Kamminga S, Sidorov IA, Tadesse M, van der Meijden E, de Brouwer C, Zaaijer HL, Feltkamp MC, Gorbalenya AE. Translating genomic exploration of the family
Polyomaviridae into confident human polyomavirus detection.
iScience 2022;
25:103613. [PMID:
35036862 PMCID:
PMC8749223 DOI:
10.1016/j.isci.2021.103613]
[Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/27/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.
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