López-Alvarez Diana, Rivera-Franco Nelson, Aristizabal Erica, Solarte Melissa, Castillo Andrés, Pardo Carlos A, Parra Beatriz
Grupo VIREM-Virus Emergentes y Enfermedad, Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Cali 760043, Colombia.
Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia, Palmira 763533, Colombia.
Viruses. 2025 May 30;17(6):800. doi: 10.3390/v17060800.
In Cali, Colombia, 405,689 COVID-19 cases were reported until March 2023, with 2463 complete genome sequences available for analysis. SARS-CoV-2 genomic data from Cali were analyzed to determine the prevalence of variants as well as the mutation frequencies. This study identified Nextstrain clades, Pango lineages, and specific mutations in key viral proteins. A total of 23 Nextstrain clades and 118 Pango lineages were detected, including variants of interest (Lambda, Mu) and variants of concern (Alpha, Gamma, Delta, Omicron). Analysis identified 2424 missense mutations, with notable frequencies in NSP3 (465), S (367), NSP2 (205), N (180), ORF3a (144), NSP12b (113), and NSP13 (108). The study also observed a high prevalence of simultaneous transmission of multiple variants. The COVID-19 epidemic waves in Cali were shaped more by social and economic dynamics than by the emergence of specific SARS-CoV-2 variants. These findings highlight the importance of context-specific public health interventions to mitigate future outbreaks effectively.
在哥伦比亚的卡利，截至2023年3月报告了405,689例新冠病毒病例，其中有2463个完整基因组序列可供分析。对来自卡利的新冠病毒基因组数据进行了分析，以确定变异株的流行情况以及突变频率。本研究确定了Nextstrain分支、Pango谱系以及关键病毒蛋白中的特定突变。共检测到23个Nextstrain分支和118个Pango谱系，包括感兴趣的变异株（拉姆达、缪）和值得关注的变异株（阿尔法、伽马、德尔塔、奥密克戎）。分析确定了2424个错义突变，在非结构蛋白3（465个）、刺突蛋白（367个）、非结构蛋白2（205个）、核衣壳蛋白（180个）、开放阅读框3a（144个）、非结构蛋白12b（113个）和非结构蛋白13（108个）中频率显著。该研究还观察到多种变异株同时传播的高流行率。卡利的新冠疫情浪潮更多地是由社会和经济动态形成的，而非特定新冠病毒变异株的出现。这些发现凸显了因地制宜的公共卫生干预措施对于有效缓解未来疫情爆发的重要性。
