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Coltiviruses, belonging to the genus Coltivirus within the family Spinareoviridae, are predominantly tick-borne viruses. Some of these species have been implicated in human diseases; however, their diversity, geographical distribution, and evolutionary dynamics remain inadequately. Therefore, this study was undertaken to explore the phylogenetic evolution of coltiviruses and related viruses. Our results revealed the detection of novel coltivirus-related sequences in adult female Haemaphysalis megaspinosa ticks collected from Kanagawa Prefecture, Japan. Molecular phylogenetic analysis revealed a close association between the sequences and the genome sequences of known coltivirus-related viruses, namely Qinghe tick reovirus and Fennes virus. The putative coltivirus-related virus was tentatively designated the Nakatsu tick virus. This study provides insights into the phylogenetic evolution of coltiviruses and related viruses.

In 2010, Jingmen tick virus (JMTV) was discovered in ticks in China and has been shown to be distributed in several regions worldwide. Recently, cases of JMTV infection in humans have been reported in China and Kosovo, and have attracted much attention as an emerging tick-borne disease. In this study, we detected the JMTV genome in Amblyomma testudinarium ticks collected in Kanagawa Prefecture, Japan, during tick-borne virus surveillance conducted in the Kanto Region. Phylogenetic analysis revealed that the new JMTV strain was closely related to previous strains detected in Japan. This suggests that JMTV may have been maintained during an independent natural transmission cycle in Japan. In addition, unlike other countries and regions, all JMTV strains in Japan were detected only in A. testudinarium ticks, suggesting that this tick species is the primary JMTV vector in Japan. This is the first report of JMTV in the Kanto Region. Further studies are required to elucidate the potential risk of infection with this tick-borne virus in Japan. In particular, the prevalence of JMTV in wild animals should be examined to clarify its geographical distribution, host range, and transmission cycle.

Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis-interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and IIIoriginal viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma- LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broadhost- range viruses like those in group II. [ABSTRACT FROM AUTHOR]

In Asia, Culex mosquitoes are of particular interest because of their role in maintaining endemic mosquito-borne viral diseases, including the Japanese encephalitis virus (JEV). Nonetheless, host-feeding preferences, along with naturally infecting RNA viruses in certain Culex species, remain understudied. In this study, selected blood-fed mosquitoes were processed for avian and mammalian blood meal source identification. Concurrently, cell culture propagation and high-throughput sequencing (HTS) approaches were used to determine the RNA virome of Culex mosquitoes collected in Ishikawa Prefecture, Japan. The identification of blood meal sources from wild-caught Culex spp. revealed that Culex (Culex) tritaeniorhynchus Giles, 1901, has a robust preference toward wild boar (62%, 26/42), followed by heron (21%, 9/42). The other two species, Culex (Oculeomyia) bitaeniorhynchus Giles, 1901, and Culex (Culex) orientalis Edwards, 1921, showed a distinct preference for avian species, including migratory birds. From the HTS results, 34 virus sequences were detected, four of which were newly identified virus sequences of unclassified Aspiviridae, Qinviridae, Iflaviridae, and Picornaviridae. The absence of observable cytopathic effects in mammalian cells and phylogenetic analysis suggested that all identified virus sequences were insect-specific. Further investigations involving other mosquito populations collected in different areas are warranted to explore previously unknown vertebrate hosts that may be linked to JEV dispersal in nature., (© The Author(s) 2023. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Jingmen tick virus (JMTV) and the related jingmenvirus-termed Alongshan virus are recognized as globally emerging human pathogenic tick-borne viruses. These viruses have been detected in various mammals and invertebrates, although their natural transmission cycles remain unknown. JMTV and a novel jingmenvirus, tentatively named Takachi virus (TAKV), have now been identified during a surveillance of tick-borne viruses in Japan. JMTV was shown to be distributed across extensive areas of Japan and has been detected repeatedly at the same collection sites over several years, suggesting viral circulation in natural transmission cycles in these areas. Interestingly, these jingmenviruses may exist in a host tick species-specific manner. Vertical transmission of the virus in host ticks in nature was also indicated by the presence of JMTV in unfed host-questing Amblyomma testudinarium larvae. Further epidemiological surveillance and etiological studies are necessary to assess the status and risk of jingmenvirus infection in Japan. [ABSTRACT FROM AUTHOR]

Viruses belonging to the genus Quaranjavirus in the family Orthomyxoviridae are known as argasid tick-borne viruses. Some viruses in this genus or an unassigned quaranjavirus-like variant can infect humans, although little is known about their pathogenicity. During the surveillance of tick-borne viruses in ixodid ticks in Ehime Prefecture, Japan, novel quaranjavirus-like sequences were detected in 3 pooled samples of Haemaphysalis histricis nymphs. Phylogenetic analysis revealed that the detected viruses formed a cluster with quaranjaviruses and other related viruses. Specifically, the viruses were closely related to Zambezi tick virus 1 and Uumaja virus, which are quaranjavirus-like viruses recently discovered in ixodid ticks in Africa and Europe, respectively. These findings indicate that the viruses detected in this study were probably new members of the Quaranjavirus genus or a related group. The viruses were tentatively named "Ohshima virus" even though only limited sequences of their genomes were available. This is the first report on the detection of a quaranjavirus-like virus in the East Asian region. Further investigations are needed to discern its infectivity and pathogenicity against humans and other animals and to determine the potential risk of an emerging tick-borne viral disease.

With the increasing prevalence of colorectal cancer (CRC), extending the present biomarkers for the diagnosis of colorectal cancer is crucial. Previous studies have highlighted the importance of bacteriophages in gastrointestinal diseases, suggesting the potential value of gut phageome in early CRC diagnostic. Here, based on 317 metagenomic samples of three discovery cohorts collected from China (Hong Kong), Austria, and Japan, five intestinal bacteriophages, including Fusobacterium nucleatum, Peptacetobacter hiranonis, and Parvimonas micra phages were identified as potential CRC biomarkers. The five CRC enriched bacteriophagic markers classified patients from controls with an area under the receiver-operating characteristics curve (AUC) of 0.8616 across different populations. Subsequently, we used a total of 80 samples from China (Hainan) and Italy for validation. The AUC of the validation cohort is 0.8197. Moreover, to further explore the specificity of the five intestinal bacteriophage biomarkers in a broader background, we performed a confirmatory meta-analysis using two inflammatory bowel disease cohorts, ulcerative colitis (UC) and Crohn's disease (CD). Excitingly, we observed that the five CRC-enriched phage markers also exhibited high discrimination in UC (AUC = 78.02%). Unfortunately, the five CRC-rich phage markers did not show high resolution in CD (AUC = 48.00%). The present research expands the potential of microbial biomarkers in CRC diagnosis by building a more accurate classification model based on the human gut phageome, providing a new perspective for CRC gut phagotherapy. IMPORTANCE Worldwide, by 2020, colorectal cancer has become the third most common cancer after lung and breast cancer. Phages are strictly host-specific, and this specificity makes them more accurate as biomarkers, but phage biomarkers for colorectal cancer have not been thoroughly explored. Therefore, it is crucial to extend the existing phage biomarkers for the diagnosis of colorectal cancer. Here, we innovatively constructed a relatively accurate prediction model, including: three discovery cohorts, two additional validation cohorts and two cross-disease cohorts. A total of five possible biomarkers of intestinal bacteriophages were obtained. They are Peptacetobacter hiranonis Phage, Fusobacterium nucleatum animalis 7_1 Phage, Fusobacterium nucleatum polymorphum Phage, Fusobacterium nucleatum animalis 4_8 Phage, and Parvimonas micra Phage. This study aims at identifying fine-scale species-strain level phage biomarkers for colorectal cancer diseases, so as to expand the existing CRC biomarkers and provide a new perspective for intestinal phagocytosis therapy of colorectal cancer.

Vitis coignetiae samples were collected from several locations in the northern area of Japan, and virome analysis using a high-throughput sequencing technique was performed. The data indicated that some of the collected samples were in mixed infections by various RNA viruses. Among these viruses, three were identified as newly recognized species with support of sequence identity and phylogenetic analysis. The viruses have been provisionally named the Vitis varicosavirus, Vitis emaravirus, and Vitis crypticvirus, and were assigned to the genus Varicosavirus, Emaravirus, and Deltapartitivirus, respectively. [ABSTRACT FROM AUTHOR]

• A new nyavirus, designated Sekira virus (SEKRV), was detected from Argas japonicus ticks in Japan. • SEKRV lacks the genes encoding matrix protein (M) and glycoprotein (G). • This is the first report of a nyavirus deficient in M and G genes in nature. Viruses are highly diverse and are the sole agents that can infect organisms in all domains of life. Viruses are defined as capsid-encoding organisms as opposed to ribosome-encoding cellular organisms. However, recent advances in virology indicate the existence of unique viruses that do not meet this basic definition, such as capsidless viruses. During virome analysis of the soft tick Argas japonicus , we identified virus-like sequences closely related to the members of genus Nyavirus (family Nyamiviridae). Further analysis revealed sequences derived from a novel nyavirus that lacks two structural protein genes, matrix (M) and glycoprotein (G). This unique nyavirus is tentatively named Sekira virus (SEKRV). To our knowledge, this is the first study to report a nyavirus deficient in M and G genes in nature. The mechanism of infection, replication, and persistence of SEKRV remain unknown, yet this finding provides new insight into virus evolution and the diverse way of viral life in nature. [ABSTRACT FROM AUTHOR]

Japanese encephalitis (JE) remains a public health concern in several countries, and the Culex mosquito plays a central role in its transmission cycle. Culex mosquitoes harbor a wide range of viruses, including insect-specific viruses (ISVs), and can transmit a variety of arthropod-borne viruses (arboviruses) that cause human and animal diseases. The current trend of studies displays enhanced efforts to characterize the mosquito virome through bulk RNA sequencing due to possible arbovirus–ISV interactions; however, the extent of viral diversity in the mosquito taxon is still poorly understood, particularly in some disease vectors. In this study, arboviral screening and RNA virome analysis of Culex tritaeniorhynchus and C. pseudovishnui, which are part of the Culex vishnui subgroup mosquitoes, were performed. Results from these two mosquito species, known as the major vectors of JE virus (JEV) in Asia, collected in three prefectures in Japan were also compared with the sympatric species C. inatomii. A total of 27 viruses, including JEV, were detected from these Culex mosquitoes. Molecular and phylogenetic analyses of the detected viruses classified 15 of the 27 viruses as novel species, notably belonging to the Flaviviridae, Rhabdoviridae, Totiviridae, and Iflaviridae families. The successful isolation of JEV genotype I confirmed its continuous presence in Japan, suggesting the need for periodic surveillance. Aside from JEV, this study has also reported the diversity of the RNA virome of disease vectors and broadened the knowledge on mosquito virome profiles containing both arbovirus and ISV. Mosquito taxon seemed to contribute largely to the virome structure (e.g., virome composition, diversity, and abundance) as opposed to the geographical location of the mosquito species. This study therefore offers notable insights into the ecology and evolution of each identified virus and viral family. To the authors' knowledge, this is the first study to characterize the viromes of the major JE vectors in Japan. [ABSTRACT FROM AUTHOR]

Tick-borne viruses have emerged recently in many parts of the world, and the discoveries of novel tick-borne viruses have been accelerated by the development of high-throughput sequencing technology. In this study, a cost-efficient small benchtop next-generation sequencer, the Illumina MiniSeq, was used for the RNA virome analysis of questing ticks collected from Hokuriku District, Japan, and assessed for their potential utility in a tick-borne virus surveillance system. We detected two phleboviruses [Kabuto Mountain virus (KAMV) and Okutama tick virus (OKTV)], a coltivirus [Tarumizu tick virus (TarTV)], and a novel iflavirus [Hamaphysalis flava iflavirus (HfIFV)] from tick homogenates and/or cell culture supernatants after virus isolation processes. The number of sequence reads from KAMV and TarTV markedly increased when cell culture supernatants were used, indicating a successful isolation of these viruses. In contrast, OKTV and HfIFV were detected only in tick homogenates but not from cell culture supernatants, suggesting a failure to isolate these viruses. Furthermore, we performed genomic and phylogenetic analyzes of these detected viruses. OKTV and some phleboviruses discovered recently by NGS-based methods were probably deficient in the M genome segment, which are herein proposed as M segment-deficient phlebovirus (MdPV). A phylogenetic analysis of phleboviruses, including MdPV, suggested that Uukuniemi and Kaisodi group viruses and kabutoviruses evolved from an ancestral MdPV, which provides insights into the evolutionary dynamics of phleboviruses as emerging pathogens., (Copyright © 2019 Elsevier GmbH. All rights reserved.)

Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis -interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and III-original viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma-LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broad-host-range viruses like those in group II. IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa is thought to have diversified its population through the interactions between host and viruses in antiviral defense systems. However, current knowledge of viral genomes and infection programs is limited to those of Microcystis virus Ma-LMM01, which was a narrow host range in which it can escape from the highly abundant host defense systems. Our metagenomic approaches unveiled the cooccurrence of narrow- and broad-host-range Microcystis viruses, which included fifteen viral genomic fragments from Microcystis blooms that were classified into three groups. Interestingly, Microcystis antiviral defense genes were expressed against viral infection in the environment, unlike what was seen in a culture experiment with Ma-LMM01. Given that viruses with a broad host range often induce antiviral responses within alternative hosts, our findings suggest that antiviral responses inhibit viral reproduction, especially that of broad-range viruses like those in group II. This paper augments our understanding of the interactions between M. aeruginosa and its viruses and fills an important knowledge gap., (Copyright © 2019 American Society for Microbiology.)