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