Inter-laboratory testing as a strategy for external quality assessment for qualitative detection of SARS-CoV-2 by real-time RT-PCR testing in India

To implement the strategy of test, track and treat to tackle the ongoing COVID-19 pandemic, the number of real-time RT-PCR–based testing laboratories was increased for diagnosis of SARS-CoV-2 in the country. To ensure reliability of the laboratory results, the Indian Council of Medical Research initiated external quality assessment (EQA) by deploying inter-laboratory quality control (ILQC) activity for these laboratories by nominating 34 quality control (QC) laboratories. This report presents the results of this activity for a period of September 2020 till November 2020. A total of 597 laboratories participated in this activity and 86 per cent of these scored ?90 per cent concordance with QC laboratories. This ILQC activity showcased India’s preparedness in quality diagnosis of SARS-CoV-2.

COVID-19 and isolation: Risks and implications in the scenario of new variants

Abstract With the emergence of new variants of SARS-CoV-2, questions about transmissibility, vaccine efficacy, and impact on mortality are important to support decision-making in public health measures. Modifications related to transmissibility combined with the fact that much of the population has already been partially exposed to infection and/or vaccination, have stimulated recommendations to reduce the isolation period for COVID-19. However, these new guidelines have raised questions about their effectiveness in reducing contamination and minimizing impact in work environments. Therefore, a collaborative task force was developed to review the subject in a non-systematic manner, answering questions about SARS-CoV-2 variants, COVID-19 vaccines, isolation/quarantine periods, testing to end the isolation period, and the use of masks as mitigation procedures. Overall, COVID-19 vaccines are effective in preventing severe illness and death but are less effective in preventing infection in the case of the Omicron variant. Any strategy that is adopted to reduce the isolation period should take into consideration the epidemiological situation of the geographical region, individual clinical characteristics, and mask for source control. The use of tests for isolation withdrawal should be evaluated with caution, due to results depending on various conditions and may not be reliable.

Validación y evaluación de una prueba de RT-PCR en tiempo real in house para la detección de SARS-CoV-2 usando un gen específico RdRp y control endógeno GAPDH / Validation and evaluation of RT-PCR real time in house test to detection of SARS-CoV-2 using specific RdRp gene and GAPDH endogen control

RESUMEN Se validó y evaluó un método de RT-PCR en tiempo real usando cebadores y sondas específicas para los genes RdRP de SARS-CoV-2 y GAPDH de humanos; este último fue usado como control endógeno. Se evaluó la especificidad y sensibilidad; además, se evaluó otros parámetros como la robustez, la repetibilidad, reproducibilidad, comparabilidad y el límite de detección. La sensibilidad, especificidad, los valores predictivos positivo y negativo, la robustez, comparabilidad y la repetibilidad-reproducibilidad de la prueba de RT-PCR en tiempo real dúplex fue de 100%, con un límite de detección de 100 copias/µL, de acuerdo con los criterios de aceptación establecidos para validación del protocolo. Esta prueba estandarizada es una buena alternativa para el diagnóstico de COVID-19; además, la prueba fue aplicada de manera exitosa en personas sospechosas de la enfermedad permitiendo controlar el número de falsos negativos.

ABSTRACT The present work validated and evaluated a duplex real-time RT-PCR using specific primers and probes for genes RdRp from SARS-CoV-2 and GAPDH from humans; the latter was used as an endogenous control in all reactions. We evaluated the specificity, the sensitivity, the robustness, the reproducibility, the repeatability, the comparability, and the limit of detection. The predictive positive and negative values (PPV and PNV, respectively) and all the parameters evaluated using our duplex real-time RT-PCR was 100%. The detection limit was 100 copies/µL according to the acceptance criteria established for the validation of this protocol. Our duplex real-time RT-PCR demonstrated to be a good alternative for the diagnosis of COVID-19; in addition, this PCR was used adequately in suspicion of COVID-19, allowing it to control the number of false-negatives.

Origen, características estructurales, medidas de prevención, diagnóstico y fármacos potenciales para prevenir y controlar COVID-19 / Origin, structural characteristics, prevention measures, diagnosis and potential drugs to prevent and COVID-19

El síndrome respiratorio agudo severo coronavirus 2 (SARS-CoV-2) es responsable de la enfermedad denominada COVID-19 (acrónimo del inglés Coronavirus Disease-2019). Esta enfermedad fue detectada inicialmente en la ciudad de Wuhan, China en diciembre de 2019. Las personas contagiadas con COVID-19 presentan síntomas variados, dependiendo de su estado de salud y edad. Los síntomas más comunes son fiebre, tos, mialgia, fatiga, odinofagia y disnea. También se ha observado que en algunos pacientes, la infección es asintomática. Los adultos mayores de 60 años infectados son el grupo de pacientes más susceptibles a desarrollar estados severos de COVID-19 y se presenta comorbilidad en presencia de enfermedades crónicas. Por otra parte, también es importante disponer de pruebas que permitan detectar al SARS-COV-2 y seguir la evolución de COVID-19 de forma rápida, confiable y barata. Para lograr esto, existen pruebas de reacción en cadena de la polimerasa de transcripción inversa en tiempo real (RT-PCR), de amplificación isotérmica de ácido nucleico y de inmunoestimulación enzimática. Actualmente, no existen tratamientos para la prevención del contagio y combatir los efectos del virus en la salud humana. Sin embargo, en el mundo hay grupos de investigación que están realizando pruebas in vitro, in vivo e in silico para encontrar fármacos que sean capaces de prevenir y/o controlar la infección en humanos con SARS-CoV-2. La cloroquina, hidroxicloroquina, remdesivir, interferon-2b y oseltamivir son algunas de las opciones farmacológicas que están siendo evaluadas en pruebas clínicas para la profilaxis de COVID-19. El objetivo de la presente revisión consiste en establecer un marco de referencia de la clasificación taxonómica del SARS-CoV-2 y la relación que guardan con otros coronavirus, así como su estructura y forma de propagarse en el ser humano. También se presentan las características y síntomas de pacientes con COVID-19, los métodos de detección y potenciales tratamientos.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes COVID-19 (Coronavirus disease 2019). This disease was detected in the city of Wuhan in China in December 2019. People infected with COVID-19 shows varying manifestations, depending on their health and age. The most common symptoms are fever, cough, myalgia, fatigue, odynophagia, and dyspnea. Infected adults older 60 years of age are the group of patients most susceptible to severe COVID-19 states and present comor-bidity in the presence of chronic diseases. On the other hand, it is also essential to have tests to detect SARS-COV-2 in people and follow the evolution of COVID-19 quickly, reliably, and cheap. To achieve this, there are real-time reverse transcription pol-ymerase chain reaction (RT-PCR) tests, isothermal nucleic acid amplification, and enzyme immunostimulation. Currently, there are no drug treatments to prevent infection and to combat the virus's effects. However, different research groups that are conduct-ing in vitro, in vivo, and in silico tests to find drugs able to provide an immune response and to control infection in humans with SARS-CoV-2. Chloroquine, hydroxychloroquine, remdesivir, interferon-2b, and oseltamivir are some pharmacological options evaluated in clinical trials for prophylaxis of COVID-19. The purpose of this review is to establish a reference framework for taxonomic classification of SARS-CoV-2 and the relationship they have with other CoVs, as well as their structure and propaga-tion pathways in humans. The characteristics and symptoms presented by patients with COVID-19, the detection methods, and possible treatments are also presented.