Biology subjects

Kishimoto, M.

Publications and source records attributed to Kishimoto, M..

17 recordsLinked to original sources

bioRxiv2026

Systematic analysis of intracellular replication competence of mammalian, avian, and reptilian kolmioviruses.

Kolmioviruses (KoVs) are circular, single-stranded RNA viruses whose evolution may have involved host switching between vertebrate classes. However, the host specificity of their intracellular replication remains poorly understood. Here, we examined six mammalian, one avian, and one reptilian KoVs using cell lines derived from the same three vertebrate classes. We transfected cells with plasmids encoding 1.2x genome-length KoV sequences and assessed persistent replication by monitoring delta antigen-positive cells for up to 18 days. Four mammalian KoVs replicated persistently only in mammalian cell lines, whereas avian and reptilian KoVs replicated persistently only in both avian and reptilian cell lines. By contrast, the remaining two mammalian KoVs, nested within the clade whose deepest lineages are the avian and reptilian KoVs, replicated in cell lines from all three vertebrate classes. The observed patterns of persistent replication are concordant with the phylogenetic grouping of the KoVs. Our findings support a possible evolutionary scenario in which the common ancestor of the two mammalian KoVs in the avian-reptilian clade acquired compatibility with mammalian cells while retaining the capacity to replicate in avian and reptilian cells, contributing to the transition of this lineage to mammalian hosts.

microbiology↗

bioRxiv2026

Identification of novel kolmioviruses in diverse invertebrates.

Kolmioviruses (KoVs; family Kolmioviridae) are circular, single-stranded RNA viruses that have recently been discovered in a wide range of animal species. However, invertebrate-associated KoVs have so far been identified only in termites and their diversity and evolution remain largely unexplored. Here, we comprehensively analyzed publicly available animal RNA-seq datasets and identified six novel KoVs associated with one fish and five invertebrate species: coho salmon (Oncorhynchus kisutch [Walbaum, 1792]), spotted babylon (Babylonia areolata [Link, 1807]), Atlantic pearl oyster (Pinctada imbricata [Roding, 1798]), small emerald moth (Hemistola chrysoprasaria [Esper, 1795]), codling moth (Cydia pomonella [Linnaeus, 1758]), and cocoa pod borer (Conopomorpha cramerella [Snellen, 1904]).

microbiology↗

bioRxiv2026

Identification of novel hepaciviruses in rock pigeon (Columba livia )

Recent advances in sequencing technology and transcriptome mining have revealed highly divergent hepaciviruses in birds. However, only a limited number of avian hepaciviruses have been identified to date, leaving their diversity and evolutionary history poorly understood. Moreover, deep phylogenetic gaps among known avian hepaciviruses suggest that additional lineages remain undiscovered. Here, we screened publicly available RNA-seq data and identified three previously undescribed hepaciviruses from rock pigeon (Columba livia), rusty-margined flycatcher (Myiozetetes cayanensis), and Hispaniolan amazon (Amazona ventralis), named rock pigeon hepacivirus (RpHV), rusty-margined flycatcher hepacivirus (RfHV), and Hispaniolan amazon hepacivirus (HaHV). Although these three viruses meet the ICTV species demarcation criteria relative to their closest known relatives, the NS5B-based criterion was not satisfied between RfHV and HaHV. Notably, however, their genome sequence identity is low at 43.2%, and their hosts differ at the order level, suggesting that their classification warrants further consideration. Our phylogenetic analysis showed that avian hepaciviruses, including those found in this study, are monophyletic, but phylogenetic incongruence was observed between avian hepaciviruses and their hosts, suggesting past cross-species transmission among avian hepaciviruses. Overall, this study provides novel insights into the diversity and evolution of hepaciviruses.

microbiology↗

bioRxiv2026

Spatial distribution of ticks and tick-borne pathogens in central Hokkaido, Japan and associated ecological factors revealed by intensive short-term survey in 2024

Tick-borne pathogens are transmitted by tick bites to cause infectious diseases in humans and domestic animals. To anticipate the occurrence of tick-borne diseases, it is required to understand high resolution distribution of infection risk and associated ecological factors. The aim of the present study is to reveal the spatial distribution of ticks and ticks infected with pathogens in central Hokkaido, Japan. Adult and nymphal ticks were collected with a constant effort at 171 sites from 13 May to 26 June 2024, followed by screening tick-borne pathogens. The potential suitable habitats of seven tick species and the endemic tick-borne pathogens in the study area (i.e. tick-borne encephalitis virus, Yezo virus, Beiji nairovirus, Lyme disease group borreliae, and relapsing fever group borreliae) were predicted using ecological niche modeling. Ixodes persulcatus and Ixodes ovatus were identified as the primary ticks to determine the distributions of all the pathogens. Besides, the predicted suitable habitats were specific to each pathogen/tick species. Among the environmental variables considered for modeling, snow depth appeared to significantly contribute to the distribution differences between ticks and pathogens. The findings of this study expand our understanding of the spatial risk distribution of tick-borne pathogen infections and its ecological context.

ecology↗

bioRxiv2026

Identification of a novel and divergent reptarenavirus in an Amazon coral snake (Micrurus spixii )

Reptarenaviruses are viruses belonging to the genus Reptarenavirus within the family Arenaviridae, which infect snakes and cause inclusion body disease (IBD), a fatal condition characterized by behavioral abnormalities and wasting. Although many reptarenaviruses have been identified thus far, the phylogenetic gaps between reptarenaviruses and the other arenaviruses suggest the existence of yet-to-be-identified reptarenaviruses filling the gaps. In this study, we identified a novel reptarenavirus from publicly available RNA-seq data derived from Amazon coral snake (Micrurus spixii) and tentatively named it Amazon coral snake virus 1 (ACSV-1). We identified four ACSV-1 contigs containing the putative full-length open reading frames of the NP, GP, and L genes, as well as the partial Z gene. Phylogenetic analyses showed that ACSV-1 is highly divergent from known reptarenaviruses. The NP, GP, and L genes showed 48.3%, 42.3%, and 45.7% nucleotide sequence identities, respectively, with those of the closest relatives. Based on the International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria, ACSV-1 can be assigned to a novel species of virus within the genus Reptarenavirus. This study expands our understanding of the diversity and evolution of reptarenaviruses.

microbiology↗

bioRxiv2025

Identification of a novel nidovirus in the common chameleon (Chamaeleo chamaeleon recticrista )

Nidoviruses (the order Nidovirales) are positive strand RNA viruses, and the order currently contains 14 families, 48 genera, and 130 species. Novel nidoviruses have been identified in a variety of animal hosts, but many phylogenetic gaps remain, suggesting the presence of yet-to-be-identified viruses. In this study, we identified a novel nidovirus from publicly available RNA-seq data obtained from the blood of the common chameleon (Chamaeleo chamaeleon recticrista [Boettger, 1880]), and tentatively named it common chameleon nidovirus 1 (CCNV-1). Phylogenetic analysis showed that CCNV-1 is clustered with a member of the family Nanhypoviridae and some unclassified viruses designated as arteriviruses. Further, CCNV-1 genetically distinct from known viruses, exhibiting 50.9% amino acid identity in the RdRp sequence to its closest relative, Jingmen rodent arterivirus 1. Thus, this study provides novel insights into the diversity of nidoviruses.

microbiology↗

bioRxiv2025

Detection and genetic characterization of pigeon gammacoronavirus

Most members of the genus Gammacoronavirus infect avian hosts, but far fewer viruses have been characterized than in the other coronavirus genera, leaving their diversity largely unclear. Pigeon gammacoronaviruses were previously detected by consensus PCR, but only partial sequences were determined. In this study, we comprehensively analyzed public RNA-seq datasets and reconstructed two nearly complete genomes of pigeon gammacoronaviruses. Molecular evolutionary analyses showed pigeon gammacoronaviruses belong to the subgenus Igacovirus, and their pairwise distances to the members of this subgenus meet the International Committee on Taxonomy of Viruses (ICTV) species demarcation criteria, supporting their designation as a novel species in this subgenus. Notably, although nucleotide sequences are highly conserved gammacoronaviruses, their 3'-genomic region exhibited differences in gene organization among pigeon coronavirus variants. These findings expand our knowledge of the diversity of gammacoronaviruses.

microbiology↗

bioRxiv2025

Identification of an ambisense kolmiovirus from birds

Circular RNA replicons share compact, highly self-complementary genomes that impose severe constraints on genome organization and coding capacity. Recent studies have uncovered a broad diversity of such replicons, but their transcriptional and coding strategies remain inferred largely from sequence analyses. Here we show experimentally that some kolmioviruses (family Kolmioviridae), which have been described as negative-sense circular RNA satellite viruses, use ambisense transcription to expand coding capacity. We identify avian bornaviruses as helper viruses for Serinus canaria kolmiovirus (scKoV) and show that ambisense transcription drives expression of a previously unrecognized gene, open reading frame 2 (ORF2), that promotes helper-dependent transmission. Comparative analyses reveal ambisense gene expression in additional kolmiovirus lineages, suggesting independent acquisition during evolution. These findings provide experimental evidence that circular RNA replicons with highly constrained genomes can acquire additional protein-coding genes through ambisense transcription.

microbiology↗

bioRxiv2024

Detection of a novel parahenipavirus from northern short-tailed shrews (Blarina brevicauda )

Parahenipaviruses (genus Parahenipavirus) are non-segmented negative strand RNA viruses belonging to the family Paramyxoviridae of the order Mononegavirales. Parahenipaviruses have been detected in shrews and rodents, some of which have been reported to be associated with human diseases. Although many parahenipaviruses have been identified thus far, there still exist large phylogenetic gaps in parahenipaviruses, suggesting the existence of yet-to-be-identified parahenipaviruses. In this study, we analyzed public RNA-seq data and identified a novel parahenipavirus from northern short-tailed shrews (Blarina brevicauda [Say, 1823]), tentatively named Blarina brevicauda virus (BbV). Based on sequence comparisons between BbV and its most closely related viruses, BbV meets the International Committee on Taxonomy of Viruses species demarcation criteria, and therefore we propose that BbV is a novel species of virus in the genus Parahenipavirus. Furthermore, mapping analysis using RNA-seq data derived from multiple tissues of northern short-tailed shrews suggested that BbV is kidney-tropic. This study provides novel insights into the diversity of parahenipaviruses, which would contribute to a deeper understanding of their evolution and control of infectious diseases.

microbiology↗

bioRxiv2023

Combination therapy with oral antiviral and anti-inflammatory drugs improves the efficacy of delayed treatment in severe COVID-19

Pulmonary infection with SARS-CoV-2 stimulates host immune responses and can also result in the progression of dysregulated and critical inflammation. Throughout the pandemic, the management and treatment of COVID-19 has been continuously updated with a range of antiviral drugs and immunomodulators. Monotherapy with oral antivirals has proven to be effective in the treatment of COVID-19. However, the treatment should be initiated in the early stages of infection to ensure beneficial therapeutic outcomes, and there is still room for further consideration on therapeutic strategies using antivirals. Here, we show that the oral antiviral ensitrelvir combined with the anti-inflammatory corticosteroid methylprednisolone has higher therapeutic effects and better outcomes in a delayed dosing model of SARS-CoV-2 infected hamsters compared to the monotherapy with ensitrelvir or methylprednisolone alone. Combination therapy with these drugs improved respiratory conditions and the development of pneumonia in hamsters even when the treatment was started after 2 days post infection. The combination therapy led to a differential histological and transcriptomic pattern in comparison to either of the monotherapies, with reduced lung damage and down-regulated expressions of genes involved in inflammatory response. Furthermore, we found that the combination treatment is effective in infection with both highly pathogenic delta and circulating omicron variants. Our results demonstrate the advantage of combination therapy with antiviral and corticosteroid drugs in COVID-19 treatment. Since both drugs are available as oral medications, this combination therapy could provide a clinical and potent therapeutic option for COVID-19.

microbiology↗

bioRxiv2022

Morphogenesis of bullet-shaped rabies virus particles requires a functional interplay between the viral matrix protein and ESCRT-I component TSG101

Viral protein assembly and virion budding are tightly regulated to enable the proper formation of progeny virions. At this late stage in the virus life cycle, some enveloped viruses take advantage of the host ESCRT (endosomal sorting complex required for transport) machinery, which contributes to the physiological functions of membrane modulation and abscission. Bullet-shaped viral particles are unique morphological characteristics of rhabdoviruses; however, the involvement of host factors in rhabdovirus infection, and specifically the molecular mechanisms underlying virion formation are not fully understood. In the present study, we used a siRNA screening approach and found that the ESCRT-I component TSG101 contributes to the propagation of rabies virus (RABV). We demonstrated that the matrix protein (M) of RABV interacts with TSG101 via the late-domain containing the PY and YL motifs, which are conserved in various viral proteins. Loss of the YL motif in the RABV M or the downregulation of host TSG101 expression resulted in the intracellular aggregation of viral proteins and abnormal virus particle formation, indicating a defect in the RABV assembly and budding processes. These results indicate that the interaction of the RABV M and TSG101 is pivotal for not only the efficient budding of progeny RABV from infected cells but also for the bullet-shaped virion morphology. ImportanceEnveloped-viruses bud from cells with the host lipid bilayer. Generally, the membrane modulation and abscission are mediated by host ESCRT (endosomal sorting complex required for transport) complexes. Some enveloped-viruses utilize their late (L)-domain to interact with ESCRTs, which promotes viral budding. Rhabdoviruses form characteristic bullet-shaped enveloped-virions, but the underlying molecular mechanisms involved remain elusive. Herein, we showed that TSG101, one of ESCRT components, supports rabies virus (RABV) budding and proliferation. TSG101 interacted with RABV matrix protein via L-domain, and the absence of this interaction resulted in intracellular virion accumulation and distortion of the morphology of progeny virions. Our study reveals that virion formation of RABV is highly regulated by TSG101 and the virus matrix protein.

microbiology↗

bioRxiv2022

Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5

Unremitting emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants imposes us to continuous control measurement. Given the rapid spread, new Omicron subvariant named BA.5 is urgently required for characterization. Here we analyzed BA.5 with the other Omicron variants BA.1, BA.2, and ancestral B.1.1 comprehensively. Although in vitro growth kinetics of BA.5 is comparable among the Omicron subvariants, BA.5 become much more fusogenic than BA.1 and BA.2. The airway-on-a-chip analysis showed that the ability of BA.5 to disrupt the respiratory epithelial and endothelial barriers is enhanced among Omicron subvariants. Furthermore, in our hamster model, in vivo replication of BA.5 is comparable with that of the other Omicrons and less than that of the ancestral B.1.1. Importantly, inflammatory response against BA.5 is strong compared with BA.1 and BA.2. Our data suggest that BA.5 is still low pathogenic compared to ancestral strain but evolved to induce enhanced inflammation when compared to prior Omicron subvariants.

microbiology↗

bioRxiv2022

Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5

After the global spread of SARS-CoV-2 Omicron BA.2 lineage, some BA.2-related variants that acquire mutations in the L452 residue of spike protein, such as BA.2.9.1 and BA.2.13 (L452M), BA.2.12.1 (L452Q), and BA.2.11, BA.4 and BA.5 (L452R), emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these L452R/M/Q-bearing BA.2-related Omicron variants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1 and BA.2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. Furthermore, infection experiments using hamsters indicated that BA.4/5 is more pathogenic than BA.2. Altogether, our multiscale investigations suggest that the risk of L452R/M/Q-bearing BA.2-related Omicron variants, particularly BA.4 and BA.5, to global health is potentially greater than that of original BA.2. HighlightsO_LISpike L452R/Q/M mutations increase the effective reproduction number of BA.2 C_LIO_LIBA.4/5 is resistant to the immunity induced by BA.1 and BA.2 infections C_LIO_LIBA.2.12.1 and BA.4/5 more efficiently spread in human lung cells than BA.2 C_LIO_LIBA.4/5 is more pathogenic than BA.2 in hamsters C_LI

microbiology↗

bioRxiv2022

A comprehensive list of the replication promoters of Bunyavirales reveals a unique promoter structure in Nairoviridae differing from other virus families

Bunyaviruses belong to the order Bunyavirales, the largest group of RNA viruses. They infect a wide variety of host species around the world, including plants, animals and humans, and pose a major threat to public health. Major families in the order Bunyavirales have tri-segmented negative-sense RNA genomes, the 5 and 3 ends of which form complementary strands that serve as a replication promoter. Elucidation of the mechanisms by which viral RNA-dependent RNA polymerase recognizes the promoter to initiates RNA synthesis is important for understanding viral replication and pathogenesis, and for developing antivirals. A list of replication promoter configuration patterns may provide details on the differences in the replication mechanisms among bunyaviruses. Here, by using public sequence data of all known bunyavirus species, we constructed a comprehensive list of the replication promoters comprising 40 nucleotides in both the 5 and 3 ends of the genome that form a specific complementary strand. We showed that among tri-segmented bunyaviruses, viruses belonging to the family Nairoviridae, including the highly pathogenic Crimean-Congo hemorrhagic fever virus, have evolved a GC-rich promoter structure that differs from that of other bunyaviruses. The unique promoter structure might be related to the large genome size of the family Nairoviridae among bunyaviruses. It is possible that the large genome architecture confers a pathogenic advantage. The promoter list provided in this report is expected to be useful for predicting virus family-specific replication mechanisms of segmented negative-sense RNA viruses.

microbiology↗

bioRxiv2022

Virological characteristics of SARS-CoV-2 BA.2 variant

Soon after the emergence and global spread of a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron lineage, BA.1 (ref1, 2), another Omicron lineage, BA.2, has initiated outcompeting BA.1. Statistical analysis shows that the effective reproduction number of BA.2 is 1.4-fold higher than that of BA.1. Neutralisation experiments show that the vaccine-induced humoral immunity fails to function against BA.2 like BA.1, and notably, the antigenicity of BA.2 is different from BA.1. Cell culture experiments show that BA.2 is more replicative in human nasal epithelial cells and more fusogenic than BA.1. Furthermore, infection experiments using hamsters show that BA.2 is more pathogenic than BA.1. Our multiscale investigations suggest that the risk of BA.2 for global health is potentially higher than that of BA.1.

microbiology↗

bioRxiv2022

Oral administration of S-217622, a SARS-CoV-2 main protease inhibitor, decreases viral load and accelerates recovery from clinical aspects of COVID-19

In parallel with vaccination, oral antiviral agents are highly anticipated to act as countermeasures for the treatment of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Oral antiviral medication demands not only high antiviral activity but also target specificity, favorable oral bioavailability, and high metabolic stability. Although a large number of compounds have been identified as potential inhibitors of SARS-CoV-2 infection in vitro, few have proven to be effective in vivo. Here, we show that oral administration of S-217622, a novel inhibitor of SARS-CoV-2 main protease (Mpro, also known as 3C-like protease), decreases viral load and ameliorates the disease severity in SARS-CoV-2-infected hamsters. S-217622 inhibited viral proliferation at low nanomolar to sub-micromolar concentrations in cells. Oral administration of S-217622 demonstrated eminent pharmacokinetic properties and accelerated recovery from acute SARS-CoV-2 infection in hamster recipients. Moreover, S-217622 exerted antiviral activity against SARS-CoV-2 variants of concern (VOCs), including the highly pathogenic Delta variant and the recently emerged Omicron variant. Overall, our study provides evidence that S-217622, an antiviral agent that is under evaluation in a phase II/III clinical trial, possesses remarkable antiviral potency and efficacy against SARS-CoV-2 and is a prospective oral therapeutic option for COVID-19.

microbiology↗

bioRxiv2022

Frequency of a nucleotide overhang at the 5' end of hemorrhagic fever mammarenavirus genomes in public sequence data

Mammarenaviruses, such as Lassa virus and South American hemorrhagic fever (SAHF) virus, cause severe hemorrhagic fevers in humans, and pose major threats to public health. Mammarenaviruses consist of a bi-segmented negative-sense RNA genome in which the 5 and 3 ends form complementary strands that serve as a replication promoter. Some mammarenaviruses have a nucleotide overhang at the 5 genome end. By examining the complementarity of 5 and 3 genome ends using public mammarenavirus genome sequences, we found that the 5 guanine overhang (5-G overhang) was present more frequently in Lassa and SAHF viruses than in other viruses. The 5-G overhang in the Lassa and SAHF virus sequences was found to be restricted to the L and S segments, respectively. If the genome end sequence data in the public database are accurate, the 5-G overhang may be related to the high pathogenicity of mammarenaviruses in humans.

microbiology↗