European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

Abstract

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.

Nosocomial transmission clusters and lineage diversity characterized by SARS-CoV-2 genomes from two large hospitals in Paris, France, in 2020

“…These clades emerged during the second part of the year in Europe whereas they remained anecdotal in other regions of the world 35 . Overall, the SARS-CoV-2 molecular diversity we described in the Paris urban area is in accordance with the diversity described in different European countries over 2020 36 , 37 . Because of the same catchment area and the shared population of patients, the molecular epidemiology between the two hospitals was similar, except for the rare clades 20B and 20D from the first wave.…”

The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe

“…We have found instances of heteroplasmy that corresponds to the published results (Hryhorowicz et al, 2020), but the somewhat smaller heteroplasmy rate is likely due to the more stringent quality filtration in this study.…”

Demographic and Clinical Overview of Hospitalized COVID-19 Patients during the First 17 Months of the Pandemic in Poland

“…Moreover, this phase was also characterized by patients exhibiting significantly increased levels of inflammatory markers, including IL-6, as well as differences in blood morphology: higher WBC and neutrophils counts but lower counts of lymphocytes and platelets. This may be due to the increase of the G superclade frequency in SARS-CoV-2 variants circulating in Poland in 2020 [ 16 ]. Its hallmark D614G substitution in spike protein was associated with increased transmissibility and higher viral loads [ 17 ].…”