Impact of nanopore-based metagenome sequencing on tick-borne virus detection

Koray Ergunay; Ender Dincer; Silvia A Justi; Brian P Bourke; Suppaluck P Nelson; Hsiao-Mei Liao; Mehmet Ozkan Timurkan; Bekir Oguz; Ismail Sahindokuyucu; Omer Faruk Gokcecik; Drew D Reinbold-Wasson; Le Jiang; Nicole L Achee; John P Grieco; Yvonne-Marie Linton

doi:10.3389/fmicb.2023.1177651

Impact of nanopore-based metagenome sequencing on tick-borne virus detection

Front Microbiol. 2023 May 30:14:1177651. doi: 10.3389/fmicb.2023.1177651. eCollection 2023.

Authors

Koray Ergunay^{1

2

3

4}, Ender Dincer⁵, Silvia A Justi^{1

2

3}, Brian P Bourke^{1

2

3}, Suppaluck P Nelson^{1

2

3}, Hsiao-Mei Liao^{6

7}, Mehmet Ozkan Timurkan⁸, Bekir Oguz⁹, Ismail Sahindokuyucu¹⁰, Omer Faruk Gokcecik¹⁰, Drew D Reinbold-Wasson¹¹, Le Jiang^{6

7}, Nicole L Achee¹², John P Grieco¹², Yvonne-Marie Linton^{1

2

3}

Affiliations

¹ Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, United States.
² One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, United States.
³ Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC, United States.
⁴ Department of Medical Microbiology, Virology Unit, Faculty of Medicine, Hacettepe University, Ankara, Türkiye.
⁵ Department of Virology, Faculty of Veterinary Medicine, Dokuz Eylül University, Izmir, Türkiye.
⁶ Naval Medical Research Center (NMRC), Silver Spring, MD, United States.
⁷ Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.
⁸ Department of Virology, Faculty of Veterinary Medicine, Ataturk University, Yakutiye, Erzurum, Türkiye.
⁹ Department of Parasitology, Faculty of Veterinary Medicine, Van Yuzuncu Yil University, Van, Türkiye.
¹⁰ Bornova Veterinary Control Institute, Veterinary Control Institute Directorates, Ministry of Agriculture and Forestry, Izmir, Türkiye.
¹¹ U.S. Army Medical Research Diriectorate-Georgia (USAMRD-G), Tbilisi, Georgia.
¹² Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States.

Abstract

Introduction: We evaluated metagenomic nanopore sequencing (NS) in field-collected ticks and compared findings from amplification-based assays.

Methods: Forty tick pools collected in Anatolia, Turkey and screened by broad-range or nested polymerase chain reaction (PCR) for Crimean-Congo Hemorrhagic Fever Virus (CCHFV) and Jingmen tick virus (JMTV) were subjected to NS using a standard, cDNA-based metagenome approach.

Results: Eleven viruses from seven genera/species were identified. Miviruses Bole tick virus 3 and Xinjiang mivirus 1 were detected in 82.5 and 2.5% of the pools, respectively. Tick phleboviruses were present in 60% of the pools, with four distinct viral variants. JMTV was identified in 60% of the pools, where only 22.5% were PCR-positive. CCHFV sequences characterized as Aigai virus were detected in 50%, where only 15% were detected by PCR. NS produced a statistically significant increase in detection of these viruses. No correlation of total virus, specific virus, or targeted segment read counts was observed between PCR-positive and PCR-negative samples. NS further enabled the initial description of Quaranjavirus sequences in ticks, where human and avian pathogenicity of particular isolates had been previously documented.

Discussion: NS was observed to surpass broad-range and nested amplification in detection and to generate sufficient genome-wide data for investigating virus diversity. It can be employed for monitoring pathogens in tick vectors or human/animal clinical samples in hot-spot regions for examining zoonotic spillover.

Keywords: metagenome; nanopore; tick; tick-borne; virus; zoonoses.

Grants and funding

This study was financially supported by the Armed Forces United States Army Medical Research and Development Command under contract no. W81XWH-21-C-0001 (to NLA, JPG, LJ, and Y-ML) and AFHSD-GEIS sustainment funding to the Walter Reed Biosystematics Unit (WRBU) (P0065_22_WR) and US Army Medical Detachment-Georgia (USAMRD-G) (P0008_21_GA).