Browsing by Author "Contreras, A. M."

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    Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
    (2022) Angulo, J.; Martinez Valdebenito, C.; Pardo Roa, C.; Almonacid, L. I.; Fuentes Luppichini, E.; Contreras, A. M.; Maldonado, C.; Le Corre, N.; Melo Ledermann, Francisco Javier; Medina, R. A.; Ferrés, M.
    Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
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    Evaluation of direct immunofluorescent assay (DFA) and rapid antigen test (RAT) for diagnosis of new pandemic influenza A H1N1 2009 (FLU AH1N1) during first wave in Santiago, Chile
    (ELSEVIER SCI LTD, 2010) Vizcaya, C.; Ferres, M.; Perret Pérez, Cecilia; Martinez, C.; Godoy, P.; Contreras, A. M.; Ferrer, P.; Azocar, T.
    Background: Since May 17th 2009 (epidemiological week 20th), the new strain of influenza A H1N1 was detected in respiratory samples of symptomatic patients in Santiago, Chile. The circulation of the virus lasted 11 weeks, with a peak between weeks 25-27th. The objective of our study was to evaluate the performance of influenza tests for diagnosis of FLU AH1N1. Methods: Nasopharyngeal swabs were taken from in and outpatients with influenza like illness (ILI), between June 1st and July 19th of 2009 (weeks 23-29th) and the results of DFA and RAT were compared using RT-PCR FLU AH1N1 (Light mix Kit Influenza A virus M2 and Light Mix Kit FLU A swine H1Ò of TIB MOLBIOL) as gold standard. We analyzed sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of DFA (D3 Ultra 8 DFA Respiratory & Identification Kit ä de Diagnostic Hybrid) and RAT (QuickVeuÒ of Biomerieux). Results were compared by age group and over three different periods of the outbreak: increasing, peak and decreasing. Results: 510 patients had RT-PCR for FLU AH1N1 with simultaneous DFA, 385 with RAT and 48 with both tests. Average age with DFA was 25,8 years (1 month-108 years, 53% females) and with RAT 32,9 years (2 months-108 years, 51% females), (p <0,0001). Comparing periods of the outbreak, DFA sensitivity was 58%, 77% and 81% in ascending, peak and descending period, respectively (p <0,001) and specificity was 90%, 83% and 91% respectively (p>0,05). Evaluating RAT, sensitivity was 41%, 61% and 67% (p<0,001) and specificity was 87%, 96% y 92% (p> 0,05) in different periods.