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Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review

Murilo Marconi Dos Santos1,2, Tiago Souza Salles1, Gabriel Montenegro de Campos1,2

  • 1Center for Viral Surveillance and Serological Assessment (CeVIVAs), Butantan Institute, São Paulo 05503-900, Brazil.

Viruses
|December 31, 2025
PubMed

Insights

Viral metagenomics offers an unbiased method to identify the causes of acute respiratory infections (ARIs), especially in complex cases. This next-generation sequencing approach aids in detecting known and novel viruses, improving public health responses.

Area of Science:

  • * Virology
  • * Molecular Biology
  • * Public Health

Background:

  • * Acute respiratory infections (ARIs) are a major global health concern, causing significant morbidity and mortality.
  • * Traditional diagnostic methods often fail to identify the etiological agent due to the diversity of respiratory viruses.
  • * This diagnostic gap is particularly evident in vulnerable populations like children, the elderly, and immunocompromised individuals.

Purpose of the Study:

  • * To review the application of viral metagenomics, specifically next-generation sequencing (NGS), for diagnosing ARIs.
  • * To highlight the utility of metagenomics in identifying causative agents in complex and undiagnosed ARI cases.
  • * To discuss the role of metagenomics in genomic surveillance and response to emerging respiratory threats.

Main Methods:

  • * Review of literature on viral metagenomics and next-generation sequencing (NGS) applied to respiratory infections.
  • * Analysis of the strengths and limitations of metagenomic NGS for etiological diagnosis of ARIs.
  • * Examination of the role of metagenomics in viral genomic surveillance and public health.

Main Results:

  • * Viral metagenomics provides an unbiased approach to detect a wide range of known and novel respiratory viruses.
  • * Metagenomic NGS is particularly valuable in immunocompromised patients where standard diagnostics are insufficient.
  • * The technology aids in understanding the diversity of viruses contributing to ARIs and supports genomic surveillance.

Conclusions:

  • * Viral metagenomics, using NGS, is a powerful tool for the etiological investigation of ARIs, especially in challenging cases.
  • * Integrating metagenomics into clinical practice and surveillance can enhance the early detection and control of respiratory viral diseases.
  • * This approach is crucial for identifying and responding to emerging respiratory pathogens and future public health threats.
Keywords:
acute respiratory infectionsdiagnosisrespiratory virusesviral metagenomics

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