1
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Wang A. Integrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS-CoV-2. J Med Virol 2024; 96:e29557. [PMID: 38506190 DOI: 10.1002/jmv.29557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/17/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024]
Abstract
A genome, composed of a precisely ordered sequence of four nucleotides (ATCG), encompasses a multitude of specific genome features like AAA motif. Mutations occurring within a genome disrupt the sequential order and composition of these features, thereby influencing the evolutionary trajectories and yielding variants. The evolutionary relatedness between a variant and its ancestor can be estimated by assessing evolutionary distances across a spectrum of genome features. This study develops a novel, alignment-free algorithm that considers both the sequential order and composition of genome features, enabling computation of the Fréchet distance (Fr) across multiple genome features to quantify the evolutionary status of a variant. Integrating this algorithm with an artificial recurrent neural network (RNN) reveals the quantitative evolutionary trajectory and origin of SARS-CoV-2, a puzzle unsolved by alignment-based phylogenetics. The RNN generates the evolutionary trajectory from Fr data at two levels: genome sequence mutations and organism variants. At the genome sequence level, SARS-CoV-2 evolutionarily shortens its genome to enhance its infectious capacity. Mutating signature features, such as TTA and GCT, increases its infectious potential and drives its evolution. At the organism level, variants mutating a single biomarker possess low infectious potential. However, mutating multiple markers dramatically increases their infectious capacity, propelling the COVID-19 pandemic. SARS-CoV-2 likely originates from mink coronavirus variants, with its origin trajectory traced as follows: mink, cat, tiger, mouse, hamster, dog, lion, gorilla, leopard, bat, and pangolin. Together, mutating multiple signature features and biomarkers delineates the evolutionary trajectory of mink-origin SARS-CoV-2, leading to the COVID-19 pandemic.
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Affiliation(s)
- Anyou Wang
- Feinstone Center for Genomic Research, University of Memphis, Memphis, Tennessee, USA
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2
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Zhiyanov A, Shkurnikov M, Nersisyan A, Hui C, Baranova A, Tonevitsky A. The signature of SARS-CoV-2 evolution reflects selective pressures within human guts. J Med Virol 2023; 95:e28996. [PMID: 37515485 DOI: 10.1002/jmv.28996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/09/2023] [Accepted: 07/16/2023] [Indexed: 07/31/2023]
Abstract
In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation and replication. In London and Berlin samples represented in GISAID database, we traced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages and divided these sequenced in two groups, "Ancestral variants" and "Omicrons," and analyzed them through the prism of the tissue-specific binding between host miRNAs and viral messenger RNAs. We demonstrate a significant number of miRNA-binding sites in the NSP4 region of the SARS-CoV-2 genome, with evidence of evolutionary pressure within this region exerted by human intestinal miRNAs. Notably, in infected cells, NSP4 promotes the formation of double-membrane vesicles, which serve as the scaffolds for replication-transcriptional complexes and protect viral RNA from intracellular destruction. In 3 years of selection, the loss of many miRNA-binding sites in general and those within the NSP4 in particular has shaped the SARS-CoV-2 genomes. With that, the descendants of the BA.2 variants were promoted as dominant strains, which define current momentum of the pandemics.
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Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Ashot Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Cai Hui
- Department of Nanoengineering, Sun Yat-Sen University, Shenzhen, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, Virginia, USA
- Research Centre for Medical Genetics, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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3
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Deng L, Fu P, Ding L, Duan X, Feng S, Peng Y. Virome analysis provides new insights into the association between viruses and Parkinson's disease. J Med Virol 2023; 95:e28111. [PMID: 36042689 DOI: 10.1002/jmv.28111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/05/2022] [Accepted: 08/27/2022] [Indexed: 01/11/2023]
Abstract
Parkinson's disease (PD) is a kind of neurodegenerative disease that causes a huge burden to society. Previous studies have suggested the association between PD and multiple viruses. However, there is still a lack of a virome study about PD. This study systematically identified viruses from the public RNA-sequencing data of more than 700 samples from both PD patients and the control group (most were healthy people). Only nine viruses such as human betaherpesvirus 5 and Merkel cell polyomavirus have been detected in several human brain tissues of the central nervous system, the appendix, and blood of PD patients, and all of these viruses were also detected in the control group. Most viruses were observed to have low abundance in no more than three tissues. No statistically significant differences were observed between the virus abundance in the PD patients and the control group for all viruses. The positive rates of most viruses in PD patients were higher or similar to that in the control group, although those were less than 5% for most viruses. Overall, this is the first study to systematically investigate the virome in PD patients, and provides new insights into the association between viruses and PD.
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Affiliation(s)
- Li Deng
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, China
| | - Ping Fu
- Bioinformatics Center, Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha, China
| | - Ling Ding
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, China
| | - Xianlai Duan
- Department of Internal Medicine-Neurology, The Third Hospital of Changsha, Changsha, China
| | - Song Feng
- Network Information Center, Xiangya Hospital, Central South University, Changsha, China
| | - Yousong Peng
- Bioinformatics Center, Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha, China
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4
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Mingione M, Ciccozzi M, Falcone M, Maruotti A. Short-term forecasts of Monkeypox cases in multiple countries: keep calm and don't panic. J Med Virol 2023; 95:e28159. [PMID: 36124421 PMCID: PMC10087044 DOI: 10.1002/jmv.28159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 01/11/2023]
Abstract
We propose a parametric regression model for incidence indicators based on the use of the Richards' curve (a generalized logistic function) to analyse the current Monkeypox epidemic data for the most 10 affected countries worldwide. At present, results show that the outbreak is under control in most countries.
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Affiliation(s)
- Marco Mingione
- Department of Political Sciences, University of Roma Tre, Rome, Italy
| | - Massimo Ciccozzi
- Department of Medicine, Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Falcone
- Department of Clinical and Experimental Medicine, Infectious Diseases Unit, University of Pisa, Pisa, Italy
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5
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Staerk-Østergaard J, Kirkeby C, Christiansen LE, Andersen MA, Møller CH, Voldstedlund M, Denwood MJ. Evaluation of diagnostic test procedures for SARS-CoV-2 using latent class models. J Med Virol 2022; 94:4754-4761. [PMID: 35713189 PMCID: PMC9349895 DOI: 10.1002/jmv.27943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/27/2022]
Abstract
Polymerase chain reaction (PCR) and antigen tests have been used extensively for screening during the severe acute respiratory syndrome coronavirus 2 pandemics. However, the real‐world sensitivity and specificity of the two testing procedures in the field have not yet been estimated without assuming that the PCR constitutes a gold standard test. We use latent class models to estimate the in situ performance of both tests using data from the Danish national registries. We find that the specificity of both tests is very high (>99.7%), while the sensitivities are 95.7% (95% confidence interval [CI]: 92.8%–98.4%) and 53.8% (95% CI: 49.8%–57.9%) for the PCR and antigen tests, respectively. These findings have implications for the use of confirmatory PCR tests following a positive antigen test result: we estimate that serial testing is counterproductive at higher prevalence levels.
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Affiliation(s)
- Jacob Staerk-Østergaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Carsten Kirkeby
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lasse E Christiansen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Michael A Andersen
- Epidemiologisk Forskning / Modelgruppen, Staten's Serum Institute, Copenhagen, Denmark
| | - Camilla H Møller
- Epidemiologisk Forskning / Modelgruppen, Staten's Serum Institute, Copenhagen, Denmark
| | - Marianne Voldstedlund
- Epidemiologisk Forskning / Modelgruppen, Staten's Serum Institute, Copenhagen, Denmark
| | - Matthew J Denwood
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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6
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Liu C, Tang B, Gao C, Deng J, Shen M, Li C, Fu Z, Gao Z, Jiang Q, Shi H, He M, Jiang H, Jia X. Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Front Med (Lausanne) 2021; 8:783646. [PMID: 34917639 PMCID: PMC8669593 DOI: 10.3389/fmed.2021.783646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/03/2021] [Indexed: 01/08/2023] Open
Abstract
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been basically under control in China since March 2020, but the import of domestic SARS-CoV-2 has begun to increase. This study reported the first case of asymptomatic SARS-CoV-2 infection imported from Spain into Sichuan Province, China, on March 11, 2020. The infected male had a body temperature of 37.5°C, normal blood oxygen saturation levels, and a computed tomography (CT) examination showed that his lungs had no shadows. However, a throat swab from the subject tested positive for SARS-CoV-2 using qPCR assay. In this study, we conducted transcriptome sequencing on respiratory throat swabs from the subject and found that the dominant SARS-CoV-2 sequence (Gene Bank ID: MW301121) was a spike protein D614G mutant strain, which is currently popular throughout world. We downloaded and analyzed SARS-CoV-2 sequences collected from cases in China and Spain for comparison and tracing purposes. After March 11, 2020, the Chinese domestic clade was naturally divided into the imported SARS-CoV-2 D614G mutant strain and evolutionarily-related similar sequences and that of sequences collected in the original Wuhan area. The sequence reported in this study was located on a small branch, far from the evolution of Wuhan sequences. As expected, the identified sequence was closely related to the evolution of the SARS-CoV-2 D614G mutant strain circulating in Spain.
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Affiliation(s)
- Chao Liu
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China.,Basic Medical School, Chengdu Medical College, Chengdu, China
| | - Bin Tang
- The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Can Gao
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China.,Yan'an Key Laboratory of Microbial Drug Innovation and Transformation, School of Basic Medicine, Yan'an University, Yan'an, China
| | | | - Min Shen
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Chaolin Li
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Zekun Fu
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Zhan Gao
- Sichuan Mianyang 404 Hospital, Mianyang, China
| | - Qi Jiang
- Sichuan Mianyang 404 Hospital, Mianyang, China
| | - Hao Shi
- Jinniu Maternity and Child Health Hospital of Chengdu, Chengdu, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | | | - Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China.,Basic Medical School, Chengdu Medical College, Chengdu, China
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7
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Hoseinpour Dehkordi A, Alizadeh M, Derakhshan P, Babazadeh P, Jahandideh A. Understanding epidemic data and statistics: A case study of COVID-19. J Med Virol 2020; 92:868-882. [PMID: 32329522 PMCID: PMC7264574 DOI: 10.1002/jmv.25885] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022]
Abstract
The 2019 novel-coronavirus (COVID-19) has affected 181 countries with approximately 1197405 confirmed cases (by 5th April). Understanding the transmission dynamics of the infection in each country which got affected on a daily basis and evaluating the effectiveness of control policies are critical for our further actions. To date, the statistics of COVID-19 reported cases show that more than 80% of infected are mild cases of disease, around 14% of infected have severe complications, and about 5% are categorized as critical disease victims. Today's report (5th April 2020; daily updates in the prepared website) shows that the confirmed cases of COVID-19 in the United States, Spain, Italy, and Germany are 308850, 126168, 124632, and 96092, respectively. Calculating the total case fatality rate (CFR) of Italy (4th April 2020), about 13.3% of confirmed cases have passed away. Compared with South Korea's rate of 1.8% (seven times lower than Italy) and China's 4% (69% lower than Italy), the CFR of Italy is too high. Some effective policies that yielded significant changes in the trend of cases were the lockdown policy in China, Italy, and Spain (the effect observed after some days), the shutdown of all nonessential companies in Hubei (the effect observed after 5 days), combined policy in South Korea, and reducing working hours in Iran.
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Affiliation(s)
| | - Majid Alizadeh
- School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
| | - Pegah Derakhshan
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Peyman Babazadeh
- School of Engineering, Islamic Azad University Central Tehran Branch, Tehran, Iran
| | - Arash Jahandideh
- Adhesive and Resin Department, Iran Polymer and Petrochemical Institute (IPPI), Tehran, Iran
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8
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Imai S, Yamana H, Inoue N, Akazawa M, Horiguchi H, Fushimi K, Migita K, Yatsuhashi H, Sugiyama M, Mizokami M. Validity of administrative database detection of previously resolved hepatitis B virus in Japan. J Med Virol 2019; 91:1944-1948. [PMID: 31283012 PMCID: PMC6771469 DOI: 10.1002/jmv.25540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022]
Abstract
The risk of hepatitis B virus (HBV) reactivation has increased owing to advances in the immunosuppressive therapy field. However, the HBV reactivation incidence among patients with previously resolved HBV (prHBV) infection during immunosuppressive therapy for rheumatoid arthritis (RA) remains unclear. The objective of this work is to describe the validity of detecting prHBV infection from administrative data through comparisons with chart abstraction and determine the incidence of HBV reactivation during immunosuppressive therapy for RA in Japan. In this retrospective cohort study, data on selected patients were extracted from administrative claims data. To identify patients with prHBV infection and de novo hepatitis, and HBsAg carriers, we conducted chart abstraction. The incidence rate of de novo hepatitis was 1.23 of 100 person‐years. The positive predictive value (PPV) and its 95% confidence interval (CI) of administrative data for the identification of suspected prHBV infections was 85.8% (95% CI: 81.7%‐89.3%). This study evaluated the PPV of the algorithm of HBV‐DNA testing with immunosuppressive therapy performed four times or more per year for the detection of prHBV infection from administrative data. Additionally, we determined the incidence rate of HBV reactivation among preHBV infections during immunosuppressive therapy for RA to be 1.23 of 100 person‐years.
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Affiliation(s)
- Shinobu Imai
- Department of Clinical Data Management and Research, Clinical Research Center, National Hospital Organization Headquarters, Tokyo, Japan.,Department of Drug Safety and Risk Management, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Hayato Yamana
- Department of Clinical Data Management and Research, Clinical Research Center, National Hospital Organization Headquarters, Tokyo, Japan.,Department of Health Services Research, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Norihiko Inoue
- Department of Clinical Data Management and Research, Clinical Research Center, National Hospital Organization Headquarters, Tokyo, Japan.,Department of Health Policy and Informatics, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Manabu Akazawa
- Department of Public Health and Epidemiology, Meiji Pharmaceutical University, Tokyo, Japan
| | - Hiromasa Horiguchi
- Department of Clinical Data Management and Research, Clinical Research Center, National Hospital Organization Headquarters, Tokyo, Japan
| | - Kiyohide Fushimi
- Department of Clinical Data Management and Research, Clinical Research Center, National Hospital Organization Headquarters, Tokyo, Japan.,Department of Health Policy and Informatics, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Kiyoshi Migita
- Department of Rheumatology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | | | - Masaya Sugiyama
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Masashi Mizokami
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
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9
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Cella E, Riva E, Angeletti S, Fogolari M, Blasi A, Scolamacchia V, Spoto S, Bazzardi R, Lai A, Sagnelli C, Sagnelli E, Ciccozzi M. Genotype I hepatitis A virus introduction in Italy: Bayesian phylogenetic analysis to date different epidemics. J Med Virol 2018; 90:1493-1502. [PMID: 29738070 DOI: 10.1002/jmv.25220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/03/2018] [Indexed: 01/05/2023]
Abstract
Despite a significant decrease in acute hepatitis A in the last 2 decades in Italy, outbreaks were observed occurring mostly in southern Italy. In this study, Bayesian phylogenetic analysis was used to analyze the origin of these epidemics. With this aim, 5 different data sets of hepatitis A virus sequences were built to perform genotyping by the neighbor-joining method to estimate the evolutionary rates by using a Bayesian Markov chain Monte Carlo approach and to investigate the demographic history by independent Markov chain Monte Carlo runs enforcing both a strict and relaxed clock. The estimated mean value of the evolutionary rate, representing Ia and Ib strains, was 1.21 × 10-3 and 2.0 × 10-3 substitutions/site/year, respectively. The Bayesian maximum clade credibility tree of hepatitis A virus (HAV) Ia and Ib strains showed that Italian sequences mostly formed separate clusters. The root of the time for the most recent common ancestor (tMRCA) for HAV Ia and Ib strains dated back to 1981 and to 1988, respectively, showing in both cases different epidemic entrances. Phylodynamic analysis showed that genotype Ia increased in 1997, when the Apulia epidemic started, then suffered a bottleneck, probably consequent to vaccination and to the herd immunity, followed by a new increase in virus population in the years 2013-2014 consequent to the epidemic caused by the ingestion of mixed frozen berries. A similar trend without an evident bottleneck was observed also in the case of genotype Ib. In conclusion, the Bayesian phylogenetic analysis represents a good tool to measure the effectiveness of the public health plans used for HAV control.
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Affiliation(s)
- Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Elisabetta Riva
- Unit of Virology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marta Fogolari
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Aletheia Blasi
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Vittoria Scolamacchia
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Silvia Spoto
- Internal Medicine Department, University Campus Bio-Medico of Rome, Rome, Italy
| | - Riccardo Bazzardi
- Dipartimento di Igiene degli Alimenti, Istituto Zooprofilattico Sperimentale della Sardegna, Sassari, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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10
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Coghill AE, Wang CP, Verkuijilen SAWM, Yu KJ, Hsu WL, Middeldorp JM, Hildesheim A. Evaluation of nasal and nasopharyngeal swab collection for the detection of Epstein-Barr virus in nasopharyngeal carcinoma. J Med Virol 2017; 90:191-195. [PMID: 28833336 DOI: 10.1002/jmv.24918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/02/2017] [Indexed: 01/02/2023]
Abstract
Epstein-Barr virus detection using nasopharyngeal swabs has been suggested as a potential screening test that could improve the specificity of current EBV-based serological assays. However, application requires insertion of the swab deep into the nasopharynx, a procedure not amenable to non-clinic screening. We reasoned that swabbing the more easily accessible nasal cavity might provide an appealing alternative for NPC detection. Patients > 18 years of age diagnosed with histologically confirmed NPC were recruited from the Otolaryngology Department at the National Taiwan University Hospital. ENT clinicians collected both nasal and nasopharyngeal swabs. EBV DNA and cellular beta-globulin DNA were quantified using quantitative PCR targeting a highly-conserved region of the BKRF1 gene. EBV DNA was detectable (non-zero) in all 34 nasopharyngeal swabs and above the positivity threshold of 1666 EBV copies in 30 (88.2%) patients. EBV DNA was detectable in 50% of 34 nasal swabs and above the positivity threshold in four (11.8%) patients. Average EBV DNA levels were >3-fold higher (P < 0.001) in nasopharyngeal compared to nasal swabs. Among the 17 NPC patients with detectable EBV DNA in both swab types, we observed correlation (P < 0.01) between EBV DNA measurements. Our data represent the first evaluation of EBV DNA collected from nasal swabs. Given current EBV DNA amplification techniques, nasopharyngeal swabs remain more sensitive than nasal swabs for NPC detection.
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Affiliation(s)
- Anna E Coghill
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Cheng-Ping Wang
- Department of Otolaryngology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | | | - Kelly J Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Wan-Lun Hsu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jaap M Middeldorp
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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11
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de Planell-Mas E, Martínez-Garriga B, Zalacain AJ, Vinuesa T, Viñas M. Human papillomaviruses genotyping in plantar warts. J Med Virol 2016; 89:902-907. [PMID: 27736001 DOI: 10.1002/jmv.24713] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2016] [Indexed: 11/08/2022]
Abstract
Plantar warts are caused by human papillomaviruses (HPVs) and have been associated with several HPV genotypes. However, there are few studies focused exclusively on plantar warts. In this work, we aim to identify the HPV genotypes of plantar warts and explore their relation to demographic and clinical characteristics of patients. A total of 72 patients diagnosed with plantar warts were recruited at the Laser unit at Podiatric Hospital, University of Barcelona, Spain. Inner hyperkeratosis laminar sections of warts were collected and DNA of samples were extracted. Amplification of a conserved region of the HPV L1 gene was performed with the SK-Polymerase chain reaction method. DNA amplicons were sequenced and HPV types identified. The most prevalent genotypes detected among the 105 analyzed plantar warts were HPV-57 (37.1%), HPV-27 (23.8%), HPV-1a (20.9%), HPV-2 (15.2%), and HPV-65 (2.8%). The majority of patients (78%) presented one single plantar wart, whereas multiple warts were detected in 22.2% of patients. One patient with multiple warts presented HPV types from two different genera, suggesting the spread of warts by self-inoculation as well as by de novo infection. No significant differences between the number of warts in toes, midfoot and heel were found. The most prevalent HPV types detected in all areas belonged to the alpha genus. This work provides new insight on plantar warts and their associated HPV genotypes, and evidences the usefulness and reliability of both the sample collection procedure and the PCR method used for HPV detection and typing. J. Med. Virol. 89:902-907, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Elena de Planell-Mas
- Laboratory of Molecular Microbiology and Antimicrobials, Faculty of Medicine, Department of Pathology and Experimental Therapeutics, Podiatric Hospital, University of Barcelona, Barcelona, Spain.,Podiatric Hospital, University of Barcelona, Barcelona, Spain
| | - Blanca Martínez-Garriga
- Laboratory of Molecular Microbiology and Antimicrobials, Faculty of Medicine, Department of Pathology and Experimental Therapeutics, Podiatric Hospital, University of Barcelona, Barcelona, Spain
| | - Antonio Jesús Zalacain
- Laboratory of Molecular Microbiology and Antimicrobials, Faculty of Medicine, Department of Pathology and Experimental Therapeutics, Podiatric Hospital, University of Barcelona, Barcelona, Spain.,Podiatric Hospital, University of Barcelona, Barcelona, Spain
| | - Teresa Vinuesa
- Laboratory of Molecular Microbiology and Antimicrobials, Faculty of Medicine, Department of Pathology and Experimental Therapeutics, Podiatric Hospital, University of Barcelona, Barcelona, Spain
| | - Miguel Viñas
- Laboratory of Molecular Microbiology and Antimicrobials, Faculty of Medicine, Department of Pathology and Experimental Therapeutics, Podiatric Hospital, University of Barcelona, Barcelona, Spain
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