Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification
Juliana Vanessa Cavalcante Souza,
Hazerral de Oliveira Santos,
Anderson Brandão Leite,
Marta Giovanetti,
Rafael dos Santos Bezerra,
Eneas de Carvalho,
Jardelina de Souza Todão Bernardino,
Vincent Louis Viala,
Rodrigo Haddad,
Massimo Ciccozzi,
Luiz Carlos Junior Alcantara,
Sandra Coccuzzo Sampaio,
Dimas Tadeu Covas,
Simone Kashima,
Maria Carolina Elias,
Svetoslav Nanev Slavov
Affiliations
Juliana Vanessa Cavalcante Souza
Central Laboratory of Public Health, Maceio 57036-860, Brazil
Hazerral de Oliveira Santos
Central Laboratory of Public Health, Maceio 57036-860, Brazil
Anderson Brandão Leite
Central Laboratory of Public Health, Maceio 57036-860, Brazil
Marta Giovanetti
Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, 00185 Rome, Italy
Rafael dos Santos Bezerra
Blood Center of Ribeirao Preto, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Rua Tenente Catão Roxo 2501, Ribeirao Preto, Sao Paulo 14051-140, Brazil
Eneas de Carvalho
Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil
Jardelina de Souza Todão Bernardino
Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil
Vincent Louis Viala
Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil
Rodrigo Haddad
Faculty of Ceilandia, University of Brasilia, Federal District, Brasília 70904-970, Brazil
Massimo Ciccozzi
Epidemiology and Statistic Unit, University of Campus Bio-Medico di Roma, 00185 Rome, Italy
Luiz Carlos Junior Alcantara
Laboratory of Flaviviruses, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
Sandra Coccuzzo Sampaio
Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil
Dimas Tadeu Covas
Blood Center of Ribeirao Preto, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Rua Tenente Catão Roxo 2501, Ribeirao Preto, Sao Paulo 14051-140, Brazil
Simone Kashima
Blood Center of Ribeirao Preto, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Rua Tenente Catão Roxo 2501, Ribeirao Preto, Sao Paulo 14051-140, Brazil
Maria Carolina Elias
Department of Biotechnology (NuCEL), Butantan Institute, Sao Paulo 05503-900, Brazil
Svetoslav Nanev Slavov
Blood Center of Ribeirao Preto, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Rua Tenente Catão Roxo 2501, Ribeirao Preto, Sao Paulo 14051-140, Brazil
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—dengue (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—were 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.
