The COVID-19 pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to implement effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, the SARS-CoV-2 lineage A/G, containing mostly sequences from North America, and the lineage B/S containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized fourteen independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represent local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described in the country. Within this Mexican cluster, we also identified an H49Y amino acid change in the spike protein. This mutation is a homoplasy occurring independently through time and space, and may function as a molecular marker to follow on any further spread of these viral variants throughout the country. Our results depict the general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.

中文翻译：

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墨西哥引进的SARS-CoV-2早期菌株的基因组分析

COVID-19大流行影响了世界上大多数国家。研究不同国家的进化和传播方式对于实施有效的疾病控制和预防策略至关重要。在这项工作中，我们介绍了17个SARS-CoV-2分离株的完整基因组序列，对应于墨西哥最早的抽样病例。全球和局部系统基因组学，加上突变分析，一致表明这些病毒序列分布在两个已知谱系中，SARS-CoV-2谱系A / G主要包含来自北美的序列，而谱系B / S主要包含序列来自欧洲。基于病例的接触史和系统学分析，我们表征了十四个独立的引进事件。另外，确定了三例没有旅行史的病例。我们发现有证据表明，这些案例中有两个代表了2020年3月中旬在墨西哥发生的本地传播案例，表明该国描述的最早事件。在这个墨西哥集群中，我们还发现了刺突蛋白中的H49Y氨基酸变化。这种突变是同质异形体，在时间和空间上独立发生，并且可以充当分子标记，跟随这些病毒变体在全国的任何进一步传播。我们的结果描述了在墨西哥爆发初期引入的SARS-CoV-2变体的概况，为以后的监视工作奠定了基础。我们还确定了刺突蛋白中的H49Y氨基酸变化。这种突变是同质异形体，在时间和空间上独立发生，并且可以充当分子标记，跟随这些病毒变体在全国的任何进一步传播。我们的结果描述了在墨西哥爆发初期引入的SARS-CoV-2变体的概况，为以后的监视工作奠定了基础。我们还确定了刺突蛋白中的H49Y氨基酸变化。这种突变是同质异形体，在时间和空间上独立发生，并且可以充当分子标记，跟随这些病毒变体在全国的任何进一步传播。我们的结果描述了在墨西哥爆发初期引入的SARS-CoV-2变体的概况，为以后的监视工作奠定了基础。