Project acronym NIRV_HOST_INT

Recent discoveries clearly show that non-retroviral RNA viruses, despite not coding for reverse transcriptase and integrase, can transfer genetic material to their hosts, similarly to DNA viruses and retroviruses. The distribution of non-retroviral integrated RNA viruses (NIRVs) in host populations, mechanisms of NIRVs formation and effects on hosts are unclear. The main objective of this proposal is to uncover the complex biological interactions between non- retroviral RNA viruses and their hosts using the model system “Aedes albopictus and Flavivirus”. This system is ideal because Ae. albopictus is a known vector of non-retroviral RNA viruses, including several highly relevant for public health such as dengue viruses (Flaviviridae, Flavivirus) and NIRVs phylogenetically related to Flaviviruses have been identified in its genome. First, a population genomic approach will be used to interrogate the genome of Ae. albopictus from different geographic populations at their DNA and RNA levels. This approach will permit the systematic characterization of the distributions of NIRVs in natural host populations, the analyses of correlations between the presence of NIRVs and viral infections and the description of NIRVs genomic context, from which insights on mechanisms of NIRVs formation can be derived. Secondly, tissue-specificity of the NIRVs, their trans-generational stability and impact on mosquito biology will be analysed in a controlled laboratory environment. Somatic integrations could contribute to acquired immunity to their respective viruses or establishment of persistent viral infection. Germ- line integrations could have an evolutionary impact. If NIRVs affect Ae. albopictus vector competence or the genome of emerging viral populations, they could be manipulated for vector control purposes. Additionally, results on NIRV distribution in natural host populations and mechanisms of NIRVs formation will have implications in medicine because several non-retroviral RNA viruses are emerging as delivery systems for gene therapy applications.

Related Publicatons
  1. Pischedda E1, Scolari F1,Valerio F1, Carballar-Lejarazú R2, Catapano PL1, Waterhouse RM3, Bonizzoni M.1 2019. Insights into an unexplored component of the mosquito repeatome: distribution and variability of viral sequences integrated into the genome of the arboviral vector Aedes albopictus
    Frontiers in Genetics. 10.3389/fgene.2019.00093

    Author information:
    1Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
    2Department of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, CA, United States
    3Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
    Electronic address:

    ABSTRACT: The Asian tiger mosquito Aedes albopictus is an invasive mosquito and a competent vector for public-health relevant arboviruses such as Chikungunya (Alphavirus), Dengue and Zika (Flavivirus) viruses. Unexpectedly, the sequencing of the genome of this mosquito revealed an unusually high number of integrated sequences with similarities to non-retroviral RNA viruses of the Flavivirus and Rhabdovirus genera. These Non-retroviral Integrated RNA Virus Sequences (NIRVS) are enriched in piRNA clusters and coding sequences and have been proposed to constitute novel mosquito immune factors. However, given the abundance of NIRVS and their variable viral origin, their relative biological roles remain unexplored. Here we used an analytical approach that intersects computational, evolutionary and molecular methods to study the genomic landscape of mosquito NIRVS. We demonstrate that NIRVS are differentially distributed across mosquito genomes, with a core set of seemingly the oldest integrations with similarity to Rhabdoviruses. Additionally, we compare the polymorphisms of NIRVS with respect to that of fast and slow-evolving genes within the Ae. albopictus genome. Overall, NIRVS appear to be less polymorphic than slow-evolving genes, with differences depending on whether they occur in intergenic regions or in piRNA clusters. Finally, two NIRVS that map within the coding sequences of genes annotated as Rhabdovirus RNA-dependent RNA polymerase and the nucleocapsid-encoding gene, respectively, are highly polymorphic and are expressed, suggesting exaptation possibly to enhance the mosquito's antiviral responses. These results greatly advance our understanding of the complexity of the mosquito repeatome and the biology of viral integrations in mosquito genomes.

    Copyright © 2019 Pischedda, Scolari, Valerio, Carballar-Lejarazú, Catapano, Waterhouse and Bonizzoni.
    DOI: 10.3389/fgene.2019.00093
    PMID: 30809249
  2. Olson K E 1, Bonizzoni M.2 2017. Nonretroviral integrated RNA viruses in arthropod vectors: an occasional event or something more?
    Current Opinion in Insect Science. 10.1016/j.cois.2017.05.010

    Author information:
    1Department of Microbiology, Immunology and Pathology, Arthropod-Borne and Infectious Disease Laboratory, Colorado State University, Fort Collins, CO, USA.
    2Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
    Electronic address:

    ABSTRACT: With few exceptions, all arthropod-borne viruses (arboviruses) are nonretroviral RNA viruses (NRVs). Despite NRVs do not encode reverse transcriptases and integrases, NRVs-DNA fragments are detected in mosquito cells and mosquitoes at early stages of infection as episomal DNA forms. Additionally, next generation sequencing and bioinformatics analyses have convincingly shown NRVs-vDNA integrated in vector genomes. We hypothesize vDNA role may be linked to host immunity and viral persistence. Key questions remain about nonretroviral integrated RNA virus sequences (NIRVS) in mosquitoes such as what is driving vDNA synthesis from NRVs, how does integration occur and what is their biological function. Here we review current knowledge about NIRVS highlighting connections with host immunity and virus-vector co-evolution and we suggest directions for future research.

    Copyright © 2017 Elsevier Inc. All rights reserved.
    DOI: 10.1016/j.cois.2017.05.010
    PMID: 28805638
  3. Palatini U1, Miesen P2, Carballar-Lejarazu R1, Ometto L3, Rizzo E4, Tu Z5, Van Rij RP2, Bonizzoni M1. 2017. Comparative Genomics Shows That Viral Integrations Are Abundant And Express piRNAs In The Arboviral Vectors Aedes aegypti and Aedes albopictus.
    BMC Genomics. 10.1186/s12864-017-3903-3.

    Author information:
    1Department of Biology and Biotechnology, University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
    2Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, Nijmegen, The Netherlands.
    3Indepenent Researcher, Mezzocorona, Trento, Italy.
    4Engenome srl, Via Ferrata 5, Pavia, Italy.
    5Department of Biochemistry and Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
    Electronic address:

    BACKGROUND: Arthropod-borne viruses (arboviruses) transmitted by mosquito vectors cause many important emerging or resurging infectious diseases in humans including dengue, chikungunya and Zika. Understanding the co-evolutionary processes among viruses and vectors is essential for the development of novel transmission-blocking strategies. Episomal viral DNA fragments are produced from arboviral RNA upon infection of mosquito cells and adults. Additionally, sequences from insect-specific viruses and arboviruses have been found integrated into mosquito genomes.

    RESULTS: We used a bioinformatic approach to analyse the presence, abundance, distribution, and transcriptional activity of integrations from 425 non-retroviral viruses, including 133 arboviruses, across the presently available 22 mosquito genome sequences. Large differences in abundance and types of viral integrations were observed in mosquito species from the same region. Viral integrations are unexpectedly abundant in the arboviral vector species Ae. aegypti and Ae. albopictus, in which they are approximately ~10-fold more abundant than in other mosquito species analysed. Additionally, viral integrations are enriched in piRNA clusters of both the Ae. aegypti and Ae. albopictus genomes and, accordingly, they express piRNAs, but not siRNAs.

    CONCLUSIONS: Differences in the number of viral integrations in the genomes of mosquito species from the same geographic area support the conclusion that integrations of viral sequences is not dependent on viral exposure, but that lineage-specific interactions exist. Viral integrations are abundant in Ae. aegypti and Ae. albopictus, and represent a thus far underappreciated component of their genomes. Additionally, the genome locations of viral integrations and their production of piRNAs indicate a functional link between viral integrations and the piRNA pathway. These results greatly expand the breadth and complexity of small RNA-mediated regulation and suggest a role for viral integrations in antiviral defense in these two mosquito species.

    DOI: 10.1186/s12864-017- 3903-3
    PMCID: PMC5497376
    PMID: 28676109