Interactions between RNA viruses, the respiratory microbiome and host responses during an acute respiratory infection impact the onset, progression and severity of disease. However, methods to explore these interactions directly in clinical samples are limited.
Seesandra Rajagopala, PhD, Suman Das, PhD, and colleagues have now optimized a metatranscriptomics (RNA sequencing) method to simultaneously characterize respiratory viruses, microbiome and host response in nasal swab samples.
The researchers found a high frequency of respiratory syncytial virus (RSV) and coronavirus (related to, but not the virus that causes COVID-19) in samples from healthy children collected between November 2018 and February 2019. In samples from RSV-positive children, they detected both RSV-A and RSV-B and showed upregulation of the innate immune system, antiviral response and inflammasome pathway. The method identified microbiota (bacteria and fungi) at the species level.
The approach, published in Cell Reports Methods, should be broadly applicable to studies of respiratory infections, the authors suggest.
This research was supported by the National Institutes of Health (grants AI149262, AI154016, AI142321, AI095227, AI110819, HL146401, TR000445), Edward P. Evans Foundation, and Vanderbilt University Medical Center.
