Cutavirus: A newly discovered parvovirus on the rise

Journal Pre-proof Cutavirus: A newly discovered parvovirus on the rise

Tung Phan, Kristin Nagaro PII:

S1567-1348(20)30007-1

DOI:

https://doi.org/10.1016/j.meegid.2020.104175

Reference:

MEEGID 104175

To appear in:

Infection, Genetics and Evolution

Received date:

13 December 2019

Revised date:

3 January 2020

Accepted date:

5 January 2020

Please cite this article as: T. Phan and K. Nagaro, Cutavirus: A newly discovered parvovirus on the rise, Infection, Genetics and Evolution(2020), https://doi.org/10.1016/ j.meegid.2020.104175

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© 2020 Published by Elsevier.

Journal Pre-proof

Cutavirus: a newly discovered parvovirus on the rise Tung Phan1,* [email protected], Kristin Nagaro2 1

Division of Clinical Microbiology, University of Pittsburgh and University of Pittsburgh

Medical Center, Pittsburgh, Pennsylvania, USA 2

Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine,

Indiana University School of Medicine, Indianapolis, Indiana, USA *

Corresponding author.

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Abstract Cutavirus is a new member of the Parvoviridae family. It was first discovered in 2016 through

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unbiased metagenomics performed on fecal samples collected from patients with diarrhea, and also in skin biopsies collected from patients with cutaneous T-cell lymphoma (CTCL, also

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known as mycosis fungoides). We have systematically reviewed the literature to describe the

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discovery, genomic organization, prevalence, and geographic distribution of cutavirus. Keywords: cutavirus, cancer, skin, mycosis fungoides

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Introduction

Next-generation sequencing has evolved so rapidly that it now has the capability to identify

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previously unidentifiable organisms. As such, viral metagenomics provides a more comprehensive analysis of clinical specimens, giving it a distinct advantage over conventional

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viral detection methods (Quiñones-Mateu et al., 2014; Forbes et al., 2017). This emerging

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approach has revolutionized the realm of viral detection, allowing for the discovery of new viruses associated with human diseases. One of the recently discovered candidates is cutavirus. Discovery

This new virus was first discovered in 2016 when viral metagenomics was carried out on 255 fecal samples collected from Brazilian children with unexplained diarrhea, and a virus with genomic similarity to parvovirus was repeatedly observed (Phan et., 2016). In order to search for nucleotide sequences closely related to this new parvovirus genome, MegaBlast was used to query the pre-existing database of multiple next-generation sequencing datasets generated from humans, animals, and environmental samples. Nucleotide sequences of the new parvovirus genome was found in one dataset generated three years earlier from skin biopsies in French

Journal Pre-proof patients with CTCL. Therefore, the new parvovirus was named “Cutavirus” for cutaneous parvovirus (Phan et., 2016).

Taxonomy The family Parvoviridae consists of single-stranded DNA viruses with small, non-enveloped capsids. Cutavirus is classified within the subfamily Parvovirinae and further identified as a member of the genus Protoparovirus, which contains several pathogens associated with diseases in humans and animals (Mäntylä et al., 2017; Väisänen et al., 2017). In addition, cutavirus is the

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founding member of the species Primate protoparvovirus 3 (Söderlund-Venermo, 2019).

Genomic organization

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At this time, there are four cutavirus genomes that contain near-complete coding sequences available in GenBank (accession numbers KX685945, KT868811, KT868815, and KT868814).

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One genome was amplified and sequenced from human diarrheal feces; the remaining three

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genomes originated from skin biopsies from patients with CTCL or melanoma (Phan et al., 2016; Mollerup et al., 2017). The cutavirus genomes contain two major open reading frames (ORFs), with the left and right ORFs encoding NS1 (659 aa) and VP1 (707 aa), respectively. NS1

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contains helicase with characteristic NTP-binding domains A, B and C. VP1 has phospholipase A2 and glycine-rich regions. A minor middle ORF encodes a theoretical protein of unknown

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function. In addition to the three ORFs described above, another small ATG-initiated ORF

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located over the VP2 coding region is revealed, and it does not show any similarity to any existing parvovirus genomes (Phan et., 2016). At this time, the structure of the cutavirus capsid has not been defined.

Genetic diversity In our genetic analysis of the near-complete coding sequences of the four cutaviruses, the aa identity of the NS1 region is 93% to 98%, and the aa identity of the VP1 region is 96% to 99%. The high identity value of non-structural and structural proteins suggests the existence of a single genotype of cutavirus. The major difference between cutavirus strains is found in the intergenic region, likely representing the hypervariable region (Figure 1).

Journal Pre-proof Molecular epidemiology To date, cutavirus has been detected in human feces, skin, and lymph nodes (Figure 2). Cutavirus DNA was also tested, but not detected from blood and prostate tissue (Vaisanen et al., 2019). Two recent studies reported the absence of cutavirus DNA in biopsies from pseudocarcinomatous hyperplasia, juvenile nasopharyngeal angiofibroma, and oral & oropharyngeal squamous cell carcinoma (Kreuter et al., 2018a; Dickinson et al., 2019). Cutavirus was detected in a total of five fecal samples originating from both Brazilian (4/345) and Botswanan patients (1/100) with diarrhea by PCR. Cutavirus was also found in 4/17 (23.5%)

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CTCL biopsies while all 31 non-CTCL biopsies in the French control groups were negative

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(Phan et al., 2016). Cutavirus was subsequently reported in a sample of cutaneous malignant melanoma from a Danish patient (Mollerup et al., 2017). Later, Kreuter et al. (2018b) screened a

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total of 189 paraffin-embedded biopsies from 130 German patients with different types of cutaneous lymphomas. Cutavirus was detected in 6/189 (3.2%) cutaneous lymphoma biopsies.

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Interestingly, cutavirus was exclusively detected in patients diagnosed with early stage CTCL.

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Cutavirus DNA loads ranged between 1.3 and 85.0 copies per β-globin gene copy. According to this research group, cutavirus DNA was detected in only 2/185 (1.1%) melanoma biopsies, and in 0/52 (0%) melanoma metastases (Wieland et al., 2019). In contrast, cutavirus DNA was absent

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in 55 CTCL samples using real-time PCR in Italy (Bergallo et al., 2018). A recent study reported the detection of cutavirus DNA in skin biopsies of 4/25 (16.0%) CTCL

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and 4/136 (2.9%) solid organ transplant patients, but not in 159 skin biopsies from 98 healthy

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adults in Finland (Väisänen et al., 2019). However, cutavirus DNA was also found in 9 skin swabs of 237 (3.8%) healthy people, and 35 skin swabs from 205 (17.1%) HIV-positive men in Germany (Wieland et al., 2019). It is noteworthy that cutavirus DNA was found in both nonmalignant and malignant skin samples from three patients, and that cutavirus DNA loads were higher in malignant skin. The highest cutavirus DNA quantity was 7x10 8 copies per 1 million cells in a patient diagnosed with triple cancers: CTCL, melanoma, and prostate cancer (Väisänen et al., 2019).

Serological epidemiology Vaisanen et al. (2018) successfully expressed and purified cutavirus VP2 virus-like particles (VLPs), which were used to develop the cutavirus enzyme immunoassay (EIA) to investigate the

Journal Pre-proof prevalence of cutavirus IgG antibody in various populations. The prevalence of cutavirus IgG varied in healthy adult cohorts, but it is generally low, ranging from 1.0% in Iraq to 5.6% in Iran. While cutavirus seroprevalence was 4.9% in Finnish healthy adults, cutavirus IgG was not detected in healthy adults in the United States. Testing 226 serum samples from adult and pediatric Kenyan patients with fever found the average cutavirus seroprevalence was 3.1%; seroprevalance in the pediatric cohort was 1.9%, but 4.2% in the adult cohort (Vaisanen et al. 2018). The second study by Vaisanen and colleagues (2019) investigated the cutavirus IgG

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seroprevalence in different cohorts in Finland. The cutavirus IgG seroprevalence in CTCL

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patients was 9.5%, followed by 6.5% in solid organ transplant recipients, and 3.8% in healthy adults. In three transplant patients with paired biopsies and sera available, both cutavirus DNA

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and IgG were positive (Vaisanen et al. 2019).

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Unanswered questions and future perspectives

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Transmission is a central tenet of disease biology and infectious disease epidemiology, and the mechanism of cutavirus transmission remains unknown. Although cutavirus has been found in human skin, it is unclear whether cutavirus can be directly transmitted person-to-person via

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direct contact. For many viruses, one of the key steps in the emergence process is the jump from animals to humans, but at this time there have been no reports of the cutavirus in animals. Thus,

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the zoonotic potential of cutavirus remains unknown.

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Whether or not cutavirus infection causes any significant health impacts in humans is currently under investigation. Even the causative role of cutavirus in CTCL has been suggested, but not yet confirmed. Strongly positive cells were detected in 2/4 CTCL tissues by in-situ hybridization (Phan et al., 2016), reflecting possible ongoing replication or viral expression of cutavirus. This low level of positivity leaves enough uncertainty as to the causative role of cutaviruses in CTCL that additional studies are warranted for clarification of this question. Some studies also report the detection of cutavirus in a small number of malignant melanomas (Mollerup et al., 2017; Wieland et al., 2019). Cutavius DNA was not found in the malignant cells, but on the surface of malignant melanomas (Wieland et al., 2019). These findings seem to argue against an oncogenic role of cutavirus in malignant melanoma.

Journal Pre-proof Like the gut microbiome, the skin microbiome is diverse, and may directly impact the risk of skin cancers. Most notably, cutavirus is found in a fraction of tissues collected from CTCL patients. While several forces can be associated with CTCL, an indirect mechanism of carcinogenesis called hit-and-runner is a possibility in explaining the role of cutavirus. Cutavirus has been detected in CTCL patients by PCR with specific primers in most of epidemiological studies, but the risk for potential co-infection with other viruses has not been fully expounded upon. In general, parvoviruses are not considered oncogenic viruses. Rat parvovirus H-1, another member of the genus Protoparvovirus, replicates preferentially in cancer cells, and has natural

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oncolytic and oncosuppressive activities (Bretscher and Marchini, 2019). At this time, it is

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unknown whether cutavirus has any oncolytic effects. It has been recovered from the skin of healthy adults, but is less frequently found on the skin of immunosuppressed patients. It is

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possible that cutavirus could be part of the normal human skin virome; however, immunosuppression more commonly increases that risk of cancers that are associated with viral

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infection. Cutavirus has not been cultured in any cell lines, so in-vitro replication and

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cytopathogenic effect in different cell lines are not known. Additional studies are needed to gain further insights about its pathogenicity, and to delineate whether or not cutavirus is an orphan organism or a possible pathogen.

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Acknowledgement

We acknowledge support from Division of Clinical Microbiology, University of Pittsburgh

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Medical Center. We would also like to show our gratitude to the many people who have offered

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us their experience in the course of our work.

Conflicts of interest

The authors declare no competing financial interests.

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positive primary cutaneous anaplastic large cell lymphoma with coexistent pseudocarcinomatous hyperplasia. Clin Exp Dermatol., 43 (2018a), 585-588.

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infection in primary cutaneous B- and T-cell lymphoma. JAMA Dermatol., 154 (2018b), 965967.

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Herrera, T. Steiniche, T. Mourier, S. Willerslev, J. Izarzugaza, A. Hansen, L. Nielsen. Cutavirus in cutaneous malignant melanoma. Emerg. Infect. Dis., 23 (2017), 363-365.

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Siqueira, A. Knol, F. Halary, J. Dantal, K. Alexander, P. Pesavento, E. Delwart, A new protoparvovirus in human fecal samples and cutaneous T cell lymphomas (mycosis fungoides). Virology., 496 (2016), 299-305. M.E. Quiñones-Mateu, S. Avila, G. Reyes-Teran, M.A. Martinez. Deep sequencing: becoming a critical tool in clinical virology. J. Clin. Virol. 61(2014), 9–19. M. Söderlund-Venermo. Emerging human parvoviruses: the rocky road to fame. Annu. Rev. Virol., 6 (2019), 71-91. E. Väisänen, U. Mohanraj, M.P. Kinnunen, P. Pikka Jokelainen, H. Al-Hello, M.A. Barakat, M. Sadeghi, A.F. Jalilian, A. Majlesi, M. Masika, D. Mwaengo, O. Anzala, E. Delwart, O. Vapalahti, K. Hedman, M. Söderlund-Venermo. Global distribution of human protoparvoviruses. Emerg. Infect. Dis., 24 (2018), 1292-1299.

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Figure 1. Genomic organization of cutavirus and sliding window of percent nucleotide

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similarity.

Figure 2. Timeline of cutavirus from discovery to current insights. CTCL, cutaneous T cell

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lymphoma; JNA, juvenile nasopharyngeal angiofibroma; OSCC/OPSCC, oral squamous cell carcinoma/oropharyngeal squamous cell carcinoma; C-ALCL, cutaneous anaplastic large cell

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lymphoma.

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Highlights

Next-generation sequencing has revolutionized the realm of viral detection, allowing



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for the discovery of cutavirus.

We have systematically reviewed the literature to describe the discovery, genomic

To date, cutavirus has been detected in human feces, skin, and lymph nodes, and it

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

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organization, prevalence, and geographic distribution of cutavirus.

may be associated with cutaneous T-cell lymphoma.