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

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Cavalcante Souza, Juliana Vanessa ; Santos, Hazerral de Oliveira ; Leite, Anderson Brandao ; Giovanetti, Marta ; Bezerra, Rafael dos Santos ; de Carvalho, Eneas ; Todao Bernardino, Jardelina de Souza ; 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

• Tipo de documento: Artigo Científico
• Fonte: Viruses-Basel; v. 14, n. 9, p. 8-pg., 2022-09-01.

Resumo

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. (AU)

• Processo FAPESP: 17/23205-8 - Avaliação do impacto de vírus emergentes e re-emergentes em hemoterapia e transplante de células-tronco por meio de técnicas moleculares avançadas
• Beneficiário: Svetoslav Nanev Slavov
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores
• Processo FAPESP: 18/15826-5 - Avaliação do impacto de vírus emergentes e re-emergentes em hemoterapia e transplante de células-tronco por meio de técnicas moleculares avançadas
• Beneficiário: Svetoslav Nanev Slavov
• Modalidade de apoio: Bolsas no Brasil - Jovens Pesquisadores
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• Beneficiário: Victória Simionatto Zucherato
• Modalidade de apoio: Bolsas no Brasil - Mestrado
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• Beneficiário: Sandra Coccuzzo Sampaio Vessoni
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Ciência para o Desenvolvimento
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• Beneficiário: Victória Simionatto Zucherato
• Modalidade de apoio: Bolsas no Brasil - Programa Capacitação - Treinamento Técnico
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• Beneficiário: Rafael dos Santos Bezerra
• Modalidade de apoio: Bolsas no Brasil - Mestrado