Tandel Kundan, Niveditha Divya, Singh Sanjay Pratap, Anand Kavita Bala, Shinde Vaishnavi, Ghedia Mayank, Sondakar Ashwini, Reddy Mahesh
Department of Microbiology, Armed Forces Medical College, Wanowarie, Pune 411040, Maharashtra, India.
Department of Microbiology, Armed Forces Medical College, Wanowarie, Pune 411040, Maharashtra, India.
Diagn Microbiol Infect Dis. 2025 Mar;111(3):116705. doi: 10.1016/j.diagmicrobio.2025.116705. Epub 2025 Jan 23.
The coronavirus disease 2019 (COVID-19) pandemic, driven by the rapid evolution of the SARS-CoV-2 virus, has led to the emergence of multiple variants with significant impacts on global health. This study aims to analyze the evolutionary trends and mutational landscape of SARS-CoV-2 variants circulating in Pune, Maharashtra, India, from August 2022 to April 2024. Using comprehensive genomic surveillance data, we identified the predominance of variants such as BA.2.75, XBB.x, and the newly emerged subvariants JN.1, KP.1, and KP.2. These subvariants, belonging to the BA.2.86 lineage, have raised concerns owing to their potential for increased transmissibility and immune evasion.
Phylogenetic analysis of 84 sequenced samples from Pune revealed 18 distinct lineages, with JN.1 and KP.2 forming a novel branch compared with their ancestral lineage, BA.2. Detailed mutational analysis highlighted key mutations in the N-terminal domain (NTD) and receptor-binding domain (RBD) of the spike protein, affecting viral stability, ACE2 binding affinity, and neutralizing antibody escape. Our findings, along with the predictions of SpikePro, suggest that the combination of these mutations enhances the viral fitness of JN.1 and KP.2, contributing to their rapid emergence and spread.
This study underscores the importance of continuous genomic surveillance and advanced computational modeling to track and predict the evolutionary trajectories of SARS-CoV-2 variants. The insights gained from this research are crucial for informing public health strategies, vaccine updates, and therapeutic interventions to mitigate the impact of current and future SARS-CoV-2 variants.
由严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）病毒的快速进化驱动的2019冠状病毒病（COVID-19）大流行，导致出现了多个对全球健康产生重大影响的变种。本研究旨在分析2022年8月至2024年4月在印度马哈拉施特拉邦浦那市流行的SARS-CoV-2变种的进化趋势和突变情况。利用全面的基因组监测数据，我们确定了BA.2.75、XBB.x等变种以及新出现的亚变种JN.1、KP.1和KP.2的优势地位。这些属于BA.2.86谱系的亚变种，因其潜在的传播性增加和免疫逃逸能力而引发了关注。
对来自浦那的84个测序样本进行系统发育分析，发现了18个不同的谱系，与它们的祖先谱系BA.2相比，JN.1和KP.2形成了一个新的分支。详细的突变分析突出了刺突蛋白的N端结构域（NTD）和受体结合结构域（RBD）中的关键突变，这些突变影响病毒稳定性、血管紧张素转换酶2（ACE2）结合亲和力和中和抗体逃逸。我们的研究结果以及SpikePro的预测表明，这些突变的组合提高了JN.1和KP.2的病毒适应性，促进了它们的迅速出现和传播。
本研究强调了持续的基因组监测和先进的计算建模对于追踪和预测SARS-CoV-2变种进化轨迹的重要性。从这项研究中获得的见解对于为公共卫生策略、疫苗更新和治疗干预提供信息以减轻当前和未来SARS-CoV-2变种的影响至关重要。
