Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses

Giant RNA genomes: Roles of host, translation elongation, genome architecture, and proteome in nidoviruses

Positive-strand RNA viruses of the order Nidovirales have the largest known RNA genomes of vertebrate and invertebrate viruses with 36.7 and 41.1 kb, respectively. The acquisition of a proofreading exoribonuclease (ExoN) by an ancestral nidovirus enabled crossing of the 20 kb barrier. Other factors constraining genome size variations in nidoviruses remain poorly defined. We assemble 76 genome sequences of invertebrate nidoviruses from >500.000 published transcriptome experiments and triple the number of known nidoviruses with >36 kb genomes, including a 64 kb RNA genome. Many of the identified viral lineages acquired putative enzymatic and other protein domains linked to genome size, host phyla, or virus families. The inserted domains may regulate viral replication and virion formation, or modulate infection otherwise. We classify ExoN-encoding nidoviruses into seven groups and four subgroups, according to canonical and noncanonical modes of viral replicase expression by ribosomes and genomic organization (reModes). The most-represented group employing the canonical reMode comprises invertebrate and vertebrate nidoviruses, including coronaviruses. Six groups with noncanonical reModes include invertebrate nidoviruses with 31-to-64 kb genomes. Among them are viruses with segmented genomes and viruses utilizing dual ribosomal frameshifting that we validate experimentally. Moreover, largest polyprotein length and genome size in nidoviruses show reMode- and host phylum-dependent relationships. We hypothesize that the polyprotein length increase in nidoviruses may be limited by the host-inherent translation fidelity, ultimately setting a nidovirus genome size limit. Thus, expansion of ExoN-encoding RNA virus genomes, the vertebrate/invertebrate host division, the control of viral replicase expression, and translation fidelity are interconnected.

Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the Flaviviridae

The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RNA viruses related to classical orthoflaviviruses and pestiviruses but quite different genome lengths and configurations, and with a hugely expanded host range that spans multiple animal phyla, including molluscs, cnidarians and stramenopiles,, and plants. Grouping of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flavivirus and 'flavi-like' viruses into four divergent clades and multiple lineages within them was congruent with helicase gene phylogeny, PPHMM profile comparisons, and comparison of RdRP protein structure predicted by AlphFold2. These results support their classification into the established order, Amarillovirales, in three families (Flaviviridae, Pestiviridae, and Hepaciviridae), and 14 genera. This taxonomic framework informed by RdRP hallmark gene evolutionary relationships provides a stable reference from which major genome re-organisational events can be understood.

Tertiary Structures of Haseki Tick Virus Nonstructural Proteins Are Similar to Those of Orthoflaviviruses

Currently, a large number of novel tick-borne viruses potentially pathogenic to humans are discovered. Studying many of them by classical methods of virology is difficult due to the absence of live viral particles or a sufficient amount of their genetic material. In this case, the use of modern methods of bioinformatics and synthetic and structural biology can help. Haseki tick virus (HSTV) is a recently discovered tick-borne unclassified ssRNA(+) virus. HSTV-positive patients experienced fever and an elevated temperature. However, at the moment, there is no information on the tertiary structure and functions of its proteins. In this work, we used AlphaFold 3 and other bioinformatic tools for the annotation of HSTV nonstructural proteins, based on the principle that the tertiary structure of a protein is inextricably linked with its molecular function. We were the first to obtain models of tertiary structures and describe the putative functions of HSTV nonstructural proteins (NS3 helicase, NS3 protease, NS5 RNA-dependent RNA-polymerase, and NS5 methyltransferase), which play a key role in viral genome replication. Our results may help in further taxonomic identification of HSTV and the development of direct-acting antiviral drugs, POC tests, and vaccines.

Insights into the virome of Hyalomma marginatum in the Danube Delta: a major vector of Crimean-Congo hemorrhagic fever virus in Eastern Europe

BACKGROUND

Ticks are significant vectors of pathogens, including viruses, bacteria, and protozoa. With approximately 900 tick species worldwide, many are expanding their geographical range due to changing socioeconomic and climate factors. The Danube Delta, one of Europe's largest wetlands, is an ecosystem that, despite its ecological importance, remains understudied concerning the risk of introducing new tick-borne viruses. This region serves as a critical habitat for migratory birds, which can carry ticks over long distances, potentially introducing exotic tick species and their pathogens into the local ecosystem. Hyalomma marginatum ticks, the primary vector of Crimean-Congo hemorrhagic fever virus (CCHFV), are of particular concern due to their expanding presence in Europe and potential to spread other arboviruses. In addition to being the primary vector for CCHFV, Hyalomma sp. ticks are capable of transmitting other pathogens of medical and veterinary importance, including Dugbe virus, West Nile virus, African horse sickness virus, and Kyasanur forest disease virus. Therefore, it is essential to monitor the presence of Hyalomma sp. ticks while simultaneously surveilling arbovirus circulation in tick populations to mitigate the risk of arboviral outbreaks.

METHODS

In this work, we used an RNA sequencing technique to analyze the virome of H. marginatum ticks collected from the Danube Delta Biosphere Reserve, Romania, one of the major bird migration hubs from Africa to Europe.

RESULTS

Among the viral taxa detected in H. marginatum ticks, sequences belonging to Volzhskoe tick virus (VTV), Balambala tick virus (BMTV) and Bole tick virus 4 (BTV4) were identified. In addition, we report the first identification of a novel Rhabdoviridae-related virus, Hyalomma marginatum rhabdovirus (HMRV). No CCHFV or any CCHFV-related nairovirus were detected in this study.

CONCLUSIONS

To summarize, detecting new viruses is essential for monitoring potential viral outbreaks. Our research expands the understanding of virus diversity in Eastern Europe, including the identification of novel viruses. This insight is crucial for monitoring viruses that may pose risks to both animal and human health, such as CCHFV.

Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses

In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete and partial virus genomes up to a length of 37 kb were identified, with noda-like and reo-like viruses being most abundant, followed by bunya-like and birna-like viruses. Viruses related to the Permutotetraviridae, Nidovirales, Flaviviridae, Rhabdoviridae and Chuviridae as well as the unclassified Jῑngmén virus and Negev virus groups were also present. The results indicate a broad extent of recombinant virus genomes, supporting the concept of the modularity of eukaryotic viruses. For example, novel combinations of genes encoding replicase and structural proteins with a jellyroll fold have been observed. Less than 35 viruses could be assigned to existing virus genera. These are (i) an avian deltacoronavirus which was represented by only one short contig, albeit with 98% similarity, (ii) a seadornavirus and a rotavirus, and (iii) some 30 nodaviruses. All remaining viruses are novel and too diverse for accommodation in existing genera. Many of the virus genomes exhibit ORFans encoding hypothetical proteins of up to 2000 amino acids without conserved protein domains.

Discovery of the first sea turtle adenovirus and turtle associated circoviruses

Turtles are an evolutionarily unique and morphologically distinctive order of reptiles, and many species are globally endangered. Although a high diversity of adenoviruses in scaled reptiles is well-documented, turtle adenoviruses remain largely understudied. To investigate their molecular diversity, we focused on the identification and characterisation of adenoviruses in turtle-derived organ, swab and egg samples. Since reptile circoviruses have been scarcely reported and no turtle circoviruses have been documented to date, we also screened our samples for circoviruses. Host-virus coevolution is a common feature of these viral families, so we aimed to investigate possible signs of this as well. Two screening projects were conducted: one on Brazilian samples collected from animals in their natural habitat, and the other on Hungarian pet shop samples. Nested PCR systems were used for the detection of adeno- and circoviruses and purified PCR products were Sanger sequenced. Phylogenetic trees for the viruses were reconstructed based on the adenoviral DNA polymerase and hexon genes, circoviral Rep genes, and for the turtle hosts based on mitochondrial cytochrome b amino acid sequences. During the screening, testadeno-, siadeno-, and circovirus strains were detected. The circovirus strains were classified into the genus Circovirus, exhibiting significant evolutionary divergence but forming a monophyletic clade within a group of fish circoviruses. The phylogenetic tree of turtles reflected their taxonomic relationships, showing a deep bifurcation between suborders and distinct monophyletic clades corresponding to families. A similar clustering pattern was observed among the testadenovirus strains in their phylogenetic tree. As a result, this screening of turtle samples revealed at least three new testadenoviruses, including the first sea turtle adenovirus, evidence of coevolution between testadenoviruses and their hosts, and the first turtle associated circoviruses. These findings underscore the need for further research on viruses in turtles, and more broadly in reptiles, to better understand their viral diversity and the evolutionary processes shaping host-virus interactions.

Classical swine fever: Unveiling the complexity through a multifaceted approach

Classical swine fever (CSF), sometimes referred to as hog cholera, is a highly contagious, virally based, systemic illness that affects both domestic and wild pigs. The virus known as classical swine fever virus (CSFV) is a member of the Flaviviridae family, specifically the genus Pestivirus. This disease is thought to be endemic in many Asian countries that produce pork as well as in several countries in Central and South America, the Caribbean, and elsewhere. As previously indicated, depending on the virulence of the virus strain involved and several host circumstances, clinical indications of CSFV infection can vary greatly, ranging from abrupt fatality to an occult course. CSF diagnosis can be made by serological detection, antigen, RNA, and isolation. CSF's highly varied symptoms and post-mortem pathology resemble those of African swine fever (ASF). ASF, the kind of CSFV, the pig's age, and its susceptibility all affect the clinical symptoms. Pigs that contract CSFV, a highly infectious and economically significant virus. The great economic significance of the swine business makes the CSFV a potential bioterrorism threat. Live attenuated CSF vaccinations have been around for many years and are quite safe and effective. Controlling epidemics in CSFV-free zones requires quick action. Pigs that are impacted must be slaughtered, and the carcasses must be buried or burned.

Predicting novel mosquito-associated viruses from metatranscriptomic dark matter

The exponential growth of metatranscriptomic studies dedicated to arboviral surveillance in mosquitoes has yielded an unprecedented volume of unclassified sequences referred to as the virome dark matter. Mosquito-associated viruses are classified based on their host range into Mosquito-specific viruses (MSV) or Arboviruses. While MSV replication is restricted to mosquito cells, Arboviruses infect both mosquito vectors and vertebrate hosts. We developed the MosViR pipeline designed to identify complex genomic discriminatory patterns for predicting novel MSV or Arboviruses from viral contigs as short as 500 bp. The pipeline combines the predicted probability score from multiple predictive models, ensuring a robust classification with Area Under ROC (AUC) values exceeding 0.99 for test datasets. To assess the practical utility of MosViR in actual cases, we conducted a comprehensive analysis of 24 published mosquito metatranscriptomic datasets. By mining this metatranscriptomic dark matter, we identified 605 novel mosquito-associated viruses, with eight putative novel Arboviruses exhibiting high probability scores. Our findings highlight the limitations of current homology-based identification methods and emphasize the potentially transformative impact of the MosViR pipeline in advancing the classification of mosquito-associated viruses. MosViR offers a powerful and highly accurate tool for arboviral surveillance and for elucidating the complexities of the mosquito RNA virome.

Mapping glycoprotein structure reveals Flaviviridae evolutionary history

Viral glycoproteins drive membrane fusion in enveloped viruses and determine host range, tissue tropism and pathogenesis1. Despite their importance, there is a fragmentary understanding of glycoproteins within the Flaviviridae2, a large virus family that include pathogens such as hepatitis C, dengue and Zika viruses, and numerous other human, animal and emergent viruses. For many flaviviruses the glycoproteins have not yet been identified, for others, such as the hepaciviruses, the molecular mechanisms of membrane fusion remain uncharacterized3. Here we combine phylogenetic analyses with protein structure prediction to survey glycoproteins across the entire Flaviviridae. We find class II fusion systems, homologous to the Orthoflavivirus E glycoprotein in most species, including highly divergent jingmenviruses and large genome flaviviruses. However, the E1E2 glycoproteins of the hepaciviruses, pegiviruses and pestiviruses are structurally distinct, may represent a novel class of fusion mechanism, and are strictly associated with infection of vertebrate hosts. By mapping glycoprotein distribution onto the underlying phylogeny, we reveal a complex evolutionary history marked by the capture of bacterial genes and potentially inter-genus recombination. These insights, made possible through protein structure prediction, refine our understanding of viral fusion mechanisms and reveal the events that have shaped the diverse virology and ecology of the Flaviviridae.

A novel hypovirulence-associated Hadaka virus 1 (HadV1-LA6) in Fusarium oxysporum f. sp. cubense

Fusarium oxysporum f. sp. cubense (Foc) poses a significant threat to banana crops as a lethal fungal pathogen. The global spread of Foc underscores the formidable challenges associated with traditional management methods in combating this pathogen. This study delves into the hypovirulence-associated mycovirus in Foc. From Foc strain LA6, we isolated and characterized a novel member of the Hadakaviridae family, named Hadaka virus 1 strain LA6 (HadV1-LA6). HadV1-LA6 comprises 10 genomic RNA segments, with RNA1 to RNA7 sharing 80.9%-95.0% amino acid sequence identity with known HadV1-7n, while RNA8 to RNA10 display significantly lower identity. HadV1-LA6 demonstrates horizontal transmission capabilities in an all-or-none fashion between different Foc strains via coculturing. Phenotypic comparisons highlight that HadV1-LA6 significantly reduces the growth rates of its host fungus under cell wall stress and oxidative stress conditions. Importantly, HadV1-LA6 attenuates Foc's virulence in detached leaves and banana plants. This study represents the first introduction of a novel hypovirulence-associated Hadaka virus 1 in Foc.IMPORTANCEFusarium wilt of banana (FWB) is a severe fungal disease caused by soil-borne Fusarium oxysporum f. sp. cubense (Foc). Among various strategies, biocontrol emerges as a safe, ecologically friendly, and cost-effective approach to managing FWB. In this study, we focus on exploring the potential of a novel hypovirulent member of hadakavirid, HadV1-LA6. Previous reports suggest that HadV1 shows no apparent effect on the host. However, through phenotypic assessments, we demonstrate that HadV1-LA6 significantly impedes the growth rates of its host fungus under stress conditions. More importantly, HadV1-LA6 exhibits a remarkable capacity to attenuate Foc's virulence in detached leaves and banana plants. Furthermore, HadV1-LA6 could be horizontally transmitted between different Foc strains, presenting a promising resource for revealing the molecular mechanism of the interaction between Hadaka virus 1 and its host.

A ~40-kb flavi-like virus does not encode a known error-correcting mechanism

It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order Nidovirales (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb. The recent discovery of large-genome flavi-like viruses (Flaviviridae), which comprise genomes up to 27 kb in length yet seemingly do not encode exonuclease domains, has led to the proposal that a proofreading mechanism is required to facilitate the expansion of nonsegmented RNA virus genomes above 30 kb. Herein, we describe a ~40 kb flavi-like virus identified in a Haliclona sponge metatranscriptome that does not encode a known exonuclease. Structural analysis revealed that this virus may have instead captured cellular domains associated with nucleic acid metabolism that have not been previously found in RNA viruses. Phylogenetic inference placed this virus as a divergent pesti-like lineage, such that we have provisionally termed it "Maximus pesti-like virus." This virus represents an instance of a flavi-like virus achieving a genome size comparable to that of the Nidovirales and demonstrates that RNA viruses have evolved multiple solutions to overcome the error threshold.

Hard ticks (Ixodida: Ixodidae) in the Colombian Caribbean harbor the Jingmen tick virus: an emerging arbovirus of public health concern

BACKGROUND

Ticks are obligate hematophagous ectoparasites involved in transmitting viruses of public health importance. The objective of this work was to identify the Jingmen tick virus in hard ticks from the Colombian Caribbean, an arbovirus of importance for public health.

METHODS

Ticks were collected in rural areas of Córdoba and Cesar, Colombia. Taxonomic identification of ticks was carried out, and pools of 13 individuals were formed. RNA extraction was performed. Library preparation was performed with the MGIEasy kit, and next-generation sequencing (NGS) with MGI equipment. Bioinformatic analyses and taxonomic assignments were performed using the Galaxy platform, and phylogenetic analyses were done using IQ-TREE2.

RESULTS

A total of 766 ticks were collected, of which 87.33% (669/766) were Rhipicephalus microplus, 5.4% (42/766) Dermacentor nitens, 4.2% (32/766) Rhipicephalus linnaei, and 3.0% (23/766) Amblyomma dissimile. Complete and partial segments 1, 2, 3, and 4 of Jingmen tick virus (JMTV) were detected in the metatranscriptome of the species R. microplus, D. nitens, and A. dissimile. The JMTVs detected are phylogenetically related to JMTVs detected in Aedes albopictus in France, JMTVs detected in R. microplus in Trinidad and Tobago, JMTVs in R. microplus and A. variegatum in the French Antilles, and JMTVs detected in R. microplus in Colombia. Interestingly, our sequences clustered closely with JMTV detected in humans from Kosovo.

CONCLUSIONS

JMTV was detected in R. microplus, D. nitens, and A. dissimile. JMTV could pose a risk to humans. Therefore, it is vital to establish epidemiological surveillance measures to better understand the possible role of JMTV in tropical diseases.

Identification and Genome Characterization of a Novel Nege-like Virus Isolated from Aphids (Aphis gossypii) in Yunnan Province

Negeviruses are insect-specific enveloped RNA viruses that exhibit a wide geographic distribution. A novel nege-like virus, tentatively named Aphis gossypii nege-like virus (AGNLV, GenBank: OR880429.1), was isolated from aphids (Aphis gossypii) in Lijiang City, Yunnan, China. AGNLV has a genome sequence of 9258 nt (excluding the polyA tail) encoding three open reading frames (ORFs). ORF1 (7149 nt) encodes a viral methyltransferase, a viral RNA helicase, and an RNA-dependent RNA polymerase. ORF2 (1422 nt) encodes a DiSB-ORF2_chro domain and ORF3 encodes an SP24 domain. The genome sequence of AGNLV shares the highest nucleotide identity of 60.0% and 59.5% with Wuhan house centipede virus 1 (WHCV1) and Astegopteryx formosana nege-like virus (AFNLV), respectively. Phylogenetic analysis based on the RNA-dependent RNA polymerase shows that AGNLV is clustered with other negeviruses and nege-like viruses discovered in aphids, forming a distinct "unclassified clade". Interestingly, AGNLV only encodes three ORFs, whereas AFNLV and WHCV1 have four ORFs. Structure and transmembrane domain predictions show the presence of eight alpha helices and five transmembrane helices in the AGNLV ORF3. Translational enhancement of the AGNLV 5' UTR was similar to that of the 5' UTR of plant viruses. Our findings provide evidence of the diversity and structure of nege-like viruses and are the first record of such a virus from a member of the genus Aphis.

Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles

During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.

A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase

Jingmenviruses are a category of emerging segmented viruses that have garnered global attention in recent years, and are close relatives of the flaviviruses in the Flaviviridae family. One of their genome segments encodes NSP1 homologous to flavivirus NS5. NSP1 comprises both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRP) modules playing essential roles in viral genome replication and capping. Here we solved a 1.8-Å resolution crystal structure of the NSP1 RdRP module from Jingmen tick virus (JMTV), the type species of jingmenviruses. The structure highly resembles flavivirus NS5 RdRP despite a sequence identity less than 30%. NSP1 RdRP enzymatic properties were dissected in a comparative setting with several representative Flaviviridae RdRPs included. Our data indicate that JMTV NSP1 produces characteristic 3-mer abortive products similar to the hepatitis C virus RdRP, and exhibits the highest preference of terminal initiation and shorter-primer usage. Unlike flavivirus NS5, JMTV RdRP may require the MTase for optimal transition from initiation to elongation, as an MTase-less NSP1 construct produced more 4-5-mer intermediate products than the full-length protein. Taken together, this work consolidates the evolutionary relationship between the jingmenvirus group and the Flaviviridae family, providing a basis to the further understanding of their viral replication/transcription process.

The infection kinetics and transmission potential of two Guaico Culex viruses in Culex quinquefasciatus mosquitoes

Guaico Culex virus (GCXV) is a newly identified segmented Jingmenvirus from Culex spp. mosquitoes in Central and South America. The genome of GCXV is composed of four or five single-stranded positive RNA segments. However, the infection kinetics and transmission capability of GCXV in mosquitoes remain unknown. In this study, we used reverse genetics to rescue two GCXVs (4S and 5S) that contained four and five RNA segments, respectively, in C6/36 ​cells. Further in vitro characterization revealed that the two GCXVs exhibited comparable replication kinetics, protein expression and viral titers. Importantly, GCXV RNAs were detected in the bodies, salivary glands, midguts and ovaries of Culex quinquefasciatus at 4-10 days after oral infection. In addition, two GCXVs can colonize Cx. quinquefasciatus eggs, resulting in positive rates of 15%-35% for the second gonotrophic cycle. In conclusion, our results demonstrated that GCXVs with four or five RNA segments can be detected in Cx. quinquefasciatus eggs during the first and second gonotrophic cycles after oral infection.

Orthoflavivirus Lammi in Russia: Possible Transovarial Transmission and Trans-Stadial Survival in Aedes cinereus (Diptera, Culicidae)

In the last few years, there has been a dramatic increase in the number of discovered viruses that are transmitted by arthropods. Some of them are pathogenic for humans and mammals, and the pathogenic potential of others is unknown. The genus Orthoflavivirus belongs to the family Flaviviridae and includes arboviruses that cause severe human diseases with damage to the central nervous system and hemorrhagic fevers, as well as viruses with unknown vectors and viruses specific only to insects. The latter group includes Lammi virus, first isolated from a mosquito pool in Finland. It is known that Lammi virus successfully replicates in mosquito cell lines but not in mammalian cell cultures or mice. Lammi virus reduces the reproduction of West Nile virus during superinfection and thus has the potential to reduce the spread of West Nile virus in areas where Lammi virus is already circulating. In this work, we isolated Lammi virus from a pool of adult Aedes cinereus mosquitoes that hatched from larvae/pupae collected in Saint Petersburg, Russia. This fact may indicate transovarial transmission and trans-stadial survival of the virus.

Mechanisms of Yellow Fever Transmission: Gleaning the Overlooked Records of Importance and Identifying Problems, Puzzles, Serious Issues, Surprises and Research Questions

In viral disease research, few diseases can compete with yellow fever for the volume of literature, historical significance, richness of the topics and the amount of strong interest among both scientists and laypersons. While the major foci of viral disease research shifted to other more pressing new diseases in recent decades, many critically important basic tasks still remain unfinished for yellow fever. Some of the examples include the mechanisms of transmission, the process leading to outbreak occurrence, environmental factors, dispersal, and viral persistence in nature. In this review, these subjects are analyzed in depth, based on information not only in old but in modern literatures, to fill in blanks and to update the current understanding on these topics. As a result, many valuable facts, ideas, and other types of information that complement the present knowledge were discovered. Very serious questions about the validity of the arbovirus concept and some research practices were also identified. The characteristics of YFV and its pattern of transmission that make this virus unique among viruses transmitted by Ae. aegypti were also explored. Another emphasis was identification of research questions. The discovery of a few historical surprises was an unexpected benefit.

Characterisation of putative novel tick viruses and zoonotic risk prediction

Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.

Viromes of Tabanids from Russia

Advances in sequencing technologies and bioinformatics have greatly enhanced our knowledge of virus biodiversity. Currently, the viromes of hematophagous invertebrates, such as mosquitoes and ixodid ticks, are being actively studied. Tabanidae (Diptera) are a widespread family, with members mostly known for their persistent hematophagous behavior. They transmit viral, bacterial, and other pathogens, both biologically and mechanically. However, tabanid viromes remain severely understudied. In this study, we used high-throughput sequencing to describe the viromes of several species in the Hybomitra, Tabanus, Chrysops, and Haematopota genera, which were collected in two distant parts of Russia: the Primorye Territory and Ryazan Region. We assembled fourteen full coding genomes of novel viruses, four partial coding genomes, as well as several fragmented viral sequences, which presumably belong to another twelve new viruses. All the discovered viruses were tested for their ability to replicate in mammalian porcine embryo kidney (PEK), tick HAE/CTVM8, and mosquito C6/36 cell lines. In total, 16 viruses were detected in at least one cell culture after three passages (for PEK and C6/36) or 3 weeks of persistence in HAE/CTVM8. However, in the majority of cases, qPCR showed a decline in virus load over time.

Structural and functional basis of low-affinity SAM/SAH-binding in the conserved MTase of the multi-segmented Alongshan virus distantly related to canonical unsegmented flaviviruses

Alongshan virus (ALSV), a newly discovered member of unclassified Flaviviridae family, is able to infect humans. ALSV has a multi-segmented genome organization and is evolutionarily distant from canonical mono-segmented flaviviruses. The virus-encoded methyltransferase (MTase) plays an important role in viral replication. Here we show that ALSV MTase readily binds S-adenosyl-L-methionine (SAM) and S-adenosyl-L-homocysteine (SAH) but exhibits significantly lower affinities than canonical flaviviral MTases. Structures of ALSV MTase in the free and SAM/SAH-bound forms reveal that the viral enzyme possesses a unique loop-element lining side-wall of the SAM/SAH-binding pocket. While the equivalent loop in flaviviral MTases half-covers SAM/SAH, contributing multiple hydrogen-bond interactions; the pocket-lining loop of ALSV MTase is of short-length and high-flexibility, devoid of any physical contacts with SAM/SAH. Subsequent mutagenesis data further corroborate such structural difference affecting SAM/SAH-binding. Finally, we also report the structure of ALSV MTase bound with sinefungin, an SAM-analogue MTase inhibitor. These data have delineated the basis for the low-affinity interaction between ALSV MTase and SAM/SAH and should inform on antiviral drug design.

Quantitative Polymerase Chain Reaction System for Alongshan Virus Detection

The recently discovered Jingmenvirus group includes viruses with a segmented genome, RNA of a positive polarity, and several proteins with distant homology to the proteins of the members of the genus Orthoflavivirus. Some Jingmenvirus group members, namely the Alongshan virus (ALSV) and Jingmen tick virus, are reported to be tick-borne human pathogens that can cause a wide variety of symptoms. The ALSV is widely distributed in Eurasia, yet no reliable assay that can detect it exists. We describe a qPCR system for ALSV detection. Our data showed that this system can detect as little as 104 copies of the ALSV in a sample. The system showed no amplification of the common tick-borne viruses circulating in Eurasia, i.e., the Yanggou tick virus-which is another Jingmenvirus group member-or some known members of the genus Orthoflavivirus. The qPCR system was tested and had no nonspecific signal for the Ixodes ricinus, I. persulcatus, Dermacentor reticulatus, D. marginatus, Haemaphysalis concinna, and H. japonica ticks. The qPCR system had no nonspecific signal for human and sheep serum as well. Overall, the qPCR system described here can be used for reliable and quantitative ALSV detection.

GB Virus B and Hepatitis C Virus, Distantly Related Hepaciviruses, Share an Entry Factor, Claudin-1

Due to increased and broadened screening efforts, the last decade has seen a rapid expansion in the number of viral species classified into the Hepacivirus genus. Conserved genetic features of hepaciviruses suggest that they have undergone specific adaptation and have evolved to hijack similar host proteins for efficient propagation in the liver. Here, we developed pseudotyped viruses to elucidate the entry factors of GB virus B (GBV-B), the first hepacivirus described in an animal after hepatitis C virus (HCV). GBV-B-pseudotyped viral particles (GBVBpp) were shown to be uniquely sensitive to the sera of tamarins infected with GBV-B, validating their usefulness as a surrogate for GBV-B entry studies. We screened GBVBpp infection of human hepatoma cell lines that were CRISPR/Cas9 engineered to ablate the expression of individual HCV receptors/entry factors and found that claudin-1 is essential for GBV-B infection, indicating the GBV-B and HCV share an entry factor. Our data suggest that claudin-1 facilitates HCV and GBV-B entry through distinct mechanisms since the former requires the first extracellular loop and the latter is reliant on a C-terminal region containing the second extracellular loop. The observation that claudin-1 is an entry factor shared between these two hepaciviruses suggests that the tight junction protein is of fundamental mechanistic importance during cell entry. IMPORTANCE Hepatitis C virus (HCV) is a major public health burden; approximately 58 million individuals have chronic HCV infection and are at risk of developing cirrhosis and liver cancer. To achieve the World Health Organization's target of eliminating hepatitis by 2030, new therapeutics and vaccines are needed. Understanding how HCV enters cells can inform the design of new vaccines and treatments targeting the first stage of infection. However, the HCV cell entry mechanism is complex and has been sparsely described. Studying the entry of related hepaciviruses will increase the knowledge of the molecular mechanisms of the first stages of HCV infection, such as membrane fusion, and inform structure-guided HCV vaccine design; in this work, we have identified a protein, claudin-1, that facilitates the entry of an HCV-related hepacivirus but with a mechanism not described for HCV. Similar work on other hepaciviruses may unveil a commonality of entry factors and, possibly, new mechanisms.

Shotgun Metagenomic Sequencing Reveals Virome Composition of Mosquitoes from a Transition Ecosystem of North-Northeast Brazil

A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex, Haemagogus, and Sabethes from a transition area between the Amazon, Cerrado, and Caatinga biomes in Brazil. Metagenomic high-throughput sequencing was used to characterize the virome of 20 mosquito pools. A total of 15 virus-like genomes were identified, comprising species genomically close to insect-specific viruses of the families Iflaviridae, Metaviridae, Lispiviridae, Rhabdoviridae, Xinmoviridae, and Parvoviridae and species of plant viruses of the families Solemoviridae, Virgaviridae, and Partitiviridae. However, sequences of viruses associated with human and animal diseases were not detected. Most of the recovered genomes were divergent from those previously described. These findings reveal that there are a large number of unknown viruses to be explored in the middle-north of Brazil.

Identification of novel Jingmen tick virus from parasitic ticks fed on a giant panda and goats in Sichuan Province, southwestern China

Introduction

Tick-borne viruses (TBVs) pose a significant risk to the health of humans and other vertebrates. A class of multisegmented flavi-like viruses, Jingmen tick virus (JMTV) was first discovered in Rhipicephalus microplus ticks collected from Jingmen of Hubei Province, China in 2010. JMTV has been confirmed to have a relatively wide distribution in vectors and hosts and is associated with human diseases.

Methods

Parasitic and host-seeking ticks were collected in Wolong Nature Reserve, Sichuan Province. Total RNA was extracted and then enriched the viral RNA. The DNA library was constructed and then were sequenced with MGI High-throughput Sequencing Set (PE150). After the adaptor sequences,low-quality bases and host genome were removed, resulting reads classified as a virus were subsequently de novo assembled into contigs, which were then compared to the NT database. Those annotated under the kingdom virus were initially identified as potential virus-associated sequences. Phylogenetic and Reassortment analysis of sequences were performed using MEGA and SimPlot software, respectively.

Results and discussion

Two host-seeking ticks and 17 ticks that fed on giant pandas and goats were collected. Through high-throughput sequencing, whole virus genomes were attained from four tick samples (PC-13, PC-16, PC-18, and PC-19) that shared 88.7-96.3% similarity with known JMTV. Phylogenetic tree showed that it was a novel JMTV-like virus, referred to as Sichuan tick virus, which also had the signals of reassortment with other JMTV strains, suggesting a cross-species transmission and co-infection of segmented flavi-like viruses among multiple tick hosts.

Conclusion

We discovered and confirmed one new Jingmen tick virus, Sichuan tick virus. Further investigation is required to determine the pathogenicity of Sichuan tick virus to humans and animals, as well as its epidemiological characteristics in nature.

A global dataset of sequence, diversity and biosafety recommendation of arbovirus and arthropod-specific virus

Arthropod-borne virus (arbovirus) and arthropod-specific virus (ASV) are viruses circulating amongst hematophagous arthropods that are broadly transmitted in ecological systems. Arbovirus may replicate in both vertebrates and invertebrates and some are known to be pathogenic to animals or humans. ASV only replicate in invertebrate arthropods yet they are basal to many types of arboviruses. We built a comprehensive dataset of arbovirus and ASV by curating globally available data from the Arbovirus Catalog, the arbovirus list in Section VIII-F of the Biosafety in Microbiological and Biomedical Laboratories 6th edition, Virus Metadata Resource of International Committee on Taxonomy of Viruses, and GenBank. Revealing the diversity, distribution and biosafety recommendation of arbovirus and ASV at a global scale is essential to the understanding of potential interactions, evolution, and risks associated with these viruses. Moreover, the genomic sequences associated with the dataset will enable the investigation of genetic patterns distinguishing the two groups, as well as aid in predicting the vector/host relationships of the newly discovered viruses.

Human pegivirus viremia in HCV/HIV co-infected patients: Direct acting antivirals exert anti-pegivirus effects

BACKGROUND

Human pegivirus (HPgV) is a single-stranded RNA virus​ that is closely related to hepatitis C virus (HCV)​. HPgV has also been shown to infect patients with human immunodeficiency virus (HIV). The mechanisms and disease outcomes of HPgV infections are largely unknown, although it has been implicated in both cancer and neurological diseases. There are no established therapies for HPgV.

OBJECTIVES

To estimate the prevalence of HPgV in a cohort of HCV/HIV co-infected patients undergoing treatment for HCV with direct acting antivirals (DAA) and investigate the effect of DAA therapy on HPgV infection.

STUDY DESIGN

RNA was extracted from plasma samples collected at time points before, during, and after DAA. HPgV RNA abundance was quantified by droplet digital PCR assays targeting the NS5A and 5'UTR domains and confirmed by RT-qPCR. Clinical, demographic and treatment data were analysed.

RESULTS

HPgV RNA was detected and quantified in 26 of 100 patients' plasma (26%) before starting DAA. Patients with detectable HPgV were more likely to be male, had higher peak HIV plasma levels, and a history of injection drug use. Patients receiving sofosbuvir/ledipasvir (n = 9) displayed significantly lower HPgV levels at time of DAA completion and had lower post-DAA HPgV rebound​ levels compared to patients receiving sofosbuvir/velpatasvir (n = 11) although both regimens significantly reduced viremia directly following DAA completion. Sustained suppression of HPgV was ​also observed among patients (n = 2) receiving pegylated-interferon.

CONCLUSIONS

HPgV RNA ​was frequently detected in HCV/HIV co-infected patients and ​was​ supressed by DAA and pegylated interferon therapies with sofosbuvir-ledipasvir showing greatest antiviral activity. These findings suggest potential treatment strategies for HPgV infections​.

Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance

Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.

The Coordinating Research on Emerging Arboviral Threats Encompassing the Neotropics (CREATE-NEO)

Arthropod-borne viruses, such as dengue, Zika and Mayaro, are emerging at an accelerating rate in the neotropics. The Coordinating Research on Emerging Arboviral Threats Encompassing the Neotropics (CREATE-NEO) project, a part of the NIH funded Centers for Research in Emerging Infectious Diseases (CREID) network provides a nimble and flexible network of surveillance sites in Central and South America coupled to cutting-edge modeling approaches in order to anticipate and counter these threats to public health. Collected data and generated models will be utilized to inform and alert local, regional and global public health agencies of enzootic arboviruses with high risk of spillover, emergence and transmission among humans, and/or international spread. Critically, CREATE-NEO builds capacity in situ to anticipate, detect and respond to emerging arboviruses at their point of origin, thereby maximizing the potential to avert full-blown emergence and widespread epidemics.

Conserved Sequences in the 5' and 3' Untranslated Regions of Jingmenvirus Group Representatives

The Jingmenvirus group (JVG), with members such as Jingmen tick virus (JMTV), Alongshan virus (ALSV), Yanggou tick virus (YGTV), and Takachi virus (TAKV), is drawing attention due to evidence of it causing disease in humans and its unique genome architecture. In the current work, complete untranslated regions (UTRs) of four strains of ALSV and eight strains of YGTV were obtained. An analysis of these sequences, as well as JVG sequences from GenBank, uncovered several regions within viral UTRs that were highly conserved for all the segments and viruses. Bioinformatics predictions suggested that the UTRs of all the segments of YGTV, ALSV, and JMTV could form similar RNA structures. The most notable feature of these structures was a stable stem-loop with one (5' UTR) or two (3' UTR) AAGU tetraloops on the end of a hairpin.

First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing

Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.

Syncytial and Congregative Effects of Dengue and Zika Viruses on the Aedes Albopictus Cell Line Differ among the Viral Strains

Objective

Dengue viruses (DENV) and Zika viruses (ZIKV) are transmitted from human to human or from non-human primates to humans by mosquito biting, so the viral interaction with mosquito cells is one key step within the viral life cycle. Therefore, our objective is to know how DENV or ZIKV interacts with mosquito cells.

Methods

Immunofluorescence assay and a direct visualization system are combined to monitor the syncytial or congregative effects of DENVs and ZIKVs on C6/36 cells. we studied the cytopathic effects of DENVs and ZIKVs on the mosquito cells, C6/36 which are widely used in the laboratory for the infections of DENV and ZIKV.

Results

Our results show that all strains of DENV-1 and DENV-2, most DENV-4 and some DENV-3 strains caused syncytial effects on C6/36 cells, while some DENV-3 and DENV-4 strains, and all the tested ZIKV strains caused cell congregation after infection but no cell fusion. In addition, we detected a range of pH environments from 6.0 to 8.0 that support the virus-caused cell fusion and figured out that the optimal pH condition is 7.5 at which the viral production is also the best. Furthermore, viral replication may be required for DENV's syncytial effects on C6/36 cells because the UV-inactivated virus failed to cause cell fusion.

Conclusion

Syncytial and congregative effects of DENV and ZIKV on the Aedes albopictus cells differ among the viral strains. Syncytial effects of DENV on C6/36 are important for viral replication.

Virome diversity of Hyalomma dromedarii ticks collected from camels in the United Arab Emirates

Background and Aim: Viruses are important components of the microbiome of ticks. Ticks are capable of transmitting several serious viral diseases to humans and animals. Hitherto, the composition of viral communities in Hyalomma dromedarii ticks associated with camels in the United Arab Emirates (UAE) remains unexplored. This study aimed to characterize the RNA virome diversity in male and female H. dromedarii ticks collected from camels in Al Ain, UAE. Materials and Methods: We collected ticks, extracted, and sequenced RNA, using Illumina (NovaSeq 6000) and Oxford Nanopore (MinION). Results: From the total generated sequencing reads, 180,559 (~0.35%) and 197,801 (~0.34%) reads were identified as virus-related reads in male and female tick samples, respectively. Taxonomic assignment of the viral sequencing reads was accomplished based on bioinformatic analyses. Further, viral reads were classified into 39 viral families. Poxiviridae, Phycodnaviridae, Phenuiviridae, Mimiviridae, and Polydnaviridae were the most abundant families in the tick viromes. Notably, we assembled the genomes of three RNA viruses, which were placed by phylogenetic analyses in clades that included the Bole tick virus. Conclusion: Overall, this study attempts to elucidate the RNA virome of ticks associated with camels in the UAE and the results obtained from this study improve the knowledge of the diversity of viruses in H. dromedarii ticks. Keywords: camels, Hyalomma dromedarii, nanopore technology, UAE, viral diversity, virome analysis, whole genome sequencing.

Novel Flavi-like virus in ixodid ticks and patients in Russia

Novel Haseki tick virus (HSTV) was detected in ixodid ticks and patients in the Asian part of Russia. Sequencing of the genome fragments corresponding whole polyprotein and viral RdRp demonstrated that HSTV is genetically close to unclassified Flavi-like viruses. Phylogenetic analysis of HSTV sequences showed that these viruses were close to Bole tick virus 4 (BLTV 4), which was detected early in Asia, Europe, Africa and the Caribbean region. The organization of the genome predicts that HSTV and BLTV 4 may also be classified as putative new genera within Flaviviridae with enlarged Flavi-like positive-sense ssRNA viral genomes. Cases of HSTV putative human incidents after Ixodes persulcatus attack were discovered in hospital patients with tick-borne infections in Vladivostok (Russia). The illness was associated with 3-5 days of fever, accompanied by acute respiratory lesions. Mixed human tick-borne infections (TBIs) were also detected for these patients as dual or triple coinfections for tick-borne encephalitis virus, Borrelia spp., Anaplasma spp., and HSTV. Thus, it is necessary to study HSTV antibody tests, virus isolation, and surveillance for HSTV sequences in different species of ticks, different geographical regions and patients after tick attacks.

Virome diversity of ticks feeding on domestic mammals in China

Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 ​G (5.88 ​× ​10⁷) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.

Diversity of RNA viruses of three dominant tick species in North China

Background

A wide range of bacterial pathogens have been identified in ticks, yet the diversity of viruses in ticks is largely unexplored.

Methods

Here, we used metagenomic sequencing to characterize the diverse viromes in three principal tick species associated with pathogens, Haemaphysalis concinna, Dermacentor silvarum, and Ixodes persulcatus, in North China.

Results

A total of 28 RNA viruses were identified and belonged to more than 12 viral families, including single-stranded positive-sense RNA viruses (Flaviviridae, Picornaviridae, Luteoviridae, Solemoviridae, and Tetraviridae), negative-sense RNA viruses (Mononegavirales, Bunyavirales, and others) and double-stranded RNA viruses (Totiviridae and Partitiviridae). Of these, Dermacentor pestivirus-likevirus, Chimay-like rhabdovirus, taiga tick nigecruvirus, and Mukawa virus are presented as novel viral species, while Nuomin virus, Scapularis ixovirus, Sara tick-borne phlebovirus, Tacheng uukuvirus, and Beiji orthonairovirus had been established as human pathogens with undetermined natural circulation and pathogenicity. Other viruses include Norway mononegavirus 1, Jilin partitivirus, tick-borne tetravirus, Pico-like virus, Luteo-like virus 2, Luteo-likevirus 3, Vovk virus, Levivirus, Toti-like virus, and Solemo-like virus as well as others with unknown pathogenicity to humans and wild animals.

Conclusion

In conclusion, extensive virus diversity frequently occurs in Mononegavirales and Bunyavirales among the three tick species. Comparatively, I. persulcatus ticks had been demonstrated as such a kind of host with a significantly higher diversity of viral species than those of H. concinna and D. silvarum ticks. Our analysis supported that ticks are reservoirs for a wide range of viruses and suggested that the discovery and characterization of tick-borne viruses would have implications for viral taxonomy and provide insights into tick-transmitted viral zoonotic diseases.

Skin infectome of patients with a tick bite history

Introduction

Ticks are the most important obligate blood-feeding vectors of human pathogens. With the advance of high-throughput sequencing, more and more bacterial community and virome in tick has been reported, which seems to pose a great threat to people.

Methods

A total of 14 skin specimens collected from tick-bite patients with mild to severe symptoms were analyzed through meta-transcriptomic sequencings.

Results

Four bacteria genera were both detected in the skins and ticks, including Pseudomonas, Acinetobacter, Corynebacterium and Propionibacterium, and three tick-associated viruses, Jingmen tick virus (JMTV), Bole tick virus 4 (BLTV4) and Deer tick mononegavirales-like virus (DTMV) were identified in the skin samples. Except of known pathogens such as pathogenic rickettsia, Coxiella burnetii and JMTV, we suggest Roseomonas cervicalis and BLTV4 as potential new agents amplified in the skins and then disseminated into the blood. As early as 1 day after a tick-bite, these pathogens can transmit to skins and at most four ones can co-infect in skins.

Discussion

Advances in sequencing technologies have revealed that the diversity of tick microbiome and virome goes far beyond our previous understanding. This report not only identifies three new potential pathogens in humans but also shows that the skin barrier is vital in preventing horizontal transmissions of tick-associated bacteria or virus communities to the host. It is the first research on patients' skin infectome after a tick bite and demonstrates that more attention should be paid to the cutaneous response to prevent tick-borne illness.

Molecular detection and genetic characterization of bovine hepacivirus identified in ticks collected from cattle in Harbin, northeastern China

Bovine hepacivirus (BovHepV) is a member of the genus Hepacivirus of the family Flaviviridae, which can cause acute or persistent infections in cattle. Currently, BovHepV strains identified in cattle populations worldwide can be classified into two genotypes with eight subtypes in genotype 1. BovHepV has been identified in a wide geographic area in China. Interestingly, the viral RNA of BovHepV has also been detected in ticks in Guangdong province, China. In this study, Rhipicephalus microplus tick samples were collected in Heilongjiang province, northeastern China, and BovHepV was screened with an overall positive rate of 10.9%. Sequence comparison and phylogenetic analysis showed that the BovHepV strains detected in this study belong to the subtype G. This is the first report about the detection of BovHepV in ticks in Heilongjiang province, China, which expands our knowledge that ticks may be a transmission vector of BovHepV.

Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes

The increasing prevalence and expanding distribution of tick-borne viruses globally have raised health concerns, but the full repertoire of the tick virome has not been assessed. We sequenced the meta-transcriptomes of 31 different tick species in the Ixodidae and Argasidae families from across mainland China, and identified 724 RNA viruses with distinctive virome compositions among genera. A total of 1,801 assembled and complete or nearly complete viral genomes revealed an extensive diversity of genome architectures of tick-associated viruses, highlighting ticks as a reservoir of RNA viruses. We examined the phylogenies of different virus families to investigate virome evolution and found that the most diverse tick-associated viruses are positive-strand RNA virus families that demonstrate more ancient divergence than other arboviruses. Tick-specific viruses are often associated with only a few tick species, whereas virus clades that can infect vertebrates are found in a wider range of tick species. We hypothesize that tick viruses can exhibit both 'specialist' and 'generalist' evolutionary trends. We hope that our virome dataset will enable much-needed research on vertebrate-pathogenic tick-associated viruses.

Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians

The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the timescale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta sowerbii, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the diversity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include amphibians, reptiles, and ray-finned fish. Through co-phylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68 per cent), including a cross-species transmission event between bats and rodents, although long-term virus-host co-divergence was still a regular occurrence (median, 23 per cent). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group, which includes a variety of invertebrate and vertebrate viruses. Combined, these data attest to an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750-800 million years ago.

A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats

BACKGROUND AND METHODS

To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing.

RESULTS

Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified.

CONCLUSIONS

Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.

Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China

BACKGROUND

Ticks act as important vectors of infectious agents, and several emerging tick-borne viruses have recently been identified to be associated with human diseases in northeastern China. However, little is known about the tick virome in northeastern China.

METHODS

Ticks collected from April 2020 to July 2021 were pooled for metagenomic analysis to investigate the virome diversity in northeastern China.

RESULTS

In total, 22 RNA viruses were identified, including four each in the Nairoviridae and Phenuiviridae families, three each in the Flaviviridae, Rhabdoviridae, and Solemoviridae families, two in the Chuviridae family, and one each in the Partitiviridae, Tombusviridae families and an unclassified virus. Of these, eight viruses were of novel species, belonging to the Nairoviridae (Ji'an nairovirus and Yichun nairovirus), Phenuiviridae (Mudanjiang phlebovirus), Rhabdoviridae (Tahe rhabdovirus 1-3), Chuviridae (Yichun mivirus), and Tombusviridae (Yichun tombus-like virus) families, and five members were established human pathogens, including Alongshan virus, tick-borne encephalitis virus, Songling virus, Beiji nairovirus, and Nuomin virus. I. persulcatus ticks had significant higher number of viral species than H. japonica, H. concinna, and D. silvarum ticks. Significant differences in tick viromes were observed among Daxing'an, Xiaoxing'an and Changbai mountains.

CONCLUSIONS

These findings showed an extensive diversity of RNA viruses in ticks in northeastern China, revealing potential public health threats from the emerging tick-borne viruses. Further studies are needed to explain the natural circulation and pathogenicity of these viruses.

Distribution and Characterisation of Tick-Borne Flavi-, Flavi-like, and Phenuiviruses in the Chelyabinsk Region of Russia

In this work, we presented data from a two-year study of flavi-, flavi-like, and phenuiviruses circulation in the population of ixodid ticks in the Chelyabinsk region. We isolated three tick-borne encephalitis virus (TBEV) strains from I. persulcatus, which was not detected in the ticks of the genus Dermacentor. The virus prevalence ranged from 0.66% to 2.28%. The Yanggou tick virus (YGTV) is widespread in steppe and forest-steppe zones and is mainly associated with ticks of the genus Dermacentor. We isolated 26 strains from D. reticulatus, D. marginatus, and I. persulcatus ticks in the HAE/CTVM8 tick cell line. The virus prevalence ranged from 1.58% to 4.18% in D. reticulatus, ranged from 0.78% to 3.93% in D. marginatus, and was 0.66% in I. persulcatus. There was combined focus of TBEV and YGTV in the territory of the Chelyabinsk region. The Alongshan virus (ALSV) was found to be associated with I. persulcatus ticks and is spread in forest zone. We detected 12 amplicons and isolated 7 strains of ALSV in tick cells. The virus prevalence ranged from 1.13% to 6.00%. The phlebovirus Gomselga and unclassified phenuivirus Stavropol were associated with I. persulcatus and D. reticulatus ticks, respectively. Virus prevalence of the unclassified phenuivirus Stavropol in the Chelyabinsk region is lower than that in neighbouring regions.

The Characterization of Three Novel Insect-Specific Viruses Discovered in the Bean Bug, Riptortus pedestris

Insect-specific virus (ISV) is one of the most promising agents for the biological control of insects, which is abundantly distributed in hematophagous insects. However, few ISVs have been reported in Riptortus pedestris (Fabricius), one of the major pests threatening soybeans and causing great losses in yield and quality. In this work, field Riptortus pedestris was collected from six soybean-producing regions in China, and their virome was analyzed with the metatranscriptomic approach. Altogether, seven new insect RNA viruses were identified, three of which had complete RNA-dependent RNA polymerase (RdRp) and nearly full-length genome sequences, which were named Riptortus pedestris alphadrosrha-like virus 1 (RpALv1), Riptortus pedestris alphadrosrha-like virus 2 (RpALv2) and Riptortus pedestris almendra-like virus (RiALv). The three identified novel ISVs belonged to the family Rhabdoviridae, and phylogenetic tree analysis indicated that they were clustered into new distinct clades. Interestingly, the analysis of virus-derived small-interfering RNAs (vsiRNAs) indicated that only RiALv-derived siRNAs exhibited 22 nt length preference, whereas no clear 21 or 22 nt peaks were observed for RpALv1 and RpALv2, suggesting the complexity of siRNA-based antiviral immunity in R. pedestris. In conclusion, this study contributes to a better understanding of the microenvironment in R. pedestris and provides viral information for the development of potential soybean insect-specific biocontrol agents.

Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China

Background

The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China.

Materials and methods

We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships.

Results

In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics.

Conclusion

Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.

Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.

Identification of Jingmen tick virus (JMTV) in Amblyomma testudinarium from Fujian Province, southeastern China

Background

Jingmen tick virus (JMTV) is a newly discovered tick-borne virus that can cause disease in humans. This virus has been authenticated as being extremely widespread worldwide and as posing a significant threat to public health and safety.

Methods

We collected 35 ticks belonging to two tick species from wild boars in Nanping, Fujian Province, China. JMTV-specific genes were amplified by qRT-PCR and nested PCR to confirm the presence of this pathogen.

Results

More than one third of of all ticks collected (11/35) were positive for JMTV. Viral sequences were obtained from three of the JMTV-positive ticks, including the complete genomic sequence from one tick. This was the first time that JMTV was identified in the hard-bodied tick Amblyomma testudinarium. Phylogenetic analysis revealed that JMTV from Fujian Province shared > 90% identity with other isolates derived from China, but was distinct from those reported in France and Cambodia.

Conclusions

JMTV is characterized by relatively low mutations and has its own local adaptive characteristics in different regions. Our findings provide molecular evidence of the presence of JMTV in an overlooked tick species from an area not unrecognized as being endemic. They also suggest that JMTV occupies a wider geographical distribution than currently believed and is a potential disease vector.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05478-2.

Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites

Arthropods harbor a largely undocumented diversity of RNA viruses. Some arthropods, like mosquitoes, can transmit viruses to vertebrates but are themselves parasitized by other arthropod species, such as mites. Very little is known about the viruses of these ectoparasites and how they move through the host-parasite relationship. To address this, we determined the virome of both mosquitoes and the mites that feed on them. The mosquito Aedes communis is an abundant and widely distributed species in Sweden, in northern Europe. These dipterans are commonly parasitized by water mite larvae (Trombidiformes: Mideopsidae) that are hypothesized to impose negative selection pressures on the mosquito by reducing fitness. In turn, viruses are dual-host agents in the mosquito-mite interaction. We determined the RNA virus diversity of mite-free and mite-detached mosquitoes, as well as their parasitic mites, using meta-transcriptomic sequencing. Our results revealed an extensive RNA virus diversity in both mites and mosquitoes, including thirty-seven putative novel RNA viruses that cover a wide taxonomic range. Notably, a high proportion of viruses (20/37) were shared between mites and mosquitoes, while a limited number of viruses were present in a single host. Comparisons of virus composition and abundance suggest potential virus transfer between mosquitoes and mites during their symbiotic interaction. These findings shed light on virome diversity and ecology in the context of arthropod host-parasite-virus relationships.