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Population genomics of co-evolution between non-retroviral RNA viruses and their hosts

Periodic Reporting for period 3 - NIRV_HOST_INT (Population genomics of co-evolution between non-retroviral RNA viruses and their hosts)

Reporting period: 2019-05-01 to 2020-10-31

The project NIRV_HOST_INT aims at studying integrations of sequences from nonretroviral RNA viruses in the genome of their eukaryotic hosts. Nonretroviral RNA viruses are the most common viruses that infect eukaryotes and include arboviruses (i.e. viruses transmitted by an arthropod host) with high public health relevance, such as Dengue, Zika and West Nile viruses (Flavivirus genus). Despite having different genome structures and replication strategies, all nonretroviral RNA viruses do not encode for reverse transcriptase and integrase. As a consequence, nonretroviral RNA viruses should be present in host cells transiently, a property that favoured their application in medicine as delivery vectors for vaccine and drugs. However, the application of next-generation sequencing technologies and metagenomic analyses led to the discovery of sequences from nonretroviral RNA viruses integrated into the genome of many eukaryotes. The safe application of nonretroviral RNA viruses in medicine requires the understanding of which viral species integrate into host genomes and under which circumstances this phenomenon occurs. Sequences from nonretroviral RNA viruses have been found integrated also into the genomes of arboviral vectors, including the Asian tiger mosquito Aedes albopictus. It is still unclear whether viral integrations are transcribed, facilitate the establishment and the progression of viral infection or, on the contrary, they prevent further infections with cognate viruses. Understanding the impact of viral integrations on mosquito vectors is important because virus-vector interaction processes could be manipulated to develop novel genetic-based strategies of mosquito control.
This project uses the model system “Aedes albopictus-Flavivirus” and combines molecular work in a laboratory setting with sampling of mosquitoes in the wild to investigate whether integration of sequences from nonretroviral RNA viruses is a common phenomenon in nature, which viruses integrate into the genome of Ae. albopictus, whether there are hot spot of integrations in the genome which could lead to hypothesis on mechanisms of integrations and whether the presence of viral integrations affect the outcome of subsequent viral infections.
"This project studies nonretroviral integrated RNA virus sequences (NIRVs) through two aims, each with different goals. Work performed and main achievements are reported below, under each aim.

Aim 1) Population genomics analyses of NIRVs in Ae. albopictus
TASK. Characterise the pattern of viral integrations in wild-caught mosquitoes from the native home range and derived populations. Assess the prevalence of viral integrations in natural populations and correlate NIRVs presence with flavivirus infections.
WORK PERFORMED and RESULTS. We generated a new genome assembly of Ae. albopicuts based on long read sequencing approaches (published in Genome Biology in August 2020, 21:215) and a bioinformatic program called ViR (posted in BioArchive in June 2020) and annotated viral integrations in the genome of Ae. albopictus. Using these resources we looked for viral integrations in wild-collected mosquitoes and were able to identify a total of 11. We demonstrated that viral integrations occur in repetitive regions of the genome in close association with trasposable elements, mostly in piRNA clusters and produce piRNAs.
We also generated a public database ( for the viral integrations of Aedes spp. mosquitoes

Aim 2) Biological Impact of NIRVs in Ae. albopictus.
WORK PERFORMED and RESULTS. Life-table parameters of different Ae. albopictus strains were built and data are being analysed.
WORK PERFORMED and RESULTS. We generated an Ae. albopictus transgenic line by inserting into a viral integration within a piRNA cluster a synthetic viral integration made of fragments from the genome of different viruses. We aim to use this line to test for fitness and impact on subsequent infection.
WORKED PERFORMED and RESULTS. Data from infection experiments with different Ae. albopictus strains and the arboviruses Dengue and Chukungunya viruses, which were done at the Institut Pasteur were analysed and are part of the publication currently under review in PLOS NTDs (MS PNTD-D-20-01726 ""Unravelling the crosstalk between small RNA response and transcriptional changes during persistent Chikungunya virus infection in Aedes albopictus"")."
The new genome assembly of Ae. albopictus (AalbF2) represents the most up-to-date collective knowledge of the Ae. albopictus genome and is expected to aid in the understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures. The database of viral integrations we produced ( will foster new investigations on the role and widespread distribution of viral integrations. The Aedes albopictus transgenic line we produced will be instrumental in testing the biological role of viral integrations from different viral species with respect to cognate viruses
home page of the database for viral integration