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

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 alpha 2,3 and alpha 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.

Automated summary

Human influenza viruses can be detected in the stools of influenza patients, and two distinct mutation patterns were found in fecal viruses. Despite limited mutations, Set I viruses were able to replicate at higher titers than Set II viruses. Functional analysis showed that fecal influenza viruses can efficiently replicate in different cells and bind to receptors.