Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
Lenmed-Bokamoso Private Hospital, Gaborone, Botswana.
Int J Infect Dis. 2024 Jan;138:91-96. doi: 10.1016/j.ijid.2023.11.011. Epub 2023 Nov 11.
We investigated intra-host genetic evolution using two SARS-CoV-2 isolates from a fully vaccinated (primary schedule x2 doses of AstraZeneca plus a booster of Pfizer), >70-year-old woman with a history of lymphoma and hypertension who presented a SARS-CoV-2 infection for 3 weeks prior to death due to COVID-19. Two full genome sequences were determined from samples taken 13 days apart with both belonging to Pango lineage FL.2: the first detection of this Omicron sub-variant in Botswana. FL.2 is a sub-lineage of XBB.1.9.1. The repertoire of mutations and minority variants in the Spike protein differed between the two time points. Notably, we also observed deletions within the ORF1a and Membrane proteins; both regions are associated with high T-cell epitope density. The internal milieu of immune-suppressed individuals may accelerate SARS-CoV-2 evolution; hence, close monitoring is warranted.
我们对两名完全接种疫苗（两剂阿斯利康加一剂辉瑞加强针）、70 岁以上、有淋巴瘤和高血压病史的女性体内的病毒遗传进化进行了研究，该患者因感染 SARS-CoV-2 而死亡。从相隔 13 天的两个样本中确定了两个完整的基因组序列，均属于 Pango 谱系 FL.2：这是博茨瓦纳首次发现这种奥密克戎亚变体。FL.2 是 XBB.1.9.1 的一个子谱系。Spike 蛋白中的突变和少数变体在两个时间点有所不同。值得注意的是，我们还观察到 ORF1a 和膜蛋白内的缺失；这两个区域都与高 T 细胞表位密度有关。免疫抑制个体的内部环境可能会加速 SARS-CoV-2 的进化；因此，需要密切监测。
