Abstract: Various embodiments are directed to analyzing host gene expression levels and microbial diversity in a biological sample, to determine a likelihood of lower-respiratory tract infection (LRTI) in subjects. Embodiments can include determining a probability value of a subject having LRTI based on differential gene expression of the subject and reference levels of control subjects. Embodiments can also include determining the likelihood of LRTI in subjects based on amicrobial diversity index or abundance levels of microbes that are considered as potential pathogens. Embodiments can also include applying an integrated classifier to gene expression levels, virus abundance levels, and microbial diversity to determine the likelihood of LRTI in subjects.

Abstract: Provided herein are lists of combined host-viral gene markers that can be used for identifying COVID-19 in a subject and/or determining severity of disease. The host-viral diagnostic methods, compositions and systems disclosed herein are used to classify human subjects pre-diagnosis, with or without symptoms of COVID-19, based on the expression levels of the identified gene markers.