The research, led by Xuan Dong of the Yellow Sea Fisheries Research Institute at the Chinese Academy of Fishery Sciences together with Weifeng Shi of Shanghai Jiao Tong University School of Medicine and a large international team, drew on an unusually rich collection of 403 samples gathered over six years, from 2019 through 2024. Sampling spanned a remarkable geographic range: the seas near the Antarctic Peninsula and the South Shetland Islands, the South Orkney Islands, and South Georgia Island in Western Antarctica, along with the Cosmonauts Sea in Eastern Antarctica. Specimens were collected with the assistance of the crews of the research icebreakers Xuelong and Xuelong 2 and scientific observers working with the Chinese krill fishery, an arrangement that allowed the team to reach remote waters across multiple seasons.

Technically, the study relied on metatranscriptomic sequencing, an approach that captures the total RNA present in a sample rather than targeting a single gene or organism. Because RNA viruses must replicate through RNA intermediates, sequencing the transcriptomes of host tissues and associated microbes simultaneously surfaces viral genomes that would be missed by DNA-based methods. The team screened the resulting data using RdRp-scan, a pipeline built around hidden Markov model profiles that detect the RNA-dependent RNA polymerase, the hallmark enzyme conserved across RNA virus lineages. Candidates passing initial screening were then subjected to increasingly conservative validation criteria, including DIAMOND-based similarity searches, to distinguish genuine viral polymerases from cellular genes or sequencing artifacts. This two-tier strategy, combining a sensitive discovery scan with a stringent confirmation analysis, allowed the researchers to characterize both complete viral genomes and highly fragmented sequences that hint at even more diversity lurking in the data.

The viral inventory that emerged was dominated by positive-sense single-stranded RNA viruses, with 37 representatives, a group that includes many of the most familiar virus families infecting animals and plants. Sixteen double-stranded RNA viruses and five negative-sense single-stranded RNA viruses rounded out the collection. Among the named discoveries were Lawrence virus and Vespucci virus, along with a member of the Picornaviridae, a family that includes poliovirus and foot-and-mouth disease virus among its terrestrial relatives. The sheer proportion of novel agents underscores how little is known about viral life in polar ecosystems, where cold, ice-covered waters and isolated food webs may have fostered long, independent evolutionary histories for their microbial inhabitants.

To understand how these viral communities are organized, the researchers applied alpha and beta diversity analyses, standard ecological tools for measuring within-sample richness and between-sample compositional differences. The alpha diversity comparisons, whether based on RdRp-scan results or the more stringent dataset, showed no statistically significant differences in viral richness or Shannon diversity across host species or sampling locations, with one-way ANOVA yielding p-values above 0.05 in every comparison. In other words, no single host or site carried a categorically richer virome than another. Beta diversity told a different story: the composition of viral communities differed significantly among host species, indicating that host identity, not geography, is the dominant force structuring which viruses live where. The authors note that the influence of geographic location on virome composition warrants further study, particularly given the wide and seasonally variable sampling range.

The most consequential finding, however, came from comparing viral sequences across the Antarctic food web. The team detected near-identical strains of Lawrence virus, sharing 99.35 percent identity in the RNA-dependent RNA polymerase gene, in both Antarctic krill and their predators. Vespucci virus strains found in krill and fish shared 97.70 to 99.08 percent RdRp identity with sequences from the same predators, and a picornavirus showed a similar pattern. The predators in question were the chinstrap penguin, Pygoscelis antarcticus, and the Antarctic fur seal, Arctocephalus gazella, two species that feed heavily on krill and fish in the Southern Ocean. Such high sequence identity between viruses found in prey and their consumers is suggestive of cross-species transmission moving up the food chain, although the authors are careful to frame this as a potential route rather than a proven one.

Antarctic krill, Euphausia superba, sit at the center of this transmission story for good reason. The shrimp-like crustacean is among the most abundant animals on the planet by biomass and forms the dietary backbone for penguins, seals, whales, and countless fish species. Any virus capable of persisting in krill populations has, in principle, a ready-made vehicle for reaching a wide range of vertebrate hosts through predation. The near-identical viral sequences in krill, fish, penguins, and fur seals provide the first genomic evidence that this trophic pathway may carry RNA viruses between distantly related animals in the Southern Ocean, a dynamic that has been hypothesized for other ecosystems but rarely documented in polar waters.

Beyond its ecological implications, the study carries practical weight for biosecurity. Warming temperatures and expanding human activity, from tourism to fisheries to scientific operations, are increasing the movement of people, equipment, and potentially pathogens into and out of the Antarctic. At the same time, shifting sea ice and changing prey distributions may alter contact patterns among wildlife species, creating new opportunities for viral exchange. The authors position their dataset as an essential baseline for assessing these risks, arguing that understanding which viruses currently circulate in Antarctic aquatic animals is a prerequisite for detecting any future incursions or range expansions. The evolutionary adaptability of RNA viruses, whose high mutation rates allow rapid adjustment to new hosts and conditions, makes this baseline all the more urgent to establish.

The work also demonstrates how modern genomic surveillance can be extended to environments where traditional virology has struggled to gain a foothold. Cold-chain logistics, remote fieldwork, and the difficulty of culturing polar pathogens have long limited virus discovery in Antarctica, but metatranscriptomics sidesteps many of these barriers by reading viral genetic material directly from field samples. The detection of 160 distinct RNA-dependent RNA polymerase groups in the broader screening analysis, many of them recurring across multiple libraries, suggests that the 58 fully characterized viruses represent only a portion of the diversity present. As sequencing costs continue to fall and reference databases expand, similar surveys in other polar and deep-sea ecosystems are likely to reveal comparable hidden reservoirs.

For now, the study stands as a reminder that even the planet’s most isolated continent is not virologically empty. Its waters host a diverse and largely novel array of RNA viruses, shaped primarily by the hosts they infect and connected to top predators through the food they eat. Whether any of these agents pose risks to wildlife health, fisheries, or human activity remains an open question, but the answer will depend on the kind of systematic, multi-year surveillance this research exemplifies. With the Southern Ocean changing faster than almost any marine environment on Earth, cataloging its viral inhabitants before the ecosystem shifts further may prove to be one of the most time-sensitive tasks in polar science.

Subject of Research: Diversity and food-web transmission of RNA viruses in Antarctic aquatic animals

Article Title: Underexplored diversity and transmission of RNA viruses in Antarctic aquatic animals

Article References: Dong, X., Zhou, Q., Luo, J., Su, Q., Wang, X., Zhu, J., Fan, G., Zhang, J., Ying, Y., Zhao, Y., Liu, L., Xu, Q., Liu, S., Wang, X., Li, J., Li, C., Yan, Y., Meng, F., Li, X., … Shi, W. (2026). Underexplored diversity and transmission of RNA viruses in Antarctic aquatic animals. Microbiome. https://doi.org/10.1186/s40168-026-02544-0

Image Credits: AI Generated

DOI: 10.1186/s40168-026-02544-0

Keywords: Antarctica, RNA viruses, virome, metatranscriptomics, Antarctic krill, chinstrap penguin, Antarctic fur seal, viral transmission, virus discovery, Southern Ocean, biodiversity, biosecurity

Previous metagenomic surveys of human breast milk had revealed an abundance of viral genetic material, much of it phage DNA, hinting that these viruses might be active participants in the early-life microbiome. But metagenomics alone cannot distinguish between free-floating DNA fragments, prophage genomes quietly embedded in bacterial chromosomes, and fully formed virions capable of infection. Demonstrating the presence of actual phage particles requires a different approach: culturing a susceptible bacterial host and showing that something in the milk sample can lyse it, producing the clear plaques on a bacterial lawn that have been the calling card of phage hunters for more than a century.

That is precisely what the team, led by Steven De Soir of UCLouvain and the Queen Astrid Military Hospital in Brussels, together with colleagues at KU Leuven, the University of Minho, and Monash University, set out to do. Working with breast milk samples collected from a lactating donor under written informed consent, the researchers succeeded in isolating six distinct bacteriophages capable of infecting P. aeruginosa, along with a co-occurring strain of the bacterium itself. The identification of the Pseudomonas isolates was carried out with the support of the microbiology laboratory of the Cliniques universitaires Saint-Luc in Brussels, ensuring that the host bacterium recovered from the milk was unambiguously characterized.

The genomic characterization of the six phages revealed a striking diversity. Four of the isolates proved to be strictly lytic, meaning they replicate inside and destroy their bacterial hosts rather than integrating into the host genome. The remaining two were temperate phages, the kind that can choose between a lytic cycle and a lysogenic lifestyle in which their genome becomes a quiet passenger within the bacterium. Across the six isolates, the genomes spanned multiple genera, indicating that a single sample of human breast milk can harbor phages drawn from several branches of the viral tree of life, all targeting the same bacterial species.

Among the four lytic phages, three showed highly similar host ranges and produced comparable plaque morphologies, suggesting they may be closely related despite being recovered as separate isolates. This kind of redundancy is a familiar feature of phage ecology, where dominant viral lineages can appear repeatedly within a single ecological niche. Whether these three represent genuinely distinct entities or variants of a locally dominant phage is one of the questions the study leaves open for future work, but their coexistence in the same sample underscores how concentrated phage activity against a single host species can be within this body fluid.

Host-range profiling, the standard method for determining which bacteria a given phage can infect and kill, showed that the newly isolated phages display broad activity against P. aeruginosa. Critically, that activity included the co-occurring P. aeruginosa strain recovered from the very same milk sample. This observation is significant because it demonstrates that the phages and their bacterial host were not merely passive co-travelers; the viruses were capable of infecting the bacterium found alongside them, raising the possibility of active phage-host dynamics unfolding within the milk itself.

Perhaps the most intriguing laboratory finding concerns synergy. The researchers observed synergistic interactions between pairs of lytic phages, as well as between lytic phages and one of the temperate isolates. In practical terms, synergy means that combinations of phages can suppress bacterial growth more effectively than the sum of their individual effects, a property that underpins the design of phage cocktails in therapeutic applications. That such interactions should be detectable among phages recovered from breast milk suggests that the viral community in this fluid is not a random assortment but potentially a functionally coordinated ensemble shaped by coevolution with its bacterial targets.

The implications extend in two directions. The first concerns neonatal biology. P. aeruginosa is an opportunistic pathogen of considerable clinical importance, notorious for its antibiotic resistance and its role in hospital-acquired infections, particularly in immunocompromised patients and those with cystic fibrosis. Yet Pseudomonas species are also documented members of the early-life microbiome, and the presence of both the bacterium and its phages in breast milk raises the possibility that infants ingest a miniature predator-prey system with every feed. Such a system could influence which bacterial strains colonize the infant gut, modulate bacterial population sizes, and even shape the developing immune system’s encounter with microbial antigens. The authors note that these findings elicit questions toward phage-host dynamics in human breast milk and highlight implications for neonatal microbial colonization and immune modulation.

The second direction concerns phage therapy and biotechnology. Phages active against P. aeruginosa are of intense interest because of the pathogen’s inclusion on lists of priority antibiotic-resistant bacteria. Discovering that novel, genetically characterized lytic phages with broad host ranges can be recovered from an unexpected and easily accessible human source adds to the growing catalog of candidate therapeutic agents. The Belgian research community involved in this study, including the Laboratory for Molecular and Cellular Technology at the Queen Astrid Military Hospital, has a long-standing track record in phage therapy research, and the isolation methods demonstrated here could inform future searches for phages in other human-associated niches. The work was supported by Innoviris, the Brussels regional research funder, and by the Belgian FRS-FNRS, with fellowship support for early-career researchers.

There are, of course, important caveats. The study reports findings from breast milk of a single lactating woman, so the prevalence of active Pseudomonas phages in breast milk across the broader population remains unknown. It is also not yet clear whether the phages and the bacterium were produced locally within the mammary gland, transported there from elsewhere in the maternal body, or introduced through environmental contact. The entero-mammary pathway, by which maternal gut immune cells and microbes are thought to traffic to the breast, offers one plausible route, but confirming the origin of these phages will require further study. What the work establishes beyond doubt is that functional phage particles targeting a clinically significant pathogen exist in human breast milk, transforming what was once a metagenomic hint into a demonstrable biological reality. As researchers begin to probe the dynamics between these viruses, their bacterial hosts, and the infant recipients of both, breast milk may prove to be one of the most accessible windows into the hidden ecology of the human virome.

Subject of Research: Isolation of active Pseudomonas aeruginosa bacteriophages and their bacterial host from human breast milk

Article Title: Isolation of active Pseudomonas aeruginosa bacteriophages and of their host from human breast milk

Article References: De Soir, S., Sáez Moreno, D., Wagemans, J., Glorieux, A., Lavigne, R., Pirnay, J.-P., Merabishvilli, M., Barr, J. J., Van Bambeke, F., & De Vos, D. (2026). Isolation of active Pseudomonas aeruginosa bacteriophages and of their host from human breast milk. npj Viruses. https://doi.org/10.1038/s44298-026-00235-z

Image Credits: AI Generated

DOI: 10.1038/s44298-026-00235-z

Keywords: bacteriophages, Pseudomonas aeruginosa, human breast milk, virome, neonatal microbiome, phage therapy, lytic phages, temperate phages, host range, phage-host dynamics, microbiome development, antibiotic resistance

The research team collected water samples from three sites along the Haridwar stretch of the river, all chosen for their high levels of human activity: the Daksheshwar Mahadev temple, the famous bathing ghat of Har ki Pauri, and Chandi Devi Ghat along the Eastern Ganga canal road. Samples from all three locations were gathered on the same day, transported at 4 degrees Celsius in sterile centrifuge tubes, and pooled in equal proportions before being stored at minus 20 degrees Celsius. From this pooled sample, the researchers extracted both metagenomic DNA and RNA using commercial kits, verifying quality by gel electrophoresis and spectrophotometry before constructing sequencing libraries.

The laboratory workflow followed established metagenomic protocols. DNA and RNA-derived cDNA were fragmented into roughly 600 base-pair segments using the KAPA HyperPlus kit, end-repaired, A-tailed, and ligated to sequencing adapters. After library amplification with Illumina primers and purification with Ampure beads, the libraries were quantified with a Qubit high-sensitivity assay and sequenced on an Illumina HiSeq 4000 platform. The run produced 22.4 million paired-end sequences of 151 base pairs each, with a GC content of 59 percent and low duplication rates of 4.9 percent for forward reads and 2.5 percent for reverse reads, indicating a robust and technically consistent sequencing depth suitable for downstream analysis.

Bioinformatic processing began with quality assessment using FastQC, followed by trimming and filtering with fastp and Trim Galore. Taxonomic classification was then performed with Kraken 2, a k-mer-based classifier that matches short sequence fragments against a reference database of complete bacterial, archaeal and viral genomes from NCBI RefSeq. Low-abundance taxa represented by fewer than ten reads or less than 0.01 percent of classified reads were excluded to remove likely false positives. Phylogenetic relationships among the identified phages were reconstructed using ETE 3 for visualization and VICTOR, the genome-based virus classification service of the Leibniz Institute DSMZ. The raw sequence data have been deposited in the NCBI Sequence Read Archive under BioProject accession PRJNA1207791.

The results revealed a strikingly diverse viral community. In total, the sample contained 6,543 distinct viral species, from which 549,515 sequence reads were obtained. Seventeen viral phyla were identified, dominated overwhelmingly by Uroviricota, the phylum that encompasses tailed bacteriophages, with 3,575 hits. Negarnaviricota and Pisuviricota followed with 474 and 460 reads respectively, while Artverviricota and Kitrinoviricota contributed 361 and 338. At the class level, Caudoviricetes, the tailed phages, stood out dramatically with 3,575 bacteriophages, far ahead of Revtraviricetes at 360 and Pisoniviricetes at 287. Among classified orders, Crassvirales led with 867 hits and Kirjokansivirales followed with 795, but the single largest category was the unclassified group, containing 1,488 reads, a clear sign that a substantial fraction of the river’s virome remains scientifically undescribed.

At the family level, one group dominated the dataset to a remarkable degree. Casjensviridae accounted for 516,163 generated sequences, dwarfing every other phage family; Rountreeviridae followed with 10,094 sequences, then Peduoviridae with 5,734 and Autographiviridae with 2,614. Kyanoviridae, Herelleviridae, Schitoviridae, Demerecviridae, Mesyanzhinovviridae and Crevaviridae completed the top ten. Among genera, the unclassified category again led with 300,671 sequences, followed by Chivirus with 205,535 and Copernicusvirus with 8,607. At the species level, the Salmonella phage Chivirus iEPS5 was the most abundant organism in the entire sample with 300,245 reads, followed by the Vibrio phage Valbvirus ValB1MD2 at 124,213 reads and the Staphylococcus phage Andhravirus andhra at 68,758. Abundance fell steeply beyond these top few, indicating a strongly skewed phage population structure.

Many of the dominant phages have well-characterized host ranges documented in earlier studies, and their presence in the Ganga carries ecological significance. Chivirus iEPS5 is a flagellatropic Salmonella phage that depends on the counterclockwise-rotating flagellar filament of Salmonella enterica serovar Typhimurium for adsorption and injects its DNA through the filament during infection. ValB1MD2 kills Vibrio alginolyticus, an emerging foodborne pathogen linked to contaminated seafood. Andhravirus andhra, originally classified among the podoviruses, infects Staphylococcus epidermidis, and its proteins Andhra_gp10 and Andhra_gp14 have been shown to inhibit bacterial growth and disintegrate staphylococcal cell walls. Rosenblumvirus CSA13, another Staphylococcus phage, can prevent biofilm formation across multiple environments, marking it as a candidate biocontrol agent.

The phylogenetic analysis added further texture to the picture. Five Pandoravirus species appeared among the 25 most prevalent viral species, making it the most species-rich genus in that set. Chivirus iEPS5, Zhonglingvirus SAP012, Andhravirus andhra and Rosenblumvirus CSA13 all belong to the class Caudoviricetes, with the first two sharing the family Casjensviridae and thus a closer taxonomic relationship. Other caudoviricetes including Elvirus EL, Efquatrovirus LY0322, which infects the drug-resistant bacterium Enterococcus faecalis, the Agrobacterium phage Atu_ph07 and the Pseudomonas phage Psa21 formed related clusters. Psa21 has previously been recognized as a potential biocontrol agent against bacterial canker of kiwifruit, while Atu_ph07 specifically infects Agrobacterium tumefaciens, the plant pathogen responsible for crown gall disease.

The study’s context stretches back more than a century. In 1896, the bacteriologist Ernest Hanbury Hankin reported antibacterial activity in the waters of the Ganga and Yamuna, noting that the activity was filterable and heat-labile and limited the spread of cholera, an observation made decades before the formal discovery of bacteriophages. Today, with an estimated 10 to the power of 31 viruses on Earth, phages are understood as key regulators of microbial populations and environmental processes. The authors note that the Ganga’s phages, each with particular host bacterial species, appear to reduce the potency and lethality of their pathogenic hosts, and that phage genes linked to bacterial virulence and antibiotic resistance underscore the ecological role of phages in shaping microbial dynamics and bacterial evolution in the river.

The findings arrive at a moment when phage therapy is regaining momentum as a response to multidrug-resistant bacteria, since lytic phages can selectively destroy infected bacterial cells and multiply within their hosts, advantages that become critical as antibiotic resistance genes spread through aquatic environments. The authors caution that their approach has limitations: Kraken 2 relies on exact k-mer matches and can therefore miss divergent or erroneous sequences, read-level classification offers limited resolution at the species level in complex metagenomes, and read counts as proxies for abundance are biased toward larger viral genomes that generate more mappable fragments. Even so, the work provides a genomic baseline for the phageome of the upper Ganga, a system never analyzed in this way before, and points toward phage-driven strategies for environmental monitoring, pollution management and the eventual development of bacteriophage-based therapeutic interventions rooted in the river’s own viral diversity.

Subject of Research: Bacteriophage diversity in the Ganga River ecosystem revealed by metagenomic sequencing

Article Title: Analysis of bacteriophage diversity in Ganga river ecosystem: insights from metagenome-based sequencing

Article References: Katara, A., Chand, S., Chaudhry, V., Vishwakarma, S., Dubey, R. C., Chandra, H., Shilbayeh, S. A. R., Khan, S.-U.-D., Vohra, S., Poddar, N. K., & Khan, S. (2026). Analysis of bacteriophage diversity in Ganga river ecosystem: insights from metagenome-based sequencing. International Microbiology. https://doi.org/10.1007/s10123-026-00901-5

Image Credits: AI Generated

DOI: 10.1007/s10123-026-00901-5

Keywords: bacteriophages, metagenomics, Ganga River, virome, Caudoviricetes, Casjensviridae, water microbiology, phage therapy, antibiotic resistance, viral ecology, freshwater ecosystem, Haridwar

The scale of the viral discovery is striking. Across 23 RNA-seq libraries, the researchers identified 416 viral sequences representing related members of 13 virus families, including Metaviridae, Chuviridae, Xinmoviridae, Flaviviridae, and Rhabdoviridae. Notably, the viromes were dominated not by known human pathogens but by insect-specific viruses, or ISVs, a diverse group of viruses that persist in insect populations without apparently infecting vertebrates. These viruses are increasingly recognized as important players in vector biology: some can modulate the ability of mosquitoes to transmit arboviruses by competing for cellular resources or priming the insect immune system. The Colombian data confirm that ISVs form the backbone of the virome in these hematophagous insects, while also revealing that virome structure is not dictated solely by host species identity—a finding that complicates simple assumptions about virus-vector relationships.

That variability is itself a key message of the study. Two insects of the same species collected from different sites, or even different pools from the same area, could carry markedly different viral assemblages. This extensive virome variability suggests that local ecological conditions—habitat type, available hosts, environmental microbes, and perhaps human land use—shape which viruses persist in vector populations. For surveillance programs, the implication is sobering: sampling a single location or season may give a misleading picture of the viral diversity circulating in a region. Continuous, spatially distributed metatranscriptomic monitoring may be required to track how these communities shift over time, particularly as climate change and urbanization alter the distributions of both vectors and their microbes.

Methodologically, the study relied on RNA sequencing of pooled insect specimens, followed by computational assembly and taxonomic classification of the resulting reads. The researchers confirmed host species identity by assembling partial cytochrome c oxidase subunit I (COI) barcode sequences from each metatranscriptome and comparing them against NCBI and BOLD databases, building maximum likelihood phylogenetic trees to verify assignments. Viral contigs were assigned to families by similarity to known relatives, with metrics such as percent identity, alignment coverage, and e-values documented for each assignment. Bacterial taxa were quantified using transcripts per million (TPM) normalization, allowing the team to distinguish transcriptionally active members of the microbiome from dormant or contaminating DNA. This activity-based view is important because it captures which microbes are actually metabolizing inside the insects, not merely which are present.

The bacterial side of the analysis revealed complex, active microbiomes with clear patterns of ecological structure. Wolbachia, the famous intracellular symbiont capable of blocking arbovirus transmission and manipulating host reproduction, was prominently represented in Culex, Coquillettidia, and Aedes albopictus specimens. Its presence in these genera is consistent with its known distribution, but its transcriptional activity in wild Colombian populations underscores its potential relevance for biocontrol strategies, including the deployment of Wolbachia-infected mosquitoes to suppress diseases such as dengue. The detection of the symbiont across multiple genera and habitat types suggests it is a stable feature of the local vector fauna, providing a natural baseline for future interventions.

Perhaps more surprising was the detection of bacterial genera typically associated with humans, including Cutibacterium, Faecalibacterium, Prevotella, Hallela, and Escherichia, at lower abundances in the insect microbiomes. Their presence, the authors suggest, may reflect exposure to human-impacted environments—urban and peri-urban settings where vectors breed in water contaminated with human waste or feed on human hosts. This finding blurs the boundary between the insect microbiome and the microbial ecology of the surrounding human landscape. It also raises practical questions: if vector microbiomes mirror environmental contamination, they could potentially serve as sentinels for monitoring microbial pollution, while simultaneously acting as vehicles through which human-associated bacteria, and the genes they carry, circulate between environments and arthropod hosts.

That last concern becomes concrete in the study’s resistome findings. The researchers identified transcriptionally active antimicrobial resistance genes (ARGs) conferring resistance to several major antibiotic classes, including fluoroquinolones, aminoglycosides, and tetracyclines, along with instances of multidrug resistance associated with efflux pump systems—cellular machinery that pumps diverse toxic compounds out of bacterial cells. Critically, statistical analysis showed that resistome composition differed significantly among insect species (pseudo-F = 1.91, p = 0.028) but not among habitat categories, indicating that the host’s own microbial community structure, rather than simply the collection site, drives which resistance genes are present and expressed. The genes were detected through TPM-normalized transcript counts, meaning they were not just present as DNA but actively being transcribed by living bacteria within the insects.

Even more consequential was the finding that some ARGs were associated with sequences linked to mobile genetic elements, such as plasmids and transposons, which can move between bacteria through horizontal gene transfer. This suggests that the microbiomes of hematophagous insects could function as arenas where resistance genes are exchanged, reshuffled, and potentially passed between environmental bacteria, human-associated pathogens, and symbionts. The authors are careful to frame this as a hypothesis requiring further work: they call for studies incorporating environmental matrices—soil, water, and other samples from the same sites—and functional validation to determine whether these insects genuinely amplify or disseminate antimicrobial resistance, or merely reflect the resistance burden of their surroundings. Still, the mere demonstration that active ARGs circulate in the microbiomes of mosquitoes and sand flies adds a new dimension to antimicrobial resistance surveillance, which has traditionally focused on clinical settings, livestock, and water systems.

The study also contributes to a growing appreciation of endogenous viral elements, sequences of viral origin integrated into host genomes, as part of the picture of vector viromes. By cataloging viral sequences across multiple families and host species, the dataset provides raw material for distinguishing true infectious viruses from genomic fossils and for understanding how insect viruses and their hosts have co-evolved. Combined with the bacterial and resistome data, the work exemplifies the power of metatranscriptomics as a single-lens approach to vector biology: one sequencing workflow yields simultaneous insight into pathogens, symbionts, environmental microbes, and resistance genes, all filtered through the constraint of transcriptional activity.

For Colombia, a country spanning Caribbean coastlines, Andean valleys, and Amazonian rainforest, the findings carry direct implications for public health planning. The confirmation that vector viromes are dominated by insect-specific viruses is reassuring in one sense, but the extensive variability among pools and sites means that pathogen emergence could be difficult to anticipate from limited sampling. The presence of Wolbachia in key vector species offers a foundation for biocontrol programs already proven elsewhere, while the detection of human-associated bacteria and active resistance genes ties vector surveillance to the broader agenda of antimicrobial resistance monitoring. The authors, led by Daniel F. Largo and Harold D. Gomez Rosero with corresponding authors Rafael J. Vivero-Gómez and Claudia Ximena Moreno-Herrera, emphasize that further studies with environmental sampling and functional validation are needed before the full significance of the resistome findings can be assessed. What is already clear, however, is that the microbes inhabiting these disease vectors form a dynamic, interconnected ecosystem—one that reflects the environments humans have built and may, in turn, shape the health risks those environments carry back to us.

Subject of Research: Virome, microbiome, and antimicrobial resistance gene profiles of mosquitoes and sand flies in Colombia

Article Title: Metatranscriptomic insights into mosquitoes and sand flies from Colombia reveal extensive virome variability and detection of bacterial and viral-related resistomes

Article References: Largo, D. F., Gomez Rosero, H. D., Gómez, G. F., Junca, H., Cadavid-Restrepo, G. E., Vivero-Gómez, R. J., & Moreno-Herrera, C. X. (2026). Metatranscriptomic insights into mosquitoes and sand flies from Colombia reveal extensive virome variability and detection of bacterial and viral-related resistomes. Parasites & Vectors. https://doi.org/10.1186/s13071-026-07710-9

Image Credits: AI Generated

DOI: 10.1186/s13071-026-07710-9

Keywords: mosquitoes, sand flies, virome, metatranscriptomics, insect-specific viruses, Wolbachia, antimicrobial resistance, resistome, microbiome, Colombia, RNA-seq, horizontal gene transfer

The study, published in Virology Journal, focused on Culex pipiens sensu lato and Culiseta annulata, two species that dominate the UK mosquito fauna and are considered among the most plausible vectors should arboviruses such as West Nile or Usutu virus establish local transmission cycles. Between 2021 and 2022, the team collected adult mosquitoes across the grounds of the two zoological collections, sites chosen deliberately because zoos concentrate large numbers of animals in outdoor enclosures where mosquitoes feed readily. That combination of abundant vectors, diverse vertebrate hosts and regular human visitors makes zoological collections potential interfaces for virus exchange between mosquitoes, animals and people, and therefore valuable sentinel locations for surveillance.

In total, 4,042 mosquitoes were processed and sequenced across 44 pools. The researchers extracted total nucleic acids and applied a metagenomic sequencing strategy designed to capture both RNA and DNA viruses, allowing them to recover viral genomes without relying on prior assumptions about which viruses might be present. Bioinformatic assembly and taxonomic classification of the resulting reads yielded 26 viral genomes, a striking haul for a country whose mosquito viromes have remained comparatively understudied. Nine of these represented entirely novel species, distributed across both RNA and DNA virus families, underscoring how much basic viral diversity in northern European mosquitoes still awaits description.

A consistent pattern emerged across the sampling sites: several viruses were detected in every pool analysed, indicating substantial overlap in virome composition between the two zoos. This shared core of viruses suggests that certain mosquito-associated viruses are widespread and stable components of the local mosquito fauna rather than isolated curiosities confined to a single habitat. Such ubiquity matters for risk assessment, because a virus that maintains itself efficiently across geographically separated mosquito populations has, by definition, the ecological flexibility that emergence requires, even if most of these viruses ultimately prove harmless to vertebrates.

The headline findings are two novel orthobunyaviruses, named Atherstone virus and Deva virus, belonging to the family Peribunyaviridae. Orthobunyaviruses are a genus with a serious pedigree: it includes recognised human and animal pathogens such as Schmallenberg virus, which devastated European ruminant farming after its emergence in 2011, and Oropouche virus, a growing public health concern in the Americas. The tripartite RNA genomes of orthobunyaviruses encode a viral RNA-dependent RNA polymerase on the large segment, surface glycoproteins on the medium segment, and nucleoprotein plus accessory proteins on the small segment. Finding two previously unknown members of this genus in British mosquitoes immediately elevates them to candidates for closer scrutiny.

Not all orthobunyaviruses pose equal risk, and the study went beyond simple detection to ask which of the two new viruses resembles a genuine arbovirus, capable of replicating in both mosquitoes and vertebrate hosts. The team employed MosViR, a machine-learning classification tool trained on known mosquito viruses to predict whether a given virus is likely to be mosquito-restricted or arthropod-borne. For Atherstone virus, detected at both zoos, the prediction pointed towards arbovirus status, a result that alone would justify follow-up. More compelling still was the genomic evidence: Atherstone virus carries an open reading frame encoding a non-structural protein S, or NSs, a well-characterised virulence factor in orthobunyaviruses that antagonises host antiviral responses, including the interferon system, and is a hallmark of pathogenic members of the genus.

Deva virus tells a different story. Its small segment lacks an NSs open reading frame altogether, and MosViR did not predict it to be an arbovirus. The absence of NSs, combined with the absence of a vertebrate-infecting signature, is consistent with Deva virus being an insect-specific virus, locked into replication within mosquito cells and their close relatives. Insect-specific viruses of this kind are increasingly recognised as common and sometimes abundant residents of mosquito viromes. Although they do not infect vertebrates directly, they are far from biologically irrelevant: they can modulate mosquito immunity, compete with arboviruses for cellular resources, and in some cases reduce the ability of mosquitoes to transmit pathogenic viruses, making them subjects of interest both for basic virology and for potential interference-based control strategies.

The broader viral inventory recovered in the study reinforces this picture of a layered virome. Alongside the orthobunyaviruses, the sequencing identified viruses spanning multiple families, including flavivirus-like and other RNA virus groups as well as DNA viruses, with several classified as novel species. Distinguishing arboviruses from insect-specific viruses is one of the central analytical challenges in mosquito metagenomics, because both can be present in the same sample and their genomes can be difficult to interpret from sequence data alone. Tools such as MosViR, combined with comparative genomics against reference databases and catalogues of known arboviruses, provide a probabilistic framework for triage, flagging which discoveries warrant experimental characterisation in cell culture and vertebrate systems and which can be provisionally set aside as likely insect-restricted.

Why does this matter for the United Kingdom specifically? The country sits at the northern edge of the range of many mosquito species, and climate warming, changes in land use and the movement of animals and goods are all expected to alter the dynamics of mosquito-borne disease in temperate Europe. Usutu virus has already established itself in British birds and mosquitoes, and West Nile virus circulates periodically in neighbouring countries. Risk frameworks built around these known threats are essential, but the new study argues that they should be complemented by surveillance for the unknown: viruses already resident in local vectors whose properties have never been tested. A virus that today appears to be insect-specific could, through reassortment with a related pathogen or through evolutionary change, acquire new capabilities. Orthobunyaviruses are particularly notable in this respect because their segmented genomes can reassort when mosquitoes are co-infected with related viruses, generating novel combinations with unpredictable host ranges.

The authors are careful not to overstate the immediate danger. Detection of a viral genome in a mosquito does not demonstrate that the virus infects or harms vertebrates, and neither Atherstone nor Deva virus has been shown to cause disease. What the study provides is a prioritised list of candidates and a demonstration of method: that large-scale metagenomic surveillance of UK mosquitoes is feasible, productive and capable of revealing both the diversity of local viromes and the specific viruses that merit laboratory follow-up. Isolation of Atherstone virus, characterisation of its host range, and serological surveys of animals and humans near the sampling sites would be the logical next steps. In the meantime, the work adds the United Kingdom to the growing map of regions where the viruses closest to home, rather than those arriving from abroad, are proving to be the first order of business for emerging infection surveillance.

Subject of Research: Metagenomic surveillance of mosquito viromes at two UK zoos reveals novel mosquito-associated orthobunyaviruses

Article Title: Emergence risks from within? Metagenomic analysis of mosquito viromes from two zoos reveals mosquito-associated orthobunyaviruses in the UK

Article References: Pilgrim, J., Seechurn, N., Cunningham-Oakes, E., Gillespie, L., Dobbs, P., Lopez, J., Kohl, A., Hughes, G. L., Blagrove, M. S. C., Baylis, M., & Darby, A. C. (2026). Emergence risks from within? Metagenomic analysis of mosquito viromes from two zoos reveals mosquito-associated orthobunyaviruses in the UK. Virology Journal. https://doi.org/10.1186/s12985-026-03305-z

Image Credits: AI Generated

DOI: 10.1186/s12985-026-03305-z

Keywords: orthobunyavirus, mosquito, virome, metagenomics, arbovirus, Culex pipiens, Culiseta annulata, surveillance, zoonotic risk, insect-specific virus, United Kingdom, Peribunyaviridae

The research team, led by Ying Shi of the Shanghai Academy of Agricultural Sciences together with colleagues including Fengwu Zhou of Fudan University and corresponding author Huili Liu, set out to test the conventional view that stray animals necessarily harbor greater viral richness than owned pets. Urbanization reshapes the environments in which companion animals live, and these changes may alter their viromes in ways that matter for zoonotic disease surveillance. Yet the dynamics of the viral microbiome in urban household and stray pets, and the forces that drive the assembly of these viral communities, had remained poorly characterized. Rather than assuming that street life means more viral exposure, the researchers measured it directly.

To do so, the team collected a total of 245 fecal or rectal swabs from household and stray cats and dogs across Shanghai. The laboratory workflow was deliberately comprehensive. Each sample underwent enrichment for virus-like particles, a step that concentrates viral genetic material while filtering out the overwhelming bulk of bacterial and host DNA. The researchers then co-extracted both viral DNA and RNA, recognizing that viruses spanning these two broad genetic classes could differ in their epidemiological relevance. After amplification, the material was sequenced on an Illumina paired-end platform, generating the short-read data from which the viral communities would be reconstructed computationally.

Identifying genuine viral sequences in metagenomic data is a notoriously difficult problem, and the team approached it with redundancy. Viral contigs were identified using four complementary tools: VirSorter2, DeepVirFinder, VirFinder and geNomad. Only sequences passing through this multi-tool gauntlet, and then further validated with the quality-assessment program CheckV, were retained for analysis. The resulting set of viral contigs was classified taxonomically, placed into phylogenetic context, and subjected to standard ecological statistics, including alpha and beta diversity measures, redundancy analysis and network co-occurrence modeling. This combination allowed the researchers to ask not only which viruses were present, but how the communities were structured and what factors best explained their composition.

The sequencing effort yielded 123 vertebrate viral operational taxonomic units, or vOTUs, drawn from virus families that include Coronaviridae, Poxviridae and Parvoviridae. These are groups of considerable public-health interest: coronaviruses in particular have repeatedly demonstrated the capacity to move between animal and human hosts, while parvoviruses are important pathogens of domestic carnivores. Cataloguing such viruses in animals that share close, daily contact with humans is a foundational step for any urban zoonotic surveillance program, and the Shanghai dataset provides one of the most detailed pictures to date of what those animals carry.

The headline result was a surprise. Household dogs exhibited the highest Chao1 richness, an estimator of total species richness, among all four host groups examined, and their viral richness was significantly higher than that of household cats, stray cats and stray dogs, according to Wilcoxon rank-sum tests corrected for multiple comparisons using the Benjamini-Hochberg false discovery rate procedure, with adjusted p-values below 0.05. Household dogs also harbored 73.7 percent of all host-specific vOTUs found in the study, fourteen out of nineteen, and every one of those unique viral units belonged to the Coronaviridae. In addition, household dogs showed the highest richness of vertebrate-associated viruses from families with recognized zoonotic potential. For dogs at least, life indoors appears to come with a more varied viral repertoire, not a narrower one.

Intriguingly, the excess richness in household dogs did not translate into a fundamentally different viral community. When the researchers compared overall community composition between household and stray dogs using PERMANOVA, a permutation-based test of differences between groups, the result was not statistically significant, with an effect size of R-squared equal to 0.07 and a p-value of 0.115. In other words, the household-stray contrast in dogs was richness-specific rather than reflecting a broad compositional shift. Household dogs carried more viral types, but the overall character of their viral communities resembled that of stray dogs. This distinction between the number of viral lineages present and the identity of those lineages is one of the study’s central conceptual contributions, separating elevated viral richness from genuine compositional differentiation.

Beyond the household-versus-stray comparison, the data revealed striking host specificity in urban pet viromes. Only about 15 percent of vOTUs were shared between cats and dogs, and network analysis of viral co-occurrence showed clear modular separation between the two host species. This modularity suggests that host identity, rather than shared urban space alone, strongly constrains which viruses circulate in which animals. The team also identified 59 putative novel viral lineages, defined as sequences showing less than 80 percent amino acid similarity to known lineages. Such a substantial reservoir of uncharacterized diversity in familiar companion animals underscores how much of the urban viral landscape remains unmapped, even in species that have lived alongside humans for thousands of years.

Perhaps the most policy-relevant finding came from the multivariate modeling of viral community assembly. Community composition was significantly influenced by socio-environmental factors, specifically human population density and green space coverage. This points to the roles of host density and urban greening as drivers of viral community structure: places where animals and people are packed more tightly together, or where green corridors alter the ecology of urban wildlife and pets, appear to shape which viruses pets carry. For surveillance planners, the message is that viral risk is not distributed uniformly across a city but varies with the urban fabric itself.

The authors conclude that both host identity and urban environmental context need to be incorporated into One Health surveillance frameworks, the integrated approach that recognizes the interconnected health of people, animals and ecosystems. The study was supported by the SAAS Program for Excellent Research Team 2025 and the Shanghai Agriculture Applied Technology Development Program, and all animal procedures were approved by the Animal Care and Use Committee of the Shanghai Academy of Agricultural Science, with owner consent obtained for household sampling and stray animals sampled humanely after capture by local authorities. As cities grow denser and greener in parallel, understanding how those design choices sculpt the viral communities of our closest animal companions may prove to be an essential component of preparing for the next viral emergence.

Subject of Research: Viral microbiome diversity and community assembly in urban household and stray cats and dogs

Article Title: Higher viral microbiome diversity in household than stray pets: insights into urban community assembly

Article References: Shi, Y., Zhou, F., Tao, J., Li, B., Cheng, J., Tang, P., Li, Q., & Liu, H. (2026). Higher viral microbiome diversity in household than stray pets: insights into urban community assembly. Microbiome. https://doi.org/10.1186/s40168-026-02525-3

Image Credits: AI Generated

DOI: 10.1186/s40168-026-02525-3

Keywords: viral microbiome, virome, household pets, stray animals, cats, dogs, metagenomics, vOTUs, Coronaviridae, zoonotic surveillance, urbanization, One Health