Do the shape and size of quasispecies reflect the host range of viruses?
Viruses exist as dynamic populations of closely related viral genomes arising from mutations, known as quasispecies. We hypothesise that viruses use their quasispecies to expand their evolutionary potential, making them critical for adaptation to new hosts and for resistance to host defences or immunity. Yet, the evolutionary trajectories of viruses cannot be fully understood without considering their ecological context. Host range and environmental conditions act as powerful filters and drivers of viral diversification, raising fundamental research questions at the interface of viral ecology and evolution: How do host interactions and environmental factors shape the emergence, stability, and adaptability of viral quasispecies? If the genetic diversity of the quasispecies reflects the evolutionary potential and ecological interactions of the virus, by which molecular mechanisms do viruses exploit their quasispecies for host range evolution? To address these fundamental questions at the core of our project, we will develop and apply a novel suite of computational tools based on Sequence Variation Graphs (SVGs). SVGs are increasingly utilised for population structure analysis in higher organisms, but their application in virology is limited due to the high mutation rates and genomic diversity of viruses. Nevertheless, they offer potential for analysing data from both genomic and metagenomic samples. In work package WP 1, we will build a quasispecies Sequence Variation Graph (qs-SVG) toolkit that can store sequencing data of viral populations, and we will use and further improve the tool in the remaining work packages. Once the tool is built, we will first apply it to an ideal case where abundant data is available, i.e., SARS-CoV-2 and influenza viruses before, taking on a more challenging case, i.e., bacteriophages found in environmental metagenomes.
The central hypothesis of our project is that viruses use their quasispecies for host range evolution, with specific hypotheses including: (1) Viral quasispecies are shaped by host- and virus-specific factors, and by environmental context; (2) Quasispecies are shaped by targeted mutations, specifically of host interaction genes, leading to host switching.
By combining these two study systems in our project, we will be able to test different functionalities of the qs-SVG toolkit and develop an optimal bioinformatic solution. In WP 2, we will exploit new and existing data on the quasispecies of human viruses and bacteriophages with broad and narrow host ranges, to test the specific hypothesis that viruses with a broad host range also have a large quasispecies. In WP 3, we will investigate under what conditions viruses evolve their quasispecies. We will examine the relationship between quasispecies, host diversity, and the environment, using both in vitro data from isolates, and in situ data by screening metagenomic data sets derived from environmental samples. Finally, in WP 4 we will focus on the underlying mutational mechanisms. How does quasispecies sequence variation arise? Can viruses exploit mutation to expand their host range, and what molecular mechanisms enable this?
The qs-SVG toolkit will provide immediate access to mutations and genetic functions, enabling us to explore the association of these features with variable sites. We will also chart the distribution of the mutational mechanisms across ecosystems and host types (G3). Thus, our new tool suite will facilitate describing, quantifying, and understanding emerging viruses (G1) and offer new perspectives for studying their evolution (G2) in the context of host range.
WP 1: Development of a tool to formally quantify quasispecies (Dutilh)
WP 2: Measuring the effect of quasispecies on host range and other phenotypic characters (Dutilh/Küsel)
WP 3: Measuring quasispecies in natural ecosystems and targeted microcosm incubations (Küsel/Dutilh)
WP 4: Ecological imprint of evolvability mechanisms and implications for classification (Dutilh/Küsel)
Team Members
N. N.
Doctoral Researcher
N. N.
Doctoral Researcher
Project-Specific Publications
2025
Ultrafast and accurate sequence alignment and clustering of viral genomes. Journal Article
In: Nat Methods, vol. 22, iss. 6, pp. 1191–1194, 2025, ISSN: 1548-7105.
Hidden viral players: Diversity and ecological roles of viruses in groundwater microbiomes Journal Article
In: 2025.
2024
Graphite: Painting genomes using a colored de Bruijn graph Journal Article
In: NAR Genom Bioinform, vol. 6, no. 4, 2024, ISSN: 2631-9268.
Genome streamlining in Parcubacteria transitioning from soil to groundwater Journal Article
In: Environ Microbiome, vol. 19, no. 1, 2024, ISSN: 2524-6372.
2023
A social niche breadth score reveals niche range strategies of generalists and specialists Journal Article
In: Nat Ecol Evol, vol. 7, no. 5, pp. 768–781, 2023.
2022
Carbon fixation rates in groundwater similar to those in oligotrophic marine systems Journal Article
In: Nat Geosci, vol. 15, no. 7, pp. 561–567, 2022, ISSN: 1752-0908.
High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems Journal Article
In: Curr Biol, vol. 32, iss. 1, pp. 220–227.e5, 2022.
2019
Marine DNA viral macro- and microdiversity from pole to pole Journal Article
In: Cell, vol. 177, iss. 5, no. 5, pp. 1109–1123.e14, 2019, ISSN: 0092-8674.
Molecular and evolutionary determinants of bacteriophage host range Journal Article
In: Trends Microbiol, vol. 27, iss. 1, pp. 51–63, 2019.
2018
Growth promotion and inhibition induced by interactions of groundwater bacteria. Journal Article
In: FEMS Microbiol Ecol, vol. 94, iss. 11, 2018, ISSN: 1574-6941.