Ivan Topolsky
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View article: Predicting COVID-19 case counts using SARS-CoV-2 genetic diversity from wastewater
Predicting COVID-19 case counts using SARS-CoV-2 genetic diversity from wastewater Open
Wastewater monitoring is a promising, cost-effective method for pathogen surveillance, particularly when individual patient testing is limited. A typical approach is to estimate viral concentrations using PCR-based quantification of viral …
View article: Characterizing influenza A virus lineages and clinically relevant mutations through high-coverage wastewater sequencing
Characterizing influenza A virus lineages and clinically relevant mutations through high-coverage wastewater sequencing Open
Influenza A virus poses significant public health challenges, causing seasonal outbreaks and pandemics. Its rapid evolution motivates continuous monitoring of circulating influenza genomes to inform vaccine and antiviral development. Waste…
View article: Wastewater sequencing reveals the genomic landscape of Influenza A virus in Switzerland
Wastewater sequencing reveals the genomic landscape of Influenza A virus in Switzerland Open
Influenza A virus poses significant public health challenges, causing seasonal outbreaks and pandemics. Its rapid evolution motivates continuous monitoring of circulating influenza genomes to inform vaccine and antiviral development. Waste…
View article: Wastewater-based sequencing of Respiratory Syncytial Virus enables tracking of lineages and identifying mutations at antigenic sites
Wastewater-based sequencing of Respiratory Syncytial Virus enables tracking of lineages and identifying mutations at antigenic sites Open
Respiratory Syncytial Virus (RSV) infections pose a substantial health burden, especially for vulnerable populations such as infants and the elderly. While novel immunoprophylaxis offer promising protection, many countries lack robust surv…
View article: Assessing different next-generation sequencing technologies for wastewater-based epidemiology
Assessing different next-generation sequencing technologies for wastewater-based epidemiology Open
Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of the disease burden as compared to clinical tes…
View article: VILOCA: Sequencing quality-aware haplotype reconstruction and mutation calling for short- and long-read data
VILOCA: Sequencing quality-aware haplotype reconstruction and mutation calling for short- and long-read data Open
RNA viruses exist in large heterogeneous populations within their host. The structure and diversity of virus populations affects disease progression and treatment outcomes. Next-generation sequencing allows detailed viral population analys…
View article: Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data Open
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2…
View article: Assessing different next-generation sequencing technologies for wastewater-based epidemiology
Assessing different next-generation sequencing technologies for wastewater-based epidemiology Open
Wastewater-based epidemiology has proven to be an important public health asset during the COVID-19 pandemic. It can provide less biassed and more cost-effective population-level monitoring of the disease burden as compared to clinical tes…
View article: Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data Open
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2…
View article: Exploring the landscape of the genomic wastewater surveillance ecosystem: a roadmap towards standardization
Exploring the landscape of the genomic wastewater surveillance ecosystem: a roadmap towards standardization Open
The landscape of genomic wastewater surveillance in the context of infectious disease monitoring is rapidly evolving, and this came into sharp focus during the COVID-19 pandemic. Here we highlight the significance of wastewater surveillanc…
View article: V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation Open
The large amount and diversity of viral genomic datasets generated by next-generation sequencing technologies poses a set of challenges for computational data analysis workflows, including rigorous quality control, adaptation to higher sam…
View article: How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort
How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort Open
Background During the SARS-CoV-2 pandemic, many countries directed substantial resources towards genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillan…
View article: Executing workflows in the cloud with WESkit
Executing workflows in the cloud with WESkit Open
With the exponential increase in genomic data, analyzing and processing large datasets has become a challenging task in healthcare. To address this issue, the Global Alliance for Genomics and Health (GA4GH) has proposed a set of community …
View article: Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data
Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data Open
Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 20…
View article: Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with<i>LolliPop</i>
Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with<i>LolliPop</i> Open
During the COVID-19 pandemic, wastewater-based epidemiology has progressively taken a central role as a pathogen surveillance tool. Tracking viral loads and variant outbreaks in sewage offers advantages over clinical surveillance methods b…
View article: Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC Open
View article: Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study
Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study Open
AIMS OF THE STUDY: Wastewater-based epidemiology has contributed significantly to the comprehension of the dynamics of the current COVID-19 pandemic. Its additional value in monitoring SARS-CoV-2 circulation in the population and identifyi…
View article: Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example Open
View article: Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data
Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data Open
Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 SARS-CoV-2 genomes from Switzerland in 2020 - the 6th largest effort globally. Using a repr…
View article: Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland Open
View article: Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland Open
Background In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a tra…
View article: Detection and surveillance of SARS-CoV-2 genomic variants in wastewater
Detection and surveillance of SARS-CoV-2 genomic variants in wastewater Open
The emergence of SARS-CoV-2 mutants with altered transmissibility, virulence, or immunogenicity emphasizes the need for early detection and epidemiological surveillance of genomic variants. Wastewater samples provide an opportunity to asse…
View article: V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data Open
Motivation High-throughput sequencing technologies are used increasingly not only in viral genomics research but also in clinical surveillance and diagnostics. These technologies facilitate the assessment of the genetic diversity in intra-…
View article: Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data Open
Pathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage bec…
View article: Within-patient genetic diversity of SARS-CoV-2
Within-patient genetic diversity of SARS-CoV-2 Open
SARS-CoV-2, the virus responsible for the current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viru…
View article: V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data Open
High-throughput sequencing technologies are used increasingly, not only in viral genomics research but also in clinical surveillance and diagnostics. These technologies facilitate the assessment of the genetic diversity in intra-host virus…
View article: "First steps with": a training course series to launch life scientists on the road towards bioinformatics
"First steps with": a training course series to launch life scientists on the road towards bioinformatics Open