Biology subjects

Nino Barreat, J. G.

Publications and source records attributed to Nino Barreat, J. G..

4 recordsLinked to original sources

bioRxiv2023

Deep-mining of vertebrate genomes reveals an unexpected diversity of endogenous viral elements

Endogenous viral elements (EVEs) are key to our understanding of the diversity, host range and evolutionary history of viruses. Given the increasing amounts of virus and host sequence data, a systematic search for EVEs is becoming computationally challenging. We used ElasticBLAST on the Google Cloud Platform to perform a comprehensive search for EVEs (kingdoms Shotokuvirae and Orthornavirae) across vertebrates. We provide evidence for the first EVEs belonging to the families Chuviridae, Paramyxoviridae, Nairoviridae and Benyviridae in vertebrate genomes. We also find an EVE from the Hepacivirus genus of flaviviruses with orthology across murine rodents. Phylogenetic analysis of hits closely related to reptarenavirus and filovirus ectodomains suggest three independent captures from a retroviral source. Our findings increase the family-level diversity of non-retroviral EVEs in vertebrates by 44%. In particular, our results shed light on key aspects of the natural history and evolution of viruses in the phyla Negarnaviricota and Kitrinoviricota.

evolutionary biology↗

bioRxiv2023

Ecological and evolutionary dynamics of cell-virus-virophage systems

Microbial eukaryotes can be infected by giant viruses, which can be infected by virophages. Virophages are parasites of the virus transcription machinery and can interfere with virus replication, resulting in a benefit to the eukaryotic host population. Surprisingly, virophages can integrate into the genomes of their cell or virus hosts, and have been shown to reactivate during coinfection. This raises interesting questions about the role of integration in the dynamics of cell-virus-virophage systems. Here, we use mathematical models and computational simulations to understand the effect of virophage integration on populations of cells and viruses. We also investigate programmed-cell death (PCD) and multicellularity as potential antiviral defence strategies used by cells. We found that virophages which enter the cell independently of the host virus, such as Mavirus, are expected to integrate commonly into the genomes of their cell hosts. In contrast, we show that virophages like Sputnik which form a complex with the giant virus, should rarely be found integrated in cell genomes. Alternatively, we found that Sputnik virophages can stably persist integrated in the virus population, as long as they do not completely inhibit virus replication. We also show that increasing virophage inhibition can stabilise oscillatory dynamics, which may explain the long-term persistence of viruses and virophages in the environment. Our results demonstrate that inhibition by virophages, PCD and multicellularity are effective antiviral strategies that may act in synergy against viral infection in microbial species.

evolutionary biology↗

bioRxiv2022

An ancient endogenous DNA virus in the human genome

The genomes of eukaryotes preserve a striking diversity of ancient viruses in the form of endogenous viral elements (EVEs). Study of this genomic fossil record provides insights into the diversity, origin and evolution of viruses across geological timescales. In particular, Mavericks have emerged as one of the oldest groups of viruses infecting vertebrates ([≥]419 My). They have been found in the genomes of fish, amphibians and non-avian reptiles but had been overlooked in mammals. Thus, their evolutionary history and the causes of their demise in mammals remain puzzling questions. Here, we conduct a detailed evolutionary study of two Maverick-like integrations found on human chromosomes 7 and 8. We performed a comparative analysis of the integrations and determined their orthology across placental mammals (Eutheria) via the syntenic arrangement of neighbouring genes. The integrations were absent at the orthologous sites in the genomes of marsupials and monotremes. These observations allowed us to reconstruct a time-calibrated phylogeny and infer the age of their most recent common ancestor at 268.61 (199.70-344.54) My. In addition, we estimate the age of the individual integrations at ~105 My which represent the oldest non-retroviral EVEs found in the human genome. Our findings suggest that active Mavericks existed in the ancestors of modern mammals ~172 My ago (Jurassic Period) and potentially to the end of the Early Cretaceous. We hypothesise Mavericks could have gone extinct in mammals from the evolution of an antiviral defence system or from reduced opportunities for transmission in terrestrial hosts. ImportanceThe genomes of vertebrates preserve an enormous diversity of endogenous viral elements (remnants of ancient viruses that accumulate in host genomes over evolutionary time). Although retroviruses account for the vast majority of these elements, diverse DNA viruses have also been found and novel lineages are being described. Here we analyse two elements found in the human genome belonging to an ancient group of DNA viruses called Mavericks. We study their evolutionary history, finding that the elements are shared between humans and many different species of placental mammals. These observations suggest the elements inserted at least ~105 Mya in the most recent common ancestor of placentals. We further estimate the age of the viral ancestor around 268 My. Our results provide evidence for some of the oldest viral integrations in the human genome and insights into the ancient interactions of viruses with the ancestors of modern-day mammals.

evolutionary biology↗

bioRxiv2021

Evidence for a billion-years arms race between viruses, virophages and eukaryotes

Bamfordviruses are arguably the most diverse group of viruses infecting eukaryotes. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs), virophages, adenoviruses, Mavericks and Polinton-like viruses. Two main hypotheses for their origins have been proposed: the "nuclear-escape" and "virophage-first" hypotheses. The "nuclear-escape" hypothesis proposes an endogenous, Maverick-like ancestor which escaped from the nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the "virophage-first" hypothesis proposes that NCLDVs coevolved with protovirophages; Mavericks then evolved from virophages that became endogenous, with adenoviruses escaping from the nucleus at a later stage. Here, we test the predictions made by both models and consider alternative evolutionary scenarios. We use a data set of the four core virion proteins sampled across the diversity of the lineage, together with Bayesian and maximum-likelihood hypothesis-testing methods, and estimate rooted phylogenies. We find strong evidence that adenoviruses and NCLDVs are not sister groups, and that Mavericks and Mavirus acquired the rve-integrase independently. We also found strong support for a monophyletic group of virophages (family Lavidaviridae) and a most likely root placed between virophages and the other lineages. Our observations support alternatives to the nuclear-escape scenario and a billion years evolutionary arms-race between virophages and NCLDVs.

microbiology↗