.issued2021
dc.identifier.citationwww.sciencedirect.com/science/article/pii/S1567134821001696es_ES
dc.identifier.issn1567-1348
dc.identifier.urihttps://hdl.handle.net/10669/85924
dc.description.abstractGenome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest-hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. In Costa Rica, from the first detected case on March 6th to December 31st almost 170,000 cases have been reported. We analyzed the genomic variability during the SARS-CoV-2 pandemic in Costa Rica using 185 sequences, 52 from the first months of the pandemic, and 133 from the current wave. Three GISAID clades (G, GH, and GR) and three PANGOLIN lineages (B.1, B.1.1, and B.1.291) were predominant, suggesting multiple re-introductions from other regions. The whole-genome variant calling analysis identified a total of 283 distinct nucleotide variants, following a power-law distribution with 190 single nucleotide mutations in a single sequence, and only 16 mutations were found in >5% sequences. These mutations were distributed through the whole genome. The prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. This variant has been observed in less than 1% of the GISAID reported sequences worldwide in 2020. Structural modeling of the Spike protein with the T1117I mutation suggests a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of the COVID-19 pandemic in Costa Rica suggest the introduction of lineages from other countries and the detection of mutations in line with other studies, but pointing out the local increase in the detection of Spike-T1117I variant. The genomic features of this virus need to be monitored and studied in further analyses as part of the surveillance program during the pandemic.es_ES
dc.description.sponsorshipInstituto Costarricense de Investigación y Enseñanza en Nutrición y Salud/[]/INCIENSA/Costa Ricaes_ES
dc.description.sponsorshipUniversidad de Costa Rica/[803-C0-196]/UCR/Costa Ricaes_ES
dc.description.sponsorshipCOINGESA-CR Consorcio Interinstitucional de Estudios Genómicos del SARS-CoV-2 Costa Ricaes_ES
dc.language.isoenges_ES
dc.sourceInfection, Genetics and Evolution, vol.92, pp.1-9.es_ES
dc.subjectSARS-CoV-2es_ES
dc.subjectCOVID-19es_ES
dc.subjectCOSTA RICAes_ES
dc.subjectGenomic surveillancees_ES
dc.subjectPandemices_ES
dc.titleSARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutationes_ES
dc.typeartículo científicoes_ES
dc.identifier.doi10.1016/j.meegid.2021.104872
dc.description.procedenceUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET)es_ES
dc.description.procedenceUCR::Vicerrectoría de Docencia::Salud::Facultad de Microbiologíaes_ES
dc.identifier.codproyecto803-C0-196


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