Biology subjects

Arias, C. F.

Publications and source records attributed to Arias, C. F..

At least 19 recordsLinked to original sources

bioRxiv2026

The gene ivory:mir-193 controls scale type differentiation in Heliconius butterflies

The ivory:mir-193 locus is a genetic hotspot underlying melanic wing pattern variation across Lepidoptera, acting as a master regulator of melanic scale fate. This includes the genus Heliconius, where aposematic mimicry is driven by three scale cell types: light Type I, dark-melanic Type II, and red Type III scales. We tested functions of ivory:mir-193 in Heliconius using CRISPR-induced somatic mosaic knockouts of ivory and mir-193 across multiple pattern morphs. Knockouts converted Type II scales to Type I scales. Effects on Type III scales varied among and within individuals, indicating that ivory:mir-193 is permissive for Type III development. Using single-nucleus RNA-seq, we profiled the transcriptional landscape of H. melpomene-{Delta}78k mutants lacking mir-193. Loss of mir-193 produced readthrough transcription, consistent with a model where miR-193 acts as a co-transcriptional terminator. These data show that ivory drives wing pattern variation, while mir-193 mediates downstream diversity in scale fate across Lepidoptera.

evolutionary biology↗

bioRxiv2025

Comparative genomic analyses of trans-ithmanian reef fishes reveals different molecular targets of environmental adaptation in different families.

The extent to which selection acts upon the same molecular targets when faced with the same environmental changes has important implications for our understanding of the repeatability and predictability of evolutionary processes. Replicated natural experiments are well positioned to provide insight, however often these involve closely related species or populations of the same species. Given that the similarity of genetic background makes the same molecular change more likely, it is essential to evaluate the extent to which molecular parallelism occurs in more distantly related species. The rise of the Isthmus of Panama presents an ideal natural experiment to investigate the prevalence of parallel molecular changes in distantly related lineages exposed to the same environmental regimes of temperature, salinity and primary productivity in the two newly formed oceans. Here, we generate high-quality reference genomes for two replicate pairs of geminate reef fishes, one in the family Pomacentridae and one in the Serranidae. Comparative analyses of positive selection in protein-coding genes and of gene family evolution revealed multiple signals of potentially adaptive divergence between geminate species in response to environmental regime. Common targets of selection between families included MAPK signalling (MAP3K10), solute transport (SLC46A2) and reproduction (ZPL3L), as well as expansions in immune and MAPK related gene families. Overall, however, we found minimal evidence of parallelism between families either at the gene level or when considering higher functional categories. Our findings suggest that phylogenetic constraints may limit the levels of molecular parallelism in distant lineages even when faced with comparable selective pressures. Significance StatementUnderstanding the extent to which species exposed to similar environmental conditions may adapt using similar genetic solutions has important implications for our understanding of evolutionary processes and how we may expect species to adapt in the future. However, systems where multiple, independent lineages are faced with the same shift in conditions are rare. The rise of the Isthmus of Panama provides a unique, natural experiment where multiple marine species have been divided and exposed to radically different environmental conditions. Here, we generate genomes for separated species in two distantly related families of reef fishes and compare genome-wide patterns of divergence. Our analyses identified signals of selection in protein-coding genes and shifts in gene family size consistent with adaptation to the distinct environments, however the specific genes and pathways involved predominantly differed between the families, revealing that, even under shared selective pressures, molecular mechanisms may differ across more distant lineages.

evolutionary biology↗

bioRxiv2025

Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii)

The uplift of the Central American Isthmus (CAI) represents a natural laboratory for the study of allopatric speciation in marine organisms. Several geminate species pairs of both vertebrates and invertebrates formed following the uplift of the CAI, including damselfishes of the Pomacentridae family. However, to date no studies have explored the genomic differences among geminate species in the Pacific and Atlantic Oceans. In this study we present genome assemblies for the transisthmian species pair consisting of the Sergeant Major Abudefduf saxatilis (Tropical Atlantic) and the Panamic Sergeant Major Abudefduf troschelii (Tropical Eastern Pacific) derived from PacBio long-read sequencing. The new genomes are near-chromosome level, and among the highest-quality genomes currently available for coral reef fishes. We show that large structural variants distinguish the two species, including a 9 megabase inversion in linkage group (putative chromosome) 6. Additionally, we show through an analysis of demographic history that alleles within the two genomes have different coalescence time distributions, which may be due to different effective population sizes, population structures, and/or selection regimes in the two oceans. Finally, we highlight gene families that were significantly expanded or contracted between A. troschelii and A. saxatilis. Some of these are related to the environmental conditions that differ between the two oceans, such as gamma crystallin M (crygm), which is linked to vision, and vitellogenin (vtg), which is associated with egg provisioning. These genomes set the stage for comparative analyses of genetic structure and selection on the marine organisms that originated with the formation of the CAI. Significance StatementUnderstanding speciation in oceans has represented a historical challenge, given the high rates of dispersal during larval stages for most marine groups. There are few geologic events that have propelled marine biodiversity while completely blocking the genetic exchange during the speciation process. The final closure of the Central American Isthmus (CAI), 2.8 million years ago, is one of these few examples where marine populations from the tropical Pacific and Atlantic oceans have been completely isolated, providing the opportunity to study how genomes diverge in the absence of gene flow. Here, we present the first comparative genomics study of marine organisms separated by the CAI, showing that genomes on the two sides of the CAI differ structurally. We also identify contractions and expansions of various gene families between the two species, which are potentially associated with adaptations to the different environmental conditions in the two oceans. This represents a relevant first step for comparative genomics of geminate species isolated by a major geologic event.

genomics↗

bioRxiv2025

Metabolic overflow prevents ecological collapse in microbial populations

Metabolic overflow is defined by the excretion of partially oxidized byproducts, such as acetate, ethanol, and lactate, which could otherwise be used to produce energy. This behavior, widespread across diverse biological systems, is paradoxical because it suggests a seemingly wasteful use of resources that could instead be employed to maximize energy production. In this work, we investigate the ecological implications of metabolic overflow, using bacterial acetate metabolism as a model. We formulate a second-order generalization of the logistic growth equation, incorporating resource availability and acceleration dynamics to provide an explicit mechanistic link between metabolic overflow and ecological collapse. We demonstrate that acetate-mediated growth deceleration reduces the risk of overshoot and collapse, especially under conditions of resource oversupply. By inhibiting excessive proliferation, acetate overflow enhances the survival and stability of bacterial communities in fluctuating environments. In this context, acetate acts as a quorum-sensing signal, coordinating population-wide responses and enabling the active regulation of growth rates before resource exhaustion occurs. Our findings suggest that overflow metabolism is an adaptive strategy evolved to mitigate the risk of ecological collapse and stabilize microbial populations. These insights highlight the dual role of metabolic byproducts as both inhibitors of growth and regulators of population dynamics, with significant implications for microbial ecology and biotechnological applications.

ecology↗

bioRxiv2025

When blood needs to flow: The role of the complement system in red blood cell clearance during immune responses

The complement system is a crucial component of the innate immune response, primarily recognized for its defensive role against pathogens. Increased red blood cell (RBC) mortality due to complement activation during infections is often considered collateral damage of this defensive role. In this study, we propose that this phenomenon results from the active regulation of RBC mortality by the complement system during acute immune responses. Traditionally, RBC homeostasis has been explained by the need to ensure adequate oxygen delivery. However, RBCs are also critical determinants of blood viscosity, which directly influences tissue perfusion. Efficient immune responses require increased blood flow to infected tissues, but changes in plasma proteins during acute-phase responses can increase blood viscosity, hindering perfusion. We suggest that the complement system selectively removes less elastic RBCs, compensating for the rise in plasma viscosity and optimizing tissue perfusion during infections. Our findings reveal a previously unrecognized role of the complement system in regulating blood flow, highlighting the intricate balance between complements homeostatic and defensive functions in maintaining physiological stability.

immunology↗

bioRxiv2024

Discovery of three novel neutralizing antibody epitopes on the human astrovirus capsid spike and mechanistic insights into virus neutralization

Human astroviruses (HAstVs) are a leading cause of viral childhood diarrhea that infect nearly every individual during their lifetime. Although human astroviruses are highly prevalent, no approved vaccine currently exists. Antibody responses appear to play an important role in protection from HAstV infection, however knowledge about the neutralizing epitope landscape is lacking, as only 3 neutralizing antibody epitopes have previously been determined. Here, we structurally define the epitopes of 3 uncharacterized HAstV-neutralizing monoclonal antibodies: antibody 4B6 with X-ray crystallography to 2.67 [A], and antibodies 3H4 and 3B4 simultaneously with single-particle cryogenic-electron microscopy to 3.33 [A]. We assess the epitope locations relative to conserved regions on the capsid spike and find that while antibodies 4B6 and 3B4 target the upper variable loop regions of the HAstV spike protein, antibody 3H4 targets a novel region near the base of the spike that is more conserved. Additionally, we found that all 3 antibodies bind with high affinity, and they compete with receptor FcRn binding to the capsid spike. These studies inform which regions of the HAstV capsid can be targeted by monoclonal antibody therapies and could aid in rational vaccine design. ImportanceHuman astroviruses infect nearly every child in the world, causing diarrhea, vomiting, and fever. Despite the prevalence of human astroviruses, little is known about how antibodies block virus infection. Here, we determined high-resolution structures of the astrovirus capsid protein in complex with three virus-neutralizing antibodies. The antibodies bind distinct sites on the capsid spike domain. We find that the antibodies block virus attachment to human cells and prevent capsid spike interaction with the human neonatal Fc receptor. These findings support the use of the human astrovirus capsid spike as an antigen in a vaccine to prevent astrovirus disease.

microbiology↗

bioRxiv2024

Antigenic determinants of HAstV-VA1 neutralization and their relevance in the human immune response

Astroviruses are highly divergent and infect a wide variety of animal hosts. In 2009, a genetically divergent human astrovirus (HAstV) strain VA1 was first identified in an outbreak of acute gastroenteritis. This strain has also been associated with fatal central nervous system disease. In this work, we report the isolation of three high-affinity neutralizing monoclonal antibodies (Nt-MAbs) targeting the capsid spike domain of HAstV-VA1. These antibodies (7C8, 2A2, 3D8) were used to select individual HAstV-VA1 mutants resistant to their neutralizing activity and also select a HAstV-VA1 triple mutant that escapes neutralization from all three Nt-MAbs. Sequencing of the virus genome capsid region revealed escape mutations that map to the surface of the capsid spike domain, define three potentially independent neutralization epitopes, and help delineate four antigenic sites in rotaviruses. Notably, two of the escape mutations were found to be present in the spike sequence of the HAstV-VA1-PS strain isolated from an immunodeficient patient with encephalitis, suggesting that those mutations arose as a result of the immune pressure generated by the patients immunotherapy. In accordance with this observation, human serum samples exhibiting strong neutralization activity against wild-type HAstV-VA1 had a 2.6-fold reduction in neutralization titer when evaluated against the triple-escape HAstV-VA1 mutant, indicating shared neutralization epitopes between the mouse and human antibody response. The isolated Nt-MAbs reported in this work will help characterize the functional sites of the virus during cell entry and have the potential for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1. ImportanceHuman astroviruses (HAstVs) have been historically associated with acute gastroenteritis. However, the genetically divergent HAstV-VA1 strain has been associated with central nervous system disease. This work isolated high-affinity neutralizing monoclonal antibodies directed to HAstV-VA1. The proposed binding sites for these antibodies, together with previously reported sites for neutralizing antibodies against classical HAstVs, suggest the existence of at least four neutralization sites on the capsid spike of astroviruses. Our data show that natural infection with human astrovirus VA1 elicits a robust humoral immune response that targets the same antigenic sites recognized by the mouse monoclonal antibodies and strongly suggests the emergence of a variant HAstV-VA1 virus in an immunodeficient patient with prolonged astrovirus infection. The isolated Nt-MAb reported in this work will be helpful in defining the functional sites of the virus involved in cell entry and hold promise for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1.

microbiology↗

bioRxiv2023

Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific

Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: i) assembled and annotated the nuclear genome of the King Angelfish (Holacanthus passer), and ii) examined the demographic history of H. passer in the TEP. We generated 43.8 Gb of ONT and 97.3 Gb Illumina reads representing 75X and 167X coverage, respectively. The final genome assembly size was 583 Mb with a contig N50 of 5.7 Mb, which captured 97.5% complete Actinoterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs). Repetitive elements account for 5.09% of the genome, and 33,889 protein-coding genes were predicted, of which 22,984 have been functionally annotated. Our demographic model suggests that population expansions of H. passer occurred prior to the last glacial maximum (LGM) and were more likely shaped by events associated with the closure of the Isthmus of Panama. This result is surprising, given that most rapid population expansions in both freshwater and marine organisms have been reported to occur globally after the LGM. Overall, this annotated genome assembly will serve as a resource to improve our understanding of the evolution of Holacanthus angelfishes while facilitating novel research into local adaptation, speciation, and introgression in marine fishes.

evolutionary biology↗

bioRxiv2023

Sex chromosome - autosome fusions in Heliconius butterflies

Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sara/sapho clade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We found that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs showed subsequent fusions between the W and chromosomes 9 or 14, respectively. These sequential fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of WGS technology to detect neo-sex chromosomes even when sex chromosomes are not explicitly assembled. Author SummaryFusions between sex chromosomes and autosomes are thought to have the potential to resolve sexual conflict and enhance local adaptation or reproductive isolation between species. Here, we discovered such fusions in Heliconius butterflies. Heliconius butterflies mostly have a very stable karyotype with 21 chromosomes and high synteny across species. However, the five species in the sapho subclade have up to 60 chromosomes, suggesting that they have undergone many chromosomal fissions. We document that in addition to the fissions, the sapho subclade also showed multiple fusions between the female-specific sex chromosome (W) and autosomes. We found a W-4 fusion shared by all five species and additional W fusions with chromosomes 9 and 14 shared by two species each. Even though in many sapho subclade species the autosomes have undergone fissions, the chromosomes fused with the W represent the full-length autosomes, as seen in other Heliconius species, suggesting that fusing to the W protected them from fissions. Our study reveals the power of short-read sequencing to discover neo-sex chromosomes and showcases Heliconius butterflies as a promising system for studying the causes and consequences of sex chromosome evolution.

evolutionary biology↗

bioRxiv2022

Regional epidemic dynamics and Delta variant diversity resulted in varying rates of spread of Omicron-BA.1 in Mexico

The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In Mexico, this subvariant began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in the country. Unlike previous SARS-CoV-2 variants, BA.1 did not acquire local substitutions nor exhibited a geographically distinct circulation pattern in Mexico. However, a regional difference in the speed of the replacement of the Delta variant was observed, as some northern states showed persistence of Delta lineages well into February 2022. Mexican states were divided into four regions (North, Central North, Central South, and Southeast) based on the lineage circulation before the dominance of BA.1 to study possible causes for this difference. For each region, the time to fixation of BA.1, the diversity of Delta sublineages in the weeks preceding BA.1 entry, the population density, and the level of virus circulation during the inter-wave interval were determined. An association between a faster Omicron spread and lower Delta diversity, as well as fewer COVID-19 cases during the Delta-BA.1.x inter-wave period, was observed. For example, the North region exhibited the slowest spread but had the highest diversity of Delta sublineages and the greatest number of inter-wave cases relative to the maximum amount of the virus circulating in the region, whereas the Southeast region showed the opposite. Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics. Nonetheless, if there is a significant difference in the fitness of the variants or the time allowed for the competition is sufficient, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico. Impact statementThe surveillance of lineage circulation of SARS-CoV-2 has helped identify variants that have a transmission advantage and are of concern to public health and to track the virus dispersion accurately. However, many factors contributing to differences in lineage spread dynamics beyond the acquisition of specific mutations remain poorly understood. In this work, a description of BA.1 entry and dispersion within Mexico is presented, and which factors potentially affected the spread rates of the Omicron variant BA.1 among geographical regions in the country are analyzed, underlining the importance of population density, the proportion of active cases, and viral lineage diversity and identity before the entry of BA.1. Data summaryThis work was carried out using data shared through the GISAID initiative. All sequences and metadate are available through GISAID with the accession EPI_SET_220927gw, accession numbers and metadata are also reported in the supplemental material of this article. Epidemiological data was obtained though the Secretaria de Salud website (https://www.gob.mx/salud/documentos/datos-abiertos-152127),

microbiology↗

bioRxiv2022

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

evolutionary biology↗

bioRxiv2022

The virtualome: a computational framework toevaluate microbiome analyses

Microbiomes have been the focus of a substantial research effort in the last decades. The composition of microbial populations is normally determined by comparing DNA sequences sampled from those populations with the sequences stored in genomic databases. Therefore, the amount of information available in databanks should be expected to constrain the accuracy of microbiome analyses. Albeit normally ignored in microbiome studies, this constraint could severely compromise the reliability of microbiome data. To test this hypothesis, we generated virtualomes, virtual bacterial populations that exhibit the ecological structure of real-world microbiomes. Confronting the analyses of virtualomes with their original composition revealed critical issues in the current approach to characterizing microbiomes, issues that were empirically confirmed by analyzing the microbiome of Galleria mellonella larvae. To reduce the uncertainty of microbiome data, the effort in the field must be channeled towards significantly increasing the amount of available genomic information.

bioinformatics↗

bioRxiv2022

Mature rotavirus particles contain equivalent amounts of 7meGpppGcap and noncapped viral positive-sense RNAs

Viruses have evolved different strategies to overcome their recognition by the host innate immune system. Addition of cap at their 5RNA ends is an efficient mechanism to ensure escape from detection by the innate immune system, but also to ensure the efficient synthesis of viral proteins. Rotavirus mRNAs contain a type 1 cap structure at their 5end that is added by the viral capping enzyme VP3. This is a multifunctional protein with all the enzymatic activities necessary to add the cap, and also functions as an antagonist of the OAS-RNase L pathway. Here, the relative abundance of capped and noncapped viral RNAs during the replication cycle of rotavirus was determined. We found that both classes of rotaviral +RNAs are encapsidated, and they were present in a 1:1 ratio in the mature infectious particles. The capping of viral +RNAs is dynamic since different ratios of capped and noncapped RNAs were detected at different times post infection. Similarly, when the relative amount of capped and uncapped viral +RNAs produced in an in vitro transcription system was determined, we found that the proportion was very similar to that in the mature viral particles and in infected cells, suggesting that the capping efficiency of VP3 both, in vivo and in vitro, might be close to 50%. Unexpectedly, when the effect of simultaneously knocking down the expression of VP3 and RNase L on the cap status of viral +RNAs was evaluated, we found that even though at late times post infection there was an increased proportion of capped viral RNAs in infected cells, the viral particles isolated from this condition contained an equal ratio of capped and noncapped viral RNA, suggesting that there might be a selective packaging of capped-noncapped RNAs. SIGNIFICANCERotaviruses have a genome composed of eleven segments of double stranded RNA. Whether all 5 ends of the positive sense genomic RNA contained in the mature viral particles are modified by a cap structure is unknown. In this work, using a direct quantitative assay we characterized the relative proportion of capped and noncapped viral RNA in rotavirus infected cells and in viral particles. We found that independently of the relative proportions of cap/noncapped RNA present in rotavirus infected cells, there is a similar proportion of these two kinds of 5-modified positive sense RNAs in the viral particles.

microbiology↗

bioRxiv2022

The capsid precursor protein of astrovirus VA1 is proteolytically processed intracellularly

Human astrovirus VA1 has been associated with neurological disease in immunocompromised patients, and its recent propagation in cell culture has opened the possibility to study its biology. Unlike classical human astroviruses, VA1 growth was found to be independent of trypsin during virus replication in vitro. In this work, we show that despite its independence on trypsin activation for cell infection, the VA1 capsid precursor protein, of 86 kDa (VP86), is processed intracellularly, and this proteolytic processing is important for astrovirus VA1 infectivity. Antibodies raised against different regions of the capsid precursor showed that the polyprotein can be processed starting at either its amino-or carboxy-terminal end, and they allowed us to identify that proteins of about 33 (VP33) and 38 (VP38) kDa constitute the core and the spike proteins of the mature infectious virus particles, respectively. The amino-terminal end of the spike protein was found to be Thr-348. Whether the protease involved in intracellular cleavage of the capsid precursor is of viral or cellular origin remains to be determined, but the cleavage is independent of caspases. Also, trypsin is able to degrade the capsid precursor but has no effect on VP34 and VP38 proteins when assembled into virus particles. These studies provide the basis for advancement of the knowledge of astrovirus VA1 cell entry and replication. IMPORTANCEHuman astrovirus VA1 has been associated with neurological disease in immunocompromised patients. Its recent propagation in cell culture has facilitated the study of its biology. In this work, we show that despite the ability of this virus to grow in the absence of trypsin, a marked feature of human classical astroviruses, the capsid precursor protein of astrovirus VA1 is cleaved intracellularly to yield the mature infectious particles, formed by two polypeptides, VP33 that constitutes the core domain of the virus particle, and V38 that forms the spike of the virus. These studies provide a platform to advance our knowledge on astrovirus VA1 cell entry and replication.

microbiology↗

bioRxiv2022

Wax worm saliva and the enzymes therein are the key to polyethylene degradation by Galleria mellonella

Plastic degradation by biological systems with re-utilization of the by-products can be the future solution to the global threat of plastic waste accumulation. We report that the saliva of Galleria mellonella larvae (wax worms) is capable of oxidizing and depolymerizing polyethylene (PE), one of the most produced and sturdy polyolefin-derived plastics. This effect is achieved after a few hours exposure at room temperature and physiological conditions (neutral pH). The wax worm saliva can indeed overcome the bottleneck step in PE biodegradation, that is the initial oxidation step. Within the saliva, we identified two enzymes that can reproduce the same effect. This is the first report of enzymes with this capability, opening up the way to new ground-breaking solutions for plastic waste management through bio-recycling/up-cycling.

molecular biology↗

bioRxiv2021

The association of human astrovirus with extracellular vesicles facilitates cell infection and protects the virus from neutralizing antibodies

Viral gastroenteritis has a global distribution and represents a high risk for vulnerable population and children under 5 years because of acute diarrhea, fever and dehydration. Human astroviruses (HAstV) have been identified as the third most important cause of viral gastroenteritis in pediatric and immunocompromised patients. Furthermore, HAstV has been reported in biopsies taken from patients with encephalitis, meningitis and acute respiratory infection, yet it is not clear how the virus reaches these organs. In this work we tested the possibility that the released astrovirus particles could be associated with extracellular vesicles. Comparison between vesicles purified from astrovirus- and mock-infected cells showed that infection with HAstV Yuc8 enhances production of vesicles larger than 150 nm. These vesicles contain CD63 and Alix, two markers of vesicular structures. Some of the extracellular virus was found associated with vesicular membranes, and this association facilitates cell infection in the absence of trypsin activation and protects virions from neutralizing antibodies. Our findings suggest a new pathway for HAstV spread and might represent an explanation for the extraintestinal presence of some astrovirus strains. ImportanceAstroviruses are an important cause of diarrhea in children; recently some reports have found these viruses in extra-intestinal organs, including the central nervous system, causing unexpected clinical disease. In this work we found that human astrovirus strain Yuc8 associates with extracellular vesicles, possibly during or after their cell egress. The association with vesicles seems to increase astrovirus infectivity in less susceptible cells, and renders virus particles insensitive to neutralization by antibodies. These data suggest that extracellular vesicles could represent a novel pathway for astrovirus to disseminate outside the gastrointestinal tract.

microbiology↗

bioRxiv2020

The gut virome of healthy children during the first year of life is diverse and dynamic

In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infants immune system or on the health of the infants later in life, remains to be investigated.

microbiology↗

bioRxiv2020

Saliva sampling is an excellent option to increase the number of SARS CoV2 diagnostic tests in settings with supplies shortages

As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for SARS CoV-2. Detection of the viral genome through RT-qPCR is the golden standard for this test, however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR test has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve as a suitable source for viral RNA detection that is cheaper and can be as efficient as the classical protocol that involves column purification of the viral RNA. In addition, it surpasses the need for swab sampling, decreases the risk of the healthcare personnel involved in this process, and accelerates the diagnostic procedure.

microbiology↗