SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation

Abstract

Genome 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.

The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe

“…This leads to relatively slow mutation rate of 1-2 mutations per month along with the SARS-CoV-2 genome. Analysis of different local SARS-CoV-2 genomic surveillance revealed 3-22 mutations per genome in comparison to reference sequence (Mora et al, 2021) which is in line with our results (7-17 mutations per genome). Among 41 Serbian isolates 148 different genome variants were detected, of which the top four amino acid changes are also some of the most prominent amino acid changes worldwide (nsp12_P323L, Spike_D614G, N_R203K, and N_G204R).…”

E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil

“…Its appearance is likely to have arisen independently ( Faria et al, 2021 ). Without previous introductions in other Latin American countries, which have been affected by their own specific mutations, such as the convergent evolution of the S:T1117I in Costa Rica ( Molina-Mora et al, 2021 ) the E484K mutation arose independently in Brazil and was identified in the Rio de Janeiro state (Southeast Brazil) in early-October carried by the P.2 lineage ( Voloch et al, 2020 ).…”

Clinical profiles at the time of diagnosis of COVID-19 in Costa Rica during the pre-vaccination period using a machine learning approach

“…This situation reminds us that the clinical profiles depend on the viral agent and human host conditions. The human genetic, comorbidities, and risk conditions have been described as the predominant factor in the clinical outcome of the COVID-19 disease, as found in several studies (LoPresti et al, 2020;Molina-Mora et al, 2021;Sironi et al, 2020;Toyoshima et al, 2020).…”

“…(Tsui, Deng, & Pan, 2020). In our previous work, we focused on the analysis of the genomic diversity of SARS-CoV-2 sequences from Costa Rica during 2020 (Molina-Mora et al, 2021) and we now studied the symptoms at the time of diagnosis of COVID-19 as clinical profiles.…”