Genomic analysis of hyperparasitic viruses associated with entomopoxviruses
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PROVIDER: S-EPMC11296320 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:Metchnikovellidae are a group of unusual microsporidians that lack some of the defining ultrastructural features characteristic of derived Microsporidia and are thought to be one of their earliest-branching lineages. The basal position of metchnikovellids was never confirmed by molecular phylogeny in published research, and thus far no genomic data for this group were available. In this work, we obtain a partial genome of metchnikovellid Amphiamblys sp. using multiple displacement amplification, next-generation sequencing, and metagenomic binning approaches. The partial genome, which we estimate to be close to 90% complete, displays genome compaction on par with gene-dense microsporidian genomes, but contains an unusual repertoire of unique repeat elements. Phylogenetic analyses of multigene datasets place Amphiamblys sp. as the first branch of the microsporidian lineage following the divergence of a mitochondriate microsporidian Mitosporidium. We find evidence for a mitochondrial remnant presumably functionally equivalent to a mitosome in Amphiamblys sp. and the common enzymatic complement for microsporidian anaerobic metabolism. Comparative genomic analyses identify the conservation of components for clathrin vesicle formation as one of the key features distinguishing the metchnikovellid from its highly derived relatives. The presented data confirm the notion of Metchnikovellidae as a less derived microsporidian group, and provide an additional stepping stone for reconstruction of an evolutionary transition from the early diverging parasitic fungi to derived Microsporidia.
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Project description:Hyperparasitism is a common pattern in nature that is not limited to cellular organisms. Giant viruses infecting protists can be hyperparasitized by smaller ones named virophages. In addition, both may carry episomal DNA molecules known as transpovirons in their particles. They all share transcriptional regulatory elements that dictate the expression of their genes within viral factories built by giant viruses in the host cytoplasm. This suggests the existence of interactions between their respective transcriptional networks. Here we investigated Acanthamoeba castellanii cells infected by a giant virus (megavirus chilensis), and coinfected with a virophage (zamilon vitis) and/or a transpoviron (megavirus vitis transpoviron). Infectious cycles were monitored through time-course RNA sequencing to decipher the transcriptional program of each partner and its impact on the gene expression of the others. We found highly diverse transcriptional responses. While the giant virus drastically reshaped the host cell transcriptome, the transpoviron had no effect on the gene expression of any of the players. In contrast, the virophage strongly modified the giant virus gene expression, albeit transiently, without altering the protein composition of mature viral particles. The virophage also induced the overexpression of transpoviron genes, likely through the indirect upregulation of giant virus-encoded transcription factors. Together, these analyses document the intricated transcriptionally regulated networks taking place in the infected cell.
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Project description:The complete genome sequences of two Sulfolobus spindle-shaped viruses (SSVs) from acidic hot springs in Kamchatka (Russia) and Yellowstone National Park (United States) have been determined. These nonlytic temperate viruses were isolated from hyperthermophilic Sulfolobus hosts, and both viruses share the spindle-shaped morphology characteristic of the Fuselloviridae family. These two genomes, in combination with the previously determined SSV1 genome from Japan and the SSV2 genome from Iceland, have allowed us to carry out a phylogenetic comparison of these geographically distributed hyperthermal viruses. Each virus contains a circular double-stranded DNA genome of approximately 15 kbp with approximately 34 open reading frames (ORFs). These Fusellovirus ORFs show little or no similarity to genes in the public databases. In contrast, 18 ORFs are common to all four isolates and may represent the minimal gene set defining this viral group. In general, ORFs on one half of the genome are colinear and highly conserved, while ORFs on the other half are not. One shared ORF among all four genomes is an integrase of the tyrosine recombinase family. All four viral genomes integrate into their host tRNA genes. The specific tRNA gene used for integration varies, and one genome integrates into multiple loci. Several unique ORFs are found in the genome of each isolate.
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Project description:Transposable elements (TEs) are repeated DNA sequences that can constitute a substantial part of genomes. Studying TEs' activity, interactions, and accumulation dynamics is thus of major interest to understand genome evolution. Here, we describe the transposition dynamics of cut-and-paste mariner elements during experimental (short- and longer-term) evolution in Drosophila melanogaster Flies with autonomous and nonautonomous mariner copies were introduced in populations containing no active mariner, and TE accumulation was tracked by quantitative PCR for up to 100 generations. Our results demonstrate that (i) active mariner elements are highly invasive and characterized by an elevated transposition rate, confirming their capacity to spread in populations, as predicted by the "selfish-DNA" mechanism; (ii) nonautonomous copies act as parasites of autonomous mariner elements by hijacking the transposition machinery produced by active mariner, which can be considered as a case of hyperparasitism; (iii) this behavior resulted in a failure of active copies to amplify which systematically drove the whole family to extinction in less than 100 generations. This study nicely illustrates how the presence of transposition-competitive variants can deeply impair TE dynamics and gives clues to the extraordinary diversity of TE evolutionary histories observed in genomes.
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Project description:Baloxavir marboxil (baloxavir) is an FDA-approved inhibitor of the influenza virus polymerase acidic (PA) protein. Here, we used next-generation sequencing to compare the genomic mutational profiles of IAV H1N1 and H3N2, and IBV wild type (WT) and mutants (MUT) viruses carrying baloxavir resistance-associated substitutions (H1N1-PA I38L, I38T, and E199D; H3N2-PA I38T; and IBV-PA I38T) during passaging in normal human bronchial epithelial (NHBE) cells. We determined the ratio of nonsynonymous to synonymous nucleotide mutations (dN/dS) and identified the location and type of amino acid (AA) substitutions that occurred at a frequency of ≥30%. We observed that IAV H1N1 WT and MUT viruses remained relatively stable during passaging. While the mutational profiles for IAV H1N1 I38L, I38T, and E199D, and IBV I38T MUTs were relatively similar after each passage compared to the respective WTs, the mutational profile of the IAV H3N2 I38T MUT was significantly different for most genes compared to H3N2 WT. Our work provides insight into how baloxavir resistance-associated substitutions may impact influenza virus evolution in natural settings. Further characterization of the potentially adaptive mutations identified in this study is needed.
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Project description:An increase in the availability of data on the influenza A viruses (IAV) has enabled the identification of the potential determinants of IAV host specificity using computational approaches. In this study, we proposed an alternative approach, based on the adjusted Rand index (ARI), for the evaluation of genomic signatures of IAVs and their ability to distinguish hosts they infected. Our experiments showed that the host-specific signatures identified using the ARI were more characteristic of their hosts than those identified using previous measures. Our results provided updates on the host-specific genomic signatures in the internal proteins of the IAV based on the sequence data as of February 2013 in the National Center for Biotechnology Information (NCBI). Unlike other approaches for signature recognition, our approach considered not only the ability of signatures to distinguish hosts (according to the ARI), but also the chronological relationships among proteins. We identified novel signatures that could be mapped to known functional domains, and introduced a chronological analysis to investigate the changes in host-specific genomic signatures over time. Our chronological analytical approach provided results on the adaptive variability of signatures, which correlated with previous studies' findings, and indicated prospective adaptation trends that warrant further investigation.
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Project description:South Africa has a small but growing olive industry. Until now, no virological research has been carried out on this crop locally. Seventeen samples were collected from various olive cultivars from a single producer in the Stellenbosch growing area of South Africa. RNAseq was performed on total RNA, and the compositions of the metaviromes were determined. Olive leaf yellowing-associated virus was detected for the first time in South Africa, as well as four novel viruses from the family Closteroviridae and one each from the families Tymoviridae and Solemoviridae.
| S-EPMC11427506 | biostudies-literature
Project description:Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages. Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country. Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.
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Project description: Not available
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Project description:The genomes of two positive-strand RNA viruses have recently been cloned from the serum of a GB agent-infected tamarin by using representational difference analysis. The two agent, GB viruses A and B (GBV-A and GBV-B, respectively), have genomes of 9,493 and 9,143 nucleotides, respectively, and single large open reading frames that encode potential polyprotein precursors of 2,972 and 2,864 amino acids, respectively. The genomes of these agents are organized much like those of other pestiviruses and flaviviruses, with genes predicted to encode structural and nonstructural proteins located at the 5' and 3' ends, respectively. Amino acid sequence alignments and subsequent phylogenetic analysis of the RNA-dependent RNA polymerases (RdRps) of GBV-A and GBV-B show that they possess conserved sequence motifs associated with supergroup II RNA polymerases of positive-strand RNA viruses. On the basis of similar analyses, the GBV-A- and GBV-B-encoded helicases show significant identity with the supergroup II helicases of positive-strand RNA viruses. Within the supergroup II RNA polymerases and helicases, GBV-A and GBV-B are most closely related to the hepatitis C virus group. Across their entire open reading frames, the GB agents exhibit 27% amino sequence identity to each other, approximately 28% identity to hepatitis C virus type 1, and approximately 20% identity to either bovine viral diarrhea virus or yellow fever virus. The degree of sequence divergence between GBV-A and GBV-B and other Flaviviridae members demonstrates that the GB agents are representatives of two new genera within the Flaviviridae family.
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