| Full text | |
| Author(s): Show less - |
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
Total Authors: 16
|
| Document type: | Journal article |
| Source: | Viruses-Basel; v. 14, n. 9, p. 8-pg., 2022-09-01. |
| Abstract | |
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) | |
| FAPESP's process: | 17/23205-8 - Evaluation of the impact of emerging and reemerging viruses in the field of hemotherapy and stem cell transplantation by multiple-research approach |
| Grantee: | Svetoslav Nanev Slavov |
| Support Opportunities: | Research Grants - Young Investigators Grants |
| FAPESP's process: | 18/15826-5 - Evaluation of the impact of emerging and reemerging viruses in the field of hemotherapy and stem-cell transplantation by multiple-research approach |
| Grantee: | Svetoslav Nanev Slavov |
| Support Opportunities: | Scholarships in Brazil - Young Researchers |
| FAPESP's process: | 21/09446-8 - Application of portable minion sequencing technology for viral metagenomics analysis |
| Grantee: | Victória Simionatto Zucherato |
| Support Opportunities: | Scholarships in Brazil - Master |
| FAPESP's process: | 21/11944-6 - Continuous improvement of vaccines: Center for Viral Surveillance and Serological Assessment (CeVIVAS) |
| Grantee: | Sandra Coccuzzo Sampaio Vessoni |
| Support Opportunities: | Research Grants - Science Centers for Development |
| FAPESP's process: | 20/13194-1 - Evaluation of the prevalence and application of next generation sequencing methods for identification of emerging viruses in the area of hemotherapy |
| Grantee: | Victória Simionatto Zucherato |
| Support Opportunities: | Scholarships in Brazil - Technical Training Program - Technical Training |
| FAPESP's process: | 19/08528-0 - Application of bioinformatic procedures for identification of the impact of the viral infections in hemotherapy |
| Grantee: | Rafael dos Santos Bezerra |
| Support Opportunities: | Scholarships in Brazil - Master |