To provide a comprehensive analysis of the SARS-CoV-2 sequence diversity in Poland in the European context. All publicly available (n = 115; GISAID database) whole-genome SARS-Cov-2 sequences from Polish samples, including those obtained during coronavirus testing performed in our COVID-19 Lab, were examined. Multiple sequence alignment of Polish isolates, phylogenetic analysis (ML tree), and multidimensional scaling (based on the pairwise DNA distances) were complemented by the comparison of the coronavirus clades frequency and diversity in the subset of over 5000 European GISAID sequences. Approximately seventy-seven percent of isolates in the European dataset carried frequent and ubiquitously found haplotypes; the remaining haplotype diversity was population-specific and resulted from population-specific mutations, homoplasies, and recombinations. Coronavirus strains circulating in Poland represented the variability found in other European countries. The prevalence of clades circulating in Poland was shifted in favor of GR, both in terms of the diversity (number of distinct haplotypes) and the frequency (number of isolates) of the clade. Polish-specific haplotypes were rare and could be explained by changes affecting common European strains. The analysis of the whole viral genomes allowed detection of several tight clusters of isolates, presumably reflecting local outbreaks. New mutations, homoplasies, and, to a smaller extent, recombinations increase SARS-CoV-2 haplotype diversity, but the majority of these variants do not increase in frequency and remains rare and population-specific. The spectrum of SARS-CoV-2 haplotypes in the Polish dataset reflects many independent transfers from a variety of sources, followed by many local outbreaks. The prevalence of the sequences belonging to the GR clade among Polish isolates is consistent with the European trend of the GR clade frequency increase.

旨在对欧洲背景下波兰的 SARS-CoV-2 序列多样性进行全面分析。对来自波兰样本的所有公开可用（n  = 115；GISAID 数据库）全基因组 SARS-Cov-2 序列（包括在我们的 COVID-19 实验室进行的冠状病毒检测期间获得的序列）进行了检查。通过比较 5000 多个欧洲 GISAID 序列子集中的冠状病毒进化枝频率和多样性，对波兰分离株的多重序列比对、系统发育分析（ML 树）和多维缩放（基于成对 DNA 距离）进行了补充。欧洲数据集中大约 77% 的分离株携带频繁且普遍存在的单倍型；其余的单倍型多样性是群体特异性的，是由群体特异性突变、同质性和重组造成的。在波兰传播的冠状病毒株代表了在其他欧洲国家发现的变异性。在波兰流行的分支的流行度向有利于 GR 的方向转变，无论是在分支的多样性（不同单倍型的数量）还是频率（分离株的数量）方面。波兰特有的单倍型很少见，可以用影响常见欧洲菌株的变化来解释。对整个病毒基因组的分析可以检测到几个紧密的分离群，这可能反映了当地的疫情爆发。新的突变、同质性以及较小程度的重组增加了 SARS-CoV-2 单倍型多样性，但其中大多数变异的频率并未增加，并且仍然罕见且具有人群特异性。波兰数据集中的 SARS-CoV-2 单倍型谱反映了来自各种来源的许多独立转移，以及随后发生的许多当地疫情。波兰分离株中属于 GR 进化枝的序列的流行率与欧洲 GR 进化枝频率增加的趋势一致。