Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland

Wiederkehr, Myriam Anja; Qi, Weihong; Schoenbaechler, Katja; Fraefel, Cornel; Kubacki, Jakub

doi:10.3390/v14091911

Cited by 9 publications

(6 citation statements)

References 126 publications

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“…In accordance with the study objectives, bacteriophage sequences were not investigated further. Encountering bacterial virus sequences is common in studies of chiropteran viromes [ 18 , 35 , 36 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis

Pinheiro,

Rodrigues,

Paiva

et al. 2024

Microorganisms

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Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats.

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Section: Discussionmentioning

confidence: 99%

Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis

Pinheiro,

Rodrigues,

Paiva

et al. 2024

Microorganisms

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“…Primates have additional TRIM duplications on chromosome 11 close to the TRIM5/6/22/34 cluster, including TRIM49 and 64 ( 120 ). Bats host many types of viruses ( 123 – 125 ) and have duplications of TRIM5 and 22 ( 107 , 126 ). There are other species-specific differences of C-IV members in bats, including duplications of TRIM25, 41, 60, and 75 ( 126 ).…”

Section: Discussionmentioning

confidence: 99%

Evolution and expression of the duck TRIM gene repertoire

2023

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Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a de novo assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck (Anas platyrhynchos), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.

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“…This means that the host usually carries a low viral load and is able to tolerate some viral replication. Studies have shown that bats have unique immunological approaches to enable coexistence with viral infections, causing no disease, while allowing enough viral replication for transmission (30)(31)(32). Screening the virome for over 4000 healthy bats from 40 different species of both Yangochiroptera and Yinpterochiroptera suborders, revealed an array of viruses belonging to diverse families, the most prevalent being Herpesviridae, Papillomaviridae, Retroviridae, Adenoviridae and Astroviridae, but also Coronaviridae, Caliciviridae, Polyomaviridae, Rhabdoviridae, among others (33), confirming bats as reservoirs of various virus.…”

Section: Divergence Analysismentioning

confidence: 99%

Evolution of guanylate binding protein genes shows a remarkable variability within bats (Chiroptera)

Pinheiro,

Borges,

Côrte-Real

et al. 2024

Front. Immunol.

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BackgroundGBPs (guanylate binding proteins), an evolutionary ancient protein family, play a key role in the host’s innate immune response against bacterial, parasitic and viral infections. In Humans, seven GBP genes have been described (GBP1-7). Despite the interest these proteins have received over the last years, evolutionary studies have only been performed in primates, Tupaia and rodents. These have shown a pattern of gene gain and loss in each family, indicative of the birth-and-death evolution process.ResultsIn this study, we analysed the evolution of this gene cluster in several bat species, belonging to the Yangochiroptera and Yinpterochiroptera sub-orders. Detailed analysis shows a conserved synteny and a gene expansion and loss history. Phylogenetic analysis showed that bats have GBPs 1,2 and 4-6. GBP2 has been lost in several bat families, being present only in Hipposideidae and Pteropodidae. GBPs1, 4 and 5 are present mostly as single-copy genes in all families but have suffered duplication events, particularly in Myotis myotis and Eptesicus fuscus. Most interestingly, we demonstrate that GBP6 duplicated in a Chiroptera ancestor species originating two genes, which we named GBP6a and GBP6b, with different subsequent evolutionary histories. GBP6a underwent several duplication events in all families while GBP6b is present as a single copy gene and has been lost in Pteropodidae, Miniopteridae and Desmodus rotundus, a Phyllostomidae. With 14 and 15 GBP genes, Myotis myotis and Eptesicus fuscus stand out as having far more copies than all other studied bat species. Antagonistically, Pteropodidae have the lowest number of GBP genes in bats.ConclusionBats are important reservoirs of viruses, many of which have become zoonotic diseases in the last decades. Further functional studies on bats GBPs will help elucidate their function, evolutionary history, and the role of bats as virus reservoirs.

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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland

Cited by 9 publications

References 126 publications

Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis

Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis

Evolution and expression of the duck TRIM gene repertoire

Evolution of guanylate binding protein genes shows a remarkable variability within bats (Chiroptera)

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