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Literature detail

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.
PMID 42263510 2026 Virology eng aheadofprint
PubMed DOI Browse context

Article

Publication summary

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.

Alongshan virus Flaviviridae Jingmen tick virus Metagenome Tick

Structured evidence records

Evidence records

2 total
Reservoir Ecology 1 records
Reservoir Ecology Extraction confidence 0.85
Key finding

Globally distributed complete JMTV genomes showed considerable geographic partitioning of diversity and formation of two supported virus clades, indicating structured tick-associated reservoir diversity.

Virus
JMTV
Host
Ixodida
Location
global Kenya Belize United States
Supporting text

Analysis of globally distributed complete JMTV genomes revealed a considerable geographic partitioning of diversity and two significantly supported virus clades.

Method
genome analysis | phylogenetic analysis
Study design
comparative genomics
Transmission direction
animal reservoir only
Event type
tick reservoir distribution and genome diversity
Geographic raw
global | Kenya | Belize | United States
Country inferred
KEN | USA
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.90
Key finding

Metagenomic surveillance detected Jingmen tick virus and related arbo-jingmenviruses in multiple tick species across continents, yielding complete viral genome assemblies and revealing geographic partitions of viral diversity.

Virus
JMTV
Host
Ixodida
Location
Kenya Belize Arkansas, United States
Supporting text

Using an unbiased metagenomics approach based on long read sequencing, we screened field-collected ticks (n = 3232) ... Signals of virus detection were observed in 32.9% of the pooled samples... 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.

Method
long read sequencing | unbiased metagenomics
Sample type
ticks | tick pools | larvae | nymphs | adults
Study design
metagenomic surveillance
Transmission direction
animal reservoir only
Event type
tick-associated virus field screening
Geographic raw
Kenya | Belize | Arkansas, United States
Country inferred
KEN
Genes or proteins
non-structural virus proteins