Detection of dicistroviruses RNA in blood of febrile Tanzanian children

Metatranscriptomic identification of novel RNA viruses from raccoon dog (Nyctereutes procyonoides) feces in Japan

The raccoon dog (Nyctereutes procyonoides), classified in the order Carnivora within the family Canidae, is native to East Asia and widely distributed throughout Japan due to its adaptability to various environments. Despite the close relationship between raccoon dogs and other animals, viruses infecting raccoon dogs have not been thoroughly investigated in Japan. In this study, we performed metatranscriptomic analyses using fecal samples collected from latrines of wild raccoon dogs in two locations on mainland Japan. Nearly complete viral genomes were identified, including viruses belonging to the genus Kobuvirus (CaKoV), an unclassified canine sapelovirus within the subfamily Ensavirinae (CaSaV), the Genius Mamastrovirus (CaAstV), unclassified hepe-astro-like virus (bastrovirus-like) (Bast-like V), and an unclassified dicistrovirus (DiciV) within the family Dicistroviridae. Phylogenetic analyses revealed that raccoon dog CaKoV, CaSaV, and CaAstV are related to canine strains but form independent clusters specific to raccoon dogs, suggesting they have evolved within this host population. Bast-like V, detected for the first time in raccoon dogs, showed high sequence identity with viruses previously identified in Chinese shrews. The shared insectivorous nature of these hosts and in silico host range predictions suggest that Bast-like Vs may originate from arthropod viruses. Although DiciV is likely of dietary origin due to its arthropod hosts, the large number of sequence reads detected and the phylogenetic clustering of raccoon dog DiciVs with mammalian DiciVs indicate the need to assess their potential infectivity in mammals and the risk of spillover. These findings suggest that raccoon dogs harbor endemic viruses within the canine population and may act as potential vectors for viruses with unknown infectivity in mammals but with spillover risk.

A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics

Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.

Metagenomic characterization of viruses in the serum of children with newly diagnosed cancer

BACKGROUND AND OBJECTIVES

A large cohort of pediatric patients with various forms of childhood cancer was investigated for the presence of viruses using metagenomics. A total of 476 patient samples, collected between 1989 and 2018, were analyzed, representing various pediatric oncological diagnoses and a control group of non-malignant diagnoses.

STUDY DESIGN

The study was carried out using metagenomic sequencing of serum samples. Viruses were identified and analyzed using bioinformatics methods, followed by Polymerase chain reaction (PCR) confirmation RESULTS: The results indicate that a wide range of viruses can be detected in the bloodstream of children with newly diagnosed cancer. Nine viral genomes were identified: Human Pegivirus (HPgV), Hepatitis C virus, Parechovirus 1, Rhinovirus C, Human papillomavirus 116, Human polyomavirus 10, Parvovirus B19, and different variants of Torque Teno Virus (TTV). In this study, a previously unknown virus was found belonging to the Iflavirdae family in the order Picornavirales. HPGV was significantly more common in patients with leukemia compared to other conditions.

CONCLUSIONS

These results highlight the abundance of systemic virus infections in children, and the value of metagenomic sequencing for hypothesis forming regarding the associations between virus infections and cancer.

The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses

Amphibians are an essential class in the maintenance of global ecosystem equilibrium, but they face serious extinction risks driven by climate change and infectious diseases. Unfortunately, the virus diversity harbored by these creatures has been rarely investigated. By profiling the virus flora residing in different tissues of 100 farmed black-spotted frogs (Rana nigromaculata) using a combination of DNA and RNA viromic methods, we captured 28 high-quality viral sequences covering at least 11 viral families. Most of these sequences were remarkably divergent, adding at least 10 new species and 4 new genera within the families Orthomyxoviridae, Adenoviridae, Nodaviridae, Phenuiviridae, and Picornaviridae. We recovered five orthomyxovirus segments, with three distantly neighboring two Chinese fish-related viruses. The recombination event of frog virus 3 occurred among the frog and turtle strains. The relative abundance and molecular detection revealed different tissue tropisms of these viruses, with the orthomyxovirus and adenoviruses being enteric and probably also neurotropic, but the new astrovirus and picornavirus being hepatophilic. These results expand the spectrum of viruses harbored by anurans, highlighting the necessity to continuously monitor these viruses and to investigate the virus diversity in a broader area with more diverse amphibian species.

Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis

Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats.

Small Molecules Targeting Viral RNA

The majority of antivirals available target viral proteins; however, RNA is emerging as a new and promising antiviral target due to the presence of highly structured RNA in viral genomes fundamental for their replication cycle. Here, we discuss methods for the identification of RNA-targeting compounds, starting from the determination of RNA structures either from purified RNA or in living cells, followed by in silico screening on RNA and phenotypic assays to evaluate viral inhibition. Moreover, we review the small molecules known to target the programmed ribosomal frameshifting element of SARS-CoV-2, the internal ribosomal entry site of different viruses, and RNA elements of HIV.

Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.

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.

An atlas of the blood virome in healthy individuals

Emerging evidence indicates that gut virome plays a role in human health and disease, however, much less is known about the viral communities in blood. Here we conducted a direct metatranscriptomic sequencing of virus-like-particles in blood from 1200 healthy individuals, without prior amplification to avoid potential amplification bias and with a strictly bioinformatic and manual check for candidate viral reads to reduce false-positive matches. We identified 55 different viruses from 36 viral families, including 24 human DNA, RNA and retroviruses in 70% of the studied pools. The study showed that anelloviruses are widely distributed and dominate the blood virome in healthy individuals. Human herpesviruses and pegivirus-1 are commonly prevalent in asymptomatic humans. We identified the prevalence of RNA viruses often causing acute infection, like HEV, HPIV, RSV and HCoV-HKU1, revealing of a transmissible risk of asymptomatic infection. Several viruses possible related to transfusion safety were identified, including human Merkel cell polyomavirus, papillomavirus, parvovirus B19 and herpesvirus 8 in addition to HBV. In addition, phages in Caudovirales and Microviridae, were commonly found in pools of samples with a very low abundance; a few sequences for invertebrate, plant and giant viruses were found in some of individuals; however, the remaining 31 viruses mostly reflect extensive contamination from commercial reagents and the work environments. In conclusion, this study is the first comprehensive investigation of blood virome in healthy individuals by metatranscriptomic sequencing of VLP in China. Further investigation of potential false positives representing a major challenge for the identification of novel viruses in mNGS, will offer a systemic idea and means to reveal true viral infections of human.

Unveiling Mycoviromes Using Fungal Transcriptomes

Viruses infecting fungi are referred to as mycoviruses. Here, we carried out in silico mycovirome studies using public fungal transcriptomes mostly derived from mRNA libraries. We identified 468 virus-associated contigs assigned to 5 orders, 21 families, 26 genera, and 88 species. We assembled 120 viral genomes with diverse RNA and DNA genomes. The phylogenetic tree and genome organization unveiled the possible host origin of mycovirus species and diversity of their genome structures. Most identified mycoviruses originated from fungi; however, some mycoviruses had strong phylogenetic relationships with those from insects and plants. The viral abundance and mutation frequency of mycoviruses were very low; however, the compositions and populations of mycoviruses were very complex. Although coinfection of diverse mycoviruses in the fungi was common in our study, most mycoviromes had a dominant virus species. The compositions and populations of mycoviruses were more complex than we expected. Viromes of Monilinia species revealed that there were strong deviations in the composition of viruses and viral abundance among samples. Viromes of Gigaspora species showed that the chemical strigolactone might promote virus replication and mutations, while symbiosis with endobacteria might suppress virus replication and mutations. This study revealed the diversity and host distribution of mycoviruses.

Viral metagenomics unveiled extensive communications of viruses within giant pandas and their associated organisms in the same ecosystem

Cross-species transmission events were commonplace, with numerous cases of host-switching during the viral evolutionary history, but relatively little evidence for onward transmission in different species living in the same ecosystem. For understanding the communications of viruses in giant pandas (Ailuropoda melanoleuca) and their associated organisms, based on a large size of samples (N = 2305) collected between 2015 and 2020 from giant panda (N = 776) and other four giant panda-associated organisms in the same ecosystem, red pandas (N = 700), stray cats (N = 32), wild rats (N = 42), and mosquitoes (N = 755), viromics was used for the virus identification and subsequent virus traceability. The results showed that a feline panleukopenia virus (FPV) was found in giant pandas with clinical signs of vomiting and mild diarrhea. Meanwhile, the same FPV strain was also prevalent in the healthy red panda (Ailurus fulgens) population. From the viromes of the five different organisms, 250 virus genomes were determined. Our data revealed that besides FPV, other putative pathogenic viruses, such as red panda amdoparvoviruses (RPAVs) and Getah viruses (GETVs) were responsible for previous disease or death of some red pandas. We also demonstrated that a number of viruses were involved in potential interspecies jumping events between giant pandas and their associated species. Collectively, our results shed light on the genetic diversity and relationship of diverse viral pathogens in 'Giant pandas-Associated animals-Arthropods' and report some cases of possible viral host-switching among these host species living in the same ecosystem.

Blood virosphere in febrile Tanzanian children

Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An in-depth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes. Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half of the patients (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.Trial registration: ClinicalTrials.gov identifier: NCT02225769.

A novel dicistrovirus in a captive red squirrel (Sciurus vulgaris)

Dicistroviruses are single-stranded RNA viruses in the family Dicistroviridae. The viruses have mainly been detected in arthropods and are the cause of several devastating diseases in many of these species such as honeybees. Increasingly, dicistroviruses have also been detected in both mammalian and avian species in faeces, blood and liver, but with unconfirmed pathology. Here, we report a novel dicistrovirus detected in the intestinal content of a captive red squirrel with enteritis along with the disease history, pathology and genomic characterisation of the virus. Virus particle morphology resembled those of picornaviruses with a diameter of 28-32 nm but failed to be detected using a mammalian/avian pan viral microarray. Next-generation sequencing confirmed a dicistrovirus having a typical dicistrovirus genome organization, but with the polyprotein 1 being shorter by about 100 amino acids, compared to that of other dicistroviruses. Phylogenetic analysis of ORF1 and ORF2 sequences clustered the virus with two yet unassigned dicistroviruses detected in Gorilla gorilla and a freshwater arthropod and likely to be designated to a new genus. Our data further highlights the ever-growing diversity of dicistroviruses, but the clinical significance of the virus in mammalian species and particularly red squirrels has yet to be established.

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity

The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus.

Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus

Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses.

Next-Generation Sequencing on Insectivorous Bat Guano: An Accurate Tool to Identify Arthropod Viruses of Potential Agricultural Concern

Viruses belonging to the Dicistroviridae family have attracted a great deal of attention from scientists owing to their negative impact on agricultural economics, as well as their recent identification as potential aetiological agents of febrile illness in human patients. On the other hand, some Dicistroviruses are also studied for their potential biopesticide properties. To date, Dicistrovirus characterized in African mainland remain scarce. By using High-Throughput Sequencing technology on insectivorous bat faeces (Hipposideros Caffer) sampled in a cave used by humans to collect bat guano (bat manure) as fertilizer in Zimbabwe, we characterized the full-length sequences of three Dicistrovirus belonging to the Cripavirus and Aparavirus genus: Big Sioux River Virus-Like (BSRV-Like), Acute Bee Paralysis Virus (ABPV), and Aphid Lethal Paralysis Virus (ALPV). Phylogenetic analyses of ORF-1 and ORF-2 genes showed a complex evolutionary history between BSRV and close viruses, as well as for the Aparavirus genus. Herewith, we provide the first evidence of the presence of Dicistrovirus in Zimbabwe and highlight the need to further document the impact of such viruses on crops, as well as in beekeeping activities in Zimbabwe which represent a crucial source of income for Zimbabwean people.