{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:16:38Z","timestamp":1792790198069,"version":"4.5.0"},"reference-count":14,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,8,31]],"date-time":"2022-08-31T00:00:00Z","timestamp":1661904000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation (FAPESP)","doi-asserted-by":"publisher","award":["2017\/23205-8"],"award-info":[{"award-number":["2017\/23205-8"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation (FAPESP)","doi-asserted-by":"publisher","award":["2018\/15826-5"],"award-info":[{"award-number":["2018\/15826-5"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation (FAPESP)","doi-asserted-by":"publisher","award":["2019\/08528-0"],"award-info":[{"award-number":["2019\/08528-0"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation (FAPESP)","doi-asserted-by":"publisher","award":["2020\/13194-1"],"award-info":[{"award-number":["2020\/13194-1"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation (FAPESP)","doi-asserted-by":"publisher","award":["2021\/09446-8"],"award-info":[{"award-number":["2021\/09446-8"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"S\u00e3o Paulo Research Foundation (FAPESP)","doi-asserted-by":"publisher","award":["2021\/11944-6"],"award-info":[{"award-number":["2021\/11944-6"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["2017\/23205-8"],"award-info":[{"award-number":["2017\/23205-8"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["2018\/15826-5"],"award-info":[{"award-number":["2018\/15826-5"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["2019\/08528-0"],"award-info":[{"award-number":["2019\/08528-0"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["2020\/13194-1"],"award-info":[{"award-number":["2020\/13194-1"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["2021\/09446-8"],"award-info":[{"award-number":["2021\/09446-8"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["2021\/11944-6"],"award-info":[{"award-number":["2021\/11944-6"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Viral metagenomics is increasingly being used for the identification of emerging and re-emerging viral pathogens in clinical samples with unknown etiology. The objective of this study was to shield light on the metavirome composition in clinical samples obtained from patients with clinical history compatible with an arboviral infection, but that presented inconclusive results when tested using RT-qPCR. The inconclusive amplification results might be an indication of the presence of an emerging arboviral agent that is inefficiently amplified by conventional PCR techniques. A total of eight serum samples with inconclusive amplification results for the routinely tested arboviruses\u2014dengue (DENV), Zika (ZIKV), and Chikungunya (CHIKV) obtained during DENV and CHIKV outbreaks registered in the state of Alagoas, Northeast Brazil between July and August 2021\u2014were submitted to metagenomic next-generation sequencing assay using NextSeq 2000 and bioinformatic pipeline for viral discovery. The performed bioinformatic analysis revealed the presence of two arboviruses: DENV type 2 (DENV-2) and CHIKV with a high genome coverage. Further, the metavirome of those samples revealed the presence of multiple commensal viruses apparently without clinical significance. The phylogenetic analysis demonstrated that the DENV-2 genome belonged to the Asian\/American genotype and clustered with other Brazilian strains. The identified CHIKV genome was taxonomically assigned as ECSA genotype, which is circulating in Brazil. Together, our results reinforce the utility of metagenomics as a valuable tool for viral identification in samples with inconclusive arboviral amplification. Viral metagenomics is one of the most potent methods for the identification of emerging arboviruses.<\/jats:p>","DOI":"10.3390\/v14091933","type":"journal-article","created":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T03:55:38Z","timestamp":1662004538000},"page":"1933","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification"],"prefix":"10.3390","volume":"14","author":[{"given":"Juliana Vanessa Cavalcante","family":"Souza","sequence":"first","affiliation":[{"name":"Central Laboratory of Public Health, Maceio 57036-860, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hazerral de Oliveira","family":"Santos","sequence":"additional","affiliation":[{"name":"Central Laboratory of Public Health, Maceio 57036-860, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anderson Brand\u00e3o","family":"Leite","sequence":"additional","affiliation":[{"name":"Central Laboratory of Public Health, Maceio 57036-860, Brazil"},{"name":"Laboratory of Pharmacology and Immunity, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceio 57051-090, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5849-7326","authenticated-orcid":false,"given":"Marta","family":"Giovanetti","sequence":"additional","affiliation":[{"name":"Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00185 Rome, Italy"},{"name":"Laboratory of Flaviviruses, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael dos Santos","family":"Bezerra","sequence":"additional","affiliation":[{"name":"Blood Center of Ribeirao Preto, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Rua Tenente Cat\u00e3o Roxo 2501, Ribeirao Preto, Sao Paulo 14051-140, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eneas de","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jardelina de Souza Tod\u00e3o","family":"Bernardino","sequence":"additional","affiliation":[{"name":"Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2267-9985","authenticated-orcid":false,"given":"Vincent Louis","family":"Viala","sequence":"additional","affiliation":[{"name":"Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4699-164X","authenticated-orcid":false,"given":"Rodrigo","family":"Haddad","sequence":"additional","affiliation":[{"name":"Faculty of Ceilandia, University of Brasilia, Federal District, Bras\u00edlia 70904-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3866-9239","authenticated-orcid":false,"given":"Massimo","family":"Ciccozzi","sequence":"additional","affiliation":[{"name":"Epidemiology and Statistic Unit, University of Campus Bio-Medico di Roma, 00185 Rome, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz Carlos Junior","family":"Alcantara","sequence":"additional","affiliation":[{"name":"Laboratory of Flaviviruses, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra 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(2021). Epidemiology and Laboratory Diagnostics of Dengue, Yellow Fever, Zika, and Chikungunya Virus Infections in Africa. Pathogens, 10.","DOI":"10.3390\/pathogens10101324"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e000530","DOI":"10.1136\/bmjgh-2017-000530","article-title":"Zika, chikungunya and dengue: The causes and threats of new and re-emerging arboviral diseases","volume":"3","author":"Teixeira","year":"2018","journal-title":"BMJ Glob. Health"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1038\/s41467-018-03772-1","article-title":"Performance of the Trioplex real-time RT-PCR assay for detection of zika, dengue, and chikungunya viruses","volume":"9","author":"Santiago","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_4","first-page":"1","article-title":"The Use of real-time PCR for arboviruses diagnosis: Integrative review","volume":"57","author":"Ayres","year":"2021","journal-title":"J. Bras. Patol. Med. 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