SARS-CoV-2 spread across the Colombian-Venezuelan border

Abstract

Introduction: Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region.

Methods: We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages 'Pangolin' tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference.

Results: We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome.

Conclusions: Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.

Keywords: Border; COVID-19; Colombia; Coronavirus; SARS-CoV-2; Venezuela.

Fig. 1

Regional comparative genomic analysis of SARS-CoV-2. A. Geographical distribution of the sequences from Venezuelan genomes and the available Colombian genomes analyzed in this study. The pink symbols indicate the Venezuelan patients identified in Colombia with their respective Venezuelan state origin. B. Stacked bar plot of the number of genomes per lineage determined using Phylogenetic Assignment of Named Global Outbreak LINeages ‘Pangolin’ tool. Three SARS-CoV-2 genomes from Venezuela were compared with 376 assemblies from other 7 South American countries (Argentina, Brazil, Chile, Colombia, Ecuador, Peru and Uruguay) using the publicly available GISAID EpiCoV™ database (https://www.gisaid.org/). Frequencies are discriminated by country of origin. The Venezuelan lineages are identified by black arrows. C. Maximum likelihood tree built in IQtree shows the phylogenetic relationships between genomes from Venezuela (pink dots) and the closest Colombian regions (yellow dots) with other South American genomes. The branches were colored according to the country of origin, using the color code of A panel. The clustering of the most frequent pangolin lineages (n > 10) is represented on the right side. The black dots represent highly supported nodes. D. Multiple alignment of the Nucleocapsid gene showing the substitutions found using the Wuhan-1 sequence as reference.