The virome of bronchoalveolar lavage fluid from patients with fever of unknown origin

Background: Viral metagenomics, a high-throughput sequencing combined with virus sequence-independent amplification by random PCR, allows for unbiased detection of virtually any viruses present in samples. Materials & methods: In order to investigate the virome of bronchoalveolar lavage fluid from patients with fever of unknown origin, 58 samples collected from diseased patients were characterized and compared. Results: Some representatives of Anelloviridae were identified, we found the torque teno virus (TTV) accounts for the majority of virus communities and were more prevalent in the specimens of febrile patients. Phylogenetic analysis suggested that these anellovirus isolates were close to the previous TTV available in GenBank®. Conclusion: All these data indicate that the human anellovirus species TTV may associated with fever of unknown origin.

Sosialisasi Infografis Kesehatan Gigi dan Mulut Pada Masa Pandemi di Kelurahan Sungai Ulin

An understanding of the importance of maintaining dental and oral health in this pandemic era will determine the overall health of the community in order to avoid exposure to the Covid-19 virus. Communities are required to be able to overcome their own dental problems. The use of infographics in print and electronic media is the most effective way to attract people to want to read and understand the contents of the Importance of Maintaining Dental and Oral Health during the Covid-19 Pandemic for the Community South Kalimantan. This socialization is in the form of a series of activities carried out to socialize the importance of maintaining dental and oral health during a pandemic by guiding the infographics in 2 languages, namely Indonesian and Banjarese. This activity was carried out at Sungai Ulin Health Center, Sungai Ulin Village, North Banjarbaru District, Banjarbaru City with limited counseling participants namely 20 people. The results of community service supported by questionnaire data illustrated the importance of effective communication media in conveying information about the importance of maintaining oral health during a pandemic. Infographic socialization about the importance of maintaining dental and oral health during a pandemic was needed to support the level of public knowledge in maintaining dental and oral health. The knowledge provided could be the basis to be realized in the behavior of daily life and in checking the dentist during a pandemic.

Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds

Emerging viral pathogens are a significant concern, with potential consequences for human, animal and environmental health. Over the past several decades, many novel viruses have been found in animals, including birds, and often pose a significant threat to vulnerable species. However, despite enormous interest in virus research, little is known about virus communities (viromes) in Australian Neophema birds. Therefore, this study was designed to characterise the viromes of Neophema birds and track the evolutionary relationships of recently emerging psittacine siadenovirus F (PsSiAdV-F) circulating in the critically endangered, orange-bellied parrot (OBP, Neophema chrysogaster), using a viral metagenomic approach. This study identified 16 viruses belonging to the families Adenoviridae, Circoviridae, Endornaviridae, Picobirnaviridae and Picornaviridae. In addition, this study demonstrated a potential evolutionary relationship of a PsSiAdV-F sequenced previously from the critically endangered OBP. Strikingly, five adenoviral contigs identified in this study show the highest identities with human adenovirus 2 and human mastadenovirus C. This highlights an important and unexpected aspects of the avian virome and warrants further studies dedicated to this subject. Finally, the findings of this study emphasise the importance of testing birds used for trade or in experimental settings for potential pathogens to prevent the spread of infections.

Soil viral communities are structured by pH at local and global scales

Viruses shape microbial community structures, impacting metabolic pathways and influencing biogeochemical cycles. Despite their importance, the influence of biotic and abiotic factors on viral community structures across environmental gradients in soil is relatively unknown compared to their prokaryotic hosts. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil virus communities. In this study, prokaryotic and viral communities were characterized in soils sampled from the extremes of a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations were compared to those in a variety of soil ecosystems ranging in pH (4.0 - 7.5). Prokaryotic and viral community structure were significantly influenced by soil pH at the local scale. Of 1,910 viral operational taxonomic units (vOTUs), 99% were restricted to pH 4.5 or 7.5 soil only. These were compared in gene sharing networks of populations from six other European and North American soil systems. A selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. Results indicate that as with prokaryotes, soil pH is a factor structuring viral communities at the local and global scale.

Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities

High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection – often in the absence of disease symptoms – and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.

Direct and indirect viral associations predict coexistence in wild plant virus communities

Integration of community ecology with disease biology is viewed as a promising avenue for uncovering determinants of pathogen diversity, and for predicting disease risks. Plant-infecting viruses represent a vastly underestimated component of biodiversity with potentially important ecological and evolutionary roles. We performed hierarchal spatial analysis of wild plant populations to characterise the diversity and coexistence structure of within-host virus communities, and their predictors. Our results show that these virus communities are characterised by single infections of few, dominating virus taxa as well as diverse, non-random coinfections. Using a novel graphical modelling framework we demonstrate that after accounting for environmental heterogeneity at the level of both individual host plants and populations, most virus co-occurrence patterns can be attributed to virus-virus associations. Moreover, we show that conditioning variables changed virus association networks especially through their indirect effects. This highlights a previously underestimated mechanism of how human-driven environmental change can influence disease risks.

Analysis of different size fractions provides a more complete perspective of viral diversity in a freshwater embayment

Inspired by recent discoveries of the prevalence of large viruses in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 datasets derived from < 0.45 μm and > 0.45 μm size fractions to compare the diversity of viruses in these fractions. At the level of virus order/family we observed highly diverse and distinct virus communities in the > 0.45 μm size fractions, whereas the < 0.45 μm size fractions were comprised primarily of Caudovirales. The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions with higher relative abundances of cyanophages in the > 0.45 μm size fractions potentially indicating replication within cells during ongoing infections. Many viruses of eukaryotes, such as Mimiviridae, Phycodnaviridae, Iridoviridae and Poxviridae were detected exclusively in the often disregarded > 0.45 μm size fractions. In addition to observing unique virus communities associated with each size fraction from every site we examined, we detected viruses common to both fractions suggesting that these are candidates for further exploration because they could be the product of ongoing or recent lytic events. Most importantly, our observations indicate that analysis of either fraction alone provides only a partial perspective of dsDNA viruses in the environment, highlighting the need for more comprehensive approaches for analyzing virus communities inferred from metagenomic sequencing. IMPORTANCE Most studies of aquatic virus communities analyze DNA sequences derived from the smaller, “free virus” size fraction. Our study demonstrates that analysis of virus communities using only the smaller size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger, > 0.45 μm size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data shows that examining only the smaller size fraction can lead to underestimations of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.

Comparative viral metagenomics from chicken feces and farm dust in the Netherlands

ABSTRACTLivestock animals housed in close proximity to humans can act as sources or intermediate hosts facilitating animal-to-human transmission of zoonotic diseases. Understanding virus diversity in livestock is important for identifying potential zoonotic threats and for ensuring animal health and safe livestock production. Here, we report viral metagenomic characterization of chicken feces (N=51) and paired farm dust samples (N=13) using metagenomic deep sequencing. Samples were collected at 4-5 time points in three broiler farms in the Netherlands. Viruses in the Parvoviridae and Picornaviridae families were the most prevalent, detected in all feces and dust samples and in all feces and 85% of dust samples, respectively. Virus composition found in chicken feces and corresponding dust samples were similar. Great genomic diversity was identified in Picornaviridae and 46 sequences from five picornavirus genera (Sicinivirus, Megrivirus, Anatvirus, Gallivirus and Avisvirus) were detected. For calicivirus, Basovirus and an unclassified novel chicken calicivirus were identified in 13 fecal and 1 dust samples. Two distinct types of chicken astroviruses were identified. Phylogenetic analyses of identified virus sequences from Picornaviridae, Astroviridae and Caliciviridae suggested that viral sequences obtained from different farms are often more closely related to each other than global reference sequences, and sequences from feces and paired dust samples also clustered together. Importantly, our sequencing methodology enabled the recover viral genome sequences from farm dusts, allowing the tracking of virus chatter between livestock animals and their farm environment. This study, albeit relative sample size, does expand current knowledge of virus communities in chickens and surrounding dusts.IMPORTANCEChickens may harbor various zoonotic pathogens, some of which can cause severe clinical outcomes in animals and humans. Farm dust can act as vector to facilitate zoonoses transmission. Here, we report the metagenomic characterization of virus communities of chicken feces and paired farm dust samples collected at multiple time points during the production cycle in broiler farms in the Netherlands. Parvoviridae and Picornaviridae were most frequently detected. We also identified novel astrovirus and calicivirus sequences that would inform future virus taxonomy classification. This is the first study to characterize virus communities in farmed chickens and paired farm dust samples. We also describe a dust sequencing strategy that can be adapted for future dust metagenomic characterization. Our study could help setting up a surveillance baseline for tracking virus flow between chickens and their farm environment which could guide zoonotic outbreak preparedness and health risk assessment of farm exposure.

Comparing the diversity and relative abundance of free and particle-associated aquatic viruses

ABSTRACTMetagenomics has enabled rapid increases in virus discovery, in turn permitting revisions of viral taxonomy and our understanding of the ecology of viruses and their hosts. Inspired by recent discoveries of large viruses prevalent in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before sequencing. We studied assembled contigs derived from < 0.45 μm and > 0.45 μm size fractions that were annotated as viral to determine the diversity and relative abundances of virus groups from each fraction. Virus communities were vastly different when comparing the size fractions, indicating that analysis of either fraction alone would provide only a partial perspective of environmental viruses. At the level of virus order/family we observed highly diverse and distinct virus communities in the > 0.45 μm size fractions, whereas the < 0.45 μm size fractions were comprised primarily of highly diverse Caudovirales. The relative abundances of Caudovirales for which hosts could be inferred varied widely between size fractions with higher relative abundances of cyanophages in the > 0.45 μm size fractions potentially indicating replication within cells during ongoing infections. Many of the Mimiviridae and Phycodnaviridae, and all Iridoviridae and Poxviridae were detected exclusively in the often disregarded > 0.45 μm size fractions. In addition to observing unique virus communities associated with each size fraction, we detected viruses common to both fractions and argue that these are candidates for further exploration because they may be the product of ongoing or recent lytic events.IMPORTANCEMost studies of aquatic virus communities analyze DNA sequences derived from the smaller, “free virus” size fraction. Our study demonstrates that analysis of virus communities using only the smaller size fraction can lead to erroneously low diversity estimates for many of the larger viruses such as Mimiviridae, Phycodnaviridae, Iridoviridae, and Poxviridae, whereas analyzing only the larger, > 0.45 μm size fraction can lead to underestimates of Caudovirales diversity and relative abundance. Similarly, our data shows that examining only the smaller size fraction can lead to underestimation of virophage and cyanophage relative abundances that could, in turn, cause researchers to assume their limited ecological importance. Given the considerable differences we observed in this study, we recommend cautious interpretations of environmental virus community assemblages and dynamics when based on metagenomic data derived from different size fractions.