Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey View Full Text


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Article Info

DATE

2017-07-14

AUTHORS

Ender Dinçer, Annika Brinkmann, Olcay Hekimoğlu, Sabri Hacıoğlu, Katalin Földes, Zeynep Karapınar, Pelin Fatoş Polat, Bekir Oğuz, Özlem Orunç Kılınç, Peter Hagedorn, Nurdan Özer, Aykut Özkul, Andreas Nitsche, Koray Ergünay

ABSTRACT

BackgroundTicks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick- associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014–2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens.ResultsA total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. Major portions of the CCHFV genomic segments were obtained via NGS. Phlebovirus sequencing revealed several tick-associated virus clades, including previously-characterized Antigone, Lesvos, KarMa and Bole tick viruses, as well as a novel clade. A wider host range for tick-associated virus strains has been observed. NGS provided near-complete sequences of the L genomic segments of Antigone and KarMa clades, as well as Antigone partial S segment. Co- infections of CCHFV and KarMa or novel phlebovirus clades were detected in 2.1% of the specimens.ConclusionsWidespread circulation of various tick-associated phlebovirus clades were documented for the first time in Anatolia. Genomes of CCHFV AP92 strains were identified in previously unexplored locations. NGS provided the most detailed genomic characterization of the Antigone and KarMa viruses to date. The epidemiological and health-related consequences must be elucidated. More... »

PAGES

335

References to SciGraph publications

  • 2007-09-07. Geographical distribution of ticks in Turkey in PARASITOLOGY RESEARCH
  • 2014-11-17. Fast and sensitive protein alignment using DIAMOND in NATURE METHODS
  • <error retrieving object. in <ERROR RETRIEVING OBJECT
  • 2015. Family Bunyaviridae in GLOBAL VIROLOGY I - IDENTIFYING AND INVESTIGATING VIRAL DISEASES
  • 2009-06-10. The first clinical case due to AP92 like strain of Crimean-Congo Hemorrhagic Fever virus and a field survey in BMC INFECTIOUS DISEASES
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13071-017-2279-1

    DOI

    http://dx.doi.org/10.1186/s13071-017-2279-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1090678468

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28705183


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    20 schema:description BackgroundTicks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick- associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014–2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens.ResultsA total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. Major portions of the CCHFV genomic segments were obtained via NGS. Phlebovirus sequencing revealed several tick-associated virus clades, including previously-characterized Antigone, Lesvos, KarMa and Bole tick viruses, as well as a novel clade. A wider host range for tick-associated virus strains has been observed. NGS provided near-complete sequences of the L genomic segments of Antigone and KarMa clades, as well as Antigone partial S segment. Co- infections of CCHFV and KarMa or novel phlebovirus clades were detected in 2.1% of the specimens.ConclusionsWidespread circulation of various tick-associated phlebovirus clades were documented for the first time in Anatolia. Genomes of CCHFV AP92 strains were identified in previously unexplored locations. NGS provided the most detailed genomic characterization of the Antigone and KarMa viruses to date. The epidemiological and health-related consequences must be elucidated.
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    31 Black Sea
    32 Bunyaviridae
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    34 Flaviviridae
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    36 Mediterranean
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    38 Province
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    40 S segment
    41 Sea
    42 Thrace
    43 Turkey
    44 acid amplification
    45 amplification
    46 assays
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    48 characterization
    49 circulation
    50 clade
    51 clusters
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    53 consequences
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    57 distinct clusters
    58 eastern region
    59 family Flaviviridae
    60 fever virus
    61 first time
    62 flaviviruses
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    65 genome
    66 genome characterization
    67 genomic characterization
    68 genomic segments
    69 genus Flavivirus
    70 health impacts
    71 health-related consequences
    72 hemorrhagic fever virus
    73 host range
    74 identification
    75 impact
    76 incidence
    77 infection
    78 karma
    79 like strains
    80 location
    81 major portion
    82 morphological identification
    83 next-generation sequencing
    84 novel
    85 novel clade
    86 nucleic acid amplification
    87 partial S segment
    88 phleboviruses
    89 pool
    90 portion
    91 range
    92 region
    93 related strains
    94 screening
    95 segments
    96 sequence
    97 sequencing
    98 significant health impacts
    99 species
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    101 strains
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    103 tick species
    104 tick-associated viruses
    105 tick-borne viral infection
    106 tick-borne viruses
    107 ticks
    108 time
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    111 unexplored locations
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