I contacted one of the authors regarding their interesting findings with questions I had, many of which were also asked in this forum. As such I thought it might be interesting if I provided some of the answers, to be precise my own interpretation of the answers, that I received.
The stool analysis they performed was on a relatively small subset of patients from the Penn cohort. These patients had their last known infection months to more than a year before the stool was collected. Overall, it seems that they didn’t analyse the stool data in more depth because the sample size is too small to say something meaningful.
They believe that one of the reasons why the viral RNA findings sometimes come back positive and sometimes negative is that PCR tests aren’t sufficiently sensitive, especially when it comes to people who have low a RNA load in the gut.
That is why they are planing to do a larger trial where they will also measure IFN. Regarding inconsistent findings of IFN, which don’t support their paper, they believe that the standard ELISA tests for IFN are not sensitive enough in PASC and as such they are planning to use the Simoa assay. This was news to me and seems interesting, even though I can't say anything about IFN tests not being sensitive enough.
Finally the brain serotonin levels in mice were normal and only the peripheral serotonin levels were reduced, so they aren’t expecting any difference in brain serotonin levels based on their results.
I still can’t say that I properly understand the reasoning to trial an SSRI but they are apparently still in the process of deciding which one to use since some might work better than others. They are also considering Vagal stimulation as a possible study arm.