ABSTRACT
Objective: To determine the effectiveness of vaccination against SARS-CoV-2 in preventing illness and death from COVID-19 in Córdoba, Argentina, during the period from January through June 2021. Methods: A retrospective cohort study was conducted among 1,139,458 residents of the province of Córdoba. Multiple logistic regression models were developed to describe the relationship between vaccination and the presence of SARS-CoV-2 or death from COVID-19, while taking account of comorbidities and chronic disease risk factors and adjusting for sex and age. Results: Among the general population, having received one or two doses of vaccine reduced the risk of illness by 98.8% and 99.3%, respectively, and the risk of dying by 83% and 96.5%, respectively. Among those who developed COVID-19, the probability of dying was reduced by 57% and 80%, respectively. Regarding probability of death, risk increased with age, with being male, and with obesity, arterial hypertension, and diabetes mellitus. Conclusion: Vaccination is effective and protects against the risk of getting COVID-19, developing severe disease, or dying. Having obesity, arterial hypertension, or diabetes mellitus, in descending order, increases the risk of death.
Objetivo: Conhecer a eficácia da vacinação contra SARS-CoV-2 para prevenir o desenvolvimento de doença e morte por COVID-19 em Córdoba, Argentina, no período de janeiro a junho de 2021. Métodos: Foi realizado um estudo de coorte retrospectivo em 1.139.458 residentes da província de Córdoba. Foram construídos modelos de regressão logística múltipla que relacionaram a vacinação à presença de SARS-CoV-2 ou morte por COVID-19, considerando comorbidades e fatores de risco para doenças crônicas e ajustando por sexo e idade. Resultados: Ter recebido uma ou duas doses da vacina na população geral reduziu o risco de adoecimento em 98,8% e 99,3%, respectivamente; e de morrer, em 83% e 96,5%, respectivamente. Naqueles que contraíram COVID-19, a probabilidade de morrer foi reduzida em 57% e 80%, respectivamente. Em relação à probabilidade de morte, o risco aumentou com o aumento da idade e para o sexo masculino, ou com a presença de obesidade, hipertensão arterial ou diabetes mellitus. Conclusão: A vacinação é efetiva e protege contra a possibilidade de contrair COVID-19, desenvolver doença grave ou morrer. A presença de obesidade, hipertensão arterial ou diabetes mellitus, em ordem decrescente, aumenta o risco de morte.
ABSTRACT
La explosión de casos de COVID-19 resaltó el papel fundamental que desempeñan las pruebas de diagnóstico en la toma de decisiones médicas y de salud pública, para contener y mitigar la pandemia de SARS-CoV-2. Este estudio reporta la evaluación e implementación de diferentes tests para la detección molecular de SARS-CoV-2 en la región central de Argentina. Evaluamos 3 kits de RT-PCR en tiempo real (GeneFinder COVID-19 Plus RealAmp Kit, DisCoVery SARS-CoV-2 RT-PCR Detection kit y WGene SARS-CoV-2 RT Detection), 2 métodos de extracción de ácidos nucleicos [MagaBio plus Virus DNA/RNA Purification Kit II (BioFlux), 35-minutes vs. 9-minutes], un reactivo pre-analítico (FlashPrep®) y 2 tests de amplificación isotérmica (Neokit Plus and ELA CHEMSTRIP®). El orden de rendimiento de los 3 kits de RT-PCR en tiempo real evaluados fue el siguiente: DisCoVery>GeneFinderTM>WGene. Los 2 métodos de extracción de RNA mostraron buenos y similares resultados;se seleccionó MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-min debido a su rápido tiempo de procesamiento. El reactivo FlashPrep® mostró excelente resultado para realizar detección directa de RNA. Los ensayos de amplificación isotérmica mostraron valores de sensibilidad y especificidad aceptables (>80%), excepto en muestras con Ct>30. Nuestros resultados muestran kits de RT-PCR en tiempo real óptimos, como así también métodos moleculares alternativos para el diagnóstico de SARS-CoV-2 que resultan aceptables para su uso en contextos adversos, de descentralización y en diferentes escenarios epidemiológicos, para la detección rápida y precisa del SARS-CoV-2.
ABSTRACT
The rocketing number of COVID-19 cases highlighted the critical role that diagnostic tests play in medical and public health decision-making to contain and mitigate the SARS-CoV-2 pandemic. This study reports the evaluation and implementation of different tests for the molecular detection of SARS-CoV-2 in the central region of Argentina. We evaluated 3 real time RT-PCR kits (GeneFinder COVID-19 Plus RealAmp Kit, DisCoVery SARS-CoV-2 RT-PCR Detection Kit and WGene SARS-CoV-2 RT Detection), 2 nucleic acid extraction methods [MagaBio plus Virus DNA/RNA Purification Kit II (BioFlux), 35-min vs. 9-min], a pre-analytical reagent (FlashPrep®) and 2 isothermal amplification tests (Neokit Plus and ELA CHEMSTRIP®). The order according to the best performance of the 3 real-time RT-PCR kits evaluated was: DisCoVery>GeneFinderTM>WGene. The 2 RNA extraction methods showed similar good results: MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-min was selected due to its faster performance. FlashPrep® reagent showed excellent results to perform direct RNA detection. Isothermal amplification assays showed acceptable sensitivity and specificity values (>80%), except in samples with Ct>30. Our data show optimal real time RT-PCR kits and alternative molecular methods for SARS-CoV-2 diagnostic. These alternative assays proved to be acceptable for their use in adverse contexts, decentralization, and different epidemiological scenarios, for rapid and accurate SARS-CoV-2 detection.
ABSTRACT
SARS-CoV-2 variants of concern (VOC) and interest (VOI) present mutations in reference to the original virus, being more transmissible. We implemented a rapid strategy for the screening of SARS-CoV-2 VOC/VOIs using real time RT-PCR and performed monitoring and surveillance of the variants in our region. Consecutive real-time RT-PCRs for detection of the relevant mutations/deletions present in the Spike protein in VOC/VOIs (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems) were implemented. A total of 6,640 SARS-CoV-2 RNA samples (Cts < 30) from infected individuals in Central Argentina during 2021 were analyzed using different algorithms that were gradually adapted to the changing scenarios of local variant circulation. The strategy developed allowed the early detection and the identification of VOC/VOIs that circulated through the year, with a 100% of concordance with the WGS. The analyses of the samples showed introductions of VOCs Alpha and Gamma in February and March 2021, respectively. Gamma showed an exponential increase, with a peak of detection in July (72%), being responsible of the second wave of COVID19 in Argentina. Since VOC Delta entered into the region, it increased gradually, together with VOI Lambda, replacing VOC Gamma, until being the main variant (84.9%) on November. By December, these variants were replaced by the emergent VOC Omicron in a term of 2 weeks, producing the third wave. We report a useful tool for VOC/VOI detection, capable to quickly and cost-effectively monitor currently recognized variants in resource-limited settings, which allowed to track the recent expansion of Omicron in our region, and contributed to the implementation of public health measures to control the disease spread.
ABSTRACT
Seroepidemiological studies help identify the indirect distribution of diseases, detecting serological markers of immunity and demonstrating undiagnosed infections in the general population. The objectives were to estimate the seroprevalence of SARS-CoV-2 antibodies in Córdoba, Argentina, from December 2020 to January 2021 and to identify factors associated with the virus' contagiousness. A population-based cross-sectional observational study was performed in 3,225 individuals over two years of age living in Córdoba city, selected by multiple-stage random sampling proportional to distribution by gender, age group, and socioeconomic status in the city's population. Clinical characteristics, anthropometry, and comorbidities were collected by interview. Qualitative serological testing was performed for detection of SARS-CoV-2 nucleocapsid IgG antibodies (ARCHITECT, Abbott). SARS-CoV-2 seroprevalence was estimated for the total population and by age group, sex, socioeconomic status, and presence of target diseases. Prevalence ratios (PR) were estimated using a log-binomial regression model. SARS-CoV-2 seropositivity was 16.68% (95%CI: 15.41-18.01). Age 2 to 18 years, living in neighborhoods with low socioeconomic status, and obesity increased the odds of seropositivity (PR = 1.50; 95%CI: 1.10-2.04, PR = 1.91; 95%CI: 1.34-2.67 and PR = 1.39; 95%CI: 1.04-1.85). The results indicate that the city of Córdoba displays differential attributes that increase the likelihood of a positive SARS-CoV-2 antibody test. This allows targeting epidemiological surveillance strategies to reduce the spread of the virus.
Los estudios seroepidemiológicos permiten conocer la distribución indirecta de las enfermedades, detectando marcadores séricos de inmunidad y demostrando infecciones no diagnosticadas en la población general. El objetivo fue estimar la seroprevalencia de anticuerpos contra el SARS-CoV-2, en Córdoba, Argentina, entre diciembre de 2020 y enero de 2021, e identificar factores asociados a la contagiosidad del virus. Se realizó un estudio observacional transversal, de base poblacional, con 3.225 individuos mayores de 2 años, residentes en Córdoba Capital, que fueron seleccionados mediante un diseño de muestreo aleatorio en múltiples etapas, proporcional a la distribución por género, franja etaria y nivel socioeconómico de la población de Córdoba. Las características clínicas, antropometría y comorbilidades se recogieron mediante entrevistas. Se realizó un test serológico cualitativo para la detección de anticuerpos IgG antinucleocápside para SARS-CoV-2 (ARCHITECT, Abbott). La seroprevalencia del SARS-CoV-2 se estimó en la población y por franja de edad, sexo, nivel socioeconómico y presencia de las patologías estudiadas. Las razones de prevalencia (RP) se estimaron usando un modelo de regresión log-binomial. La seropositividad para SARS-CoV-2 fue de 16,68% (IC95%: 15,41-18,01). Tener entre 2 y 18 años, residir en barrios con nivel socioeconómico bajo y la presencia de obesidad, aumentaron la oportunidad de seropositividad (RP = 1,50; IC95%: 1,10-2,04, RP = 1,91; IC95%: 1,34-2,67 y RP = 1,39; IC95%: 1,04-1,85). Los resultados indican que en Córdoba Capital existen atributos diferenciales que aumentan la posibilidad de ser seropositivo para SARS-CoV-2. Esto permite dirigir estrategias de vigilancia epidemiológica para reducir la propagación del virus.
Os estudos soroepidemiológicos permitem conhecer a distribuição indireta das doenças, detectando marcadores séricos de imunidade e demonstrando infecções não diagnosticadas na população geral. O objetivo foi estimar a soroprevalência de anticorpos contra o SARS-CoV-2, em Córdoba, Argentina, entre dezembro de 2020 e janeiro de 2021, e identificar fatores associados à contagiosidade do vírus. Um estudo observacional transversal foi realizado, de base populacional, com 3.225 indivíduos maiores de 2 anos, residentes em Córdoba Capital, que foram selecionados por meio de um delineamento de amostragem aleatória em múltiplos estágios, proporcional à distribuição de gênero, a faixa etária e o nível socioeconômico da população de Córdoba. As características clínicas, antropometria e comorbidades foram coletadas por meio de entrevistas. Um teste sorológico qualitativo foi realizado para a detecção de anticorpos IgG anti-nucleocapsídeo para SARS-CoV-2 (ARCHITECT, Abbott). A soroprevalência do SARS-CoV-2 foi estimada na população e por faixa etária, sexo, nível socioeconômico e presença das patologias estudadas. Razões de prevalência (RP) foram estimadas usando um modelo de regressão log-binomial. A soropositividade para SARS-CoV-2 foi de 16,68% (IC95%: 15,41-18,01). Ter entre 2 e 18 años, residir em bairros com nível socioeconômico baixo e a presença de obesidade aumentaram a chance de soropositividade (RP = 1,50; IC95%: 1,10-2,04, RP = 1,91; IC95%: 1,34-2,67 e RP = 1,39; IC95%: 1,04-1,85). Os resultados indicam que em Córdoba Capital existem atributos diferenciais que aumentam a possibilidade de ser soropositivo para SARS-CoV-2. Isso permite direcionar estratégias de vigilância epidemiológica para reduzir a propagação do vírus.
Subject(s)
COVID-19 , Adolescent , Antibodies, Viral , Argentina/epidemiology , Brazil , COVID-19/epidemiology , Child , Child, Preschool , Cross-Sectional Studies , Humans , Immunoglobulin G , SARS-CoV-2 , Seroepidemiologic StudiesABSTRACT
BACKGROUND: The current COVID-19 pandemic has overloaded the diagnostic capacity of laboratories by the gold standard method rRT-PCR. This disease has a high spread rate and almost a quarter of infected individuals never develop symptoms. In this scenario, active surveillance is crucial to stop the virus propagation. METHODS: Between July 2020 and April 2021, 11,580 oropharyngeal swab samples collected in closed and semi-closed institutions were processed for SARS-CoV-2 detection in pools, implementing this strategy for the first time in Córdoba, Argentina. Five-sample pools were constituted before nucleic acid extraction and amplification by rRT-PCR. Comparative analysis of cycle threshold (Ct) values from positive pools and individual samples along with a cost-benefit report of the whole performance of the results was performed. RESULTS: From 2,314 5-sample pools tested, 158 were classified as positive (6.8%), 2,024 as negative (87.5%), and 132 were categorized as indeterminate (5.7%). The Ct value shift due to sample dilution showed an increase in Ct of 2.6±1.53 cycles for N gene and 2.6±1.78 for ORF1ab gene. Overall, 290 pools were disassembled and 1,450 swabs were analyzed individually. This strategy allowed correctly identifying 99.8% of the samples as positive (7.6%) or negative (92.2%), avoiding the execution of 7,806 rRT-PCR reactions which represents a cost saving of 67.5%. CONCLUSION: This study demonstrates the feasibility of pooling samples to increase the number of tests performed, helping to maximize molecular diagnostic resources and reducing the work overload of specialized personnel during active surveillance of the COVID-19 pandemic.
Subject(s)
COVID-19 , Pandemics , COVID-19/diagnosis , COVID-19/epidemiology , Humans , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity , Specimen Handling/methods , Watchful WaitingABSTRACT
Although the nasopharyngeal swab (NPS) is considered the gold standard for the diagnosis of the SARS-CoV-2 infection, the Nasal Mid-Turbinate swab (NMTS) is often used due to its higher tolerance among patients. We compared the diagnostic performance of the NPS and the NMTS for the Panbio™ COVID-19 antigen-detecting rapid diagnostic test (Ag-RDT). Two hundred and forty-three individuals were swabbed three times by healthcare professionals: a NMTS and a NPS specimen for the Ag-RDT and an oropharyngeal swab for real time RT-PCR. Forty-nine participants were RNA-SARS-CoV-2 positive by real time RT-PCR: 45 and 40 were positive by the Ag-RDT with NPS and NMTS, respectively. The overall sensitivity and specificity were 91.8% (95% CI: 83.2-100.0) and 99.5% (95% CI: 98.2-100.0) for Ag-RDT with NPS, and 81.6% (95% CI: 69.8-93.5) and 100.0% (95% CI: 99.7-100.0) for the Ag-RDT with NMTS. The Cohen's kappa index was 0.92 (95% CI: 0.85-0.98). Among asymptomatic individuals, the Ag-RDT with both sampling techniques showed a high sensitivity [100.0% (95% CI: 95.5-100.0) with NPS; 90.9% (95% CI: 69.4-100.0) with NMTS], while the performance of the test decreased in samples with Ct≥ 30 and in patients tested after the first 7 days from symptom onset. Although the NMTS yielded a lower sensitivity compared to NPS, it might be considered a reliable alternative, as it presents greater adherence among patients, enabling scaling of antigen testing strategies, particularly in countries with under-resourced health systems.
Subject(s)
COVID-19 , Antigens, Viral , COVID-19/diagnosis , Humans , SARS-CoV-2 , Sensitivity and Specificity , TurbinatesABSTRACT
BACKGROUND: To analyze the infectious extent of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) in different settings where prevention strategies are critical to limit infection spread, we evaluated SARS-COV-2 viability to guide public health policies regarding isolation criteria and infection control. METHODS: We attempted viral isolation in 82 nasopharyngeal swabs from 72 patients with confirmed SARS-COV-2 infection. Study population was divided into four groups: (i) Patients during the first week of symptoms; (ii) Patients with prolonged positive PCR; (iii) Healthcare workers from a hospital participating of an outbreak investigation, with SARS-COV-2 infection confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) and (iv) Recipients of convalescent immune plasma (CIP).Vero Cl76 cell-line (ATCC CRL-587) was used in assays for virus isolation. Plasma samples of CIP recipients were also tested with plaque-reduction neutralization test. RESULTS: We obtained infectious SARS-COV-2 isolates from 15/84 nasopharyngeal swabs. The virus could not be isolated from upper respiratory tract samples collected 10-day after onset of symptoms (AOS) in patients with mild-moderate disease. CONCLUSION: The knowledge of the extent of SARS-CoV-2 infectivity AOS is relevant for effective prevention measures. This allows to discuss criteria for end isolation despite persistence of positive PCR and improve timing for hospital discharge with consequent availability of critical beds.