Mirjana Novkovic1*, Bojana Banovic Djeri1, Sasa Todorovic1, and Valentina Djordjevic1
1Institute of Molecular Genetics and Genetic Engineering University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
mirjananovkovic [at] imgge.bg.ac.rs
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic, resulting in significant morbidity and mortality worldwide. Understanding the evolutionary dynamics and genetic diversity of the virus were crucial for virus control and management strategies. With that aim we conducted genomic surveillance and phylogenetic analysis of SARS-CoV-2 variants in Serbia, spanning from March 2020 to the end of January 2023.
Sequencing was conducted using three different platforms: Oxford Nanopore, Ion Torrent AmpliSeq and BGISEQ-500. Consensus sequences obtained using platforms respective software were deposited in the GISAID database. In this study 2109 good-quality sequences were included (doi.10.55876/gis8.230411qh). Pangolin and Nextclade software were utilized for clade, lineage and variant determination, while sequence alignment and construction of the phylogenetic tree was performed using Nextstrain web-based application.
Variant analysis revealed over 125,000 mutations across the 2109 sequences, of which 38% occurred in the S protein encoding gene. The most common mutations involved intragenic single nucleotide variants (88%), followed by intragenic deletions (5%). All sequences were assigned to following 16 clades: 20A, 20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F.
Temporal analysis of the variants in Serbia revealed that the Alpha variant was predominant during 2020 and the first three months of 2021. The Delta variant emerged in June 2021, dominating until the end of December 2021, when Omicron variant was detected for the first time, overtaking the dominance for the remaining surveillance period. Notably, the Gamma and Epsilon variants were not detected in the analyzed samples.
Phylogenetic analysis demonstrated that the SARS-CoV-2 variants circulating in Serbia were largely comparable to the variants found in Europe. However, a slight delay in their emergence was observed, potentially attributed to a lower travel rate during that period and a decreased frequency of sequencing in certain months.
Keywords: Sars-CoV-2 variants, Next-generation sequencing, phylogeny, surveillance, Serbia
Acknowledgement: We would like to thank all researchers involved in testing and collecting Sars-Co-2 samples in Huo Yan National Laboratories for molecular detection of infectious agents (Clinical Center of Serbia in Belgrade and Clinical Center of Nis), Clinical Center of Vojvodina, Institute of Virology Vaccines and Sera “Torlak”, Veterinary Specialist Institute “Kraljevo”, Scientific Veterinary Institute “Novi Sad”, and The Directorate for National Reference Laboratories. Further we would like to thank all the researchers who were involved in sequencing, analyzing and submitting data to GISAID from the Institute of Molecular Genetics and Genetic Engineering University of Belgrade (UB), Faculty of Medicine UB, Faculty of Biology UB, and especially to the Veterinary Specialist Institute Kraljevo who were the first to start SARS-CoV-2 sequencing in Serbia in the very beginning of pandemic.
