More Like this

1. A hybrid stochastic-deterministic approach to explore multiple infection and evolution in HIV

   https://doi.org/10.1371/journal.pcbi.1009713  

   Kreger, Jesse; Komarova, Natalia L.; Wodarz, Dominik (December 2021, PLOS Computational Biology)

   Pascual, Mercedes (Ed.)

   To study viral evolutionary processes within patients, mathematical models have been instrumental. Yet, the need for stochastic simulations of minority mutant dynamics can pose computational challenges, especially in heterogeneous systems where very large and very small sub-populations coexist. Here, we describe a hybrid stochastic-deterministic algorithm to simulate mutant evolution in large viral populations, such as acute HIV-1 infection, and further include the multiple infection of cells. We demonstrate that the hybrid method can approximate the fully stochastic dynamics with sufficient accuracy at a fraction of the computational time, and quantify evolutionary end points that cannot be expressed by deterministic models, such as the mutant distribution or the probability of mutant existence at a given infected cell population size. We apply this method to study the role of multiple infection and intracellular interactions among different virus strains (such as complementation and interference) for mutant evolution. Multiple infection is predicted to increase the number of mutants at a given infected cell population size, due to a larger number of infection events. We further find that viral complementation can significantly enhance the spread of disadvantageous mutants, but only in select circumstances: it requires the occurrence of direct cell-to-cell transmission through virological synapses, as well as a substantial fitness disadvantage of the mutant, most likely corresponding to defective virus particles. This, however, likely has strong biological consequences because defective viruses can carry genetic diversity that can be incorporated into functional virus genomes via recombination. Through this mechanism, synaptic transmission in HIV might promote virus evolvability. 

   more » « less
2. Genomic analysis reveals an exogenous viral symbiont with dual functionality in parasitoid wasps and their hosts

   https://doi.org/10.1371/journal.ppat.1009069  

   Coffman, Kelsey A.; Burke, Gaelen R. (November 2020, PLOS Pathogens)

   Roossinck, Marilyn J. (Ed.)

   Insects are known to host a wide variety of beneficial microbes that are fundamental to many aspects of their biology and have substantially shaped their evolution. Notably, parasitoid wasps have repeatedly evolved beneficial associations with viruses that enable developing wasps to survive as parasites that feed from other insects. Ongoing genomic sequencing efforts have revealed that most of these virus-derived entities are fully integrated into the genomes of parasitoid wasp lineages, representing endogenous viral elements (EVEs) that retain the ability to produce virus or virus-like particles within wasp reproductive tissues. All documented parasitoid EVEs have undergone similar genomic rearrangements compared to their viral ancestors characterized by viral genes scattered across wasp genomes and specific viral gene losses. The recurrent presence of viral endogenization and genomic reorganization in beneficial virus systems identified to date suggest that these features are crucial to forming heritable alliances between parasitoid wasps and viruses. Here, our genomic characterization of a mutualistic poxvirus associated with the wasp Diachasmimorpha longicaudata , known as Diachasmimorpha longicaudata entomopoxvirus (DlEPV), has uncovered the first instance of beneficial virus evolution that does not conform to the genomic architecture shared by parasitoid EVEs with which it displays evolutionary convergence. Rather, DlEPV retains the exogenous viral genome of its poxvirus ancestor and the majority of conserved poxvirus core genes. Additional comparative analyses indicate that DlEPV is related to a fly pathogen and contains a novel gene expansion that may be adaptive to its symbiotic role. Finally, differential expression analysis during virus replication in wasps and fly hosts demonstrates a unique mechanism of functional partitioning that allows DlEPV to persist within and provide benefit to its parasitoid wasp host. 

   more » « less
3. A Mutualistic Poxvirus Exhibits Convergent Evolution with Other Heritable Viruses in Parasitoid Wasps

   https://doi.org/10.1128/JVI.02059-19  

   Coffman, Kelsey A.; Harrell, Taylor C.; Burke, Gaelen R.; Shisler, Joanna L. (March 2020, Journal of Virology)

   ABSTRACT For insects known as parasitoid wasps, successful development as a parasite results in the death of the host insect. As a result of this lethal interaction, wasps and their hosts have coevolved strategies to gain an advantage in this evolutionary arms race. Although normally considered to be strict pathogens, some viruses have established persistent infections within parasitoid wasp lineages and are beneficial to wasps during parasitism. Heritable associations between viruses and parasitoid wasps have evolved independently multiple times, but most of these systems remain largely understudied with respect to viral origin, transmission and replication strategies of the virus, and interactions between the virus and host insects. Here, we report a detailed characterization of Diachasmimorpha longicaudata entomopoxvirus (DlEPV), a poxvirus found within the venom gland of Diachasmimorpha longicaudata wasps. Our results show that DlEPV exhibits similar but distinct transmission and replication dynamics compared to those of other parasitoid viral elements, including vertical transmission of the virus within wasps, as well as virus replication in both female wasps and fruit fly hosts. Functional assays demonstrate that DlEPV is highly virulent within fly hosts, and wasps without DlEPV have severely reduced parasitism success compared to those with a typical viral load. Taken together, the data presented in this study illustrate a novel case of beneficial virus evolution, in which a virus of unique origin has undergone convergent evolution with other viral elements associated with parasitoid wasps to provide an analogous function throughout parasitism. IMPORTANCE Viruses are generally considered to be disease-causing agents, but several instances of beneficial viral elements have been identified in insects called parasitoid wasps. These virus-derived entities are passed on through wasp generations and enhance the success of the wasps’ parasitic life cycle. Many parasitoid-virus partnerships studied to date exhibit common features among independent cases of this phenomenon, including a mother-to-offspring route of virus transmission, a restricted time and location for virus replication, and a positive effect of virus activity on wasp survival. Our characterization of Diachasmimorpha longicaudata entomopoxvirus (DlEPV), a poxvirus found in Diachasmimorpha longicaudata parasitoid wasps, represents a novel example of beneficial virus evolution. Here, we show that DlEPV exhibits functional similarities to known parasitoid viral elements that support its comparable role during parasitism. Our results also demonstrate unique differences that suggest DlEPV is more autonomous than other long-term viral associations described in parasitoid wasps. 

   more » « less
4. Why do viruses make aphids winged?

   https://doi.org/10.1111/imb.12860  

   Rozo‐Lopez, Paula; Parker, Benjamin J. (December 2023, Insect Molecular Biology)

   Abstract Aphids are hosts to diverse viruses and are important vectors of plant pathogens. The spread of viruses is heavily influenced by aphid movement and behaviour. Consequently, wing plasticity (where individuals can be winged or wingless depending on environmental conditions) is an important factor in the spread of aphid‐associated viruses. We review several fascinating systems where aphid‐vectored plant viruses interact with aphid wing plasticity, both indirectly by manipulating plant physiology and directly through molecular interactions with plasticity pathways. We also cover recent examples where aphid‐specific viruses and endogenous viral elements within aphid genomes influence wing formation. We discuss why unrelated viruses with different transmission modes have convergently evolved to manipulate wing formation in aphids and whether this is advantageous for both host and virus. We argue that interactions with viruses are likely shaping the evolution of wing plasticity within and across aphid species, and we discuss the potential importance of these findings for aphid biocontrol. 

   more » « less
5. Host Competitive Asymmetries Accelerate Viral Evolution in a Microbe–Virus Coevolutionary System

   https://doi.org/10.1111/ele.70153  

   Liaghat, Armun; Guillemet, Martin; Whitaker, Rachel; Gandon, Sylvain; Pascual, Mercedes (June 2025, Ecology Letters)

   ABSTRACT Microbial host populations evolve traits conferring specific resistance to viral predators via various defence mechanisms, while viruses reciprocally evolve traits to evade these defences. Such coevolutionary dynamics often involve diversification promoted by negative frequency‐dependent selection. However, microbial traits conferring competitive asymmetries can induce directional selection, opposing diversification. Despite extensive research on microbe–virus coevolution, the combined effect of both host trait types and associated selection remains unclear. Using a CRISPR‐mediated coevolutionary system, we examine how the co‐occurrence of both trait types impacts viral evolution and persistence, previously shown to be transient and nonstationary in computational models. A stochastic model incorporating host competitive asymmetries via variation of intrinsic growth rates reveals that competitively advantaged host clades generate the majority of immune diversity. Greater asymmetries extend viral extinction times, accelerate viral adaptation locally in time and augment long‐term local adaptation. These findings align with previous experiments and provide further insights into long‐term coevolutionary dynamics. 

   more » « less