Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
Infect Genet Evol. 2020 Dec;86:104616. doi: 10.1016/j.meegid.2020.104616. Epub 2020 Nov 4.
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.
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.
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.
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.
委内瑞拉和哥伦比亚在应对 COVID-19 大流行时都采取了遏制措施。然而，委内瑞拉持续的人道主义危机摧毁了其医疗体系，并迫使数以百万计的委内瑞拉人通过与哥伦比亚接壤的漏洞百出的边境逃离。两国之间广泛的共同边界以及通过两国之间临时小道的非法跨境过境，是公共卫生当局面临的主要挑战。我们报告了来自委内瑞拉的第一批 SARS-CoV-2 基因组，并展示了哥伦比亚-委内瑞拉边境地区 SARS-CoV-2 流行病学特征的快照。
我们使用基于自定义参考的分析管道从鼻咽（NP）临床标本中提取的总 RNA 对病毒基因组进行测序和组装。使用 Phylogenetic Assignment of Named Global Outbreak LINeages 'Pangolin' 工具对获得的三个组装体进行分型。总共从 GISAID 数据库中获得了来自南美洲的 376 个公开的 SARS-CoV-2 基因组，以进行比较基因组分析。此外，还使用了武汉-1 株作为参考。
我们发现，来自委内瑞拉的两个 SARS-CoV-2 基因组属于 B1 谱系，第三个属于 B.1.13 谱系。我们在所有三个委内瑞拉基因组中都观察到 Spike 蛋白基因（D614G 取代）的点突变，此前该突变与增加的传染性有关。此外，在一个委内瑞拉基因组的核衣壳（N）基因中存在三个突变（R203K/G204R 取代）。
基因组测序表明，来自委内瑞拉的 SARS-CoV-2 谱系与从哥伦比亚和巴西接壤地区的患者以及从哥伦比亚邻国收集的病毒相似，尽管采取了包括封锁在内的行政措施，但仍存在跨境过境现象。我们报告的 3 个委内瑞拉基因组和来自邻国边境地区的哥伦比亚 SARS-CoV-2 基因组中存在与增加传染性相关的突变，可能会给拉丁美洲国家复杂的流行病学环境中 SARS-CoV-2 传播的控制带来额外挑战。公共卫生当局应密切关注该大流行的进展及其对该地区流离失所人口的影响。
