Virus Family Research Articles

Viral Diversity in Benthic Abyssal Ecosystems: Ecological and Methodological Considerations.

Viruses are the most abundant 'biological entities' in the world's oceans. However, technical and methodological constraints limit our understanding of their diversity, particularly in benthic abyssal ecosystems (>4000 m depth). To verify advantages and limitations of analyzing virome DNA subjected either to random amplification or unamplified, we applied shotgun sequencing-by-synthesis to two sample pairs obtained from benthic abyssal sites located in the North-eastern Atlantic Ocean at ca. 4700 m depth. One amplified DNA sample was also subjected to single-molecule long-read sequencing for comparative purposes. Overall, we identified 24,828 viral Operational Taxonomic Units (vOTUs), belonging to 22 viral families. Viral reads were more abundant in the amplified DNA samples (38.5-49.9%) compared to the unamplified ones (4.4-5.8%), with the latter showing a greater viral diversity and 11-16% of dsDNA viruses almost undetectable in the amplified samples. From a procedural point of view, the viromes obtained by direct sequencing (without amplification step) provided a broader overview of both ss and dsDNA viral diversity. Nevertheless, our results suggest that the contextual use of random amplification of the same sample and long-read technology can improve the assessment of viral assemblages by reducing off-target reads.

Vibrio cyclitrophicus phage encoding gene transfer agent fragment, representing a novel viral family

Vibrio is a prevalent bacterial genus in aquatic environments and exhibits diverse metabolic capabilities, playing a vital role in marine biogeochemical cycles. This study isolated a novel virus infecting Vibrio cyclitrophicus, vB_VviC_ZQ26, from coastal waters near Qingdao, China. The vB_VviC_ZQ26 comprises a linear double-stranded DNA genome with a length of 42,982 bp and a G + C content of 43.21 %, encoding 72 putative open reading frames (ORFs). Transmission electron microscope characterization indicates a siphoviral-morphology of vB_VviC_ZQ26. Nucleic-acids-wide analysis indicates a tetranucleotide frequency deviation for genomic segments encoding putative gene transfer agent protein (GTA) and coil-containing protein, implying divergent origins occurred in different parts of viral genomes. Phylogenetic and genome-content-based analysis suggest that vB_VviC_ZQ26 represents a novel vibriophage-specific family designated as Coheviridae. From the result of biogeographic analysis, Coheviridae is mainly colonized in the temperate and tropical epipelagic zones. This study describes a novel vibriophage infecting V. cyclitrophicus, shedding light on the evolutionary divergence of different parts of the viral genome and its ecological footprint in marine environments.

Prevention of Oncogenic Gammaherpesvirinae (EBV and HHV8) Associated Disease in Solid Organ Transplant Recipients.

Long-term risk for malignancy is higher among solid organ transplant (SOT) recipients compared to the general population. Four non-hepatitis viruses have been recognized as oncogenic in SOT recipients-EBV, cause of EBV-associated lymphoproliferative diseases; human herpes virus 8 (HHV8), cause of Kaposi sarcoma, primary effusion lymphoma and multicentric Castleman disease; human papilloma virus, cause of squamous cell skin cancers, and Merkel cell polyomavirus, cause of Merkel cell carcinoma. Two of these viruses (EBV and HHV8) belong to the human herpes virus family. In this review, we will discuss key aspects regarding the clinical presentation, diagnosis, treatment, and prevention of diseases in SOT recipients associated with the two herpesviruses.

Tumor Tropism of DNA Viruses for Oncolytic Virotherapy.

Oncolytic viruses (OVs) have emerged as one of the most promising cancer immunotherapy agents that selectively target and kill cancer cells while sparing normal cells. OVs are from diverse families of viruses and can possess either a DNA or an RNA genome. These viruses also have either a natural or engineered tropism for cancer cells. Oncolytic DNA viruses have the additional advantage of a stable genome and multiple-transgene insertion capability without compromising infection or replication. Herpes simplex virus 1 (HSV-1), a member of the oncolytic DNA viruses, has been approved for the treatment of cancers. This success with HSV-1 was achievable by introducing multiple genetic modifications within the virus to enhance cancer selectivity and reduce the toxicity to healthy cells. Here, we review the natural characteristics of and genetically engineered changes in selected DNA viruses that enhance the tumor tropism of these oncolytic viruses.

Viral proteins length distributions: A comparative analysis

In this work, we perform a comparative analysis of length distributions of proteins belonging to two virus families, namely Flaviviridae and Coronaviridae. Both families of viruses are highly contagious and represent severe threats to global health systems. To perform the comparative analysis, we retrieved data from the databases Virus Pathogen Database and Analysis Resource (ViPR) and National Center for Biotechnology Information (NCBI). In our investigation, we have considered four distinct Cumulative Distribution Functions (CDFs) of protein length: q-Exponential-CDF and q-Gaussian-CDF, q-Weibull-CDF, and κ-Maxwellian-CDF. Our results show that q-Weibull-CDF is the least appropriate for length distributions among the four CDFs. Also, the q-Exponential, q-Gaussian, and κ-Maxwellian distribution functions fit the cumulative distributions of viral protein lengths with remarkable agreement. Furthermore, our findings suggest that the correlations for viral protein lengths are identical for both species, even though their average lengths differ.

Remote teaching for health academics in the COVID-19 pandemic

During the COVID-19 pandemic, a global shift to remote education has occurred. This study investigated the impact of remote teaching on health students at a public university in Amazonas, Brazil. The participants were students of the Nursing, Medicine and Dentistry courses, submitted to completely remote learning. Data collection was carried out online, followed by statistical analysis. In total, 175 students participated, representing 17.6% from Nursing, 20.6% from Medicine and 19.7% from Dentistry. Most participants were female (68.0%) and entered through the capital's admission system (65.1%). Considering the negative impact of the pandemic, 46.3% of students reported feeling frequently harmed by fully remote teaching. According to the students' perception, most professors were not adequately prepared for distance learning and active educational strategies proved to be ineffective; the lack of motivation among the students themselves was also reported. However, academic tutoring received positive evaluations. In this scenario, 48.0% of students reported a negative impact on academic performance, with concerns about virus transmission and family infections being significant factors. These results underscore the need for further research to understand the true nature of remote learning outcomes and guide future educational practices. It is crucial to adequately prepare professors for distance learning and to develop effective strategies that promote student motivation and improve their academic performance in crisis situations such as the COVID-19 pandemic.

Genetic diversity of RNA viruses infecting invertebrate pests of rice.

Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

Five families of diverse DNA viruses comprehensively restructure the nucleus.

Many viruses have evolved ways to restructure their host cell's nucleus profoundly and unexpectedly upon infection. In particular, DNA viruses that need to commandeer their host's cellular synthetic functions to produce their progeny can induce the condensation and margination of host chromatin during productive infection, a phenomenon known as virus-induced reorganization of cellular chromatin (ROCC). These ROCC-inducing DNA viruses belong to 5 families (herpesviruses, baculoviruses, adenoviruses, parvoviruses, and geminiviruses) that infect a wide range of hosts and are important for human and ecosystem health, as well as for biotechnology. Although the study of virus-induced ROCC is in its infancy, investigations are already raising important questions, such as why only some DNA viruses that replicate their genomes in the nucleus elicit ROCC. Studying the shared and distinct properties of ROCC-inducing viruses will provide valuable insights into viral reorganization of host chromatin that could have implications for future therapies that target the viral life cycle.

To Assess The Knowledge And Perceptions Regarding Novel Coronavirus (Covid-19) During The First Surge Among Healthcare Workers Of Banke District, Nepal

Background: Human Coronaviruses (HCoVs), a large family of single-stranded RNA viruses in humans causes mainly respiratory tract infections. The current outbreak of coronavirus disease 2019 has emerged as pandemic causing severe public health issue of international concern. This study aims to assess the knowledge and perception regarding novel coronavirus (COVID-19) during first wave of pandemic among healthcare workers working at various Health care institutions. Method: This web-based cross-sectional study was conducted among 174 health care workers of Banke district, Nepal between May-July 2020 during first wave of COVID-19 pandemic using an online self-administered questionnaire. A 35-item self-administered survey instrument was developed using WHO course materials on emerging respiratory viruses, including COVID-19, and covered the domains of HCWs characteristics, knowledge, and perceptions of HCWs related to COVID-19. Descriptive statistics were reported as proportion and frequencies. Bivariate analysis was performed using chi-square test to assess the association of level of knowledge, and perception about COVID-19 with participants’ characteristics. A p-value of less than 0.05 was considered statistically significant. All the statistical analysis was performed using IBM SPSS software, version 23. Findings: Most of the participants (94.8%) had known about the virus from news (70.1%) and social media (68.4%). Among them only 36.2% participants had the opportunities to attend lectures, discussions, and training about the virus COVID-19. Overall, 55.7%, and 52.9% of the HCWs had adequate knowledge, and positive perception about COVID-19, respectively. Bivariate analysis showed no significant association of knowledge regarding COVID-19 among health care worker with participants characteristics whereas, the variables such as gender, occupation, working department showed significant association of perception regarding COVID-19 among health care worker. Conclusion: This study revealed lower level of knowledge and positive perception regarding COVID-19 and infection control measures among HCWs. There is a need of adequate training to enhance the knowledge and perception about covid-19 and safety measures to the HCWs.

Molecular characterization of a novel benyvirus infecting wheat in China.

In this study, a novel positive single-stranded RNA (+ ssRNA) virus named wheat yellow stripe associated virus (WYSAV) was identified in wheat plants in China. Molecular characterization revealed that the complete genome of WYSAV is divided into two segments, RNA1 and RNA2, which are 6,460 and 4,935 nucleotides (nt) in length, excluding their respective poly(A) tails. RNA1 contains one large opening reading frame (ORF), encoding a replication-associated protein. RNA2 contains six ORFs, encoding a coat protein (CP), a coat protein readthrough domain protein (CP-RTD), triple gene block protein 1 (TGB1), triple gene block protein 2 (TGB2), triple gene block protein 3 (TGB3), and a cysteine-rich protein (CRP). Phylogenetic analysis showed that WYSAV is related to members of the genus Benyvirus in the family Benyviridae. Thus, WYSAV is proposed to be a new member of the genus Benyvirus. Wheat (Triticum aestivum L.) is one of the most important food crops and ranked third in the world in terms of production, only behind rice and maize [1]. During its growth cycle, wheat faces several biotic and abiotic stresses. Wheat soil-borne virus disease is an important disease that is difficult to control and causes severe yield loss in China each year [2]. The main pathogens causing wheat soil-borne virus disease are Chinese wheat mosaic virus (CWMV) and wheat yellow mosaic virus (WYMV), and their transmission vector is Polymyxa graminis [3-5]. Members of the viral family Benyviridae usually have two to five genomic RNA segments and are transmitted by root-infecting vectors belonging to the family "Plasmodiophoridae". Although few members of the family Benyviridae, of which beet necrotic yellow vein virus is the type member, have been identified [6], several recently identified viruses have been found to be phylogenetically related to benyviruses but are not classified as members of the family Benyviridae. These "unclassified benyviruses" include red clover RNA virus 1, Arceuthobium sichuanense virus 3, Dactylorhiza hatagirea beny-like virus, goji berry chlorosis virus [7], Guiyang benyvirus 1, Guiyang benyvirus 2, Mangifera indica latent virus [8], Rhizoctonia solani beny-like virus 1 [9], Sanya benyvirus 1 [10], and Sclerotium rolfsii beny-like virus 1 [11].In this study, we identified a novel + ssRNA virus in symptomatic leaf samples collected from cultivated wheat in the city of Zhumadian, Henan Province, China. We propose to name this virus "wheat yellow stripe associated virus" (WYSAV), and we have deposited its full-length sequence in the GenBank database under the accession numbers OQ547804 (RNA1) and OQ547805 (RNA2).

Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses.

Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.

Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems

The global decline in biodiversity driven by anthropogenic factors necessitates biomonitoring of ecosystems. However, current approaches are limited to targeted detection of taxa and fail to capture the total biodiversity of ecosystems. We postulated that extracellular environmental DNA (eDNA) represents a genetic repertoire of all the life forms in an ecosystem, which can be retrieved by deep sequencing. The feasibility and effectiveness of this approach were tested through a spatiotemporal study in Chilika Lagoon, a large and biodiverse Ramsar wetland ecosystem in India. Extracellular eDNA was enriched from large-volume filtered water samples using lysis-free methods and over 10.96 billion extracellular eDNA fragments were sequenced from 16 PCR-free shotgun sequencing libraries. The taxonomic classification results show that organisms from all the domains of life, including the low-abundant non-microbial taxa, can be detected with high sensitivity for taxonomic families with representative genomes. Interestingly, despite Bacteria representing a large proportion (87%) of the taxonomically classified reads, Eukaryotes showed the highest taxonomic diversity (73%). Further, using incidence-based asymptotic richness analysis, the total taxonomic diversity of Chilika was estimated to be 1071 families across the tree of life, comprising approximately 799 families of Eukaryotes, 230 families of Bacteria, 27 families of Archaea, and 13 families of DNA Viruses. We also quantified the compositional changes using Bray-Curtis dissimilarity and showed that extracellular eDNA can resolve the broad-scale spatiotemporal variation of biodiversity across the tree of life. These results demonstrate that PCR-free deep sequencing of extracellular eDNA is an effective approach for taxonomic diversity assessment across the tree of life in large ecosystems. With the increasing genomic resources and decreasing sequencing costs, we foresee its widespread application to monitor future biodiversity loss and support conservation, restoration, and management efforts in the Anthropocene.

Molecular and Cellular Mechanisms Underlying Neurologic Manifestations of Mosquito-Borne Flavivirus Infections.

Flaviviruses are a family of enveloped viruses with a positive-sense RNA genome, transmitted by arthropod vectors. These viruses are known for their broad cellular tropism leading to infection of multiple body systems, which can include the central nervous system. Neurologic effects of flavivirus infection can arise during both acute and post-acute infectious periods; however, the molecular and cellular mechanisms underlying post-acute sequelae are not fully understood. Here, we review recent studies that have examined molecular and cellular mechanisms that may contribute to neurologic sequelae following infection with the West Nile virus, Japanese encephalitis virus, Zika virus, dengue virus, and St. Louis encephalitis virus. Neuronal death, either from direct infection or due to the resultant inflammatory response, is a common mechanism by which flavivirus infection can lead to neurologic impairment. Other types of cellular damage, such as oxidative stress and DNA damage, appear to be more specific to certain viruses. This article aims to highlight mechanisms of cellular damage that are common across several flavivirus members and mechanisms that are more unique to specific members. Our goal is to inspire further research to improve understanding of this area in the hope of identifying treatment options for flavivirus-associated neurologic changes.

On the Molecular Structure of Remdesivir Compound Applied for the Treatment of Corona Virus

Coronavirus is a family of viruses that cause upper respiratory infections in humans. Drug properties can be obtained by studying the molecular structure of corresponding drugs. The calculation of the topological index of a drug structure enables scientists to have a better understanding of the physical chemistry and biological characteristics of drugs. In this paper, we study topological indices and find the exact formulas for general topological indices and By the appropriate choice of parameters γ and η, several new/old inequalities that reveal topological indices are obtained.

Evidence for Dicot Plants as Alternative Hosts of Banana Bunchy Top Virus and Its Alphasatellites in South-East Asia.

Banana bunchy top virus is a multicomponent circular ssDNA virus (family Nanoviridae) that causes one of the most devastating diseases of cultivated bananas and plantains (family Musaceae). It is transmitted by the aphids Pentalonia nigronervosa and P. caladii among host plants of Musaceae and some other families of monocots. Our Illumina sequencing reconstruction of virome components of BBTV-infected banana plants and their neighbor non-banana plants sampled in Vietnam and Laos revealed the monocot Commelina sp. (Commelinaceae) and the dicots Bidens pilosa and Chromolaena odorata (both Asteraceae) as hosts of BBTV and circular ssDNA alphasatellites (family Alphasatellitidae). Counting the proportions and relative abundances of Illumina reads representing BBTV genome components and alphasatellites suggested that Chromolaena and Commelina are poor hosts for BBTV and one to three alphasatellite species, whereas Bidens is a permissive host for BBTV and four alphasatellite species representing two genera of Alphasatellitidae. Our findings provide evidence for the dicot plants of family Asteraceae as alternative hosts of BBTV and its alphasatellites, which warrants further investigation of these and other dicots as a potential refuge and source of BBTV and multiple alphasatellites that become associated with this virus and likely affect its replication, transmission, and host range.

Wastewater sequencing reveals community and variant dynamics of the collective human virome

Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.

Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.

We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.

Physicochemical and sequence determinants of antiviral peptides.

Antiviral peptides (AVPs) open new possibilities as an effective antiviral therapeutic in the current scenario of evolving drug-resistant viruses. Knowledge about the sequence and structure activity relationship in AVPs is still largely unknown. AVPs and antimicrobial peptides (AMPs) share several common features but as they target different life forms (living organisms and viruses), exploring the differential sequence features may facilitate in designing specific AVPs. The current work developed accurate prediction models for discriminating (a) AVPs from AMPs, (b) Coronaviridae AVPs from other virus family specific AVPs and (c) highly active AVPs (HAA) from lowly active AVPs (LAA). Further explainable machine learning methods (using model agnostic global interpretable methods) are utilized for exploring and interpreting the physicochemical spaces of AVPs, Coronaviridae AVPs and highly active AVPs. To further understand the association of physicochemical space distribution with pIC50 values, regression models were developed and analyzed using accumulated local effects and interaction strength analysis. An independent sample t-test is used to filter out the significant compositional differences between the smaller length HAA and longer length HAA groups. AVPs prefer lower charge/length ratio and basic residues in comparison with AMPs. Coronaviridae family-specific AVPs have lower propensities for basic amino acids, charge and preference for aspartic acid. Further there is prevalence for basic residues in lowly active AVPs as compared to highly active AVPs. Sequence order effects captured in terms of average amino acid pair distances proved to be more constructive in deciphering the sequences of AVPs.

ICTV Virus Taxonomy Profile: Xinmoviridae 2023.

Xinmoviridae is a family of viruses with negative-sense RNA genomes of 9-14 kilobases. Xinmovirids typically infect beneficial and pest insects but their host range has not yet been investigated systematically and hence may be broader. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family of Xinmoviridae, which is available at ictv.global/report/xinmoviridae.

Long-Read-Based Genome Assembly Reveals Numerous Endogenous Viral Elements in the Green Algal Bacterivore Cymbomonas tetramitiformis.

The marine tetraflagellate Cymbomonas tetramitiformis has drawn attention as an early diverging green alga that uses a phago-mixotrophic mode of nutrition (i.e., the ability to derive nourishment from both photosynthesis and bacterial prey). The Cymbomonas nuclear genome was sequenced previously, but due to the exclusive use of short-read (Illumina) data, the assembly suffered from missing a large proportion of the genome's repeat regions. For this study, we generated Oxford Nanopore long-read and additional short-read Illumina data and performed a hybrid assembly that significantly improved the total assembly size and contiguity. Numerous endogenous viral elements were identified in the repeat regions of the new assembly. These include the complete genome of a giant Algavirales virus along with many genomes of integrated Polinton-like viruses (PLVs) from two groups: Gezel-like PLVs and a novel group of prasinophyte-specific PLVs. The integrated ∼400 kb genome of the giant Algavirales virus is the first account of the association of the uncultured viral family AG_03 with green algae. The complete PLV genomes from C. tetramitiformis ranged between 15 and 25 kb in length and showed a diverse gene content. In addition, heliorhodopsin gene-containing repeat elements of putative mirusvirus origin were identified. These results illustrate past (and possibly ongoing) multiple alga-virus interactions that accompanied the genome evolution of C. tetramitiformis.