ICTV Virus Taxonomy Profile: Kolmioviridae 2024

Kolmioviridae is a family for negative-sense RNA viruses with circular, viroid-like genomes of about 1.5-1.7 kb that are maintained in mammals, amphibians, birds, fish, insects and reptiles. Deltaviruses, for instance, can cause severe hepatitis in humans. Kolmiovirids encode delta antigen (DAg) and replicate using host-cell DNA-directed RNA polymerase II and ribozymes encoded in their genome and antigenome. They require evolutionary unrelated helper viruses to provide envelopes and incorporate helper virus proteins for infectious particle formation. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Kolmioviridae, which is available at ictv.global/report/kolmioviridae.

Reverse genetics of parrot bornavirus 4 reveals a unique splicing of the glycoprotein gene that affects viral propagation

Viruses can utilize host splicing machinery to enable the expression of multiple genes from a limited-sized genome. Orthobornaviruses use alternative splicing to regulate the expression level of viral proteins and achieve efficient viral replication in the nucleus. Although more than 20 orthobornaviruses have been identified belonging to eight different viral species, virus-specific splicing has not been demonstrated. Here, we demonstrate that the glycoprotein (G) transcript of parrot bornavirus 4 (PaBV-4; species Orthobornavirus alphapsittaciforme), a highly virulent virus in psittacines, undergoes mRNA splicing and expresses a soluble isoform termed sGP. Interestingly, the splicing donor for sGP is not conserved in other orthobornaviruses, including those belonging to the same orthobornavirus species, suggesting that this splicing has evolved as a PaBV-4-specific event. We have also shown that exogenous expression of sGP does not affect PaBV-4 replication or de novo virion infectivity. In this study, to investigate the role of sGP in viral replication, we established a reverse genetics system for PaBV-4 by using avian cell lines and generated a recombinant virus lacking the spliced mRNA for sGP. Using the recombinant viruses, we show that the replication of the sGP-deficient virus is significantly slower than that of the wild-type virus and that the exogenous expression of sGP cannot restore its propagation efficiency. These results suggest that autologous or controlled expression of sGP by splicing may be important for PaBV-4 propagation. The reverse genetics system for avian bornaviruses developed here will be a powerful tool for understanding the replication strategies and pathogenesis of avian orthobornaviruses. IMPORTANCE Parrot bornavirus 4 (PaBV-4) is the dominant cause of proventricular dilatation disease, a severe gastrointestinal and central nervous system disease among avian bornaviruses. In this study, we discovered that PaBV-4 expresses a soluble isoform of glycoprotein (G), called sGP, through alternative splicing of the G mRNA, which is unique to this virus. To understand the role of sGP in viral replication, we generated recombinant PaBV-4 lacking the newly identified splicing donor site for sGP using a reverse genetics system and found that its propagation was significantly slower than that of the wild-type virus, suggesting that sGP plays an essential role in PaBV-4 infection. Our results provide important insights not only into the replication strategy but also into the pathogenesis of PaBV-4, which is the most prevalent bornavirus in captive psittacines worldwide.

Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)

In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

The hidden diversity of ancient bornaviral sequences from X and P genes in vertebrate genomes

Endogenous bornavirus-like elements (EBLs) are heritable sequences derived from bornaviruses in vertebrate genomes that originate from transcripts of ancient bornaviruses. EBLs have been detected using sequence similarity searches such as tBLASTn, whose technical limitations may hinder the detection of EBLs derived from small and/or rapidly evolving viral X and P genes. Indeed, no EBLs derived from the X and P genes of orthobornaviruses have been detected to date in vertebrate genomes. Here, we aimed to develop a novel strategy to detect such 'hidden' EBLs. To this aim, we focused on the 1.9-kb read-through transcript of orthobornaviruses, which encodes a well-conserved N gene and small and rapidly evolving X and P genes. We show a series of evidence supporting the existence of EBLs derived from orthobornaviral X and P genes (EBLX/Ps) in mammalian genomes. Furthermore, we found that an EBLX/P is expressed as a fusion transcript with the cellular gene, ZNF451, which potentially encodes the ZNF451/EBLP fusion protein in miniopterid bat cells. This study contributes to a deeper understanding of ancient bornaviruses and co-evolution between bornaviruses and their hosts. Furthermore, our data suggest that endogenous viral elements are more abundant than those previously appreciated using BLAST searches alone, and further studies are required to understand ancient viruses more accurately.

Nyamanini Virus Nucleoprotein and Phosphoprotein Organize Viral Inclusion Bodies That Associate with Host Biomolecular Condensates in the Nucleus

Many mononegaviruses form inclusion bodies (IBs) in infected cells. However, little is known about nuclear IBs formed by mononegaviruses, since only a few lineages of animal-derived mononegaviruses replicate in the nucleus. In this study, we characterized the IBs formed by Nyamanini virus (NYMV), a unique tick-borne mononegavirus undergoing replication in the nucleus. We discovered that NYMV forms IBs, consisting of condensates and puncta of various sizes and morphologies, in the host nucleus. Likewise, we found that the expressions of NYMV nucleoprotein (N) and phosphoprotein (P) alone induce the formation of condensates and puncta in the nucleus, respectively, even though their morphologies are somewhat different from the IBs observed in the actual NYMV-infected cells. In addition, IB-like structures can be reconstructed by co-expressions of NYMV N and P, and localization analyses using a series of truncated mutants of P revealed that the C-terminal 27 amino acid residues of P are important for recruiting P to the condensates formed by N. Furthermore, we found that nuclear speckles, cellular biomolecular condensates, are reorganized and recruited to the IB-like structures formed by the co-expressions of N and P, as well as IBs formed in NYMV-infected cells. These features are unique among mononegaviruses, and our study has contributed to elucidating the replication mechanisms of nuclear-replicating mononegaviruses and the virus-host interactions.

Characterization of Megabat-Favored, CA-Dependent Susceptibility to Retrovirus Infection

The isolation of the Koala retrovirus-like virus from Australian megabats and the identification of endogenous retroviruses in the bat genome have raised questions on bat susceptibility to retroviruses in general. To answer this, we studied the susceptibility of 12 cell lines from 11 bat species to four well-studied retroviruses (human and simian immunodeficiency viruses [HIV and SIV] and murine leukemia viruses [B- and N-MLV]). Systematic comparison of retroviral susceptibility among bats revealed that megabat cell lines were overall less susceptible to the four retroviruses than microbat cell lines, particularly to HIV-1 infection, whereas lineage-specific differences were observed for MLV susceptibility. Quantitative PCR of reverse transcription (RT) products, infection in heterokaryon cells, and point mutation analysis of the capsid (CA) revealed that (i) HIV-1 and MLV replication were blocked at the nuclear transport of the pre-integration complexes and before and/or during RT, respectively, and (ii) the observed lineage-specific restriction can be attributed to a dominant cellular factor constrained by specific positions in CA. Investigation of bat homologs of the three previously reported post-entry restriction factors constrained by the same residues in CA, tripartite motif-protein 5α (TRIM5α), myxovirus resistance 2/B (Mx2/MxB), and carboxy terminus-truncated cleavage and polyadenylation factor 6 (CPSF6-358), demonstrated poor anti-HIV-1 activity in megabat cells, whereas megabat TRIM5α restricted MLV infection, suggesting that the major known CA-dependent restriction factors were not dominant in the observed lineage-specific susceptibility to HIV-1 in bat cells. Therefore, HIV-1 susceptibility of megabat cells may be determined in a manner distinct from that of primate cells. IMPORTANCE Recent studies have demonstrated the circulation of gammaretroviruses among megabats in Australia and the bats' resistance to HIV-1 infection; however, the origins of these viruses in megabats and the contribution of bats to retrovirus spread to other mammalian species remains unclear. To determine the intrinsic susceptibility of bat cells to HIV-1 infection, we investigated 12 cell lines isolated from 11 bat species. We report that lineage-specific retrovirus restriction in the bat cell lines can be attributed to CA-dependent factors. However, in the megabat cell lines examined, factors known to bind capsid and block infection in primate cell culture, including homologs of TRIM5α, Mx2/MxB, and CPSF6, failed to exhibit significant anti-HIV-1 activities. These results suggested that the HIV-1 susceptibility of megabat cells occurs in a manner distinct from that of primate cells, where cellular factors, other than major known CA-dependent restriction factors, with lineage-specific functions could recognize retroviral proteins in megabats.

Large-scale investigation of zoonotic viruses in the era of high-throughput sequencing

Zoonotic diseases considerably impact public health and socioeconomics. RNA viruses reportedly caused approximately 94% of zoonotic diseases documented from 1990 to 2010, emphasizing the importance of investigating RNA viruses in animals. Furthermore, it has been estimated that hundreds of thousands of animal viruses capable of infecting humans are yet to be discovered, warning against the inadequacy of our understanding of viral diversity. High-throughput sequencing (HTS) has enabled the identification of viral infections with relatively little bias. Viral searches using both symptomatic and asymptomatic animal samples by HTS have revealed hidden viral infections. This review introduces the history of viral searches using HTS, current analytical limitations, and future potentials. We primarily summarize recent research on large-scale investigations on viral infections reusing HTS data from public databases. Furthermore, considering the accumulation of uncultivated viruses, we discuss current studies and challenges for connecting viral sequences to their phenotypes using various approaches: performing data analysis, developing predictive modeling, or implementing high-throughput platforms of virological experiments. We believe that this article provides a future direction in large-scale investigations of potential zoonotic viruses using the HTS technology.

2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Calmodulinopathy is a common cause of critical cardiac phenotypes in fetus and infancy

Background

Cardiac calmodulinopathy is a life-threatening arrhythmia syndrome which presents several phenotypes of inherited primary arrhythmia syndrome (IPAS), and caused by mutations in calmodulin-encoded genes (CALM1–3). We aimed clarify the frequency and their clinical characteristics of calmodulinopathy in our IPAS cohort.

Methods

By using next generation sequencing, we screened arrhythmia related genes including calmodulin-encoding genes in 322 unrelated symptomatic children (0–12 years) who were suspected as IPAS; they included 40 cases with lethal arrhythmic attacks (LAE) under 6-year-old. After gene screening, we investigated their physiological and clinical characteristics about mutation carriers.

Results

Among 322 children, we identified 6 mutations of calmodulin-encoded genes in 9 probands (2.8%); one CALM1 in 2 probands (N98S), and 5 CALM2 in 7 probands (E46K, D96V, D96G, N98S, E141K). Their clinical diagnoses were long QT syndrome (LQTS, n=4), catecholaminergic polymorphic ventricular tachycardia (CPVT, n=3) and both (n=2). Their age of diagnosis ranges at 0–9 with the median of 5 years. There were three major clinical phenotypes; 1) CALM2-D96V, and E141K: two infants with advanced atrio-ventricular block, significant QTc prolongation, severe heart failure from their fetal period – both of them deceased within 1.5-year-old. Their clinical phenotypes resembled classical Timothy syndrome caused by CACNA1C mutations. 2) CALM1-N98S (n=2), CALM2-N98S (n=2), and CALM2-D96G: four preschoolers with LAEs and one syncope: all of them were 3–5 years old. In addition, a T wave morphology of CALM2-D96G carrier was very similar to LQT1. 3) CALM2-E46K (n=2): two were first diagnosed with neurological and developmental disorders, and showed phenotype of CPVT: their cardiac phenotypes were milder compared with that of 1) or 2). Overall, these phenotypes seemed to be mutation specific (indicated in figure). Their cardiac features were severer, and the onset of LAEs was earlier compared with other genotypes of LQTS/CPVT. As the treatment, β-blocker was effective for control of LAEs.

Conclusion

Cardiac calmodulinopathy presented serious and potentially lethal phenotypes in fetus or infancy. To prevent cardiac death in them, we must correctly diagnose and start the treatment as earlier as possible.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): MEXT KAKENHI from the Ministry of Education, Culture, Sports, Science, and Technology of Japan

Different prognosis of ARVC patients between DSG2 and PKP2 variant carriers

Background

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiomyopathy mainly caused by desmosomal gene variants. In Europe and North America, pathogenic variants in PKP2 were identified in most of the ARVC patients. On the other hand, we have reported that the genetic backgrounds of ARVC in Japanese were different from those in European; pathogenic variants in DSG2 were predominant in Japanese. Genotype-phenotype correlations, however, have not been clarified yet.

Purpose

In this study, we aimed to examine whether the genotype affect the phenotype and outcome in Japanese ARVC patients.

Methods and results

This study included 167 Japanese ARVC patients who received genetic testing (128 males [77%]). Their median age at diagnosis was 44 [24–55] years old and median follow-up duration was 10 [4–21] years. We found 90 patients with pathogenic variants: 52 in DSG2 (31%), 30 in PKP2 (18%), 3 in DSP (1.8%), 1 in DSC (0.6%), 1 in JUP (0.6%) and 3 in DES (1.8%). The age of the first sustained ventricular arrhythmia (SVT) were older in the patients with DSG2 than those with PKP2 variants (48±15 years vs. 35±15 years, P=0.008) but younger in DSG2 variant carriers at the first hospitalization for heart failure (41 [22–61] years vs. 67 [61–74] years, P=0.03). The left ventricular ejection fractions of DSG2 variant carriers were significantly lower at diagnosis than that of PKP2 (52 [41–60] % vs. 61 [56–66] %, P=0.002). Kaplan-Meier survival curve for lethal arrhythmic events including SVT, ventricular fibrillation and sudden death revealed that the event rate of DSG2 variant carriers was significantly lower than that of PKP2 (log-rank test, P=0.02) (Fig. 1).

Among 11 patients who had both SVT and hospitalizations for HF, 7 PKP2 variant carriers had SVT first, then, hospitalized for HF (48 [35–53] years and 67 [55–71] years, P=0.02). Contrary, the clinical course of 4 DSG2 variants carriers were different from those with PKP2 (54 [40–68] years for SVT and 65 [56–70, P=0.1] years for HF) (Fig. 2).

Conclusion

The patients with DSG2, which is the major causative gene for ARVC in Japanese, show different phenotype and outcome from those with PKP2. We should examine the effect of variants on the prognosis of ARVC patients in more large population including various ethnics.

Funding Acknowledgement

Type of funding sources: None.

Squalomix: shark and ray genome analysis consortium and its data sharing platform

The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages of vertebrates with a tantalizing collection of species occupying critical aquatic habitats. To overcome the current limitation in molecular resources, we launched the Squalomix Consortium in 2020 to promote a genome-wide array of molecular approaches, specifically targeting shark and ray species. Among the various bottlenecks in working with elasmobranchs are their elusiveness and low fecundity as well as the large and highly repetitive genomes. Their peculiar body fluid composition has also hindered the establishment of methods to perform routine cell culturing required for their karyotyping. In the Squalomix consortium, these obstacles are expected to be solved through a combination of in-house cytological techniques including karyotyping of cultured cells, chromatin preparation for Hi-C data acquisition, and high fidelity long-read sequencing. The resources and products obtained in this consortium, including genome and transcriptome sequences, a genome browser powered by JBrowse2 to visualize sequence alignments, and comprehensive matrices of gene expression profiles for selected species are accessible through https://github.com/Squalomix/info.

Borna disease virus phosphoprotein triggers the organization of viral inclusion bodies by liquid-liquid phase separation

Inclusion bodies (IBs) are characteristic biomolecular condensates organized by the non-segmented negative-strand RNA viruses belonging to the order Mononegavirales. Although recent studies have revealed the characteristics of IBs formed by cytoplasmic mononegaviruses, that of Borna disease virus 1 (BoDV-1), a unique mononegavirus that forms IBs in the cell nucleus and establishes persistent infection remains elusive. Here, we characterize the IBs of BoDV-1 in terms of liquid-liquid phase separation (LLPS). The BoDV-1 phosphoprotein (P) alone induces LLPS and the nucleoprotein (N) is incorporated into the P droplets in vitro. In contrast, co-expression of N and P is required for the formation of IB-like structure in cells. Furthermore, while BoDV-1 P binds to RNA, an excess amount of RNA dissolves the liquid droplets formed by N and P in vitro. Notably, the intrinsically disordered N-terminal region of BoDV-1 P is essential to drive LLPS and to bind to RNA, suggesting that both abilities could compete with one another. These features are unique among mononegaviruses, and thus this study will contribute to a deeper understanding of LLPS-driven organization and RNA-mediated regulation of biomolecular condensates.

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

A comprehensive profiling of innate immune responses in Eptesicus bat cells

Bats (the order Chiroptera), including those of the genus Eptesicus, have been reported to serve as reservoirs of several zoonotic viruses. Notably, bats have been reported to lack obvious symptoms of infection with such viruses and are thought to have unique immune system responses. However, the responses of their innate immune system, the first line of immunity, remain largely unclear. Here, we comprehensively analyzed the expression profiles in two Eptesicus bat cell lines to investigate their innate immune responses. The gene expression profiles after polyinosinic-polycytidylic acid (poly (I:C)) induction were similar between the two bat cell lines, but uniquely upregulated differentially expressed genes were also identified. We also revealed that the upregulated genes of Eptesicus bat cells were distinct from those of human epithelial cells in response to induction. Moreover, the basal expression levels of several immune-related genes were higher in bat cells than in human cells. We also identified unannotated novel transcripts that were upregulated after induction and novel microRNAs expressed in bat cells, some of which were upregulated by poly (I:C) treatment. This is the first report to illustrate the innate immune response in Eptesicus bat cells; therefore, this study provides basic and novel insights into bat innate immunity. Our data represent a valuable resource for future studies into bat immunity and the biology of Eptesicus bats. This article is protected by copyright. All rights reserved.

Early onset of heart failure in Japanese ARVC patients with pathogenic desmosomal gene variants

Background

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiomyopathy mainly caused by desmosomal gene variants. Although there are a lot of reports regarding to European ARVC patients, the ones in Asian are a few, and the characteristics of Asian ARVC have been still unclear. We have reported that the genetic backgrounds in Japanese ARVC patients were different from those in European ones. In this study, we aimed to examine the phenotype and outcome of Japanese ARVC patients with specific genetic backgrounds.

Methods and results

This study included 104 Japanese ARVC patients who were diagnosed as definite in the 2010 Task Force Criteria for ARVC and received genetic analysis (79 males [76%]; median age at diagnosis, 40 years [IQR 22–53 years].) Fifty-seven patients carried variants in desmosomal genes classified as pathogenic based on ACMG guideline: 30 in DSG2 (29%), 22 in PKP2 (21%), 2 in DSC2 (2%) and 3 in DSP (3%). The median age of diagnosis was significantly younger in the patients with the pathogenic variants than in those without (37 years [IQR 21–49 years] vs. 46 years [IQR 34–58 years], P=0.01). During a median follow-up of 9.3 years (IQR 3.5–20.9 years), 10 patients died and 2 were received heart transplantation. Sixty-two suffered lethal arrhythmic events including cardiopulmonary arrest, ventricular fibrillation, sustained ventricular tachycardia and appropriate shocks by implantable cardioverter defibrillator. Twenty-two were hospitalized for heart failure. There was no difference in these events rate between the two groups. However, survival analysis revealed that patients with pathogenic variants hospitalized for heart failure significantly earlier in their life than those without (P=0.04, log-rank test, Figure 1).

Conclusions

The Japanese ARVC patients with pathogenic variants in desmosomal genes are diagnosed and hospitalize for heart failure at younger age than those without. These findings have not been reported in other ethnics. Our study warns that we should be cautious for not only the prevention of lethal arrhythmic events but also the progress of the heart failure in Japanese ARVC patients with pathogenic variants.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Japan Agency for Medical Research and Development Figure 1

Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases

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

BUD23-TRMT112 interacts with the L protein of Borna disease virus and mediates the chromosomal tethering of viral ribonucleoproteins

Persistent intranuclear infection is an uncommon infection strategy among RNA viruses. However, Borna disease virus 1 (BoDV-1), a nonsegmented, negative-strand RNA virus, maintains viral infection in the cell nucleus by forming structured aggregates of viral ribonucleoproteins (vRNPs), and by tethering these vRNPs onto the host chromosomes. To better understand the nuclear infection strategy of BoDV-1, we determined the host protein interactors of the BoDV-1 large (L) protein. By proximity-dependent biotinylation, we identified several nuclear host proteins interacting with BoDV-1 L, one of which is TRMT112, a partner of several RNA methyltransferases (MTase). TRMT112 binds with BoDV-1 L at the RNA-dependent RNA polymerase domain, together with BUD23, an 18S rRNA MTase and 40S ribosomal maturation factor. We then discovered that BUD23-TRMT112 mediates the chromosomal tethering of BoDV-1 vRNPs, and that the MTase activity is necessary in the tethering process. These findings provide us a better understanding on how nuclear host proteins assist the chromosomal tethering of BoDV-1, as well as new prospects of host-viral interactions for intranuclear infection strategy of orthobornaviruses. This article is protected by copyright. All rights reserved.

Identification of a novel filovirus in a common lancehead (Bothrops atrox (Linnaeus, 1758))

I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae). I identified a coding-complete sequence of a filovirus from the common lancehead (Bothrops atrox (Linnaeus, 1758)), tentatively named Tapajós virus (TAPV). Although the genome organization of TAPV is similar to mammalian filoviruses, our phylogenetic analysis showed that TAPV forms a cluster with a fish filovirus. However, TAPV is still distantly related to all the known filoviruses, suggesting that TAPV can be assigned as a species of a novel genus in Filoviridae. To our knowledge, this is the first report identifying a filovirus in reptiles, and thus contributes to a deeper understanding of the diversity and evolution of filoviruses.

RNA Viral Metagenome Analysis of Subnanogram dsRNA Using Fragmented and Primer Ligated dsRNA Sequencing (FLDS)

Fragmented and primer ligated dsRNA sequencing (FLDS) is a sequencing method applicable to long double-stranded RNA (dsRNA) that enables the complete genome sequencing of both double- and single-stranded RNA viruses. However, the application of this method on a low amount of dsRNA has been hindered by adaptor dimer formation during cDNA amplification and sequence library preparation. We herein developed FLDS ver. 3 by optimizing the terminal modification of an oligonucleotide adaptor and the conditions of adaptor ligation. We also examined the concentration of Mg²⁺ in the PCR reaction for cDNA amplification and the purification method of amplified cDNA. Fine sequence reads were successfully obtained from metagenomic shotgun sequencing libraries constructed from 10 and 100 pg dsRNA, and these libraries exhibited weaker detection sensitivity for low-abundance dsRNAs (viral genomes and genome segments) than that constructed from 1‍ ‍ng of dsRNA. We also report the utility of capillary electrophoresis for dsRNA quantification. The FLDS ver. 3 package expands the frontiers of our knowledge in RNA virus diversity and evolution.

Identification of novel avian and mammalian deltaviruses provides new insights into deltavirus evolution

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

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Evolutionary Selection of the Nuclear Localization Signal in the Viral Nucleoprotein Leads to Host Adaptation of the Genus Orthobornavirus

Adaptation of the viral life cycle to host cells is necessary for efficient viral infection and replication. This evolutionary process has contributed to the mechanism for determining the host range of viruses. Orthobornaviruses, members of the family Bornaviridae, are non-segmented, negative-strand RNA viruses, and several genotypes have been isolated from different vertebrate species. Previous studies revealed that some genotypes isolated from avian species can replicate in mammalian cell lines, suggesting the zoonotic potential of avian orthobornaviruses. However, the mechanism by which the host specificity of orthobornaviruses is determined has not yet been identified. In this study, we found that the infectivity of orthobornaviruses is not determined at the viral entry step, mediated by the viral glycoprotein and matrix protein. Furthermore, we demonstrated that the nuclear localization signal (NLS) sequence in the viral nucleoprotein (N) has evolved under natural selection and determines the host-specific viral polymerase activity. A chimeric mammalian orthobornavirus, which has the NLS sequence of avian orthobornavirus N, exhibited a reduced propagation efficiency in mammalian cells. Our findings indicated that nuclear transport of the viral N is a determinant of the host range of orthobornaviruses, providing insights into the evolution and host adaptation of orthobornaviruses.

Identification of a reptile lyssavirus in Anolis allogus provided novel insights into lyssavirus evolution

Lyssaviruses (genus Lyssavirus) are negative-strand RNA viruses belonging to the family Rhabdoviridae. Although a lyssa-like virus (frog lyssa-like virus 1 [FLLV-1]), which is distantly related to lyssaviruses, was recently identified in frogs, a large phylogenetic gap exists between those viruses, and thus the evolution of lyssaviruses is unclear. In this study, we detected a lyssa-like virus from publicly available RNA-seq data obtained using the brain and skin of Anolis allogus (Spanish flag anole), which was designated anole lyssa-like virus 1 (ALLV-1), and determined its complete coding sequence. Via mapping analysis, we demonstrated that ALLV-1 was actively replicating in the original brain and skin samples. Phylogenetic analyses revealed that ALLV-1 is more closely related to lyssaviruses than FLLV-1. Overall, the topology of the tree is compatible with that of hosts, suggesting the long-term co-divergence of lyssa-like and lyssaviruses and vertebrates. The ψ region, which is a long 3' untranslated region of unknown origin present in the G mRNA of lyssaviruses (approximately 400-700 nucleotides), is also present in the genome of ALLV-1, but it is much shorter (approximately 180 nucleotides) than those of lyssaviruses. Interestingly, FLLV-1 lacks the ψ region, suggesting that the ψ region was acquired after the divergence of the FLLV-1 and ALLV-1/lyssavirus lineages. To the best of our knowledge, this is the first report to identify a lyssa-like virus in reptiles, and thus, our findings provide novel insights into the evolution of lyssaviruses.

Preclinical proof-of-concept study: antisense-mediated knockdown of CALM as a therapeutic strategy for calmodulinopathy

Background

Calmodulin (CaM) is a ubiquitous Ca2+ sensor molecule encoded by three distinct calmodulin genes, CALM1–3, and has an important role for cardiac ion channel function. Recently, heterozygous missense mutations in CALM genes were reported to cause a new category of life-threatening genetic arrhythmias such as long-QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT), which is called as “calmodulinopathy”. The patients with calmodulinopathy show poor prognosis and there is no effective treatment for them.

Purpose

Considering the dominant-negative effect of mutant calmodulin proteins produced by heterozygous missense mutations in CALMs, we aimed to prove the concept of antisense-based therapy to treat calmodulinopathy using human iPS cell-derived cardiomyocyte (hiPSC-CM) model.

Methods

We designed multiple locked nucleic acid (LNA) gapmer-antisense oligonucleotides (ASOs) targeting CALM2 and analyzed the silencing efficiency and toxicity in cultured cells to select the most potent ASO. Using CMs differentiated from hiPSCs which were generated form a 12-year-old boy with LQTS carrying a heterozygous CALM2-N98S mutation, CALM2 expression and action potentials (APs) were analyzed to evaluate the efficacy of ASOs.

Results

We identified several ASOs which reduced CALM2 expression without affecting cell viability in human cultured cells (HepG2) (ASO 50 nM, n=2; Figure 1A). Considering further experiments in vivo mouse model, we investigated the CALM2 silencing activity in mouse cultured cells (3T3-L1) without transfection (free-uptake) (ASO 1 μM, n=2; †ASOs have homologous sequence between human and mouse; Figure B). After free-uptake CALM2 silencing analysis in 3T3-L1 cells, we identified that ASO #2 has the most potent CALM2 silencing activity and low cytotoxicity (Figure 1B). ASO #2 effectively reduced CALM2 expression even in hiPSC-CMs (ASO(−): n=3, lipofection: n=4, free-uptake: n=3; P<0.05; Figure 1C). In action potential recordings, we demonstrated that ASO #2 ameliorated prolonged AP durations (APD90) in N98S-hiPSC-CMs at 0.5 Hz pacing (ASO(−): 666±123 ms (n=7), lipofection: 329±21 ms (n=8), free-uptake: 388±34 ms (n=12); P<0.05; Figure 1D).

Conclusion

Our results using patient-derived hiPSC-CM model suggest that ASO-based therapy might be a promising strategy for the treatment of calmodulinopathy.

Figure 1

Funding Acknowledgement

Type of funding source: Private company. Main funding source(s): Nissan Chemical Corporation

Atenolol is not effective in reducing ventricular arrhythmia severity on exercise stress test in patients with catecholaminergic polymorphic ventricular tachycardia

 

Patients with catecholaminergic polymorphic ventricular tachycardia (CPVT) are at risk for malignant ventricular arrhythmias during exercise and emotions which may lead to sudden cardiac death. Beta-blockers (BB) are the mainstay of therapy in patients with CPVT, but studies comparing the efficacy of different types of BB are scarce. Our objective was to determine the efficacy of different types of BB in reducing the ventricular arrhythmia (VA) severity on exercise stress test (EST) in patients with CPVT.

Data was derived from the International CPVT Registry, a large retrospective cohort study. We included patients who had an EST before (pre-EST) and after start of BB (post-EST). We divided the cohort into five groups based on the first prescribed BB and compared pre-EST and post-EST.

We included 428 patients (median age 18.5 [11.7–39.6] years, 240 (56.%) female), 155 (36.2%) probands) of whom 38 (8.9%) used atenolol, 131 (30.6%) bisoprolol, 82 (19.2%) metoprolol, 124 (29.0%) nadolol and 53 (12.4%) propranolol. Sex and history of aborted cardiac arrest were similar in all groups. The age at start of BB differed (p<0,001): patients using bisoprolol were oldest (35.0 [15.7–35.3]) while patients using propranolol were youngest (12.3 [8.8–24.9]). Median daily BB dose in mg/kg was: 1.0 [0.8–2.3] for atenolol, 0.06 [0.05–0.10] for bisoprolol, 0.9 [0.6–1.5] for metoprolol, 1.1 [0.9–1.6] for nadolol and 1.5 [1.1–2.8] for propranolol. Resting heart rate on pre-EST and post-EST was similar in all groups. Patients using metoprolol had a significantly higher maximum heart rate post-EST compared to nadolol and propranolol (161±18 vs 136±19 and 130±22 bpm, p=0,002 and p=0,001, respectively). The VA severity decreased significantly after BB (147 (37.9%) (non-sustained) ventricular tachycardia ((NS)VT) and 120 (30.9%) no or isolated ventricular premature beat (iVPB) pre-EST vs 46 (11.4%) (NS)VT and 184 (45.7%) iVPB post-EST, p<0,001). Examining the different groups, the VA severity decreased significantly after BB in all but atenolol (13 (40.6%) (NS)VT and 8 (25.0%) iVPB pre-EST vs 9 (25.0%) (NS)VT and 15 (41.7%) iVPB post-EST, p=0,103).

Based on these results we conclude that all beta-blockers except atenolol are effective in reducing the VA severity on EST in patients with CPVT.

Funding Acknowledgement

Type of funding source: Public grant(s) – EU funding. Main funding source(s): E-Rare Joint Transnational Call for Proposals 2015 “Improving Diagnosis and Treatment of Catecholaminergic Polymorphic Ventricular Tachycardia: Integrating Clinical and Basic Science”

Clinical aspects of pediatric Brugada syndrome

Introduction

Brugada syndrome (BrS) is an inherited arrhythmia characterized by a coved-type ST elevation and sudden death, especially in middle-aged males and more common in Asia. Mutations in SCN5A are detected in 15–20% and reported to be associated with poor prognosis. Among children, BrS is rare and the risk factors in pediatric BrS are unknown, especially in Asian population.

Purpose

The purpose of this study is to elucidate the risk factors for fatal arrhythmic events in Japanese pediatric patients with BrS.

Methods

We enrolled 52 Japanese children with BrS younger than 20 years, and performed genetic analysis and collected the clinical information.

Results

The mean age of initial symptoms was 10.7±5.5 years, and the mean follow-up period was 3.9±5.5 years. Ninety percent of patients were probands. No subjective symptom was confirmed in 28 of the patients, but aborted cardiac arrest (ACA) in 4, ventricular tachycardia in 4, ventricular fibrillation in 1, and syncope in 11. We identified mutations in SCN5A in 63%. There was no significant gender difference in ≤10 years, but a significant male predominance appeared in >10 years. And no gender difference was confirmed in the incidence of severe cardiac events in ≤10 years.

Conclusion

No gender difference was confirmed in ≤10 years in this study about Asian children. And being girls did not reduce the risk in ≤10 years. The frequency of SCN5A mutations was higher than adults, but decreased from childhood (68%) to adolescence (59%). In BrS, genetical and environmental factors may be more effective in childhood and adulthood, respectively.

Funding Acknowledgement

Type of funding source: None

Long-read sequence confirmed a large deletion of MYH6 and MYH7 in a family with atrial septal defect

Background

Genome structural variants (SVs) have larger effect on human genome functions than single nucleotide variants (SNVs). Although short-read sequencing (SRS) is current major next generation sequencing method and has given us a great benefit to elucidate the genetic background of inherited diseases, it does not detect SVs accurately. Long-read sequencing (LRS) produces tens to thousands of kilobases reads and detects the breakpoints of complex SVs. This study aimed to confirm a large deletion, which was suspected by SRS, using LRS by Oxford Nanopore technology (ONT).

Methods

Genomic libraries for SRS was prepared with HaloPlex. Targeted SRS was performed for 58 genes with MiSeq. Genomic libraries for LRS were prepared using the Ligation sequencing 1D kit SQK-LSK109 (ONT). Whole genome LRS was performed with GridION X5 and R9.4 flow cells (ONT).

Results

The patient was a five-month-old boy with atrial septal defect (ASD) and atrial tachycardia. Though SRS failed to identify any causative SNVs, the results with SureCall software (Agilent) suspected a deletion between exon 3 to exon 26 in MYH6 encoding α heavy chains of cardiac myosin. The variants in MYH6 are known to be associated with ASD. Because a deletion between MYH6 exon 26 and MYH7 exon 27 was reported as esv2748480 on the Database of Genomic Variants, we performed long-range PCR from MYH6 intron26 to MYH7 exon26 and found an abnormal 1.5K bases PCR product only in the case. Due to high homology of MYH6 and MYH7, Sanger sequencing failed to detect the break point.

In LRS, 3 flow cells generated 3.8M base-called reads containing 42G bases with N50 of 13K bases. We used NGMLR, which is a long-read mapper, to align the reads to the human reference genome (hg38). SVs were called by Sniffles detecting all types of SVs. The deletion was found to range from chr14: 23390037 to 23419824 (see figure) and did not contain other SVs. There was no pathogenic SV on ACTC1, GATA4, TBX20 and TLL1 which are genes related to ASD on Genetic Testing Registry.

His mother had also ASD and harbored the same deletion.

Conclusions

This is the first report to identify a large deletion between MYH6 and MYH7 in the family with ASD. The combination of SRS and LRS is useful to detect SVs in patients with suspected inherited diseases but carried no causative SNVs.

Funding Acknowledgement

Type of funding source: None

Systematic Evaluation of KCNQ1 variant using ACMG/AMP Guidelines and Risk Stratification in Long QT Syndrome Type 1

Background

Mutation/variant-site specific risk stratification in long-QT syndrome type 1 (LQT1) has been well investigated, but it is still challenging to adopt current enormous genomic information to clinical aspects caused by each mutation/variant. We assessed a novel variant-specific risk stratification in LQT1 patients.

Methods

We classified a pathogenicity of 142 KCNQ1 variants among 927 LQT1 patients (536 probands and 391 family members) based on the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines and evaluated whether the ACMG/AMP-based classification was associated with arrhythmic risk in LQT1 patients.

Results

Among 142 KCNQ1 variants, 60 (42.3%), 58 (40.8%), and 24 (16.9%) variants were classified into pathogenic (P), likely pathogenic (LP), and variant of unknown significance (VUS), respectively. The ACMG/AMP guideline-based classification was significantly associated with syncopal events (particularly those during exercise) and LQT risk score (Schwartz score) in overall population. On the other hand, arrhythmic risk was completely different between probands and families even in the same variants. The baseline QTc interval and variant location could stratify the risk in family members but not in probands, however, the ACMG/AMP-based KCNQ1 variant classification stratified the risk in LQT1 probands as well as family members. Multivariate analysis showed that proband (HR=2.52; 95% CI: 1.93–3.30; p<0.0001), longer QTc interval (≥500ms) (HR=1.41; 95% CI: 1.11–1.79; p<0.0001), variants at membrane spanning (MS) (vs. those at N/C terminus) (HR=1.40; 95% CI: 1.07–1.85; p=0.02), C-loop (vs. N/C terminus) (HR=1.58; 95% CI: 1.11–2.24; p=0.01), and P variants [(vs. LP) (HR=1.71; 95% CI: 1.33–2.23; p<0.0001), (vs. VUS) (HR=1.96; 95% CI: 1.19–3.46; p=0.007)] were significantly associated with syncopal events. A clinical score (0–4) based on the proband, QTc (≥500ms), variant location (MS or C-loop) and P variant by the ACMG/AMP guidelines allowed identification of patients more likely to have arrhythmic events (Figure A and B).

Conclusion

Comprehensive evaluation of clinical findings and pathogenicity of KCNQ1 variants based on the ACMG/AMP-based evaluation may stratify arrhythmic risk of congenital long-QT syndrome type 1.

Figure 1

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Health Science Research Grant from the Ministry of Health,Labor and Welfare of Japan for Clinical Research on Measures for Intractable Diseases (H24-033, H26-040, H27-032) and a research grant from the Japan Agency for Medical Research and Development (AMED) (15km0305015h0101, 16ek0210073h0001)

Splice site mutation of LMNA causes severe dilated cardiomyopathy via strong dominant reduction of total lamin expression

Objective

LMNA is a known causative gene of dilated cardiomyopathy (DCM) and familial cardiac conduction disturbance (CCD). Genetic variants affecting the pre-mRNA splicing process often lead to premature stop codons and result in nonsense-mediated mRNA decay (NMD), followed by degradation of mutated alleles. The misssense variant LMNA c. 936G>C was previously reported in a French family affected by muscular dystrophy, CCD, and DCM, but no detailed analysis has been performed. We so far identified the same variant in two Japanese families affected by CCD and DCM. In this study, we investigated the molecular consequences of the variant located at the last codon of LMNA exon5 to demonstrate its pathogenicity.

Methods

Genomic DNA and total RNA were isolated from patients' peripheral blood lymphocytes or cardiac tissue. LMNA-coding exons were screened by direct sequencing. Complementary DNAs (cDNAs) were generated by reverse transcription PCR from RNA. Quantitative PCR (qPCR) was performed to quantify the LMNA cDNA amount by using specific primers for lamins A and C. The protein expressions of both isoforms were analyzed by western blotting.

Results

We detected the heterozygous LMNA c.936 G>C (p. Q312H) variant at the end of exon 5 by genomic DNA sequencing in two unrelated Japanese families (figure. pedigree) affected by DCM and CCD. In a genomic database survey, we did not find the variant in either gnomAD, TogoVar, or the Human Genetic Variation Database. The two commonly used splice site predictor tools, NetGene2 and FSPLICE, estimated that this site was a splice donor site. Sequencing of cDNA demonstrated that the mutated allele was absent. By qPCR assay, we confirmed a 90% reduction in LMNA cDNA. Western blot analysis revealed that lamin A and C expression was reduced far more than 50% (figure. western blot).

Conclusions

We report a LMNA missense mutation found in two families, which disrupts a normal splicing site, leads to NMD, and resulted in severe cardiac laminopathy. The drastic reductions of lamin expression at the cDNA and protein levels suggested that other co-existing mechanisms may also have suppressed the expression of the healthy wild type allele.

Pedigree and western blot assay

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Japan Society for the Promotion of Science KAKENHI

Interactions among eukaryotes, retrotransposons and riboviruses: endogenous riboviral elements in eukaryotic genomes

Riboviruses are viruses that have RNA genomes and replicate only via RNA intermediates. Although they do not require a DNA phase for replication and do not encode reverse transcriptase, the presence of DNA forms of riboviral sequences in ribovirus-infected cells has been reported since the 1970s. Additionally, heritable ribovirus-derived sequences, called riboviral endogenous viral elements (EVEs), have been found in the genomes of many eukaryotes. These are now thought to be formed by the reverse transcription machineries of retrotransposons within eukaryotic genomes sometimes referred to as selfish elements. Surprisingly, some reverse-transcribed riboviral DNAs (including EVEs) provide physiological functions for their hosts, suggesting the occurrence of novel interactions among eukaryotic genomes, retrotransposons and riboviruses, and opening the door to new avenues of investigation. Here I review current knowledge on these triangular interactions, and discuss future directions in this field.

299 The prevalence and role of SCN10A variants in Han Chinese patients with Brugada syndrome: the SADS-TW BrS registry

On Behalf

SADS-TW BrS registry

Background

Brugada syndrome (BrS) is an inheritable arrhythmic disease responsible for sudden cardiac death. Information on the prevalence and role of SCN10A variants in BrS is limited and equivocal.

Purpose

We aimed to investigate the prevalence and role of SCN10A variants in BrS in Han Chinese.

Methods

From 2000 to 2017, we prospectively and consecutively enrolled 176 unrelated BrS patients from the Han Chinese population in Taiwan (the SADS-TW BrS registry). Thirty-four BrS-related genes were screened by next-generation sequencing, using Taiwan Biobank as the population reference. The pathogenicity was evaluated by literature review and in silico analyses, including the SKAT-O algorithm.

Results

The SKAT-O algorithm showed that rare variants of SCN10A, but not common variants, were significantly different between BrS patients and healthy controls in the additive and dominant models (p-value <0.001), suggesting that rare SCN10A variants may play a role in BrS. Six likely pathogenic SCN10A variants were found in 6 patients and were compared to 25 pathogenic or likely pathogenic SCN5A variants found in 29 patients. The patients with likely pathogenic SCN10A variants tended to exhibit sudden death in older age and have a shorter QRS interval than those carrying pathogenic or likely pathogenic SCN5A variants or no variants in either gene (p = 0.06, 0.07, respectively). Collectively, the prevalence of likely pathogenic SCN10A variants was 3.4% in Han Chinese patients with BrS in Taiwan.

Conclusions

SCN10A likely pathogenic variants were present in 3.4% of Han Chinese BrS patients. Rare SCN10A variants may play a role in BrS, and may have impact on clinical and electrocardiographic manifestations.

Table 1. Patient Nucleotide Amino acid TWB gnomAD_EA REVEL CADD PHRED SIFT Polyphen-2 GERP++ 1 c.5789A > T p.D1930V 0.001318 0.0008700 0.479 24.5 Damaging Possibly damaging 4.22 2 c.2341G > A p.G781R 0 0.00005301 0.866 33 Damaging Probably damaging 4.83 3 c.5587C > T p.R1863W 0.000502 0 0.832 27.8 Damaging Probably damaging 1.97 4 c.2161C > T p.P721S 0.000989 0.0009016 0.933 28.5 Damaging Probably damaging 4.19 5 c.3749G > A p.R1250Q 0 0 0.907 31 Damaging Probably damaging 4.23 6 c.1825A > T p.R609W 0.000659 0.0001591 0.811 32 Damaging Probably damaging 4.28 Clinical and predicted functional characteristics of 6 likely pathogenic SCN10A variants. EA = East Asian; GERP = Genomic Evolutionary Rate Profiling; TWB = Taiwan Biobank. Transcript: NM_006514.3.

Abstract 299 Figure. Location of the SCN10A variants

P2865Mutation specific clinical characteristics in long QT syndrome type 8; severe phenotype in Timothy syndrome patients

Background

Long QT syndrome type 8 (LQT8) caused by mutations in CACNA1C has been classified as a very rare and severe type of long QT syndrome accompanied with Timothy syndrome (TS) with extra-cardiac phenotype. Recently, various mutations in CACNA1C have been identified in non-TS patients. However, mutation specific severity in LQT8 has not been elucidated yet, especially for non-TS patients.

Purpose

We aimed to clarify the clinical characteristics of LQT8 patients.

Methods

The study consists of 26 LQT8 patients (21 probands and 5 family members). We evaluated their phenotype.

Results

Table summarizes the clinical characteristics of LQT8 patients. TS patients diagnosed in younger age than those of non-TS. Four TS and one non-TS patients were diagnosed at the age of 0, though the non-TS patient was a son of a patient and asymptomatic. Nine patients suffered symptoms including 7 with cardiac arrest. We identified three TS mutations; classical p.G406R in two and p.G402S in two, and a new TS mutation, p.412M in one. Four of TS patients were symptomatic and two died suddenly at the age of 4 and 5. In contrast, no one died in non-TS patients. Five non-TS patients suffered symptoms in the age of 4,9,15,54 and 64, and the mutations were p.S643F, p.R858H (2 patients), p.K1518E and p.K1591T.

Characteristics of TS and non-TS patient TS Non-TS P N (male) 5 (2) 21 (9) Age (range) 0 (0–7) 12 (0–64) 0.004 Symptom Syncope 4 5 0.034 CPA 3 4 0.101 ECG characteristics   QT interval 603±40 507±14 0.011   T wave alternans 5 2 <0.001   AV Block 4 1 0.002 Therapy (4 unknown)   Beta-blocker 4 7 0.311   Mexiletine 3 1 0.024   ICD implantation 2 2 0.21

Conclusions

Although TS patients showed severe phenotype, most of the non-TS patients were asymptomatic. The phenotype in LQT8 are diversely different depend on the mutations, especially between patients with TS and non-TS.

P3827Low dose of quinidine is effective to normalize the slow inactivation in mutant Kv4.3 channel identified in an early repolarization syndrome patient

Background

Early repolarization syndrome (ERS) is characterized by J-point elevation in the ECG and ventricular fibrillation (VF). Several mutations in genes encoding cardiac ion channels have been reported as the causes for ERS. For the treatment of ERS, clinical studies have shown that quinidine is effective for the suppression of electrical storm. However, the mechanism or the optimal concentration for quinidine to suppress the electrical storm has not been elucidated yet.

Purpose

The aim of the present study is to clarify pharmacological effect of quinidine on mutant Kv4.3 channel by electrophysiological analysis and to establish theoretically effective treatment for ERS.

Methods

A KCND3 mutation, p.G306A, identified heterozygously in a 12-year-old boy was examined by whole-cell patch-clamp methods using CHO cells. We performed functional analysis of the Kv4.3 channels encoded by KCND3 of wild-type (WT), heterozygous (WT/G306A), or homozygous (G306A) mutants. Pharmacological normalizing effects of quinidine to the WT and mutant channels were investigated by loading test in various concentration. The sensitivity of quinidine was evaluated in terms of the concentration of the clinical course and the loading test.

Results

The patient suffered VF while sleeping or under sedation. Significant J-point elevations in multiple leads were recorded and he was diagnosed as ERS. Quinidine administration in the serum concentration of 1.2 to 3.1 μM was effective to stop his VF storm. Mutant Kv4.3 currents showed significantly slow inactivation time course (Fig 1), which meant that the mutation caused the gain-of-function channel. Quinidine loading to the mutant Kv4.3 normalized the inactivation time course in concentration-dependent manner (Fig 2, 3). In the loading concentration of 1 μM, the peak currents were not changed regardless of the voltage (Fig 4). The optimal serum concentration of quinidine in clinical use as multi-ion-channels blocker is 6 to 15 μM and the concentration was higher than that of the patient to stop the VF storm. The electrophysiological analysis showed that the low dose loading of quinidine was effective to prevent the gain-of function change of mutant Kv4.3 channels.

Electrophysiological analysis

Conclusions

We showed the pharmacological mechanism of quinidine against the mutant Kv4.3 channels identified in an ERS patient. Even the low concentration of quinidine was effective to normalize the slow inactivation, gain-of-function, in mutant Kv4.3 channels. Our data would be helpful to confirm the optimal concentration of quinidine for ERS patients to avoid adverse effect.

P5025Structural insights into catecholaminergic polymorphic ventricular tachycardia-associated RyR2 mutant channels using a three-dimensional in silico model

Background

The cardiac ryanodine receptors (RyR2) are large tetrameric calcium-permeant ion channels found in cardiac muscle sarcoplasmic reticulum, which play an important role in the control of intracellular Ca2+ release and cardiac contraction. Mutations in the RYR2 gene are associated with lethal arrhythmia diseases including catecholaminergic polymorphic ventricular tachycardia (CPVT) resulting from increased diastolic Ca2+ leak from mutant channels. RyR2 is a huge protein that each subunit of tetramer is comprised of 4967 amino acids, which hampers the detailed in vitro analysis of RyR2 mutant channels.

Purpose

We aimed to analyze the structural features of RyR2 mutant channels identified in our cohort with inherited arrhythmias using RyR2 three-dimensional (3D) in silico model to reveal the arrhythmogenic mechanisms.

Methods

A targeted next-generation sequencing panel for inherited arrhythmias was employed for genetic diagnosis of the patients. Then, we mapped the identified mutations on RyR2 3D structural model developed by cryo-EM images (PDB: 5go9, 5goa, Peng Science 2016) and investigated the relationship between the location of the mutations and specific functional sites.

Results

As a result of genetic analysis, we identified 93 RYR2 mutations from 112 probands with CPVT (n=93) or long-QT syndrome (LQTS) (n=19).64 of 93 (69%) RYR2 mutations are located in three “hot-spot” area (N-terminal (residues 77–466), central (2246–2534), and channel (3778–4959) hotspot. RyR2 3D in silico modeling revealed that the mutations are regionally distributed mainly in three parts: N-terminal, periphery, and channel part (Figure A). In N-terminal part (1–642 amino acid), 9 of 13 mutations alter the charges of the amino acids (Figure B). Especially, R169L, R169Q, and G172E are close to the interface between two neighboring subunits (∼20Å). These mutations which change the amino acid charge may cause a complete disruption of the ionic pair network and result in largest structural changes, which facilitates RyR2 channel opening. In periphery part (643–3528aa), 22 of 33 mutations are close to the two predicted binding sites of FKBP12.6, a stabilizer of RyR2 (∼5–40Å, Figure C). The mutations are supposed to disturb the binding affinity to the FKBP12.6 resulting in RyR2 channel instability. In channel part (3613–4968aa), 16 of 40 mutations are located near two interface. (FigureD) 12 mutations are close to the Ca2+ sensor and the other 4 mutations are adjacent to the pore-forming segment. Especially, V4821I is just located on this segment and strongly expected to impair the channel function. Above all, RyR2 3D in silico modeling revealed that 63 of all 93 (68%) identified mutations are supposed to be pathogenic.

Location of RYR2 mutations in 3D model

Conclusion

3D structural model of RyR2 is useful for the investigation of the pathogenic mechanisms of CPVT-related mutations. Further studies are needed to elucidate the relationship between the location of the mutations and clinical phenotypes.

Identification of a distinct lineage of aviadenovirus from crane feces

Viruses are believed to be ubiquitous; however, the diversity of viruses is largely unknown because of the bias of previous research toward pathogenic viruses. Deep sequencing is a promising and unbiased approach to detect viruses from animal-derived materials. Although cranes are known to be infected by several viruses such as influenza A viruses, previous studies targeted limited species of viruses, and thus viruses that infect cranes have not been extensively studied. In this study, we collected crane fecal samples in the Izumi plain in Japan, which is an overwintering site for cranes, and performed metagenomic shotgun sequencing analyses. We detected aviadenovirus-like sequences in the fecal samples and tentatively named the discovered virus crane-associated adenovirus 1 (CrAdV-1). We determined that our sequence accounted for approximately three-fourths of the estimated CrAdV-1 genome size (33,245 bp). The GC content of CrAdV-1 genome is 34.1%, which is considerably lower than that of other aviadenoviruses. Phylogenetic analyses revealed that CrAdV-1 clusters with members of the genus Aviadenovirus, but is distantly related to the previously identified aviadenoviruses. The protein sequence divergence between the DNA polymerase of CrAdV-1 and those of other aviadenoviruses is 45.2-46.8%. Based on these results and the species demarcation for the family Adenoviridae, we propose that CrAdV-1 be classified as a new species in the genus Aviadenovirus. Results of this study contribute to a deeper understanding of the diversity and evolution of viruses and provide additional information on viruses that infect cranes, which might lead to protection of the endangered species of cranes.

Taxonomy of the order Mononegavirales: update 2019

In February 2019, following the annual taxon ratification vote, the order Mononegavirales was amended by the addition of four new subfamilies and 12 new genera and the creation of 28 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Gender difference in clinical and genetic characteristics of Brugada syndrome: SADS-TW BrS registry

BACKGROUND

Brugada syndrome (BrS) is a heritable sudden cardiac death (SCD) disease with male predominance. Information on gender difference of BrS remains scarce.

AIM

To investigate the gender difference of BrS in Han Chinese.

DESIGN

We consecutively enrolled 169 BrS patients (153 males and 16 females) from Han Chinese in Taiwan from 1998 to 2017.

METHODS

Clinical characteristics, electrocardiographic parameters and SCN5A mutation status were compared between genders.

RESULTS

The percentage of family history of SCD in females was slightly higher (31.3% vs. 15%, P = 0.15). Females exhibited longer QTc (457.8 ± 33.0 vs. 429.5 ± 42.1 ms, P < 0.01). Regarding cumulative event occurrence by age, Mantel-Cox test showed females had earlier age of onset of first cardiac events (SCD or syncope) than males (P = 0.049), which was mainly attributed to syncope (P < 0.01). Males with SCD exhibited longer QRS duration (114.2 ± 26.8 vs. 104.8 ± 15.3 ms, P = 0.02) and QTc (442.5 ± 57.4 vs. 422.9 ± 28.8 ms, P = 0.02). Males with syncope exhibited longer PR interval (181.2 ± 33.7 vs. 165.7 ± 27.1 ms, P = 0.01), whereas females with SCD or syncope had a trend towards slower heart rates (69.1 ± 9.6 vs. 82.2 ± 16.3 bpm, P = 0.10) than female with no or mild symptoms. There was no difference in the percentage of SCN5A mutation between genders.

CONCLUSION

Gender difference is present in BrS. Females have longer QTc and suffer from syncope earlier than males. Risk of SCD in males is associated with boarder QRS complex and longer QTc, whereas risk of syncope is associated with longer PR interval in males and slower heart rate in females.

Development of a Model of Porcine Epidemic Diarrhea in Microminipigs

Porcine epidemic diarrhea virus (PEDV) induces an often fatal gastrointestinal disease in piglets. In this study, we performed a PEDV infection experiment with the Microminipig, the smallest of experimental minipigs, as a novel small animal model. We orally inoculated a neonatal Microminipig with an intestinal homogenate of a PEDV-infected pig and housed it in a small cage originally designed for rats in an animal biosafety level 2 facility. The infected Microminipig showed the typical signs of porcine epidemic diarrhea (PED), such as watery diarrhea, loss of appetite and weight loss. We also recognized a high amount of excreted PEDV in its rectal swabs and villus atrophy of the small intestine. These results suggest that the Microminipig is a good small animal model for PED, which may contribute to a better understanding of the pathogenesis of PEDV.

Phylogenetic variations of highly pathogenic H5N6 avian influenza viruses isolated from wild birds in the Izumi plain, Japan, during the 2016-17 winter season

During the 2016-2017 winter season, we isolated 33 highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype and three low pathogenic avian influenza viruses (LPAIVs) from debilitated or dead wild birds, duck faeces, and environmental water samples collected in the Izumi plain, an overwintering site for migratory birds in Japan. Genetic analyses of the H5N6 HPAIV isolates revealed previously unreported phylogenetic variations in the PB2, PB1, PA, and NS gene segments and allowed us to propose two novel genotypes for the contemporary H5N6 HPAIVs. In addition, analysis of the four gene segments identified close phylogenetic relationships between our three LPAIV isolates and the contemporary H5N6 HPAIV isolates. Our results implied the co-circulation and co-evolution of HPAIVs and LPAIVs within the same wild bird populations, thereby highlighting the importance of avian influenza surveillance targeting not only for HPAIVs but also for LPAIVs.