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Nicolás-Párraga S, Torres M, Alemany L, Félix A, Cruz E, de Sanjosé S, Bosch FX, Bravo IG. Human DNA decays faster with time than viral dsDNA: an analysis on HPV16 using pathology archive samples spanning 85 years. Virol J 2021; 18:65. [PMID: 33781303 PMCID: PMC8008572 DOI: 10.1186/s12985-021-01529-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/05/2021] [Indexed: 12/01/2022] Open
Abstract
Background Quality of the nucleic acids extracted from Formalin Fixed Paraffin Embedded (FFPE) samples largely depends on pre-analytic, fixation and storage conditions. We assessed the differential sensitivity of viral and human double stranded DNA (dsDNA) to degradation with storage time. Methods We randomly selected forty-four HPV16-positive invasive cervical cancer (ICC) FFPE samples collected between 1930 and 1935 and between 2000 and 2004. We evaluated through qPCR the amplification within the same sample of two targets of the HPV16 L1 gene (69 bp, 134 bp) compared with two targets of the human tubulin-β gene (65 bp, 149 bp). Results Both viral and human, short and long targets were amplified from all samples stored for 15 years. In samples archived for 85 years, we observed a significant decrease in the ability to amplify longer targets and this difference was larger in human than in viral DNA: longer fragments were nine times (CI 95% 2.6–35.2) less likely to be recovered from human DNA compared with 1.6 times (CI 95% 1.1–2.2) for viral DNA. Conclusions We conclude that human and viral DNA show a differential decay kinetics in FFPE samples. The faster degradation of human DNA should be considered when assessing viral DNA prevalence in long stored samples, as HPV DNA detection remains a key biomarker of viral-associated transformation. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01529-9.
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Affiliation(s)
- Sara Nicolás-Párraga
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Montserrat Torres
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Laia Alemany
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ana Félix
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Lisbon), Lisbon, Portugal
| | - Eugenia Cruz
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Coimbra), Coimbra, Portugal
| | - Silvia de Sanjosé
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Sexual and Reproductive Health, PATH, Seattle, USA.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Francesc Xavier Bosch
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Biomedical Research Networking Centre On Cancer (CIBERONC), Madrid, Spain.,Universitat Oberta de Catalunya, Barcelona, Spain
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.,Laboratory MIVEGEC (CNRS IRD Univ Montpellier), French National Center for Scientific Research (CNRS), Montpellier, France.,Center for Research On the Ecology and Evolution of Diseases (CREES), Montpellier, France
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Tighe AJ, Gallagher MD, Carlsson J, Matejusova I, Swords F, Macqueen DJ, Ruane NM. Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7). DISEASES OF AQUATIC ORGANISMS 2020; 142:203-211. [PMID: 33331288 DOI: 10.3354/dao03546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive 'piscine alphavirus'.
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Affiliation(s)
- Andrew J Tighe
- Fish Health Unit, Marine Institute, Oranmore H91 R673, Ireland
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Abstract
Potyviridae is the largest family of plant-infecting RNA viruses, encompassing over 30% of known plant viruses. The family is closely related to animal picornaviruses such as enteroviruses and belongs to the picorna-like supergroup. Like all other picorna-like viruses, potyvirids employ polyprotein processing as a gene expression strategy and have single-stranded, positive-sense RNA genomes, most of which are monopartite with a long open reading frame. The potyvirid polyproteins are highly conserved in the central and carboxy-terminal regions. In contrast, the N-terminal region is hypervariable and contains position-specific mutations resulting from transcriptional slippage during viral replication, leading to translational frameshift to produce additional viral proteins essential for viral infection. Some potyvirids even lack one of the N-terminal proteins P1 or helper component-protease and have a genus-specific or species-specific protein instead. This review summarizes current knowledge about the conserved and divergent features of potyvirid genomes and biological relevance and discusses future research directions.
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Affiliation(s)
- Hongguang Cui
- College of Plant Protection, Hainan University, Haikou, Hainan 570228, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Haikou, Hainan 570228, China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada
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Huang CH, Tai CH, Lin RS, Chang CJ, Jan FJ. Biological, Pathological, and Molecular Characteristics of a New Potyvirus, Dendrobium Chlorotic Mosaic Virus, Infecting Dendrobium Orchid. PLANT DISEASE 2019; 103:1605-1612. [PMID: 30998416 DOI: 10.1094/pdis-10-18-1839-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dendrobium smillieae is one of the popular orchids in Taiwan. This report describes a new potyvirus tentatively named Dendrobium chlorotic mosaic virus (DeCMV) causing chlorotic and mosaic symptoms in D. smillieae. Enzyme-linked immunosorbent assay (ELISA) tests using six antisera against orchid-infecting viruses revealed that only a monoclonal antibody against the potyvirus group reacted positively with crude saps prepared from a symptomatic dendrobium orchid. Potyvirus-like, flexuous, filamentous particles were observed under an electron microscope, measuring approximately 700 to 800 nm in length and 11 to 12 nm in diameter. Sequence analyses revealed that DeCMV coat protein gene shared 59.6 to 66.0% nucleotide sequence identity and 57.6 to 66.0% amino acid sequence identity, whereas the DeCMV complete genome shared 54.1 to 57.3% nucleotide sequence identity and 43.7 to 49.5% amino acid sequence identity with those other known potyviruses. These similarity levels were much lower than the criteria set for species demarcation in potyviruses. Thus, DeCMV can be considered a new potyvirus. The whole DeCMV genome contains 10,041 nucleotides (GenBank accession no. MK241979) and encodes a polyprotein that is predicted to produce 10 proteins by proteolytic cleavage. In a pathogenicity test, results of inoculation assays demonstrated that DeCMV can be transmitted to dendrobium orchids by grafting and mechanical inoculation, as verified by ELISA and western blot analyses using the DeCMV polyclonal antiserum and by reverse transcription polymerase chain reaction using the coat protein gene-specific primers. The inoculated orchids developed similar chlorotic and mosaic symptoms. In conclusion, DeCMV is a novel orchid-infecting potyvirus, and this is the first report of a new potyvirus that infects dendrobium orchids in Taiwan.
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Affiliation(s)
- Chih-Hung Huang
- 1 Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
- 2 Department of Plant Pathology, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Chia-Hsing Tai
- 2 Department of Plant Pathology, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Ruey-Song Lin
- 3 Department of Horticulture, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Chung-Jan Chang
- 4 Department of Plant Pathology, University of Georgia, Griffin, GA 30223, U.S.A.; and
| | - Fuh-Jyh Jan
- 1 Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
- 2 Department of Plant Pathology, National Chung-Hsing University, Taichung 40227, Taiwan
- 5 Advanced Plant Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
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Zhang L, Shang J, Jia Q, Li K, Yang H, Liu H, Tang Z, Chang X, Zhang M, Wang W, Yang W. Genetic evolutionary analysis of soybean mosaic virus populations from three geographic locations in China based on the P1 and CP genes. Arch Virol 2019; 164:1037-1048. [PMID: 30747339 DOI: 10.1007/s00705-019-04165-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/11/2019] [Indexed: 01/14/2023]
Abstract
Soybean mosaic virus (SMV) is one of the major pathogens causing serious soybean losses. Little is known about the genetic structure and evolutionary biology of the SMV population in southwestern China. In this study, 29 SMV isolates were obtained from Sichuan Province, and the genomic regions encoding the first protein (P1) and coat protein (CP) were sequenced. Combined with SMV isolates from the southeastern and northeastern regions of China, the genetic and molecular evolution of SMV was studied. Recombination analysis revealed that intraspecific and interspecific recombination had occurred in the SMV population. A phylogenetic tree based on the P1 gene reflected the geographic origin of the non-interspecific recombinant SMV (SMV-NI), while a tree based on the CP gene did not. Though frequent gene flow of the SMV-NI populations was found between the southeastern and northeastern populations, the southwestern population was relatively independent. Genetic differentiation was significant between the SMV interspecific recombinant (SMV-RI) and the non-interspecific recombinant (SMV-NI) populations. It was interesting to note that there was an almost identical recombination breakpoint in SMV-RI and Watermelon mosaic virus (WMV). Population dynamics showed that SMV-RI might be in an expanding state, while the SMV-NI population is relatively stable.
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Affiliation(s)
- Lei Zhang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Shang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Qi Jia
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Li
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, China
| | - Hui Yang
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huanhuan Liu
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongqin Tang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoli Chang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Zhang
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenming Wang
- College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenyu Yang
- Sichuan Engineering Research Center for Crop Strip Intercropping System and Key Laboratory of Crop Eco‑physiology and Farming System in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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Shan H, Pasin F, Tzanetakis IE, Simón‐Mateo C, García JA, Rodamilans B. Truncation of a P1 leader proteinase facilitates potyvirus replication in a non-permissive host. MOLECULAR PLANT PATHOLOGY 2018; 19:1504-1510. [PMID: 29115017 PMCID: PMC6638051 DOI: 10.1111/mpp.12640] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/25/2017] [Accepted: 11/03/2017] [Indexed: 05/08/2023]
Abstract
The Potyviridae family is a major group of plant viruses that includes c. 200 species, most of which have narrow host ranges. The potyvirid P1 leader proteinase self-cleaves from the remainder of the viral polyprotein and shows large sequence variability linked to host adaptation. P1 proteins can be classified as Type A or Type B on the basis, amongst other things, of their dependence or not on a host factor to develop their protease activity. In this work, we studied Type A proteases from the Potyviridae family, characterizing their host factor requirements. Our in vitro cleavage analyses of potyvirid P1 proteases showed that the N-terminal domain is relevant for host factor interaction and suggested that the C-terminal domain is also involved. In the absence of plant factors, the N-terminal end of Plum pox virus P1 antagonizes protease self-processing. We performed extended deletion mutagenesis analysis to define the N-terminal antagonistic domain of P1. In viral infections, removal of the P1 protease antagonistic domain led to a gain-of-function phenotype, strongly increasing local infection in a non-permissive host. Altogether, our results shed new insights into the adaptation and evolution of potyvirids.
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Affiliation(s)
- Hongying Shan
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
| | - Fabio Pasin
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
- Present address:
Agricultural Biotechnology Research CenterAcademia Sinica11529 TaipeiTaiwan
| | - Ioannis E. Tzanetakis
- Department of Plant Pathology, Division of AgricultureUniversity of Arkansas SystemFayettevilleAR 72701USA
| | - Carmen Simón‐Mateo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
| | - Juan Antonio García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
| | - Bernardo Rodamilans
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB‐CSIC)Campus Universidad Autónoma de Madrid, Darwin 3Madrid 28049Spain
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Molecular archeological evidence in support of the repeated loss of a papillomavirus gene. Sci Rep 2016; 6:33028. [PMID: 27604338 PMCID: PMC5015084 DOI: 10.1038/srep33028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/16/2016] [Indexed: 11/08/2022] Open
Abstract
It is becoming clear that, in addition to gene gain, the loss of genes may be an important evolutionary mechanism for many organisms. However, gene loss is often associated with an increased mutation rate, thus quickly erasing evidence from the genome. The analysis of evolutionarily related sequences can provide empirical evidence for gene loss events. This paper analyzes the sequences of over 300 genetically distinct papillomaviruses and provides evidence for a role of gene loss during the evolution of certain papillomavirus genomes. Phylogenetic analysis suggests that the viral E6 gene was lost at least twice. Despite belonging to distant papillomaviral genera, these viruses lacking a canonical E6 protein may potentially encode a highly hydrophobic protein from an overlapping open reading frame, which we designate E10. Evolutionary pressure working on this alternative frame, may explain why, despite having lost the E6 open reading frame between 20 and 60 million years ago, evidence of an E6-like protein is conserved.
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Félez-Sánchez M, Vergara M, de Sanjosé S, Castellsagué X, Alemany L, Bravo IG. Searching beyond the usual papillomavirus suspects in squamous carcinomas of the vulva, penis and head and neck. INFECTION GENETICS AND EVOLUTION 2016; 45:198-204. [PMID: 27600594 DOI: 10.1016/j.meegid.2016.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/02/2016] [Indexed: 01/17/2023]
Abstract
Human Papillomaviruses (HPVs) are involved in the etiology of anogenital and head and neck cancers. The HPV DNA prevalence greatly differs by anatomical site. Indeed, the high rates of viral DNA prevalence in anal and cervical carcinomas contrast with the lower fraction of cancer cases attributable to HPVs in other anatomical sites, chiefly the vulva, the penis and head and neck. Here we analyzed 2635 Formalin Fixed Paraffin Embedded surgical samples that had previously tested negative for the presence of HPVs DNA using the SPF10/DEIA procedure, in order to identify the presence of other PVs not explicitly targeted by standard molecular epidemiologic approaches. All samples were reanalyzed using five broad-PV PCR primer sets (CP1/2, FAP6064/FAP64, SKF/SKR, MY9/MY11, MFI/MFII) targeting the main PV main clades. In head and neck carcinoma samples (n=1141), we recovered DNA from two BetaHPVs, namely HPV20 and HPV21, and from three cutaneous AlphaPVs, namely HPV2, HPV57 and HPV61. In vulvar squamous cell carcinoma samples (n=902), we found one of the samples containing DNA of one cutaneous HPV, namely HPV2, and 29 samples contained DNA from essentially mucosal HPVs. In penile squamous cell carcinoma samples (n=592), we retrieved the DNA of HPV16 in 16 samples. Our results show first that the SPF10/DEIA is very sensitive, as we recovered only 2.1% (55/2635) false negative results; second, that although the DNA of cutaneous HPVs can be detected in cancer samples, their relative contribution remains anyway minor (0.23%; 6/2635) and may be neglected for screening and vaccination purposes; and third, their contribution to malignancy is not necessarily warranted and needs to be elucidated.
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Affiliation(s)
- Marta Félez-Sánchez
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO) L'Hospitalet de Llobregat, Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marleny Vergara
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO) L'Hospitalet de Llobregat, Barcelona, Spain
| | - Silvia de Sanjosé
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO) L'Hospitalet de Llobregat, Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública (CIBERESP). Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Castellsagué
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO) L'Hospitalet de Llobregat, Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Alemany
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO) L'Hospitalet de Llobregat, Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO) L'Hospitalet de Llobregat, Barcelona, Spain; Bellvitge Institute of Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; MIVEGEC, National Center for Scientific Research (CNRS), Montpellier, France.
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