From Alpha to Delta—Genetic Epidemiology of SARS-CoV-2 (hCoV-19) in Southern Poland

Abstract

In Poland, the first case of SARS-CoV-2 infection was confirmed in March 2020. Since then, many circulating virus lineages fueled rapid pandemic waves which inflicted a severe burden on the Polish healthcare system. Some of these lineages were associated with increased transmissibility and immune escape. Mutations in the viral spike protein, which is responsible for host cell recognition and serves as the primary target for neutralizing antibodies, are of particular importance. We investigated the molecular epidemiology of the SARS-CoV-2 clades circulating in Southern Poland from February 2021 to August 2021. The 921 whole-genome sequences were used for variant identification, spike mutation, and phylogenetic analyses. The Pango B.1.1.7 was the dominant variant (n = 730, 89.68%) from March 2021 to July 2021. In July 2021, the B.1.1.7 was displaced by the B.1.617.2 lineage with 66.66% in July 2021 and 92.3% in August 2021 frequencies, respectively. Moreover, our results were compared with the sequencing available on the GISAID platform for other regions of Poland, the Czech Republic, and Slovakia. The analysis showed that the dominant variant in the analyzed period was B.1.1.7 in all countries and Southern Poland (Silesia). Interestingly, B.1.1.7 was replaced by B.1.617.2 earlier in Southern Poland than in the rest of the country. Moreover, in the Czech Republic and Slovakia, AY lineages were predominant at that time, contrary to the Silesia region.

Ensitrelvir is effective against SARS-CoV-2 3CL protease mutants circulating globally

“…Global Initiative on Sharing Avian Influenza Data (GISAID) is one of the SARS-CoV-2 WGS public databases. SARS-CoV-2 WGS and information on SARS-CoV-2 mutations circulating around the world are used for various kinds of analyses, such as on the prevalence of SARS-CoV-2 variants and the spread of such variants in specific regions [ 6 , 7 ].…”

Reinfections from SARS-CoV-2: A Retrospective Study from the Gyncentrum Genetic Laboratory in Sosnowiec, Poland, April 2020 to July 2022

“…There was also no available information about detected SARS-CoV-2 variants because tests specifically for this purpose were implemented with a delay. The time period in which these tests were performed was described in detail in our previous study [ 27 ]. The samples were also collected in a relatively small area of Poland (the analysis was conducted at a single center), making it difficult to generalize the results to the entire country.…”

A Retrospective Population Study of 385 191 Positive Real-Time Reverse Transcription–Polymerase Chain Reaction Tests For SARS-CoV-2 from a Single Laboratory in Katowice, Poland from April 2020 to July 2022

“…The beginning of 2021 witnessed a gradual loosening of restrictions, adopting solutions regulating travel, and promoting vaccinations [ 32 ]. Nevertheless, infections increased in March and April 2021, when variant B.1.1.7 (alpha) dominated, and again in November and December 2021 [ 33 ].…”