The Viromes of Mosquitoes from the Natural Landscapes of Western Siberia

The metagenomic analysis of mosquitoes allows for the genetic characterization of mosquito-associated viruses in different regions of the world. This study applied a metagenomic approach to identify novel viral sequences in seven species of mosquitoes collected from the Novosibirsk region of western Siberia. Using NGS sequencing, we identified 15 coding-complete viral polyproteins (genomes) and 15 viral-like partial sequences in mosquitoes. The complete sequences for novel viruses or the partial sequences of capsid proteins, hypothetical viral proteins, and RdRps were used to identify their taxonomy. The novel viral sequences were classified within the orders Tymovirales and Picornavirales and the families Partitiviridae, Totiviridae, Tombusviridae, Iflaviridae, Nodaviridae, Permutotetraviridae, and Solemoviridae, with several attributed to four unclassified RNA viruses. Interestingly, the novel putative viruses and viral sequences were mainly associated with the mosquito Coquillettidia richardii. This study aimed to increase our understanding of the viral diversity in mosquitoes found in the natural habitats of Siberia, which is characterized by very long, snowy, and cold winters.

[1]  A. Simon,et al.  Conserved Structure Associated with Different 3′CITEs Is Important for Translation of Umbraviruses , 2023, Viruses.

[2]  E. Protopopova,et al.  Detection of tick-borne pathogens in wild birds and their ticks in Western Siberia and high level of their mismatch. , 2021, Folia parasitologica.

[3]  F. Gao,et al.  Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs , 2021, Viruses.

[4]  B. Misof,et al.  Viromics of extant insect orders unveil the evolution of the flavi-like superfamily , 2021, Virus evolution.

[5]  A. Blomström,et al.  Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes , 2019, Viruses.

[6]  R. Jarman,et al.  Metagenomic Analysis Reveals Three Novel and Prevalent Mosquito Viruses from a Single Pool of Aedes vexans nipponii Collected in the Republic of Korea , 2019, Viruses.

[7]  H. Liu,et al.  Metagenomic Analysis of Flaviviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes From Dengue and Zika Viruses , 2018, Front. Cell. Infect. Microbiol..

[8]  C. Barker,et al.  Virome of > 12 thousand Culex mosquitoes from throughout California. , 2018, Virology.

[9]  Bo Zhang,et al.  Mosquito-Associated Viruses in China , 2018, Virologica Sinica.

[10]  E. Gould,et al.  Emerging arboviruses: Why today? , 2017, One health.

[11]  M. Shi,et al.  High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia , 2017, Journal of Virology.

[12]  A. Powers,et al.  A decade of arboviral activity—Lessons learned from the trenches , 2017, PLoS neglected tropical diseases.

[13]  T. Dermody,et al.  Chikungunya virus: epidemiology, replication, disease mechanisms, and prospective intervention strategies , 2017, The Journal of clinical investigation.

[14]  T. de Oliveira,et al.  Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo , 2017, Journal of Virology.

[15]  Edward C. Holmes,et al.  Redefining the invertebrate RNA virosphere , 2016, Nature.

[16]  M. Berg,et al.  Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique , 2016, PloS one.

[17]  A. F. van den Hurk,et al.  The insect-specific Palm Creek virus modulates West Nile virus infection in and transmission by Australian mosquitoes , 2016, Parasites & Vectors.

[18]  Anthony S Fauci,et al.  Zika Virus in the Americas--Yet Another Arbovirus Threat. , 2016, The New England journal of medicine.

[19]  Vishwesh P. Mokashi,et al.  Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses , 2016, Evolutionary bioinformatics online.

[20]  J. Hobson-Peters,et al.  Commensal Viruses of Mosquitoes: Host Restriction, Transmission, and Interaction with Arboviral Pathogens , 2016, Evolutionary bioinformatics online.

[21]  Samuel H. Lewis,et al.  Twenty-Five New Viruses Associated with the Drosophilidae (Diptera) , 2016, bioRxiv.

[22]  R. Tesh,et al.  Insect-specific viruses and their potential impact on arbovirus transmission. , 2015, Current opinion in virology.

[23]  G. Ebel,et al.  Potential for Co-Infection of a Mosquito-Specific Flavivirus, Nhumirim Virus, to Block West Nile Virus Transmission in Mosquitoes , 2015, Viruses.

[24]  R. Tesh,et al.  Eilat virus induces both homologous and heterologous interference. , 2015, Virology.

[25]  C. Drosten,et al.  Evolutionary and phenotypic analysis of live virus isolates suggests arthropod origin of a pathogenic RNA virus family , 2015, Proceedings of the National Academy of Sciences.

[26]  N. Pardigon,et al.  The challenge of West Nile virus in Europe: knowledge gaps and research priorities. , 2015, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[27]  E. Holmes,et al.  Evolution of Genome Size and Complexity in the Rhabdoviridae , 2015, PLoS pathogens.

[28]  M. Shi,et al.  Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses , 2015, eLife.

[29]  A. Brault,et al.  Characterization of a novel insect-specific flavivirus from Brazil: potential for inhibition of infection of arthropod cells with medically important flaviviruses. , 2014, The Journal of general virology.

[30]  Kirsten A. Duda,et al.  Global spread of dengue virus types: mapping the 70 year history , 2014, Trends in microbiology.

[31]  C. Drosten,et al.  Virus discovery and recent insights into virus diversity in arthropods , 2013, Current Opinion in Microbiology.

[32]  H. Vetten,et al.  The complete genome sequences of a Peruvian and a Colombian isolate of Andean potato latent virus and partial sequences of further isolates suggest the existence of two distinct potato-infecting tymovirus species. , 2013, Virus research.

[33]  J. Hobson-Peters,et al.  A New Insect-Specific Flavivirus from Northern Australia Suppresses Replication of West Nile Virus and Murray Valley Encephalitis Virus in Co-infected Mosquito Cells , 2013, PloS one.

[34]  H. Guzmán,et al.  Negevirus: a Proposed New Taxon of Insect-Specific Viruses with Wide Geographic Distribution , 2012, Journal of Virology.

[35]  C. G. Moore,et al.  Transmission dynamics of an insect-specific flavivirus in a naturally infected Culex pipiens laboratory colony and effects of co-infection on vector competence for West Nile virus. , 2012, Virology.

[36]  C. King,et al.  Measuring the burden of arboviral diseases: the spectrum of morbidity and mortality from four prevalent infections , 2011, Population health metrics.

[37]  R. Tesh,et al.  Quaranfil, Johnston Atoll, and Lake Chad Viruses Are Novel Members of the Family Orthomyxoviridae , 2009, Journal of Virology.

[38]  Chonticha Klungthong,et al.  Dengue Virus Detection Using Whole Blood for Reverse Transcriptase PCR and Virus Isolation , 2007, Journal of Clinical Microbiology.

[39]  R. Charrel,et al.  Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes. , 2004, The Journal of general virology.

[40]  V. L. Gromashevskiĭ,et al.  [Detection of West Nile virus in birds in the territories of Baraba and Kulunda lowlands (West Siberian migration way) during summer-autumn of 2002]. , 2004, Voprosy virusologii.

[41]  P. Keese,et al.  The tymobox, a sequence shared by most tymoviruses: its use in molecular studies of tymoviruses. , 1990, Nucleic acids research.

[42]  E. Protopopova,et al.  [Cases of West Nile fever in Novosibirsk region in 2004, and the genotyping of its viral pathogen]. , 2007, Vestnik Rossiiskoi akademii meditsinskikh nauk.

[43]  A. G. Mirzaeva,et al.  [Species composition of mosquitoes (Diptera, Culicidae) and possibility of the West Nile virus natural foci formation in the South of Western Siberia]. , 2007, Parazitologiya.

[44]  X. de Lamballerie,et al.  Liao ning virus, a new Chinese seadornavirus that replicates in transformed and embryonic mammalian cells. , 2006, The Journal of general virology.