Browsing by Autor "Garcia, Lineth"

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Multiplex RT-qPCR strategy for SARS-CoV-2 variants detection in developing countries without ngs: The Bolivian experience.
(2025) Parrado, Rudy; Cuba-Grandy, Carolina X; Fuentes-Luppichini, Eugenia; Torrico Villarroel, Nattaly Grecia; Mamani-Ortiz, Yercin; Mendez, Jaqueline; Melgarejo, Betty; Coronado-Arrázola, Irenice; Montaño, Nair A; Almonacid, Leonardo I; Medina, Rafael A; Garcia, Lineth; Pardo-Roa, Catalina
The rapid evolution of SARS-CoV-2 has led to the emergence of variants of concern (VOCs) characterized by increased transmissibility, pathogenicity, and resistance to neutralizing antibodies. Identifying these variants is essential for guiding public health efforts to control COVID-19. Although whole genome sequencing (WGS) is the gold standard for variant identification, its implementation is often limited in developing countries due to resource constraints. In Bolivia, genomic surveillance is a challenge due to its limited technological infrastructure and resources. An RT-qPCR-based strategy was designed to address these limitations and detect the mutations associated with VOCs and variants of interest (VOIs). The multiplex RT-qPCR commercial kits AllplexTM Master and Variants I (Seegene®) and the ValuPanelTM (Biosearch®) were used to target mutations such as HV69/70del, E484K, N501Y, P681H, and K417N/T. They are characteristic of the Alpha (B.1.1.7), Beta (B.1.531), Gamma (P.1), Omicron (B.1.1.529), Mu (B.1.621), and Zeta (P.2) variants. A total of 157 samples collected in Cochabamba from January to November 2021 were evaluated, identifying 44 Gamma, 2 Zeta, 20 Mu, and 10 Omicron were identified. The strategy's effectiveness was validated against WGS data generated with Oxford NanoporeTM technology, showing a concordance rate of 0.96. This highlights the value of the RT-qPCR strategy in guiding the selection of samples for WGS, enabling broader detection of new variants that cannot be identified by RT-qPCR alone.
Supplementary Data and Materials for: Statistical Analysis of Larval Postspiracular Filament Length in Anopheles pseudopunctipennis
(European Organization for Nuclear Research, 2025) Lardeux, Frédéric; Vasquez, Deysi; Lardeux, Rosenka; Aliaga, Claudia; Garcia, Lineth; Torrez, Libia
This repository provides the complete dataset and all scripts used in the study “Statistical analysis of larval postspiracular filament length reveals continuous variation in Bolivian Anopheles pseudopunctipennis (Diptera: Culicidae)”, recommended by PCI Zoology.It includes the raw morphometric measurements, transformed datasets used for statistical modelling, all R scripts used for data processing and analyses, and the full set of outputs generated during the workflow. These materials enable full reproducibility of the study and allow further investigation of caudal filament variation across populations from Mataral and El Chaco (Bolivia). Contents Raw data: original morphometric measurements of larval postspiracular filaments and head-collar length. Processed datasets: outputs of measurement verification, allometric correction, and data preparation for downstream analyses. R scripts (8 scripts): measurement validation, allometry correction, site comparison, descriptive statistics, distribution fitting, mixture modelling, outlier detection, and tail-analysis procedures. Outputs: tables and figures associated with each analysis step for both sites. Supplementary tables: reassigned measurements and Pickands moment estimates for Mataral and El Chaco. Repository structure data/ (raw and transformed datasets) scripts/ (colas_1_mean.R to colas_8_tail_analysis.R) outputs/ (results for Mataral and El Chaco, structured by script) Supplementary_Tables/ (CSV files referenced in the manuscript) README.txt (detailed documentation) Data descriptionDatasets include individual larval identifiers, site information, left and right filament lengths, head-collar length, and all allometry-corrected variables (ratios, log-ratios, OLS/RLM/GAM residuals, SMA-derived predictions). Variable names are consistent across files. Software and reproducibilityAnalyses were performed in R (≥ 4.3.0). All required packages are listed in the repository documentation. Scripts are fully executable in the order described, and each step generates structured outputs. LicenseAll files are distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. CitationIf using these data or scripts, please cite:Lardeux F., Vasquez D., Lardeux R., Aliaga C., Garcia L., Torrez L. (2025). Statistical analysis of larval postspiracular filament length reveals continuous variation in Bolivian Anopheles pseudopunctipennis (Diptera: Culicidae). PCI Zoology.(See repository for DOI.)
Supplementary Data and Materials for: Statistical Analysis of Larval Postspiracular Filament Length in Anopheles pseudopunctipennis
(European Organization for Nuclear Research, 2025) Lardeux, Frédéric; Vasquez, Deysi; Lardeux, Rosenka; Aliaga, Claudia; Garcia, Lineth; Torrez, Libia
This repository provides the complete dataset and all scripts used in the study “Statistical analysis of larval postspiracular filament length reveals continuous variation in Bolivian Anopheles pseudopunctipennis (Diptera: Culicidae)”, recommended by PCI Zoology.It includes the raw morphometric measurements, transformed datasets used for statistical modelling, all R scripts used for data processing and analyses, and the full set of outputs generated during the workflow. These materials enable full reproducibility of the study and allow further investigation of caudal filament variation across populations from Mataral and El Chaco (Bolivia). Contents Raw data: original morphometric measurements of larval postspiracular filaments and head-collar length. Processed datasets: outputs of measurement verification, allometric correction, and data preparation for downstream analyses. R scripts (8 scripts): measurement validation, allometry correction, site comparison, descriptive statistics, distribution fitting, mixture modelling, outlier detection, and tail-analysis procedures. Outputs: tables and figures associated with each analysis step for both sites. Supplementary tables: reassigned measurements and Pickands moment estimates for Mataral and El Chaco. Repository structure data/ (raw and transformed datasets) scripts/ (colas_1_mean.R to colas_8_tail_analysis.R) outputs/ (results for Mataral and El Chaco, structured by script) Supplementary_Tables/ (CSV files referenced in the manuscript) README.txt (detailed documentation) Data descriptionDatasets include individual larval identifiers, site information, left and right filament lengths, head-collar length, and all allometry-corrected variables (ratios, log-ratios, OLS/RLM/GAM residuals, SMA-derived predictions). Variable names are consistent across files. Software and reproducibilityAnalyses were performed in R (≥ 4.3.0). All required packages are listed in the repository documentation. Scripts are fully executable in the order described, and each step generates structured outputs. LicenseAll files are distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. CitationIf using these data or scripts, please cite:Lardeux F., Vasquez D., Lardeux R., Aliaga C., Garcia L., Torrez L. (2025). Statistical analysis of larval postspiracular filament length reveals continuous variation in Bolivian Anopheles pseudopunctipennis (Diptera: Culicidae). PCI Zoology.(See repository for DOI.)
Usefulness of Serial Blood Sampling and PCR Replicates for Treatment Monitoring of Patients with Chronic Chagas Disease.
(2019) Parrado, Rudy; Ramirez, Juan Carlos; de la Barra, Anabelle; Alonso-Vega, Cristina; Juiz, Natalia; Ortiz, Lourdes; Illanes, Daniel; Torrico, Faustino; Gascon, Joaquim; Alves, Fabiana; Flevaud, Laurence; Garcia, Lineth; Schijman, Alejandro G; Ribeiro, Isabela
This work evaluated a serial blood sampling procedure to enhance the sensitivity of duplex real-time quantitative PCR (qPCR) for baseline detection and quantification of parasitic loads and posttreatment identification of failure in the context of clinical trials for treatment of chronic Chagas disease, namely, DNDi-CH-E1224-001 (ClinicalTrials.gov registration no. NCT01489228) and the MSF-DNDi PCR Sampling Optimization Study (NCT01678599). Patients from Cochabamba (n = 294), Tarija (n = 257), and Aiquile (n = 220) were enrolled. Three serial blood samples were collected at each time point, and qPCR triplicates were tested for each sample. The first two samples were collected during the same day and the third one 7 days later. A patient was considered PCR positive if at least one qPCR replicate was detectable. Cumulative results of multiple samples and qPCR replicates enhanced the proportion of pretreatment sample positivity from 54.8% to 76.2%, 59.5% to 77.8%, and 73.5% to 90.2% in Cochabamba, Tarija, and Aiquile cohorts, respectively. This strategy increased the detection of treatment failure from 72.9% to 91.7%, 77.8% to 88.9%, and 42.9% to 69.1% for E1224 low-, short-, and high-dosage regimens, respectively, and from 4.6% to 15.9% and 9.5% to 32.1% for the benznidazole arm in the DNDi-CH-E1224-001 and MSF-DNDi studies, respectively. The addition of the third blood sample and third qPCR replicate in patients with nondetectable PCR results in the first two samples gave a small, non-statistically significant improvement in qPCR positivity. No change in clinical sensitivity was seen with a blood volume increase from 5 to 10 ml. The monitoring of patients treated with placebo in the DNDi-CH-E1224-001 trial revealed fluctuations in parasitic loads and occasionally nondetectable results. In conclusion, a serial sampling strategy enhanced PCR sensitivity to detecting treatment failure during follow-up and has the potential for improving recruitment capacity in Chagas disease trials, which require an initial positive qPCR result for patient admission.