<b>Mutation Profile Analysis of 3,252 SARS-CoV-2 Genomes from January to Early May 2025: Evidence of High Diversity and Limited Convergent Evolution in NSP7, NSP8, NSP12, and NSP14</b>

This study presents a mutation profile analysis of <b>3,252 SARS-CoV-2 genomes </b>collected between <b>January and early May 2025 </b>, focusing on non-structural proteins (NSP7, NSP8, NSP12, and NSP14).<b>It is suggested that there is high diversity, low convergence</b> which suggests ongoing evolutionary process with no fixed substitutions in key replicase components (nsp7, nsp8, nsp12, nsp14) as of early May 2025.After rigorous alignment, filtering, and quality control steps, sequences were reduced due to gaps, misalignment, or incomplete coverage. No recurrent mutations were identified at standard thresholds (≥1% frequency), suggesting <b>high genomic diversity </b>and limited convergent evolution during this period.QC check was set to 90%This analysis began with <b>3,252 SARS-CoV-2 genome accessions </b>downloaded from NCBI, covering samples collected between January and early May 2025. Following alignment using MAFFT and extensive quality control to remove duplicates, incomplete sequences, and misaligned entries, the dataset was reduced to <b>2,731 high-quality sequences </b>. Mutation matrices were generated for four key non-structural protein regions: <b>nsp7, nsp8, nsp12, and nsp14 </b>. Despite lowering mutation frequency thresholds down to 0.1%, no recurrent mutations were identified across these genes that indicate a high degree of genetic diversity and limited evidence of convergent evolution during this time window.The results highlight the importance of <b>careful sequence curation </b>when analyzing public NCBI surveillance data. Most observed changes were rare or private, indicating an evolving population without dominant variants emerging by early May 2025.All mutation matrices are provided for reproducibility.<br>

本研究针对**2025年1月至5月初采集的3252份严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）基因组**开展突变谱分析，重点聚焦非结构蛋白（NSP7、NSP8、NSP12及NSP14）。
**研究表明，该数据集呈现高多样性、低趋同性特征**，提示截至2025年5月初，关键复制酶组分（nsp7、nsp8、nsp12、nsp14）尚未出现固定替代突变，演化过程仍在持续。
经过严格的序列比对、筛选及质量控制流程后，因存在序列缺口、比对错误或覆盖不全问题，部分序列被剔除。在标准阈值（频率≥1%）下未检出复发性突变，这一结果反映出该时间段内**高基因组多样性**，且趋同演化的证据有限。本次质量控制阈值设为90%。
本分析初始数据集为从美国国家生物技术信息中心（NCBI）下载的**3252份SARS-CoV-2基因组登录序列**，样本采集时间覆盖2025年1月至5月初。经MAFFT软件完成序列比对，并通过严格质控剔除重复序列、不完整序列及比对错误的条目后，最终得到**2731条高质量序列**。
随后针对**nsp7、nsp8、nsp12及nsp14**这4个关键非结构蛋白区域生成突变矩阵。即便将突变频率阈值降至0.1%，仍未在上述基因中检出复发性突变，进一步印证了该时间段内基因组多样性较高，且趋同演化的证据有限。
研究结果凸显了在分析NCBI公共监测数据时，**严谨的序列整理质控**的重要性。本次观测到的多数变异均为罕见或私人变异，提示病毒种群仍处于演化过程中，截至2025年5月初尚未出现优势变异株。
所有突变矩阵均已提供，可保障研究结果可复现。

搜集汇总

背景与挑战

背景概述

该数据集包含2025年1月至5月初期间3,252个SARS-CoV-2基因组的突变分析数据，重点关注非结构蛋白NSP7、NSP8、NSP12和NSP14的突变矩阵。分析显示，这些基因组具有高多样性且趋同进化有限，未发现复发突变，表明在2025年5月初前病毒种群仍在进化，没有固定变异或优势变异出现。