Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice

Ouwendijk, W. J.; Roychoudhury, P.; Cunningham, A. L.; Jerome, K. R.; Koelle, D. M.; Kinchington, P. R.; Mohr, I.; Wilson, A. C.; Verjans, G. M. G. M.; Depledge, D. P.

doi:10.1101/2023.07.17.549345

bioRxiv · 10.1101/2023.07.17.549345

Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice

Ouwendijk, W. J.·Roychoudhury, P.·Cunningham, A. L.·Jerome, K. R.·Koelle, D. M.·Kinchington, P. R.·Mohr, I.·Wilson, A. C.·Verjans, G. M. G. M.·Depledge, D. P.

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Abstract

Most individuals are latently infected with herpes simplex virus type 1 (HSV-1) and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent virus is also present in immune cells recovered from ganglia in a mouse model used for studying latency. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for this conclusion. Unexpectedly, off-target priming in 3 scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1 latency-associated transcript (LAT) intronic RNAs. However, LAT reads were near-exclusively detected in a mixed population of cells undergoing cell death. Specific loss of HSV-1 LAT and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained by inaccuracies in the data analyses.

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Ouwendijk, W. J., Roychoudhury, P., Cunningham, A. L., Jerome, K. R., Koelle, D. M., Kinchington, P. R., Mohr, I., Wilson, A. C., Verjans, G. M. G. M., Depledge, D. P.. 2023-07-18. Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice. https://doi.org/10.1101/2023.07.17.549345

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