{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T15:09:41Z","timestamp":1784732981930,"version":"3.55.0"},"reference-count":53,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2024,3,16]],"date-time":"2024-03-16T00:00:00Z","timestamp":1710547200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Coordination of Superior Level Staff Improvement","award":["88887.636483\/2021-00"],"award-info":[{"award-number":["88887.636483\/2021-00"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/microorganisms12030593","type":"journal-article","created":{"date-parts":[[2024,3,18]],"date-time":"2024-03-18T06:58:39Z","timestamp":1710745119000},"page":"593","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8830-505X","authenticated-orcid":false,"given":"Lucas Rafael Santana","family":"Pinheiro","sequence":"first","affiliation":[{"name":"Graduate Program in Virology, Hemorrhagic Fevers and Arbovirology Section (SAARB), Evandro Chagas Institute (IEC), BR-316 Highway, km 7, Levil\u00e2ndia, Ananindeua 67030-000, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c9rika Dayane Leal","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Hemorrhagic Fevers and Arbovirology Section (SAARB), Evandro Chagas Institute (IEC), BR-316 Highway, km 7, Levil\u00e2ndia, Ananindeua 67030-000, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco Amilton dos Santos","family":"Paiva","sequence":"additional","affiliation":[{"name":"Hemorrhagic Fevers and Arbovirology Section (SAARB), Evandro Chagas Institute (IEC), BR-316 Highway, km 7, Levil\u00e2ndia, Ananindeua 67030-000, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4607-9346","authenticated-orcid":false,"given":"Ana Cec\u00edlia Ribeiro","family":"Cruz","sequence":"additional","affiliation":[{"name":"Hemorrhagic Fevers and Arbovirology Section (SAARB), Evandro Chagas Institute (IEC), BR-316 Highway, km 7, Levil\u00e2ndia, Ananindeua 67030-000, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniele Barbosa de Almeida","family":"Medeiros","sequence":"additional","affiliation":[{"name":"Hemorrhagic Fevers and Arbovirology Section (SAARB), Evandro Chagas Institute (IEC), BR-316 Highway, km 7, Levil\u00e2ndia, Ananindeua 67030-000, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre do Ros\u00e1rio","family":"Casseb","sequence":"additional","affiliation":[{"name":"Health and Animal Production Institute, Federal and Rural University of Amazon (UFRA), Bel\u00e9m 66077-830, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7185-4538","authenticated-orcid":false,"given":"Sandro Patroca da","family":"Silva","sequence":"additional","affiliation":[{"name":"Hemorrhagic Fevers and Arbovirology Section (SAARB), Evandro Chagas Institute (IEC), BR-316 Highway, km 7, Levil\u00e2ndia, Ananindeua 67030-000, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8578-9984","authenticated-orcid":false,"given":"Livia Medeiros Neves","family":"Casseb","sequence":"additional","affiliation":[{"name":"Hemorrhagic Fevers and Arbovirology Section (SAARB), Evandro Chagas Institute (IEC), BR-316 Highway, km 7, Levil\u00e2ndia, Ananindeua 67030-000, PA, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,3,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1590\/S0034-89101999000600016","article-title":"Isolamento Do V\u00edrus R\u00e1bico Em Molossus Ater (Chiroptera: Molossidae) No Estado de S\u00e3o Paulo","volume":"33","author":"Silva","year":"1999","journal-title":"Rev. Sa\u00fade P\u00fablica"},{"key":"ref_2","first-page":"215","article-title":"Preda\u00e7\u00e3o oportun\u00edstica de Molossus molossus (Pallas, 1766) (Chiroptera: Molossidae) por Rhinella jimi (Stevaux, 2002) (Anura: Bufonidae) na Caatinga, Pernambuco, Brasil","volume":"23","author":"Silva","year":"2010","journal-title":"Biotemas"},{"key":"ref_3","first-page":"143","article-title":"First record of Molossus coibensis (Chiroptera: Molossidae) in the brazilian amazon","volume":"20","author":"Costa","year":"2013","journal-title":"Mastozoolog\u00eda Neotrop."},{"key":"ref_4","first-page":"23","article-title":"Quir\u00f3pteros hospedeiros de zoonoses no Brasil","volume":"67","author":"Lazar","year":"2013","journal-title":"Bol. Soc. Bras. Mastozool"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Salmier, A., Tirera, S., Thoisy, B., Franc, A., Darcissac, E., Donato, D., Bouchier, C., Lacoste, V., and Lavergne, A. (2017). Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0186943"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/ncomms1796","article-title":"Bats Host Major Mammalian Paramyxoviruses","volume":"3","author":"Drexler","year":"2012","journal-title":"Nat. Commun."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1099\/jgv.0.001328","article-title":"ICTV virus taxonomy profile: Paramyxoviridae","volume":"100","author":"Rima","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_8","unstructured":"Strauss, J.H., and Strauss, E.G. (2008). Viruses and Human Disease, Elsevier. [2nd ed.]. EUA."},{"key":"ref_9","unstructured":"King, A.M., Lefkowitz, E., Adams, M.J., and Carstens, E.B. (2012). Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses, Elsevier Science. EUA."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"162","DOI":"10.26605\/medvet-n3-1776","article-title":"Cinomose Canina: Revis\u00e3o de Literatura","volume":"11","author":"Portela","year":"2017","journal-title":"Med. Vet. (UFRPE)"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Lee, B., Ikegame, S., Carmichael, J., Wells, H., Furler, R., Acklin, J., Chiu, H.-P., Oguntuyo, K., Cox, R., and Patel, A. (2021). Zoonotic Potential of a Novel Bat Morbillivirus. Res. Sq., preprint.","DOI":"10.21203\/rs.3.rs-926789\/v1"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Kingsbury, D.W. (1991). The Paramyxoviruses, Springer. [1st ed.]. The Viruses; EUA.","DOI":"10.1007\/978-1-4615-3790-8"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"104036","DOI":"10.1016\/j.meegid.2019.104036","article-title":"Krykf\u00e9ie Dicistrovirus: A Novel Dicistrovirus in Velvety Free-Tailed Bats from Brazil","volume":"75","author":"Fumagalli","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1146\/annurev-ento-112408-085457","article-title":"Dicistroviruses","volume":"55","author":"Bonning","year":"2010","journal-title":"Annu. Rev. Entomol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"e00068-16","DOI":"10.1128\/genomeA.00068-16","article-title":"Draft Genome Sequence of Goose Dicistrovirus","volume":"4","author":"Greninger","year":"2016","journal-title":"Genome Announc."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"3453","DOI":"10.1007\/s00705-014-2212-2","article-title":"Novel Dicistrovirus from Bat Guano","volume":"159","author":"Reuter","year":"2014","journal-title":"Arch. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Bourgarel, M., No\u00ebl, V., Pfukenyi, D., Michaux, J., Andr\u00e9, A., Becquart, P., Cerqueira, F., Barrachina, C., Bou\u00e9, V., and Talignani, L. (2019). Next-Generation Sequencing on Insectivorous Bat Guano: An Accurate Tool to Identify Arthropod Viruses of Potential Agricultural Concern. Viruses, 11.","DOI":"10.3390\/v11121102"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Dacheux, L., Cervantes-Gonzalez, M., Guigon, G., Thiberge, J.-M., Vandenbogaert, M., Maufrais, C., Caro, V., and Bourhy, H. (2014). A Preliminary Study of Viral Metagenomics of French Bat Species in Contact with Humans: Identification of New Mammalian Viruses. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0087194"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.virol.2018.12.009","article-title":"Diverse RNA Viruses of Arthropod Origin in the Blood of Fruit Bats Suggest a Link between Bat and Arthropod Viromes","volume":"528","author":"Bennett","year":"2019","journal-title":"Virology"},{"key":"ref_20","unstructured":"Pereira, R.H.M., and Gon\u00e7alves, C.N. (2023, November 21). Geobr: Loads Shapefiles of Official Spatial Data Sets of Brazil. GitHub Repository. Available online: https:\/\/github.com\/ipeaGIT\/geobr."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e107","DOI":"10.1002\/imt2.107","article-title":"Ultrafast One-pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp","volume":"2","author":"Chen","year":"2023","journal-title":"iMeta"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast Gapped-Read Alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41586-020-2486-3","article-title":"Six Reference-Quality Genomes Reveal Evolution of Bat Adaptations","volume":"583","author":"Jebb","year":"2020","journal-title":"Nature"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3211","DOI":"10.1093\/bioinformatics\/bts611","article-title":"SortMeRNA: Fast and Accurate Filtering of Ribosomal RNAs in Metatranscriptomic Data","volume":"28","author":"Kopylova","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and Sensitive Protein Alignment Using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ondov, B.D., Bergman, N.H., and Phillippy, A.M. (2011). Interactive Metagenomic Visualization in a Web Browser. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-385"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An Ultra-Fast Single-Node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: A Self-Training Method for Prediction of Gene Starts in Microbial Genomes. Implications for Finding Sequence Motifs in Regulatory Regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-Scale Protein Function Classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/S0022-2496(02)00028-7","article-title":"Tutorial on Maximum Likelihood Estimation","volume":"47","author":"Myung","year":"2003","journal-title":"J. Math. Psychol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2307\/2408678","article-title":"Confidence Limits on Phylogenies: An Approach Using the Bootstrap","volume":"39","author":"Felsenstein","year":"1985","journal-title":"Evolution"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/s00705-020-04825-x","article-title":"Detection of Multiple Viruses in Oropharyngeal Samples from Brazilian Free-Tailed Bats (Tadarida brasiliensis) Using Viral Metagenomics","volume":"166","author":"Cibulski","year":"2021","journal-title":"Arch. Virol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Wiederkehr, M.A., Qi, W., Schoenbaechler, K., Fraefel, C., and Kubacki, J. (2022). Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses, 14.","DOI":"10.3390\/v14091911"},{"key":"ref_37","first-page":"Doc16","article-title":"Mimiviridae, Marseilleviridae, and Virophages as Emerging Human Pathogens Causing Healthcare-Associated Infections","volume":"9","author":"Kutikhin","year":"2014","journal-title":"GMS Hyg. Infect. Control"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1038\/s41579-022-00754-5","article-title":"Giant Virus Biology and Diversity in the Era of Genome-Resolved Metagenomics","volume":"20","author":"Schulz","year":"2022","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_39","unstructured":"International Committee on Taxonomy of Viruses (ICTV) (2023, January 17). Current ICTV Taxonomy Release. Available online: https:\/\/ictv.global\/taxonomy\/."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1007\/s002390010215","article-title":"Viral Eukaryogenesis: Was the Ancestor of the Nucleus a Complex DNA Virus?","volume":"53","year":"2001","journal-title":"J. Mol. Evol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e01941-21","DOI":"10.1128\/mBio.01941-21","article-title":"Retroviruses of Bats: A Threat Waiting in the Wings?","volume":"12","author":"Hayward","year":"2021","journal-title":"mBio"},{"key":"ref_42","first-page":"4152","article-title":"In vitro transmission and propagation of the bovine leukemia virus in monolayer cell cultures","volume":"36","author":"Graves","year":"1976","journal-title":"Cancer Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"5180","DOI":"10.1128\/JVI.03452-14","article-title":"A Novel Endogenous Betaretrovirus in the Common Vampire Bat (Desmodus rotundus) Suggests Multiple Independent Infection and Cross-Species Transmission Events","volume":"89","author":"Mendoza","year":"2015","journal-title":"J. Virol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.coviro.2017.07.020","article-title":"Retroviruses of the RDR Superinfection Interference Group: Ancient Origins and Broad Host Distribution of a Promiscuous Env Gene","volume":"25","author":"Sinha","year":"2017","journal-title":"Curr. Opin. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1007\/s00705-022-05500-z","article-title":"Classification of New Morbillivirus and Jeilongvirus Sequences from Bats Sampled in Brazil and Malaysia","volume":"167","author":"Wells","year":"2022","journal-title":"Arch. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/S0163-4453(03)00045-8","article-title":"Measles Infection in Pregnancy","volume":"47","author":"Chiba","year":"2003","journal-title":"J. Infect."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Ohishi, K., Maruyama, T., Seki, F., and Takeda, M. (2019). Marine Morbilliviruses: Diversity and Interaction with Signaling Lymphocyte Activation Molecules. Viruses, 11.","DOI":"10.3390\/v11070606"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/bs.aivir.2017.12.003","article-title":"Morbillivirus Pathogenesis and Virus\u2013Host Interactions","volume":"Volume 100","author":"Pfeffermann","year":"2018","journal-title":"Advances in Virus Research"},{"key":"ref_49","unstructured":"Christian, P.D., and Scotti, P.D. (2008). Encyclopedia of Virology, Elsevier."},{"key":"ref_50","unstructured":"Santos, J.L. (2019). Manual de Manejo e Monitoramento de Morcegos em \u00c1reas Urbanas. Final Paper, Biologist. [Ph.D. Thesis, Federal University of Pernambuco]."},{"key":"ref_51","unstructured":"(2023, February 05). FCTViva. Available online: https:\/\/www.viva.fct.unl.pt\/mamiferos\/pipistrellus-pipistrellus."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1007\/s11262-017-1514-3","article-title":"Sera of Peruvians with Fever of Unknown Origins Include Viral Nucleic Acids from Non-Vertebrate Hosts","volume":"54","author":"Phan","year":"2018","journal-title":"Virus Genes"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1080\/22221751.2019.1603791","article-title":"Detection of Dicistroviruses RNA in Blood of Febrile Tanzanian Children","volume":"8","author":"Cordey","year":"2019","journal-title":"Emerg. Microbes Infect."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/3\/593\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:14:34Z","timestamp":1760105674000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/12\/3\/593"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,16]]},"references-count":53,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2024,3]]}},"alternative-id":["microorganisms12030593"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms12030593","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,16]]}}}