Nanopore sequencing of non-oncogenic oral Papillomaviruses from people living with HIV

Objective To explore the diversity of non-oncogenic papillomaviruses in saliva samples from people living with HIV using nanopore amplicon-based sequencing for detection and typing. Methods This was a secondary analysis of data from the nanopore sequencing of amplicons obtained from polymerase chain reaction detection of papillomaviruses from 127 samples of people living with HIV. The sequencing data was cleaned and analyzed using a series of bash, Python and R scripts to produce output based on comparisons with the PAVE reference database for all known non-oncogenic papillomaviruses. Results A total of 171,194 reads corresponding to 201 known papillomavirus types were obtained from the data. Most of these reads (69%), belonged to the human non-oncogenic papillomavirus types. The most abundant nonhuman and non-oncogenic PV, Trichechus manatus latirostris papillomavirus 4 in 99% of the samples. There were nine other less abundant non-oncogenic papillomaviruses that were found in 95% or more of the samples as mixed infections. Conclusions This study demonstrates that there are many non-oncogenic PV infections in samples from PLHIV, most of which are mixed infections from this setting. It is important to note that the non-human non-oncogenic PVs, as a potential one health concern, were highly prevalent in this population.