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

Paniz-Mondolfi A.,
Muñoz M.,
Florez C.,
Gómez S.,
Rico A.,
Pardo L.,
Barros E.C.,
Hernandez C.,
Delgado L.,
Jaimes J.E.,
Pérez L.,
Teherán A.A.,
Alshammary H.A.,
Obla A.,
Khan Z.,
Dutta J.,
van de Guchte A.,
Gonzalez-Reiche A.S.,
Hernandez M.M.,
Sordillo E.M.,
Simon V.,
van Bakel H.,
Llewellyn M.S.,
Ramírez J.D.
Document Type
Source Title
Infection, Genetics and Evolution
Elsevier B.V.


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. © 2020

Migration angle
Region/Country (by coverage)
Index Keywords

virus spike protein; 5' untranslated region; amino acid substitution; analytic method; Article; Colombia; comparative genomics; coronavirus disease 2019; epidemiological data; factual database; gene identification; genetic association; genetic database; health impact assessment; human; infection control; mutational analysis; nasopharynx; nonhuman; nose smear; pandemic; phylogeny; point mutation; population migration; priority journal; protocol compliance; public health service; RNA extraction; RNA sequence; sequence analysis; Severe acute respiratory syndrome coronavirus 2; South America; Venezuela; virus genome; virus infection; virus infectivity; virus nucleocapsid; virus strain; virus transmission; classification; epidemiology; genetics; mutation; single nucleotide polymorphism; virology; Colombia; COVID-19; Genome, Viral; Humans; Mutation; Polymorphism, Single Nucleotide; SARS-CoV-2; Venezuela