Biology subjects

Kawasaki, J.

Publications and source records attributed to Kawasaki, J..

9 recordsLinked to original sources

bioRxiv2026

Quantitative host-response mapping enables phenotypic profiling of viruses detected by virome sequencing

Animal-derived viruses have repeatedly caused human outbreaks, motivating efforts to identify and characterize viruses circulating in animals. Virome sequencing has accelerated animal virus discovery, but phenotypic characterization remains difficult to scale. Although generated for viral detection, virome RNA-seq data also capture host transcriptional responses to infection. Here, we developed ViroChart, a comparative transcriptomic framework that quantifies activities across biological pathways and maps diverse mammalian host responses into a common, interpretable low-dimensional space. ViroChart enables clustering of infected samples by host response pattern and quantitative assessment of host response similarity between samples. In virome data sets from wild and farmed animals, some lung samples infected with poorly characterized betacoronaviruses showed host responses resembling those induced by viruses capable of causing fatal disease. ViroChart also revealed host-response heterogeneity in natural infections: among rats with zoonotic rodent-borne viruses, most showed weak responses, consistent with asymptomatic infection, but some showed pronounced inflammation characteristic of acute infection. ViroChart thus enables phenotypic characterization and prioritization of newly detected viruses by leveraging the same RNA-seq data from which their genomes were detected.

microbiology↗

bioRxiv2026

Host innate immune response profiling reveals hidden viral infections across diverse animal species

Virus discovery using RNA-seq data from wildlife and livestock offers a powerful strategy for identifying unknown pathogens with pandemic potential. However, conventional approaches rely on homology-based searches that have limited sensitivity for highly divergent viruses, are computationally intensive at scale, and cannot distinguish true infections from contamination. Viral infection induces interferon-stimulated genes (ISGs), key components of the frontline antiviral defense, and their expression serves as a robust indicator of viral infection. Here, we developed a host-response-based virus discovery framework that rapidly quantifies ISG expression and predicts viral infection status. Applying this framework to [~]210,000 RNA-seq data sets from diverse mammalian and avian species, we identified hidden viral infections across diverse hosts, including those caused by highly divergent viruses missed by a conventional approach. Our framework complements existing virus discovery strategies by adding host innate immune response context and enabling computationally efficient prescreening for scalable viral surveillance. HighlightsO_LIHost response-based virus discovery in wildlife and livestock RNA-seq data C_LIO_LIQuantify interferon-stimulated gene (ISG) expression and predict viral infection C_LIO_LIAnalysis of [~]210,000 RNA-seq data sets reveals hidden viral infections C_LIO_LIDetects highly divergent viruses and scalable viral surveillance through rapid prescreening C_LI

microbiology↗

bioRxiv2025

Genotype-first approach revealed unrecognized breed-specific genetic diseases in dogs

Numerous dogs are affected by genetic diseases because of their unique breeding situation. The identification of pathogenic variants in dogs not only has veterinary benefits but also leads to the development of new human disease models. However, fewer pathogenic variants have been identified in dogs than in humans, and standard genetic approaches, such as large-scale case/control studies and family analyses, often fail to identify novel causative variants in dogs. To address this, we applied a genotype-first approach by developing a multiplex polymerase chain reaction (PCR)-based targeted sequencing method for dogs, analyzing 203 genes--most of which are related to human disease--from 6,333 dogs collected from a veterinary hospital, and characterizing pathogenic variant carriers. In total, 120 pathogenic variants in 83 genes were identified. Frequent pathogenic variants were enriched in specific dog breeds. Dogs homozygous for a pathogenic CHEK2 variant, frequently identified in French Bulldogs (5.74%, homozygous), showed a five-fold increased risk of cancer (P = 3.45 x 10-2). A pathogenic NOD2 variant was detected in half of the Italian Greyhounds. However, their medical records did not document the typical clinical symptoms observed in humans with NOD2 deficiency. Some pathogenic variants were present in three or fewer dogs, and 11.0% of these dogs exhibited symptoms potentially associated with gene defects. These rare variants could become common within a short period due to the canine breeding system to induce breed-specific genetic diseases. These findings suggest that the genotype-first approach successfully identified unrecognized breed-specific genetic diseases. Further characterization of dogs with pathogenic variants enable to define clinical diagnosis, providing an important spontaneous model for human genetic diseases.

genomics↗

bioRxiv2025

Functional analysis of promoter element 2 within the viral polymerase gene of an emerging paramyxovirus, Sosuga virus

Paramyxovirus genomes carry bipartite promoters at the 3 ends of both their genome and antigenome, thereby initiating RNA synthesis, which requires the viral polymerase to recognize two elements: the primary promoter element 1 (PE1) and the secondary promoter element 2 (PE2). We have previously shown that the antigenomic PE2 (agPE2) in many viruses in the Rubulavirinae subfamily is located within the coding region of the viral RNA polymerase L gene. Sosuga virus (SOSV), belonging to the Rubulavirinae subfamily, is highly pathogenic to humans, thus necessitating high-level containment facilities for infectious virus research. The use of a minigenome system permits studies of viral RNA synthesis at lower biosafety levels. Because minigenomes of negative-strand RNA viruses generally comprise only the untranslated regions, agPE2 within the L coding region--such as those found in Rubulavirinae like SOSV--are typically omitted. However, generating an SOSV minigenome that retains agPE2 led to a pronounced increase in activity, enabling a detailed examination of the role of agPE2 in SOSV replication. In many Rubulavirinae, the agPE2 not only acts as a promoter but also encodes part of the L protein, resulting in a distinct motif at the C-terminus of the L protein. We have further shown that this motif is preserved even in Rubulavirinae that no longer contain the agPE2 within the L gene. ImportanceParamyxoviruses are classified into three major subfamilies: Orthoparamyxovirinae, Avulavirinae and Rubulavirinae. All paramyxovirus genomes and antigenomes possess bipartite promoters, comprising two elements: promoter element 1 (PE1) at the 3 end and promoter element 2 (PE2) located internally. We previously revealed that, in many Rubulavirinae, the antigenomic PE2 lies within the coding region of the viral RNA polymerase L gene. In this study, we used Sosuga virus, a member of the Rubulavirinae subfamily, to elucidate the role of antigenomic PE2 in viral replication. Because the PE2 region encodes part of the L protein, its presence leads to a distinctive motif at the C-terminus of L protein. Notably, this motif is conserved in all Rubulavirinae, including those that do not harbor the antigenomic PE2 within their L gene, indicating its importance in viral propagation.

microbiology↗

bioRxiv2024

Hidden Challenges in Evaluating Spillover Risk of Zoonotic Viruses using Machine Learning Models

Machine learning models have been deployed to assess the zoonotic spillover risk of viruses by identifying their human infectivity potential. However, the scarcity of comprehensive datasets poses a major challenge, limiting the predictable range of viruses. Our study addressed this limitation through two key strategies: constructing expansive datasets across 26 viral families and developing new models leveraging large language models pre-trained on extensive nucleotide sequences. Our approaches substantially boosted our model performance. This enhancement was particularly notable in segmented RNA viruses, which are involved with severe zoonoses but have been overlooked due to limited data availability. Furthermore, models trained on data up to 2018 displayed strong generalization capability for viruses emerging post-2018. Nonetheless, we also found remaining challenges in alerting the zoonotic potential of specific viral lineages, including SARS-CoV-2. Our study elaborates on the models and datasets for predicting viral infectivity and highlights the unresolved issues to fully exploit machine learning in preparing for future zoonotic threats.

microbiology↗

bioRxiv2023

FeLIX is a restriction factor for mammalian retrovirus infection

Endogenous retroviruses (ERVs) are remnants of ancestral viral infections. Feline leukemia virus (FeLV) is an exogenous and endogenous retrovirus in domestic cats. It is classified into several subgroups (A, B, C, D, E, and T) based on viral receptor interference properties or receptor usage. ERV-derived molecules benefit animals, conferring resistance to infectious diseases. However, the soluble protein encoded by the defective envelope (env) gene of endogenous FeLV (enFeLV) functions as a co-factor in FeLV subgroup T infections. Thus, whether the gene emerged to facilitate viral infection is unclear. Based on the properties of ERV-derived molecules, we hypothesized that the defective env genes possess antiviral activity that would be advantageous to the host because FeLV subgroup B (FeLV-B), a recombinant virus derived from enFeLV env, is restricted to viral transmission among domestic cats. When soluble truncated Env proteins from enFeLV were tested for their inhibitory effects against enFeLV and FeLV- B, they inhibited viral infection. Notably, this antiviral machinery was extended to infection with the Gibbon ape leukemia virus, Koala retrovirus-A, and Hervey pteropid gammaretrovirus. Although these viruses used feline phosphate transporter1 (fePit1) or fePit1 and phosphate transporter2 (fePit2) as receptors, the inhibitory mechanism involved competitive receptor binding in a fePit1-dependent manner. The shift of receptor usage may have occurred to avoid the inhibitory effect. Overall, these findings highlight the possible emergence of soluble truncated Env proteins from enFeLV as a restriction factor against retroviral infection, and might help in the control of retroviral spread for host immunity and antiviral defense. ImportanceRetroviruses are unique in using reverse transcriptase to convert RNA genomes into DNA, infecting germ cells, and transmitting to offspring. A large amount of ancient retroviral sequences are known as endogenous retroviruses (ERVs). Soluble Env protein derived from ERVs have been identified to function as a co-factor that assists in FeLV-T infection. However, herein, we show that the soluble Env protein exhibits antiviral activity and provides resistance to mammalian retrovirus infection through competitive receptor binding. In particular, this finding may explain why FeLV-B transmission is not observed among domestic cats. ERV-derived molecules can benefit animals in an evolutionary arm race, highlighting the double-edged sword nature of ERVs.

microbiology↗

bioRxiv2021

Hidden viral sequences in public sequencing data and warning for future emerging diseases

RNA viruses cause numerous emerging diseases, mostly due to transmission from mammalian and avian reservoirs. Large-scale surveillance of RNA viral infections in these animals is a fundamental step for controlling viral infectious diseases. Metagenomic analysis is a powerful method for virus identification with low bias and has substantially contributed to the discovery of novel viruses. Deep sequencing data have been collected from diverse animals and accumulated in public databases, which can be valuable resources for identifying unknown viral sequences. Here, we screened for infections of 33 RNA viral families in publicly available mammalian and avian sequencing data and found approximately 900 hidden viral infections. We also discovered six nearly complete viral genomes in livestock, wild, and experimental animals: hepatovirus in a goat, hepeviruses in blind mole-rats and a galago, astrovirus in macaque monkeys, parechovirus in a cow, and pegivirus in tree shrews. Some of these viruses were phylogenetically close to human pathogenic viruses, suggesting the potential risk of causing disease in humans upon infection. Furthermore, the infections of five novel viruses were identified in several different individuals, indicating that their infections may have already spread in the natural host population. Our findings demonstrate the reusability of public sequencing data for surveying viral infections and identifying novel viral sequences, presenting a warning about a new threat of viral infectious disease to public health. ImportanceMonitoring the spread of viral infections and identifying novel viruses capable of infecting humans through animal reservoirs are necessary to control emerging viral diseases. Massive amounts of sequencing data collected from various animals are publicly available, and these data may contain sequences originating from a wide variety of viruses. Here, we analyzed more than 46,000 public sequencing data and identified approximately 900 hidden RNA viral infections in mammalian and avian samples. Some viruses discovered in this study were genetically similar to pathogens that cause hepatitis, diarrhea, or encephalitis in humans, suggesting the presence of new threats to public health. Our study demonstrates the effectiveness of reusing public sequencing data to identify known and unknown viral infections, indicating that future continuous monitoring of public sequencing data by metagenomic analyses would help prepare and mitigate future viral pandemics.

microbiology↗

bioRxiv2020

One hundred million years history of bornavirus infections hidden in vertebrate genomes

Although viruses have threatened our ancestors for millions of years, prehistoric epidemics of viruses are largely unknown. Endogenous bornavirus-like elements (EBLs) are ancient viral sequences that have been integrated into animal genomes. These elements can be used as molecular fossil records to trace past bornaviral infections. In this study, we systematically identified EBLs in vertebrate genomes and revealed the history of bornavirus infections over nearly 100 million years. We found that ancient bornaviral infections have occurred in diverse vertebrate lineages, especially in primate ancestors. Phylogenetic analyses indicated that primate ancestors had been infected with various bornaviral lineages during evolution. Moreover, EBLs in primate genomes formed clades according to their integration ages, suggesting that epidemic lineages of bornaviruses had changed chronologically. However, we found that some bornaviral lineages coexisted with primate ancestors and underwent repeated endogenizations for tens of millions of years. Furthermore, this viral lineage that coexisted with primate ancestors was also endogenized in some ancestral bats. Notably, the geographic distributions of these bat ancestors have been reported to overlap with the migration route of primate ancestors, suggesting that long-term virus-host coexistence could have expanded the geographic distributions of the viral lineage and might have spread their infections to new hosts. Thus, our findings describe hidden virus-host co-evolutionary history over geological timescales, including chronological change in epidemic bornaviral lineages, long-term virus-host coexistence, and expansion of viral infections.

microbiology↗

bioRxiv2020

Identifications of novel avian and mammalian deltaviruses filled the large evolutionally gaps and revealed inter-family transmission of deltaviruses

Hepatitis delta virus (HDV) is a satellite virus that requires hepadnavirus envelope proteins for its transmission. Although recent studies identified HDV-related deltaviruses in certain animals, the evolution of deltaviruses, such as the origin of HDV and the mechanism of its coevolution with its helper viruses, is unknown, mainly because of the phylogenetic gaps among deltaviruses. Here we identified novel deltaviruses of passerine birds, woodchucks, and white-tailed deer by extensive database searches and molecular surveillance. Phylogenetic and molecular epidemiological analyses suggest that HDV originated from mammalian deltaviruses and the past interspecies transmission of mammalian and passerine deltaviruses. Further, metaviromic and experimental analyses suggest that the satellite-helper relationship between HDV and hepadnavirus was established after the divergence of the HDV lineage from non-HDV mammalian deltaviruses. Our findings enhance our understanding of deltavirus evolution, diversity, and transmission, indicating the importance of further surveillance for deltaviruses.

microbiology↗