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Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification

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 c...

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Autores principales: Souza, Juliana Vanessa Cavalcante, Santos, Hazerral de Oliveira, Leite, Anderson Brandão, Giovanetti, Marta, Bezerra, Rafael dos Santos, de Carvalho, Eneas, Bernardino, Jardelina de Souza Todão, Viala, Vincent Louis, Haddad, Rodrigo, Ciccozzi, Massimo, Alcantara, Luiz Carlos Junior, Sampaio, Sandra Coccuzzo, Covas, Dimas Tadeu, Kashima, Simone, Elias, Maria Carolina, Slavov, Svetoslav Nanev
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505086/
https://www.ncbi.nlm.nih.gov/pubmed/36146740
http://dx.doi.org/10.3390/v14091933
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author Souza, Juliana Vanessa Cavalcante
Santos, Hazerral de Oliveira
Leite, Anderson Brandão
Giovanetti, Marta
Bezerra, Rafael dos Santos
de Carvalho, Eneas
Bernardino, Jardelina de Souza Todão
Viala, Vincent Louis
Haddad, Rodrigo
Ciccozzi, Massimo
Alcantara, Luiz Carlos Junior
Sampaio, Sandra Coccuzzo
Covas, Dimas Tadeu
Kashima, Simone
Elias, Maria Carolina
Slavov, Svetoslav Nanev
author_facet Souza, Juliana Vanessa Cavalcante
Santos, Hazerral de Oliveira
Leite, Anderson Brandão
Giovanetti, Marta
Bezerra, Rafael dos Santos
de Carvalho, Eneas
Bernardino, Jardelina de Souza Todão
Viala, Vincent Louis
Haddad, Rodrigo
Ciccozzi, Massimo
Alcantara, Luiz Carlos Junior
Sampaio, Sandra Coccuzzo
Covas, Dimas Tadeu
Kashima, Simone
Elias, Maria Carolina
Slavov, Svetoslav Nanev
author_sort Souza, Juliana Vanessa Cavalcante
collection PubMed
description 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.
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spelling pubmed-95050862022-09-24 Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification Souza, Juliana Vanessa Cavalcante Santos, Hazerral de Oliveira Leite, Anderson Brandão Giovanetti, Marta Bezerra, Rafael dos Santos de Carvalho, Eneas Bernardino, Jardelina de Souza Todão Viala, Vincent Louis Haddad, Rodrigo Ciccozzi, Massimo Alcantara, Luiz Carlos Junior Sampaio, Sandra Coccuzzo Covas, Dimas Tadeu Kashima, Simone Elias, Maria Carolina Slavov, Svetoslav Nanev Viruses Communication 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. MDPI 2022-08-31 /pmc/articles/PMC9505086/ /pubmed/36146740 http://dx.doi.org/10.3390/v14091933 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Communication
Souza, Juliana Vanessa Cavalcante
Santos, Hazerral de Oliveira
Leite, Anderson Brandão
Giovanetti, Marta
Bezerra, Rafael dos Santos
de Carvalho, Eneas
Bernardino, Jardelina de Souza Todão
Viala, Vincent Louis
Haddad, Rodrigo
Ciccozzi, Massimo
Alcantara, Luiz Carlos Junior
Sampaio, Sandra Coccuzzo
Covas, Dimas Tadeu
Kashima, Simone
Elias, Maria Carolina
Slavov, Svetoslav Nanev
Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification
title Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification
title_full Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification
title_fullStr Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification
title_full_unstemmed Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification
title_short Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification
title_sort viral metagenomics for the identification of emerging infections in clinical samples with inconclusive dengue, zika, and chikungunya viral amplification
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505086/
https://www.ncbi.nlm.nih.gov/pubmed/36146740
http://dx.doi.org/10.3390/v14091933
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