Unveiling viral pathogens in acute respiratory disease: Insights from viral metagenomics in patients from the State of Alagoas, Brazil

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de Campos, Gabriel Montenegro ; Santos, Hazerral de Oliveira ; Lima, Alex Ranieri Jeronimo ; Leite, Anderson Brandao ; Ribeiro, Gabriela ; Bernardino, Jardelina de Souza Todao ; do Nascimento, Jean Phellipe Marques ; Souza, Juliana Vanessa Cavalcante ; de Lima, Loyze Paola Oliveira ; Lima, Marlon Breno Zampieri ; de Araujo, Mykaella Andrade ; Giovanetti, Marta ; Kallas, Esper Georges ; Sampaio, Sandra Coccuzzo ; Elias, Maria Carolina ; Slavov, Svetoslav Nanev

• Document type: Journal article
• Source: PLoS Neglected Tropical Diseases; v. 18, n. 9, p. 11-pg., 2024-09-01.

Abstract

Background Respiratory illness affects individuals across all age demographics on a global scale, often precipitated by viral infections. The symptomatic manifestations of these diseases bear clinical resemblance, complicating the accurate determination of their etiological origins. Furthermore, the diagnostic panels for respiratory pathogens used within local medical practices, may not encompass the full spectrum of viral agents responsible for such ailments. Consequently, a significant number of clinically important viral pathogens may remain undetected.Methods and findings In the light of this, we conducted a metagenomic examination of 66 nasopharyngeal swab specimens, obtained from patients presenting with acute respiratory conditions yet tested negative by the standard diagnostic panels available locally. These specimens were obtained from the Public Health Laboratory, Maceio, State of Alagoas. Our findings indicate a predominant diagnostic escape of rhinoviruses and notably enterovirus D68. Moreover, our study identified a substantial quantity of sequence reads attributed to human respirovirus 3 (human parainfluenza 3) along with various herpresviruses including human herpesvirus-1, Epstein-Barr virus (Human herpesvirus-4), Human herpesviruses 6 and 7 and human parvovirus B19 (B19V). Notably, the metagenomic analysis uncovered a widespread presence of the emerging human vientovirus FB in most of sample pools, though its clinical importance remains to be elucidated.Conclusions The obtained results in this study underscore the invaluable role of viral metagenomics in the identification of underrecognized viruses bearing clinical relevance. Furthermore, it offers insights into the dissemination of these pathogens within the studied area, thereby informing public health strategies aimed at enhancing diagnostic accuracy and improving patient care. The emergence of SARS-CoV-2 has reshaped our understanding of respiratory viruses, highlighting the challenges in etiological diagnosis due to symptom similarities. Metagenomics, an innovative approach, has revolutionized respiratory infection diagnosis by unbiasedly sequencing all genetic material in a sample, enabling the identification of previously unknown or unsuspected viruses where traditional methods often fail. In a study conducted in Alagoas, a Northeast Brazilian state with low human development indexes, samples obtained from patients with flu-like symptoms negative for locally applied diagnostic kits revealed diagnostic escape of rhinoviruses and a notably prevalent enterovirus D68. Additionally, substantial reads attributed to human respirovirus 3 (parainfluenza virus 3) and various herpesviruses, including human herpesvirus-1, Epstein-Barr virus, human herpesviruses 6 and 7, and human parvovirus B19, were identified. These findings are pivotal for differentiating viruses not detected by routinely implemented diagnostic procedures. Metagenomics shows great promise in diagnosing and surveilling respiratory viruses, providing insights into their epidemiology, evolution, and public health impact. (AU)

• 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: 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: 22/00910-6 - Development and application of bioinformatic pipelines for metagenomic analysis of clinical samples
• Grantee: Gabriel Montenegro de Campos
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• FAPESP's process: 23/12155-0 - Machine Learning Algorithms applied for Virus Identification in Dark Matter sequencing data from Next Generation Sequencing
• Grantee: Gabriel Montenegro de Campos
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 22/14958-0 - Molecular diagnosis and next-generation sequencing for emerging viral infections in different clinical samples
• Grantee: Marlon Breno Zampieri Lima
• Support Opportunities: Scholarships in Brazil - Technical Training Program - Technical Training