Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland

Abstract

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed variant identification, spike mutation pattern analysis, and phylogenetic and evolutionary analyses for 1106 high-coverage whole-genome sequences, implementing maximum likelihood, multiple continuous-time Markov chain, and Bayesian birth–death skyline models. For time trends, logistic regression was used. In the dataset, virus B.1.221 lineage was predominant (15.37%), followed by B.1.258 (15.01%) and B.1.1.29 (11.48%) strains. Three clades were identified, being responsible for 74.41% of infections over the analyzed period. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. In population dynamics inferences, three periods with exponential increase in infection were observed, beginning in March, July, and September 2020, respectively, and were driven by different virus clades. Additionally, a notable increase in infections caused by the B.1.1.7 lineage since February 2021 was noted. Over time, the virus accumulated mutations related to optimized transmissibility; therefore, faster dissemination is reflected by the second wave of epidemics in Poland.

SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains

“…Even though there are different approaches to full-genome sequencing, the multiplex PCR amplicon method is currently one of the cheapest, while also proving to be superior to capture-based sequencing in the analysis of challenging samples [4]. For the purpose of the project founded by the Polish National Centre For Research and Development "Development of modern laboratory technologies, IT and bioinformatics dedicated to the diagnosis and prevention of SARS-CoV-2 infections" [27], we chose the AmpliSeq chemistry and panel (Ion AmpliSeq SARS-CoV-2 Research Panel) with IonTorrent sequencing technology for the sequencing of the whole SARS-CoV-2 genomes, with the additional aim to improve the efficiency of the chemistry on low-template samples.…”

Phylodynamic Dispersal of SARS-CoV-2 Lineages Circulating across Polish–German Border Provinces

“…Interestingly, only one B.1.177.86|20E.EU1| sequence was identified in Poland (region of West Pomerania), so there were no substantial binational transmission clusters for this lineage, but the timeline of this variant European dominance coincided with limited mobility between border provinces [ 41 ]. Of note, in PL-De-Interreg, the two subsequent prevalent lineages, B.1.258|20A| and B.1.221|20A|, from the second wave had been circulating extensively, and it appears to be congruent with patterns of incidence observed in West Poland [ 11 ] and East Germany [ 42 ].…”

“…More than 22,647,197 COVID-19 cases were registered in Germany as of 4 April 2022, compared to 5,978,215 incidences in Poland, meaning that these countries were within the top six most affected European Union (EU) states (Available online: ) (accessed on 15 April 2022)). During the expansion of the epidemic’s first wave, phylogenetic analyses revealed multiple independent introductions of the virus to the most populated EU member states, including variants classified as A1|19B|, A5|19 B|, B.1|20A|, B.1.1|20 B| and B.1.5|20A| [ 8 , 9 , 10 , 11 ]. In late March 2020, most EU countries introduced social distancing and lockdown policies [ 12 ], but this did not limit the second wave, which was largely dominated by B.1.1.177|20E.EU1| and B.1.160|20A.EU2) in Europe [ 13 ].…”

Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic

“…One of the purposes of this study was to provide information about the distribution of SARS-CoV-2 genome variants within isolates collected during the first year (March 2020–February 2021) of COVID-19 pandemic in the Czech Republic. In comparison to neighbouring countries, namely Austria [ 18 ], Poland [ 19 ], or Germany ( accessed on 24 July 2021), the Czech Republic developed no sustained countrywide effort focused on the sequencing of SARS-CoV-2-positive samples during the first year of the pandemic. For the purpose of our study, we have adopted formerly tested library preparation solutions for massive parallel sequencing [ 14 ] of isolates of nucleic acids from nasopharyngeal swabs of SARS-CoV-2-positive patients collected since early spring 2020 (March 2020) until February 2021 [ 20 , 21 , 22 ] in diagnostic laboratories located in five major hospitals (see Materials and Methods) selected to represent the progress of the pandemic within the entire country.…”