Publications by authors named "Karyna Rosario"

Circovirids have a circular single-stranded DNA genome packed into a small icosahedral capsid. They are classified within two genera, Circovirus and Cyclovirus, in the family Circoviridae (phylum Cressdnaviricota, class Arfiviricetes, order Cirlivirales). Over the last five years, a number of new circovirids have been identified, and, as a result, 54 new species have been created for their classification based on the previously established species demarcation criterion, namely, that viruses classified into different species share less than 80% genome-wide pairwise sequence identity.

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Turtlegrass virus X, which infects the seagrass , is the only potexvirus known to infect marine flowering plants. We investigated potexvirus distribution in seagrasses using a degenerate reverse transcription polymerase chain reaction (RT-PCR) assay originally designed to capture potexvirus diversity in terrestrial plants. The assay, which implements Potex-5 and Potex-2RC primers, successfully amplified a 584 nt RNA-dependent RNA polymerase (RdRp) fragment from TVX-infected seagrasses.

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Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the CZ ID AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data.

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Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data.

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Article Synopsis
  • Research on aquatic plant viruses is less advanced than that of land plant viruses, prompting a study to identify viruses in freshwater macrophytes, which are large aquatic plants visible to the naked eye.
  • Using next generation sequencing, the study detected 156 viral sequences linked to freshwater macrophytes, indicating a diverse range of viruses and suggesting similarities with viruses found in terrestrial plants.
  • Notably, the study found that some terrestrial plant viruses might also infect underwater plants, highlighting a possible connection between terrestrial and aquatic plant viruses and underscoring the need to explore the virome of aquatic plants for better understanding virus evolution.
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Because parasites have an inextricable relationship with their host, they have the potential to serve as viral reservoirs or facilitate virus host shifts. And yet, little is known about viruses infecting parasitic hosts except for blood-feeding arthropods that are well-known vectors of zoonotic viruses. Herein, we uncovered viruses of flatworms (phylum Platyhelminthes, group Neodermata) that specialize in parasitizing vertebrates and their ancestral free-living relatives.

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Article Synopsis
  • The symbiont-associated (SA) environmental package is an expansion of the MIxS standards created by the Parasite Microbiome Project and the Genomics Standard Consortium, focusing on symbiont-associated microbiota.
  • This package provides a framework for collecting and reporting metadata related to symbionts, such as their life history, interactions with hosts, and the type of relationships they have ranging from mutualism to parasitism.
  • A key feature of the SA package is its ability to allow users to co-localize samples and nest metadata packages, making it easier to report complex sampling designs from various environments.
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Interest in developing food, feed, and other useful products from farmed insects has gained remarkable momentum in the past decade. Crickets are an especially popular group of farmed insects due to their nutritional quality, ease of rearing, and utility. However, production of crickets as an emerging commodity has been severely impacted by entomopathogenic infections, about which we know little.

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  • * A study at Manatee Springs found a dramatic increase in prokaryotic and viral abundance as water moved from the spring to the Suwannee River, with few spring species remaining in the river environment.
  • * The composition of these microbial communities varied by location and season, indicating that environmental factors like flow and water chemistry influence community dynamics, with distinct communities supported by different first-magnitude springs.
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Parasitic flatworms (Neodermata) infect all vertebrates and represent a significant health and economic burden worldwide due to the debilitating diseases they cause. This study sheds light for the first time into the virome of a tapeworm by describing six novel RNA virus candidate species associated with Schistocephalus solidus, including three negative-strand RNA viruses (order Jingchuvirales, Mononegavirales, and Bunyavirales) and three double-stranded RNA viruses. Using in vitro culture of S.

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  • Aquifers are vital underground freshwater sources, and this study focuses on the microbial life in the outflow from five springs in northern Florida, shedding light on communities in the Floridan aquifer, known for its productivity.
  • The research found that the abundance of virus-like particles and prokaryotic cells in these springs was slightly lower compared to other groundwater systems, while molecular sequencing revealed distinct microbial communities shaped by local land usage.
  • The study also identified 58 new viral genomes, highlighting the prevalence of single-stranded DNA viruses in these springs, suggesting a rich biodiversity in these understudied ecosystems that warrants further exploration.
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Spiders (order Araneae, class Arachnida) are an important group of predatory arthropods in terrestrial ecosystems that have been recently identified as an untapped reservoir of single-stranded (ss)DNA viruses. Specifically, spiders harbour a diversity of ssDNA viruses encoding a replication-associated protein (Rep) within a circular genome. However, little is known about the ecology of novel circular Rep-encoding ssDNA (CRESS DNA) viruses.

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Here, we present the complete genome sequences of three circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS DNA) viruses detected in secondary treated and disinfected wastewater effluent. The discovered viruses, named astewater RESS NA irus (WCDV)-1 to -3, represent novel viral species that seem to persist in wastewater effluent.

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While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.

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We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases.

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Article Synopsis
  • Viruses with a replication-associated protein (Rep) in a single-stranded DNA genome are the smallest known viruses affecting eukaryotes, including important crops and livestock.
  • A study identified 44 new CRESS DNA viral genomes in arthropods, covering spiders, insects, and millipedes, revealing substantial diversity beyond what was previously known.
  • Most of these newly identified viruses are distantly related to current CRESS DNA classifications, emphasizing the significant unexplored viral diversity in invertebrates and highlighting similarities in findings from RNA virus research in under-researched organisms.
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  • Phages, which are viruses that infect bacteria, play a vital role in the gut ecosystem, but their full diversity and functions are not well understood.
  • This study focused on the relatively underexplored group of single-stranded DNA (ssDNA) phages in the gut, identifying 258 genomes, primarily from a new subfamily as well as several known phylogenetic groups.
  • Results showed that the gut of the studied marine invertebrate exhibits a unique and diverse community of ssDNA phages, highlighting its potential as a model system for further research on phage roles in animal health.
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Here, we describe four novel circular single-stranded DNA viruses discovered in fungus-farming termites ( sp.). The viruses, named termite-associated circular virus 1 (TaCV-1) through TaCV-4, are most similar to members of the family and were widely detected in African termite mounds.

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Viral metagenomic analysis of heating, ventilation, and air conditioning (HVAC) filters recovered the near-complete genome sequence of a novel virus, named HVAC-associated NA irus 1 (HVAC-RV1). The HVAC-RV1 genome is most similar to those of picorna-like viruses identified in arthropods but encodes a small domain observed only in negative-sense single-stranded RNA viruses.

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The characteristics and risk factors of pigeon paramyxovirus type 1 (PPMV-1) infection in humans are poorly known. We performed virological, pathological, and epidemiological analyses of a Dutch case, and compared the results with those of a US case. Both infections occurred in transplant patients under immunosuppressive therapy and caused fatal respiratory failure.

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Diverse bacterial and fungal communities inhabit human-occupied buildings and circulate in indoor air; however, viral diversity in these man-made environments remains largely unknown. Here we investigated DNA and RNA viruses circulating in the air of 12 university dormitory rooms by analyzing dust accumulated over a one-year period on heating, ventilation, and air conditioning (HVAC) filters. A metagenomic sequencing approach was used to determine the identity and diversity of viral particles extracted from the HVAC filters.

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The genome sequence of the obligate chemolithoautotroph Hydrogenovibrio crunogenus paradoxically predicts a complete oxidative citric acid cycle (CAC). This prediction was tested by multiple approaches including whole cell carbon assimilation to verify obligate autotrophy, phylogenetic analysis of CAC enzyme sequences and enzyme assays. Hydrogenovibrio crunogenus did not assimilate any of the organic compounds provided (acetate, succinate, glucose, yeast extract, tryptone).

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