Na Jia

Ticks, which are globally distributed, transmit a wide range of human and animal pathogens. Soft and hard ticks are two major tick families exhibiting distinct vector capacities and blood-feeding abilities. However, understanding the genetic basis of these differences is hindered by the scarcity of high-quality tick genomes, particularly for soft ticks. Here, we present high-quality genomes of two soft and two hard tick species of both evolutionary and medical importance, and compare the genomic characteristics of the two tick families. Compared with soft ticks, hard ticks exhibited faster genome evolution, characterized by larger genome sizes, higher rates of gene gain and loss, and a greater number of positively selected genes. Both tick families exhibited frequent positive selection across metabolism and organismal systems, sharing a core set of adaptive genes but undergoing refinement at different sites. Gene families underpinning various vector capacities, including those involved in cuticle structure, heme biosynthesis, egg waxing, and immune pathways, were identified. Additionally, we assembled the genomes of two novel Rickettsia endosymbionts from soft ticks, revealing high genomic divergence and lineage-specific adaptations to their hosts. These genomic resources provide fundamental insights into the genetic basis of tick biology and vector capacity, highlighting the divergent evolutionary strategies of blood-feeding arthropods shaped by their ecological niches.

We report genomic characterization and molecular detection of a previously unrecognized Anaplasma species, provisionally named Candidatus Anaplasma cheelooensis, in goats and ticks in Shandong Province, China. During 2021–2022, metagenomic sequencing of blood from a sick goat kid yielded a 1.13-Mb Anaplasma genome with 45.3% G+C content and only 77.0%–77.6% nucleotide identity to recognized Anaplasma species. Whole-genome and gltA-based phylogenies placed the organism in a distinct lineage related to A. phagocytophilum, A. platys, and A. bovis. Specific PCR detected the organism in 37/53 goat blood samples and 7/145 Haemaphysalis longicornis ticks from the same region; gltA sequences shared 97.9%–100% identity. These findings provide genome-level evidence for a candidate novel Anaplasma species circulating in small ruminants and ticks. Its pathogenicity, vector competence, host range, and zoonotic potential require further investigation.

Emerging and re-emerging tick-borne viruses (TBVs) have caused numerous outbreaks recently, yet the factors driving their emergence and pathogenicity in humans remain poorly understood across viral taxa. A large-scale analysis integrating epidemiological and genomic data of pathogenic TBVs reveal that highly pathogenic TBVs (HPTBVs) tend to exhibit ecological generalism. Specifically, HPTBVs infect a broader range of tick species, animal hosts, and ecotypes, which likely enhance their transmission to humans. Bird migration is identified as the primary driver for geographic spread of HPTBVs through modeling and phylogeographic analyses, while livestock density and TBVs’ diversity they carry determine HPTBVs local persistence. HPTBVs experience stronger positive selection in genes related to host interactions, with specific mutations associated with lineage adaptation. Notably, the positively selected D170N mutation in severe fever with thrombocytopenia syndrome virus is predicted to be an enhanced binding affinity to human receptors, which correlate with increased infectivity. In this work, using TBV as a model system, we verify our hypothesis that ecological generalism is associated with increased pathogenicity and adaptability. These findings highlight the ecological and evolutionary mechanisms that drive the generalization of TBV and underscore their potential implications for public health risk.

RNA viruses exhibit high mutation rates and strong host adaptive capacity, posing major public health challenges. Although meta-transcriptomic studies have uncovered vast numbers of novel RNA viral sequences, identifying those with spillover risks remains difficult. Current virus host-prediction methods can only predict a narrow set of host labels at coarse taxonomic levels (e.g., kingdom or order), which hampers precise evaluation of cross-species transmission risk and may overlook potential zoonotic hosts. To overcome these limitations, we developed UniVH, a unified virus–host association prediction framework trained on an exceptionally broad spectrum of 90 viral families and 240 host families, enabling robust prediction even for phylogenetically distant or data-scarce hosts. UniVH achieved a host prediction accuracy of 71.2% for novel viruses discovered after 2020, representing a 15.3% improvement over conventional BLASTp-based homology approaches. Feature interpretation revealed that viral structural genes and host immune- and metabolism-related genes contributed most significantly to predictive performance. Model predictions indicated widespread host-range expansion, with 20 mammalian virus families doubling their documented mammalian host ranges and several showing marked increases in viruses with human-infection potential. This unified, interpretable framework represents an important methodological advance for future RNA virus spillover-risk evaluation and emerging virus prioritization.

The Haemaphysalis longicornis tick, an important arthropod vector native to East Asia, has expanded its range to Oceania and the American continents, where populations are exclusively parthenogenetic females. While the parthenogenetic population possesses a stable triploid genetic system, the absence of a triploid genome assembly has prohibited us from understanding their genetic evolution and biological traits. Here, we present a chromosome-level, haplotype-resolved triploid genome assembly of the parthenogenetic population by integrating ultra-deep long-read high-fidelity, short-read high-throughput chromosome conformation capture, and isoform sequencing technologies. The phylogenetic analysis suggested that triploid genome originated from an autopolyploid event rather than interspecific hybridization. We identified functional genes that enable parthenogenetic ticks to complete embryogenesis without fertilization. Parthenogenetic ticks showed higher tolerance to Rickettsia and virus infections, with more differential expressed genes compared to bisexual ticks. They exhibited lower levels of deleterious mutations across the genome and a broader global distribution predicted by ecological niche modeling.

Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host–microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases.

Emerging and re-emerging tick-borne viruses (TBVs) have caused numerous outbreaks recently, yet the factors driving their emergence and pathogenicity in humans remain unclear. A global analysis integrating epidemiological and genomic data of all known pathogenic TBVs revealed that highly pathogenic TBVs (HPTBVs) tend to exhibit ecological generalism. Specifically, HPTBVs infect a broader range of tick species, animal hosts, and ecotypes, which likely enhance their transmission to humans. Bird migration is the primary driver for geographic spread of HPTBVs, while livestock density and TBVs’ diversity they carry determine HPTBVs local persistence. HPTBVs experience stronger positive selection in genes related to host interactions, with specific mutations associated with lineage adaptation. Notably, the positively selected D170N mutation in severe fever with thrombocytopenia syndrome virus revealed an enhanced binding affinity to human receptors, which correlated with increased infectivity. These findings underscore ecological and evolutionary factors facilitating TBV generalization, thereby posing significant public health risks.