SARS-CoV-2 in Transit: Characterization of SARS-CoV-2 Genomes From Venezuelan Migrants in Colombia

Abstract

Objectives: To evaluate the genomic epidemiology of SARS-CoV-2 from Venezuelan migrants living in Colombia.

Methods: This study sequenced SARS-CoV-2 from 30 clinical specimens collected from Venezuelan migrants. Genomes were compared with the Wuhan reference genome to identify polymorphisms, reconstruct phylogenetic relationships and perform comparative genomic analyses. Geographic, sociodemographic and clinical data were also studied across genotypes.

Results: This study demonstrated the presence of six distinct SARS-CoV-2 lineages circulating among Venezuelan migrants, as well as a close relationship between SARS-CoV-2 genomic sequences obtained from individuals living in the Venezuelan-Colombian border regions of La Guajira (Colombia) and Zulia (Venezuela). Three clusters (C-1, C-2 and C-3) were well supported by phylogenomic inference, supporting the hypothesis of three potential transmission routes across the Colombian-Venezuelan border. These genomes included point mutations previously associated with increased infectivity. A mutation (L18F) in the N-terminal domain of the spike protein that has been associated with compromised binding of neutralizing antibodies was found in 2 of 30 (6.6%) genomes. A statistically significant association was identified with symptomatology for cluster C2.

Conclusion: The close phylogenetic relationships between SARS-CoV-2 genomes from Venezuelan migrants and from people living at the Venezuela-Colombian border support the importance of human movements for the spread of COVID-19 and for emerging virus variants.

Keywords: L18F; Lineages; Mutations; SARS-CoV-2; Venezuelan-Colombian border.

Figure 1

Phylogenomic relationships of evaluated SARS-CoV-2 genomes in the global context. A dataset with 2,958 genomes (30 genomes from Venezuelans in Colombia (Ven_Col), 10 from Venezuela, 277 from Colombia, and 2,641 from other countries) was analyzed from the alignment with a length of 5,209 positions, corresponding to the whole genome single-nucleotide polymorphisms (SNP) excluding untranslated regions. A) Maximum likelihood tree from whole genome SNPs for the complete dataset. Clusters consisting of 23 of the 30 Ven_Col genomes are highlighted in orange (C-1 to C-3), which are depicted in B) at a greater magnification to visualize all genomes included in each cluster. These clusters support the hypothesis of three potential transmission routes across the Colombian-Venezuelan border.

Figure 2

Nucleotide diversity between 30 Ven_Col genomes. Single nucleotide polymorphisms (SNP) found in the 30 Ven_Col SARS-CoV-2 isolates (Genome ID) compared with the Wuhan reference sequence (NC_045512). The positions of each SNP that is represented in ≥ 5% of all genomes are shown. If the SNP is a non-synonymous substitution, the corresponding amino acid change is indicated below the nucleotide position. All SNPs are annotated across an annotated SARS-CoV-2 genome.

Figure 3

Geographic distribution of Colombian and Ven_Col SARS-CoV-2 isolates in Colombia. Using geographical coordinates for sequenced genomes, quantities of A) Colombian and B) Ven_Col isolates characterized by evolutionary lineage are depicted as circles across Colombian departments. Circles are proportional in size (see scale) to the number of genomes sequenced that correspond to a given color-coded PANGO lineage.