OmniVira

Unbiased long read metagenomic screening reveals diverse jingmen tick virus genomes across continents.

Koray Ergunay1 Brian P Bourke2 Maureen Kamau3 Benedicte Fustec4 Cameron J Osborne5 Janerose Mutura3 Rashid Lebunge3 Griphin Ochieng3 Tevin Onyango3 Alvaro Cruz6 Mariely Campos6 Marie C Pott6 Uziel Romero6 Anna Grace Deakins5 Julia Paoli7,8 Hsiao-Mei Liao9,10 Michael E von Fricken7,8 Emily G McDermott5 Le Jiang11 John P Grieco4 Nicole L Achee4 Yvonne-Marie Linton2
Affiliations 11 institutions
  1. Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA. Electronic address: [email protected].
  2. Department of Entomology, Smithsonian Institution National Museum of Natural History, Washington, DC, USA.
  3. Mpala Research Centre, Nanyuki, Laikipia, Kenya.
  4. Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.
  5. Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, USA.
  6. Belize Vector Ecology Center, Orange Walk, Belize.
  7. One Health Center of Excellence, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
  8. Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
  9. Naval Medical Research Command, Silver Spring, MD, USA
  10. Henry M Jackson Foundation of the Advancement of Military Medicine, Bethesda, MD, USA.
  11. Naval Medical Research Command, Silver Spring, MD, USA.
PMID42263510 DOI10.1016/j.virol.2026.110999 Year2026 Journal Virology Languageeng Statusaheadofprint

Abstract

Jingmen tick virus (JMTV) is an emerging tick-associated virus related to flaviviruses. Substantial information gaps remain on the epidemiology and public health impact of JMTV, despite evidence for symptomatic human infections, detection in potential zoonotic reservoirs and widespread global circulation. Using an unbiased metagenomics approach based on long read sequencing, we screened field-collected ticks (n = 3232) of various life stages from locations of spillover risk across continents, from Eastern Africa (Kenya), Central America (Belize), and North America (Arkansas, United States). Signals of virus detection were observed in 32.9% of the pooled samples comprising adult, nymph and larvae stages. JMTV genome segments were assembled in 16.7% of the pools with initial virus detection. Adult ticks comprising Amblyomma gemma, Hyalomma rufipes, Rhipicephalus. evertsi and Rhipicephalus pulchellus from Kenya yielded complete JMTV genome assemblies. Evidence for tick-associated arbo-jingmenviruses was described for the first time in Belize, identified as complete genome segments encoding for non-structural virus proteins in pooled larvae. Analysis of globally distributed complete JMTV genomes revealed a considerable geographic partitioning of diversity and two significantly supported virus clades and genomic underrepresentation in many regions with documented virus activity. Further investigations and expanded screening are needed to elucidate JMTV and arbo-jingmenvirus global epidemiology.

Supporting text Virus Host Location
Alongshan virus 1 Flaviviridae 6 Jingmen tick virus 4 Metagenome 8 Tick 6

Evidence records

3 total
Zoonotic Surveillance
2 records · 1 evidence types
Evidence type Viral Detection
2 records
OVE11298 Viral Detection
Key finding

Tick-associated arbo-jingmenviruses were detected for the first time in Belize, with complete genome segments encoding non-structural proteins identified in pooled tick larvae.

Virus
arbo-jingmenviruses
Host
ticks Ixodida Natural host
Location
Belize
Supporting text

Evidence for tick-associated arbo-jingmenviruses was described for the first time in Belize, identified as complete genome segments encoding for non-structural virus proteins in pooled larvae.

Method
metagenomic screening | genome segment sequencing | long read sequencing
Sample type
pooled larvae
Geographic raw
Belize
OVE11297 Viral Detection
Key finding

Metagenomic screening detected Jingmen tick virus signals in 32.9% of pooled tick samples collected from Kenya, Belize, and the United States.

Virus
Jingmen tick virus
Host
ticks Ixodida Natural host
Location
Kenya Belize United States
Supporting text

Using an unbiased metagenomics approach based on long read sequencing, we screened field-collected ticks (n = 3232) of various life stages from locations of spillover risk across continents, from Eastern Africa (Kenya), Central America (Belize), and North America (Arkansas, United States). Signals of virus detection were observed in 32.9% of the pooled samples comprising adult, nymph and larvae stages.

Method
metagenomic screening | long read sequencing
Sample type
pooled tick samples | adult ticks | nymph ticks | larvae ticks
Geographic raw
Kenya | Belize | Arkansas | United States
Country inferred
KEN | USA
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE11300 Phylogenetic Evolution
Key finding

Phylogenetic analysis of complete Jingmen tick virus (JMTV) genomes identified two well-supported global clades and indicated geographic partitioning of viral diversity.

Virus
Jingmen tick virus
Host
Not specified
Location
Not specified
Supporting text

Analysis of globally distributed complete JMTV genomes revealed a considerable geographic partitioning of diversity and two significantly supported virus clades and genomic underrepresentation in many regions with documented virus activity.

Genes or proteins
complete genome
Analysis methods
phylogenetic analysis | comparative genomic analysis