{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T21:31:49Z","timestamp":1761168709097,"version":"build-2065373602"},"reference-count":44,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministerio de Ciencias, Tecnolog\u00eda e Innovaci\u00f3n","award":["798"],"award-info":[{"award-number":["798"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Acute respiratory infections and other infectious diseases causing acute febrile syndrome are major public health concerns in Colombia, particularly among vulnerable populations such as the Wayuu Indigenous community in Manaure, La Guajira. To investigate their viral etiology, 55 nasopharyngeal swabs and 58 serum samples were collected from febrile Wayuu individuals in Manaure. RT-qPCR screening identified Coronavirus, Enteroviruses, Adenovirus, and Influenza A\/B in respiratory samples, while no arboviruses were detected in serum. Sixteen representative samples underwent metatranscriptomic next-generation sequencing (mtNGS) using the Chan-Zuckerberg ID (CZ-ID) platform. This analysis confirmed RT-qPCR findings and additionally revealed six viral contigs related to Orthopicobirnavirus hominis. Sequencing coverage enabled the reconstruction of a consensus RdRp segment, which was phylogenetically compared with sequences from diverse hosts. The virus clustered within genogroup 1, alongside Colombian isolates linked to severe acute respiratory infection. The absence of strict host-specific clustering suggests possible interspecies transmission. These findings underscore the complementary roles of targeted and unbiased approaches: RT-qPCR detected common respiratory viruses, whereas mtNGS uncovered a virus previously unreported in this community. Overall, mtNGS emerges as a powerful tool to support viral surveillance and provide baseline evidence in indigenous populations, emphasizing the need to decentralize advanced molecular diagnostics and strengthen public health capacity in Colombia.<\/jats:p>","DOI":"10.3390\/v17101397","type":"journal-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T13:42:03Z","timestamp":1761054123000},"page":"1397","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Metatranscriptomic Analysis of Oropharyngeal Samples Reveals Common Respiratory Viruses and a Potential Interspecies Transmitted Picobirnavirus in the Wayuu Population, La Guajira, Colombia"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0498-783X","authenticated-orcid":false,"given":"Beatriz Elena","family":"De arco-Rodr\u00edguez","sequence":"first","affiliation":[{"name":"Grupo de Gen\u00f3mica de Microorganismos Emergentes, Direcci\u00f3n de Investigaci\u00f3n en Salud P\u00fablica, Instituto Nacional de Salud, Bogot\u00e1 111321, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5437-5831","authenticated-orcid":false,"given":"Jhindy Tatiana","family":"P\u00e9rez-Lozada","sequence":"additional","affiliation":[{"name":"Grupo de Gen\u00f3mica de Microorganismos Emergentes, Direcci\u00f3n de Investigaci\u00f3n en Salud P\u00fablica, Instituto Nacional de Salud, Bogot\u00e1 111321, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1383-3127","authenticated-orcid":false,"given":"Katherine","family":"Laiton-Donato","sequence":"additional","affiliation":[{"name":"Grupo de Gen\u00f3mica de Microorganismos Emergentes, Direcci\u00f3n de Investigaci\u00f3n en Salud P\u00fablica, Instituto Nacional de Salud, Bogot\u00e1 111321, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4752-8358","authenticated-orcid":false,"given":"Dioselina","family":"Pel\u00e1ez-Carvajal","sequence":"additional","affiliation":[{"name":"Grupo de Gen\u00f3mica de Microorganismos Emergentes, Direcci\u00f3n de Investigaci\u00f3n en Salud P\u00fablica, Instituto Nacional de Salud, Bogot\u00e1 111321, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8577-0228","authenticated-orcid":false,"given":"Gloria Mercedes","family":"Puerto-Castro","sequence":"additional","affiliation":[{"name":"Grupo de Micobacterias, Direcci\u00f3n de Investigaci\u00f3n en Salud P\u00fablica, Instituto Nacional de Salud, Bogot\u00e1 111321, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6534-0079","authenticated-orcid":false,"given":"Diego Alejandro","family":"\u00c1lvarez-D\u00edaz","sequence":"additional","affiliation":[{"name":"Grupo de Gen\u00f3mica de Microorganismos Emergentes, Direcci\u00f3n de Investigaci\u00f3n en Salud P\u00fablica, Instituto Nacional de Salud, Bogot\u00e1 111321, Colombia"},{"name":"Grupo de Investigaci\u00f3n y Desarrollo de Vacunas y Biol\u00f3gicos Estrat\u00e9gicos en Salud P\u00fablica, Direcci\u00f3n de Producci\u00f3n, Instituto Nacional de Salud, Bogot\u00e1 111321, Colombia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1016\/j.jiph.2022.10.015","article-title":"Prevalence, incidence, and severity associated with viral respiratory tract infections in Colombian adults before the COVID-19 pandemic","volume":"15","author":"Fuentes","year":"2022","journal-title":"J. Infect. Public Health"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Yozwiak, N.L., Skewes-Cox, P., Stenglein, M.D., Balmaseda, A., Harris, E., and DeRisi, J.L. (2012). Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing. PLoS Negl. Trop. Dis., 6.","DOI":"10.1371\/journal.pntd.0001485"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"100595","DOI":"10.1016\/j.onehlt.2023.100595","article-title":"The global burden of neglected zoonotic diseases: Current state of evidence","volume":"17","author":"Venkateswaran","year":"2023","journal-title":"One Health"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"107680","DOI":"10.1016\/j.actatropica.2025.107680","article-title":"Repercussions of the end of the armed conflict in Colombia and its influence on the emergence of zoonotic pathogens related to acute undifferentiated febrile illness: Future challenges to be addressed","volume":"267","author":"Hidalgo","year":"2025","journal-title":"Acta Trop."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1177\/01632787241263370","article-title":"Consistency Between Administrative Health Records and Self-Reported Health Status and Health Care Use Among Indigenous Wayuu Health Insurance Enrollees: La Guajira, Colombia","volume":"48","author":"Hinds","year":"2024","journal-title":"Eval. Health Prof."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Instituto Nacional de Salud (INS) (2024). Infecci\u00f3n Respiratoria Aguda\u2014IRA Comportamiento Epidemiol\u00f3gico, Instituto Nacional de Salud (INS).","DOI":"10.33610\/416904nrcqpn"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"758","DOI":"10.2105\/AJPH.92.5.758","article-title":"Housing and Health: Time Again for Public Health Action","volume":"92","author":"Krieger","year":"2011","journal-title":"Am. J. Public Health"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Parsania, M., Poopak, B., Pouriayevali, M.H., Haghighi, S., Amirkhani, A., and Nateghian, A. (2016). Detection of Human Metapneumovirus and Respiratory Syncytial Virus by Real-Time Polymerase Chain Reaction Among Hospitalized Young Children in Iran. Jundishapur J. Microbiol., 9.","DOI":"10.5812\/jjm.32974"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2000045","DOI":"10.2807\/1560-7917.ES.2020.25.3.2000045","article-title":"Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR","volume":"25","author":"Corman","year":"2020","journal-title":"Eurosurveillance"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/j.jcv.2013.03.016","article-title":"Field evaluation of TaqMan Array Card (TAC) for the simultaneous detection of multiple respiratory viruses in children with acute respiratory infection","volume":"57","author":"Weinberg","year":"2013","journal-title":"J. Clin. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/j.jviromet.2016.05.020","article-title":"Quantitative real-time PCR assays for detection and type-specific identification of the endemic species C human adenoviruses","volume":"237","author":"Lu","year":"2016","journal-title":"J. Virol. Methods"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Aamir, U.B., Alam, M.M., Sadia, H., Zaidi, S.S.Z., and Kazi, B.M. (2015). Correction: Molecular Characterization of Circulating Respiratory Syncytial Virus (RSV) Genotypes in Gilgit Baltistan Province of Pakistan during 2011\u20132012 Winter Season. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0145599"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.jcv.2004.11.025","article-title":"Real-time RT-PCR detection of 12 respiratory viral infections in four triplex reactions","volume":"33","author":"Gunson","year":"2005","journal-title":"J. Clin. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3390\/v1010057","article-title":"More and More Coronaviruses: Human Coronavirus HKU1","volume":"1","author":"Woo","year":"2009","journal-title":"Viruses"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1086\/521308","article-title":"Human Coronavirus Infections in Rural Thailand: A Comprehensive Study Using Real-Time Reverse-Transcription Polymerase Chain Reaction Assays","volume":"196","author":"Dare","year":"2007","journal-title":"J. Infect. Dis."},{"key":"ref_16","unstructured":"World Health Organization (2025, January 10). Information Forthe Molecular Detectionof Influenza Viruses, Available online: https:\/\/cdn.who.int\/media\/docs\/default-source\/influenza\/molecular-detention-of-influenza-viruses\/protocols_influenza_virus_detection_2024.pdf?sfvrsn=df7d268a_8."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Berg, M.G., Forberg, K., Perez, L.J., Luk, K.C., Meyer, T.V., and Cloherty, G.A. (2021). Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness. Viruses, 13.","DOI":"10.3390\/v13122534"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"113677","DOI":"10.1016\/j.jviromet.2019.113677","article-title":"Novel pan-serotype control RNA for dengue virus typing through real-time reverse transcription-polymerase chain reaction","volume":"271","author":"Quintero","year":"2019","journal-title":"J. Virol. Methods"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"104967","DOI":"10.1016\/j.meegid.2021.104967","article-title":"An updated RT-qPCR assay for the simultaneous detection and quantification of chikungunya, dengue and zika viruses","volume":"93","author":"Rivera","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref_20","unstructured":"(2025, August 20). Chan Zuckerberg ID\u2014Detect & Track Infectious Diseases. Available online: https:\/\/czid.org\/."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Knox, M.A., Gedye, K.R., and Hayman, D.T.S. (2018). The Challenges of Analysing Highly Diverse Picobirnavirus Sequence Data. Viruses, 10.","DOI":"10.3390\/v10120685"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Perez, L.J., Cloherty, G.A., and Berg, M.G. (2021). Understanding the genetic diversity of picobirnavirus: A classification update based on phylogenetic and pairwise sequence comparison approaches. Viruses, 13.","DOI":"10.3390\/v13081476"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e02693-23","DOI":"10.1128\/spectrum.02693-23","article-title":"Parallel evolution of picobirnaviruses from distinct ancestral origins","volume":"11","author":"Perez","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Alhamid, G., Tombuloglu, H., Rabaan, A.A., and Al-Suhaimi, E. (2022). SARS-CoV-2 detection methods: A comprehensive review. Saudi J. Biol. Sci., 29.","DOI":"10.1016\/j.sjbs.2022.103465"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1128\/JVI.00681-19","article-title":"Effect of Geographic Isolation on the Nasal Virome of Indigenous Children","volume":"93","author":"Altan","year":"2019","journal-title":"J. Virol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"100091","DOI":"10.1016\/j.crmeth.2021.100091","article-title":"Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples","volume":"1","author":"Rajagopala","year":"2021","journal-title":"Cell Rep. Methods"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e00321-24","DOI":"10.1128\/msystems.00321-24","article-title":"Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements","volume":"9","author":"Martyn","year":"2024","journal-title":"mSystems"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e38380","DOI":"10.1016\/j.heliyon.2024.e38380","article-title":"Functional metagenomics highlights varied infection states with dynamics of pathogens and antibiotic resistance in lower respiratory tract infections","volume":"10","author":"Shamim","year":"2024","journal-title":"Heliyon"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s13073-025-01480-2","article-title":"Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline","volume":"17","author":"Lu","year":"2024","journal-title":"Genome Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1016\/j.jgg.2021.08.005","article-title":"An efficient metatranscriptomic approach for capturing RNA virome and its application to SARS-CoV-2","volume":"48","author":"Meng","year":"2021","journal-title":"J. Genet. Genomics."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Zeng, Y., Wang, G., Yang, H., Li, H., Guo, Y., Liu, H., Xu, X., and Zhang, C. (2025). Estimating the prevalence of six common respiratory viral infections in Zhangzhou, China using nasopharyngeal swabs in adults and throat swabs in Children. Sci. Rep., 15.","DOI":"10.1038\/s41598-024-84822-1"},{"key":"ref_33","unstructured":"(2025, September 30). NS: Infecci\u00f3n Respiratoria Aguda Colombia, Available online: https:\/\/www.ins.gov.co\/buscador-eventos\/BoletinEpidemiologico\/2025_Boletin_epidemiologico_semana_16.pdf."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Jo, K.J., Choi, S.-H., Oh, C.E., Kim, H., Choi, B.S., Jo, D.S., and Park, S.E. (2022). Epidemiology and Clinical Characteristics of Human Coronaviruses-Associated Infections in Children: A Multi-Center Study. Front. Pediatr., 10.","DOI":"10.3389\/fped.2022.877759"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"van der Hoek, L., Sure, K., Ihorst, G., Stang, A., Pyrc, K., Jebbink, M.F., Petersen, G., Forster, J., Berkhout, B., and \u00dcberla, K. (2005). Croup Is Associated with the Novel Coronavirus NL63. PLoS Med., 2.","DOI":"10.1371\/journal.pmed.0020240"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"340","DOI":"10.7705\/biomedica.7168","article-title":"Seroprevalencia de HCoV-NL63 y HCoV-HKU1 y su relaci\u00f3n con las caracter\u00edsticas cl\u00ednicas de pacientes con COVID-19 de Villavicencio, Colombia","volume":"44","author":"Castillo","year":"2024","journal-title":"Biom\u00e9dica"},{"key":"ref_37","unstructured":"(2025, August 18). INS: Los Virus Respiratorios Como La Influenza, Rinovirus, Enterovirus, El Sincitial Respiratorio, Entre Otros, Son Virus Respiratorios Estacionales Ya Conocidos, Available online: https:\/\/www.ins.gov.co\/Noticias\/Paginas\/INS-explica-la-circulaci%C3%B3n-de-virus-respiratorios-en-el-pa%C3%ADs.aspx."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/ve\/veae033","article-title":"Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts","volume":"10","author":"Sadiq","year":"2024","journal-title":"Virus Evol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Roux, S., Matthijnssens, J., and Dutilh, B.E. (2021). Metagenomics in Virology. Encyclopedia of Virology, Academic Press. [4th ed.]. Available online: https:\/\/www.sciencedirect.com\/science\/article\/abs\/pii\/B9780128096338209576?via%3Dihub.","DOI":"10.1016\/B978-0-12-809633-8.20957-6"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.tim.2020.05.021","article-title":"Challenges of Studying the Human Virome\u2014Relevant Emerging Technologies","volume":"29","author":"Mirzaei","year":"2021","journal-title":"Trends Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"199551","DOI":"10.1016\/j.virusres.2025.199551","article-title":"Meta-transcriptomic sequencing reveals divergent RNA viruses in geckos","volume":"354","author":"Liu","year":"2025","journal-title":"Virus Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1093\/cid\/ciy656","article-title":"Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda","volume":"68","author":"Cummings","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.3201\/eid1809.120507","article-title":"Picobirnaviruses in the human respiratory tract","volume":"18","author":"Smits","year":"2012","journal-title":"Emerg. Infect. Dis."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.jviromet.2005.02.010","article-title":"Complete nucleotide sequences of two RNA segments of human picobirnavirus","volume":"126","author":"Wakuda","year":"2005","journal-title":"J. Virol. Methods"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/10\/1397\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T01:07:40Z","timestamp":1761095260000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/10\/1397"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,21]]},"references-count":44,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2025,10]]}},"alternative-id":["v17101397"],"URL":"https:\/\/doi.org\/10.3390\/v17101397","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2025,10,21]]}}}