Molecular and biological characterization of influenza A viruses isolated from human fecal samples

Abstract

Human influenza viruses are occasionally detected in the stools of influenza patients. Objectives: Here, we investigated the molecular and biological characteristics of intestinal influenza viruses and their potential role in virus transmission. Methods: Fecal samples were first screened for the presence of influenza viral RNA using RT-qPCR. Positive fecal samples were subjected to cell culture. Isolated viruses were then sequenced using MiSeq platform. Replication kinetics and receptor binding affinity were also evaluated. Results: Influenza RNA was detected in stool samples of 41% (36/87) of influenza A positive patients. Among the 36 stool samples subjected to viral isolation, 5 showed virus growth. Sequence analysis of isolated viruses revealed two distinct mutation patterns in fecal viruses. Set I viruses was able to replicate to higher titers in cell culture despite the limited number of mutations (6 mutations) compared to set II viruses (>10 mutations). Functional analysis of both sets revealed the ability to replicate efficiently in differentiated human bronchial cells. Receptor binding testing has also demonstrated their ability to bind α 2,3 and α 2,6 sialic acid receptors. Conclusion: The ability of fecal influenza viruses to replicate in intestinal cells and human 3D bronchial cells might suggest their possible contribution in virus transmission.