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Merkel Cell Polyomavirus (MCPyV) in the Context of Immunosuppression: Genetic Analysis of Noncoding Control Region (NCCR) Variability among a HIV-1-Positive Population

1
IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-Degenerative Pathologies, 00166 Rome, Italy
2
Department of Public Health and Infectious Diseases, “Sapienza” University, 00185 Rome, Italy
3
IRCCS San Raffaele Pisana, Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, 00166 Rome, Italy
4
Infectious Diseases Clinic, Policlinic Tor Vergata, 00133 Rome, Italy
5
Department of System Medicine, Tor Vergata University of Rome, 00133 Rome, Italy
6
Department of Public Health and Infectious Diseases, Institute Pasteur, Cenci-Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
7
Laboratory of Clinical Microbiology and Virology, Polyclinic Tor Vergata Foundation, 00133 Rome, Italy
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Viruses 2020, 12(5), 507; https://doi.org/10.3390/v12050507
Received: 17 April 2020 / Revised: 28 April 2020 / Accepted: 30 April 2020 / Published: 4 May 2020
(This article belongs to the Special Issue Polyomaviruses)
Background: Since limited data are available about the prevalence of Merkel cell polyomavirus (MCPyV) and the genetic variability of its noncoding control region (NCCR) in the context of immunosuppression, this study aimed to investigate the distribution of MCPyV in anatomical sites other than the skin and the behavior of NCCR among an HIV-1-positive population. Methods: Urine, plasma, and rectal swabs specimens from a cohort of 66 HIV-1-positive patients were collected and subjected to quantitative real-time polymerase chain reaction (qPCR) for MCPyV DNA detection. MCPyV-positive samples were amplified by nested PCR targeting the NCCR, and NCCRs alignment was carried out to evaluate the occurrence of mutations and to identify putative binding sites for cellular factors. Results: MCPyV DNA was detected in 10/66 urine, in 7/66 plasma, and in 23/66 rectal samples, with a median value of 5 × 102 copies/mL, 1.5 × 102 copies/mL, and 2.3 × 103 copies/mL, respectively. NCCR sequence analysis revealed a high degree of homology with the MCC350 reference strain in urine, whereas transitions, transversions, and single or double deletions were observed in plasma and rectal swabs. In these latter samples, representative GTT and GTTGA insertions were also observed. Search for putative binding sites of cellular transcription factors showed that in several strains, deletions, insertions, or single base substitutions altered the NCCR canonical configuration. Conclusions: Sequencing analysis revealed the presence of numerous mutations in the NCCR, including insertions and deletions. Whether these mutations may have an impact on the pathogenic features of the virus remains to be determined. qPCR measured on average a low viral load in the specimens analyzed, with the exception of those with the GTTGA insertion. View Full-Text
Keywords: Merkel cell polyomavirus; HIV-1-positive population; noncoding control region; GTT and GTTGA insertions; putative binding sites Merkel cell polyomavirus; HIV-1-positive population; noncoding control region; GTT and GTTGA insertions; putative binding sites
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Prezioso, C.; Obregon, F.; Ambroselli, D.; Petrolo, S.; Checconi, P.; Rodio, D.M.; Coppola, L.; Nardi, A.; de Vito, C.; Sarmati, L.; Andreoni, M.; Palamara, A.T.; Ciotti, M.; Pietropaolo, V. Merkel Cell Polyomavirus (MCPyV) in the Context of Immunosuppression: Genetic Analysis of Noncoding Control Region (NCCR) Variability among a HIV-1-Positive Population. Viruses 2020, 12, 507.

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