Cryphonectria parasitica fungus, the causal agent of chestnut blight, by virus infection (hypovirulence) is an effective control strategy against chestnut blight in Europe and some parts of North America. The most studied mycovirus is the Cryphonectria hypovirus 1 (CHV1) type species of the Hypoviridae family. In this study, the CHV1 virus was studied within some highly infected British isolates of Cryphonectria parasitica, gained in the past through co-culture transmissions. The effects of six temperatures  on six infected isolates  and their respective negative non-infected controls, three isogenic virulent fungal isolates, were examined. Experiments were performed with the nine isolate types with three replicates on potato dextrose agar (PDA) with cellophane sheets per isolate and temperature. A recently developed rapid, specific, quantitative reverse transcription PCR (RT-qPCR) screening method was used. This enabled quantifying the concentration (nanograms per microliter or copy numbers) of the virus within each isolate repetition. The presence of the virus had a significant negative effect between 20 and 25 °C on the C. parasitica growth rate, which was anyway highly influenced by and positively correlated with the temperature. The temperature clearly determined the virus accumulation and its recovery from cold or heat, and the virus optimum temperature was estimated at 15–25 °C.Biological control of  Chrysoviridae, Spinoreoviridae, Partitiviridae, Totiviridae, Polymycoviridae, Quadriviridae, Megabirnaviridae, Amalgaviridae, and Curvulaviridae) and the genus Botybirnavirus, twelve single-stranded RNA families , two reverse-transcribing virus families Metaviridae and Pseudoviridae, and one ssDNA family Genomoviridae , where Avogadro’s number is the number of copies per mole, DNA concentration is given in grams per microliter, and the molecular weight of one plasmid is in grams per mole, assuming a plasmid size of 2627 bp and a 1 bp molecular weight of 660 g/mole. The threshold cycle values permitted also calculating the viral concentration (in nanograms per microliter) after building up an equation with a four points serial dilution of known concentrations standard . The fragment copy number, actual number of CHV1 virus particles, was estimated using a ten point 1:10 serial dilution of the plasmid and subsequent posterior regression equation analyses B. For castandard A submittThe complete experimental protocol but without cellophane was repeated to test for potential recoveries from cold or heat. After the temperature treatments, a 5 mm diameter mycelial plug per repetition was further incubated in 1 mL malt extract broth (MEB) in 2-mL Eppendorf tubes at 25 °C for one week, before quantifying the virus concentration and copy number as above.Differences in virus load were analysed in two ways–using viral concentration in nanograms per microliter and by using the variable virus copy number per microliter. Multivariate general linear model ANOVA-type-III analyses were used to assess for significant differences, using Tukey’s HSD adjustments for determining statistical significance with IBM SPSS 13.0 software, and building up regression equations when appropriate.C. parasitica colonies along the trial with cellophane, was influenced by the original virus concentration in the inoculated plugs , and the temperature, but was independent of the haplotype of the two tested virus strains  supported building up respective regression equations relating the fungal growth diameter and the temperature to the viral negative and positive isolate repetitions   B.The capacity of the viral strain E-5 to recover in concentration and copy numbers was always greater than that of strain L-18 A,B, at aC. parasitica by reducing pathogenic growth and sporulation, hence the virus is used in Europe for disease control. The virus has been introduced into continental Europe on multiple occasions in association with C. parasitica from countries such as Japan, China, and Korea, which are known to be the geographical origin of the fungus. Since those introductions, both C. parasitica and CHV1 have spread widely. Originally, such introductions are most likely to have occurred through the plant trade and/or the importation of Asiatic planting stock, often intended for use in breeding resistance programs to chestnut ink disease caused by Phytophthora cinnamomi and P. cambivora. Six genetically distinct CHV1 subtypes have been identified in Europe  [Cryphonectria hypovirus 1 is known to induce hypovirulence in 2 and G) . Subtype2 and G) ,24, is t2 and G) , Bosnia 2 and G) , Croatia2 and G) , Sloveni2 and G) , Macedon2 and G) , Turkey 2 and G) , and now2 and G) ,24, wher2 and G) .To the best of our knowledge, this is the first time that the effect of temperature on CHV1 has been evaluated. The fact that the biological replicate effect was not significant along the different models, and the original virus concentration being significant, gave a high level of confidence to the whole assay.The low prevalence of CHV1 (17 out of 350 isolates) and the naturally low virus concentration in these isolates  in ECurvularia protuberata [Heterobasidion annosum sensu lato [That temperature can modulate the outcome of the chestnut blight fungus and its CHV1 hypovirus interaction was already suggested by a previous study . Somehowtuberata  and somensu lato .C. parasitica. The results revealed a clear relationship between the virus concentration and temperature. The accumulation of CHV1 within all six virus-infected cultures was shown to be higher between 15 to 25 °C than at lower or higher temperatures.Considering the mentioned hypothesis, we analysed the accumulation of the CHV1 virus at different temperatures and its possible effect on the growth of highly infected (gained by transmissions ) BritishC. parasitica in the present study, which could explain why the chestnut blight situation in England is also quite stable, as temperatures are generally much lower than this [C. parasitica at 5, 10, 15 and 30 °C but had a reducing effect at 20 and 25 °C, which makes sense with the highest detected transcription levels. The same fungal isolates proved to be less pathogenic in a previous study compared to non-infected isolates when inoculated into chestnut branches and seedlings that were constantly kept at 25 °C [On the other hand, temperature regulates the fungal growth, with 30 °C the optimum temperature for han this . Taken tat 25 °C .One conclusion noted is that the distribution of the virus load along the different parts of a fungal colony is not uniform, tending to be more concentrated in the central parts than in the periphery of the colony, as suggested here in


In this study, a deterministic model for the dynamics of Marburg virus transmission that incorporates the impact of public health education is being formulated and analyzed. The Caputo fractional-order derivative is used to extend the traditional integer model to a fractional-based model. The model’s positivity and boundedness are also under investigation. We obtain the basic reproduction number  These outbreaks were associated with laboratory work involving African green monkeys imported from Uganda. Since then, sporadic outbreaks of Marburg virus disease have occurred in various countries in Africa, including Uganda, Angola, and Kenya4. The natural reservoir for Marburg virus is believed to be fruit bats of the Pteropodidae family, which are found throughout sub-Saharan Africa. The virus is transmitted to humans through direct contact with the bodily fluids of infected individuals or animals5. The incubation period for the virus ranges from 2 to 21 days, with symptoms typically appearing between 5 and 10 days after infection6. Marburg virus causes severe and often fatal hemorrhagic fever in humans and nonhuman primates. The virus attacks multiple organs and systems in the body, leading to a range of symptoms, including fever, headache, muscle pain, vomiting, and diarrhea. In severe cases, the virus can cause hemorrhagic fever, which is characterized by bleeding from the eyes, ears, and mouth, as well as internal bleeding. The case fatality rate for Marburg virus disease ranges from 24% to 88%, depending on the outbreak and the quality of care available7. The impact of Marburg virus on the African continent has been significant. Given the severity of Marburg virus disease and the potential for outbreaks to cause significant harm, it is crucial that public health officials remain vigilant and prepared to respond to any new cases or outbreaks. The recent Marburg virus infection in sub-Saharan African countries, namely Equatorial Guinea, Tanzania, Ghana, Guinea, and Uganda has been considered to be significant which called for World Health Organization’s (WHO) in-depth epidemiological investigation, intervention and potential treatment9.Marburg virus is a highly infectious virus that belongs to the Filoviridae family, which also includes the Ebola virus. The virus was first identified in 1967, during simultaneous outbreaks in Marburg, Germany11. When an infectious disease first appears, the first priority is to rapidly inform the public about the illness and its protective measures. Although widespread vaccination is the most effective method of disease management, vaccination is expensive and sometimes only temporarily confers immunity. In developing and underdeveloped countries, public health educational initiatives on Marburg virus infection are essential for managing and preventing the disease and can raise people’s health literacy and awareness of the virus. The awareness campaigns not only educate the public about the Marburg virus, but also recommend important preventive measures like the use of face masks, improved hygiene, and avoidance of congregated areas, among others, which can sometimes alter people’s behaviour and lower the risk of infection.It was widely recognized that the social behaviour of individuals within a society has had a significant impact on the occurrence of any epidemic. It was noted that behaviour modification was crucial in the spread of disease. It was noted that behavioural change played a very important role in the spread of the disease14. In a broad range of systems and processes, fractional derivatives are an effective tool for explaining memory and hereditary characteristics17. With fractional-order modelling, we have such an additional variable (order of the derivative) that is helpful for numerical techniques. The dynamics of many disease transmission have been investigated using fractional-order modelling. For instance, mathematical model for HIV/AIDS18, Ebola-malaria co-infection model19, smoke age-specific model20, monkeypox transmission dynamics23 Middle East Lungs Coronavirus dynamism transmission model24, COVID-19 model26, Hepatitis E disease model27 are all examples of fractional model used in the past. For more application on fractional derivatives see, for instance29, and references therein. The Caputo fractional order derivative is very helpful for discussing actual situations since it enables the inclusion of conventional starting and boundary conditions in the derivation and because the derivative of a constant is zero, unlike the Riemann-Liouville fractional derivative.While dealing with an epidemic, it is crucial to anticipate future events, understand how to stop the virus from spreading, and provide the required instructions so that the situation may be handled before it gets out of hand. The forecasting, investigation, and creation of significant strategies to battle infectious diseases have been made possible by numerous researchers from a broad range of disciplines. Several scientists have used mathematical modelling to understand the intricacies of how viruses spread32 areas of infectious diseases, this work consider Caputo fractional model to discuss how various variables affect the mathematical simulation of the dynamics of Marburg virus transmission incorporating public health education. It is important to note that this is relatively the first time a fractional order model has been presented to simulate the aforemention topic. The following highlight the innovative nature of our study: i.A novel fractional model defined in the Caputo sense is used to examine the dynamics of Marburg virus transmission incorporating the impact of public health education.ii.The reproduction number iii.We demonstrate the existence and uniqueness solutions of the dynamics of Marburg virus transmission incorporating the impact of public health education by employing the Banach contraction mapping principle.iv.The fractional controlling system of equations underwent a stability study using the Hyers-Ulam-type stability criteria.v.To validate the theoretical components and conclusions of the suggested model, an effective numerical technique is adopted.vi.The obtained results demonstrate the effectiveness of the suggested model in providing some new insights into the dynamics of the Marburg virus infection as well as some preventative actions.The paper is structured in the manner described below. In Section "Inspired by the advantages of Caputo derivative that gives standard beginning and steady state in the derivation over other fractional derivatives which have been used in other researchn this section, we recall some critical concepts, lemmas, and definitions to study our proposed model.33 The Caputo fractional derivative of order 34 Assume that n, thenS(t); susceptible humans with public health education P(t); Exposed individuals H, respectively. Considering the interrelationship, the infection model used in analyzing the dynamics of Marburg virus transmission incorporating the impact of public health education is given by the following deterministic system of nonlinear differential equations35, our considered Caputo fractional order derivative model for the dynamics of Marburg virus transmission is defined as follows;In this section, we present the formulation of the model, which we will be studying in this paper. For this, we have considered only human population and divided it into seven different compartments, which are susceptible humans without public health education about the Marburg virus transmission (at a time) mentclass2pt{minimmentclass2pt{minimIn this section, we give positivity, boundedness and existence of unique solution to projected model.Assume Since the coefficients of (2) are positive constants, we haveLet some parameters of system (2) beThe disease-free equilibrium Consider a Lyapunov function:T] with the norm Let us write the system (2) in the compact form for easy description as follows:We show the analysis for Let Define an operator Step 1: Prove that the operator (1) Prove that Duo to From Step 2: Show that the system (6) has a unique solution.For any (HU stability) Assume that For solution In this section, the numerical solution of system (2) is given by corrector-predictor iterative scheme in Caputos sense. LetFor the purpose of validating our created iterative scheme, we present our numerical simulation in this part. For this, we start with initial values for each compartment of our proposed model 1); ; \documeentclass1pt{minimaentclass1pt{minimaentclass1pt{minimaentclass1pt{minimaR. We noticed that dynamics has significant impact on our proposed model. These results give public policymakers a note on how and where resources allocate are needed in order to prevent and control Marburg virus spread.Furthermore, considering the contributions of some of the sensitive parameters in our proposed model, we maintain the fractional operator to be fixed at In recent years, numerous deadly diseases have appeared in many countries around the globe. If the limitations of established methodologies, ideas, and procedures are updated, questioned, and amended in response to contemporary scientific findings and the emergence of unforeseen physical phenomena, the dynamics of infectious diseases can be better understood and even predicted. We have comprehensively analyzed a new deterministic mathematical model for Marburg virus in a homogeneously mixing human population under Caputo fractional order derivative in this paper. We have investigated the qualitative aspect of the spread of the Marburg virus by analysing the positiveness, boundedness, equilibrium point, and fundamental reproductive number


A 68‐year‐old female patient was referred to our hospital with a 30‐mm polyp in the second portion of the duodenum found via esophagogastroduodenoscopy. The polyp had an irregular, lobular surface and a thick stalk. In addition, white dots were detected on the surface. Magnifying endoscopy with narrow‐band imaging showed a white material deep in the loop‐shaped microvessels on the white dots. Endoscopic ultrasonography showed a hypoechoic elevated lesion from the mucosal layer, and a feeding vessel traversing the stalk to supply the head of the polyp. Endoscopic biopsy did not provide a definitive diagnosis. Endoscopic resection was conducted for a definitive diagnosis and treatment. The resected specimen showed a branching bundle of smooth muscle fibers covered by hyperplastic mucosa, consistent with a hamartomatous polyp. The patient had no mucocutaneous pigmentation or familial history of the hamartomatous polyp. The polyp was finally diagnosed as a solitary Peutz‐Jeghers‐type polyp. No recurrence has been observed for seven years postoperatively. Peutz‐Jeghers (PJ) syndrome is a rare autosomal dominant syndrome caused by mutations in the serine/threonine kinase 11 genes, which is characterized by gastrointestinal hamartomatous polyps, mucocutaneous pigmentation, and an increased risk of cancer.A hamartomatous polyp without associated mucocutaneous pigmentation or a family history of PJ syndrome is diagnosed as a solitary PJ‐type polyp.This case report discusses a patient with a solitary PJ‐type polyp in the duodenum treated by endoscopic resection and includes a review of the literature.A 68‐year‐old female patient with a history of hypertension and diabetes mellitus was referred to our hospital with a pedunculated polyp in the duodenum identified by routine esophagogastroduodenoscopy. Physical examination and blood tests revealed no significant findings. Contrast‐enhanced computed tomography revealed a well‐circumscribed mass in the 2nd portion of the duodenum Figure ; arrows.A previous case series that included 51 patients with a solitary PJ‐type gastrointestinal polyp reported that the sigmoid colon was most frequently involved, followed by the rectum, duodenum, transverse colon, jejunum, and cecum.A MEDLINE search of the well‐documented English language literature up to 2022 using the terms “hamartomatous polyp” and “duodenum” revealed 15 studies (including the current study), including 21 patients with a solitary PJ‐type polyp in the duodenum Table . The meaThe differential diagnosis based on morphological features is difficult as PJ‐type polyps present with various colors, including normal, erythematous, and white, and often present with pedunculated or semi‐pedunculated morphology, which is similar to duodenal neoplastic lesions. In addition, differentiation of PJ‐type polyp from neoplastic lesions in the duodenum is difficult by endoscopic ultrasonography. Sonoda et al. reported knacks of endoscopic differentiation between PJ‐type and neoplastic polyps that included: (1) due to the branching bundles of smooth muscle fibers, PJ‐type polyps have more irregular lobules than neoplastic polyps; and (2) PJ‐type polyps have white dots, which represents lymphatic congestion rather than whitened epithelium as often seen in neoplastic polyps, which can be confirmed by narrow‐band imaging magnifying endoscopy.To date, there is no definitive therapeutic strategy for solitary PJ‐type polyps in the duodenum. A definitive diagnosis by endoscopic biopsy is difficult as PJ‐type polyps are typically covered by the hyperplastic duodenal mucosa. Most of the 11 cases with well‐documented biopsy results in the literature were not definitively diagnosed  Endoscopic ultrasonography showed a hypoechoic elevated lesion from the mucosal layer, and a luminal‐like structure was observed inside the stalk (arrows).(b) Color Doppler imaging showed an abundant blood flow inside the luminal‐like structure (arrows).Click here for additional data file.Figure S2 Endoscopic resection.(a) The Peutz‐Jeghers‐type polyp is shown in the second portion of the duodenum.(b) The polyp is snared.(c) An ulcer after endoscopic resection.(d) The resected specimen is shown.Click here for additional data file.Doc S1 Reference articles in Table 1.Click here for additional data file.


Dear Editor,Marburgvirus. It is closely related to the Ebola virus. Marburg marburgvirus, only species causing a zoonotic disease called Marburg virus disease (MVD) in humans, manifests as skin rash, nausea, vomiting, malaise, hemorrhage, and feverRousettus aegyptiacus. Since African fruit bats reside in caves and are extensively distributed across Africa; these might have infected humans, although the exact mechanism of transmission from fruit bats to humans is still unknownMarburg virus (MARV) is a rare yet deadly pathogen, an RNA virus belonging to the order: Mononegavirales, family: Filoviridae, genus: MVD is a fatal infection with a significant potential to become an epidemicDue to ongoing COVID-19 pandemic and overlapping features between COVID-19 and MVD, it becomes difficult for a physician to accurately differentiate COVID-19 and MVD. Table No antiviral has been accepted as the appropriate treatment for MVD, neither is any approved vaccine for itWorld is already afflicted with multiple outbreaksNot commissioned, externally peer reviewed.Not applicable.None.Conceptualization and editing: A.N. Writing: A.N., S.T., S.M.H.Z., Q.M., F.N., S.G., A.A.W. Review with critical comments: A.N. and S.T.The authors declare that they have no financial conflict of interest with regard to the content of this report.Not applicable.All authors.


DNA viruses into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a virus integration site (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein–Barr virus based on the next-generation sequencing (NGS) data, literature, and experimental data. There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database, comprising 47 virus genotypes and 17 disease types. The VIS Atlas database provides (1) a genome browser for NGS breakpoint quality check, visualization of VISs, and the local genomic context; (2) a novel platform to discover integration patterns; and (3) a statistics interface for a comprehensive investigation of genotype-specific integration features. Data collected in the VIS Atlas aid to provide insights into virus pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at https://www.vis-atlas.tech/.Integration of oncogenic  The VIS Atlas was designed and the interactive interface was built using Vue  and Ant Design . The ECharts  was used as a graphical visualization framework, and JBrowse  was used as the browser framework. We recommend using the database with a modern web browser that supports HTML5, such as Firefox, Google Chrome, Safari, Opera, or IE 10.0+. VIS Atlas is freely available to the research community, and users are not required to register or login to access information in the database.The general workflow of VIS Atlas was developed by MySQL  with the authorization of Sun Yat-sen University. (2) The Sequence Read Archive (SRA) database: all raw sequencing data were retrieved by statements of virus full names, virus abbreviations, full names of virus-related cancers, or abbreviations of virus-related cancers, and then filtered by public source and DNA strategy. All metadata of the aforementioned results were examined to exclude the runs of epigenomics strategy, experimental intervened samples, or the third-generation sequencing platform. Then, runs of 2043 samples were downloaded by the Linux wget command. (3) The European Bioinformatics Institute (EBI) database: some candidate data searched from SRA were deposited and only could be accessed in EBI. (4) In-house samples: all 6075 cervical exfoliative cell samples, Raji cell line samples, and C666.1 cell line samples from Zheng Hu Lab were conducted with virus capture technology accompanied by NGS. For literature/experiment-validated breakpoints, data from Dr.VIS v2.0 were downloaded before they were inactive, and 11 papers were kept with integration sequences for curation. Publications were also searched from PubMed and Google Scholar with the authorization of Sun Yat-Sen University by the statements of virus integration, virus full names, or virus abbreviations. Some papers already employed in Dr.VIS v2.0 were checked for accuracy and completeness. Then, we kept 25 papers, which were not employed in Dr.VIS v2.0 otherwise with correct information. We also detected HPV breakpoints for 397 samples by detection of integrated papillomavirus sequences by ligation-mediated PCR (DIPS-PCR) technology.Two kinds of data sources were involved in this study, computational breakpoints and curated breakpoints. For NGS-based computational breakpoints, the raw data collection included three databases. (1) The Cancer Genome Atlas (TCGA) database: under the TCGA-CESC project, we downloaded all 615 bam files with sequencing reads (Data Category) and whole-exome sequencing (WES)  filter conditions for all 307 cases. The download activities were finished by binary Genomic Data Commons (GDC) Data Transfer Tool, gdc-client from GDC Data Portal . (1) Quality control (QC): quality of all collected raw WES data was tested by FastQC followed by simple QC by fastp http://genome.ucsc.edu/). Representative virus genome references were downloaded from the Papillomavirus Episteme (PaVE) genome database (http://pave.niaid.nih.gov), Hepatitis B Virus Database , and the National Center for Biotechnology Information . (3) Virus infection identification: BWA-MEM was used to map clean data to the mixed reference of human and all viruses to identify the dominant infection virus type. (4) Remap: clean data were mapped to (i) mixed reference of human and detected virus genotype; (ii) human reference; and (iii) detected virus genotype reference by BWA-MEM, followed by removing duplication by SAMtools (samtools v-0.1.19) and Picard MarkDuplicates (Picard tools v-1.117) command. (5) Soft-clip read extraction: soft-clip reads, defined as reads spanning the junction sites of human and virus genomes (pair-end soft-clip reads and one-end soft-clip reads), were extracted based on the aforementioned mapping results. These reads were re-aligned against the human reference, respectively, and virus reference by BLASTN (BLAST v-2.7.1). Only reads with consistent alignment results of BWA and BLAST were retained for the next step. (6) Human–virus breakpoint identification: the junction positions of soft-clip reads were merged according to the junction positions in both human and virus genomes, and supported soft-clip reads were calculated for each position. (7) Annotation and consensus sequence generation: junction positions were annotated by ANNOVAR (version 2017-07-17) for the human genome and in-house scripts for the virus genome. For EBV, the VISs located in the repeat region of the EBV genome were excluded. Then, we conducted multiple alignments of supported soft-clip reads by ClustalW, and used EMBOSS Cons to generate consensus junctional sequences. Finally, detailed breakpoint information that met the filtering standard (soft-clip reads ≥ 2) for HPV, HBV, and EBV was generated. (8) The mapping results of soft-clip reads were extracted for manual visualization.The related steps were listed below . (1) QuaFor literature/experiment-validated breakpoints, including the Dr.VIS v2.0 database, updated publications, and DIPS-PCR-detected VISs, the sequencing results were collected followed by BLASTN against the unified human and virus genome references to curate the positions and filter unreliable ones in data processing. By this method, we kept 201, 268, and 354 breakpoints of the Dr.VIS v2.0 database, updated publications, and DIPS-PCR-detected VISs, respectively.Overview of the VIS Atlas database is shown in In the VIS Atlas database, we constructed a universal dataset of VISs for oncogenic viruses. Altogether, 63,179 accurate VISs involved in three most prevalent DNA oncoviruses  were included. According to the detection strategy and stringency, the breakpoints in the VIS Atlas database could be classified into three categories, NGS soft-clip reads ≥ 2, NGS soft-clip reads ≥ 3, or non-NGS source . Unlike This content consisted of integration information and sample metadata. The integration information included virus type, genotype, accurate integration positions in both the human and virus genomes, integration genes and their cytobands in the human genome , and integration genes in the virus genome (annotated according to the PaVE database by Perl script). The metadata contained clinical disease type, pathology, stage, integration detection strategy, and publication information . In addiEach VIS from the NGS data source is accompanied by a link that could visualize the raw mapping results of supported NGS soft-clip reads B. The viOur database provided numerous high-resolution junctional sequences, which play an important role in the sentence in analyzing integration patterns. As an advantage, at the bottom of the detailed page for each human–virus junction sequence, we further displayed MH-mediated patterns http://www.vis-atlas.tech/, and allows users to browse, search, visualize, analyze, and download our integration data , human gene annotations (UCSC source), RepeatMasker (UCSC source), fragile sites (UCSC source), DNase clusters (UCSC source), open chromatin (ENCODE source), gene enhancer (UCSC source), CpG island (UCSC source) tracks To display the genome content for a single VIS, we developed a comprehensive genome browser, VIS BrowserIn addition, high-resolution human–virus junctional sequences could help explore the integration patterns of double-strand DNA viruses. Based on the results analyzed by VIPA, we discovered that a certain quantity of breakpoints may be generated from MH-mediated patterns PVT1 (n = 73), CASC8 (n = 70), CASC11 (n = 48), LINC00392 (n = 50), ERRB2 (n = 49), KLF5 (n = 46), C14orf177 (n = 45), SOX2-OT (n = 41), IRF4 (n = 38), and BCL3 (n = 37) (TERT (n = 120) and MIR4457 (n = 36)], chromosome 19 [KMT2B (n = 30) and CCNE1 (n = 18)], and chromosome 2 [FN1 (n = 61)] (SGK1 (n = 4), HMGA1P7 (n = 4), PROS1 (n = 3), and TAF6 (n = 3) , and EBV Type 1 (NC007605) were the most high-risk genotypes and had 16,024 (45.06%), 10,451 (88.21%), and 1245 (87.80%) integration events (NGS soft-clip reads ≥ 3), respectively A–C. For (n = 37) D. HBV Tyn = 61)] E. EBV Ty (n = 3) F.Figure CASC8, CASC11, CASC21, LINC00392, KLF5, FHIT, and ERBB2) co-existed in more than 10 samples (NGS soft-clip reads ≥ 3 and integration hotspots in ≥ 15 samples) (TERT had co-existing integration relationship with CCNE1 and ANKRD26P1 in 3 samples (NGS soft-clip reads ≥ 3 and integration hotspots in ≥ 3 samples)  at least 3, 5, 10, 15, and 20 integrated samples for hotspot genes, and (2) at least 3, 5, 10, 15, and 20 samples for co-existing relationship. We found that for HPV16, each pair among the seven hotspot integration genes (samples) . For HBVsamples) . Similar samples .CNTN4, EVI5, FZD1, LOC105371703, and PROS1) were found in HPV, HBV, and EBV . When NGS soft-clip reads ≥ 3 and total unique integration times ≥ 10, 5 common integration genes  Initially chimeric mapping results against the mixed reference of specific virus genotype and human were re-checked by mapping to specific virus genotype and human alone via BWA-MEM to avoid align errors. (2) When all soft-clip reads were clustered by genome coordinate, BLASTN was utilized to check the human and virus positions of reads to exclude inaccurate results. We believe the strategies mentioned above could achieve reliability and sensitivity in detecting HPV, HBV, and EBV integration, and could construct a consistent breakpoint database based on different NGS data sources.As most current genome browsers have no double-strand virus genome and annotation configuration, we developed VIS Browser as the first customized genome browser to visualize and explore NGS computational VISs. The VIS Browser could help users not only to visualize both collected and their own computational results, but also to understand the potential impact of local genomic context on viral integration. For instance, open chromatin and DNase clusters reflect the more accessible genome regions Furthermore, we focused on the genotype-based VISs in Browse, Search, Visualization, and Statistic modules. The virus genotypes showed differences in integration frequencies, human hotspots, and associated disease stages. Our results support the viewpoint that the prevention and treatment strategies for oncogenic viruses should be based on virus genotypes and even sub-genotypes The understanding of oncogenic viral integration mechanisms could provide important information for both preventive and therapeutic strategies against the corresponding virus persistent infections and their related cancers As NGS becomes the most popular detection approach for VISs, the need to develop a computational VIS database is required. The VIS Atlas database based on integration sequences from NGS data sources makes the study of integration patterns possible. Additionally, we will continue to maintain and improve our database in the future by following strategies: (1) adding breakpoints of other viruses, such as molluscum contagiosum virus (MCV) and herpes simplex virus (HSV); (2) expanding more disease types and samples; and (3) acquiring accurate VISs and sequences by taking virus integration heterogeneity into account.As the first universal resource for NGS integration breakpoints, the VIS Atlas database is expected to help promote research into oncogenic virus integration mechanisms during carcinogenesis and the development of preventive and therapeutic strategies for virus-related cancers.http://www.vis-atlas.tech/.The VISs identified in this study with their annotations and sequences can be directly downloaded at The authors have declared no competing interests.Ye Chen: Investigation, Validation, Methodology, Writing – review & editing. Yuyan Wang: Software, Formal analysis, Methodology, Writing – review & editing. Ping Zhou: Methodology, Investigation, Funding acquisition. Hao Huang: Methodology, Investigation, Formal analysis. Rui Li: Investigation, Validation, Resources. Zhen Zeng: Investigation, Validation, Resources. Zifeng Cui: Writing – original draft. Rui Tian: Resources, Methodology. Zhuang Jin: Formal analysis. Jiashuo Liu: Data curation. Zhaoyue Huang: Data curation. Lifang Li: Visualization. Zheying Huang: Visualization. Xun Tian: Conceptualization, Project administration, Funding acquisition. Meiying Yu: Resources, Methodology, Project administration. Zheng Hu: Conceptualization, Methodology, Project administration, Funding acquisition, Supervision, Writing – original draft, Writing – review & editing. All authors have read and approved the final manuscript.


Severe fever with thrombocytopenia syndrome (SFTS) is a new infectious disease first discovered in Ta-pieh Mountains in central China in 2009. It is caused by a novel bunyavirus infection (SFTSV). Since the first discovery of SFTSV, there have been case reports and epidemiological studies on SFTS in several East Asian countries, such as South Korea, Japan, Vietnam and so on. With the rising incidence of SFTS and the rapid spread of the novel bunyavirus around the world, it is clear that the virus has a pandemic potential and may pose a threat to global public health in the future. Early studies have suggested that ticks are an important medium for the transmission of SFTSV to humans; in recent years, it has been reported that there is also human-to-human transmission. In endemic areas, potential hosts include a variety of livestock and wildlife. When people are infected with SFTV, the main clinical manifestations are high fever, thrombocytopenia, leukocytopenia, gastrointestinal symptoms, liver and kidney function damage, and even MODS, with a mortality rate of about 10–30%. This article reviews the latest progress of novel bunyavirus, including virus transmission vector, virus genotypic diversity and epidemiology, pathogenesis, clinical manifestation and treatment. Severe fever with thrombocytopenia syndrome(SFTS) is an infectious disease caused by viral infection. It was first reported in 2009 in the Ta-pieh Mountains in central China, and then in 2010, Yu et al. . The M sThe life cycle and mechanism of continuous transmission of SFTSV in nature are not clear . ThroughSFTS RNA can be detected in arthropods of ticks such as Haemaphysalis, Ixodes minimus, Ixodes tortoise, Ixodes asiatica and Ixodes japonicus in the endemic areas of SFTSV. Another feature of these tick species is that they can reproduce parthenogenetically and survive in a variety of environmental conditions . AlthougSFTSV maintains virus replication in nature through tick-to-tick cycles . In the tick cycle, ticks act not only as a carrier, but also as a host of SFTSV  Fig. 1)1).Fig. 1SFTSV can also be detected in livestock and wild animals. Most animals are found to be subclinical infected with SFTSV. The reason for subclinical infection is that infected animals do not have prolonged symptoms of viremia and viral infection. SFTSV's RNA can be detected in cattle, goats, pigs, chickens, dogs, cats, deer, hedgehogs and minks, but these animals did not develop the disease. The novel bunyavirus is transmitted to these vertebrates through tick bites, which serve as storage hosts for SFTSV. This cycle makes SFTSV spread in nature to achieve a lasting cycle. Human beings usually have a lot of contact with domestic animals and need special precautions. There is also a potential risk of cross-regional transmission of migratory birds infected with SFTSV . DiffereTick bites are the main route of transmission of SFTSV, as initial epidemiological reports show that patients diagnosed with SFTS have a history of tick bites before the onset of SFTS . With thHaemaphysalis longicornis of Asia undergo three unique life stages . At each stage, they are parasitic on a variety of wild and domestic animals, including birds, livestock, etc.There is a close relationship between humans and animals, especially in SFTSV-endemic areas, which increases the risk of SFTS epidemic . Ticks sSFTS was first reported in the Ta-pieh Mountains in central China in 2009, and quickly spread to Zhejiang, Jiangsu, Shandong and other regions. Japan and South Korea also reported cases of SFTS in 2012 , 27. RecThe mechanism of rapid spread of severe fever with thrombocytopenia syndrome is unclear. However, the spread of the virus is usually attributed to two main mechanisms:increased contact between wildlife and human populations and geographical spread of hematophagous arthropod vector or their vertebrate host outside the area of endemicity. Haemaphysalis longicornis is also a common parasite of migratory birds, which usually breeds and migrates between the endemic areas of China, Korea and Japan, and the endemic areas of STFS match the migration routes of migratory birds . HoweverSeveral studies have highlighted the genetic diversity of SFTSV. The novel bunyavirus consists of several gene fragments. Because it is a RNA virus, the gene mutation caused by lack of proofreading function of SFTSV in viral RNA replication and transcription, which will lead to gene recombination. As a result, genetic diversity and new genome lines have emerged in different hosts . AccordiThe main clinical symptoms of SFTSV infection are fever and thrombocytopenia. In addition to these two major clinical manifestations, it also includes gastrointestinal symptoms such as poor anorexia of nausea and vomiting, leukocytopenia, low lymphocyte count, coagulation dysfunction and hemorrhagic tendency. In addition, there are also reported cases of atypical and asymptomatic SFTS infection . The incAs early as 2013, according to the clinical characteristics of Chinese patients, clinical experts divided the severity of SFTS into mild, severe and critical. After classification, it is beneficial to focus on treatment and find critical patients in time. The patients with T < 38 ℃, muscle soreness, digestive system symptoms such as anorexia, diarrhea, nausea and vomiting, no systemic bleeding tendency, clear mind and no nervous system symptoms were divided into mild symptoms. The patients with T > 38 ℃, obvious symptoms of general fatigue, severe anorexia; mental malaise, accompanied by neurological symptoms, such as lethargy, muscle tremor, systemic involuntary tremor, convulsions, convulsions and delirium are divided into severe cases.On the basis of severe cases, patients with any of the following conditions such as: ARDS, heart failure, AKI, sepsis or septic shock; DIC, encephalitis, that is, summarized as critical . The aboPathological study is of great significance for understanding the pathogenesis of the virus. Autopsy of patients who died of SFTS can better understand it’s pathogenesis. A pathological study of SFTS suggests that biopsy of lymph nodes near tick bites indicates necrotizing lymphadenitis, which is consistent with the signs of SFTS patients. These patients are prone to enlarged lymph nodes at the bitten site . In addiThe immunopathogenesis of SFTSV infection is complex, which includes a cascade of reactions involving a wide range of immune cells, inflammatory mediators, inflammasomes and signaling pathways . SFTSV aAt present, the main treatment for SFTS disease is symptomatic treatment and traditional Chinese medicine treatment. Symptomatic treatment is to deal with fever, give drugs to increase platelet and leukocyte use.For example, the Chinese medicine Xuebijing injection can reduce SIRS reaction. It can also reduce the DIC score of SFTS and restore the platelets to normal . AccordiFavipiravir, discovered and synthesized by Toyama Chemical Co., Ltd., Japan, is a new antiviral drug so far. It has a wide range of activities against a variety of RNA viruses, including influenza virus, Bunya virus, West Nile virus, yellow fever virus and foot-and-mouth disease virus . It’s meIn many animal models of SFTSV infection, the efficacy of Favipiravir in vivo has been fully verified. One study showed that when treatment began 3 days or earlier after SFTSV infection, all mice treated with Favipiravir survived, even though mice treated 4 and 5 days after infection showed a survival rate of 83% and 50%, respectively . At pres2+ levels and are widely used in the treatment of various cardiovascular diseases, including hypertension, angina pectoris and supraventricular arrhythmias. In recent years, some studies have shown that CCBs has strong antiviral activity against Ebola virus, Marburg virus and Japanese encephalitis virus [2+ replication by reducing virus-induced SFTSV influx [Calcium channel blockers(CCBs) can reduce intracellular Cais virus , 51. AmoV influx . ProfessV influx . It was V influx . In the IVIG plays an important role in the treatment of various viral diseases by triggering complement activation, virus neutralization, antibody-dependent cytotoxicity and conditioning. Based on the mechanism of immunosuppression and inflammatory factor disorder in the pathogenesis of SFTS, we believe that IVIG can help reduce viral load in patients with SFTS, inhibit SFTSV transmission, and effectively inhibit cytokine storm. However, there are only a few cases of successful use of IVIG in patients with severe SFTS . The mecSevere SFTS can lead to rapid deterioration of the disease, and patients are easy to die of septic shock and MODS,DIC. The key to this pathogenic process is the cytokine storm. Considering the pathogenesis of SFTS, clinicians believe that steroids are a therapeutic option for suppressing the immune system of patients with severe SFTS. Kim et al.  reportedSFTSV infection can lead to a storm of cytokines all over the body, which can damage organ function. Plasma exchange may be a possible rescue method for the removal of cytokines. Korean scholars have done much research on this therapy. A Korean hospital reported 2 cases of SFTS treated with therapeutic Plasma exchange(TPE) and oral ribavirin . AnotherVaccine is the most effective way to deal with infectious diseases, and the development of a vaccine against the novel bunyavirus can provide mass immunity to people living in epidemic areas. In 2019, researchers at the University of the Chinese Academy of Sciences published a paper on a novel bunyavirus vaccine using recombinant vesicular stomatitis virus (rVSV) as a vector. In this study, VSV has been developed as a promising attenuated virus vaccine vector to induce the production of neutralizing antibodies that can effectively resist the deadly challenges of a variety of pathogens, including Hendra virus, Lassa virus, Ebola virus, Marburg virus, Nipah virus, etc. .VSV is classified as a RNA virus of the family Rhabdoviridae, which is covered with an envelope protein when it sprouts. The envelope protein is composed of two substances, one is lipid bilayer and the other is anchoring protein derived from glycoprotein. The reason why VSV is used as a vaccine vector and model is that it’s envelope protein can be recombined with foreign virus envelope protein to form virus particles, and the antigen composition remains unchanged. The effects of recombinant vesicular stomatitis virus in invading the body, being recognized by the immune cells of the body, binding to the receptor, and producing neutralizing specific antibodies are basically similar to that produced by SFTSV invading the body , 62. TheSFTS is prone to sepsis and MODS . In prinThe cause of MODS was actively eliminated. For SFTS patients, the cause was the storm of cellular inflammatory factors caused by viral infection. If septic shock is present, tissue and organ perfusion should be improved as soon as possible to avoid further aggravating organ function damage. If a bacterial infection presents clinically, combined antibiotic therapy is required .The main measures to improve oxygen metabolism and correct tissue hypoxia include increasing oxygen supply, reducing oxygen consumption and improving the ability of tissue cells to use oxygen. At present, increasing oxygen supply is the most feasible means to improve tissue hypoxia, which requires three conditions: ① normal hemoglobin content; ② Oxygen therapy, if necessary, mechanical ventilation to support breathing, so that SaO2> 90%; ③ Normal cardiac function and effective circulating blood volume. Vasoactive drugs can be used appropriately to maintain tissue and organ perfusion. Reducing oxygen consumption is often overlooked and can be achieved through sedation, hypothermia and mechanical ventilation to support breathing.Respiratory support treatment Respiratory support is one of the important means to improve oxygen delivery and reduce oxygen consumption. When selecting ventilator mode and setting ventilator parameters, attention should be paid to the prevention and treatment of ventilator related lung injury, and the influence of mechanical ventilation on organ function should be reduced as far as possible .SFTSV has the potential of pandemic, has an impact on global public health and poses a great threat. People in affected areas are at risk of being bitten by ticks when engaged in agricultural and outdoor activities. With the migration of migratory birds, virus spillovers often spread between humans, animals and ticks. Some studies have investigated the complex interaction between SFTSV and the host immune system. For example, the failure to produce a virus-specific humoral response is attributed to b-cell dysfunction. It has also been reported that B cell differentiation in secondary lymphoid organs is the main target of the virus at the end of fatal SFTSV infection. In addition, an inflammatory storm caused by an overimmune response to the virus can lead to progressive sexual organ damage and death. The mainly reasons are: First, the early pathogenesis of SFTSV infection; Second, the similarities and differences and interrelationship between the pathogenesis of fatal and surviving SFTSV infection. At present, there is no specific antiviral drug against SFTSV infection, nor is there a commercial vaccine. Redeveloping new antivirals is a promising approach, but it consumes time and resources. Therefore, more and more people are looking for candidate treatments for emerging viruses through the reuse of existing antiviral drugs. Vaccines are the most powerful tool to prevent outbreaks in response to this infectious disease, and some vaccine-related studies have been published. As the research on SFTSV is still in its infancy, there are still many problems to be solved.


Healthcare utilization among people living with inflammatory bowel disease (IBD) in Canada has shifted from inpatient management to outpatient management; fewer people with IBD are admitted to hospitals or undergo surgery, but outpatient visits have become more frequent. Although the frequency of emergency department (ED) visits among adults and seniors with IBD decreased, the frequency of ED visits among children with IBD increased. Additionally, there is variation in the utilization of IBD health services within and between provinces and across ethnocultural and sociodemographic groups. For example, First Nations individuals with IBD are more likely to be hospitalized than the general IBD population. South Asian children with Crohn’s disease are hospitalized more often than their Caucasian peers at diagnosis, but not during follow-up. Immigrants to Canada who develop IBD have higher health services utilization, but a lower risk of surgery compared to individuals born in Canada. The total direct healthcare costs of IBD, including the cost of hospitalizations, ED visits, outpatient visits, endoscopy, cross-sectional imaging, and medications are rising rapidly. The direct health system and medication costs of IBD in Canada are estimated to be $3.33 billion in 2023, potentially ranging from $2.19 billion to $4.47 billion. This is an increase from an estimated $1.28 billion in 2018, likely due to sharp increases in the use of biologic therapy over the past two decades. In 2017, 50% of total direct healthcare costs can be attributed to biologic therapies; the proportion of total direct healthcare costs attributed to biologic therapies today is likely even greater. People living with IBD in Canada are admitted to hospitals and undergo surgery less often than in past decades, but these individuals have an increasing number of outpatient visits.The frequency of emergency department (ED) visits among adults and seniors with IBD have decreased. Children with IBD are visiting EDs more often. Despite presenting to the ED for reasons related to their IBD, gastroenterologist consults during their ED visit and follow-up are uncommon.The utilization of IBD-specific health services  and medications, as well as the likelihood of undergoing surgery, vary both within and between provinces.First Nations individuals with IBD are more likely to be hospitalized than the general IBD population. Additional within and between-province studies are needed to better understand healthcare and medication utilization and the risk of surgery in First Nations individuals with IBD.South Asian children with Crohn’s disease are hospitalized more often at diagnosis than their Caucasian peers. However, these differences diminish during follow-up.Immigrants to Canada who develop IBD have higher health services utilization, but a lower risk of surgery compared to individuals born in Canada.People with IBD of low socioeconomic status are more likely to be hospitalized, undergo surgery, and require systemic steroids.People with IBD living in rural areas are more likely to be hospitalized and visit the ED than people living in urban areas, but there is no difference in their risk of surgery.The total direct healthcare costs of IBD—costs of hospitalizations, ED visits, outpatient visits, endoscopy, cross-sectional imaging, and medications—in Canada have risen rapidly and are estimated to be $3.33 billion in 2023 relative to market list price; these costs may be as low as $2.19 billion or as high as $4.47 billion.Biologic medications contributed approximately 50% of direct healthcare costs in 2017; the proportion of total direct healthcare costs attributed to biologic therapies today is likely even greater.In 2018, annual healthcare costs  of IBD in Canada were estimated to be at least $1.28 billion, but this was acknowledged as likely an underestimate due to its reliance on a Manitoba costing study using data from 2006, reflecting an era where far fewer individuals were treated with biologic therapy. Direct healthcare costs for IBD are more than double that of individuals without IBD. Prescription drug costs accounted for 42% of these costs and were continuing to rise with the increasing use of biologic therapy. The introduction of biosimilars into the marketplace was anticipated to reduce these costs. People with IBD had increasing access to gastroenterologists, yet many lacked timely access, with most individuals waiting longer than six months between symptom onset and diagnosis. Seniors, individuals living in rural areas, and nonimmigrants had less access to specialist care, which was associated with better IBD outcomes. One in five adults with Crohn’s disease and one in eight adults with ulcerative colitis were hospitalized every year. Surgery rates were declining. However, within 10 years of diagnosis, one in three people with Crohn’s disease still required surgery, and one in six people with ulcerative colitis required a colectomy.Canadians living with inflammatory bowel disease (IBD) have frequent interactions with the healthcare system, including being admitted to hospitals, care, undergoing diagnostic testing , and receiving ambulatory and long-term care. Nearly all Canadians are eligible for universal healthcare plans that cover the majority of the costs of these interactions. Most provinces also cover medication costs for seniors, individuals on social assistance, or those who are otherwise unable to afford needed medications. When these and other costs  are not covered by health plans, individuals must pay out-of-pocket or purchase private insurance. These costs, borne both by individuals and the healthcare system, comprise the direct costs of IBD.Provincial healthcare budgets are limited. Nevertheless, Canadian healthcare systems must be prepared to address the needs of a growing IBD population. Understanding the healthcare needs of people with IBD ensures Crohn’s and Colitis Canada can advocate for the resources people with IBD need. Therefore, it is critical to understand how much care is being used by Canadians with IBD, how this is changing over time, the inequities in healthcare utilization, and associated costs to provide equitable and high-quality care for people with IBD. This article outlines the direct costs of IBD borne by the Canadian health system, including medication costs (covered either through government or private pharmacare programs). For the direct costs borne by individuals (including medication costs paid out-of-pocket by a person with IBD), see Kuenzig et al. (this volume).The frequency of hospitalization for IBD has steadily decreased in most Canadian regions over the past few decades, likely resulting from a combination of evolving treatment paradigms in IBD and health system pressures  1–6). I. I1–6). P < 0.01); per-person hospitalization costs were not reported (costs in 2018 CAD)  ,8. Hospi018 CAD) . The autWhen medications are not working or IBD-related complications occur , individuals with IBD may require surgery. The type and location of surgery depends on disease location and phenotype. The most common surgery in Crohn’s disease is an intestinal resection , most ofAs IBD management has evolved, surgery rates have decreased  1–4,9,1,19,10,13The frequency of Crohn’s disease-related emergency department (ED) visits decreased from 141 95% CI: 137, 146) in 2003 to 101  in 2014 per 1,000 prevalent individuals with Crohn’s disease   .On average, people with IBD have an additional 3.7 outpatient visits per person per year compared to people without IBD . BetweenWhile people with IBD living in rural areas were more likely to visit the ED than those living in urban areas, this association was not mediated by geographic differences in access to specialist care . People People with IBD are significantly more likely to undergo abdominal imaging . One-thiThe proportion of people with an abdominal CT for Crohn’s disease increased by 11%  per year between 1999 and 2007, then decreased by 2%  per year until 2017 , data are limited to outpatient prescriptions for those eligible for provincial drug plans; in these provinces, individuals ≥65 years of age and those on social assistance are eligible for provincial drug plans. Individuals who need assistance to cover costs associated with expensive medications  may also be eligible for provincial drug plans, but off-label utilization of biologics is often funded by compassionate use programs of pharmaceutical companies, and therefore the dose/interval of their use may not be accurately reflected in provincial drug databases.Among individuals eligible for provincial drug coverage in Québec, there has been no change in corticosteroid utilization , while aMultiple Canadian provinces have reported the rapidly increasing use of biologics to treat IBD. Between 1996 and 2013, biologic use increased by 36.2%  per year among individuals with Crohn’s disease in Edmonton, Alberta . Among tP < 0.001; ulcerative colitis, 13% to 16%, P < 0.001); the proportion of people on methotrexate also increased but was much smaller  and biologic eras after 2010)  . Forty pMedications accounted for approximately 50% of all IBD direct healthcare costs in 2016  and are AntiTNF therapies dispensed for any reason , cost Canadian taxpayers nearly $1 billion in 2019; this cost estimate accounted only for antiTNFs taken by those eligible for provincial drug programs (3.9% of biologics dispensed) . The intWhile all Canadians are eligible for universal healthcare coverage, there remains significant variation in healthcare utilization among Canadians living with IBD. Two studies have specifically investigated this variation in healthcare utilization. The first compared variation in health services utilization and surgery within the first five years following IBD diagnosis among children treated at tertiary paediatric centres in Alberta, Manitoba, Nova Scotia, and Ontario . The secI2: 84%, τ: 0.1556) ; the risk of intestinal resection in children with Crohn’s disease did vary  (P = 0.01) but not in the risk of intestinal resection among seniors with Crohn’s disease   , but the 0.1556) . The ris: 0.042) . The opp = 0.08) .I2: 99%, τ: 1.33), largely attributable to between-province differences (P = 0.023), but not within five years  (Children with IBD varied in the frequency at which they visited an ED (ferences . Among O = 0.49) .P = 0.006; immunomodulators, MOR: 1.46, P = 0.001) (P = 0.34)  . In cont = 0.34) .While we cannot determine if variability in health service, medication utilization and surgery results from differential access to the healthcare system or other factors that shift an individual’s likelihood of seeking healthcare, it is important that we recognize that there are differences in access to and provision of care that may impact long-term outcomes. Canadian studies have aimed to compare health services and medication utilization across sociodemographic  and ethnocultural groups .A Manitoba study used health administrative data to compare health services utilization among people with IBD classified as having low socioeconomic status compared to those of higher socioeconomic status . In thisData from multiple provinces have described differences in healthcare utilization among people with IBD living in rural and urban regions ,25. PeopThe frequency of IBD-specific outpatient visits was similar among people living in urban and rural areas of Alberta, Manitoba, and Ontario  . FurtherPeople living with IBD in rural and urban areas of Saskatchewan were equally likely to be treated with biologic and immunomodulator therapies  . SimilarA study using health administrative data in Saskatchewan compared health services and medication utilization among First Nations individuals with IBD not living on reserves to the general IBD population . After aThere might be differences in biologic and immunomodulator therapy between First Nations individuals with IBD and people with IBD from the general population  . First NThe risk of hospitalization/surgery was compared among South Asian and non-Jewish Caucasian children using data from the Canadian Children Inflammatory Bowel Disease Network (CIDsCaNN)—a cohort study of children newly diagnosed with IBD across 12 Canadian paediatric hospitals . South AHealth services utilization among immigrants to Canada was compared to Canadian-born individuals using Ontario health administrative data linked to data from Immigration, Refugees, and Citizenship Canada . CanadiaA Manitoba study reported significantly increasing total direct healthcare costs  among people with IBD, from $3,354 per person per year in 2005 to $7,801 in 2015 (costs in 2015 CAD) . The aveIn a study combining health administrative data from Alberta, British Columbia, and Manitoba, the total estimated direct costs for individuals with IBD were $10,336  in 2016/17, a significant increase from $7,000  in 2009/10 (costs in 2020 CAD) , and then meta-analyzed to provide a pooled per-person cost . This coVariations and inequities in health services utilization exist across sociodemographic and ethnocultural groups. Since timely access to specialist care is vital for reducing adverse outcomes , efforts need to focus on ensuring equitable access to high-quality specialist care. Novel models of care for IBD, with the goal of improving outcomes (including reduced reliance on EDs), are described in Mathias et al. (this volume).Patterns of health services utilization among people living with IBD in Canada are shifting. People with IBD are being admitted to hospitals and undergoing surgery less frequently; this is accompanied by increasing outpatient visits and utilization of biologic therapy. The costs associated with hospitalizations are decreasing (Crohn’s disease) or remaining stable (ulcerative colitis). As the use of expensive biologic therapies continues to increase rapidly, medication costs will eclipse all other health system costs.The costs of IBD to the healthcare system, people living with IBD, and society are substantial. Over the course of a single year, direct health system and medication costs for IBD are estimated to be $3.33 billion. As the prevalence of IBD continues to rise and as more biologic and targeted therapies at a higher price point than traditional therapies are introduced into the marketplace, the costs of caring for people with IBD will continue to rise . Canadian healthcare systems must prepare for the growing number of people with IBD and the costs of caring for these individuals. The costs of therapies need to become more affordable.While we know that there are ethnocultural, sociodemographic and geographic inequities in access to and utilization of the healthcare system by people living with IBD, our knowledge of these inequities concerning tools used to monitor disease proactively  is limited. Understanding potential inequities is important for strategies designed to ensure that all individuals living with IBD have timely access to high-quality care that will improve their long-term outcomes.Studies on the health system impacts of biologic therapies have not demonstrated system-level improvements in health services utilization  and costs of managing IBD. Future studies evaluating the impact of biologic therapy should not only focus on the impact on the healthcare system but on broader society, including the impact of biologic therapies on disability spending, workplace productivity, and other economic benefits resulting from a healthier IBD population.Much of the data describing variation in care for people with IBD comes from regions with relatively high access to specialist care. Data on access to and utilization of the health system among individuals living in rural and remote regions, including the territories, and provinces with limited access to specialist gastroenterology care are sparse and should be a focus of future research.With the emergence of many biosimilars and new competitive advanced therapies , we should expect that the absolute and relative costs of caring for individuals with IBD will change over time. We need better transparent data to be able to accurately calculate these changing patterns.Our knowledge of the costs of IBD is derived from a subset of provinces. Differences in health system administration are likely a significant source of heterogeneity across provinces. In order to better understand the evolving costs of IBD, national data on the costs of IBD—including the true costs of medications to private and public insurance plans and individuals paying out of pocket for their medications—are needed.Patient partners underlined that the data presented in this chapter show the distressing picture of the significant direct healthcare costs of IBD (and the inequities). Timely access to outpatient care is essential to prevent negative disease outcomes and healthcare costs. The evidence of IBD healthcare utilization differences depending on where you live, income, or ethnicity is an issue that requires close attention and interventions. For example, rural residents and Firsts Nation individuals with IBD face barriers to accessing primary and specialized care which could result in suboptimal medication management, more emergency department visits, hospitalizations, and surgeries. Improving access to care for individuals with IBD could help reduce healthcare costs in the short and long term. There is an urgency to consider how to support individuals living with IBD to access innovative and holistic healthcare and treatment options. The Canadian healthcare systems need to prepare for the growing number of people with IBD and the costs of caring for them. Since biologic medications account for about 50% of the direct costs of IBD, patient partners also emphasized the need for universal pharmacare in Canada and for developing more research about biosimilars. Upcoming studies and reports could assess the impact of biosimilars on the trends of direct healthcare costs in Canada. The costs of therapies for IBD need to become affordable for individuals, healthcare systems and society overall.Crohn’s and Colitis Canada should advocate for better regulation of the cost of biologic therapies to ensure the financial viability of providing the right medication to the right person at the right time. Both government and private health insurance plans should provide financial pressure on the pharmaceutical industry to lower medication costs.Despite increasing utilization of cross-sectional imaging that does not expose people living with IBD to ionizing radiation , people living with IBD have limited time access to these imaging modalities. Improving access for people living with IBD to timely imaging for diagnosis and management is important for managing disease before complications arise and will be beneficial for the long-term outcomes of these individuals by reducing costs to individuals, their caregivers, and the healthcare system.Better access to healthcare resources is needed for individuals living in rural and remote communities and in provinces/territories with limited availability of gastroenterologists, including continued use of virtual healthcare beyond the pandemic.Efforts should be made to reduce geographic, ethnocultural, and other sociodemographic inequities in access to and utilization of health services among people living with IBD, particularly high-quality specialist care, which is important for improving the long-term outcomes of IBD.Crohn’s and Colitis Canada should advocate for universal pharmacare that includes timely access to the most effective IBD medications with the goal of improving the short- and long-term well-being of people living with IBD.This article appears as part of the supplement “The Impact of Inflammatory Bowel Disease in Canada in 2023”, sponsored by Crohn’s and Colitis Canada, and supported by Canadian Institutes of Health Research Project Scheme Operating Grant (Reference number PJT-162393).


Hendra virus (HeV) and Nipah virus (NiV) are biosafety level 4 zoonotic pathogens causing severe and often fatal neurological and respiratory disease. These agents have been recognized by the World Health Organization as top priority pathogens expected to result in severe future outbreaks. HeV has caused sporadic infections in horses and a small number of human cases in Australia since 1994. The NiV Malaysia genotype (NiV-M) was responsible for the 1998–1999 epizootic outbreak in pigs with spillover to humans in Malaysia and Singapore. Since 2001, the NiV Bangladesh genotype (NiV-B) has been the predominant strain leading to outbreaks almost every year in Bangladesh and India, with hundreds of infections in humans. The natural reservoir hosts of HeV and NiV are fruit bats, which carry the viruses without clinical manifestation. The transmission pathways of henipaviruses from bats to humans remain poorly understood. Transmissions are often bridged by an intermediate animal host, which amplifies and spreads the viruses to humans. Horses and pigs are known intermediate hosts for the HeV outbreaks in Australia and NiV-M epidemic in Malaysia and Singapore, respectively. During the NiV-B outbreaks in Bangladesh, following initial spillover thought to be through the consumption of date palm sap, the spread of infection was largely human-to-human transmission. Spillover of NiV-B in recent outbreaks in India is less understood, with the primary route of transmission from bat reservoir to the initial human infection case(s) unknown and no intermediate host established. This review aims to provide a concise update on the epidemiology of henipaviruses covering their previous and current outbreaks with emphasis on the known and potential role of livestock as intermediate hosts in disease transmission. Also included is an up-to-date summary of newly emerging henipa-like viruses and animal hosts. In these contexts we discuss knowledge gaps and new challenges in the field and propose potential future directions. The vire family  and the e family , respectus genus  and thosThe virions of henipaviruses are enveloped and pleomorphic with variable sizes from 120 to 500 nm and have an unsegmented single-stranded RNA genome of negative polarity . The henIn humans and several animal species, the major pathological consequence of henipaviral infection is a severe acute systemic vasculitis in many major organs, prominently in the brain and lung. This often leads to fatal neurological or/and respiratory disease, which also includes long-term relapsing encephalitis  . HenipavSince its emergence in 1994 in Australia, HeV has been causing sporadic infections in horses in most of the subsequent years, and on an annual basis since 2006, with the most recent case reported in July 2022 . Human iApart from the established HeV prototype, or genotype 1 (HeV-g1), a novel variant, or genotype 2 (HeV-g2), was detected in Australia in horses that suffered acute illness with signs of HeV infection as well as in fruit bats . The twoNiV, initially known as Hendra-like virus, was discovered during the 1998–1999 outbreak in farmed pigs and humans in Malaysia . The sprSince 2001, in Bangladesh and its neighboring regions of India, NiV outbreaks or isolated transmission events have been reported almost every year, mainly during the winter months, and have resulted in hundreds of infections in humans . A curreThe latest NiV case in India to our knowledge was documented in a report by the World Health Organization  and in aA possibly new type of NiV or NiV-like virus was reported from a 2014 outbreak in the Philippines . The outPteropus, family Pteropodidae are the major known reservoir hosts of henipaviruses  was not known, and no intermediate host was established. Outbreaks in pigs, which had previously contributed to human infections in Malaysia and Singapore, were not seen here . In a reHuman consumption of date palm sap suspected of henipaviral contamination from bats was found to correlate with risk of NiV-B infection and has been proposed as the most common pathway of NiV-B transmission from bats to humans . InfrareHenipaviral transmissions concerning human infections can occur from bats to intermediate hosts, from intermediate hosts to humans, potentially from bats to humans without intermediate hosts or from humans to humans. These events are commonly featured by close/direct contact with infected hosts or the proximity to bat presence, which has been well supported by scientific observations. However, specific details of the transmission mechanisms remain to be determined while a number of potential modes and vehicles of transmission have been proposed .Body fluids and excretions from henipavirus-infected bat, horse, pig or human hosts, such as saliva, urine and feces, or materials with these contaminants such as fruits partially eaten by bats and date palm saps in contact with bats have been believed to be vehicles of viral transmission. This applies to the handling or consumption of meat from infected pigs or horses as well . It was These hypotheses warrant further research as they are both theoretically feasible and have been suggested or supported to some extent by outbreak observations. Their determination will require in-depth epidemiological investigations and controlled laboratory studies.The host receptors for henipaviruses, ephrin-B2 and ephrin-B3, are highly conserved among mammalian species, which in theory allow the viruses to infect a broad range of hosts. Consistent with this, apart from the known natural hosts bats, horses and pigs, many small animals were able to be experimentally infected by henipaviruses supporting viral replication . These iDomestic ruminants including goats, sheep and cattle constitute significant part of agriculture. They have worldwide distributions in large population numbers, which also involve areas overlapping with habitats of henipaviral reservoir hosts. Particularly, for example, the estimated numbers of goats, sheep and cattle are 14.8 million, 1.9 million and 25.7 million, respectively, in Bangladesh , and 148Several signs suggest potential exposure of ruminants to henipaviruses and their possible involvement in viral transmission to humans. It was reported that in 2004 two goats owned by a Bangladesh family became ill with symptoms including “fever, difficulty walking, walking in circles, and frothing at the mouth” and both died. Within 2 weeks following the goats’ death, a boy from the family, who had played with the goats developed encephalitis and tested positive for NiV antibodies . This raThese possibilities need to be observed further in epidemiological investigations and tested in controlled experiments. Knowledge on the potential role of ruminants as amplifying hosts for henipavirus transmission, which is currently lacking, is of great veterinary and public health importance, considering the vast quantity of potential interactions between humans and henipavirus reservoir hosts connected through ruminants at the ecological interface. New research findings on whether or not ruminants do play such a role will clearly provide guidance for governments to prioritize targets for prevention, surveillance, diagnosis and further research.Henipavirus was initially created in the family Paramyxoviridae following the identification of the two prototype viruses, HeV and NiV  may be an additional host type. These bats are found in continental Africa, which has no Pteropus bats, as well as Madagascar. Antibodies to henipaviruses were detected in both Pteropus and Eidolon bats in Madagascar  and five central/west African countries   where the sequence of its RNA genome was first identified . Althougdagascar , Eidolondagascar  and Eidodagascar . In all dagascar , 2012. Td Ghana) , 2012. Tus genus . Furthermoopidae . These fmoopidae .henipavirus genus that has been reported in a non-bat reservoir host, shifting the paradigm of henipavirus reservoir host range. The virus was named after the Mòjiāng County, Yunnan Province, China, where an outbreak of pneumonia disease with unknown etiology in 2012 resulted in the death of three miners who had been working in a mine cave (CFR 100%). Following the incidence, a virome survey was conducted on anal swab samples of bats, rats and musk shrews collected from the cave, leading to the identification of MojV sequence in rats (Rattus flavipectus)  . MojV  and share a common ancestor with MojV  is the most recently reported shrew-borne henipa-like virus . A hospi to MojV . A subse to MojV . To iden to MojV .henipavirus genus. The rodent/shrew-borne clade seems to be characterized by a conserved putative protein coding region  between the M and F genes, which is not found in other paramyxoviruses  a henipa-like virus was detected, named Peixe-Boi virus (PBV) based on the location of sampling, the municipality of Peixe-Boi, Pará State, Brazil  and humans (n = 497), respectively. Human seropositivity was almost exclusively found in those who had butchered bats for meat . This prReservoir hosts of henipaviruses and emerging henipa-like viruses now have an overwhelmingly broad distribution on the planet. Climate change is expected to further increase the emergence of favorable ecological environment leading to the extension of their habitats into new locations . This wiThe resulting knowledge from these efforts will guide the development of targeted strategies to prevent and contain future henipavirus outbreaks. An extreme idea might be to remove the identified viral reservoirs, which would be practically impossible and disastrous given the large numbers and broad distribution of the reservoir hosts and the importance of these animals to the ecosystem and biodiversity. It should be noted that loss of biodiversity often leads to increased disease transmission . Under tParamyxoviridae) as but different genera  from henipaviruses. In comparison, a vaccine vector derived from CedV is expected to elicit better cross-protection due to higher extent of antigenic overlap within the henipavirus genus. Our previous study suggested that the soluble G protein vaccine was not effective in inducing cellular immunity (On a final, encouraging note, although the emergence of new henipa-like viruses signifies new challenges, it also provides new opportunities. Different characteristics among closely related viruses can be utilized in comparative functional investigations to understand aspects of henipavirus biology such as evolution, host tropism, cross-species transmission and pathogenicity. So far CedV , KV Per and MojVimmunity . We propimmunity  are antiHL and BP contributed to the conception and design of the review. HL wrote the first draft of the manuscript. J-YK generated This work was supported by funding from Canadian Food Inspection Agency.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1167085/full#supplementary-materialThe Supplementary material for this article can be found online at: Click here for additional data file.


Prorocentrum shikokuense. Our data show that P. shikokuense was infected dominantly by Mimiviridae and Phycodnaviridae viruses in both blooms. Strikingly, these viruses were transcriptionally very active during the bloom that extended for weeks, suggesting a paralleled development of both the bloom and chronic infection. Furthermore, our data indicate that these viruses maintained a stable infection process by generating polymorphic variants to sustain the exploitation of host intracellular machinery, suggesting co-adaptation between the viruses and the bloom-causative dinoflagellate. This novel insight will be valuable for fully understanding and modeling the role of viruses in regulating blooms of dinoflagellates and other algae.Viruses are generally believed to cause cell mortality and terminate algal blooms. However, how the dinoflagellate-virus interaction shapes the dynamics of host dinoflagellate blooms remains poorly understood. Here, we profile viral composition and metabolic landscape in two blooms of the widely distributed dinoflagellate in situ virus infection in dinoflagellate blooms. Our findings reveal highly similar viral assemblages that infected the bloom species Prorocentrum shikokuense and a co-adapted metabolic relationship between the host and the viruses in the blooms, which varied between the prolonged and the short-lived blooms of the same dinoflagellate species. These findings fill the gap in knowledge regarding the identity and behavior of viruses in a dinoflagellate bloom and shed light on what appears to be the complex mode of infection. The novel insight will be potentially valuable for fully understanding and modeling the role of viruses in regulating blooms of dinoflagellates and other algae.This study represents the first that investigates  Marine phytoplankton not only acts as primary producers in the food chain but also plays an essential role in the global carbon cycle and geochemical processes in the ocean. However, under certain conditions, some species’ explosive proliferation and aggregation or toxin production lead to harmful algal blooms (HABs), which cause devastating impacts on the ecosystem, economy, and human health. HABs can last for weeks and collapse within a few days under specific environmental factors. Viruses, the most abundant living entity in the ocean, are recognized as a crucial factor contributing to algal mortality and the dynamics of HABs –6.Phaeocystis pouchetii can coexist with its virus PpV-01 for 40 days after infection (Chlorella variabilis and its virus PBCV-1 was observed to maintain a 15-day stable interaction following a 30-day arms race battle (Ostreococcus and its infective double-stranded DNA (dsDNA) virus OmV2 were found to grow in parallel (Emiliania huxleyi (EhVs) can adopt a chronic infection strategy at the early stage of infection and transmit horizontally through budding without causing cell lysis, also known as pseudolysogeny or carrier states , and it aimed to characterize the interaction between viral infection and algal bloom progression. We identified the viruses infecting P. shikokuense during the blooms and found the co-evolution of their infection mode with the host bloom. We found that chronic infection was the main mode in the prolonged bloom. Furthermore, our data indicated that in the long-duration bloom, viruses might maintain the stability of functional expression through genetic polymorphism to sustain the utilization of host organelles and ensure stable chronic infection.However, the mode of interaction between viruses and harmful algae and the role of the infecting viruses in regulating the dynamics of harmful algal blooms are still poorly understood and underexplored. In particular, whether the chronic mode of viral infection occurs in dinoflagellates, the most dominant causative species of HABs, and if so, what mechanism drives the long-term virus-host coexistence in bloom outbreaks remains elusive. This study was based on time-sequential metatranscriptomics of two bloom outbreaks by P. shikokuense is the dominant species in BC and ECS, accounting for 76% and 74.2%, respectively  that were 900 km apart . Previouectively , 19. PooThe metatranscriptomes revealed distinct algae-associated viral communities in the blooms at BC and ECS. The total number of virus genes in BC  was more than twice than that in ECS (433 genes). The more abundantly expressed viral genes in BC belong to double-stranded DNA (dsDNA) and single-stranded RNA (ssRNA) viruses, accounting for 49% and 48%, respectively , whereasMimiviridae and Phycodnaviridae in both blooms  than in the ECS bloom , their proportions in the total dsDNA virus-like genes were highly similar (47.6% versus 19.6% in BC compared to 40.3% versus 17.1% in ECS).The remaining dsDNA virus data showed striking similarity between the ECS and BC blooms. The majority of dsDNA type virus-like genes belonged to families Mimiviridae and Phycodnaviridae we detected were associated with P. shikokuense, we compared the bloom-derived gene transcripts with transcripts from laboratory-cultured P. shikokuense . This result suggests that the dominant viral genes expressed in the two blooms were viruses that infected P. shikokuense.For natural bloom communities, the cell (particle)-associated viruses detected theoretically could be viruses infecting non-bloomed algae, protists, and nonliving particles. To determine if these kokuense  using BLmcp (genome assembly and release), which is usually expressed in the late stage of the viral infection, responsible for synthesizing virus capsid and participating in the assembly of new virions  and 4% 23 unigenes) showed elevated [twofold transcript per million (TPM) change] expression or exclusive expression in the ECS and BC bloom relative to the non-bloom (T0) field samples or laboratory culture . These i unigenes virions , 30.Similar to BC, most of the 13 upregulated viral genes in the ECS bloom function in the early stage of virus infection . One of P. shikokuense) responded to, or were influenced by, the infecting viruses. Genes of P. shikokuense and other major lineages of phytoplankton  , indicating that P. shikokuense was the primary host of these viruses in the blooms. Virus-related GO terms were then screened by different upregulated genes in BC and ECS belonging to P. shikokuense . We found 42 common virus-related GO terms (We investigated how host cells (e in BC) , 19 weree in BC) , 40. In GO terms  shared bGO terms .All the host-originated virus-related GO terms were clustered into two major life activity processes: virus life activity and defense against virus, which was confirmed by the GO enrichment map (over 80% of GO terms related to virus life cycle) . MoreoveP. shikokuense during blooms, we adopted Vincent’s method  abundance of psbA in each sample. psbA is a chloroplast gene that encodes D1 protein, which is constantly transcribed in algal cells due to its rapid turnover (mcp (coding for major capsid protein), which is usually expressed at the late stage of the viral infection cycle  in bloom samples. Only 6 virus-related functions (each with no more than 10 genes) were found in the other top 4 algal lineages , while there are as many as 81 functions related to responses to viruses in P. shikokuense, including the above 6 functions. In addition, we checked whether there were any Asfaviridae virus genes represented in our metatranscriptomes, because the dsDNA virus that is known to infect another dinoflagellate, Heterocapsa circularisquama, and its DNA polymerase B gene showed high similarity to African swine fever virus . These results in concert suggest that the bloom-associated viruses are likely specific to P. shikokuense. The detection of the ssRNA viruses in the close-shore BC bloom, their absence in the more offshore ECS bloom and cultured P. shikokuense, and their resemblance to mammalian viruses indicate that the potential of terrestrially sourced viruses may be transiently active and can mislead data interpretation in field work. Our finding underscores the importance to take note of the potential contamination and avoid data misinterpretation in future research.Our bloom metatranscriptomes showed that dsDNA viruses from the families  viruses –45, angellates , 46–49gellates , the taxer virus . We onlyer virus . We alsoHeterocapsa circularisquama showed that resistance against viruses happened at the stage of virus nucleic acid transcription and/or replication  cells. The GO terms associated with virus life activities functionally covered almost all stages of the infection cycle, from attachment to release, but mostly the early stage of viral infection. From studies on various groups of algae, resistance to infection can arise at any of these stages . A studylication . The col surface . Anothere to EhV , 54.P. shikokuense cells in the one-day bloom at BC. This resembled E. huxleyi, in which only after 4 hours of EhV infection, infected E. huxleyi cells released virions  were stable throughout the ECS bloom, and these two GO terms belong to virus release function. Virus release via budding is a hallmark of chronic infections in which ESCRT plays an active role , and both showed a negative correlation between the expression of organelle-related GO terms and SNP density. While the functional connection remains to be investigated in the future, this finding implies that regulating polymorphic variants might be a genetic mechanism by which the viruses modulate organelle exploitation during infection. Previous reports indicate that viruses can manipulate and rewire host metabolic pathways to facilitate infection . The virP. shikokuense sustainably and ensure the smooth progress of chronic infection warrants further investigation and critical examination. Overall, the findings and novel insight from this study will serve as the baseline for future research to fully understand and accurately model the role of viruses in regulating blooms of dinoflagellates and other algae.Host-virus interactions at microscale eventually shape ecosystem processes at geographical scales . ResolviP. shikokuense blooms in 2014 at two locations that were 900 km apart  Bloom community at night, morning, and midday; SRR9878963, SRR9878964, SRR9878965, and SRR9878966 for ECS Bloom T0 to T3, respectively. A set of transcriptomic data from P. shikokuense cultures CCMA-206 (phosphate-replete and P-depleted condition) (SRR5249183 and SRR5249152 for P-depleted and P-replete (Table S4).Metatranscriptomic data were obtained using RNA-seq. Plankton samples were collected by filtering 4–13 L surface water (0–2 m) onto 3 µm polycarbonate membranes during two km apart . The usekm apart . The othkm apart . Triplicndition)  was alsode novo into contigs using MEGAHIT  (P. shikokuense transcriptomes)  . To retrlen 200) . Contigslen 200) . Coding len 200) . The funiptomes)  using Diiptomes) . eggNOG iptomes) , 68 was iptomes) . Redundaiptomes) , with a P. shikokuense, we investigated whether such viruses have been reported to infect this species or a dinoflagellate. Furthermore, the similar expression pattern of the viral genes between the two P. shikokuense blooms and correlation between viral gene expression pattern and the evolution of the blooms were sought and used as another supporting evidence for the functional linkage between viruses and P. shikokuense.Genes with the best BLAST match to viral genes in GenBank with e-values <1e-5 were collected and named virus-like genes in this study. To associate viruses expressing these genes with the bloom dinoflagellate P. shikokuense cells, expression levels of virus-like (in viruses) and virus infection-related genes (in P. shikokuense) were measured in the BC and ECS blooms and that from P. shikokuense cultures (P-replete and P-depleted conditions) were used as the control group. Sequence reads were aligned back to predicted CDSs using bowtie2 (version 2.4.2)  , and expn 2.4.2) . Differen 2.4.2)  values opsbA and mcp as proxies of host photosynthesis and virus replication following previous reports  is usually expressed at the late stage of the viral infection cycle. psbA sequences from functional annotation result were further checked with Photo_RC (PF00124) by hmmscan , and only proteins that matched Prorocentrum in taxonomy were retained; mcp domain file (mcp.hmm) was obtained from a previously reported work   . Varianton 1.12) . After fon 1.12) . Data weon 1.12) .