Dynamics, evolutionary and epidemiological patterns of RNA viruses

Viral infections, specifically those caused by RNA viruses such as Human Immunodeficiency virus (HIV), Hepatitis C virus (HCV) or Influenza, are among the most important public health concerns to humans due to their high prevalence and associated mortality. Prevention and treatment campaigns against these viruses usually had limited efficacy, partly because their biological features allow them to reach very high levels of diversity, both at the within- and between-host levels. Research focused on understanding the processes and mechanisms involved in the evolution of RNA viruses, and on the clinical and/or epidemiological consequences of their diversification, is important for improving the management of their epidemics. The aim of this PhD thesis is to study different aspects of the mid- and long-term evolution of RNA viruses, with special interest in molecular epidemiology. For this, different datasets (viral alignments, obtained either from public databases or by sequencing patient’s derived samples from the studied populations) were obtained and analyzed by means of evolutionary and statistical approaches. Firstly, phylogenetic, coalescent and statistical analyses were performed to depict the HIV epidemic in two different Spanish regions: Euskadi (Basque Country) and Comunitat Valenciana (Valencian Community). A significant number of patients from both regions, especially those from the Comunitat Valenciana, were included in local transmission clusters. Men who have unprotected sex with men (MSM) were significantly more prone to form transmission clusters than other risk groups. The high vulnerability of MSM to HIV infection was also evidenced by the detection of an extraordinarily large transmission cluster, affecting more than 100 patients solely in the city of Valencia. Interestingly, the recent expansion of the highly pathogenic HIV CRF19_cpx among local Valencian MSM was also reported, for the first time outside Cuba. Secondly, by means of Bayesian coalescent analyses, the genomic evolutionary rates of different HIV-1 subtypes (A1, B, C, D, G) and CRFs (CRF01_AE, CRF02_AG) were estimated and compared. The results obtained revealed that HIV-1 A1, C and CRF01_AE evolve significantly faster than subtypes B, D, G and CRF02_AG. Thirdly, datasets containing sequences from the 6 major genotypes causing the HCV pandemic were analyzed, inferring the prevalence, evolutionary history and genetic barrier of naturally-occurring resistance mutations (RAVs) to direct acting antivirals (DAAs) in these genotypes. The obtained results demonstrate that RAVs are common in all HCV genotypes, and that there is an overall low genetic barrier for the selection of RAVs. Interestingly, some of these resistance mutations present a high potential to be transmitted between patients at risk. In the fourth place, the distribution of positively selected sites along the genomes of HCV subtypes 1a and 1b was analyzed. The results show that positive selection is acting in all HCV genes, and that positively selected sites are associated with the presence of CD8 epitopes, while conserved sites are associated with RNA secondary structure and CD4 epitopes. Finally, the effect of using RNA substitution models on the phylogenetic inference of viroids and RNA viruses was assessed. Such models were found to fit best for all the species analyzed. Compared to viral phylogenies inferred only from DNA models, using RNA models usually leads to significantly longer tree length estimates, while has no significant effect on tree topology inference. The results obtained from this work will not only have direct applications to HIV control campaigns in Spain and HCV treatment refinement, but also provide new insights into different aspects of the evolution of RNA viruses.Viral infections, specifically those caused by RNA viruses such as Human Immunodeficiency virus (HIV), Hepatitis C virus (HCV) or Influenza, are among the most important public health concerns to humans due to their high prevalence and associated mortality. Prevention and treatment campaigns against these viruses usually had limited efficacy, partly because their biological features allow them to reach very high levels of diversity, both at the within- and between-host levels. Research focused on understanding the processes and mechanisms involved in the evolution of RNA viruses, and on the clinical and/or epidemiological consequences of their diversification, is important for improving the management of their epidemics. The aim of this PhD thesis is to study different aspects of the mid- and long-term evolution of RNA viruses, with special interest in molecular epidemiology. For this, different datasets (viral alignments, obtained either from public databases or by sequencing patient’s derived samples from the studied populations) were obtained and analyzed by means of evolutionary and statistical approaches. Firstly, phylogenetic, coalescent and statistical analyses were performed to depict the HIV epidemic in two different Spanish regions: Euskadi (Basque Country) and Comunitat Valenciana (Valencian Community). A significant number of patients from both regions, especially those from the Comunitat Valenciana, were included in local transmission clusters. Men who have unprotected sex with men (MSM) were significantly more prone to form transmission clusters than other risk groups. The high vulnerability of MSM to HIV infection was also evidenced by the detection of an extraordinarily large transmission cluster, affecting more than 100 patients solely in the city of Valencia. Interestingly, the recent expansion of the highly pathogenic HIV CRF19_cpx among local Valencian MSM was also reported, for the first time outside Cuba. Secondly, by means of Bayesian coalescent analyses, the genomic evolutionary rates of different HIV-1 subtypes (A1, B, C, D, G) and CRFs (CRF01_AE, CRF02_AG) were estimated and compared. The results obtained revealed that HIV-1 A1, C and CRF01_AE evolve significantly faster than subtypes B, D, G and CRF02_AG. Thirdly, datasets containing sequences from the 6 major genotypes causing the HCV pandemic were analyzed, inferring the prevalence, evolutionary history and genetic barrier of naturally-occurring resistance mutations (RAVs) to direct acting antivirals (DAAs) in these genotypes. The obtained results demonstrate that RAVs are common in all HCV genotypes, and that there is an overall low genetic barrier for the selection of RAVs. Interestingly, some of these resistance mutations present a high potential to be transmitted between patients at risk. In the fourth place, the distribution of positively selected sites along the genomes of HCV subtypes 1a and 1b was analyzed. The results show that positive selection is acting in all HCV genes, and that positively selected sites are associated with the presence of CD8 epitopes, while conserved sites are associated with RNA secondary structure and CD4 epitopes. Finally, the effect of using RNA substitution models on the phylogenetic inference of viroids and RNA viruses was assessed. Such models were found to fit best for all the species analyzed. Compared to viral phylogenies inferred only from DNA models, using RNA models usually leads to significantly longer tree length estimates, while has no significant effect on tree topology inference. The results obtained from this work will not only have direct applications to HIV control campaigns in Spain and HCV treatment refinement, but also provide new insights into different aspects of the evolution of RNA viruses

Comparative analysis of variation and selection in the HCV genome

Genotype 1 of the hepatitis C virus (HCV) is themost prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and CD8), and secondary protein structure. Less than 10% of the genome was found to be under positive selection, and purifying selection was the main evolutionary process acting in both subtypes. We found differences in the number of positively selected sites between subtypes in several genes (Core, HVR2 in E2, P7, helicase in NS3 and NS4a). Heterozygosity values in positively selected sites and the rate of non-synonymous substitutions were significantly higher in subtype HCV-1b. Logistic regression analyses revealed that similar selective forces act at the genome level in both subtypes: RNA secondary structure and CD4 T-cell epitopes are associated with conserved sites, while CD8 T-cell epitopes are associatedwith positive selection in both subtypes. These results indicate that similar selective constraints are acting along HCV-1a and HCV-1 b genomes, despite some differences in the distribution of positively selected sites at independent genes

The substitution rate of HIV-1 subtypes: a genomic approach

HIV-1M causes most infections in the AIDS pandemic. Its genetic diversity is defined by nine pure subtypes and more than sixty recombinant forms. We have performed a comparative analysis of the evolutionary rate of five pure subtypes (A1, B, C, D, and G) and two circulating recombinant forms (CRF01_AE and CRF02 AG) using data obtained from nearly complete genome coding sequences. Times to the most recent common ancestor (tMRCA) and substitution rates of these HIV genomes, and their genomic partitions, were estimated by Bayesian coalescent analyses. Genomic substitution rate estimates were compared between the HIV-1 datasets analyzed by means of randomization tests. Significant differences in the rate of evolution were found between subtypes, with subtypes C and A1 and CRF01_AE displaying the highest rates. On the other hand, CRF02_AG and subtype D were the slowest evolving types. Using a different molecular clock model for each genomic partition led to more precise tMRCA estimates than when linking the same clock along the HIV genome. Overall, the earliest tMRCA corresponded to subtype A1 (median = 1941, 95% HPD = 1943-55), whereas the most recent tMRCA corresponded to subtype G and CRF01_AE subset 3 (median = 1971, 95% HPD = 1967-75 and median = 1972, 95% HPD = 1970-75, respectively). These results suggest that both biological and epidemiological differences among HIV-1M subtypes are reflected in their evolutionary dynamics. The estimates obtained for tMRCAs and substitution rates provide information that can be used as prior distributions in future Bayesian coalescent analyses of specific HIV-1 subtypes/CRFs and genes

Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain

We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM). Although it was significantly located in the city of Valencia (n = 105), phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194). Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143), whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791). In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia

Formative research contributions to the development of Risaralda

Es importante establecer y visibilizar a los estudiantes los beneficios relacionados con la formación en investigación, dentro de los cuales encontramos el fortalecimiento de las capacidades de liderazgo así como el compromiso activo y las experiencias en independencia y colaboración. Así mismo, la formación integral hacia una mayor apreciación del valor de la literatura disciplinaria, generando de esta manera habilidades de pensamiento crítico, indagación y análisis. Además, esto permite forjar la confianza en sí mismo para presentar las propias ideas a la comunidad, permitiendo al estudiante la preparación de futuras actividades académicas, incluidos estudios de posgrado. La investigación formativa tiene como propósito la difusión de la información existente y permitir que el estudiante la integre como conocimientos, considerándolo como un aprendizaje permanente y necesario. Uno de los principales problemas que debe enfrentar la investigación formativa es el número de docentes con las capacidades necesarias para generar en el estudiante capacidades investigativas, exigiendo al profesor universitario adoptar una actitud contraria al objeto de enseñanza, generando un carácter complejo y dinámico del conocimiento.CONTENTS RETOS DE LA INVESTIGACIÓN EN PREGRADO..................................................5 CHALLENGES OF UNDERGRADUATE RESEARCH.............................................9 German Oved Acevedo Osorio CHAPTER 1 HEALTH AND SPORTS SCIENCES FACTORS ASSOCIATED WITH EXACERBATIONS OR CRISIS EVENTS OF CHRONIC NON COMMUNICABLE DISEASES.........................13 Giovanni García Castro, Sandra Milena Bedoya Gaviria, Isabela Patiño Pulgarín y Valentina Valencia Flórez ORAL ANTICOAGULATION IN PATIENTS WITH NON-VALVULAR ATRIAL FIBRILLATION IN A UNIVERSITY HOSPITAL IN COLOMBIA.....................................................................................................29 María Leonor Galindo Márquez, Adrian Giraldo Diaconeasa, Juan Darío Franco Ramírez y Eduardo Ramírez Vallejo PERFORMANCE IN INITIAL TRAUMAASSESSMENT OF EMERGENCY TEAMS FROM PREHOSPITAL CARE TEAMS..................43 Giovanni García Castro, Yamileth Estrada Berrio, Manuela Aguirre Torres e Isabella Díaz Leal ACADEMIC TRAINING AND WORKING CONDITIONS OF NURSING PROFESSIONALS IN PEREIRA - RISARALDA 2020.....................55 Miguel Ángel Gómez Puerta, Laura Isabel Orozco Santamaría, Alexandra Villa Patiño y Gladys Judith Basto Hernández EFFECTS OF DYNAMIC TAPE WITH ANTI-VALGUS APPLICATION ON VERTICAL JUMP PERFORMANCE IN PHYSICALLY ACTIVE WOMEN: A CASE STUDY ..........................................73 María Camila Arias Castro, Alejandro Gómez Rodas y Ángela María Cifuentes Ríos PROPOSAL OF CARE FOR DIAGNOSTIC PREVALENT NURSES IN AN EMERGENCY DEPARTMENT................................................................89 Tatiana Restrepo Pérez, Jessica Viviana Ríos Uribe, Anyi Daniela Lemos Córdoba, Anyi Katherine Mapura Benjumea and Mónica Margarita Barón Castro FACTORS AND CONCEPTS ASSOCIATED WITH THE INITIATION OF CIGARETTE CONSUMPTION IN UNIVERSITY STUDENTS OF PEREIRA, COLOMBIA ............................................................................... 113 Giovanni García Castro, Claudia Milena Bernal Parra, Natalia Cardona Arroyave, Brahiam Stiven Moreno Bustamante y Daniela Ospina Sierra CHAPTER 2 ECONOMIC, ADMINISTRATIVE AND ACCOUNTING SCIENCES TECHNICAL-FINANCIAL EVALUATION OF BEAN (PHASEOLUS VULGARIS) VARIETY CARGAMANTO IN THE VILLAGE OF THE MUNICIPALITY OF SIBUNDOY IN THE DEPARTMENT OF PUTUMAYO ................................................................................................ 131 Adriana María Cuervo Rubio, Alejandra Arango Baranza IMPLEMENTATION OF THE NIF IN MICRO-ENTERPRISES OF PEREIRA CITY ............................................................................................ 151 Laura Cortes Correa y Nataly Andrea Gutiérrez STRATEGIC FRAMEWORK FOR SUSTAINABLE PRODUCTION IN COLOMBIA................................................................................................... 163 Paulina Murillo Gómez, Manuela Ramírez Osorio, Laura Juliana Rodríguez Henao, Lindy Neth Perea Mosquera, Isabel Redondo Ramírez SUSTAINABLE INNOVATION IN MANUFACTURING INDUSTRY........... 179 Mariana Buitrago Zuleta, Laura Juliana Rodríguez Henao, Lindy Neth Perea Mosquera y Marlen Isabel Redondo Ramírez CHAPTER 3 ARTS, HUMANITIES AND SOCIAL SCIENCES PERSONAL AND FAMILY CHANGES OF UNDERGRADUATE PSYCHOLOGY STUDENTS. IS A PROGRAM IN PSYCHOLOGY A PATHWAY TO PERSONALAND FAMILY CHANGE?...................................197 Linda Michelle De La Torre Álvarez, Mireya Ospina Botero PREGNANT MOTHERS DEPRIVED OF LIBERTY IN COLOMBIA AND MEXICO. A LOOK FROM COMPARATIVE LAW .................................225 Mary Luz Vélez Cárdenas, Katherine Almanza Astrid Milena Calderón Cárdenas CHAPTER 4 NATURAL SCIENCES DIFFERENTIAL DIAGNOSIS AND TREATMENT OF CUTANEOUS LYMPHOMA VS MASTOCYTOMA IN A 9 YEARS OLD CANINE: CASE REPORT...................................................................................................241 Diana Patricia Diaz García, Stephany Loaiza Pulgarín, Rafael R. Santisteban Arenas y Juan C. Ramírez Ante CHAPTER 5 TECHNOLOGÍES AND ENGINEERING STUDY OF INVENTORY-ROUTING PROBLEM IRP.....................................257 Frank Alejandro Hincapié Londoño, Jhonatan Stiven García Guevara y Eliana Mirldey Toro Ocamp

Intermediate Molecular Phenotypes to Identify Genetic Markers of Anthracycline-Induced Cardiotoxicity Risk.

Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex trait with a polygenic component that is mainly unidentified. We propose that levels of intermediate molecular phenotypes (IMPs) in the myocardium associated with histopathological damage could explain CDA susceptibility, so variants of genes encoding these IMPs could identify patients susceptible to this complication. Thus, a genetically heterogeneous cohort of mice (n = 165) generated by backcrossing were treated with doxorubicin and docetaxel. We quantified heart fibrosis using an Ariol slide scanner and intramyocardial levels of IMPs using multiplex bead arrays and QPCR. We identified quantitative trait loci linked to IMPs (ipQTLs) and cdaQTLs via linkage analysis. In three cancer patient cohorts, CDA was quantified using echocardiography or Cardiac Magnetic Resonance. CDA behaves as a complex trait in the mouse cohort. IMP levels in the myocardium were associated with CDA. ipQTLs integrated into genetic models with cdaQTLs account for more CDA phenotypic variation than that explained by cda-QTLs alone. Allelic forms of genes encoding IMPs associated with CDA in mice, including AKT1, MAPK14, MAPK8, STAT3, CAS3, and TP53, are genetic determinants of CDA in patients. Two genetic risk scores for pediatric patients (n = 71) and women with breast cancer (n = 420) were generated using machine-learning Least Absolute Shrinkage and Selection Operator (LASSO) regression. Thus, IMPs associated with heart damage identify genetic markers of CDA risk, thereby allowing more personalized patient management.J.P.L.’s lab is sponsored by Grant PID2020-118527RB-I00 funded by MCIN/AEI/10.13039/ 501100011039; Grant PDC2021-121735-I00 funded by MCIN/AEI/10.13039/501100011039 and by the “European Union Next Generation EU/PRTR”, the Regional Government of Castile and León (CSI144P20). J.P.L. and P.L.S. are supported by the Carlos III Health Institute (PIE14/00066). AGN laboratory and human patients’ studies are supported by an ISCIII project grant (PI18/01242). The Human Genotyping unit is a member of CeGen, PRB3, and is supported by grant PT17/0019 of the PE I + D + i 2013–2016, funded by ISCIII and ERDF. SCLl is supported by MINECO/FEDER research grants (RTI2018-094130-B-100). CH was supported by the Department of Defense (DoD) BCRP, No. BC190820; and the National Cancer Institute (NCI) at the National Institutes of Health (NIH), No. R01CA184476. Lawrence Berkeley National Laboratory (LBNL) is a multi-program national laboratory operated by the University of California for the DOE under contract DE AC02-05CH11231. The Proteomics Unit belongs to ProteoRed, PRB3-ISCIII, supported by grant PT17/0019/0023 of the PE I + D +i, 2017–2020, funded by ISCIII and FEDER. RCC is funded by fellowships from the Spanish Regional Government of Castile and León. NGS is a recipient of an FPU fellowship (MINECO/FEDER). hiPSC-CM studies were funded in part by the “la Caixa” Banking Foundation under the project code HR18-00304 and a Severo Ochoa CNIC Intramural Project (Exp. 12-2016 IGP) to J.J.S

Dated phylogeny of the 143 sequences from the initial CV cluster.

<p>Branch lengths represent years. The CV cluster is highlighted in black. Dots on nodes represent posterior probabilities ≥ 0.90.</p

Phylogenetic tree of the HIV-1 subtype B dataset.

<p>The potential transmission cluster (n = 143) is highlighted in red, other subtype B sequences are colored in black and the reference sequences from other subtypes/CRFs are colored in grey.</p

Sampling distribution of HIV-1 subtype B sequences.

<p>Sequences from patients inhabiting the city of Valencia or its metropolitan area are represented in blue (n = 1134) and those belonging to the transmission cluster sampled in this city are shown in red (n = 105).</p