@conference{
author = "Novković, Mirjana and Banović Đeri, Bojana and Todorović, Saša and Đorđević, Valentina",
year = "2023",
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.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Genomic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Variants in Serbia: Insights into Evolutionary Dynamics and Genetic Diversity",
pages = "81-81",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2021"
}
