Biology subjects

Martinez-Recio, R.

Publications and source records attributed to Martinez-Recio, R..

6 recordsLinked to original sources

bioRxiv2025

Rodents as Potential Reservoirs for Toroviruses

Emerging zoonotic viruses pose a significant threat to global health. The order Nidovirales includes diverse viruses, such as coronaviruses, which are well known for their zoonotic potential. Toroviruses are a less-studied genus within Nidovirales primarily associated with gastrointestinal diseases in ungulates, although some evidence suggests their presence in humans. In this study, we report the discovery of a novel torovirus from a fecal sample of a dormouse (Eliomys quercinus) in Spain, which we named Dormouse torovirus (DToV). This represents the first complete genome of a rodent-associated torovirus. The 28,555-nucleotide genome encodes the six characteristic torovirus open reading frames, but these exhibit low amino acid sequence identity (44.3-86.3%) compared to other toroviruses, indicating that DToV likely represents a new viral species. Bayesian analysis of the ORF1b suggests that DToV diverged from known toroviruses approximately 1300 years ago. Moreover, the basal phylogenetic position of DToV suggests that rodents may represent a reservoir for this viral genus. Our findings expand the known torovirus host range, underscore their potential for cross-species transmission, and highlight the importance of continued surveillance of wildlife viruses. ImportanceCurrently, there is concern about the potential emergence of new viruses from natural reservoirs. This has led to an increasing search taking advantage of new massive sequencing methodologies. In our study, we have identified a complete genome of a torovirus in a rodent species in Spain. Toroviruses are a group related to coronaviruses and cause gastrointestinal diseases in ungulates, such as cows or pigs. However, they have not been studied in depth, as there is no clear evidence of their ability to infect humans. Our results suggest that rodents may be the natural reservoir of toroviruses and underline their potential for cross-species transmission. Based on the results obtained from monitoring wildlife for viruses with zoonotic potential, the next step will be to implement new approaches in the laboratory to characterise the ability of these viruses to infect humans.

microbiology↗

bioRxiv2025

Identification and characterization of novel bat coronaviruses in Spain

The zoonotic transmission of bat coronaviruses poses a threat to human health. However, the diversity of bat-borne coronaviruses remains poorly characterized in many geographical areas. Here, we recovered six complete coronavirus genomes by performing a metagenomic analysis of fecal samples from hundreds of individual bats captured in Spain, a country with high bat species diversity. Three of these genomes corresponded to potentially novel coronavirus species belonging to the alphacoronavirus genus. Phylogenetic analyses revealed that some of these viruses are closely related to coronaviruses previously described in bats from other countries, suggesting the existence of a shared viral reservoir worldwide. Using viral pseudotypes, we investigated the receptor usage of the identified viruses and found that one of them can use human and bat ACE2, highlighting its zoonotic potential. However, the receptor usage of the other viruses remains unknown. This study broadens our understanding of coronavirus diversity and identifies research priorities for the prevention of zoonotic viral outbreaks. Author summaryBats carry many viruses, some of which can cross the species barrier and infect humans, a process known as zoonosis. In particular, bat-borne coronaviruses pose a significant threat to human health. To improve our pandemic preparedness, it is essential to characterize the diversity and zoonotic potential of bat coronaviruses. However, such research efforts have historically suffered from a strong geographical bias. For example, despite the rich bat diversity in Spain, few studies have searched for coronaviruses in Iberian bats. Here, we used viral metagenomics to test for the presence of coronaviruses in more than 200 bat samples collected across Spain. We detected six complete coronaviruses, three of which were proposed to be new viral species. We characterized their relationship to previously identified viruses and their ability to use known coronavirus receptors to enter cells, demonstrating that one virus could use human ACE2 as a receptor. Our results highlight the diversity of bat-borne coronaviruses in Spain, their zoonotic potential, and the need to better characterize coronavirus diversity worldwide.

microbiology↗

bioRxiv2024

Complete genomes of DNA viruses in faecal samples from small terrestrial mammals in Spain

Viromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by emerging viruses. Regarding the latter, the main concern lies in monitoring the presence of RNA viruses, but the zoonotic potential of some DNA viruses, on which we have focused in the present study, should also be highlighted. For this purpose, we analysed 160 faecal samples from 14 species belonging to three orders of small terrestrial mammals (i.e. Rodentia, Lagomorpha and Eulypotyphla). This allowed us to identify a total of 25 complete or near-complete genomes belonging to the families Papillomaviridae, Polyomaviridae, Adenoviridae, Circoviridae and Genomoviridae, 18 of which could be considered new species or types. Our results provide a significant increase in the number of complete genomes of DNA viruses of European origin with zoonotic potential in databases, which are at present clearly under-represented compared to RNA viruses.

microbiology↗

bioRxiv2024

A new clade of pararetroviruses distantly related to hepadnaviruses and nackednaviruses

Group VII of the Baltimore classification comprises reverse-transcribing, non-integrated DNA viruses, also known as pararetroviruses. These include the hepadnaviruses, a family of small enveloped DNA viruses that infect vertebrates, but also a sister family of non-enveloped fish viruses, the nackednaviruses. Here we describe the complete sequence of a new pararetrovirus found in the feces of an insectivorous bat. This virus encodes a core protein and a reverse transcriptase but no envelope protein. A database search identified a viral sequence from a permafrost sample as its closest relative. The two viruses form a cluster that occupies a basal phylogenetic position relative to hepadnaviruses and nackednaviruses, with an estimated divergence time of 500 million years. These findings may lead to the definition of a new viral family and support the hypothesis that ancestral animal pararetroviruses were non-enveloped.

evolutionary biology↗

bioRxiv2024

Genetic diversity and cross-species transmissibility of bat-associated picornaviruses from Spain

BackgroundEmerging zoonotic diseases arise from cross-species transmission events between wild or domesticated animals and humans, with bats being one of the major reservoirs of zoonotic viruses. Viral metagenomics has led to the discovery of many viruses, but efforts have mainly been focused on some areas of the world and on certain viral families. MethodsWe set out to describe full-length genomes of new picorna-like viruses by collecting feces from hundreds of bats captured in different regions of Spain. Viral sequences were obtained by high-throughput Illumina sequencing and analyzed phylogenetically to classify them in the context of known viruses. Linear discriminant analysis (LDA) was performed to infer likely hosts based on genome composition. ResultsWe found five complete or nearly complete genomes belonging to the family Picornaviridae, including a new species of the subfamily Ensavirinae. LDA suggested that these were true vertebrate viruses, rather than viruses from the bat diet. Some of these viruses were related to picornaviruses previously found in other bat species from distant geographical regions. We also found a calhevirus genome that most likely belongs to a proposed new family within the order Picornavirales, and for which genome composition analysis suggested a plant host. ConclusionsOur findings describe new picorna-like viral species and variants circulating in the Iberian Peninsula, illustrate the wide geographical distribution and interspecies transmissibility of picornaviruses, and suggest new hosts for calheviruses.

microbiology↗

bioRxiv2024

Full genome sequencing of dozens of new DNA viruses found in Spanish bat faeces

Bats are natural hosts of multiple viruses, many of which have clear zoonotic potential. The search for emerging viruses has been aided by the implementation of metagenomic tools, which have also enabled the detection of unprecedented viral diversity. Currently, this search is mainly focused on RNA viruses, which are largely over-represented in databases. To compensate for this research bias, we analyzed fecal samples from 189 Spanish bats belonging to 22 different species using viral metagenomics. This allowed us to identify 50 complete or near-complete viral genomes belonging to the families Adenoviridae, Circoviridae, Genomoviridae, Papillomaviridae, Parvoviridae, Polyomaviridae and Smacoviridae. Of these, 28 could constitute new species, doubling the number of viruses currently described in Europe. These findings open the door to a more thorough analysis of bat DNA viruses and their zoonotic potential. IMPORTANCEMetagenomics has become a fundamental tool to characterize the global virosphere, allowing us to understand the existing viral diversity and its ecological implications, but also to identify new and emerging viruses. RNA viruses have a higher zoonotic potential, but this risk is also present for some DNA virus families. In our study, we have analyzed the DNA fraction of faecal samples from 22 Spanish bat species, identifying 50 complete or near-complete genomes of different viral families with zoonotic potential. This doubles the number of genomes currently described in Europe. Metagenomic data often produce partial genomes that can be difficult to analyse. Our work, however, has characterised a large number of complete genomes, thus facilitating their taxonomic classification and enabling different analyses to be carried out to evaluate their zoonotic potential. For example, recombination studies are relevant, since this phenomenon could play a major role in cross-species transmission.

microbiology↗