{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:43:09Z","timestamp":1760150589241,"version":"build-2065373602"},"reference-count":28,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2023,12,22]],"date-time":"2023-12-22T00:00:00Z","timestamp":1703203200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Pan American Health Organization (PAHO\/WHO)","award":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"],"award-info":[{"award-number":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"]}]},{"name":"Brazilian Ministry of Health","award":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"],"award-info":[{"award-number":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"]}]},{"name":"Programa Inova Fiocruz\/Oswaldo Cruz Foundation","award":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"],"award-info":[{"award-number":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"]}]},{"name":"National Institutes of Health USA","award":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"],"award-info":[{"award-number":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"]}]},{"name":"CRP-ICGEB RESEARCH","award":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"],"award-info":[{"award-number":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"]}]},{"name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior (CAPES)","award":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"],"award-info":[{"award-number":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"],"award-info":[{"award-number":["SCON2021-00180","U01 AI151698","CRP\/20\/03","001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The emergence and continued geographic expansion of arboviruses and the growing number of infected people have highlighted the need to develop and improve multiplex methods for rapid and specific detection of pathogens. Sequencing technologies are promising tools that can help in the laboratory diagnosis of conditions that share common symptoms, such as pathologies caused by emerging arboviruses. In this study, we integrated nanopore sequencing and the advantages of reverse transcription polymerase chain reaction (RT-PCR) to develop a multiplex RT-PCR protocol for the detection of Chikungunya virus (CHIKV) and several orthoflaviviruses (such as dengue (Orthoflavivirus dengue), Zika (Orthoflavivirus zikaense), yellow fever (Orthoflavivirus flavi), and West Nile (Orthoflavivirus nilense) viruses) in a single reaction, which provides data for sequence-based differentiation of arbovirus lineages.<\/jats:p>","DOI":"10.3390\/v16010023","type":"journal-article","created":{"date-parts":[[2023,12,22]],"date-time":"2023-12-22T04:44:40Z","timestamp":1703220280000},"page":"23","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3916-2018","authenticated-orcid":false,"given":"Joilson","family":"Xavier","sequence":"first","affiliation":[{"name":"Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5521-6448","authenticated-orcid":false,"given":"Vagner","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Organiza\u00e7\u00e3o Pan-Americana da Sa\u00fade, Organiza\u00e7\u00e3o Mundial da Sa\u00fade, Bras\u00edlia 70800-400, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Talita","family":"Adelino","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Estado de Minas Gerais, Funda\u00e7\u00e3o Ezequiel Dias, Belo Horizonte 30510-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3629-8529","authenticated-orcid":false,"given":"Felipe C. M.","family":"Iani","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Estado de Minas Gerais, Funda\u00e7\u00e3o Ezequiel Dias, Belo Horizonte 30510-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Glauco C.","family":"Pereira","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Estado de Minas Gerais, Funda\u00e7\u00e3o Ezequiel Dias, Belo Horizonte 30510-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Myrian M.","family":"Duarte","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Estado de Minas Gerais, Funda\u00e7\u00e3o Ezequiel Dias, Belo Horizonte 30510-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0830-3909","authenticated-orcid":false,"given":"Mauricio","family":"Lima","sequence":"additional","affiliation":[{"name":"Instituto Rene Rachou, Funda\u00e7\u00e3o Oswaldo Cruz, Belo Horizonte 30190-002, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3210-7342","authenticated-orcid":false,"given":"Emerson","family":"Castro","sequence":"additional","affiliation":[{"name":"Instituto Rene Rachou, Funda\u00e7\u00e3o Oswaldo Cruz, Belo Horizonte 30190-002, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0829-036X","authenticated-orcid":false,"given":"Carla","family":"Oliveira","sequence":"additional","affiliation":[{"name":"lnstituto Oswaldo Cruz, Funda\u00e7\u00e3o Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1997-5786","authenticated-orcid":false,"given":"Hegger","family":"Fritsch","sequence":"additional","affiliation":[{"name":"Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalia","family":"Guimar\u00e3es","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Estado de Minas Gerais, Funda\u00e7\u00e3o Ezequiel Dias, Belo Horizonte 30510-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ludmila O.","family":"Lamounier","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Estado de Minas Gerais, Funda\u00e7\u00e3o Ezequiel Dias, Belo Horizonte 30510-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0088-9036","authenticated-orcid":false,"given":"Fernanda Khouri","family":"Barreto","sequence":"additional","affiliation":[{"name":"Instituto Multidisciplinar em Sa\u00fade, Universidade Federal da Bahia, Vit\u00f3ria da Conquista 45029-094, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camilo M. M.","family":"Braga de Oliveira","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central de Sa\u00fade P\u00fablica do Acre, Rio Branco 69900-604, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6953-4965","authenticated-orcid":false,"given":"Crhistinne C.","family":"Maymone Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Secretaria de Sa\u00fade do estado do Mato Grosso do Sul, Campo Grande 79031-350, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danielle","family":"Malta Lima","sequence":"additional","affiliation":[{"name":"Faculty of the Graduate Program in Biotechnology (Renorbio), Universidade de Fortaleza, Fortaleza 60811-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elaine C.","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Mato Grosso, Cuiab\u00e1 78060-628, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gislene G.","family":"de Castro Lichs","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Mato Grosso do Sul, Campo Grande 79074-460, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iago","family":"Gomes","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central de Sa\u00fade P\u00fablica do Rio Grande do Norte, Natal 59037-170, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janaina","family":"Mazaro","sequence":"additional","affiliation":[{"name":"Secretaria Estadual de Sa\u00fade do estado do Acre, Rio Branco 69900-064, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janete T. N.","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central de Sa\u00fade P\u00fablica do Acre, Rio Branco 69900-604, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jayra","family":"Abrantes","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central de Sa\u00fade P\u00fablica do Rio Grande do Norte, Natal 59037-170, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1367-6272","authenticated-orcid":false,"given":"Jeov\u00e1 K. B.","family":"Colares","sequence":"additional","affiliation":[{"name":"Faculty of the Graduate Program in Biotechnology (Renorbio), Universidade de Fortaleza, Fortaleza 60811-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kleber G.","family":"Luz","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Universidade Federal do Rio Grande do Norte, Natal 59078-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luana","family":"Barbosa da Silva","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Mato Grosso, Cuiab\u00e1 78060-628, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luiz","family":"Demarchi","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Mato Grosso do Sul, Campo Grande 79074-460, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Magaly C. B.","family":"C\u00e2mara","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central de Sa\u00fade P\u00fablica do Rio Grande do Norte, Natal 59037-170, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marina C. S.","family":"Umaki Zardin","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Mato Grosso do Sul, Campo Grande 79074-460, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1856-4501","authenticated-orcid":false,"given":"Rafaela","family":"Sabatini Mello Pinheiro","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Citogen\u00e9tica, Universidade Federal do Acre, Rio Branco 69920-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rutilene","family":"Barbosa Souza","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central de Sa\u00fade P\u00fablica do Acre, Rio Branco 69900-604, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone K.","family":"Haddad","sequence":"additional","affiliation":[{"name":"Funda\u00e7\u00e3o Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto 14051-140, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephanni","family":"Figueiredo da Silva","sequence":"additional","affiliation":[{"name":"Laboratorio Central de Sa\u00fade P\u00fablica do Mato Grosso, Cuiab\u00e1 78060-628, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0805-6140","authenticated-orcid":false,"given":"Svetoslav N.","family":"Slavov","sequence":"additional","affiliation":[{"name":"Funda\u00e7\u00e3o Hemocentro de Ribeir\u00e3o Preto, Ribeir\u00e3o Preto 14051-140, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Themis","family":"Rocha","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio Central de Sa\u00fade P\u00fablica do Rio Grande do Norte, Natal 59037-170, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Noelia","family":"Morel","sequence":"additional","affiliation":[{"name":"Departamento de Laboratorios de Salud P\u00fablica, Ministerio de Salud P\u00fablica, Montevideo 11200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8713-1067","authenticated-orcid":false,"given":"Hector","family":"Chiparelli","sequence":"additional","affiliation":[{"name":"Departamento de Laboratorios de Salud P\u00fablica, Ministerio de Salud P\u00fablica, Montevideo 11200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anal\u00eda","family":"Burgue\u00f1o","sequence":"additional","affiliation":[{"name":"Departamento de Laboratorios de Salud P\u00fablica, Ministerio de Salud P\u00fablica, Montevideo 11200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victoria","family":"B\u00f3rmida","sequence":"additional","affiliation":[{"name":"Departamento de Laboratorios de Salud P\u00fablica, Ministerio de Salud P\u00fablica, Montevideo 11200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda N.","family":"Cortinas","sequence":"additional","affiliation":[{"name":"Departamento de Laboratorios de Salud P\u00fablica, Ministerio de Salud P\u00fablica, Montevideo 11200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosario S.","family":"Mart\u00edn","sequence":"additional","affiliation":[{"name":"Departamento de Laboratorios de Salud P\u00fablica, Ministerio de Salud P\u00fablica, Montevideo 11200, Uruguay"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Allan C.","family":"Pereira","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Fronteira Tabatinga, Tabatinga 69640-000, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marcelo F.","family":"dos Santos","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Fronteira Tabatinga, Tabatinga 69640-000, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Walter","family":"Andr\u00e9 J\u00fanior","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Fronteira Tabatinga, Tabatinga 69640-000, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jairo","family":"Mendez Rico","sequence":"additional","affiliation":[{"name":"Pan American Health Organization, Washington, DC 20037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leticia","family":"Franco","sequence":"additional","affiliation":[{"name":"Pan American Health Organization, Washington, DC 20037, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Rosewell","sequence":"additional","affiliation":[{"name":"Organiza\u00e7\u00e3o Pan-Americana da Sa\u00fade, Organiza\u00e7\u00e3o Mundial da Sa\u00fade, Bras\u00edlia 70800-400, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodrigo F.","family":"do Carmo Said","sequence":"additional","affiliation":[{"name":"Organiza\u00e7\u00e3o Pan-Americana da Sa\u00fade, Organiza\u00e7\u00e3o Mundial da Sa\u00fade, Bras\u00edlia 70800-400, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0581-5535","authenticated-orcid":false,"given":"Carlos F. C.","family":"de Albuquerque","sequence":"additional","affiliation":[{"name":"Organiza\u00e7\u00e3o Pan-Americana da Sa\u00fade, Organiza\u00e7\u00e3o Mundial da Sa\u00fade, Bras\u00edlia 70800-400, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ethel L.","family":"Noia Maciel","sequence":"additional","affiliation":[{"name":"Secretaria de Vigil\u00e2ncia em Sa\u00fade e Ambiente, Minist\u00e9rio da Sa\u00fade, Bras\u00edlia 70058-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00edlia","family":"Santini de Oliveira","sequence":"additional","affiliation":[{"name":"Coordena\u00e7\u00e3o Geral dos Laborat\u00f3rios de Sa\u00fade P\u00fablica, Minist\u00e9rio da Sa\u00fade, Bras\u00edlia 70058-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rivaldo","family":"Ven\u00e2ncio da Cunha","sequence":"additional","affiliation":[{"name":"Funda\u00e7\u00e3o Oswaldo Cruz, Instituto de Tecnologia em Imunobiol\u00f3gicos, Rio de Janeiro 21040-090, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Livia C.","family":"Vinhal Frutuoso","sequence":"additional","affiliation":[{"name":"Coordena\u00e7\u00e3o Geral das Arboviroses, Minist\u00e9rio da Sa\u00fade, Bras\u00edlia 70058-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana M. B.","family":"de Filippis","sequence":"additional","affiliation":[{"name":"lnstituto Oswaldo Cruz, Funda\u00e7\u00e3o Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5849-7326","authenticated-orcid":false,"given":"Marta","family":"Giovanetti","sequence":"additional","affiliation":[{"name":"Instituto Rene Rachou, Funda\u00e7\u00e3o Oswaldo Cruz, Belo Horizonte 30190-002, Brazil"},{"name":"Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, 00128 Roma, Italy"},{"name":"Climate Amplified Diseases and Epidemics (CLIMADE), Funda\u00e7\u00e3o Oswaldo Cruz, Belo Horizonte 30190-002, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6769-9931","authenticated-orcid":false,"given":"Luiz","family":"Carlos Junior Alcantara","sequence":"additional","affiliation":[{"name":"Instituto Rene Rachou, Funda\u00e7\u00e3o Oswaldo Cruz, Belo Horizonte 30190-002, Brazil"},{"name":"Climate Amplified Diseases and Epidemics (CLIMADE), Funda\u00e7\u00e3o Oswaldo Cruz, Belo Horizonte 30190-002, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,12,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1508","DOI":"10.1038\/s41564-019-0476-8","article-title":"The current and future global distribution and population at risk of dengue","volume":"4","author":"Messina","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_2","unstructured":"Pan American Health Organization (2023). Annual Arbovirus Bulletin 2022, Regional Office for the Americas of the World Health Organization."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1007\/s00705-023-05835-1","article-title":"Renaming of the genus Flavivirus to Orthoflavivirus and extension of binomial species names within the family Flaviviridae","volume":"168","author":"Postler","year":"2023","journal-title":"Arch. Virol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e101","DOI":"10.1016\/S1473-3099(16)30518-7","article-title":"Epidemic arboviral diseases: Priorities for research and public health","volume":"17","author":"Gubler","year":"2017","journal-title":"Lancet Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Kralik, P., and Ricchi, M. (2017). A basic guide to real time PCR in microbial diagnostics: Definitions, parameters, and everything. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.00108"},{"key":"ref_6","first-page":"S292","article-title":"Next generation sequencing and bioinformatics methodologies for infectious disease research and public health: Approaches, applications, and considerations for development of laboratory capacity","volume":"221","author":"Melendrez","year":"2020","journal-title":"J. Infect. Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.1038\/s41467-021-22607-0","article-title":"Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil","volume":"12","author":"Adelino","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"4413","DOI":"10.1038\/s41467-023-40099-y","article-title":"Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil","volume":"14","author":"Xavier","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1038\/s41564-022-01191-z","article-title":"Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil","volume":"7","author":"Giovanetti","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/1743-422X-10-58","article-title":"Development of one-step quantitative reverse transcription PCR for the rapid detection of flaviviruses","volume":"10","author":"Patel","year":"2013","journal-title":"Virol. J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1038\/nprot.2017.066","article-title":"Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples","volume":"12","author":"Quick","year":"2017","journal-title":"Nat. Protoc."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.3201\/eid1408.080287","article-title":"Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007","volume":"14","author":"Lanciotti","year":"2008","journal-title":"Emerging Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"764","DOI":"10.3201\/eid1305.070015","article-title":"Chikungunya virus in US travelers returning from India, 2006","volume":"13","author":"Lanciotti","year":"2007","journal-title":"Emerging Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4977","DOI":"10.1128\/JCM.43.10.4977-4983.2005","article-title":"Serotype-specific detection of dengue viruses in a fourplex real-time reverse transcriptase PCR assay","volume":"43","author":"Johnson","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"4054","DOI":"10.1128\/JCM.01799-12","article-title":"Advanced yellow fever virus genome detection in point-of-care facilities and reference laboratories","volume":"50","author":"Domingo","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Fonseca, V., Libin, P.J.K., Theys, K., Faria, N.R., Nunes, M.R.T., Restovic, M.I., Freire, M., Giovanetti, M., Cuypers, L., and Now\u00e9, A. (2019). A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLoS Negl. Trop. Dis., 13.","DOI":"10.1371\/journal.pntd.0007231"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1093\/bioinformatics\/bty695","article-title":"Genome Detective: An automated system for virus identification from high-throughput sequencing data","volume":"35","author":"Vilsker","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_18","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_19","doi-asserted-by":"crossref","first-page":"e2002169","DOI":"10.1002\/smll.202002169","article-title":"Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses","volume":"16","author":"Wang","year":"2020","journal-title":"Small"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Burgueno, A., Giovanetti, M., Fonseca, V., Morel, M.N., Lima, M., Castro, E., Guimaraes, N.R., Iani, F.C.M., Bormida, V., and Cortinas, M.N. (2023). Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023. medRxiv.","DOI":"10.1101\/2023.08.17.23294156"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1725","DOI":"10.3201\/eid2808.220550","article-title":"Emergence of dengue virus serotype 2 cosmopolitan genotype, brazil","volume":"28","author":"Giovanetti","year":"2022","journal-title":"Emerging Infect. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/s41564-018-0296-2","article-title":"Tracking virus outbreaks in the twenty-first century","volume":"4","author":"Grubaugh","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/s41592-022-01441-2","article-title":"Methods for fighting emerging pathogens","volume":"19","author":"Alcantara","year":"2022","journal-title":"Nat. Methods"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.jcv.2003.11.004","article-title":"One-Step RT-PCR protocols improve the rate of dengue diagnosis compared to Two-Step RT-PCR approaches","volume":"30","author":"Torres","year":"2004","journal-title":"J. Clin. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Naveca, F.G., Claro, I., Giovanetti, M., de Jesus, J.G., Xavier, J., de Melo Iani, F.C., do Nascimento, V.A., de Souza, V.C., Silveira, P.P., and Louren\u00e7o, J. (2019). Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon. PLoS Negl. Trop. Dis., 13.","DOI":"10.1371\/journal.pntd.0007065"},{"key":"ref_26","unstructured":"(2023, August 30). Centers for Disease Control and Prevention-CDC CDC DENV-1-4 rRT-PCR Multiplex and Trioplex rRT-PCR Assays\u2014Dengue\u2014CDC, Available online: https:\/\/www.cdc.gov\/dengue\/healthcare-providers\/testing\/molecular-tests\/assays.html."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Chan, K.R., Ismail, A.A., Thergarajan, G., Raju, C.S., Yam, H.C., Rishya, M., and Sekaran, S.D. (2022). Serological cross-reactivity among common flaviviruses. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.975398"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/nrg.2017.88","article-title":"Towards a genomics-informed, real-time, global pathogen surveillance system","volume":"19","author":"Gardy","year":"2018","journal-title":"Nat. Rev. Genet."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/1\/23\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T21:40:12Z","timestamp":1760132412000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/1\/23"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,22]]},"references-count":28,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,1]]}},"alternative-id":["v16010023"],"URL":"https:\/\/doi.org\/10.3390\/v16010023","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2023,12,22]]}}}