The first SARS-CoV-2 genetic variants of concern (VOC) in Poland: The concept of a comprehensive approach to monitoring and surveillance of emerging variants.

Charkiewicz, Radosław; Nikliński, Jacek; Biecek, Przemysław; Kiśluk, Joanna; Pancewicz, Sławomir; Moniuszko-Malinowska, Anna M; Flisiak, Robert; Krętowski, Adam J; Dzięcioł, Janusz; Moniuszko, Marcin; Gierczyński, Rafał; Juszczyk, Grzegorz; Reszeć, Joanna

PURPOSE We analyzed the SARS-CoV-2 genome using our integrated genome analysis system and present the concept of a comprehensive approach to monitoring and surveillance of emerging variants. MATERIAL/METHODS A total of 69 SARS-CoV-2 positive samples (with Ct value ​≤ ​28) were tested. Samples included in this study were selected from 7 areas of eastern Poland. All samples were sequenced on an Illumina MiSeq platform using a 300-cycle MiSeq Reagent Kit v2. BWA was used for reads mapping on the reference SARS-CoV-2 sequence. SAMTools were used for post-processing of reads to genome assembly. Pango lineage and Nexstrain were used to identify variants and amino acid mutations. Statistical analysis was performed with R 4.0.2. RESULTS This study shows the first confirmed case of SARS-CoV-2 in Poland with the lineage B.1.351 (known as 501Y.V2 South African variant), as well as another 18 cases with epidemiologically relevant lineage B.1.1.7, known as British variant. Supplementary analysis of SARS-CoV-2 sequences deposited in GISAID shows that the share of a new variant can change rapidly within one month. In addition, we show a complete, integrated concept of a networked system for analyzing the variability of the SARS-CoV-2 genome, which, used in the present study, generated data and a variant report within 6 days. CONCLUSION The analyzed viral genomes showed considerable variability with simultaneous clear distinction of local clusters of genomes showing high similarity. Implementing real-time monitoring of new SARS-CoV-2 variants in Poland is urgently needed, and our developed system is available to be implemented on a large scale.