RT-qPCR-based pool testing for the diagnosis of COVID-19

ABSTRACT This study proposes a strategy for large-scale testing among a large number of people for the early diagnosis of COVID-19 to elucidate the epidemiological situation. Pool testing involves the analysis of pooled samples. This study aimed to discuss a reverse transcription technique followed by quantitative real-time polymerase chain reaction using pool testing to detect SARS-CoV-2 in nasopharyngeal swab samples. The study proposes an innovative diagnostic strategy that contributes to resource optimization, cost reduction, and improved agility of feedback from results.

Autocoleta de swab nasofaríngeo e teste molecular em pool testing como estratégias para detecção de coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2): viabilidade em estudantes de medicina da Universidade Federal de Minas Gerais, 2021 / Autocolección de hiopados nasofaríngeos y pruebas moleculares en pool testing como estrategias para la detección del Coronavirus Síndrome Respiratorio Agudo Severo 2 (SARS-CoV-2): viabilidad en estudiantes de medicina de la Universidad Federal de Minas Gerais, Brasil, 2021 / Self-collected nasopharyngeal swab and molecular test using pool testing as strategies to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): feasibility in medical students at the Universidade Federal de Minas Gerais, Brazil, 2021

Objetivo: Demonstrar a viabilidade da utilização combinada da autocoleta de swab nasofaríngeo e pool testing para detecção do SARS-CoV-2 em inquéritos epidemiológicos. Métodos: A experiência envolveu amostra de 154 estudantes da Universidade Federal de Minas Gerais, que realizaram a autocoleta do swab nasofaríngeo em cabines individuais e sem supervisão. O teste molecular foi realizado utilizando-se a técnica de pool testing. Resultados: A obtenção de amostras durou cerca de 5 minutos por pessoa. Realizou-se análise para detecção de RNA endógeno em 40 amostras e os resultados indicaram que não houve falhas decorrentes da autocoleta. Nenhum dos pools detectou presença de RNA viral. O custo da realização do teste molecular (RT-PCR) por pool testing com amostras obtidas por autocoleta foi cerca de dez vezes menor do que nos métodos habituais. Conclusão: As estratégias investigadas mostraram-se economicamente viáveis e válidas para a pesquisa de SARS-CoV-2 em inquéritos epidemiológicos.

Objetivo: Demostrar la viabilidad del uso combinado de la auto recolección de swabs nasofaríngeos y tests por agrupamiento (pool testing) para la detección del SARS-CoV-2 en encuestas epidemiológicas. Métodos: La prueba involucró a una muestra de 154 estudiantes de la Universidade Federal de Minas Gerais, quienes realizaron e autorecolectado del hisopo nasofaríngeo en cabinas individuales sin supervisión. La prueba molecular se realizó utilizando la técnica de prueba de grupo. Resultados: La obtención de muestras duró unos 5 minutos por persona. Se realizó un análisis para detectar ARN endógeno en 40 muestras y los resultados indicaron que no hubo fallas derivadas de la autorecolección. Ninguno de los grupos detectó la presencia de ARN viral. El costo de realizar una prueba molecular (RT-PCR) por pool con muestras obtenidas por auto-recolección fue aproximadamente 10 veces menor que con los métodos habituales. Conclusión: Las estrategias investigadas demostraron ser económicamente viables y válidas para la investigación del SARS-CoV-2 en encuestas epidemiológicas.

Objective: To show the feasibility of the combined use of self-collected nasopharyngeal swab and pool testing to detect SARS-CoV-2 in epidemiological surveys. Methods: This experience included a sample of 154 students at the Universidade Federal de Minas Gerais, who performed self-collected nasopharyngeal swab in individual cabins and without supervision. The molecular test was performed using the pool testing technique. Results: It took each person 5 minutes to collect the sample. An analysis was performed to detect endogenous RNA in 40 samples. The results showed that there were no failures resulting from self-collection. None of the pools detected the presence of viral RNA. The cost of molecular testing (RT-PCR), by pool testing, with samples obtained by self-collection was about ten times lower than the usual methods. Conclusion: The strategies that were investigated proved to be economically feasible and valid for the research on SARS-CoV-2 in epidemiological surveys.

Multi-Epitope Protein as a Tool of Serological Diagnostic Development for HTLV-1 and HTLV-2 Infections

A multi-epitope protein expressed in a prokaryotic system, including epitopes of Env, Gag, and Tax proteins of both HTLV-1 and HTLV-2 was characterized for HTLV-1/2 serological screening. This tool can contribute to support the implementation of public policies to reduce HTLV-1/2 transmission in Brazil, the country with the highest absolute numbers of HTLV-1/2 infected individuals. The chimeric protein was tested in EIA using serum/plasma of HTLV-infected individuals and non-infected ones from four Brazilian states, including the North and Northeast regions (that present high prevalence of HTLV-1/2) and Southeast region (that presents intermediate prevalence rates) depicting different epidemiological context of HTLV-1/2 infection in our country. We enrolled samples from Pará (n = 114), Maranhão (n = 153), Minas Gerais (n = 225) and São Paulo (n = 59) states; they are from blood donors' candidates (Pará and Minas Gerais), pregnant women (Maranhão) and HIV+/high risk for sexually transmitted infection (STI; São Paulo). Among the HTLV-1/2 positive sera, there were co-infections with viral (HTLV-1 + HTLV-2, HIV, HCV, and HBV), bacterial (Treponema pallidum) and parasitic (Trypanosoma cruzi, Schistosma mansoni, Strongyloides stercoralis, Entamoeba coli, E. histolytica, and Endolimax nana) pathogens related to HTLV-1/2 co-morbidities that can contribute to inconclusive diagnostic results. Sera positive for HIV were included among the HTLV-1/2 negative samples. Considering both HTLV-1 and HTLV-2-infected samples from all states and different groups (blood donor candidates, pregnant women, and individuals with high risk for STI), mono or co-infected and HTLV-/HIV+, the test specificity ranged from 90.09 to 95.19% and the sensitivity from 82.41 to 92.36% with high accuracy (ROC AUC = 0.9552). Thismulti-epitope protein showed great potential to be used in serological screening of HTLV-1 and HTLV-2 in different platforms, even taking into account the great regional variation and different profile of HTLV-1 and HTLV-2 mono or co-infected individuals. (AU)

Detection of SARS-CoV-2 through pool testing for COVID-19: an integrative review

Abstract INTRODUCTION: The pool testing technique optimizes the number of tests performed and reduces the delivery time of results, which is an interesting strategy for the health crisis caused by the COVID-19 pandemic. This integrative review investigated studies in which pool testing was carried out for epidemiological or screening purposes to analyze its clinical or cost effectiveness and assessed the applicability of this method in high-, middle-, and low-income countries. METHODS: This integrative review used primary studies published in the MEDLINE, EMBASE, Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS), and Cochrane Library databases. RESULTS: A total of 435 studies were identified: 35.3% were carried out in Asia, 29.4% in Europe, 29.4% in North America, and 5.9% in Oceania. CONCLUSIONS: This review suggests that pool testing in the general population may be a useful surveillance strategy to detect new variants of SARS-CoV-2 and to evaluate the period of immunogenicity and global immunity from vaccines.

Genotypic characterization of psittacid herpesvirus isolates from Brazil

Abstract Thirty-six isolates of psittacid herpesvirus (PsHV), obtained from 12 different species of psittacids in Brazil, were genotypically characterized by restriction fragment length polymorphism (RFLP) analysis and PCR amplification. RFLP analysis with the PstI enzyme revealed four distinct restriction patterns (A1, X, W and Y), of which only A1 (corresponding to PsHV-1) had previously been described. To study PCR amplification patterns, six pairs of primers were used. Using this method, six variants were identified, of which, variants 10, 8, and 9 (in this order) were most prevalent, followed by variants 1, 4, and 5. It was not possible to correlate the PCR and RFLP patterns. Twenty-nine of the 36 isolates were shown to contain a 419 bp fragment of the UL16 gene, displaying high similarity to the PsHV-1 sequences available in GenBank. Comparison of the results with the literature data suggests that the 36 Brazilian isolates from this study belong to genotype 1 and serotype 1.

Clinical signs, diagnosis, and case reports of Vaccinia virus infections

Vaccinia virus is responsible for a zoonosis that usually affects cattle and human beings in Brazil. The initial clinical signs of the infection are focal red skin areas, fever, and general symptoms similar to those of a cold. Then, pustules and ulcerated lesions surrounded by edema and erythema follow, as well as local lymphadenopathy that can last for weeks. Cure and healing of the lesions occur over several weeks, leaving a typical scar in the skin of people and animals affected. The infection definitive diagnosis is made through morphological characterization of the virus by use of electron microscopy, followed by PCR for specific viral genes. Since 1963, circulating orthopoxviruses in infectious outbreaks in several regions of Brazil have been reported. Later, the etiological agent of those infections was characterized as samples of Vaccinia virus. In addition, the widespread use of those viruses in research laboratories and mass vaccination of militaries have contributed to increase the cases of those infections worldwide. Thus, several epidemiological and clinical studies are required, as well as studies of viral immunology, public health, and economic impact, because little is known about those Vaccinia virus outbreaks in Brazil.

Self-collection of nasopharyngeal swab and molecular test in pool testing as strategies for detecting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): feasibility in medical students at the Universidade Federal de Minas Gerais, 2021 / Autocollección de swabs nasofaríngeos y pruebas moleculares en pool testing como estrategias para la detección del Coronavirus Síndrome Respiratorio Agudo Severo 2 (SARS-CoV-2): viabilidad en estudiantes de medicina de la Universidade Federal de Minas Gerais, 2021 / Autocoleta de swab nasofaríngeo e teste molecular em pool testing como estratégias para detecção de coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2): viabilidade em estudantes de medicina da Universidade Federal de Minas Gerais, 2021

Objective: To show the feasibility of using combined nasopharyngeal swab auto-collection and pool testing to detect SARS-CoV-2 in epidemiological surveys. Methods: The study involved a sample of 154 students from the Universidade Federal de Minas Gerais, who performed the self-collection of the nasopharyngeal swab in individual booths without supervision. Molecular testing was performed using the pool testing technique. Results: Obtaining samples lasted about 5 minutes each. Analysis 6 was performed to detect endogenous RNA in 40 samples, and the results indicated that no failures resulted from self-collection. None of the pools detected the presence of viral RNA. The cost of performing the molecular test (RT-PCR) by pool testing with samples obtained by self-collection was about 10 times lower than with the usual methods. Conclusion: The investigated strategies showed to be economically feasible and valid for the research of SARS-CoV-2 in epidemiological surveys.

Objetivo: Demostrar la viabilidad de utilizar el uso combinado de la autocollección de swabs nasofaríngeos y pool testing para la detección del SARS-CoV2 en encuestas epidemiológicas. Métodos: El estudio involucró a una muestra de 154 estudiantes de la Universidade Federal de Minas Gerais, quienes realizaron la autocolección del hisopo nasofaríngeo en cabinas individuales sin supervision. La prueba molecular se realizó utilizando la técnica de prueba de grupo. Resultados: La obtención de muestras duró unos 5 minutos por persona. Se realizó un análisis para detectar RNA endógeno en 40 muestras y los resultados indicaron que no hubo fallas derivadas de la autocolección. Ninguno de los grupos detectó la presencia de RNA viral. El costo de realizar una prueba molecular (RT-PCR) por pool con muestras obtenidas por auto-recolección fue aproximadamente 10 veces menor que con los métodos habituales. Conclusión: Las estrategias investigadas demonstraram ser económicamente viables y válidas para la investigación del SARS-CoV-2 en encuestas epidemiológicas.

Objetivo: Demonstrar a viabilidade da utilização combinada da autocoleta de swab nasofaríngeo e pool testing para detecção do SARS-CoV-2 em inquéritos epidemiológicos. Métodos: O estudo envolveu amostra de 154 estudantes da Universidade Federal de Minas Gerais, que realizaram a autocoleta do swab nasofaríngeo em cabines individuais e sem supervisão. O teste molecular foi realizado utilizando-se a técnica de pool testing. Resultados: A obtenção de amostras durou cerca de 5 minutos por pessoa. Realizou-se análise para detecção de RNA endógeno em 40 amostras e os resultados indicaram que não houve falhas decorrentes da autocoleta. Nenhum dos pools detectou presença de RNA viral. O custo da realização do teste molecular (RT-PCR) por pool testing com amostras obtidas por autocoleta foi cerca de dez vezes menor do que nos métodos habituais. Conclusão: As estratégias investigadas mostraram-se economicamente viáveis e válidas para a pesquisa de SARS-CoV-2 em inquéritos epidemiológicos.