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42 results on '"prototype vector"'

1. A Two-Level, Intramutant Spectrum Haplotype Profile of Hepatitis C Virus Revealed by Self-Organized Maps

Author

Soledad Delgado, Celia Perales, Carlos García-Crespo, María Eugenia Soria, Isabel Gallego, Ana Isabel de Ávila, Brenda Martínez-González, Lucía Vázquez-Sirvent, Cecilio López-Galíndez, Federico Morán, and Esteban Domingo

Subjects
viral quasispecies, genome diversification, NS5A-NS5B amplicons, haplotype frequency, SOM network, prototype vector, Microbiology, QR1-502
Abstract

ABSTRACT RNA viruses replicate as complex mutant spectra termed viral quasispecies. The frequency of each individual genome in a mutant spectrum depends on its rate of generation and its relative fitness in the replicating population ensemble. The advent of deep sequencing methodologies allows for the first-time quantification of haplotype abundances within mutant spectra. There is no information on the haplotype profile of the resident genomes and how the landscape evolves when a virus replicates in a controlled cell culture environment. Here, we report the construction of intramutant spectrum haplotype landscapes of three amplicons of the NS5A-NS5B coding region of hepatitis C virus (HCV). Two-dimensional (2D) neural networks were constructed for 44 related HCV populations derived from a common clonal ancestor that was passaged up to 210 times in human hepatoma Huh-7.5 cells in the absence of external selective pressures. The haplotype profiles consisted of an extended dense basal platform, from which a lower number of protruding higher peaks emerged. As HCV increased its adaptation to the cells, the number of haplotype peaks within each mutant spectrum expanded, and their distribution shifted in the 2D network. The results show that extensive HCV replication in a monotonous cell culture environment does not limit HCV exploration of sequence space through haplotype peak movements. The landscapes reflect dynamic variation in the intramutant spectrum haplotype profile and may serve as a reference to interpret the modifications produced by external selective pressures or to compare with the landscapes of mutant spectra in complex in vivo environments. IMPORTANCE The study provides for the first time the haplotype profile and its variation in the course of virus adaptation to a cell culture environment in the absence of external selective constraints. The deep sequencing-based self-organized maps document a two-layer haplotype distribution with an ample basal platform and a lower number of protruding peaks. The results suggest an inferred intramutant spectrum fitness landscape structure that offers potential benefits for virus resilience to mutational inputs.

Published
2021
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5. Automatic ROI Selection Using SOM Modelling in Structural Brain MRI

Author

Ortiz García, Andrés, Górriz, Juan Manuel, Ramírez, Javier, Salas-González, Diego, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Ferrández Vicente, José Manuel, editor, Álvarez Sánchez, José Ramón, editor, de la Paz López, Félix, editor, and Toledo Moreo, Fco. Javier, editor

Published
2013
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6. Comparing One-Class Classification Algorithms for Finding Interesting Resources in Social Bookmarking Systems

Author

Godoy, Daniela, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Lacroix, Zoé, editor, and Vidal, María Esther, editor

Published
2012
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7. Application of SOM-Based Visualization Maps for Time-Response Analysis of Industrial Processes

Author

Prada, Miguel A., Domínguez, Manuel, Díaz, Ignacio, Fuertes, Juan J., Reguera, Perfecto, Morán, Antonio, Alonso, Serafín, Hutchison, David, Kanade, Takeo, Kittler, Josef, Kleinberg, Jon M., Mattern, Friedemann, Mitchell, John C., Naor, Moni, Nierstrasz, Oscar, Pandu Rangan, C., Steffen, Bernhard, Sudan, Madhu, Terzopoulos, Demetri, Tygar, Doug, Vardi, Moshe Y., Weikum, Gerhard, Diamantaras, Konstantinos, editor, Duch, Wlodek, editor, and Iliadis, Lazaros S., editor

Published
2010
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10. The Complexity of the Batch Neural Gas Extended to Local PCA

Author

Machón-González, Iván, López-García, Hilario, Calvo-Rolle, José Luís, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Cabestany, Joan, editor, Sandoval, Francisco, editor, Prieto, Alberto, editor, and Corchado, Juan M., editor

Published
2009
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11. On the Improvement of the Mapping Trustworthiness and Continuity of a Manifold Learning Model

Author

Cruz-Barbosa, Raúl, Vellido, Alfredo, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Fyfe, Colin, editor, Kim, Dongsup, editor, Lee, Soo-Young, editor, and Yin, Hujun, editor

Published
2008
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12. Fuzzy Growing Hierarchical Self-Organizing Networks

Author

Barreto-Sanz, Miguel, Pérez-Uribe, Andrés, Peña-Reyes, Carlos-Andres, Tomassini, Marco, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Kůrková, Véra, editor, Neruda, Roman, editor, and Koutník, Jan, editor

Published
2008
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13. Improving the Correlation Hunting in a Large Quantity of SOM Component Planes : Classification of Agro-Ecological Variables Related with Productivity in the Sugar Cane Culture

Author

Barreto S., Miguel A., Pérez-Uribe, Andrés, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, de Sá, Joaquim Marques, editor, Alexandre, Luís A., editor, Duch, Włodzisław, editor, and Mandic, Danilo, editor

Published
2007
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14. Fuzzy Labeled Self-organizing Map with Kernel-Based Topographic Map Formation

Author

González, Iván Machón, García, Hilario López, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, de Sá, Joaquim Marques, editor, Alexandre, Luís A., editor, Duch, Włodzisław, editor, and Mandic, Danilo, editor

Published
2007
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15. Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping

Author

Scherbart, Alexandra, Timm, Wiebke, Böcker, Sebastian, Nattkemper, Tim W., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, de Sá, Joaquim Marques, editor, Alexandre, Luís A., editor, Duch, Włodzisław, editor, and Mandic, Danilo, editor

Published
2007
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20. Semi-automatic Creation and Maintenance of Web Resources with webTopic

Author

Escudeiro, Nuno F., Jorge, Alípio M., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Ackermann, Markus, editor, Berendt, Bettina, editor, Grobelnik, Marko, editor, Hotho, Andreas, editor, Mladenič, Dunja, editor, Semeraro, Giovanni, editor, Spiliopoulou, Myra, editor, Stumme, Gerd, editor, Svátek, Vojtěch, editor, and van Someren, Maarten, editor

Published
2006
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21. WordNet-Based Word Sense Disambiguation for Learning User Profiles

Author

Degemmis, M., Lops, P., Semeraro, G., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Ackermann, Markus, editor, Berendt, Bettina, editor, Grobelnik, Marko, editor, Hotho, Andreas, editor, Mladenič, Dunja, editor, Semeraro, Giovanni, editor, Spiliopoulou, Myra, editor, Stumme, Gerd, editor, Svátek, Vojtěch, editor, and van Someren, Maarten, editor

Published
2006
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22. Implementing a Chinese Character Browser Using a Topography-Preserving Map

Author

Kirk, James S., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Wang, Jun, editor, Yi, Zhang, editor, Zurada, Jacek M., editor, Lu, Bao-Liang, editor, and Yin, Hujun, editor

Published
2006
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23. Nonlinear Exploratory Data Analysis Applied to Seismic Signals

Author

Esposito, Antonietta M., Scarpetta, Silvia, Giudicepietro, Flora, Masiello, Stefano, Pugliese, Luca, Esposito, Anna, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Apolloni, Bruno, editor, Marinaro, Maria, editor, Nicosia, Giuseppe, editor, and Tagliaferri, Roberto, editor

Published
2006
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24. A Novel Clustering Method for Analysis of Gene Microarray Expression Data

Author

Luo, Fei, Liu, Juan, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Dough, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Li, Jinyan, editor, Yang, Qiang, editor, and Tan, Ah-Hwee, editor

Published
2006
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26. Mining Promising Qualification Patterns

Author

Wagner, Ralf, Bock, H.-H., editor, Gaul, W., editor, Vichi, M., editor, Arabie, Ph., editor, Baier, D., editor, Critchley, F., editor, Decker, R., editor, Diday, E., editor, Greenacre, M., editor, Lauro, C., editor, Meulman, J., editor, Monari, P., editor, Nishisato, S., editor, Ohsumi, N., editor, Opitz, O., editor, Ritter, G., editor, Schader, M., editor, Weihs, C., editor, Baier, Daniel, editor, and Wernecke, Klaus-Dieter, editor

Published
2005
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27. Visualization of Cluster Changes by Comparing Self-organizing Maps

Author

Denny, Squire, David McG., Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Ho, Tu Bao, editor, Cheung, David, editor, and Liu, Huan, editor

Published
2005
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28. Neural Networks in Detection and Identification of Littoral Oil Pollution by Remote Sensing

Author

Lin, Bin, An, Jubai, Carl, Brown, Zhang, Hande, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Yin, Fu-Liang, editor, Wang, Jun, editor, and Guo, Chengan, editor

Published
2004
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29. Comparison of Instances Seletion Algorithms I. Algorithms Survey

Author

Jankowski, Norbert, Grochowski, Marek, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Carbonell, Jaime G., editor, Siekmann, Jörg, editor, Rutkowski, Leszek, editor, Siekmann, Jörg H., editor, Tadeusiewicz, Ryszard, editor, and Zadeh, Lotfi A., editor

Published
2004
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36. N

Author

Hazewinkel, M. and Hazewinkel, M., editor

Published
1997
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37. A Two-Level, Intramutant Spectrum Haplotype Profile of Hepatitis C Virus Revealed by Self-Organized Maps

Author

Carlos García-Crespo, Federico Morán, Soledad Delgado, Cecilio López-Galíndez, Brenda Martínez-González, Celia Perales, Lucía Vázquez-Sirvent, María Eugenia Soria, Ana Isabel de Ávila, Esteban Domingo, and Isabel Gallego

Subjects
Microbiology (medical), Physiology, Population, Viral quasispecies, Genome, Viral, Hepacivirus, Biology, Viral Nonstructural Proteins, Virus Replication, Genome, Microbiology, Deep sequencing, Virus, Evolution, Molecular, Cell Line, Tumor, Genetics, Coding region, Humans, haplotype frequency, education, genome diversification, education.field_of_study, General Immunology and Microbiology, Ecology, Haplotype, prototype vector, Chromosome Mapping, High-Throughput Nucleotide Sequencing, NS5A-NS5B amplicons, Cell Biology, Amplicon, RNA-Dependent RNA Polymerase, Adaptation, Physiological, Hepatitis C, fitness platform, QR1-502, Quasispecies, Infectious Diseases, Amino Acid Substitution, Haplotypes, Evolutionary biology, SOM network, Mutation, RNA, Viral, viral quasispecies, Research Article
Abstract

RNA viruses replicate as complex mutant spectra termed viral quasispecies. The frequency of each individual genome in a mutant spectrum depends on its rate of generation and its relative fitness in the replicating population ensemble. The advent of deep sequencing methodologies allows for the first-time quantification of haplotype abundances within mutant spectra. There is no information on the haplotype profile of the resident genomes and how the landscape evolves when a virus replicates in a controlled cell culture environment. Here, we report the construction of intramutant spectrum haplotype landscapes of three amplicons of the NS5A-NS5B coding region of hepatitis C virus (HCV). Two-dimensional (2D) neural networks were constructed for 44 related HCV populations derived from a common clonal ancestor that was passaged up to 210 times in human hepatoma Huh-7.5 cells in the absence of external selective pressures. The haplotype profiles consisted of an extended dense basal platform, from which a lower number of protruding higher peaks emerged. As HCV increased its adaptation to the cells, the number of haplotype peaks within each mutant spectrum expanded, and their distribution shifted in the 2D network. The results show that extensive HCV replication in a monotonous cell culture environment does not limit HCV exploration of sequence space through haplotype peak movements. The landscapes reflect dynamic variation in the intramutant spectrum haplotype profile and may serve as a reference to interpret the modifications produced by external selective pressures or to compare with the landscapes of mutant spectra in complex in vivo environments. IMPORTANCE The study provides for the first time the haplotype profile and its variation in the course of virus adaptation to a cell culture environment in the absence of external selective constraints. The deep sequencing-based self-organized maps document a two-layer haplotype distribution with an ample basal platform and a lower number of protruding peaks. The results suggest an inferred intramutant spectrum fitness landscape structure that offers potential benefits for virus resilience to mutational inputs.

Published
2021
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38. USING OF THE K NEAREST NEIGHBOURS ALGORITHM (k-NNs) IN THE DATA CLASSIFICATION.

Author

Natalia, Gîlcă and Gheorghe, Gîlcă

Subjects
K-nearest neighbor classification, MACHINE learning
Abstract

The article aims to implement a data classification algorithm based on the nearest k neighbors (k-NNs). To begin we propose a series of improvements to the k-NNs algorithm that can lead to the optimization of the algorithm. The simulation results in the R2012b Matlab environment highlights the accuracy in the data classification for the k-NNs algorithm. In the simulation we have considered three different classes having a different number of components: 22, 35, 45, and a value of k = 10 was taken. We have considered three classified points and the output of the system has very good results, assigning for each point one of the 3 classes which contains most neighbors from the total. [ABSTRACT FROM AUTHOR]

Published
2016

40. A new Feature-Fusion method based on training dataset prototype for surface defect recognition.

Author

Wang, Yucheng, Li, Xinyu, Gao, Yiping, Wang, Lijian, and Gao, Liang

Subjects
*SURFACE defects, *CONVOLUTIONAL neural networks, *PROTOTYPES, *FEATURE extraction
Abstract

Surface defect recognition is important to improve the surface quality of end products. In this area, there were many convolutional neural network (CNN)-based methods because CNN can extract features automatically. The extracted features determine the performance of recognition, so it is important for CNN-based methods to extract effective and sufficient features. However, feature extraction needs a large-scale dataset, which is hard to obtain. To save the cost of collecting samples and extract effective features, ensemble methods were proposed to make full use of the features extracted by CNN in order to guarantee good performance with limited samples. However, the methods are confined to utilize one sample – they extracted multi-level features from one individual sample – but ignore the vast information in a dataset. Due to the limit information in one sample, this paper turns the attention to the training dataset and attempts to mine the multi-level information in the dataset for predicting. The proposed method is named as Prototype vectors fusion-based CNN (ProtoCNN), which utilizes the prototype information in the training dataset. In training process, it trains a VGG11 as the base model, and meanwhile prototype vectors corresponding to each defect class are generated in multiple feature layers of VGG11. Then, in predicting process, the prototype vectors are fused to predict unknown samples. The experiments on three famous datasets, including NEU-CLS, wood dataset, and textile dataset indicate that the proposed ProtoCNN outperforms conventional ensemble models and other models for surface defect recognition. In these datasets, ProtoCNN has achieved the accuracy of 99.86%, 90.01%, and 81.28% respectively, which increase 1.05%, 4.07%, 19.53% compared to its base model respectively. Finally, this paper analyzes the effectiveness and practicality of prototype vectors, showing that the proposed ProtoCNN is practical for real world application. [ABSTRACT FROM AUTHOR]

Published
2021
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41. A Two-Level, Intramutant Spectrum Haplotype Profile of Hepatitis C Virus Revealed by Self-Organized Maps.

Author

Delgado S, Perales C, García-Crespo C, Soria ME, Gallego I, de Ávila AI, Martínez-González B, Vázquez-Sirvent L, López-Galíndez C, Morán F, and Domingo E

Subjects
Amino Acid Substitution genetics, Cell Line, Tumor, Chromosome Mapping, Evolution, Molecular, Hepacivirus growth & development, Hepatitis C virology, High-Throughput Nucleotide Sequencing, Humans, Mutation genetics, Quasispecies genetics, RNA, Viral genetics, Virus Replication, Adaptation, Physiological genetics, Genome, Viral genetics, Haplotypes genetics, Hepacivirus genetics, RNA-Dependent RNA Polymerase genetics, Viral Nonstructural Proteins genetics
Abstract

RNA viruses replicate as complex mutant spectra termed viral quasispecies. The frequency of each individual genome in a mutant spectrum depends on its rate of generation and its relative fitness in the replicating population ensemble. The advent of deep sequencing methodologies allows for the first-time quantification of haplotype abundances within mutant spectra. There is no information on the haplotype profile of the resident genomes and how the landscape evolves when a virus replicates in a controlled cell culture environment. Here, we report the construction of intramutant spectrum haplotype landscapes of three amplicons of the NS5A-NS5B coding region of hepatitis C virus (HCV). Two-dimensional (2D) neural networks were constructed for 44 related HCV populations derived from a common clonal ancestor that was passaged up to 210 times in human hepatoma Huh-7.5 cells in the absence of external selective pressures. The haplotype profiles consisted of an extended dense basal platform, from which a lower number of protruding higher peaks emerged. As HCV increased its adaptation to the cells, the number of haplotype peaks within each mutant spectrum expanded, and their distribution shifted in the 2D network. The results show that extensive HCV replication in a monotonous cell culture environment does not limit HCV exploration of sequence space through haplotype peak movements. The landscapes reflect dynamic variation in the intramutant spectrum haplotype profile and may serve as a reference to interpret the modifications produced by external selective pressures or to compare with the landscapes of mutant spectra in complex in vivo environments. IMPORTANCE The study provides for the first time the haplotype profile and its variation in the course of virus adaptation to a cell culture environment in the absence of external selective constraints. The deep sequencing-based self-organized maps document a two-layer haplotype distribution with an ample basal platform and a lower number of protruding peaks. The results suggest an inferred intramutant spectrum fitness landscape structure that offers potential benefits for virus resilience to mutational inputs.

Published
2021
Full Text
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