Recent Developments in Studying Human Polyomaviruses
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Journal of General Virology (2013), 94, 482–496 DOI 10.1099/vir.0.048462-0 Review From Stockholm to Malawi: recent developments in studying human polyomaviruses Mariet C. W. Feltkamp,1 Siamaque Kazem,1 Els van der Meijden,1 Chris Lauber1 and Alexander E. Gorbalenya1,2 Correspondence 1Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands Mariet Feltkamp 2Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, [email protected] 119899 Moscow, Russia Until a few years ago the polyomavirus family (Polyomaviridae) included a dozen viruses identified in avian and mammalian hosts. Two of these, the JC and BK-polyomaviruses isolated a long time ago, are known to infect humans and cause severe illness in immunocompromised hosts. Since 2007 an unprecedented number of eight novel polyomaviruses were discovered in humans. Among them are the KI- and WU-polyomaviruses identified in respiratory samples, the Merkel cell polyomavirus found in skin carcinomas and the polyomavirus associated with trichodysplasia spinulosa, a skin disease of transplant patients. Another four novel human polyomaviruses were identified, HPyV6, HPyV7, HPyV9 and the Malawi polyomavirus, so far not associated with any disease. In the same period several novel mammalian polyomaviruses were described. This review summarizes the recent developments in studying the novel human polyomaviruses, and touches upon several aspects of polyomavirus virology, pathogenicity, epidemiology and phylogeny. Introduction polyomaviruses were identified in rodents, cattle and birds, but not in humans until this century. The polyomaviruses have been recognized as a separate virus family (Polyomaviridae) consisting of several species From 2005 on, eight novel human polyomaviruses (HPyV) since 1999. Before that time they formed the genus were identified. Two of those are involved in disease Polyomavirus in the family Papovaviridae that contained development in immunosuppressed and/or elderly patients, the papillomaviruses, polyomaviruses and the simian and therefore seem to fit the ‘opportunistic’ polyomavirus vacuolating agent 40 (SV40). Nowadays, the latter virus profile characterized by symptomatic reactivations after a forms the namesake species that is designated the period of persistent latent infection. For the other novel polyomavirus type species (prototype) as listed in the HPyVs pathogenicity is still unknown. In this review, the ICTV 9th Report (Norkin et al., 2012). novel HPyVs will be discussed with respect to virological and pathogenic properties as far as they are known, addressing The first members of the polyomavirus family, mouse some epidemiological and phylogenetic aspects of poly- polyomavirus (MPyV) and SV40, were identified halfway omavirus in general. through the last century as filterable agents that caused tumours in newborn mice and hamsters (Eddy et al., 1962; Fig. 1 shows a timeline of polyomavirus (putative) species Girardi et al., 1962; Gross, 1953). SV40 contaminated many identifications at the time of writing (October 2012), animal lots of human poliovirus vaccine produced in monkey and human. A list of polyomaviruses that prototype the kidney cells. This raised a serious concern, but so far SV40 (tentative) namesake species, name abbreviations and has never been shown to be oncogenic in humans (Strickler RefSeq/GenBank numbers of genome sequences are shown et al., 1998). The first two human polyomaviruses were in Table 1. In this review, the polyomaviruses will be termed discovered in 1971. The JC-polyomavirus (JCPyV) was according to their species names and abbreviations men- identified in a brain tissue extract from a progressive tioned in the pending 2011 ICTV taxonomy proposal multifocal leukoencephalopathy (PML) patient that bore the regarding the family Polyomaviridae, as presented in a recent initials J. C. (Padgett et al., 1971). The first BK-polyomavirus publication on the subject (Johne et al., 2011). The (BKPyV) reported was isolated from the urine of a phylogenic tree composed by Johne, Norkin and collabora- nephropathic kidney transplant patient B. K. (Gardner tors is shown in Fig. 2. The most recent polyomavirus et al., 1971). Both JCPyV and BKPyV were not oncogenic discoveries are not mentioned in the pending ICTV in humans despite being closely related phylogenetically proposal. These will be termed according to their pro- with SV40 (Johne et al., 2011). Subsequently, more visional names given in their first publication, respectively. 482 048462 G 2013 SGM Printed in Great Britain Review of the new human polyomaviruses TSPyV HPyV6 HPyV7 HPyV9 OraPyV2 MasPyV OraPyV1 MWPyV MCPyV WUPyV FPyV GHPyV 2010 LPyV 2011 BKPyV 2012 2009 SA12 2008 2006 2007 MPyV 2000 1979 1971 1963 1950 1954 2012 1953 1960 1967 1971 MptV SV40 1976 HaPyV 1981 2012 2006 2007 JCPyV 2008 2009 BPyV 2011 APyV CPyV 2010 KIPyV EPyV SqPyV GggPyV1 BatPyV PtvPyV CaPyV ChPyV SLPyV Fig. 1. A time line that indicates 32 (putative) polyomavirus species discovered at the time of writing (October 2012). The year of discovery refers to the first description of the virus, not necessarily to the year that the full genome DNA sequence was obtained. The virus name abbreviations are explained in Table 1 where also the citations to the first descriptions can be found. New human polyomaviruses and methods of approach were published in a previous virus discovery paper discovery describing the identification of the human bocavirus (Allander et al., 2005). With the steady advancement of nucleic acid amplification and detection techniques, the need for cytopathic changes For the identification of WUPyV a ‘shotgun sequencing’ observed in cell culture to detect the presence of a virus was strategy was used on a single nasopharyngeal aspirate that bypassed. Recent versions of these molecular techniques proved negative for 17 known viral respiratory pathogens allow sensitive and high-throughput analyses of large in diagnostic PCR. Total nucleic acid isolated from the numbers of clinical samples that led to a revolution in virus sample was randomly amplified and PCR products were discovery. Nucleic acid isolated from both diseased and cloned and sequenced. The reads were analysed in a healthy tissues can be used as ‘a template’ for such techniques comparable fashion to the above, which revealed several and therefore the identified viruses are not necessarily sequences that displayed significant homology with JCPyV pathogenic. These techniques are frequently combined with and BKPyV (Gaynor et al., 2007). Subsequent analyses of strategies to enrich the original sample for viral DNA or the compiled WUPyV genome showed highest sequence RNA, by reducing the content of host genomic DNA. identity with the KI-polyomavirus just isolated from respiratory samples, described above. KI-polyomavirus (KIPyV) and WU-polyomavirus (WUPyV) Merkel cell polyomavirus (MCPyV) In 2007 almost coincidentally, two novel HPyV were Exciting and worrisome at the same time has been the reported, the Karolinska Institute polyomavirus (KIPyV) discovery of the MCPyV, which finally proved assumptions identified in Stockholm, Sweden and the Washington of polyomavirus involvement in human oncogenesis true. University polyomavirus (WUPyV) identified in St Louis, Merkel cell carcinomas (MCC) are rare but aggressive USA. Both were discovered in respiratory tract samples from cutaneous tumours of neuroendocrine origin that typically individuals with (acute) respiratory tract infections, but by develop in the elderly and immunocompromised patients. totally different methods. Using a technique called digital transcriptome subtraction KIPyV was identified by pooling centrifuged and filtered (Feng et al., 2007), MCPyV was identified in MCC (Feng supernatants from randomly selected DNase-treated naso- et al., 2008). This technique compares (subtracts) cDNA pharyngeal aspirates, from which DNA and RNA were libraries generated with random RT-PCR from diseased extracted (Allander et al., 2007). The nucleic acids served as a and healthy tissues and thereby identifies mRNA tran- template for random-PCR, and the products were separated scripts potentially unique for either or both. In this case by gel electrophoresis, cloned and sequenced. This resulted with the help of sophisticated software, unique sequences in several sequence reads that were subsequently trimmed, were further analysed and some of them displayed clustered and sorted using dedicated software. Finally, BLAST homology to the monkey B-lymphotrophic polyomavirus searches were performed to look for similarities with known (LPyV) and BKPyV. Through primer-genome-walking the (viral) sequences listed in GenBank. Details of the technical complete genome was sequenced. New to HPyVs, but http://vir.sgmjournals.org 483 M. C. W. Feltkamp and others Table 1. List of 32 polyomavirus names identified up to October 2012, which prototype putative species Host Polyomavirus (putative) species name First publication* RefSeq/GenBank accession no.D Human JC polyomavirus (JCPyV) Padgett et al. (1971) NC_001699 BK polyomavirus (BKPyV) Gardner et al. (1971) NC_001538 KI polyomavirus (KIPyV) Allander et al. (2007) NC_009238 WU Polyomavirus (WUPyV) Gaynor et al. (2007) NC_009539 Merkel cell polyomavirus (MCPyV) Feng et al. (2008) NC_010277 Trichodysplasia spinulosa-associated van der Meijden et al. (2010) NC_014361 polyomavirus (TSPyV) Human polyomavirus 6 (HPyV6) Schowalter et al. (2010) NC_014406 Human polyomavirus 7 (HPyV7) Schowalter