Biology subjects

Wallau, G. d. L.

Publications and source records attributed to Wallau, G. d. L..

17 recordsLinked to original sources

bioRxiv2026

Discovery of two potential new species and two novel bat-coronavirus subgenera (Phyllacovirus and Phyllobecovirus) in the Neotropics

Bats are major natural reservoirs for coronaviruses, yet complete viral genomes from South America remain scarce, limiting evolutionary and taxonomic understanding. Here, we conducted metatranscriptomic sequencing of coronavirus-positive bat samples collected across two ecologically distinct Brazilian biomes: the Atlantic Forest and the semi-arid Caatinga. We recovered seven complete or near-complete genomes belonging to Alphacoronavirus and Betacoronavirus. Phylogenetic and comparative similarity analyses of conserved replicase domains (3CLpro, NiRAN, RdRp, ZBD, HEL1), following International Committee on Taxonomy of Viruses (ICTV) demarcation criteria, revealed significant viral diversity. Within Alphacoronavirus, two genomes from Atlantic Forest phyllostomid bats (Artibeus lituratus and Carollia perspicillata) formed a deeply divergent sister lineage to Amalacovirus, exhibiting a mean amino acid similarity of 76.7% with the reference genome. Within Betacoronavirus, one genome from a Caatinga phyllostomid bat (Artibeus planirostris) clustered within the recently described Ambecovirus clade, displaying 75.9% mean amino acid similarity with mormoopid-associated reference sequences. Based on these divergence levels and non-recombinant genomic architectures, we propose two novel candidate subgenera, Phyllacovirus and Phyllobecovirus, alongside potential novel viral species. Furthermore, our findings demonstrate strong host-associated structuring and biogeographical partitioning of viral lineages across Neotropical biomes. Overall, this study expands the genomic landscape of South American bat coronaviruses and underscores the importance of continuous genomic surveillance at human-wildlife interfaces.

genomics↗

bioRxiv2025

Wolbachia introgression in Rio de Janeiro remains at sub-optimal levels 30 months after its crash: challenges in the sustainability of wMel interventions for dengue control

The deployment of the Wolbachia wMel strain is currently underway in multiple dengue-endemic municipalities across Brazil. The efficacy of this strategy in Rio de Janeiro remains uncertain, primarily due to the difficulty in sustaining high wMel prevalence in regions previously subjected to large-scale releases. A key contributing factor was the routine rotation of insecticides within the framework of Integrated Vector Management (IVM), which led to the use of the larvicide Spinosad for Aedes control in urban areas. This compound was associated with a precipitous decline in Aedes aegypti mosquitoes, regardless the wMel infection status. While wMel-uninfected population recovered within weeks, wMel-infected population remained at low levels likely due to the fitness costs imposed by wMel on egg viability. To assess the long-term persistence of wMel following this demographic collapse, we conducted mosquito sampling across 12 neighborhoods in Rio de Janeiro, 30 months after mosquito populations crashed. Our findings reveal that wMel introgression remains suboptimal, with a mean frequency of 9.87% across the sampled areas. Only two neighborhoods exhibited wMel frequencies exceeding 15%, likely reflecting ongoing localized releases. The reduced prevalence underscores the challenges of achieving self-sustaining wMel establishment in complex urban environments and highlight critical considerations for the implementation of Wolbachia-based dengue control programs in endemic regions. SponsorshipThis study was supported by grants from the CNPq - Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (312282/2022-2, 307209/2023-7) and by FAPERJ - Fundacao Carlos Chagas Filho de Amparo a Pesquisa no Estado do Rio de Janeiro (E-26/211.159/2019, E-26/204.108/2024, E26/2001.844/2017, E-26/210.335/2022, E-26/210.537/2024).

ecology↗

bioRxiv2025

Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats sheds new light on bat-borne coronaviruses evolution

Understanding the viral diversity harboured by wildlife is essential for effective prediction and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several zoonotic viral pathogens of high impact on public health, including coronaviruses responsible for SARS, the rabies virus, Marburg, Ebola, Nipah and Hendra viruses. However, the large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazil. We used a meta-transcriptomic to characterize new virus genomes found in blood, oral and anal samples collected from cave- and non-cave bats from Northeast Brazil. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nebecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain could not be identified due to high dissimilarity relative to known congeneres. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown not just in Brazil but, likely, in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.

evolutionary biology↗

bioRxiv2025

Genomics insights reveal multi-year maintenance of a new Deltacoronavirus infecting Seabirds from the Cagarras Island Archipelago Natural Monument, Brazil

Previous studies have identified various pathogens in seabirds, notably coronaviruses (CoVs) and influenza A viruses (IAVs), due to their potential to cause significant morbidity and mortality. The Cagarras Island Archipelago Natural Monument, located near Rio de Janeiro, Brazil, serves as nesting site for two species, the magnificent frigatebird (Fregata magnificens) and the brown booby (Sula leucogaster). Despite its ecological importance, no prior studies have investigated viral infections in these species, which share habitat interfaces with densely populated human areas. To address this gap, we sampled and tested seabirds for CoVs and IAVs from January 2022 to April 2024. Birds were captured and identified by species, age, and sex. Oropharyngeal and cloacal swabs, as well as blood samples, were collected. Viral RNA was extracted using the QIAamp Viral RNA Mini Kit, and the presence of IAVs was screened via real-time RT-PCR, while CoVs were screened using semi-nested RT-PCR. Sanger and metatranscriptomic sequencing were performed to identify viral strains and assess phylogenetic relationships. Of the 153 seabirds sampled, CoVs were detected in 6 individuals (9.1%) of F. magnificens and 16 individuals (18.4%) of S. leucogaster. No IAVs were found in either oropharyngeal or cloacal swabs, and all serum samples were negative for the presence of antibodies against the virus. We recovered two full deltacoronavirus genomes and eight additional draft genomes from S. leucogaster samples obtained from distinct sampling expeditions and additional enteroviruses, passeriviruses, and picornaviruses. Phylogenetic analysis revealed that the detected CoVs are closely related to avian deltacoronaviruses from environmental samples of S. leucogaster in the Sao Pedro and Sao Paulo Archipelago, indicating potential viral exchange between these seabird populations living at these distant islands. Moreover, multiple detections in different individuals at different time points are associated with specific Spike NTD deletions that have been shown to accumulate in immune escape lineages, supporting the long-term maintenance through new infections and reinfection of this virus in these bird populations. This is the first detection of CoVs in F. magnificens, highlighting their circulation in marine ecosystems. Further research is needed to understand the ecological and epidemiological implications, including potential cross-species transmission.

microbiology↗

bioRxiv2024

Detection of Deltacoronavirus in Environmental Fecal Samples from Seabirds in the Saint Peter and Saint Paul Archipelago, central equatorial Atlantic Ocean

This study investigates the presence of avian coronaviruses (CoVs), influenza A viruses (IAVs), and Avian rotaviruses (RVs) group A in seabird populations inhabiting the Saint Peter and Saint Paul Archipelago (SPSPA), an isolated and remote oceanic island situated in the equatorial region of the Atlantic Ocean. In July 2022, 95 environmental fecal samples were collected from seabird colonies and screened for the viruses by quantitative one-step real-time RT-PCR (IAVs and RVs), by the conventional pancoronavirus RT-PCR protocols and metatranscriptomics of a positive sample. Four environmental feces samples tested positive for CoVs. Avian IAVs and RVs were not detected. Phylogenetic analysis revealed CoVs closely related to avian deltacoronaviruses previously identified in waterbirds from Asia and Australia. We could not recover the CoV by metatranscriptomics but we recovered a single viral contig of an avian enterovirus. The findings contribute valuable insights into virus dynamics among seabird populations, laying the groundwork for future investigations in this field.

molecular biology↗

bioRxiv2024

Detection and full genome sequencing of a Deltacoronavirus and other bird associated viruses from feces of the kelp gull (Larus dominicanus) sampled at the South Shetland Islands Antarctica.

Bird species are known to be the main reservoir of a range of respiratory viruses such as Influenza, Newcastle and Coronaviruses. Migratory birds are particularly important for the maintenance and long distance spread of the virus to wild bird and poultry species but eventually to mammal species as well. Antarcticas pristine environment and wildlife is of immense biological value, but the spread of such deadly viruses pose a substantial threat to the regions fragile ecosystems. To investigate the presence of respiratory viruses in the region we sampled feces of different wild migratory birds at various localities in the South Shetland Islands in the Antarctic summer of 2023 and screened them for coronaviruses (CoVs) and influenza A virus (IAV). Viral screening was performed by the conventional pancoronavirus RT-PCR protocol (CoVs), by quantitative one-step real-time RT-PCR (IAVs) followed by metatranscriptomic sequencing of positive samples. During January and February of 2023, we collected and examined a total of 243 fecal samples representing Stercorarius spp (N=5), Larus dominicanus (N=16), Phalacrocorax bransfieldensis (N=3), Pygoscelis adeliae (N=19), Pygoscelis antarcticus (N=38), Pygoscelis papua (N=139), Pygoscelis spp (N=23). All tested samples were negative for influenza A and one sample from the colony of L. dominicanus at Keller Peninsula, King George Island, tested positive for CoVs. Metatranscriptomic sequencing recovered a full deltaCoV genome. Nucleotide and amino acid distance analysis revealed that the deltacoronavirus detected belongs to subgenus Buldecovirus and to the novel wild bird deltaCoV clade previously identified infecting Antarctica penguins. The identified deltaCov is most closely related to a deltacoronavirus previously identified 2014 in P. papua penguin sampled at Isla Kopaitik, Base OHiggin suggesting a potential cross species transmission. The presence of CoVs in Antarctic migratory seabirds raises concerns about their impact on the wild bird population in Antarctica and their potential role in virus dispersion through intra and intercontinental migratory routes. These findings contribute valuable insights into virus dynamics among seabird populations, laying the groundwork for future investigations in this field and warning of the importance of viral surveillance on the Antarctic fauna. RepositoriesThe raw reads were submitted to NCBI Sequence Read Archive (SRA) database and are available under project number: PRJNA1160912 and Run Accessions: SRR30664529 and SRR30664530. Impact statementThis study provides insights into the presence of respiratory viruses, specifically coronaviruses (CoVs), in Antarctic seabirds. By detecting a novel wild bird deltacoronavirus in gulls population in the South Shetland Islands, our research contributes to the growing body of literature on viral transmission in remote ecosystems. The findings highlight the potential of migratory birds to act as reservoirs and vectors of viruses in the Antarctic region and underscores the urgent need for continued viral surveillance.

genomics↗

bioRxiv2024

Genomic and phenotypic characterization of an Oropouche virus strain implicated in the 2023-24 large-scale outbreak in Brazil

The Orthobunyavirus oropoucheense in a arthropod borne zoonotic pathogen known to infect sylvatic animals and humans by means of biting midges transmission. Several large-scale human outbreaks of Oropouche virus (OROV), primarily confined to the Amazon region, were documented over the decades. However, since 2022, more widespread OROV outbreaks have been unfolding in Brazil and across South America, with cases exported to Cuba, Italy, and Germany. I In Brazil, the virus has reached and established communitary transmission in states from all major regions of the country. Here we isolated, characterized the cytopathic effect and the full genomic sequence of two OROV isolates from the current outbreak. Our data shows that OROV can readily infect and replicate in non-human primate cells, supporting the role of non-human primates as important reservoirs. Phylogenetic data supports a direct introduction of the same lineages causing the 2022-24 outbreak in Brazil from the Amazonas state, the epicenter of the epidemics in Brazil. Lastly, as case counts accumulate in the state and the Northeast region, clear evidence supports established and sustained transmission. Continued studies are critical to understand the transmission cycle in this region, the most important vectors and reservoirs, to appropriately deploy control measures.

microbiology↗

bioRxiv2024

EEfinder, a tool for identification of bacterial and viral endogenized elements in eukaryotic genomes

Horizontal transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. Genetic elements derived from horizontal transfer are known as Endogenous Bacterial Elements and Endogenous Viral Elements. Endogenous elements characterization provides a snapshot of past host-pathogen interactions and coevolution as well as a reference sequence information to remove false positive results from viral metagenomic studies. However, there is a current lack of standardized tools for endogenous elements identification, which hinder comparative studies and reproducibility within this field. Here we describe EEfinder, a new tool for identification and classification of endogenous elements derived from horizontal transfer. The tool was developed to include six standard steps performed in this type of analysis: data cleaning, pairwise alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder can systematically identify endogenous elements with bacterial/viral origin.

bioinformatics↗

bioRxiv2024

Limited stress and tissue-specific transcriptional and translational activity of transposable elements in mosquitoes

The mobilization of transposable elements (TEs) can either negatively affect the hosts fitness or contribute to the species evolution. TE protein expression is the first stage for transposition, but organisms developed defenses to control it. The intensity of regulatory mechanisms can vary among tissues, and in response to stress, it may facilitate TE activation across different species. Using hundreds of RNA-Seq and mass spectrometry experiments we calculated TE expression on twelve mosquito species. Most mosquito TE families exhibit constitutive RNA expression with abundant lncRNA production, yet only a limited number of proteins are effectively produced, in a tissue-specific manner. Under natural conditions, TEs exhibit distinct expression in somatic and germinal tissues, notably with pronounced repression in ovaries, associated with increased PIWI and AGO3 expression. Following exposure to abiotic stress and viral infection, certain TE families undergo altered expression. However, some stressors have no effects on TEs, or cause opposite effects in distinct species. Furthermore, repression predominates over induction in most cases. These data suggest that while some proteins are synthesized, the majority of TE transcripts function in a regulatory capacity. We also propose that the conventional notion of TEs being more expressed under stress conditions may not be universally valid. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/580529v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@edfebborg.highwire.dtl.DTLVardef@eebf0forg.highwire.dtl.DTLVardef@417764org.highwire.dtl.DTLVardef@56731_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America

The highly pathogenic avian influenza viruses of the clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast. Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens), fur seals (Arctocephalus australis), and terns (Sterna hirundinacea). Phylogenetic and ancestral reconstruction analysis showed that these strains have pinnipeds as the most likely ancestral host, representing a recent introduction of the clade 2.3.4.4b in Uruguay. The Uruguayan and closely related strains from Peru (sea lions) and Chile (sea lions and a human case) carry mammalian adaptative residues 591K and 701N in the viral polymerase basic protein 2 (PB2). Our findings suggest that the clade 2.3.4.4b strains in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route.

microbiology↗

bioRxiv2023

RNA virome of sylvatic mosquitoes from northeast Brazil reveals a divergent and diverse insect-specific viral community

Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISV) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome the majority are focused on few urban species and relatively little is known about the virome of sylvatic mosquitoes particularly in high biodiverse brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquitos species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RdRp amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquitoes viral community is majorly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated. These findings will help to understand the interactions and coevolution between mosquitoes and viruses in nature. ImportanceMosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as ISVs. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in depth bioinformatics approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Lastly, it also provided several complete genomes that warrants further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.

genomics↗

bioRxiv2022

Dynamic of Mayaro virus transmission between Aedes aegypti and Culex quinquefasciatus mosquitoes and a mice model

Mayaro virus (MAYV) is transmitted by Haemagogus spp. mosquitoes and has been circulating in Amazon areas in the North and Central West regions of Brazil since the 1980s, with an increase in human case notifications in the last 10 years. MAYV introduction in urban areas is a public health concern once the infection can cause severe symptoms similar to other Alphaviruses. Regarding to urban transmission, studies with Aedes aegypti demonstrate the potential vector competence of the species and the detection of MAYV in urban populations of mosquitoes. Considering the two most abundant urban mosquito species in Brazil, we investigated the dynamics of MAYV transmission by Ae. aegypti and Culex quinquefasciatus in a mice model. Mosquito colonies were artificially fed with blood containing MAYV and infection (IR) and dissemination rates (DR) were evaluated. On the 7th post-infection day (dpi), IFNAR BL/6 mice were made available as a blood source to both mosquitos species. After the appearance of clinical signs of infection, a second blood feeding was performed with a new group of non-infected mosquitoes. RT-q PCR and plaque assay were carried out with animal and mosquitos tissues. We found for Ae. aegypti a IR of 97,5-100% and a DR of 100% in both 7th and 14th dpi. Regarding Cx. quinquefasciatus, the IR found was 13.1-14.81% and DR ranged from 60% to 80%. To evaluate the mosquito-mice transmission rate, 18 mice were evaluated (Test=12 and Control=6) for Ae. aegypti and 12 animals (Test=8 and Control=4) for Cx. quinquefasciatus. All mice bitten by infected Ae. aegypti showed clinical signs of infection while all mice exposed to infected Cx. quinquefasciatus mosquitoes remained healthy. Viremia found in those animals ranged from 2.5 x 108 to 5 x 109 PFU/ml. Ae. aegypti from the second blood feeding showed a 50% infection rate. Our study showed the applicability of an efficient model to complete arbovirus transmission cycle studies and suggests that the Ae. aegypti population evaluated is a competent vector for MAYV highlighting the risk of establishment of MAYV urban cycle. The mice model employed here can be used more extensively for arthropod-vector transmission studies, with laboratory and field mosquito populations, as well as with other arboviruses. Author summaryMayaro virus (MAYV) is an arbovirus maintained mostly in a sylvan cycle in South America, circulating between Haemagogus mosquitoes and wild animals. In Brazil, MAYV has been circulating in the northern region since early 80s, but a substantial increase in human cases has been reported in the past decade. MAYV infections may go undetected, as clinical symptoms are mistaken with other arboviruses already circulating in Brazil, such as dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) viruses. The introduction of MAYV in other parts of Brazil may result in a public health concern, since the virus will find all favorable conditions in urban settings: high mosquito densities, poor sanitation and uncontrolled urbanization. Therefore, we conducted a study to test the vector competence of MAYV in the two most abundant mosquito species in Brazil: Aedes aegypti and Culex quinquefasciatus. We used an animal model to analyze the dynamics between artificially-infected mosquitos and mice. We fed mosquito colonies with blood containing MAYV and on the 7th day post-infection (dpi), mice were made available as a blood source to both mosquitos species. When these mice display signs of infection, a second blood feeding was performed with a new group of non-infected mosquitoes. We found that Ae. aegypti mosquitoes are very competent in transmitting MAYV, while Cx. quinquefasciatus presented lower rates of infection and dissemination of the virus. All mice bitten by infected Ae. aegypti showed clinical signs of infection. On the other hand, all mice exposed to infected Cx. quinquefasciatus mosquitoes remained healthy. We also found a higher viremia in animals bitten by infected-Ae. aegypti. Overall, our study showed the applicability of an efficient model to complete arbovirus transmission cycle studies and suggests that the Ae. aegypti population evaluated is a competent vector for MAYV highlighting the risk of establishment of MAYV urban cycle.

molecular biology↗

bioRxiv2022

The virome of bats inhabiting Brazilian biomes: knowledge gaps and biases towards zoonotic viruses

Bats are hosts of a large variety of viruses including some that may infect other vertebrates and humans. Research on bat-borne viruses attracted significant attention in recent years mainly due to epizootics caused by viruses having bats as hosts. The characterization of the viral communities of bats was then prioritized, but despite increasing efforts, there are large disparities in the geographical ranges covered and the methodologies employed around the world. As a result, large gaps remain in our current understanding of bat viromes and their role in disease emergence. This is particularly true for megadiverse regions in Latin America. This review aims to summarize the current understanding about bat-viruses that inhabit Brazilian biomes, one of the most bat species-rich and diverse regions of the globe. Taking into account all known bat-associated viral families studied in Brazilian biomes, we found that almost half of all bat species (86/181 species) were not investigated for viruses at all. Moreover, only a small fraction of viral lineages or families have been studied more in depth, usually employing targeted methods with limited power to characterize a broad virus diversity. Additionally, these studies relied on limited spatio-temporal sampling and small sample sizes. Therefore, our current understanding of bat viral communities in the Brazilian biomes is limited and biased at different levels, limiting zoonotic risk assessments of bat-borne viruses. Considering these limitations, we propose strategies to bridge the existing gaps in the near future.

microbiology↗

bioRxiv2020

Transposable elements are constantly exchanged by horizontal transferreshaping mosquito genomes

Transposable elements (TEs) are a set of mobile elements within a genome. Due to their complexity, an in-depth TE characterization is only available for a handful of model organisms. In the present study, we performed a de novo and homology-based characterization of TEs in the genomes of 24 mosquito species and investigated their mode of inheritance. More than 40% of the genome of Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus is composed of TEs, varying substantially among Anopheles species (0.13%-19.55%). Class I TEs are the most abundant among mosquitoes and at least 24 TE superfamilies were found. Interestingly, TEs have been continuously exchanged by horizontal transfer (212 TE families of 18 different superfamilies) among mosquitoes since 30 million years ago, representing around 6% of the genome in Aedes genomes and a small fraction in Anopheles genomes. Most of these horizontally transferred TEs are from the three ubiquitous LTR superfamilies: Gypsy, Bel-Pao and Copia. Searching more 32,000 genomes, we also uncover transfers between mosquitoes and two different Phyla--Cnidaria and Nematoda--and two subphyla--Chelicerata and Crustacea, identifying a vector, the worm Wuchereria bancrofti, that enabled the horizontal spread of a Tc1-mariner element of irritans subfamily among various Anopheles species. These data also allowed us to reconstruct the horizontal transfer network of this TE involving more than 40 species. In summary, our results suggest that TEs are constantly exchanged by common phenomena of horizontal transfers among mosquitoes, influencing genome variation and contributing to genome size expansion. Author SummaryMost eukaryotes have DNA fragments inside their genome that can multiply by inserting themselves in other regions of the genome, generating variability. These fragments are called Transposable Elements (TEs). Since they are a constituent part of the eukaryote genomes, these pieces of DNA are usually inherited vertically by the offspring. To avoid damage to the genome caused by the replication and insertion of TEs, organisms usually control them, leading to their inactivation. However, TEs sometimes get out of control and invade other species through a horizontal transfer mechanism. This dynamic is not known in mosquitoes, a group of organisms that acts as vectors of many human diseases. We collected mosquito genomes available in public databases and characterized the whole content of TEs. Using a statistic supported method, we investigate TE relations among mosquitoes and discover that horizontal transfers of transposons are common and occurred in the last 30 million years among these species. Although not as common as transfers among closely related species, transposon transfer to distant species also occur. We also identify a parasite, a filarial worm, that may have facilitated the transfer of TE to many mosquitoes. Together, horizontally transferred TEs contribute to increasing mosquito genome size and variation.

evolutionary biology↗

bioRxiv2020

In and outs of Chuviridae endogenous viral elements: origin of a retrovirus and signature of ancient and ongoing arms race in mosquito genomes

BackgroundEndogenous viral elements (EVEs) are sequences of viral origin integrated into the host genome. EVEs have been characterized in various insect genomes, including mosquitoes. A large EVE content has been found in Aedes aegypti and Aedes albopictus genomes among which a recently described Chuviridae viral family is of particular interest, owing to the abundance of EVEs derived from it, the discrepancy in the endogenized gene regions and the frequent association with retrotransposons from the BEL-Pao superfamily. In order to better understand the endogenization process of chuviruses and the association between chuvirus glycoproteins and BEL-Pao retrotransposons, we performed a comparative genomics and evolutionary analysis of chuvirus-derived EVEs found in 37 mosquito genomes. ResultsWe identified 428 EVEs belonging to the Chuviridae family confirming the wide discrepancy between the number of genomic regions endogenized: 409 glycoproteins, 18 RNA-dependent RNA polymerases and one nucleoprotein region. Most of the glycoproteins (263 out of 409) are associated specifically with retroelements from the Pao family. Focusing only on well assembled Pao retroelement copies, we estimated that 263 out of 379 Pao elements are associated with chuvirus-derived glycoproteins. Seventy-three potentially active Pao copies were found to contain glycoproteins into their LTR boundaries. Thirteen out of these were classified as complete and likely autonomous copies, with a full LTR structure and protein domains. We also found 116 Pao copies with no trace of glycoproteins and 37 solo glycoproteins. All potential autonomous Pao copies, contained highly similar LTRs, suggesting a recent/current activity of these elements in the mosquito genomes. ConclusionEvolutionary analysis revealed that most of the glycoproteins found are likely derived from a single or few glycoprotein endogenization events associated with a recombination event with a Pao ancestral element. A potential fully functional Pao-chuvirus hybrid (named Anakin) emerged and the glycoprotein was further replicated through retrotransposition. However, a number of solo glycoproteins, not associated with Pao elements, can still be found in some mosquito genomes 114 million years later, suggesting that these glycoproteins were likely domesticated by the host genome and may participate in an antiviral defense mechanism against both chuvirus and Anakin retrovirus.

evolutionary biology↗

bioRxiv2019

Time and mode of Culicidae evolutionary history

Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans and other mammals. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquitoes species. Here we sequenced the mitogenomes of mosquitoes species through low-coverage sequencing and data mining. A total of 37 draft mitogenomes were assembled representing 11 genera and 16 of those were sequenced for the first time. The recovered mitogenomes showed a coverage breadth average of 81.24%. Most of the species were clustered in monophyletic clades with other members of their own genus with exception of the Aedini tribe which was paraphyletic corroborating other findings. We established for the first time the monophyletic status of eight species from the tribe Mansoniini including both Coquillettidia and Mansonia genus and established the basal positioning of Aedeomyiini and Uranotaeniini tribes regarding the Culicinae subfamily. Molecular clock dated the Culicidae family emergence around 273 MYA and the split between Anophelinae and Culicinae subfamily around 182 MYA in the Jurassic period. Low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge generating basic fundamental information to the understanding of the role of these species as pathogen vectors.

evolutionary biology↗

bioRxiv2019

First complete genome sequences of Zika virus from Midwest Brazil, 2015.

Zika virus (ZIKV) has been intensively studied in Brazil since 2015-2016 epidemics, but little is known about the virus in Midwest region of the country. We report here two ZIKV complete genomes, which were isolated during arboviral surveillance in Sinop city, southern border of the Amazonian forest, Midwest Brazil, 2015.

genomics↗