Viral Abundance Research Articles

Isolation of a widespread giant virus implicated in cryptophyte bloom collapse.

Photosynthetic cryptophytes are ubiquitous protists that are major participants in the freshwater phytoplankton bloom at the onset of spring. Mortality due to change in environmental conditions and grazing have been recognized as key factors contributing to bloom collapse. In contrast, the role of viral outbreaks as factors terminating phytoplankton blooms remains unknown from freshwaters. Here, we isolated and characterized a cryptophyte virus contributing to the annual collapse of a natural cryptophyte spring bloom population. This viral isolate is also representative for a clade of abundant giant viruses (phylum Nucleocytoviricota) found in freshwaters all over the world.

Virus production in shallow groundwater at the bank of the Danube River.

Viruses play a crucial role in regulating prokaryotic populations, yet their impact on subsurface environments, specifically groundwater habitats, remains poorly understood. In this study, we employed the virus-dilution approach to measure lytic virus production rates in shallow groundwater located near the city of Vienna (Austria) during the period from July-November 2020. Physico-chemical parameters (pH, electrical conductivity, water temperature, concentration of dissolved oxygen), prokaryotic, and viral abundance, and viral decay rates were monitored as well. Our findings revealed low virus-to-prokaryote ratios varying between 0.9-3.9 throughout the study period and a lack of correlation between prokaryotic and viral abundance in groundwater. Virus production rates varied between 9-12% of viral abundance h-1 in July-August and between 34-36% of viral abundance h-1 in October-November. Seasonal variations in virus production rates were found to be correlated with electrical conductivity, revealing ~3.5 times higher virus production rates during periods with high electrical conductivity and low groundwater recharge in October-November compared to July-August with higher groundwater recharge and lower electrical conductivity. Our data indicate that groundwater recharge disrupts the balance between virus and prokaryotic host communities, resulting in a deficiency of suitable prokaryotic host cells for viral proliferation.

Unveiling microbial worlds: exploring viral metagenomics among waste pickers at Latin America's largest dumpsite.

Waste pickers constitute a marginalized demographic engaged in the collection of refuse, facing considerable occupational hazards that heighten their susceptibility to contract infectious diseases. Moreover, waste pickers contend with societal stigmatization and encounter barriers to accessing healthcare services. To explore the viral profile of waste pickers potentially linked to their occupational environment, we conducted a metagenomic analysis on 120 plasma specimens sampled from individuals employed at the Cidade Estrutural dumpsite in Brasilia city, Brazil. In total, 60 blood donors served as a comparative control group. Specimens were pooled and subjected to Illumina NextSeq 2000 sequencing. Viral abundance among waste pickers revealed the presence of significant pathogens, including HIV, HCV, and Chikungunya, which were not detected in the control group. Additionally, elevated levels of anelloviruses and Human pegivirus-1 were noted, with a comparable incidence in the control group. These findings underscore the utility of metagenomics in identifying clinically relevant viral agents within underserved populations. The implications of this study extend to informing public health policies aimed at surveilling infectious diseases among individuals facing socioeconomic disparities and limited access to healthcare resources.

Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells.

RNA sequencing (RNA-seq) analysis of virus-infected host cells enables researchers to study a wide range of phenomena involving host-virus interactions. This includes genomic analysis of the viral population itself, as well as analysis of the transcriptional dynamics of the virus and host during infection. In this chapter, we provide a guide for researchers interested in performing RNA-seq data analysis of virus-infected host cells or cell lines. We outline several bioinformatic protocols for quantifying viral abundance, assembling viral genomes from mixed samples, and performing differential expression analysis, among other common workflows. These workflows can be used as starting points for researchers aiming to analyze RNA-seq datasets of mixed samples containing both host and viral RNA, such as virus-infected cell lines or clinical samples.

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.

Viral infections in cardiometabolic risk and disease between old acquaintances and new enemies

Atherosclerosis is a chronic disease, characterized by chronic inflammation, endothelial dysfunction, and lipid deposition in the vessel. Although many major, well-identified risk factors for atherosclerosis [e.g., hyperlipidemia, hypertension, type 2 diabetes (T2D), smoking habit, and obesity] explain a lot about the risk, there is a considerable number of patients who develop atherosclerotic damage and undergo adverse events without presenting any of these established modifiable risk factors. This observation has stimulated an urgent need to expand knowledge towards the identification of additional, less established risk factors that may help in the assessment of risk and fill the gap of knowledge in the cardiovascular (CV) setting. Among them, the hypothesis of a possible relationship between viral infectious agents and atherosclerosis has risen since the early 1900s. However, there is still a great deal of debate regarding the onset and progression of CV disease in relation to the roles of the pathogens (as active inducers or bystanders), host genomic counterparts, and environmental triggers, affecting both virus abundance and the composition of viral communities. Accordingly, the aim of this review is to discuss the current state of knowledge on infectious agents in the atherosclerotic process, with particular focus on two environmental-related viruses, as examples of familiar (influenza) and unfamiliar [severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)] disease triggers.

Biocrust succession significantly influences soil virus composition and alpha diversity in a sandy desert

Soil viruses, which are abundant and pivotal in soil ecology, remain understudied regarding composition, alpha diversity, and their association with cyanobacteria across different biocrust successional stages. We collected cyanobacteria crust, lichen crust, moss crust, and mixed crust in the Tengger Desert and evaluated virus and cyanobacteria composition through metagenomics. Phormidium phage MIS-PhV1A, Anabaena phage A-4L, and Shewanella SPP. dominated in all biocrusts. A 75 % positive correlation in the virus-cyanobacteria co-occurrence network was observed. Higher virus richness, abundance, and alpha diversity occurred in later successional stages of biocrust and were highly correlated with cyanobacteria diversity. Our results demonstrate that biocrust succession significantly influences soil virus composition and alpha diversity in a sandy desert.

Lymphoid tissues contribute to plasma viral clonotypes early after antiretroviral therapy interruption in SIV-infected rhesus macaques.

The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood and tissues from secondary lymphoid organs (spleen, mesenteric lymph nodes, and inguinal lymph nodes) and from the colon, ileum, lung, liver, and brain were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX and RNAscope in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy, although plasma viral RNA remained below 22 copies per milliliter. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. CD4+ T cells were the main cell type harboring viral RNA after ATI. Furthermore, T cell zones in lymphoid tissues showed higher viral RNA abundance than B cell zones for most animals. These findings are consistent with lymphoid tissues contributing to the virus present in plasma early after ATI.

A widespread picornavirus affects the hemocytes of the noble pen shell (Pinna nobilis), leading to its immunosuppression.

The widespread mass mortality of the noble pen shell (Pinna nobilis) has occurred in several Mediterranean countries in the past 7 years. Single-stranded RNA viruses affecting immune cells and leading to immune dysfunction have been widely reported in human and animal species. Here, we present data linking P. nobilis mass mortality events (MMEs) to hemocyte picornavirus (PV) infection. This study was performed on specimens from wild and captive populations. We sampled P. nobilis from two regions of Spain [Catalonia (24 animals) and Murcia (four animals)] and one region in Italy [Venice (6 animals)]. Each of them were analyzed using transmission electron microscopy (TEM) to describe the morphology and self-assembly of virions. Illumina sequencing coupled to qPCR was performed to describe the identified virus and part of its genome. In 100% of our samples, ultrastructure revealed the presence of a virus (20 nm diameter) capable of replicating within granulocytes and hyalinocytes, leading to the accumulation of complex vesicles of different dimensions within the cytoplasm. As the PV infection progressed, dead hemocytes, infectious exosomes, and budding of extracellular vesicles were visible, along with endocytic vesicles entering other cells. The THC (total hemocyte count) values observed in both captive (eight animals) (3.5 × 104-1.60 × 105 ml-1 cells) and wild animals (14 samples) (1.90-2.42 × 105 ml-1 cells) were lower than those reported before MMEs. Sequencing of P. nobilis (six animals) hemocyte cDNA libraries revealed the presence of two main sequences of Picornavirales, family Marnaviridae. The highest number of reads belonged to animals that exhibited active replication phases and abundant viral particles from transmission electron microscopy (TEM) observations. These sequences correspond to the genus Sogarnavirus-a picornavirus identified in the marine diatom Chaetoceros tenuissimus (named C. tenuissimus RNA virus type II). Real-time PCR performed on the two most abundant RNA viruses previously identified by in silico analysis revealed positive results only for sequences similar to the C. tenuissimus RNA virus. These results may not conclusively identify picornavirus in noble pen shell hemocytes; therefore, further study is required. Our findings suggest that picornavirus infection likely causes immunosuppression, making individuals prone to opportunistic infections, which is a potential cause for the MMEs observed in the Mediterranean.

Zea mays genotype influences microbial and viral rhizobiome community structure

Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.

Single-cell atlas reveals characteristic changes in intrahepatic HBV-specific leukocytes.

Hepatitis B virus (HBV)-specific CD8+ T cells play a central role in the clearance of virus and HBV-related liver injury. Acute infection with HBV induces a vigorous, multifunctional CD8+ T cell response, whereas chronic one exhibits a weaker response. Our study elucidated HBV-specific T cell responses in terms of viral abundance rather than the timing of infection. We showed that in the premalignant stage, the degree of impaired T cell function was not synchronized with the viral surface antigen, which was attributed the liver's tolerance to the virus. However, after the development of hepatocellular carcinoma, T cell exhaustion was inevitable, and it was marked by the exhaustion of the signature transcription factor TOX.

Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio)

BackgroundMany studies have investigated how nanoplastics (NPs) exposure mediates nerve and intestinal toxicity through a dysregulated brain-gut axis interaction, but there are few studies aimed at alleviating those effects. To determine whether and how vitamin D can impact that toxicity, fish were supplemented with a vitamin D-low diet and vitamin D-high diet.ResultsTransmission electron microscopy (TEM) showed that polystyrene nanoplastics (PS-NPs) accumulated in zebrafish brain and intestine, resulting in brain blood–brain barrier basement membrane damage and the vacuolization of intestinal goblet cells and mitochondria. A high concentration of vitamin D reduced the accumulation of PS-NPs in zebrafish brain tissues by 20% and intestinal tissues by 58.8% and 52.2%, respectively, and alleviated the pathological damage induced by PS-NPs. Adequate vitamin D significantly increased the content of serotonin (5-HT) and reduced the anxiety-like behavior of zebrafish caused by PS-NPs exposure. Virus metagenome showed that PS-NPs exposure affected the composition and abundance of zebrafish intestinal viruses. Differentially expressed viruses in the vitamin D-low and vitamin D-high group affected the secretion of brain neurotransmitters in zebrafish. Virus AF191073 was negatively correlated with neurotransmitter 5-HT, whereas KT319643 was positively correlated with malondialdehyde (MDA) content and the expression of cytochrome 1a1 (cyp1a1) and cytochrome 1b1 (cyp1b1) in the intestine. This suggests that AF191073 and KT319643 may be key viruses that mediate the vitamin D reduction in neurotoxicity and immunotoxicity induced by PS-NPs.ConclusionVitamin D can alleviate neurotoxicity and immunotoxicity induced by PS-NPs exposure by directionally altering the gut virome. These findings highlight the potential of vitamin D to alleviate the brain-gut-virome disorder caused by PS-NPs exposure and suggest potential therapeutic strategies to reduce the risk of NPs toxicity in aquaculture, that is, adding adequate vitamin D to diet.A5myG_s1qHAhSjY9k6V2Q1Video

Biological sources and sinks of dimethylsulfide disentangled by an induced bloom experiment and a numerical model

AbstractDimethylsulfide (DMS) is a climatically active trace gas promoting cloud formation. The biochemical precursor of DMS, dimethylsulfoniopropionate (DMSP), is a phytoplankton metabolite and a source of reduced sulfur for many microbial species. Because of the complex interactions between their many producers and consumers, the dynamics of DMSP and DMS in the ocean are still poorly constrained. In this study we measure particulate DMSP, dissolved DMSP (), and DMS concentrations in seven mesocosms where two consecutive phytoplankton blooms (first, pico‐ and nano‐algae; second, Emiliania huxleyi) were induced by nutrient addition, and we build a mechanistic numerical model to identify the sources and sinks that best account for the observations. The mesocosms were designed as replicates but differ from each other by their E. huxleyi virus abundance due to stochastic differences in initial conditions. The model shows that heterotrophic bacteria cannot be the only consumers of . A fraction of dissolved must be consumed by phytoplankton to avoid excessive accumulation during the first bloom. The induced blooms increase DMS concentration by 220% on average, until an increase in the abundance of DMS‐consuming bacteria brings DMS concentration back to its pre‐bloom value, after 3 weeks of experiment. Therefore phytoplankton blooms can increase DMS emission to the atmosphere, but only during a transient regime of a few weeks. The model also shows that the DMS yield, production and emission are increased when the coccolithophore bloom is terminated by a viral infection, but decreased if the infection occurs several days before the bloom can reach its maximum.

Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2.

The emergence of SARS-CoV-2 and the subsequent pandemic have prompted extensive diagnostic and clinical efforts to mitigate viral spread. However, these strategies have largely overlooked the presence of other respiratory viruses. Acute respiratory diseases in pediatric patients can be caused by a diverse range of viral agents, and metagenomics represents a powerful tool for their characterization. This study aimed to investigate the viral abundance in pediatric patients with acute respiratory symptoms who tested negative for SARS-CoV-2 during the Omicron pandemic wave. To achieve this, viral metagenomics and next-generation sequencing were employed on 96 nasopharyngeal swab samples, which were organized into 12 pools, with each pool consisting of eight individual samples. Metagenomic analysis revealed that the most prevalent viruses associated with acute disease in pediatric patients were respiratory syncytial virus (detected in all pools) and enteroviruses, which are known to cause significant morbidity and mortality in children. Additionally, clinically significant viruses such as mumps orthorubulavirus, human metapneumovirus, influenza A, and a wide array of human herpesviruses (1, 3-7) were identified. These findings highlight the extensive potential of viral metagenomics in identifying viruses other than SARS-CoV-2 that contribute to acute infections in children. Consequently, this methodology should garner clinical attention in terms of differential diagnosis and the development of public policies to address such conditions in the global pediatric population.

Evidence of distinct response of soil viral community to a plant infection and the disease pathobiome

AbstractDespite the abundance and ubiquity of viruses in terrestrial ecosystems, the roles of soil viruses in ecosystem functions and plant diseases remain understudied. Here, we used 42 pairs of bulk soil and rhizosphere samples collected from cotton fields with different Verticillium dahliae infection conditions to investigate the responses of soil viruses to soilborne fungal pathogen infections. We found that V. dahliae infection significantly impacted the characteristics of rhizosphere viral community but not bulk soil community. In addition, our results revealed that unlike current knowledge of the impacts of plant pathogens on soil bacterial and fungal communities, the soil viral community demonstrated a lower viral network vulnerability to infection. Importantly, we provided evidence that soil viruses are a potentially important component of the pathobiome of plant disease which may help pathogen invasion and promote disease symptoms. Our study highlights distinct response of viral community and has implications for future plant disease management and agricultural productivity.

Metagenomic analysis of antibiotic-resistance genes and viruses released from glaciers into downstream habitats

Glaciers serve as effective reservoirs of antibiotic resistance genes (ARGs) and viruses for millions of years. Climate change and anthropogenic activity have accelerated the melting of glaciers, but the patterns of release of ARGs and viruses from melting glaciers into downstream habitats remain unknown. We analyzed 171 metagenomic samples from glaciers and their downstream habitats and found that the abundance and diversity of ARGs were higher in glaciers (polar and plateau glaciers) than downstream habitats (Arctic Ocean, Qinghai Lake, and Yangtze River Basin), with the diversity of viruses having the opposite pattern. Proteobacteria and Actinobacteria were the main potential hosts of ARGs and viruses, and the richness of ARGs carried by the hosts was positively correlated with viral abundance, suggesting that the transmission of viruses in the hosts could disseminate ARGs. Source tracking indicated that >18 % of the ARGs and >25 % of the viruses detected in downstream habitats originated from glaciers, demonstrating that glaciers could be one of the potential sources of ARGs and viruses in downstream habitats. Increased solar radiation and emission of carbon dioxide mainly influenced the release of the ARGs and viruses from glaciers into downstream habitats. This study provides a systematic insight demonstrating the release of ARGs and viruses from the melting glaciers, potentially increasing ecological pressure.

The analysis of HPV integration sites based on nanopore sequencing and the profiling changes along the course of photodynamic therapy

ObjectiveTo detect the HPV genotype and integration sites in patients with high-risk HPV infection at different stages of photodynamic therapy using nanopore technology and to evaluate the treatment effect.MethodsFour patients with HPV infection were selected and subjected to photodynamic therapy, and cervical exfoliated cell was sampled at before treatment, after three courses of treatment and six courses of treatment, their viral abundance and insertion sites were analyzed by nanopore technology, and pathological examinations were performed before and after treatment. In this study, we developed a novel assay that combined viral sequence enrichment and Nanopore sequencing for identification of HPV genotype and integration sites at once. The assay has obvious advantages over qPCR or NGS-based methods, as it has better sensitivity after viral sequences enrichment and can generate long-reads (kb to Mb) for better detection rate of structure variations, moreover, fast turn-around time for real-time viral sequencing and analysis.ResultsThe pathological grade was reduced in all four patients after photodynamic therapy. Virus has been cleared in two cases after treatment, the virus amount reduced after treatment but not completely cleared in one case, and two type viruses were cleared and one type virus persisted after treatment in the last patient with multiple infection. Viral abundance and the number of integration sites were positively correlated. Gene enrichment analysis showed complete viral clearance in 1 patient and 3 patients required follow-up.ConclusionNanopore sequencing can effectively monitor the abundance of HPV viruses and integration sites to show the presence status of viruses, and combined with the results of gene enrichment analysis, the treatment effect can be dynamically assessed.

Prokaryotic Plankton and Viruses in the Waters of the Fram Strait in the Winter Period

New data have been obtained on the distribution of prokaryotic plankton and pelagic viruses in the Fram Strait (the Greenland Sea) during the polar night (late November). Three main types of water masses were present in the study area: surface polar, Atlantic, and transformed Atlantic. The content of mineral biogenic elements increased with depth. The concentration of chlorophyll a had low values (0.07–0.13 mg/m3). The abundance and biomass of prokaryotes varied from 286 000 to 675 000 cells/mL and from 2.7 to 11.7 mg C/m3, respectively. The composition of prokaryotic plankton was dominated by single small cells (more than 97% of the abundance and more than 68% of the biomass). The average cell volume was 0.034–0.096 µm3. The number of viruses varied from 724 000 to 3 920 000 particles/mL, and the biomass varied from 0.040 to 0.216 μg C/m3. Against the background of local maxima in the abundance of prokaryotic plankton in the 0–25 m layer, the highest concentrations of viruses were noted in the surface layer. In the latitudinal distribution (from south to north), an increase in the number of viruses and prokaryotes was revealed. A close relationship between their abundance and biomass with hydrological parameters and phosphate content was established; the role of certain water masses in the vertical distribution of microbes was insignificant. The relatively high abundance of viruses and prokaryotes indicated their significant activity during the polar night.

Effect of wastewater collection and concentration methods on assessment of viral diversity

Monitoring of potentially pathogenic human viruses in wastewater is of crucial importance to understand disease trends in communities, predict potential outbreaks, and boost preparedness and response by public health departments. High throughput metagenomic sequencing opens an opportunity to expand the capabilities of wastewater surveillance. However, there are major bottlenecks in the metagenomic enabled wastewater surveillance, including the complexities in selecting appropriate sampling and concentration/virus enrichment methods as well as in bioinformatic analysis of complex samples with low human virus concentrations. To evaluate the abilities of two commonly used sampling and concentration methods in virus identification, virus communities concentrated with Virus Adsorption-Elution (VIRADEL) and PolyEthylene Glycol (PEG) precipitation were compared for three interceptor sites. Results indicated that more viral reads were obtained by the VIRADEL concentration method, with 2.84 ± 0.57 % viral reads in the sample. For samples concentrated with PEG, the average proportion of viral reads in the sample was 0.63 ± 0.19 %. In all wastewater samples, bacteriophage affiliated with the families Siphoviridae, Myoviridae and Podoviridae were found to be the abundant populations. Comparison against a custom Swiss-Prot human virus database indicated that the relatively abundant human viruses (average proportions in human virus community greater than 1.00 %) in samples concentrated with the VIRADEL method were Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Molluscipoxvirus, Parechovirus, Lymphocryptovirus, and Spumavirus. In samples concentrated with the PEG method, fewer human viruses were found to be relatively abundant. These were Orthopoxvirus, Rhadinovirus, Varicellovirus, Simplexvirus, Molluscipoxvirus, Lymphocryptovirus, and Betacoronavirus. Contigs of Betacoronavirus, which contains severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were identified in VIRADEL and PEG samples. Our study demonstrates the feasibility of using metagenomics in wastewater surveillance as a first screening tool and the need for selecting the appropriate virus concentration methods and optimizing bioinformatic approaches in analyzing metagenomic data of wastewater samples.

Phylogenetic diversity and functional potential of large and cell-associated viruses in the Bay of Bengal.

The BoB, the world's largest bay, is of significant economic importance to surrounding countries, particularly Bangladesh, which heavily relies on its coastal resources. Concurrently, the BoB holds substantial ecological relevance due to the region's high vulnerability to climate change-induced impacts. Yet, our understanding of the BoB's microbiome in relation to marine food web and biogeochemical cycling remains limited. Particularly, there are little or no data on the viral diversity and host association in the BoB. We examined the viral community in two distinct BoB coastal regions to reveal a multitude of viral species interacting with a wide range of microbial hosts, some of which play key roles in coastal biogeochemical cycling or potential pathogens. Furthermore, we demonstrate that the BoB coast harbors a diverse community of large and giant viruses, underscoring the importance of investigating understudied environments to discover novel viral lineages with complex metabolic capacities.