Biology subjects

Pettersson, J. H.- O.

Publications and source records attributed to Pettersson, J. H.- O..

7 recordsLinked to original sources

bioRxiv2026

Exploring the influence of mutation rates with stochastic perturbations on genome evolution

We present a stochastic version of the classical Luria-Delbruck mutation rate model using Ito calculus. Our model is used to explore implications of population growth with randomly varying mutation rates. By comparing the It&ocirc version of the Luria-Delbruck mutation rate model to the deterministic we find that stochastic effects can have profound implications for genome evolution. In particular, as the growth rate decreases below the population's carrying capacity, or another given threshold, we show that stochastic effects can dominate the evolution of a population in a feedback-based manner. Moreover, we find that the influence of stochastic effects increase as the population reaches its carrying capacity if not accounted for. Our model also suggests strategies for a population to overcome increasing mutational load and evolve 'robustness' to genetic drift. We discuss our methodology in light of the SARS-CoV-2 virus and implications for its molecular evolution. Finally, we conclude that Ito calculus incorporates stochastic effects in mathematical models in a way that is very natural to biological systems.

evolutionary biology↗

bioRxiv2024

The evolutionary and molecular history of a chikungunya virus outbreak lineage

In 2018-2019, Thailand experienced a nationwide spread of chikungunya virus (CHIKV), with approximately 15,000 confirmed cases of disease reported. Here, we investigated the evolutionary and molecular history of the East/Central/South African (ECSA) genotype to determine the origins of the 2018-2019 CHIKV outbreak in Thailand. This was done using newly sequenced clinical samples from travellers returning to Sweden from Thailand in late 2018 and early 2019 and previously published genome sequences. Our phylogeographic analysis showed that before the outbreak in Thailand, the Indian Ocean lineage (IOL) found within the ESCA, had evolved and circulated in East Africa, South Asia, and Southeast Asia for about 15 years. In the first half of 2017, an introduction occurred into Thailand from another South Asian country, most likely Bangladesh, which subsequently developed into a large outbreak in Thailand with export to neighbouring countries. Based on comparative phylogenetic analyses of the complete CHIKV genome and protein modelling, we also identified amino acid substitutions that may be associated with immune evasion, increased spread, and virulence. We identified several mutations in the E1/E2 spike complex, such as E1 K211E and E2 V264A, which are highly relevant as they may lead to changes in vector competence, transmission efficiency and pathogenicity of the virus. A number of mutations (E2 G205S, Nsp3 D372E, Nsp2 V793A), that emerged shortly before the outbreak of the virus in Thailand in 2018 may have altered antibody binding and recognition due to their position. This study not only improves our understanding of the factors contributing to the epidemic in Southeast Asia, but also has implications for the development of effective response strategies and the potential development of new vaccines. Author SummaryWe investigated the evolutionary and molecular history of the East/Central/South African (ECSA) genotype to determine the origins of the 2018-2019 chikungunya virus (CHIKV) outbreak in Thailand. We used newly sequenced clinical samples from travellers returning to Sweden from Thailand in late 2018 and early 2019 together with previously published genome sequences. Our phylogeographic analysis shows that the Indian Ocean lineage (IOL), found within ECSA, evolved in Eastern Africa, Southern Asia, and Southeast Asia for about 15 years before the outbreak in Thailand in 2018. We have also identified amino acid substitutions that may be associated with immune evasion, increased spread, and higher virulence that occurred prior to the outbreak and may have played a critical role in the rapid spread of the virus. Our study concludes that monitoring and understanding CHIKV dynamics remains critical for an effective response to the previously unpredictable outbreaks of the virus.

microbiology↗

bioRxiv2022

Discovery of a novel coronavirus in Swedish bank voles (Myodes glareolus)

We identified a novel Betacoronavirus from bank voles (Myodes glareolus) in Grimso, Sweden. Repeated detection over three years and an overall prevalence of 3.4% suggests the virus commonly occurs in bank voles. Furthermore, phylogenetic analyses indicate the virus belongs to a highly divergent Embecovirus lineage predominantly associated with bank voles.

microbiology↗

bioRxiv2020

Metagenomic identification of diverse animal hepaciviruses and pegiviruses

The RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus - each of which have a diverse host range. Members of the genus Hepacivirus are associated with a diverse array of animal species, including humans and non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa including humans. Using a combination of meta-transcriptomic and whole genome sequencing we identified four novel hepaciviruses and one novel variant of a known virus, in five species of native Australian wildlife, expanding our knowledge of the diversity in this important group of RNA viruses. The infected hosts comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). The addition of these novel viruses led to the identification of a distinct marsupial clade within the hepacivirus phylogeny that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Gecko and avian associated hepacivirus lineages were also identified. In addition, by mining the short-read archive (SRA) database we identified another five novel members of Flaviviridae, comprising three new hepaciviruses from avian and primate hosts, as well as two primate-associated pegiviruses. The large-scale phylogenetic analysis of these novel hepacivirus and pegivirus genomes provides additional support for virus-host co-divergence over evolutionary time-scales.

microbiology↗

bioRxiv2020

Circumpolar diversification of the Ixodes uriae tick virome

Ticks (order: Ixodida) are a highly diverse and ecologically important group of ectoparasitic blood-feeding organisms. One such species, the seabird tick (Ixodes uriae), is widely distributed around the circumpolar regions of the northern and southern hemispheres. It has been suggested that Ix. uriae spread from the southern to the northern circumpolar region millions of years ago and has remained isolated in these regions ever since. Such a profound biographic subdivision provides a unique opportunity to determine whether viruses associated with ticks exhibit the same evolutionary patterns as their hosts. To test this, we collected Ix. uriae specimens near a Gentoo penguin (Pygoscelis papua) colony at Neko harbour, Antarctica, and from migratory birds - the Razorbill (Alca torda) and the Common murre (Uria aalge) - on Bonden island, northern Sweden. Through meta-transcriptomic next- generation sequencing we identified 16 RNA viruses, seven of which were novel. Notably, we detected the same species, Ronne virus, and two closely related species, Bonden virus and Piguzov virus, in both hemispheres indicating that there have been at least two cross- circumpolar dispersal events. Similarly, we identified viruses discovered previously in other locations several decades ago, including Gadgets Gully virus, Taggert virus and Okhotskiy virus. By identifying the same or closely related viruses in geographically disjunct sampling locations we therefore provide evidence for virus dispersal within and between the circumpolar regions. In marked contrast, our phylogenetic analysis revealed no movement of the Ix. uriae hosts between the same locations. Combined, these data suggest that migratory birds are responsible for the movement of viruses at both the local and global scales. Author summary/ImportanceAs host populations diverge, so may those microorganisms, including viruses, that are dependent on those hosts. To examine this key issue in host-microbial evolution we compared the co-phylogenies of the seabird tick, Ixodes uriae, and their RNA viruses sampled from the far northern and southern hemispheres. Despite the huge geographic distance between them, phylogeographic analysis reveals that the same viruses were found both within and between the northern and southern circumpolar regions, most likely reflecting transfer by virus-infected migratory birds. In contrast, genomic data suggested that the Ix. uriae populations were phylogenetically distinct between the northern and southern hemispheres. This work emphasises the importance of migratory birds and ticks as vectors and sources of virus dispersal and introduction at both the local and global scales.

microbiology↗

bioRxiv2019

Meta-transcriptomic comparison of the RNA viromes of the mosquito vectors Culex pipiens and Culex torrentium in northern Europe

There is mounting evidence that mosquitoes harbour an extensive diversity of insect-specific RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes there is a major knowledge gap on the genetic diversity, evolutionary history, and spread of RNA viruses sampled from mosquitoes in northern latitudes. Here, we determined and compared the RNA virome of two common northern Culex mosquito species, Cx. pipiens and Cx. torrentium, known vectors of West Nile virus and Sindbis virus, respectively, collected in south-central Sweden. Following bulk RNA-sequencing (meta-transcriptomics) of 12 libraries, comprising 120 specimens of Cx. pipiens and 150 specimens of Cx. torrentium, we identified 40 viruses (representing 14 virus families) of which 28 were novel based on phylogenetic analysis of the RNA-dependent RNA polymerase (RdRp) protein. Hence, we found similar levels of virome diversity as in mosquitoes sampled from the more biodiverse lower latitudes. Four libraries, all from Cx. torrentium, had a significantly higher abundance of viral reads, spanning [~]7- 36% of the total amount of reads. Many of these viruses were also related to those sampled on other continents, indicative of widespread global movement and/or long host-virus co-evolution. Importantly, although the two mosquito species investigated have overlapping geographical distributions and share many viruses, approximately one quarter of the viruses were only found at a specific location, such that geography must play an important role in shaping the diversity of RNA viruses in Culex mosquitoes.\n\nImportanceRNA viruses are found in all domains of life and all global habitats. However, the factors that determine virome composition and structure within and between organisms are largely unknown. Herein, we characterised RNA virus diversity in two common mosquito vector species, Culex pipiens and Culex torrentium, sampled from northern Europe. Our analysis revealed extensive viral diversity, including 28 novel viruses, and was comparable to the levels of diversity found in other temperate and tropical regions globally. Importantly, as well as harbouring RNA viruses that are closely related to other mosquito-derived viruses sampled in diverse global locations, we also described a number of viruses that are unique to specific sampling locations in Sweden. Hence, these data showed that geographical factors can play an important role in shaping virome structure even at local scales.

evolutionary biology↗

bioRxiv2019

Novel hepatitis D-like agents in vertebrates and invertebrates

Hepatitis delta virus (HDV) is the smallest known RNA virus and encodes a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has a far longer evolutionary history. Herein, using additional meta-transcriptomic data, we show that highly divergent HDV-like viruses are also present in fish, amphibians and invertebrates. Notably, the novel viruses identified here share HDV-like genomic features such as a small genome size of ~1.7kb in length, circular genomes, and self-complementary, unbranched rod-like structures. Coiled-coil domains, leucine zippers, conserved residues with essential biological functions and isoelectronic points similar to those in the human hepatitis delta virus antigens (HDAgs) were also identified in the putative non-human HDAgs. Notably, none of these novel HDV-like viruses were associated with hepadnavirus infection, supporting the idea that the HDV-HBV association may be specific to humans. Collectively, these data not only broaden our understanding of the diversity and host range of HDV in non-human species, but shed light on its origin and evolutionary history.

evolutionary biology↗