Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection
Sergio Kamminga,
Igor A. Sidorov,
Michaël Tadesse,
Els van der Meijden,
Caroline de Brouwer,
Hans L. Zaaijer,
Mariet C.W. Feltkamp,
Alexander E. Gorbalenya
Affiliations
Sergio Kamminga
Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands; Corresponding author
Igor A. Sidorov
Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Corresponding author
Michaël Tadesse
Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
Els van der Meijden
Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
Caroline de Brouwer
Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
Hans L. Zaaijer
Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands
Mariet C.W. Feltkamp
Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Corresponding author
Alexander E. Gorbalenya
Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; Corresponding author
Summary: 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.
