Browsing by Author "Loncar, Ana (57225067864)"

Real-time reverse transcription polymerase chain reaction (RT-qPCR) is the most sensitive and specific assay and, therefore, is the “gold standard” diagnostic method for the diagnosis of SARS-CoV-2 infection. The aim of this study was to compare and analyze the detection performance of three different commercially available SARS-CoV-2 nucleic acid detection kits: Sansure Biotech, GeneFinder™, and TaqPath™ on 354 randomly selected samples from hospitalized COVID-19 patients. All PCR reactions were performed using the same RNA isolates and one real-time PCR machine. The final result of the three evaluated kits was not statistically different (p = 0.107), and also had a strong positive association and high Cohen’s κ coefficient. In contrast, the average Ct values that refer to the ORF1ab and N gene amplification were significantly different (p < 0.001 and p < 0.001, respectively), with the lowest obtained by the TaqPath™ for the ORF1ab and by the Sansure Biotech for the N gene. The results show a high similarity in the analytical sensitivities for SARS-CoV-2 detection, which indicates that the diagnostic accuracy of the three assays is comparable. However, the SanSure Biotech kit showed a bit better diagnostic performance. Our findings suggest that the imperative for improvement should address the determination of cut-off Ct values and rapid modification of the primer sets along with the appearance of new variants. © 2021 by the authors.

Real-time reverse transcription polymerase chain reaction (RT-qPCR) is the most sensitive and specific assay and, therefore, is the “gold standard” diagnostic method for the diagnosis of SARS-CoV-2 infection. The aim of this study was to compare and analyze the detection performance of three different commercially available SARS-CoV-2 nucleic acid detection kits: Sansure Biotech, GeneFinder™, and TaqPath™ on 354 randomly selected samples from hospitalized COVID-19 patients. All PCR reactions were performed using the same RNA isolates and one real-time PCR machine. The final result of the three evaluated kits was not statistically different (p = 0.107), and also had a strong positive association and high Cohen’s κ coefficient. In contrast, the average Ct values that refer to the ORF1ab and N gene amplification were significantly different (p < 0.001 and p < 0.001, respectively), with the lowest obtained by the TaqPath™ for the ORF1ab and by the Sansure Biotech for the N gene. The results show a high similarity in the analytical sensitivities for SARS-CoV-2 detection, which indicates that the diagnostic accuracy of the three assays is comparable. However, the SanSure Biotech kit showed a bit better diagnostic performance. Our findings suggest that the imperative for improvement should address the determination of cut-off Ct values and rapid modification of the primer sets along with the appearance of new variants. © 2021 by the authors.

Here, we report on a serendipitous finding of a chryso-like virus associated with Culex pipiens mosquitos in the course of study aimed to detect and characterize West Nile virus (WNV) circulating in mosquitos in Serbia, Southern Europe. Upon initial detection of unexpected product in a PCR protocol for partial WNV NS5 gene amplification, further confirmation and identification was obtained through additional PCR and Sanger sequencing experiments. Bioinformatic and phylogenetic analysis identified the obtained sequences as Xanthi chryso-like virus (XCLV). The finding is particular for the fact that it associates XCLV with a new potential vector species and documents a novel geographical area of its distribution. © 2023 by the authors.

Here, we report on a serendipitous finding of a chryso-like virus associated with Culex pipiens mosquitos in the course of study aimed to detect and characterize West Nile virus (WNV) circulating in mosquitos in Serbia, Southern Europe. Upon initial detection of unexpected product in a PCR protocol for partial WNV NS5 gene amplification, further confirmation and identification was obtained through additional PCR and Sanger sequencing experiments. Bioinformatic and phylogenetic analysis identified the obtained sequences as Xanthi chryso-like virus (XCLV). The finding is particular for the fact that it associates XCLV with a new potential vector species and documents a novel geographical area of its distribution. © 2023 by the authors.

West Nile Virus (WNV) is considered one of the most widely distributed arboviruses worldwide. In 2018, Serbia was among the European countries reporting the highest number of WNV cases. This study aimed to characterize WNV strains circulating in Serbia, and to estimate the pathways and dynamics of WNV-2 spread in the Balkans and globally through the phylogenetic approach. Fifty newly generated NS5 Serbian sequences were found to belong to WNV lineage 2. Phylodynamic analyses of the Balkan clade indicated the potential for an increase in genetic diversity and structure of virus populations. Presented phylogeographic analyses implied four instances of long-distance WNV-2 migration from Africa to Europe, during the 1940s to 1950s, while further dissemination of WNV-2 originated in Hungary in mid-1970s and subsequently spread to Austria and Serbia. Extensive dispersion took place during the 1990s–2000s, as the virus spread from Austria to central and western Europe, and from Hungary to the Balkans. Continuous phylogeography analysis of the Balkans WNV-2 clade implied the central role of Serbia for WNV dissemination across the Balkan peninsula. Furthermore, previously undocumented instance of intercontinental migration of WNV-2 from Europe to Asia was implied. In-depth phylogenetic investigation into the global distribution of WNV-2 may provide valuable insights into the prediction and prevention of potential epidemics. © 2024 Wiley Periodicals LLC.

West Nile Virus (WNV) is considered one of the most widely distributed arboviruses worldwide. In 2018, Serbia was among the European countries reporting the highest number of WNV cases. This study aimed to characterize WNV strains circulating in Serbia, and to estimate the pathways and dynamics of WNV-2 spread in the Balkans and globally through the phylogenetic approach. Fifty newly generated NS5 Serbian sequences were found to belong to WNV lineage 2. Phylodynamic analyses of the Balkan clade indicated the potential for an increase in genetic diversity and structure of virus populations. Presented phylogeographic analyses implied four instances of long-distance WNV-2 migration from Africa to Europe, during the 1940s to 1950s, while further dissemination of WNV-2 originated in Hungary in mid-1970s and subsequently spread to Austria and Serbia. Extensive dispersion took place during the 1990s–2000s, as the virus spread from Austria to central and western Europe, and from Hungary to the Balkans. Continuous phylogeography analysis of the Balkans WNV-2 clade implied the central role of Serbia for WNV dissemination across the Balkan peninsula. Furthermore, previously undocumented instance of intercontinental migration of WNV-2 from Europe to Asia was implied. In-depth phylogenetic investigation into the global distribution of WNV-2 may provide valuable insights into the prediction and prevention of potential epidemics. © 2024 Wiley Periodicals LLC.

Background: Usutu virus (USUV) is an emerging mosquito-borne Flavivirus, with birds as the main zoonotic reservoir. Humans are accidental hosts and mostly develop mild or even asymptomatic infections, although severe complications such as encephalitis can also arise. Detailed characterization of the pathogen's phylogenetics may offer valuable insights into the prediction and prevention of potential epidemics; however, lack of uniformity and the number of available USUV sequences worldwide hamper comprehensive investigation. Aim: The study aimed to investigate USUV spatio-temporal dispersal inter- and intracontinentally and to estimate the dynamics of viral spread within Europe. Methods: Phylogeographic and phylodynamic analyses were done using advanced phylogenetic methods implemented in Beast 1.10.4 and Beast 2.6.4 software packages. Results: Herein, we report on a new USUV isolate from Culex pipiens collected in 2019 from Serbia. The results of this research revealed two newly described intercontinental migration events of USUV from Africa to Germany in the 1970s and from Africa to the Middle East (Israel) in the late 90s. Finally, phylodynamic analysis substantiated the ongoing active expansion of USUV in Europe. Conclusion: The data would imply a high potential for further USUV expansion in Europe. Detailed phylogenetic characterization of the pathogen may offer valuable insights into prediction and prevention of potential epidemics; however, lack of uniformity and number of available USUV sequences worldwide hampers comprehensive investigation. This study draws attention to the need for upscaling USUV surveillance. Copyright © 2023 Siljic, Sehovic, Jankovic, Stamenkovic, Loncar, Todorovic, Stanojevic and Cirkovic.

Background: Usutu virus (USUV) is an emerging mosquito-borne Flavivirus, with birds as the main zoonotic reservoir. Humans are accidental hosts and mostly develop mild or even asymptomatic infections, although severe complications such as encephalitis can also arise. Detailed characterization of the pathogen's phylogenetics may offer valuable insights into the prediction and prevention of potential epidemics; however, lack of uniformity and the number of available USUV sequences worldwide hamper comprehensive investigation. Aim: The study aimed to investigate USUV spatio-temporal dispersal inter- and intracontinentally and to estimate the dynamics of viral spread within Europe. Methods: Phylogeographic and phylodynamic analyses were done using advanced phylogenetic methods implemented in Beast 1.10.4 and Beast 2.6.4 software packages. Results: Herein, we report on a new USUV isolate from Culex pipiens collected in 2019 from Serbia. The results of this research revealed two newly described intercontinental migration events of USUV from Africa to Germany in the 1970s and from Africa to the Middle East (Israel) in the late 90s. Finally, phylodynamic analysis substantiated the ongoing active expansion of USUV in Europe. Conclusion: The data would imply a high potential for further USUV expansion in Europe. Detailed phylogenetic characterization of the pathogen may offer valuable insights into prediction and prevention of potential epidemics; however, lack of uniformity and number of available USUV sequences worldwide hampers comprehensive investigation. This study draws attention to the need for upscaling USUV surveillance. Copyright © 2023 Siljic, Sehovic, Jankovic, Stamenkovic, Loncar, Todorovic, Stanojevic and Cirkovic.

March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations. © Copyright © 2021 Miljanovic, Milicevic, Loncar, Abazovic, Despot and Banko.

March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations. © Copyright © 2021 Miljanovic, Milicevic, Loncar, Abazovic, Despot and Banko.