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Dai Z, Wang H, Xu J, Lu X, Ni P, Yang S, Shen Q, Wang X, Li W, Wang X, Zhou C, Zhang W, Shan T. Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter. Genome Biol Evol 2024; 16:evae206. [PMID: 39327897 PMCID: PMC11463337 DOI: 10.1093/gbe/evae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 09/23/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024] Open
Abstract
Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter," the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.
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Affiliation(s)
- Ziyuan Dai
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People's Hospital, Yancheng, Jiangsu 224000, China
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Haoning Wang
- Heilongjiang Cold Region Wetland Ecology and Environment Research Key Laboratory, School of Geography and Tourism, Harbin University, Harbin, Heilongjiang 150086, China
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang 150086, China
| | - Juan Xu
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Ping Ni
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wang Li
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Xiaolong Wang
- The Key Laboratory of Wildlife Diseases and Biosecurity Management of Heilongjiang Province, Northeast Forestry University, Harbin 150006, China
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
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2
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He X, Tia AB, Yin Q, Gao L, Wang L, Tian T, Xiao K, Zhang Y, Tian F, Ma X, Harding D, Dong X. A retrospective study revealing complex viral diversity and a substantial burden of HPV infection in SARS-CoV-2 positive individuals, Sierra Leone. Virol J 2024; 21:201. [PMID: 39192225 DOI: 10.1186/s12985-024-02466-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has underscored the critical role of sequencing technology in disease control and outbreak response. However, resource limitations and challenging environments often impede such efforts in low and middle-income countries. This study aimed to investigate the spectrum of viral co-infections, particularly with human viral pathogens, in SARS-CoV-2 positive individuals in Sierra Leone using metagenomic sequencing, evaluating the feasibility of utilizing this technology for epidemiological and evolutionary surveillance of pathogens related to public health in low-income environments. METHODS We retrospectively collected and analyzed 98 nasopharyngeal swab specimens from SARS-CoV-2 positive individuals in Sierra Leone. Samples were pre-processed locally and transferred to China via FTA cards for metagenomic sequencing, which was performed using the Novaseq platform. The study focused on the identification of nasopharyngeal viruses co-infecting with SARS-CoV-2, with a deeper analysis of significant human viral pathogens such as HPV. RESULTS The study identified 22 viral taxa from 20 families, including 4 human viruses. Notably, 19.4% of samples showed HPV co-infection with 34 distinct types, predominantly beta and gamma HPVs. Multiple HPV types were found in individual samples, indicating a high complexity of viral co-infections. CONCLUSIONS The identification of a wide range of co-infecting viruses, particularly multiple HPV genotypes, highlights the complexity of viral interactions and their potential implications for public health. These findings enhance our understanding of viral co-infections and provide valuable insights for public health interventions in Sierra Leone. Further research is needed to explore the clinical significance of these findings and their impact on disease outcomes.
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Affiliation(s)
- Xiaozhou He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Alie Brima Tia
- Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra Leone
| | - Qikai Yin
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Liping Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Lili Wang
- Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Tingting Tian
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Kang Xiao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Yi Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Fengyu Tian
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Xuejun Ma
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
| | - Doris Harding
- Ministry of Health and Sanitation, 4th & 5th Floors Youyi Building, Freetown, Sierra Leone.
| | - Xiaoping Dong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
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3
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Morgan HJ, Olivero C, Shorning BY, Gibbs A, Phillips AL, Ananthan L, Lim AXH, Martuscelli L, Borgogna C, De Andrea M, Hufbauer M, Goodwin R, Akgül B, Gariglio M, Patel GK. HPV8-induced STAT3 activation led keratinocyte stem cell expansion in human actinic keratoses. JCI Insight 2024; 9:e177898. [PMID: 38916963 PMCID: PMC11383611 DOI: 10.1172/jci.insight.177898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/20/2024] [Indexed: 06/27/2024] Open
Abstract
Despite epidermal turnover, the skin is host to a complex array of microbes, including viruses, such as HPV, which must infect and manipulate skin keratinocyte stem cells (KSCs) to survive. This crosstalk between the virome and KSC populations remains largely unknown. Here, we investigated the effect of HPV8 on KSCs using various mouse models. We observed that the HPV8 early region gene E6 specifically caused Lrig1+ hair follicle junctional zone KSC proliferation and expansion, which would facilitate viral transmission. Within Lrig1+ KSCs specifically, HPV8 E6 bound intracellular p300 to phosphorylate the STAT3 transcriptional regulatory node. This induced ΔNp63 expression, resulting in KSC expansion into the overlying epidermis. HPV8 was associated with 70% of human actinic keratoses. Together, these results define the "hit-and-run" mechanism for HPV8 in human actinic keratosis as an expansion of KSCs, which lack melanosome protection and are thus susceptible to sun light-induced malignant transformation.
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Affiliation(s)
- Huw J Morgan
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Carlotta Olivero
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Boris Y Shorning
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Alex Gibbs
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Alexandra L Phillips
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Lokapriya Ananthan
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Annabelle Xiao Hui Lim
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Licia Martuscelli
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Cinzia Borgogna
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Marco De Andrea
- Viral Pathogenesis Unit, Department of Public Health and Pediatric Sciences, University of Turin Medical School, Turin, Italy
- Intrinsic Immunity Unit, Translational Research Centre for Autoimmune and Allergic Diseases, University of Eastern Piedmont, Novara, Italy
| | - Martin Hufbauer
- Institute of Virology, University of Cologne, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Richard Goodwin
- Department of Dermatology, Aneurin Bevan University Health Board, Royal Gwent Hospital, Newport, United Kingdom
| | - Baki Akgül
- Institute of Virology, University of Cologne, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Marisa Gariglio
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Girish K Patel
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, United Kingdom
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4
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Chatterjee S, Starrett GJ. Microhomology-mediated repair machinery and its relationship with HPV-mediated oncogenesis. J Med Virol 2024; 96:e29674. [PMID: 38757834 DOI: 10.1002/jmv.29674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Human Papillomaviruses (HPV) are a diverse family of non-enveloped dsDNA viruses that infect the skin and mucosal epithelia. Persistent HPV infections can lead to cancer frequently involving integration of the virus into the host genome, leading to sustained oncogene expression and loss of capsid and genome maintenance proteins. Microhomology-mediated double-strand break repair, a DNA double-stranded breaks repair pathway present in many organisms, was initially thought to be a backup but it's now seen as vital, especially in homologous recombination-deficient contexts. Increasing evidence has identified microhomology (MH) near HPV integration junctions, suggesting MH-mediated repair pathways drive integration. In this comprehensive review, we present a detailed summary of both the mechanisms underlying MH-mediated repair and the evidence for its involvement in HPV integration in cancer. Lastly, we highlight the involvement of these processes in the integration of other DNA viruses and the broader implications on virus lifecycles and host innate immune response.
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Affiliation(s)
- Subhajit Chatterjee
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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5
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Du-Thanh A, Foulongne V, Dereure O, Eloit M, Pérot P. A quantitative assay for the assessment of cutaneous human papillomaviruses and polyomaviruses over time: A proof-of-concept in two patients with atopic dermatitis and psoriasis. PLoS One 2024; 19:e0297907. [PMID: 38568962 PMCID: PMC10990162 DOI: 10.1371/journal.pone.0297907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/16/2024] [Indexed: 04/05/2024] Open
Abstract
The human skin virome, unlike commensal bacteria, is an under investigated component of the human skin microbiome. We developed a sensitive, quantitative assay to detect cutaneous human resident papillomaviruses (HPV) and polyomaviruses (HPyV) and we first used it to describe these viral populations at the skin surface of two patients with atopic dermatitis (AD) and psoriasis (PSO). We performed skin swabs on lesional and non-lesional skin in one AD and one PSO patient at M0, M1 and M3. After extraction, DNA was amplified using an original multiplex PCR technique before high throughput sequencing (HTS) of the amplicons (named AmpliSeq-HTS). Quantitative results were ultimately compared with monoplex quantitative PCRs (qPCRs) for previously detected viruses and were significantly correlated (R2 = 0.95, ρ = 0.75). Fifteen and 13 HPV types (mainly gamma and beta-HPVs) or HPyV species (mainly Merkel Cell Polyomavirus (MCPyV)) were detected on the skin of the AD and PSO patients, respectively. In both patients, the composition of the viral flora was variable across body sites but remained stable over time in non-lesional skin samples, mostly colonized with gamma-papillomaviruses. In lesional skin samples, beta-papillomaviruses and MCPyV were the major components of a viral flora more prone to vary over time especially with treatment and subsequent clinical improvement. We believe this method might be further used in extensive studies to further enhance the concept of an individual cutaneous viral fingerprint and the putative role of its alterations through various skin diseases and their treatments.
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Affiliation(s)
- Aurélie Du-Thanh
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Montpellier, France
- Département de Dermatologie, CHU de Montpellier, Montpellier, France
| | - Vincent Foulongne
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Montpellier, France
- Laboratoire de Virologie, CHU de Montpellier, Montpellier, France
| | - Olivier Dereure
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Montpellier, France
- Département de Dermatologie, CHU de Montpellier, Montpellier, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
- Ecole Nationale Vétérinaire d’Alfort, Maisons-Alfort, France
| | - Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
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6
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Moulin C, Beaupain B, Suarez F, Bertrand Y, Beaussant SC, Fischer A, Durin J, Ranta D, Espéli M, Bachelerie F, Bellanné-Chantelot C, Molina T, Emile JF, Balabanian K, Deback C, Donadieu J. CXCR4 WHIM syndrome is a cancer predisposition condition for virus-induced malignancies. Br J Haematol 2024; 204:1383-1392. [PMID: 38442908 DOI: 10.1111/bjh.19373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Warts, hypogammaglobulinaemia, infections and myelokathexis syndrome (WHIMS) is a rare combined primary immunodeficiency caused by the gain of function of the CXCR4 chemokine receptor. We present the prevalence of cancer in WHIMS patients based on data from the French Severe Chronic Neutropenia Registry and an exhaustive literature review. The median follow-up of the 14 WHIMS 'patients was 28.5 years. A central review and viral evaluation of pathological samples were organized, and we conducted a thorough literature review to identify all reports of WHIMS cases. Six French patients were diagnosed with cancer at a median age of 37.6 years. The 40-year risk of malignancy was 39% (95% confidence interval [CI]: 6%-74%). We observed two human papillomavirus (HPV)-induced vulvar carcinomas, three lymphomas (two Epstein-Barr virus [EBV]-related) and one basal cell carcinoma. Among the 155 WHIMS cases from the literature, 22 cancers were reported in 16 patients, with an overall cancer 40-year risk of 23% (95% CI: 13%-39%). Malignancies included EBV-associated lymphoproliferative disorders and HPV-positive genital and anal cancers as in the French cohort. Worldwide, nine cases of malignancy were associated with HPV and four with EBV. Immunocompromised WHIMS patients appear to be particularly susceptible to developing early malignancy, mainly HPV-induced carcinomas, followed by EBV-related lymphomas.
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Affiliation(s)
- Clémentine Moulin
- Université Paris-Cité, INSERM U1160, Institut de Recherche Saint-Louis, Paris, France
| | - Blandine Beaupain
- Centre de référence des neutropénies chroniques, Registre des neutropénies chroniques, APHP, Hôpital Trousseau Paris, Paris, France
| | - Felipe Suarez
- Service d'hématologie, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Yves Bertrand
- Institut d'hémato oncologie Pédiatrique, Hospice Civil de Lyon, Paris, France
| | - Sarah Cohen Beaussant
- Centre de référence des neutropénies chroniques, Registre des neutropénies chroniques, APHP, Hôpital Trousseau Paris, Paris, France
| | - Alain Fischer
- Centre de référence des déficits immunitaires héréditaires, Unité d'Immuno-Hématologie Pédiatrique, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Julie Durin
- Centre de référence des neutropénies chroniques, Registre des neutropénies chroniques, APHP, Hôpital Trousseau Paris, Paris, France
| | - Dana Ranta
- Service d'hématologie, CHU Nancy, Nancy, France
| | - Marion Espéli
- Université Paris-Cité, INSERM U1160, Institut de Recherche Saint-Louis, Paris, France
| | - Françoise Bachelerie
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, Orsay, France
| | | | - Thierry Molina
- Service d'anatomie pathologique Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Jean François Emile
- Service d'anatomie pathologique Hôpital Ambroise Paré, APHP, Boulogne-Billancourt, France
| | - Karl Balabanian
- Université Paris-Cité, INSERM U1160, Institut de Recherche Saint-Louis, Paris, France
| | - Claire Deback
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, Orsay, France
- Laboratoire de Virologie, Hôpitaux Universitaires Paris-Saclay, Hôpital Paul Brousse, AP-HP, Villejuif, France
| | - Jean Donadieu
- Centre de référence des neutropénies chroniques, Registre des neutropénies chroniques, APHP, Hôpital Trousseau Paris, Paris, France
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7
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Buck CB, Welch N, Belford AK, Varsani A, Pastrana DV, Tisza MJ, Starrett GJ. Widespread Horizontal Gene Transfer Among Animal Viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586562. [PMID: 38712252 PMCID: PMC11071296 DOI: 10.1101/2024.03.25.586562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.
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Affiliation(s)
| | - Nicole Welch
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: L.E.K. Consulting, Boston, MA, USA
| | - Anna K. Belford
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: University of Pittsburgh, Pittsburgh, PA, USA
| | - Arvind Varsani
- Arizona State University, Tempe, AZ, USA
- University of Cape Town, South Africa
| | | | - Michael J. Tisza
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: Baylor College of Medicine, Houston, TX, USA
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8
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Kilich G, Perelygina L, Sullivan KE. Rubella virus chronic inflammatory disease and other unusual viral phenotypes in inborn errors of immunity. Immunol Rev 2024; 322:113-137. [PMID: 38009321 DOI: 10.1111/imr.13290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Infectious susceptibility is a component of many inborn errors of immunity. Nevertheless, antibiotic use is often used as a surrogate in history taking for infectious susceptibility, thereby disadvantaging patients who present with viral infections as their phenotype. Further complicating clinical evaluations are unusual manifestations of viral infections which may be less familiar that the typical respiratory viral infections. This review covers several unusual viral phenotypes arising in patients with inborn errors of immunity and other settings of immune compromise. In some cases, chronic infections lead to oncogenesis or tumor-like growths and the conditions and mechanisms of viral-induced oncogenesis will be described. This review covers enterovirus, rubella, measles, papillomavirus, and parvovirus B19. It does not cover EBV and hemophagocytic lymphohistiocytosis nor lymphomagenesis related to EBV. EBV susceptibility has been recently reviewed. Our goal is to increase awareness of the unusual manifestations of viral infections in patients with IEI and to describe treatment modalities utilized in this setting. Coincidentally, each of the discussed viral infections can have a cutaneous component and figures will serve as a reminder of the physical features of these viruses. Given the high morbidity and mortality, early recognition can only improve outcomes.
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Affiliation(s)
- Gonench Kilich
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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9
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Roach MJ, Beecroft SJ, Mihindukulasuriya KA, Wang L, Paredes A, Cárdenas LAC, Henry-Cocks K, Lima LFO, Dinsdale EA, Edwards RA, Handley SA. Hecatomb: an integrated software platform for viral metagenomics. Gigascience 2024; 13:giae020. [PMID: 38832467 PMCID: PMC11148595 DOI: 10.1093/gigascience/giae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project-specific statistical analyses. FINDINGS Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means "a great sacrifice." In this setting, Hecatomb is "sacrificing" false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short- and long-read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome. CONCLUSION Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization, including rigorous quality control, host removal, and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools, enabling effective data interpretation for a variety of study designs. Hecatomb is hosted on GitHub (github.com/shandley/hecatomb) and is available for installation from Bioconda and PyPI.
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Affiliation(s)
- Michael J Roach
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
- Adelaide Centre for Epigenetics, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sarah J Beecroft
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Kathie A Mihindukulasuriya
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leran Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anne Paredes
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Luis Alberto Chica Cárdenas
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kara Henry-Cocks
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | | | - Elizabeth A Dinsdale
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, SA, Australia
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
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10
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McDermott DH, Velez D, Cho E, Cowen EW, DiGiovanna JJ, Pastrana DV, Buck CB, Calvo KR, Gardner PJ, Rosenzweig SD, Stratton P, Merideth MA, Kim HJ, Brewer C, Katz JD, Kuhns DB, Malech HL, Follmann D, Fay MP, Murphy PM. A phase III randomized crossover trial of plerixafor versus G-CSF for treatment of WHIM syndrome. J Clin Invest 2023; 133:e164918. [PMID: 37561579 PMCID: PMC10541188 DOI: 10.1172/jci164918] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 08/08/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUNDWarts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a primary immunodeficiency disorder caused by heterozygous gain-of-function CXCR4 mutations. Myelokathexis is a kind of neutropenia caused by neutrophil retention in bone marrow and in WHIM syndrome is associated with lymphopenia and monocytopenia. The CXCR4 antagonist plerixafor mobilizes leukocytes to the blood; however, its safety and efficacy in WHIM syndrome are undefined.METHODSIn this investigator-initiated, single-center, quadruple-masked phase III crossover trial, we compared the total infection severity score (TISS) as the primary endpoint in an intent-to-treat manner in 19 patients with WHIM who each received 12 months treatment with plerixafor and 12 months treatment with granulocyte CSF (G-CSF, the standard of care for severe congenital neutropenia). The treatment order was randomized for each patient.RESULTSPlerixafor was nonsuperior to G-CSF for TISS (P = 0.54). In exploratory endpoints, plerixafor was noninferior to G-CSF for maintaining neutrophil counts of more than 500 cells/μL (P = 0.023) and was superior to G-CSF for maintaining lymphocyte counts above 1,000 cells/μL (P < 0.0001). Complete regression of a subset of large wart areas occurred on plerixafor in 5 of 7 patients with major wart burdens at baseline. Transient rash occurred on plerixafor, and bone pain was more common on G-CSF. There were no significant differences in drug preference or quality of life or the incidence of drug failure or serious adverse events.CONCLUSIONPlerixafor was not superior to G-CSF in patients with WHIM for TISS, the primary endpoint. Together with wart regression and hematologic improvement, the infection severity results support continued study of plerixafor as a potential treatment for WHIM syndrome.TRIAL REGISTRATIONClinicaltrials.gov NCT02231879.FUNDINGThis study was funded by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- David H. McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
| | - Daniel Velez
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
| | - Elena Cho
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
| | - Edward W. Cowen
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases
| | | | | | | | | | - Pamela J. Gardner
- Office of the Clinical Director, National Institute of Dental and Craniofacial Research
| | | | | | | | - H. Jeffrey Kim
- Otolaryngology Branch, National Institute on Deafness and other Communication Disorders, and
| | - Carmen Brewer
- Otolaryngology Branch, National Institute on Deafness and other Communication Disorders, and
| | - James D. Katz
- Rheumatology Fellowship and Training Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | | | | | - Dean Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Michael P. Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Philip M. Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
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11
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Gelbard MK, Munger K. Human papillomaviruses: Knowns, mysteries, and unchartered territories. J Med Virol 2023; 95:e29191. [PMID: 37861365 PMCID: PMC10608791 DOI: 10.1002/jmv.29191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
There has been an explosion in the number of papillomaviruses that have been identified and fully sequenced. Yet only a minute fraction of these has been studied in any detail. Most of our molecular research efforts have focused on the E6 and E7 proteins of "high-risk," cancer-associated human papillomaviruses (HPVs). Interactions of the high-risk HPV E6 and E7 proteins with their respective cellular targets, the p53 and the retinoblastoma tumor suppressors, have been investigated in minute detail. Some have thus questioned if research on papillomaviruses remains an exciting and worthwhile area of investigation. However, fundamentally new insights on the biological activities and cellular targets of the high-risk HPV E6 and E7 proteins have been discovered and previously unstudied HPVs have been newly associated with human diseases. HPV infections continue to be an important cause of human morbidity and mortality and since there are no antivirals to combat HPV infections, research on HPVs should remain attractive to new investigators and biomedical funding agencies, alike.
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Affiliation(s)
- Maya K. Gelbard
- Genetics, Molecular and Cellular Biology Program, Graduate School of Biomedical Sciences
- Department of Developmental, Molecular and Cellular Biology, Tufts University School of Medicine, Boston, MA 02111
| | - Karl Munger
- Genetics, Molecular and Cellular Biology Program, Graduate School of Biomedical Sciences
- Department of Developmental, Molecular and Cellular Biology, Tufts University School of Medicine, Boston, MA 02111
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12
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Majumdar S, Pontejo SM, Jaiswal H, Gao JL, Salancy A, Stassenko E, Yamane H, McDermott DH, Balabanian K, Bachelerie F, Murphy PM. Severe CD8+ T Lymphopenia in WHIM Syndrome Caused by Selective Sequestration in Primary Immune Organs. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1913-1924. [PMID: 37133343 PMCID: PMC10247468 DOI: 10.4049/jimmunol.2200871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/10/2023] [Indexed: 05/04/2023]
Abstract
Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is an ultra-rare combined primary immunodeficiency disease caused by heterozygous gain-of-function mutations in the chemokine receptor CXCR4. WHIM patients typically present with recurrent acute infections associated with myelokathexis (severe neutropenia due to bone marrow retention of mature neutrophils). Severe lymphopenia is also common, but the only associated chronic opportunistic pathogen is human papillomavirus and mechanisms are not clearly defined. In this study, we show that WHIM mutations cause more severe CD8 than CD4 lymphopenia in WHIM patients and WHIM model mice. Mechanistic studies in mice revealed selective and WHIM allele dose-dependent accumulation of mature CD8 single-positive cells in thymus in a cell-intrinsic manner due to prolonged intrathymic residence, associated with increased CD8 single-positive thymocyte chemotactic responses in vitro toward the CXCR4 ligand CXCL12. In addition, mature WHIM CD8+ T cells preferentially home to and are retained in the bone marrow in mice in a cell-intrinsic manner. Administration of the specific CXCR4 antagonist AMD3100 (plerixafor) in mice rapidly and transiently corrected T cell lymphopenia and the CD4/CD8 ratio. After lymphocytic choriomeningitis virus infection, we found no difference in memory CD8+ T cell differentiation or viral load between wild-type and WHIM model mice. Thus, lymphopenia in WHIM syndrome may involve severe CXCR4-dependent CD8+ T cell deficiency resulting in part from sequestration in the primary lymphoid organs, thymus, and bone marrow.
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Affiliation(s)
- Shamik Majumdar
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Sergio M. Pontejo
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Hemant Jaiswal
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Ji-Liang Gao
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Abigail Salancy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Elizabeth Stassenko
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hidehiro Yamane
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - David H. McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Karl Balabanian
- Université Paris-Cité, Institut de Recherche Saint-Louis, OPALE Carnot Institute, EMiLy, INSERM U1160, Paris, France
| | - Françoise Bachelerie
- Université Paris-Saclay, INSERM, Inflammation, Microbiome and Immunosurveillance, Orsay, France
| | - Philip M. Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
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13
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Gallego C, Jaracz-Ros A, Laganà M, Mercier-Nomé F, Domenichini S, Fumagalli A, Roingeard P, Herfs M, Pidoux G, Bachelerie F, Schlecht-Louf G. Reprogramming of connexin landscape fosters fast gap junction intercellular communication in human papillomavirus-infected epithelia. Front Cell Infect Microbiol 2023; 13:1138232. [PMID: 37260709 PMCID: PMC10228504 DOI: 10.3389/fcimb.2023.1138232] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 06/02/2023] Open
Abstract
Human papillomaviruses (HPVs) are highly prevalent commensal viruses that require epithelial stratification to complete their replicative cycle. While HPV infections are most often asymptomatic, certain HPV types can cause lesions, that are usually benign. In rare cases, these infections may progress to non-replicative viral cycles associated with high HPV oncogene expression promoting cell transformation, and eventually cancer when not cleared by host responses. While the consequences of HPV-induced transformation on keratinocytes have been extensively explored, the impact of viral replication on epithelial homeostasis remains largely unexplored. Gap junction intercellular communication (GJIC) is critical for stratified epithelium integrity and function. This process is ensured by a family of proteins named connexins (Cxs), including 8 isoforms that are expressed in stratified squamous epithelia. GJIC was reported to be impaired in HPV-transformed cells, which was attributed to the decreased expression of the Cx43 isoform. However, it remains unknown whether and how HPV replication might impact on the expression of Cx isoforms and GJIC in stratified squamous epithelia. To address this question, we have used 3D-epithelial cell cultures (3D-EpCs), the only model supporting the productive HPV life cycle. We report a transcriptional downregulation of most epithelial Cx isoforms except Cx45 in HPV-replicating epithelia. At the protein level, HPV replication results in a reduction of Cx43 expression while that of Cx45 increases and displays a topological shift toward the cell membrane. To quantify GJIC, we pioneered quantitative gap-fluorescence loss in photobleaching (FLIP) assay in 3D-EpCs, which allowed us to show that the reprogramming of Cx landscape in response to HPV replication translates into accelerated GJIC in living epithelia. Supporting the pathophysiological relevance of our observations, the HPV-associated Cx43 and Cx45 expression pattern was confirmed in human cervical biopsies harboring HPV. In conclusion, the reprogramming of Cx expression and distribution in HPV-replicating epithelia fosters accelerated GJIC, which may participate in epithelial homeostasis and host immunosurveillance.
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Affiliation(s)
- Carmen Gallego
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Agnieszka Jaracz-Ros
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Marta Laganà
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Françoise Mercier-Nomé
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
- US31-UMS3679-Plateforme PHIC, Ingénierie et Plateformes au Service de l’Innovation Thérapeutique (IPSIT), INSERM, CNRS, Université Paris-Saclay, Orsay, France
| | - Séverine Domenichini
- UMS-IPSIT Plateforme MIPSIT, Université Paris-Saclay, CNRS, Inserm, Ingénierie et Plateformes au Service de l’Innovation Thérapeutique, Orsay, France
| | - Amos Fumagalli
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Philippe Roingeard
- INSERM U1259, Université de Tours et CHRU de Tours & Plateforme IBiSA des Microscopies, PPF ASB, CHRU de Tours, Tours, France
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liège, Liège, Belgium
| | | | - Françoise Bachelerie
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Géraldine Schlecht-Louf
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
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14
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Kandeel M. Oncogenic Viruses-Encoded microRNAs and Their Role in the Progression of Cancer: Emerging Targets for Antiviral and Anticancer Therapies. Pharmaceuticals (Basel) 2023; 16:ph16040485. [PMID: 37111242 PMCID: PMC10146417 DOI: 10.3390/ph16040485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Approximately 20% of all cases of human cancer are caused by viral infections. Although a great number of viruses are capable of causing a wide range of tumors in animals, only seven of these viruses have been linked to human malignancies and are presently classified as oncogenic viruses. These include the Epstein-Barr virus (EBV), human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), Merkel cell polyomavirus (MCPyV), human herpesvirus 8 (HHV8), and human T-cell lymphotropic virus type 1 (HTLV-1). Some other viruses, such as the human immunodeficiency virus (HIV), are associated with highly oncogenic activities. It is possible that virally encoded microRNAs (miRNAs), which are ideal non-immunogenic tools for viruses, play a significant role in carcinogenic processes. Both virus-derived microRNAs (v-miRNAs) and host-derived microRNAs (host miRNAs) can influence the expression of various host-derived and virus-derived genes. The current literature review begins with an explanation of how viral infections might exert their oncogenic properties in human neoplasms, and then goes on to discuss the impact of diverse viral infections on the advancement of several types of malignancies via the expression of v-miRNAs. Finally, the role of new anti-oncoviral therapies that could target these neoplasms is discussed.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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15
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Nelson CW, Mirabello L. Human papillomavirus genomics: Understanding carcinogenicity. Tumour Virus Res 2023; 15:200258. [PMID: 36812987 PMCID: PMC10063409 DOI: 10.1016/j.tvr.2023.200258] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
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Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA; Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA.
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16
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Silling S, Kreuter A, Gambichler T, Meyer T, Stockfleth E, Wieland U. Epidemiology of Merkel Cell Polyomavirus Infection and Merkel Cell Carcinoma. Cancers (Basel) 2022; 14:6176. [PMID: 36551657 PMCID: PMC9776808 DOI: 10.3390/cancers14246176] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Merkel cell polyomavirus (MCPyV) is a ubiquitous virus replicating in human dermal fibroblasts. MCPyV DNA can be detected on healthy skin in 67−90% of various body sites, and intact virions are regularly shed from the skin. Infection occurs early in life, and seropositivity increases from 37 to 42% in 1- to 6-year-olds to 92% in adults. Merkel cell carcinoma (MCC) is a rare but very aggressive neuroendocrine tumor of the skin. It develops mainly on sun-exposed areas as a fast-growing, reddish nodule. Two MCC entities exist: about 80% of MCC are MCPyV-associated. Tumorigenesis is driven by viral integration into the host genome and MCPyV oncogene expression. In MCPyV-negative MCC, UV radiation causes extensive DNA damage leading to the deregulation of the cell cycle. In recent decades, MCC incidence rates have increased worldwide, e.g., in the United States, from 0.15 in 1986 to 0.7/100,000 in 2016. Risk factors for the development of MCC include male sex, older age (>75 years), fair skin, intense UV exposure, and immunosuppression. Projections suggest that due to aging populations, an increase in immunosuppressed patients, and enhanced UV exposure, MCC incidence rates will continue to rise. Early diagnosis and prompt treatment are crucial to reducing high MCC morbidity and mortality.
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Affiliation(s)
- Steffi Silling
- Institute of Virology, National Reference Center for Papilloma- and Polyomaviruses, Faculty of Medicine, University Hospital Cologne, 50935 Cologne, Germany
| | - Alexander Kreuter
- Department of Dermatology, Venereology and Allergology, HELIOS St. Elisabeth Hospital Oberhausen, University Witten/Herdecke, 58455 Witten, Germany
| | - Thilo Gambichler
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Thomas Meyer
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Eggert Stockfleth
- Skin Cancer Center, Department of Dermatology, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Ulrike Wieland
- Institute of Virology, National Reference Center for Papilloma- and Polyomaviruses, Faculty of Medicine, University Hospital Cologne, 50935 Cologne, Germany
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17
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Hu H, Ling Y, Wang X, Wang H, Zhu N, Li Y, Xu H. Viral Metagenomics Reveals a Putative Novel HPV Type in Anogenital Wart Tissues. Pathogens 2022; 11:pathogens11121452. [PMID: 36558785 PMCID: PMC9781650 DOI: 10.3390/pathogens11121452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Viral metagenomics is widely employed to identify novel viruses in biological samples. Recently, although numerous novel human papillomavirus (HPV) types have been identified in clinical samples including anogenital warts (AGWs), many novel HPV sequences remain to be discovered. In this study, a putative novel HPV type designated as HPV-JDFY01 was discovered from library GW05 with 63 sequence reads by the viral metagenomic technique. Its complete genomic sequence was determined by PCR to bridge the gaps between contigs combining Sanger sequencing. The complete genome of HPV-JDFY01 is a 7186 bp encoding 7 open reading frames (ORFs) (E6, E7, E1, E2, E4, L2 and L1) and contains a 487 bp long control region (LCR) between L1 and E6. Sequence and phylogeny analysis indicated that HPV-JDFY01 shared the highest sequence identity of 74.2% with HPV-mSK_244 (MH777383) and well clustered into the genus Gammapapillomavirus. It has the classical genomic organization of Gammapapillomaviruses. Epidemiological investigation showed that one out of the 413 AGW tissue samples was positive for HPV-JDFY01. Further research with large size and different type of samples should be performed to elucidate the epidemiologic status of HPV-JDFY01.
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Affiliation(s)
- Huimin Hu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
- Department of Dermatology, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian 223002, China
| | - Yu Ling
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing 210004, China
| | - Xuan Wang
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Hao Wang
- Department of Dermatology, The Affiliated Huai’an Hospital of Xuzhou Medical University and The Second People’s Hospital of Huai’an, Huaian 223002, China
| | - Niannan Zhu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Yumei Li
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
| | - Hui Xu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang 212001, China
- Correspondence: ; Tel.: +86-051185026785
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18
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Yu L, Majerciak V, Zheng ZM. HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094943. [PMID: 35563334 PMCID: PMC9105396 DOI: 10.3390/ijms23094943] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/18/2022] Open
Abstract
Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.
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19
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Silling S, Kreuter A, Wieland U. [Human polyomavirus-associated skin diseases]. Hautarzt 2022; 73:426-433. [PMID: 35482045 DOI: 10.1007/s00105-022-04993-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Of the 15 currently known human polyomaviruses (HPyV), eight have been found on healthy skin. Merkel cell polyomavirus (MCPyV), HPyV6, HPyV7, and to a lesser extent Saint Louis polyomavirus (STLPyV) are considered part of the human cutaneous virome. The most important cutaneous polyomavirus, MCPyV, causes the majority of Merkel cell carcinomas (MCC). MCC is a rare but very aggressive malignant skin tumor that affects both immunocompetent and immunosuppressed patients. A steady increase in incidence rates of this skin tumor has been observed in recent decades. MCC occurs primarily on sunlight-exposed skin of fair-skinned individuals. Risk factors for MCC development include immunosuppression and advanced age. In immunocompromised individuals, primary infection with trichodysplasia spinulosa-associated polyomavirus (TSPyV) can cause the very rare skin disease trichodysplasia spinulosa (TS). Keratin spines (spicules), mainly in the center of the face, clinically characterize this disease. Skin lesions associated with further HPyV have been described exclusively in immunocompromised individuals. For HPyV6 and HPyV7, cases of epithelial proliferation and pruritic dyskeratotic dermatitis have been published. HPyV9 and New Jersey polyomavirus (NJPyV-13) were each found in different skin lesions of individual patients. The role of these polyomaviruses in the development of the skin lesions is still unclear.
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Affiliation(s)
- Steffi Silling
- Institut für Virologie, Nationales Referenzzentrum für Papillom- und Polyomaviren, Universitätsklinikum Köln und Universität zu Köln, Fürst-Pückler-Str. 56, 50935, Köln, Deutschland
| | - Alexander Kreuter
- Klinik für Dermatologie, Venerologie und Allergologie, HELIOS St. Elisabeth Klinik Oberhausen, Universität Witten/Herdecke, Oberhausen, Deutschland.,Klinik für Dermatologie, Venerologie und Allergologie, HELIOS St. Johannes Klinik Duisburg, Duisburg, Deutschland
| | - Ulrike Wieland
- Institut für Virologie, Nationales Referenzzentrum für Papillom- und Polyomaviren, Universitätsklinikum Köln und Universität zu Köln, Fürst-Pückler-Str. 56, 50935, Köln, Deutschland.
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20
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Zampella J, Cohen B. Consideration of underlying immunodeficiency in refractory or recalcitrant warts: A review of the literature. SKIN HEALTH AND DISEASE 2022; 2:e98. [PMID: 35665206 PMCID: PMC9060099 DOI: 10.1002/ski2.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/12/2022] [Accepted: 01/16/2022] [Indexed: 11/16/2022]
Abstract
Although the exact mechanisms have yet to be elucidated, it is clear that cellular immunity plays a role in clearance of human papillomavirus (HPV) infections as it relates to the development of warts. Patients with extensive, recalcitrant, or treatment‐refractory warts may have an underlying immune system impairment at the root of HPV susceptibility. Early recognition of genetic disorders associated with immunologic defects that allow for recalcitrant HPV infection may expedite appropriate treatment for patients. Early recognition is often pivotal in preventing subsequent morbidity and/or mortality that may arise from inborn errors of immunity, such as WHIM (Warts, Hypogammaglobulinemia, Infections, Myelokathexis) syndrome. Among these, cervical cancer is one of the most common malignancies associated with HPV, can be fatal if not treated early, and is seen more frequently in patients with underlying immune deficiencies. A review of diseases with susceptibility to HPV provides clues to understanding the pathophysiology of warts. We also present diagnostic guidance to facilitate the recognition of inborn errors of immunity in patients with extensive and/or recalcitrant HPV infections.
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Affiliation(s)
- J. Zampella
- Ronald O. Perelman Department of Dermatology NYU Grossman School of Medicine New York New York USA
| | - B. Cohen
- Division of Pediatric Dermatology Johns Hopkins University School of Medicine Baltimore Maryland USA
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21
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Trevino V, Oyervides M, Ramírez-Correa GA, Garza L. Generating human papillomavirus (HPV) reference databases to maximize genomic mapping. Arch Virol 2022; 167:57-65. [PMID: 34668074 DOI: 10.1007/s00705-021-05256-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/13/2021] [Indexed: 01/14/2023]
Abstract
Genomic experiments analyzing human papillomaviruses (HPVs) require a carefully selected list of sequences as a reference database to map millions of reads. The available sources, such as the Papillomavirus Episteme (PaVE), are organized based on variations in the L1 gene rather than the whole HPV sequence. Moreover, the PaVE process uses complex multiple sequence alignments containing hundreds or thousands of sequences. These issues complicate the generation of a reference database for genomics, leading to the generation of per-analysis-defined databases. Here, we propose a de novo strategy considering all HPV sequences reported in the NCBI database to define a subset of highly representative HPV sequences. The strategy is based on oligonucleotide frequency profiling of the whole sequence followed by hierarchical clustering. Using data from HPV capture experiments, we demonstrate that this strategy selects suitable sequences as a reference database to map most mappable reads unambiguously. We provide some recommendations to improve HPV mapping. The generated .fasta files can be accessed at https://github.com/vtrevino/HPV-Ref-Genomes .
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Affiliation(s)
- Victor Trevino
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, 64710, Monterrey, Nuevo León, Mexico.
| | - Mariel Oyervides
- Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, 64849, Monterrey, Nuevo León, Mexico
| | - Genaro A Ramírez-Correa
- Department of Molecular Science, UT Health Rio Grande Valley, McAllen, TX, 78502, USA.,Division of Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Lourdes Garza
- Centro Universitario Contra el Cáncer (CUCC), Servicio de Oncología, Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio Gonzáalez", 64460, Monterrey, Nuevo León, Mexico
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22
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The Application of the Skin Virome for Human Identification. Forensic Sci Int Genet 2022; 57:102662. [DOI: 10.1016/j.fsigen.2022.102662] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 01/03/2023]
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23
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Giuliani E, Rollo F, Donà MG, Garbuglia AR. Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology. Pathogens 2021; 10:pathogens10111411. [PMID: 34832567 PMCID: PMC8625118 DOI: 10.3390/pathogens10111411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Oral infection by Human Papillomavirus (HPV) has recently gained great attention because of its involvement in the development of a subset of head and neck squamous cell carcinoma. The role of specific Alpha-HPVs in this regard has been well established, whereas the contribution of other genera is under investigation. Despite their traditional classification as “cutaneous” types, Beta and Gamma HPVs are frequently detected in oral samples. Due to the lack of a standardized protocol, a large variety of methodologies have been used for oral sample collection, DNA extraction, HPV detection and genotyping. Laboratory procedures influence the evaluation of oral HPV prevalence, which largely varies also according to the population characteristics, e.g., age, gender, sexual behavior, Human Immunodeficiency Virus (HIV) status. Nevertheless, oral infection by Beta and Gamma HPVs seems to be even more common than Alpha-HPVs. The latter is 5–7% in the general population, and increases up to 30% approximately in HIV-infected men who have sex with men. Despite major advances in the evaluation of oral HPV prevalence, its natural history is still little understood, especially for Beta and Gamma HPVs. The latest technologies, such as Next Generation Sequencing (NGS), can be exploited to gain new insights into oral HPV, and to improve the identification of novel HPV types.
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Affiliation(s)
- Eugenia Giuliani
- Scientific Direction, San Gallicano Dermatological Institute IRCCS, Via Elio Chianesi 53, 00144 Rome, Italy;
| | - Francesca Rollo
- Pathology Department, Regina Elena National Cancer Institute IRCCS, Via Elio Chianesi 53, 00144 Rome, Italy;
| | - Maria Gabriella Donà
- STI/HIV Unit, San Gallicano Dermatological Institute IRCCS, Via Elio Chianesi 53, 00144 Rome, Italy
- Correspondence: ; Tel.: +39-0652665393
| | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy;
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24
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Human papillomaviruses: diversity, infection and host interactions. Nat Rev Microbiol 2021; 20:95-108. [PMID: 34522050 DOI: 10.1038/s41579-021-00617-5] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 12/13/2022]
Abstract
Human papillomaviruses (HPVs) are an ancient and highly successful group of viruses that have co-evolved with their host to replicate in specific anatomical niches of the stratified epithelia. They replicate persistently in dividing cells, hijack key host cellular processes to manipulate the cellular environment and escape immune detection, and produce virions in terminally differentiated cells that are shed from the host. Some HPVs cause benign, proliferative lesions on the skin and mucosa, and others are associated with the development of cancer. However, most HPVs cause infections that are asymptomatic and inapparent unless the immune system becomes compromised. To date, the genomes of almost 450 distinct HPV types have been isolated and sequenced. In this Review, I explore the diversity, evolution, infectious cycle, host interactions and disease association of HPVs.
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25
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Kono T, Laimins L. Genomic Instability and DNA Damage Repair Pathways Induced by Human Papillomaviruses. Viruses 2021; 13:1821. [PMID: 34578402 PMCID: PMC8472259 DOI: 10.3390/v13091821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/29/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022] Open
Abstract
Human papillomaviruses (HPV) are the causative agents of cervical and other anogenital cancers as well as those of the oropharynx. HPV proteins activate host DNA damage repair factors to promote their viral life cycle in stratified epithelia. Activation of both the ATR pathway and the ATM pathway are essential for viral replication and differentiation-dependent genome amplification. These pathways are also important for maintaining host genomic integrity and their dysregulation or mutation is often seen in human cancers. The APOBEC3 family of cytidine deaminases are innate immune factors that are increased in HPV positive cells leading to the accumulation of TpC mutations in cellular DNAs that contribute to malignant progression. The activation of DNA damage repair factors may corelate with expression of APOBEC3 in HPV positive cells. These pathways may actively drive tumor development implicating/suggesting DNA damage repair factors and APOBEC3 as possible therapeutic targets.
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Affiliation(s)
- Takeyuki Kono
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
- Department of Otolaryngology Head and Neck Surgery, School of Medicine, Keio University, Tokyo 1608582, Japan
| | - Laimonis Laimins
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
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26
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Chen Z, Utro F, Platt D, DeSalle R, Parida L, Chan PKS, Burk RD. K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses. Int J Mol Sci 2021; 22:9657. [PMID: 34502564 PMCID: PMC8432194 DOI: 10.3390/ijms22179657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 12/31/2022] Open
Abstract
Papillomaviruses (PVs) are a heterogeneous group of DNA viruses that can infect fish, birds, reptiles, and mammals. PVs infecting humans (HPVs) phylogenetically cluster into five genera (Alpha-, Beta-, Gamma-, Mu- and Nu-PV), with differences in tissue tropism and carcinogenicity. The evolutionary features associated with the divergence of Papillomaviridae are not well understood. Using a combination of k-mer distributions, genetic metrics, and phylogenetic algorithms, we sought to evaluate the characteristics and differences of Alpha-, Beta- and Gamma-PVs constituting the majority of HPV genomes. A total of 640 PVs including 442 HPV types, 27 non-human primate PV types, and 171 non-primate animal PV types were evaluated. Our analyses revealed the highest genetic diversity amongst Gamma-PVs compared to the Alpha and Beta PVs, suggesting reduced selective pressures on Gamma-PVs. Using a sequence alignment-free trimer (k = 3) phylogeny algorithm, we reconstructed a phylogeny that grouped most HPV types into a monophyletic clade that was further split into three branches similar to alignment-based classifications. Interestingly, a subset of low-risk Alpha HPVs (the species Alpha-2, 3, 4, and 14) split from other HPVs and were clustered with non-human primate PVs. Surprisingly, the trimer-constructed phylogeny grouped the Gamma-6 species types originally isolated from the cervicovaginal region with the main Alpha-HPV clade. These data indicate that characterization of papillomavirus heterogeneity via orthogonal approaches reveals novel insights into the biological understanding of HPV genomes.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China;
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Filippo Utro
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Daniel Platt
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA;
| | - Laxmi Parida
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China;
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Brancaccio RN, Robitaille A, Dutta S, Rollison DE, Tommasino M, Gheit T. MinION nanopore sequencing and assembly of a complete human papillomavirus genome. J Virol Methods 2021; 294:114180. [PMID: 33965458 PMCID: PMC8223502 DOI: 10.1016/j.jviromet.2021.114180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/26/2021] [Accepted: 05/03/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consuming and low-throughput methodologies. METHODS We report the use of the MinION nanopore sequencer to sequence the full-length genome of human papillomavirus (HPV)-ICB2 (7441 bp), which was previously characterized in our laboratory. Three independent MinION libraries were prepared and sequenced using either three consecutive 12 -h runs (Protocol A) or a single run of 48 h starting from a pool of three barcoded DNA libraries (Protocol B). A fully automated bioinformatics pipeline was developed for the reconstruction of the viral genome. RESULTS Protocols A and B generated 9,354,933 and 3,255,879 reads, respectively. Read length N50 values ranged between 6976 and 7360 nucleotides over the four sequencing runs. Bioinformatics analysis showed that both protocols allowed for the reconstruction of the whole viral genome, with pairwise percentages of identity to HPV-ICB2 of 100 % for protocol A and 99.98 % for protocol B. CONCLUSION Our results show that the use of the MinION nanopore sequencer represents an effective strategy for whole-genome sequencing of HPVs with a minimal error rate.
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Affiliation(s)
- Rosario N Brancaccio
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Alexis Robitaille
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Sankhadeep Dutta
- Chittaranjan National Cancer Institute, Department of Viral Associated Human Cancer, Kolkata, India
| | - Dana E Rollison
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Massimo Tommasino
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Tarik Gheit
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France.
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28
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Tisza MJ, Buck CB. A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. Proc Natl Acad Sci U S A 2021; 118:e2023202118. [PMID: 34083435 PMCID: PMC8201803 DOI: 10.1073/pnas.2023202118] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus-disease associations are found.
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Affiliation(s)
- Michael J Tisza
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
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29
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Arroyo Mühr LS, Hultin E, Dillner J. Transcription of human papillomaviruses in nonmelanoma skin cancers of the immunosuppressed. Int J Cancer 2021; 149:1341-1347. [PMID: 33990956 DOI: 10.1002/ijc.33683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022]
Abstract
Nonmelanoma skin cancer (NMSC) has a greatly increased incidence among the immunosuppressed and the DNA of human papillomavirus (HPV) is commonly found in these tumors. To investigate if there are any actively transcribed HPV infections in these tumors, we identified all skin cancers diagnosed after solid organ transplantation in Sweden during 1964-2011 (n = 7614 NMSCs) and requested the diagnostic tumor blocks from the corresponding pathology archives. For the present study, we selected diagnostic specimens from 345 NMSC and performed whole genome transcriptome analysis using NovaSeq (Illumina), in comparison with three cervical cancers. Although we obtained an abundance of high-quality paired reads per sample (median of 35 million reads), only 15 NMSC specimens contained HPV transcription. Three specimens had transcription of oncogenic anogenital HPVs (HPV16 and 56), six tumors had transcription of HPVs from the beta-2 species (three HPV38, two with HPV23 and one with HPV107) and then there was one observation each of transcription of HPVs 3, 26, 57, 147, 158, 168 and of two nonestablished HPV types belonging to the gamma genus. In conclusion, transcription of specific HPV types can be found in NMSC among the immunosuppressed, but this is not common.
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Affiliation(s)
| | - Emilie Hultin
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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30
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Abstract
The skin microbiome is an ecosystem comprised of a multitude of microbial species interacting with their surroundings, including other microbes and host epithelial and immune cells. These interactions are the basis of important roles within the skin microbiome that provide benefit to the host, boosting multiple aspects of barrier function, a critical function of this essential organ. However, with reward always comes risk; resident skin microbes function in a context-dependent manner, set on the backdrop of a dynamic host and microbial milieu. Here, we discuss the reward of hosting a microbial ecosystem on the skin, including protection from pathogens and tuning of the skin microenvironment. We also give consideration to how these skin residents, often termed "commensals" can cause disorder, damage, and promote skin disease.
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Affiliation(s)
- Laurice Flowers
- Department of Dermatology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth A Grice
- Department of Dermatology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.
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31
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Hošnjak L, Kocjan BJ, Pirš B, Seme K, Poljak M. The genetic diversity of human papillomavirus types from the species Gammapapillomavirus 15: HPV135, HPV146, and HPV179. PLoS One 2021; 16:e0249829. [PMID: 33956809 PMCID: PMC8101917 DOI: 10.1371/journal.pone.0249829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/25/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES To determine the prevalence, viral load, tissue tropism, and genetic variability of novel human papillomavirus (HPV) type 179, which is etiologically associated with sporadic cases of common warts in immunocompromised patients, and phylogenetically related HPV types 135 and 146. METHODS The representative collection of 850 HPV-associated clinical samples (oral/nasopharyngeal/anal, archival specimens of oral/oropharyngeal/conjunctival/cervical/skin cancer, benign lesions of the larynx/conjunctiva/skin, and eyebrows), obtained from immunocompetent individuals, was tested for the presence of HPV179, HPV135, and HPV146 using type-specific real-time PCRs. To assess the genetic diversity of the HPVs investigated in the non-coding long control region (LCR), several highly sensitive nested PCR protocols were developed for each HPV type. The genetic diversity of HPV179 was additionally determined in 12 HPV179 isolates from different anatomical sites of an only immunocompromised patient included in the study. RESULTS HPV179, HPV135, and HPV146 were detected in 1.4, 2.0, and 1.5% of the samples tested, respectively, with no preference for cutaneous or mucosal epithelial cells. One (with five single nucleotide polymorphisms; SNPs), four (with one to six SNPs), and four (with one to eight SNPs) genetic variants of HPV179, HPV135, and HPV146, respectively, were identified among eligible samples. HPV179 isolates from the immunocompromised patient exhibited the identical LCR nucleotide sequence, suggesting that HPV179 can cause generalized HPV infections. CONCLUSIONS HPV179, HPV135, and HPV146 have a mucocutaneous tissue tropism and are associated with sporadic infections in immunocompromised and immunocompetent individuals. Because the majority of mutations were found outside the major functional domains of the respective LCRs, we assume that HPV179, HPV135, and HPV146 genetic variants pathogenically do not differ from their prototypes. In addition, no association was found between specific HPV179, HPV135, and HPV146 genetic variants and anatomical sites of infection and/or specific neoplasms.
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Affiliation(s)
- Lea Hošnjak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Katja Seme
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
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32
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Hu HM, Long WG, Wang X, Li YM, Xu H. Recurrent infantile digital fibromatosis with HPV infection: a case report. AME Case Rep 2021; 5:20. [PMID: 33912809 DOI: 10.21037/acr-20-95] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/04/2020] [Indexed: 11/06/2022]
Abstract
Infantile digital fibromatosis is a rare, benign fibrous tumor among infants usually limited to fingers and toes. Most cases present themselves with round eosinophilic inclusion bodies of different sizes, similar to erythrocyte in the parakarytoplasm. Although infantile digital fibromatosis had been observed with a tendency of spontaneous regression after a rapid phase of growth in some reports, the recurrence rate of early surgical intervention remains high. And the mechanism of recurrence is still unknown. Human papillomavirus (HPV), as a circular icosahedral double-stranded DNA virus, is famous for its remarkable significant correlation with cervical cancer. However, the reports about the possible relationship of recurrent infantile digital fibromatosis and HPV infection are rare and inconsistent. Here, we report a recurrent case of infantile digital fibromatosis after surgical resection. Pathological biopsy of the recurrent site not only identified the diagnosis of infantile digital fibromatosis again, but found the sign of HPV infection. Family history indicated that the patient's grandmother had a history of verruca plana. After complete resection of recurrence, the tumor recurred again and the case is still being followed up. The unique case may serve as a clue to the pathogenesis of the relationship between recurrent infantile digital fibromatosis and HPV infection.
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Affiliation(s)
- Hui-Min Hu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wei-Guo Long
- Department of Pathology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xuan Wang
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yu-Mei Li
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Hui Xu
- Department of Dermatology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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33
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Misclassifications in human papillomavirus databases. Virology 2021; 558:57-66. [PMID: 33730650 DOI: 10.1016/j.virol.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/23/2021] [Accepted: 03/04/2021] [Indexed: 01/05/2023]
Abstract
We assessed the quality of human papillomavirus (HPV) sequences in GenBank by analyzing the possible presence of chimeras, "wrong-assembled" contigs and errors in taxonomy using an open-source script (HPVChimera_Gb) that compared 25 638 HPV-related nucleotide sequences in GenBank with the 221 numbered HPV types and another 220 complete HPV sequences. There were 110 sequences with taxonomy/naming errors (sequences reported as another HPV type than the one they corresponded to) and 1318 possibly chimeric sequences. Manual analysis found plausible explanations for most of them (e.g. sequence covering an integration site) but 114 sequences appeared to be chimeras (96/114 were already flagged as "unverified" by GenBank) and 13 had taxonomy/naming errors. When comparing all correct HPV sequences in GenBank, there appeared to exist about 800 unique putative HPV types. Systematic and regular work towards eliminating chimeric sequences and taxonomy/naming errors could increase the quality and order in HPV research.
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34
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Zhang HT, Wang H, Wu HS, Zeng J, Yang Y. Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis. Virol J 2021; 18:11. [PMID: 33407663 PMCID: PMC7789296 DOI: 10.1186/s12985-020-01482-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. METHODS To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. RESULTS Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. CONCLUSION Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.
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Affiliation(s)
- He-Teng Zhang
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, 212001, Jiangsu, China
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Hai-Sheng Wu
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 810021, Qinghai, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Yang
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, 212001, Jiangsu, China.
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35
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Dale DC, Firkin F, Bolyard AA, Kelley M, Makaryan V, Gorelick KJ, Ebrahim T, Garg V, Tang W, Jiang H, Skerlj R, Beaussant Cohen S. Results of a phase 2 trial of an oral CXCR4 antagonist, mavorixafor, for treatment of WHIM syndrome. Blood 2020; 136:2994-3003. [PMID: 32870250 PMCID: PMC7770568 DOI: 10.1182/blood.2020007197] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/16/2020] [Indexed: 12/16/2022] Open
Abstract
Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare primary immunodeficiency caused by gain-of-function mutations in the CXCR4 gene. We report the safety, tolerability, pharmacokinetics, pharmacodynamics, and preliminary efficacy of mavorixafor from a phase 2 open-label dose-escalation and extension study in 8 adult patients with genetically confirmed WHIM syndrome. Mavorixafor is an oral small molecule selective antagonist of the CXCR4 receptor that increases mobilization and trafficking of white blood cells from the bone marrow. Patients received escalating doses of mavorixafor, up to 400 mg once daily. Five patients continued on the extension study for up to 28.6 months. Mavorixafor was well tolerated with no treatment-related serious adverse events. At a median follow-up of 16.5 months, we observed dose-dependent increases in absolute neutrophil count (ANC) and absolute lymphocyte count (ALC). At doses ≥300 mg/d, ANC was maintained at >500 cells per microliter for a median of 12.6 hours, and ALC was maintained at >1000 cells per microliter for up to 16.9 hours. Continued follow-up on the extension study resulted in a yearly infection rate that decreased from 4.63 events (95% confidence interval, 3.3-6.3) in the 12 months prior to the trial to 2.27 events (95% confidence interval, 1.4-3.5) for patients on effective doses. We observed an average 75% reduction in the number of cutaneous warts. This study demonstrates that mavorixafor, 400 mg once daily, mobilizes neutrophil and lymphocytes in adult patients with WHIM syndrome and provides preliminary evidence of clinical benefit for patients on long-term therapy. The trial was registered at www.clinicaltrials.gov as #NCT03005327.
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Affiliation(s)
- David C Dale
- Department of Medicine, University of Washington, Seattle, WA
| | - Frank Firkin
- Department of Medicine and
- University of Washington, Severe Chronic Neutropenia International Registry, Seattle, WA; and
| | - Audrey Anna Bolyard
- University of Washington, Severe Chronic Neutropenia International Registry, Seattle, WA; and
| | - Merideth Kelley
- Department of Medicine, University of Washington, Seattle, WA
| | - Vahagn Makaryan
- Department of Medicine, University of Washington, Seattle, WA
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Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing. Viruses 2020; 12:v12121437. [PMID: 33327447 PMCID: PMC7764970 DOI: 10.3390/v12121437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022] Open
Abstract
In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.
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37
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Rosenstein RK, Pastrana DV, Starrett GJ, Sapio MR, Hill NT, Jo JH, Lee CCR, Iadarola MJ, Buck CB, Kong HH, Brownell I, Cowen EW. Host-Pathogen Interactions in Human Polyomavirus 7‒Associated Pruritic Skin Eruption. J Invest Dermatol 2020; 141:1344-1348.e8. [PMID: 33075349 DOI: 10.1016/j.jid.2020.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/16/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022]
Affiliation(s)
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, NCI/CCR, NIH, Bethesda, Maryland, USA
| | | | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | | | - Jay-Hyun Jo
- Dermatology Branch, NIAMS, NIH, Bethesda, Maryland, USA
| | - Chyi-Chia R Lee
- Laboratory of Pathology, NCI/CCR, NIH, Bethesda, Maryland, USA
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | | | - Heidi H Kong
- Dermatology Branch, NIAMS, NIH, Bethesda, Maryland, USA
| | | | - Edward W Cowen
- Dermatology Branch, NIAMS, NIH, Bethesda, Maryland, USA.
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38
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Detection of Human Papillomaviruses in the Nasopharynx of Breastfed Infants: New Findings and Meta-Analysis. Viruses 2020; 12:v12101119. [PMID: 33019742 PMCID: PMC7650825 DOI: 10.3390/v12101119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Vertical transmission of human papillomaviruses (HPVs) from mother to infant is known to occur during labor, delivery or breastfeeding. Infection with mucosal HPV 6 and 11 may cause recurrent respiratory papillomatosis in children, which is a rare and severe respiratory disease. The cutaneous HPV genotypes have also been described to be transmitted from mother to newborn through skin-to-skin contacts and during breastfeeding. To investigate the perinatal transmission of alpha and beta HPVs we collected nasopharyngeal specimens from 0-12-months-old infants born by vaginal delivery and breastfed at the time of sample collection. The mucosal and cutaneous HPVs were searched by nested PCR using the MY09/11-MGPs and CP65/70-CP66/69 primer sets, respectively, and genotypes identified by direct sequencing analysis. Fourteen out of 113 (12.4%) samples tested positive for HPV and sequence analysis allowed us to identify eight beta genotypes (HPV 5b, 20, 25, 100, 107, 124, 152 and RTRX7). Moreover, we performed a comprehensive review of published studies on the prevalence of mucosal and cutaneous HPVs among 5126 newborns and observed that 10% and 53% were positive for alpha and beta HPVs, respectively. In all studies there was an inverse correlation between the rate of alpha HPV positivity and age, while a significant positive trend was observed in beta HPV detection and age with the highest rate among children older than 12 months (Χ2 test for trend of 10.6, p < 0.001). Further studies are needed to confirm the hypothesis that beta HPVs are transmitted to breastfeeding infants through shedding of viruses in the breast milk or on the external breast epithelium.
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39
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Hong S, Li Y, Kaminski PJ, Andrade J, Laimins LA. Pathogenesis of Human Papillomaviruses Requires the ATR/p62 Autophagy-Related Pathway. mBio 2020; 11:e01628-20. [PMID: 32788179 PMCID: PMC7439466 DOI: 10.1128/mbio.01628-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022] Open
Abstract
High-risk human papillomaviruses (HPVs) constitutively activate the ataxia telangiectasia and Rad3-related (ATR) DNA damage response pathway, and this is required for viral replication. In fibroblasts, activated ATR regulates transcription of inflammatory genes through its negative effects on the autophagosome cargo protein p62. In addition, suppression of p62 results in increased levels of the transcription factor GATA4, leading to cellular senescence. In contrast, in HPV-positive keratinocytes, we observed that activation of ATR resulted in increased levels of phosphorylated p62, which in turn lead to reduced levels of GATA4. Knockdown of ATR in HPV-positive cells resulted in decreased p62 phosphorylation and increased GATA4 levels. Transcriptome sequencing (RNA-seq) analysis of HPV-positive cells identified inflammatory genes and interferon factors as negative transcriptional targets of ATR. Furthermore, knockdown of p62 or overexpression of GATA4 in HPV-positive cells leads to inhibition of viral replication. These findings identify a novel role of the ATR/p62 signaling pathway in HPV-positive cells.IMPORTANCE High-risk human papillomaviruses (HPVs) infect epithelial cells and induce viral genome amplification upon differentiation. HPV proteins activate the ATR DNA damage repair pathway, and this is required for HPV genome amplification. In the present study, we show that HPV-induced ATR activation also leads to suppression of expression of inflammatory response genes. This suppression results from HPV-induced phosphorylation of the autophagosome cargo protein p62 which regulates the levels of the transcription factor GATA4. Activation of p62 in normal fibroblasts results in senescence, but this is not seen in HPV-positive keratinocytes. Importantly, knockdown of p62 or overexpression of GATA4 in HPV-positive cells abrogates viral replication. This study demonstrates that activation of ATR in HPV-positive cells triggers a p62-directed pathway inducing suppression of inflammatory gene expression independent of DNA repair and facilitating HPV replication.
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Affiliation(s)
- Shiyuan Hong
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yan Li
- Center for Research Informatics, The University of Chicago, Chicago, Illinois, USA
| | - Paul J Kaminski
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, Illinois, USA
| | - Laimonis A Laimins
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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40
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Kono T, Hoover P, Poropatich K, Paunesku T, Mittal BB, Samant S, Laimins LA. Activation of DNA damage repair factors in HPV positive oropharyngeal cancers. Virology 2020; 547:27-34. [PMID: 32560902 PMCID: PMC7333731 DOI: 10.1016/j.virol.2020.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
The mechanisms regulating viral pathogenesis of human papillomavirus (HPV) associated oropharyngeal squamous cell cancers (OPSCC) are not well understood. In the cervix, activation of DNA damage repair pathways is critical for viral replication but little is known about their role in OPSCC. APOBEC factors have been shown to be increased in OPSCC but the significance of this is unclear. We therefore examined activation of DNA damage and APOBEC factors in HPV-induced OPSCC. Our studies show significantly increased levels of pCHK1, FANCD2, BRCA1, RAD51, pSMC1 and γH2AX foci in HPV-positive samples as compared to HPV-negative while the ATM effector kinase, pCHK2, was not increased. Similar differences were observed when the levels of proteins were examined in OPSCC cell lines. In contrast, the levels of APOBEC3B and 3A were found to be similar in both HPV-positive and -negative OPSCC. Our studies suggest members of ATR pathway and FANCD2 may be important in HPV-induced OPSCC.
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Affiliation(s)
- Takeyuki Kono
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Paul Hoover
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kate Poropatich
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Tatjana Paunesku
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Bharat B Mittal
- Department of Radiation Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sandeep Samant
- Department of Otolaryngology Head and Neck Surgery, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Laimonis A Laimins
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.
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41
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Howson LJ, Awad W, von Borstel A, Lim HJ, McWilliam HEG, Sandoval-Romero ML, Majumdar S, Hamzeh AR, Andrews TD, McDermott DH, Murphy PM, Le Nours J, Mak JYW, Liu L, Fairlie DP, McCluskey J, Villadangos JA, Cook MC, Turner SJ, Davey MS, Ojaimi S, Rossjohn J. Absence of mucosal-associated invariant T cells in a person with a homozygous point mutation in MR1. Sci Immunol 2020; 5:5/49/eabc9492. [PMID: 32709702 DOI: 10.1126/sciimmunol.abc9492] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
The role unconventional T cells play in protective immunity in humans is unclear. Mucosal-associated invariant T (MAIT) cells are an unconventional T cell subset restricted to the antigen-presenting molecule MR1. Here, we report the discovery of a patient homozygous for a rare Arg31His (R9H in the mature protein) mutation in MR1 who has a history of difficult-to-treat viral and bacterial infections. MR1R9H was unable to present the potent microbially derived MAIT cell stimulatory ligand. The MR1R9H crystal structure revealed that the stimulatory ligand cannot bind due to the mutation lying within, and causing structural perturbation to, the ligand-binding domain of MR1. While MR1R9H could bind and be up-regulated by a MAIT cell inhibitory ligand, the patient lacked circulating MAIT cells. This shows the importance of the stimulatory ligand for MAIT cell selection in humans. The patient had an expanded γδ T cell population, indicating a compensatory interplay between these unconventional T cell subsets.
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Affiliation(s)
- Lauren J Howson
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hui Jing Lim
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Hamish E G McWilliam
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Maria L Sandoval-Romero
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shamik Majumdar
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Abdul Rezzak Hamzeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Thomas D Andrews
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Matthew C Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Martin S Davey
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Samar Ojaimi
- Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia.,Centre for Inflammatory Diseases, Monash University, Clayton, Victoria, Australia.,Department of Allergy and Immunology, Monash Health, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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42
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Cheng L, Wang Y, Du J. Human Papillomavirus Vaccines: An Updated Review. Vaccines (Basel) 2020; 8:vaccines8030391. [PMID: 32708759 PMCID: PMC7565290 DOI: 10.3390/vaccines8030391] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 12/17/2022] Open
Abstract
Human papillomavirus (HPV) vaccines, which were introduced in many countries in the past decade, have shown promising results in decreasing HPV infection and related diseases, such as warts and precancerous lesions. In this review, we present the updated information about current HPV vaccines, focusing on vaccine coverage and efficacy. In addition, pan-gender vaccination and current clinical trials are also discussed. Currently, more efforts should be put into increasing the vaccine’s coverage, especially in low- and middle-income countries. Provision of education on HPV and vaccination is one of the most important methods to achieve this. Vaccines that target HPV types not included in current vaccines are the next stage in vaccine development. In the future, all HPV-related cancers, such as head and neck cancer, and anal cancer, should be tracked and evaluated, especially in countries that have introduced pan-gender vaccination programs. Therapeutic vaccines, in combination with other cancer treatments, should continue to be investigated.
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43
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Albert E, Laimins L. Regulation of the Human Papillomavirus Life Cycle by DNA Damage Repair Pathways and Epigenetic Factors. Viruses 2020; 12:E744. [PMID: 32664381 PMCID: PMC7412114 DOI: 10.3390/v12070744] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
Human papillomaviruses are the causative agents of cervical and other anogenital cancers along with approximately 60% of oropharyngeal cancers. These small double-stranded DNA viruses infect stratified epithelia and link their productive life cycles to differentiation. HPV proteins target cellular factors, such as those involved in DNA damage repair, as well as epigenetic control of host and viral transcription to regulate the productive life cycle. HPVs constitutively activate the ATM and ATR DNA repair pathways and preferentially recruit these proteins to viral genomes to facilitate productive viral replication. In addition, the sirtuin deacetylases along with histone acetyltransferases, including Tip60, are targeted in HPV infections to regulate viral transcription and replication. These pathways provide potential targets for drug therapy to treat HPV-induced disease.
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Affiliation(s)
| | - Laimonis Laimins
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA;
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44
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Robitaille A, Brancaccio RN, Dutta S, Rollison DE, Leja M, Fischer N, Grundhoff A, Gheit T, Tommasino M, Olivier M. PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing. BMC Bioinformatics 2020; 21:233. [PMID: 32513098 PMCID: PMC7282039 DOI: 10.1186/s12859-020-03573-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/28/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. RESULTS We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify known and potentially new Papillomaviridae sequences from NGS amplicon sequencing with degenerate PV primers. Here, we describe the features of PVAmpliconFinder and its implementation using biological data obtained from amplicon sequencing of human skin swab specimens and oral rinses from healthy individuals. CONCLUSIONS PVAmpliconFinder identified putative new HPV sequences, including one that was validated by wet-lab experiments. PVAmpliconFinder can be easily modified and applied to other viral families. PVAmpliconFinder addresses a gap by providing a solution for the analysis of NGS amplicon sequencing, increasingly used in clinical research. The PVAmpliconFinder workflow, along with its source code, is freely available on the GitHub platform: https://github.com/IARCbioinfo/PVAmpliconFinder.
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Affiliation(s)
| | | | - Sankhadeep Dutta
- International Agency for Research on Cancer, Lyon, France
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Dana E Rollison
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Marcis Leja
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Nicole Fischer
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Adam Grundhoff
- German Center for Infection Research, Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
- Heinrich Pette Institut, Leibniz Institut for Experimental Virology, Hamburg, Germany
| | - Tarik Gheit
- International Agency for Research on Cancer, Lyon, France
| | | | - Magali Olivier
- International Agency for Research on Cancer, Lyon, France.
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45
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Galati L, Brancaccio RN, Robitaille A, Cuenin C, Luzi F, Fiorucci G, Chiantore MV, Marascio N, Matera G, Liberto MC, Donà MG, Di Bonito P, Gheit T, Tommasino M. Detection of human papillomaviruses in paired healthy skin and actinic keratosis by next generation sequencing. PAPILLOMAVIRUS RESEARCH (AMSTERDAM, NETHERLANDS) 2020; 9:100196. [PMID: 32222599 PMCID: PMC7118314 DOI: 10.1016/j.pvr.2020.100196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 01/20/2023]
Abstract
Actinic keratosis (AK) arises on photo-damaged skin and is considered to be the precursor lesion of cutaneous squamous cell carcinoma (cSCC). Many findings support the involvement of β human papillomaviruses (HPVs) in cSCC, while very little is known on γ HPV types. The objective of this study was to characterize the spectrum of PV types in healthy skin (HS) and AK samples of the same immunocompetent individuals using next generation sequencing (NGS). Viral DNA of 244 AK and 242 HS specimens were amplified by PCR using two different sets of primers (FAP59/64 and FAPM1). Purified amplicons were pooled and sequenced using NGS. The study resulted in the identification of a large number of known β and γ PV types. In addition, 27 putative novel β and 16 γ and 4 unclassified PVs were isolated. HPV types of species γ-1 (e.g. HPV4) appeared to be strongly enriched in AK versus HS. The NGS analysis revealed that a large spectrum of known and novel PVs is present in HS and AK. The evidence that species γ-1 HPV types appears to be enriched in AK in comparison to HS warrants further studies to evaluate their role in development of skin (pre)cancerous lesions.
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Affiliation(s)
- Luisa Galati
- International Agency for Research on Cancer-World Health Organization, Lyon, France; "Magna Graecia" University, Catanzaro, Italy
| | | | - Alexis Robitaille
- International Agency for Research on Cancer-World Health Organization, Lyon, France
| | - Cyrille Cuenin
- International Agency for Research on Cancer-World Health Organization, Lyon, France
| | - Fabiola Luzi
- Plastic and Reconstructive Surgery, San Gallicano Dermatologic Institute IRCCS, Rome, Italy
| | - Gianna Fiorucci
- Department of Infectious Diseases, EVOR Unit, Istituto Superiore di Sanità, Rome, Italy; Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | | | | | | | | | - Paola Di Bonito
- Department of Infectious Diseases, EVOR Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Tarik Gheit
- International Agency for Research on Cancer-World Health Organization, Lyon, France
| | - Massimo Tommasino
- International Agency for Research on Cancer-World Health Organization, Lyon, France.
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46
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Bolatti EM, Hošnjak L, Chouhy D, Casal PE, Re-Louhau MF, Bottai H, Komloš KF, Poljak M, Giri AA. Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols. BMC Infect Dis 2020; 20:274. [PMID: 32264841 PMCID: PMC7140492 DOI: 10.1186/s12879-020-4893-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Background Human papillomaviruses (HPVs) have been divided into mucosal and cutaneous types according to their primary epithelial tissue tropism. However, recent studies showed the presence of several cutaneous types in mucosal lesions and healthy mucosa from different anatomical sites. Methods Here, the HPV prevalence and type-specific distribution were assessed in a variety of mucosal samples from 435 individuals using a combination of two established broad-spectrum primer systems: Gamma-PV PCR and CUT PCR. Results Overall HPV prevalence in anal canal swabs, cervical cancer biopsies, genital warts and oral swabs was 85, 47, 62 and 4%, respectively. In anal canal swabs, Alpha-PVs were most frequently found (59%), followed by Gamma- (37%) and Beta-PVs (4%). The prevalence and persistence of HPV infection in the anal canal of 226 individuals were further explored. Overall HPV, Gamma-PVs and multiple HPV infections were significantly higher in men vs. women (p = 0.034, p = 0.027 and p = 0.003, respectively); multiple HPV infections were more common in individuals ≤40 years (p = 0.05), and significantly higher prevalence of Gamma-PVs and multiple HPV infections was observed in HIV-1-positive vs. HIV-1-negative individuals (p = 0.003 and p = 0.04, respectively). Out of 21 patients with follow-up anal swabs, only one persistent infection with the same type (HPV58) was detected. Conclusions Our findings suggest that Gamma-PVs (except species Gamma-6) are ubiquitous viruses with dual muco-cutaneous tissue tropism. Anal canal Gamma-PV infections may be associated with sexual behavior and the host immune status. This study expands the knowledge on Gamma-PVs’ tissue tropism, providing valuable data on the characteristics of HPV infection in the anal canal.
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Affiliation(s)
- Elisa M Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Lea Hošnjak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Pablo E Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María F Re-Louhau
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina
| | - Hebe Bottai
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Kristina Fujs Komloš
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia.
| | - Adriana A Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina. .,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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47
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Ling Y, Wang J, Yin J, Xu J, Wu Y, Zhou R, Lu J, Yang S, Wang X, Shen Q, Zhang W. Genomic organization of a Gamma-6 papillomavirus metagenomic discovered from vaginal swab samples of Chinese pregnant women. Virol J 2020; 17:44. [PMID: 32234038 PMCID: PMC7110641 DOI: 10.1186/s12985-020-01319-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/19/2020] [Indexed: 12/17/2022] Open
Abstract
A complete genome sequence of human papillomaviruses (HPV) named as HPV-ujs-21015 was determined by viral metagenomic and PCR methods. The complete genome is 7354 bp in length with GC content of 41.7%, of which the genome was predicted to contain six ORFs (Open Reading Frame, ORF) coding for four early proteins (E7, E1, E4, and E2) and two late proteins (L1 and L2). Phylogenetic analysis based on the complete genome and the L1 protein showed that HPV-ujs-21015 belongs to a type 214 member within genus Gamma-6 papillomavirus. It is the first complete genome of Gamma-6 papillomavirus discovered from pregnant women in China.
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Affiliation(s)
- Yu Ling
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.,Department of Laboratory Medicine, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Jianqiang Wang
- Intensive Care Unit, Jintan District Hospital of Traditional Chinese Medicine, 1006 Huixian Road, Changzhou, Jiangsu, 213200, People's Republic of China
| | - Jun Yin
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Jianpu Xu
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Yufan Wu
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Rui Zhou
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Juan Lu
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Quan Shen
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.
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48
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Tisza MJ, Pastrana DV, Welch NL, Stewart B, Peretti A, Starrett GJ, Pang YYS, Krishnamurthy SR, Pesavento PA, McDermott DH, Murphy PM, Whited JL, Miller B, Brenchley J, Rosshart SP, Rehermann B, Doorbar J, Ta'ala BA, Pletnikova O, Troncoso JC, Resnick SM, Bolduc B, Sullivan MB, Varsani A, Segall AM, Buck CB. Discovery of several thousand highly diverse circular DNA viruses. eLife 2020; 9:51971. [PMID: 32014111 PMCID: PMC7000223 DOI: 10.7554/elife.51971] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/06/2020] [Indexed: 12/18/2022] Open
Abstract
Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere. When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequences, because only a fraction of the enormous diversity of viruses has been characterized. This “viral dark matter” is a major obstacle for those studying viruses. This led Tisza et al. to attempt to classify some of the unknown viral sequences in their metagenomic surveys. The search, which specifically focused on viruses with circular DNA genomes, detected over 2,500 circular viral genomes. Intensive analysis revealed that many of these genomes had similar makeup to previously discovered viruses, but hundreds of them were totally different from any known virus, based on typical methods of comparison. Computational analysis of genes that were conserved among some of these brand-new circular sequences often revealed virus-like features. Experiments on a few of these genes showed that they encoded proteins capable of forming particles reminiscent of characteristic viral shells, implying that these new sequences are indeed viruses. Tisza et al. have added the 2,500 newly characterized viral sequences to the publicly accessible GenBank database, and the sequences are being considered for the more authoritative RefSeq database, which currently contains around 9,000 complete viral genomes. The expanded databases will hopefully now better equip scientists to explore the enormous diversity of viruses and help medics and veterinarians to detect disease-causing viruses in humans and other animals.
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Affiliation(s)
- Michael J Tisza
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Diana V Pastrana
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Nicole L Welch
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Brittany Stewart
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Alberto Peretti
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Gabriel J Starrett
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Yuk-Ying S Pang
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, United States
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Jessica L Whited
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Bess Miller
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jason Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Cambridge, United States
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, United States.,Civil Environmental and Geodetic Engineering, Ohio State University, Columbus, United States
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, United States.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anca M Segall
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, United States
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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49
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Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biol 2019; 20:232. [PMID: 31690338 PMCID: PMC6833257 DOI: 10.1186/s13059-019-1841-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets. We describe several use cases, including contamination screening and retrospective analysis of metagenomes for novel genome discovery. Using this tool, we provide containment estimates for every NCBI RefSeq genome within every SRA metagenome and demonstrate the identification of a novel polyomavirus species from a public metagenome.
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Affiliation(s)
- Brian D. Ondov
- Genome Informatics section, National Human Genome Research Institute, Bethesda, MD USA
- Department of Computer Science, University of Maryland College Park, College Park, MD USA
| | - Gabriel J. Starrett
- Tumor Virus Molecular Biology section, National Cancer Institute, Bethesda, MD USA
| | - Anna Sappington
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Aleksandra Kostic
- Department of Computer Science, Princeton University, Princeton, NJ USA
| | - Sergey Koren
- Genome Informatics section, National Human Genome Research Institute, Bethesda, MD USA
| | - Christopher B. Buck
- Tumor Virus Molecular Biology section, National Cancer Institute, Bethesda, MD USA
| | - Adam M. Phillippy
- Genome Informatics section, National Human Genome Research Institute, Bethesda, MD USA
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50
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Chen Z, Long T, Wong PY, Ho WCS, Burk RD, Chan PKS. Non-human Primate Papillomaviruses Share Similar Evolutionary Histories and Niche Adaptation as the Human Counterparts. Front Microbiol 2019; 10:2093. [PMID: 31552003 PMCID: PMC6747053 DOI: 10.3389/fmicb.2019.02093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/26/2019] [Indexed: 11/13/2022] Open
Abstract
Given high genetic diversity of papillomaviruses (PV) and complex scenario of virus-host interaction, the genetic basis underlying the mechanisms of HPV carcinogenicity is not well understood. In an effort to evaluate the origin and evolution of PV pathogenicity, we collected paired oral, perianal, and genital swabs from a wild macaque population. Of the 117 surveyed macaques, 88 (75.2%) were positive for PV DNA in one or more sites, mostly common from genital swabs, followed by oral and perianal sites. All putative macaque PV types phylogenetically clustered into the genera Alpha-, Beta-, and Gammapapillomavirus, with a strong phylogeny-tropism association as observed in HPVs. Using a Bayesian Markov Chain Monte Carlo framework, we demonstrated ancient intra-host divergence of primate PVs in which multiple ancestors had split and adapted to specific host ecosystems at least 41 million years ago, prior to the speciation events of primate host species. Following subsequent divergence and niche adaptation, distinct but phylogenetically related PV types were transmitted to similar host ecosystems by closely related host animals when host speciation occurred, which may explain in part the origin of carcinogenicity of HPV type 16 (HPV16) and Macaca fascicularis PV type 3 (MfPV3) that evolved from a most recent common ancestor containing the determinants for cervicovaginal colonization and cervical cancer. The findings identifying evolutionary and biological relatedness between human and non-human primate PVs lay a genetic foundation for research on parasite-host interactions and carcinogenic outcomes, which will prove useful in further study of viral pathogenesis and host specificity.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Teng Long
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Po Yee Wong
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wendy C S Ho
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D Burk
- Department of Pediatrics, Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics, Gynecology and Woman's Health, Albert Einstein College of Medicine, The Bronx, NY, United States
| | - Paul K S Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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