Advancements in detection of SARS-CoV-2 infection for confronting COVID-19 pandemics.

As one of the major approaches in combating the COVID-19 pandemics, the availability of specific and reliable assays for the SARS-CoV-2 viral genome and its proteins is essential to identify the infection in suspected populations, make diagnoses in symptomatic or asymptomatic individuals, and determine clearance of the virus after the infection. For these purposes, use of the quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) for detection of the viral nucleic acid remains the most valuable in terms of its specificity, fast turn-around, high-throughput capacity, and reliability. It is critical to update the sequences of primers and probes to ensure the detection of newly emerged variants. Various assays for increased levels of IgG or IgM antibodies are available for detecting ongoing or past infection, vaccination responses, and persistence and for identifying high titers of neutralizing antibodies in recovered individuals. Viral genome sequencing is increasingly used for tracing infectious sources, monitoring mutations, and subtype classification and is less valuable in diagnosis because of its capacity and high cost. Nanopore target sequencing with portable options is available for a quick process for sequencing data. Emerging CRISPR-Cas-based assays, such as SHERLOCK and AIOD-CRISPR, for viral genome detection may offer options for prompt and point-of-care detection. Moreover, aptamer-based probes may be multifaceted for developing portable and high-throughput assays with fluorescent or chemiluminescent probes for viral proteins. In conclusion, assays are available for viral genome and protein detection, and the selection of specific assays depends on the purposes of prevention, diagnosis and pandemic control, or monitoring of vaccination efficacy.

[Prediction of end of lockdown post-peak of cases in first wave of the COVID-19 pandemic in Chile]. / Predicción del fin del confinamiento después del máximo de casos en la primera ola de la pandemia COVID-19 en Chile.

INTRODUCTION: The results of mandatory confinement have been detrimental in several respects. Nonetheless, they have resulted in reducing the number of active cases of COVID-19. Chile has begun the de-escalation and needs to know the best time to end the restrictions. OBJECTIVE: We discuss the best conditions and guarantees for the end of compulsory confinement. METHODS: This study is based on a trend model with prediction estimation. The data of the variables of interest were subjected to linear regression studies to determine the curve that best explained the data. The coefficient of determination, the standard deviation of y in x, and the confidence interval of the observed curve were estimated. The trend curve was chosen in accordance with the regression estimates. OUTCOMES: It was found that all dependent variables tended to decrease over time in a quadratic fashion, except for the new cases variable. In general, the R2 and MAPE estimates are satisfactory, except for the variable number of PCR tests per day. CONCLUSIONS: Gradual and cautious steps should be taken before ending mandatory confinement. In the current de-escalator, daily PCR tests should be increased, maintaining vigilance on indicators of incidence, prevalence, and positivity of PCR tests. Evidence suggests with some degree of confidence that mandatory confinement could be safely lifted as of August 30, 2020. Long-term preparations must be made to contain future waves of new cases.

INTRODUCCIÓN: Los resultados del confinamiento obligatorio han sido perjudiciales en varios aspectos. No obstante, han surtido efecto en lograr el descenso de casos activos de COVID-19. Chile ha comenzado la desescalada y precisa conocer el mejor momento para poner fin a las restricciones. OBJETIVOS: Discutir las mejores condiciones y garantías para el fin del confinamiento obligatorio sobre la base de los casos nuevos, casos activos y positividad de exámenes de reacción en cadena de la polimerasa. MÉTODOS: Estudio basado en un modelo de tendencia con estimación de predicciones. Los datos de las variables de interés fueron sometidas a estudios de regresión lineal, con el objeto de determinar la curva que mejor explicaba los datos. Se estimó el coeficiente de determinación, la desviación estándar de y en x y el intervalo de confianza de la curva observada. Posteriormente, fue escogida la curva de tendencia en concordancia con las estimaciones de regresión. RESULTADOS: Se encontró que todas las variables dependientes tendían a disminuir con el tiempo de forma cuadrática, con excepción de la variable casos nuevos. En general, las estimaciones de coeficiente de determinación (R²) y error porcentual absoluto medio son satisfactorias, con excepción de la variable: número de exámenes de reacción en cadena de la polimerasa por día. CONCLUSIONES: Se deben tomar medidas graduales y cautelosas antes de poner fin al confinamiento obligatorio. En la actual desescalada, se deben aumentar los exámenes de reacción en cadena de la polimerasa diarios y mantener vigilancia en los indicadores de incidencia, prevalencia y positividad de dichos exámenes. La evidencia sugiere con cierto grado de confiabilidad que el confinamiento obligatorio podría levantarse de forma segura a contar del día 30 de agosto de 2020. Se deben hacer preparativos a largo plazo en contención de las futuras olas, es decir, una nueva alza de casos nuevos y activos luego del descenso.