Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuelan 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. An additional 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.

中文翻译：

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SARS-CoV-2跨哥伦比亚-委内瑞拉边境蔓延

委内瑞拉和哥伦比亚都对COVID-19大流行采取了早期遏制措施。但是，委内瑞拉持续的人道主义危机使该国的医疗系统瘫痪，并迫使数百万委内瑞拉人逃离其与哥伦比亚接壤的边界。两国之间广泛的共享边界和通过简易步道的非法跨境转运是公共卫生当局的主要挑战。我们报告了委内瑞拉的第一个SARS-CoV-2基因组，并提出了哥伦比亚-委内瑞拉边境地区SARS-CoV-2流行病学景观的快照。我们使用自定义的基于参考的分析管道，从从鼻咽（NP）临床标本中提取的总RNA测序并组装了病毒基因组。使用命名的全球爆发线性穿山甲穿山甲工具的系统发育分配对获得的三个程序集进行打字。从GISAID数据库中获得了总共376个来自南美的公开可用SARS-CoV-2基因组，以进行比较基因组分析。另外，以武汉-1株为参考。我们发现委内瑞拉的两个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观察到了Spike蛋白基因中的点突变（D614G替代），以前据报道与感染性增加相关。一个委内瑞拉基因组的核衣壳（N）基因中存在另外三个突变（R203K / G204R取代）。结论：基因组测序表明，委内瑞拉的SARS-CoV-2谱系与从哥伦比亚和巴西边境地区的患者收集的病毒之间具有相似性，尽管采取了包括封锁在内的行政措施，但与跨境运输相符。我们报告的3个委内瑞拉基因组中与传染性增加相关的突变的存在，以及来自邻国边界地区的哥伦比亚SARS-CoV-2基因组可能对控制SARS-CoV-2在拉丁美洲国家的复杂流行病学格局中传播构成了额外挑战。公共卫生当局应认真跟踪大流行的进展及其对区域内流离失所者的影响。尽管采取了行政措施（包括封锁），但仍与跨境运输保持一致。我们报告的3个委内瑞拉基因组中与传染性增加相关的突变的存在，以及来自邻国边界地区的哥伦比亚SARS-CoV-2基因组可能对控制SARS-CoV-2在拉丁美洲国家的复杂流行病学格局中传播构成了额外挑战。公共卫生当局应认真跟踪大流行的进展及其对区域内流离失所者的影响。尽管采取了行政措施（包括封锁），但仍与跨境运输保持一致。我们报告的3个委内瑞拉基因组中与传染性增加相关的突变的存在，以及来自邻国边界地区的哥伦比亚SARS-CoV-2基因组可能对控制SARS-CoV-2在拉丁美洲国家的复杂流行病学格局中传播构成了额外挑战。公共卫生当局应认真跟踪大流行的进展及其对区域内流离失所者的影响。