Clinical and Virological Characterization of Severe Acute Respiratory Infection Using PCR-Based Methods and Metagenomic Sequencing: a National Registry in Saudi Arabia

Data on the burden, severity and etiology of SARI amongst critically ill patients will be expected to be of a great value in guiding the prioritization of prevention and control efforts18 and in the design of future intervention studies of antivirals and other therapeutic modalities.

Because influenza is a common cause of serious respiratory illness in Saudi Arabia, although only limited data are available on the most severely ill patients with influenza, we will conduct surveillance in SARI critically ill patients and perform typing and subtyping of influenza viruses in BAL samples. We will store samples for future examination of predisposing risk factors including genetic factors.

Multiplex PCR will reduce the cost and time to detect the respiratory pathogens. In recent years, the falling costs of Whole Genome Sequencing (WGS) technologies have has proven to be a valuable tool to understand the growing threat of emerging pathogens. Metagenomic next-generation sequencing (M-NGS) has transformative effect in the last decade to investigate and understand complex microbial communities. M-NGS is simply capturing and determining all nucleic acids in a sample which allowed to identify a mixed population of microorganisms. This powerful platform simultaneously identifies genetics materials of any organisms unbiased to other methods that used specific primers to identify specific targets.

The primary objective of the VERIFY registry is to examine the virological etiologies of SARI among mechanically ventilated critically ill patients in a geographical representative sample from Saudi Arabia in order to obtain a better estimate of viral pathogen prevalence by systematic lower respiratory tract sampling and use of serology among critically ill patients in a geographical representative sample from Saudi Arabia. Contribution of viruses may be under-estimated due to the use of upper respiratory tract specimens only, and late presentation of cases to ICU (at which time antigen is no longer detectable). Therefore a systematic approach using mini-BAL to obtain lower respiratory samples will likely yield better estimate.