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Widely available and reliable testing for SARS-CoV-2 is essential for the public health response to the COVID-19 pandemic. We estimated the diagnostic performance of reverse transcription PCR (RT-PCR) performed on saliva and the SD Biosensor STANDARD Q antigen test performed on nasopharyngeal swab compared to the reference standard, nasopharyngeal swab (NP) RT-PCR. We enrolled participants living and/or seeking care in health facilities in North Lima, Peru from November 2020 to January 2021. Consenting participants underwent same-day RT-PCR on both saliva and nasopharyngeal swab specimens, antigen testing on a nasopharyngeal swab specimen, pulse oximetry, and standardized symptom assessment. We calculated sensitivity, specificity, and predictive values for the nasopharyngeal antigen and saliva RT-PCR compared to nasopharyngeal RT-PCR. Of 896 participants analyzed, 567 (63.3%) had acute signs/symptoms of COVID-19. The overall sensitivity and specificity of saliva RT-PCR were 85.8% and 98.1%, respectively. Among participants with and without acute signs/symptoms of COVID-19, saliva sensitivity was 87.3% and 37.5%, respectively. Saliva sensitivity was 97.4% and 56.0% among participants with cycle threshold (CT) values of ≤30 and >30 on nasopharyngeal RT-PCR, respectively. The overall sensitivity and specificity of nasopharyngeal antigen were 73.2% and 99.4%, respectively. The sensitivity of the nasopharyngeal antigen test was 75.1% and 12.5% among participants with and without acute signs/symptoms of COVID-19, and 91.2% and 26.7% among participants with CT values of ≤30 and >30 on nasopharyngeal RT-PCR, respectively. Saliva RT-PCR achieved the WHO-recommended threshold of >80% for sensitivity for the detection of SARS-CoV-2, while the SD Biosensor nasopharyngeal antigen test did not. IMPORTANCE In this diagnostic validation study of 896 participants in Peru, saliva reverse transcription PCR (RT-PCR) had >80% sensitivity for the detection of SARS-CoV-2 among all-comers and symptomatic individuals, while the SD Biosensor STANDARD Q antigen test performed on nasopharyngeal swab had <80% sensitivity, except for participants whose same-day nasopharyngeal RT-PCR results showed cycle threshold values of <30, consistent with a high viral load in the nasopharynx. The specificity was high for both tests. Our results demonstrate that saliva sampling could serve as an alternative noninvasive technique for RT-PCR diagnosis of SARS-CoV-2. The role of nasopharyngeal antigen testing is more limited; when community transmission is low, it may be used for mass screenings among asymptomatic individuals with high testing frequency. Among symptomatic individuals, the nasopharyngeal antigen test may be relied upon for 4 to 8 days after symptom onset, or in those likely to have high viral load, whereupon it showed >80% sensitivity.
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COVID-19 , SARS-CoV-2 , COVID-19/diagnóstico , Teste para COVID-19 , Humanos , Nasofaringe , Pandemias , Peru/epidemiologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Transcrição Reversa , SARS-CoV-2/genética , Saliva , Manejo de EspécimesRESUMO
Abstract The World Health Organization has declared the widespread spread of SARS-CoV-2 and its associated disease (COVID-19) a public health emergency. The standard gold test for detecting the virus is the RT-PCR, performed from nasopharyngeal swab (NPS) samples. However, this test may be uncomfortable for the patient and requires specific training and attire from the health professional responsible for collecting the sample. Therefore, the search for alternative ways to collect samples that may be used in the diagnosis of COVID-19 is relevant. This study aimed to compare the results obtained from NPS and saliva samples. NPS and saliva samples were collected from 189 symptomatic outpatients suspected of COVID-19, who came to Piquet Carneiro Polyclinic. RNA extraction was performed using the Bio-Gene DNA/RNA Viral Extraction kit (Bioclin®). Real-time reverse transcriptase-polymerase chain reaction (RT-PCR) reactions used the Molecular SARS-CoV-2 (E / RP) kit (Bio-Manguinhos). The results indicated that 142 showed a non-detectable result (ND), while 47 showed a detectable result (D). Among the 142 "ND", 137 (94.4%) saliva samples obtained the same result, while 5 samples (3.4%) were "D". Among the 47 "D" swab samples, 35 (74.4%) showed the same result in the saliva samples. The sensitivity of the saliva test was 0.74 and the specificity was 0.97. The positive predictive value was 0.88 while the negative predictive value was 0.92. The results showed that detection of Sars-CoV-2 using saliva samples showed high sensitivity and specificity compared to nasopharyngeal swabs.
Resumo A Organização Mundial da Saúde declarou a disseminação generalizada do SARS-CoV-2 e sua doença associada (COVID-19) uma emergência de saúde pública. O teste padrão ouro para detecção do vírus é o RT-PCR, realizado a partir de amostras de swab nasofaríngeo (NPS). No entanto, esse exame pode ser desconfortável para o paciente e requer treinamento específico e vestimenta do profissional de saúde responsável pela coleta da amostra. Portanto, a busca por formas alternativas de coleta de amostras que possam ser utilizadas no diagnóstico de COVID-19 é relevante. O objetivo deste estudo foi comparar os resultados obtidos em amostras de NPS e saliva. Amostras de NPS e saliva foram coletadas de 189 pacientes ambulatoriais sintomáticos com suspeita de COVID-19, que procuraram a Policlínica Piquet Carneiro. A extração de RNA foi realizada com o kit Bio-Gene DNA / RNA Viral Extraction (Bioclin®) e as reações em tempo real da reação em cadeia da polimerase-transcriptase reversa (RT-PCR) usaram o kit Molecular SARS-CoV-2 (E / RP) (Bio-Manguinhos). Os resultados indicaram que 142 apresentaram resultado não detectável (ND), enquanto 47 apresentaram resultado detectável (D). Entre os 142 "ND", 137 (94,4%) amostras de saliva obtiveram o mesmo resultado, enquanto 5 amostras (3,4%) foram "D". Dentre as 47 amostras de swab "D", 35 (74,4%) apresentaram o mesmo resultado nas amostras de saliva. A sensibilidade do teste de saliva foi de 0,74 e a especificidade foi de 0,97. O valor preditivo positivo foi de 0,88, enquanto o valor preditivo negativo foi de 0,92. Os resultados mostraram que a detecção de Sars-CoV-2 em amostras de saliva apresentou alta sensibilidade e especificidade quando comparada com swabs nasofaríngeos.
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ABSTRACT Introduction: The detection of SARS-CoV-2 genetic material from nasopharyngeal swab samples by RT-PCR is the most specific and sensitive way to test suspected cases. However, factors such as the sampling process, the type of hyssop used, and the anatomical area from which the sample is collected can distort the result and cause false negatives. Objective: To evaluate the reliability of CNUERO hyssops for sample collection for the SARS-CoV-2 diagnosis versus IMPROSWAB hyssops. Material and Methods: To study the reliability of hyssops developed in Cuba for swabbing for the COVID-19 diagnosis by comparing them to other hyssops successfully used for this task, 2 swabbing samples were obtained from each patient (136). One of these two samples was taken using the hyssops made in Cuba, while the other was taken using another hyssop imported from Germany. The positive detections obtained with the use of both hyssops were compared using the Fisher's exact test. The result of the detection of each hyssop was evaluated and compared using the ROC curve. Results: The use of CNEURO hyssops allowed the detection of 45 out of 59 positive cases, while IMPROSAWAB hyssops detected 52 out of 59 true positive cases. There were no significant differences between positive cases detected with the use of each hyssop. The sensitivity of sample detection using CNEURO hyssops was 76,3 % while the one using IMPROSWAB hyssops was 88,1 %. Hence, there are no significant differences in the detection of cases using these two hyssops. Conclusion: CNEURO hyssops are safe and reliable to be used to take nasopharyngeal samples from COVID-19 patients.
RESUMEN Introducción: La detección de material genético del SARS-CoV-2 a partir de muestras de hisopos nasofaríngeos mediante RT-PCR es la forma más específica y sensible de analizar los casos sospechosos. Sin embargo, factores como el proceso de toma de muestra, el tipo de hisopo y el área anatómica de la que se extrae la muestra, pueden distorsionar el resultado y provocar falsos negativos. Objetivo: Evaluar la confiabilidad de hisopos CNUERO para la recolección de muestras en el diagnóstico de SARS-CoV-2 versus hisopos IMPROSWAB. Material y Métodos: Se obtuvieron 2 muestras de exudado de cada paciente (136). Una de estas dos muestras se tomó con hisopos CNEURO, mientras que la otra se tomó con el hisopo IMPROSWAB. Las detecciones positivas entre ambos hisopos se compararon mediante la prueba exacta de Fisher. El resultado de la detección de cada hisopo se evaluó y comparó utilizando la curva ROC. Resultados: El uso de hisopos CNEURO permitió detectar 45 de 59 casos positivos, mientras que los hisopos IMPROSAWAB detectaron 52 de 59 casos verdaderos positivos. Se detectaron diferencias no significativas entre los casos positivos detectados entre hisopos. La sensibilidad de detección de muestras utilizando hisopos CNEURO fue del 76,3 % y del 88,1 % cuando se utilizaron hisopos IMPROSWAB. Por tanto, no se detectaron diferencias significativas en la detección de casos utilizando estos dos hisopos. Conclusión: Los hisopos CNEURO son seguros y fiables para su uso en la toma de muestras nasofaríngeas de pacientes con COVID-19.
Assuntos
HumanosRESUMO
This study reported the case of a healthy male in his 40s who presented with a 3-month history of frontal headache and post-nasal drip, which did not improve with oral antibiotics. One month prior to the onset of the symptoms, he underwent a nasopharyngeal swab testing for SARS-CoV-2 (which yielded a negative result) for a history of malaise and cough. The patient claimed that the swab insertion into the nasal cavity was particularly painful on the left side. Sinus computed tomography (CT) scan showed deformity of the left middle nasal turbinate with occlusion of the osteomeatal complex, resulting in ethmoid silent sinus syndrome. This study makes a significant contribution to the literature because nasopharyngeal, midturbinate and anterior nasal swabs have been recommended as initial diagnostic specimen collection methods by the US Centers for Disease Control and Prevention (CDC) for the coronavirus disease 2019. These methods require introducing an instrument into the nasal cavity, potentially leading to adverse effects due to the delicate and complex nasal anatomy. However, complications related to swab testing for respiratory pathogens have not yet been fully discussed in the literature.
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COVID-19 , Testes Diagnósticos de Rotina , Humanos , Masculino , Nasofaringe , SARS-CoV-2 , Manejo de EspécimesRESUMO
Objetivos: El muestreo de hisopado nasofaríngeo para la detección de SARS CoV-2 es un método estándar para el diagnóstico de COVID-19, pero su recolección generalmente ocasiona incomodidad en el paciente y expone a un mayor riesgo al personal de salud. La muestra de saliva parece ser una buena alternativa con respecto a las muestras de hisopado nasofaringeo, no es invasiva, reduce el riesgo de contaminación del personal sanitario y permite la auto recolección. Este estudio tiene por objetivo comparar la capacidad de detectar al SARS CoV-2 por RT-PCR en un mismo paciente, a partir de muestras de saliva y de hisopado nasofaríngeo para analizar la concordancia de los resultados obtenidos entre ambas muestras. Métodos: Treinta muestras de saliva y de HNF de pacientes con síntomas de COVID-19 que ingresaron al servicio de emergencia del Hospital Clínico Viedma fueron tomadas en paralelo. Ambas muestras fueron analizadas por RT-PCR para la detección de SARS CoV-2. La concordancia de resultados fue calculada por el coeficiente de kappa de Cohen. Resultados: Nuestros resultados muestran que existe una buena concordancia (Índice Kappa 0,730; IC del 95%: 0,486 - 0,974) entre los dos tipos de muestras analizadas. Conclusiones: La saliva parece ser una muestra fiable y efectiva para la detección del SARS CoV-2.
Objectives: Nasopharyngeal swab sampling for the detection of SARS-CoV-2 is a standard method for the diagnosis of COVID-19, but its collection usually causes discomfort in the patient and exposes healthcare workers to a higher risk. Saliva seems to be a good alternative to nasopharyngeal swabs, as it is non-invasive, reduces the risk of contamination of healthcare workers, and allows self-collection. This study aims to compare the ability to detect SARS-CoV-2 by RT-PCR in the same patient using saliva and nasopharyngeal swab samples to analyze the concordance of the results obtained between the two samples. Methods: Thirty saliva and nasopharyngeal swab samples from patients with COVID-19 symptoms who were admitted to the emergency department of the Viedma Clinical Hospital were taken in parallel. Both samples were analyzed by RT-PCR for the detection of SARS-CoV-2. The concordance of results was calculated using the Cohen's Kappa coefficient. Results: Our results show that there is good concordance (Kappa index 0.730; 95% CI: 0.486-0.974) between the two types of samples analyzed. Conclusions: Saliva seems to be a reliable and effective sample for the detection of SARS-CoV-2.
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Introdução: Atualmente, estamos enfrentando uma pandemia causada pela síndrome respiratória aguda grave coronavirus 2 (SARS-CoV-2) que é um vírus de RNA de uma única cadeia pertencente à família de coronavírus. O método mais utilizado para confirmar o diagnóstico da infecção pelo SARSCoV-2 é através de testes moleculares usando rRT-PCR (reações em cadeia de transcrição reversa em tempo real polimerase) para detectar o RNA viral. A maneira usual de colher amostras virais é através de cotonetes nasofaríngeos. Uma das formas efetivas de controlar a transmissão dessa doença é o diagnóstico precoce e isolamento dos pacientes infectados. Nesse relato abordaremos dois casos de complicações com swab nasal na coleta de rRT-PCR para COVID-19, atendidos em um pronto socorro de otorrinolaringologia. Relato de caso: O primeiro foi de uma paciente que teve a haste do cotonete quebrada em sua fossa nasal esquerda, necessitando de remoção do corpo estranho com por nasoendoscopia. Enquanto o segundo foi de uma paciente que apresentou epistaxe grave devido trauma do cotonete em esporão no septo nasal esquerdo, necessitando de abordagem em centro cirúrgico. Conclusão: É importante ressaltar que mesmo sujeito a complicações possivelmente graves, a realização de testes RT-PCR com cotonete nasal é o padrão ouro no diagnóstico de COVID-19. É muito importante advertir que o profissional treinado ao suspeitar de algum acidente durante o exame deve, precocemente, solicitar avaliação do especialista competente para abordagem adequada. [au]
Background: We are currently facing a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is a single-stranded RNA virus belonging to the coronavirus family. The most widely used method to confirm the diagnosis of SARSCoV-2 infection is through molecular tests using rRT-PCR (real-time reverse transcription polymerase chain reaction) to detect viral RNA. The usual way to collect viral samples is through nasopharyngeal swabs. One of the effective ways to control the transmission of this disease is the early diagnosis and isolation of infected patients. In this report, we will approach two cases of complications with nasal swabs in the collection of rRT-PCR for COVID-19, treated in an otolaryngology emergency room. Case Report: The first was from a patient who had the swab rod broken in her left nasal cavity, requiring removal of the foreign body through nasoendoscopy. While the second was from a patient who had severe epistaxis due to trauma of the spur swab in the left nasal septum, requiring an approach in the surgery center. Conclusion: It is important to emphasize that, even subject to possibly serious complications, the performance of RT-PCR tests with a nasal swab is the gold standard in the diagnosis of COVID-19. It is very important to enhance that the trained professional, when suspecting an accident during the exam, should, early on, request an evaluation from the competent specialist for an adequate approach. [au]
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Resumen Introducción: La pandemia de COVID-19 ha afectado a millones de personas en todo el mundo. La identificación de sujetos infectados ha sido importante para el control. Objetivo: Evaluar el rendimiento de una reacción de polimerasa en cadena (RPC) cuantitativa en tiempo real (en inglés: RT-qPCR) para SARS-CoV-2, utilizando saliva como matriz en comparación con un hisopado nasofaríngeo (HNF). Metodología: Se reclutaron adultos en atención ambulatoria, la mayoría sintomáticos. Fueron estudiadas 530 muestras pareadas de saliva e HNF con RT-qPCR. Resultados: Fueron positivas 59 muestras de HNF y 54 de saliva. La sensibilidad con saliva fue 91%, especificidad 100%, el valor predictor positivo (VPP) 100%, valor predictor negativo (VPN) 98%. El índice Kappa fue de 0,95 y LR-0,08. En promedio, el umbral de ciclo (en inglés cycle threshold-CT) de la saliva fue 3,99 puntos más alto que los de HNF (p < 0,0001) mostrando que la carga viral (CV) es menor en saliva. La carga viral en ambas disminuyó con el tiempo después del inicio de los síntomas. El muestreo de saliva fue preferido por los sujetos en lugar de HNF. Conclusión: Este estudio demuestra que la RPC para SARS-CoV-2 utilizando saliva, es adecuada para el diagnóstico de COVID-19 en adultos ambulatorios, especialmente en la etapa temprana de los síntomas.
Abstract Background: The COVID-19 pandemic has affected millions of people around the world. Part of control strategies is testing a large proportion of the population to identify and isolate the infected subjects. Aim: To evaluate the SARS-CoV-2 detection by the performance of a reverse transcription and quantitative polymerase chain reaction (RT-qPCR) against SARS-CoV-2, using saliva as a matrix compared to a nasopharyngeal swab (NPS) to simplify obtaining a diagnostic sample. Methods: Adults in outpatient care were recruited, 95% of them symptomatic. We studied 530 paired saliva and NPS samples by SARS-CoV-2 RT-qPCR. Results: Fifty-nine individuals tested positive in NPS and 54 in saliva samples. Sensitivity for saliva sample was 91%, specificity 100%, positive predictive value (PPV) 100%, negative predictive value (NPV) 98%. The Kappa index was 0.95 and LR-0.08. On average, the cycle threshold (CT) of saliva was 3.99 points higher than those of NPS (p < 0.0001) showing that viral load (VL) is lower in saliva than in NPS. Viral load in both decreased over the time after onset of symptoms. Saliva sampling was preferred by subjects instead of NPS. Conclusion: This study demonstrates that SARS-CoV-2 RT-qPCR using saliva, even with lower VL, is suitable for the diagnosis of COVID-19 in outpatient adults, especially at early stage of symptoms.
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BACKGROUND: Healthcare workers are at increased risk of SARS-CoV-2 infection. The positivity rates in hospitals that do not receive patients with COVID-19, such as the National Cancer Institute (INCan) in Mexico, and the associated factors are unknown. OBJECTIVE: To assess the incidence and factors associated with SARS-CoV-2 infection in health workers at INCan. METHODS: A cohort study of 531 workers who were followed for 6 months. RT-PCR analysis of saliva and nasopharyngeal swab samples were used in the baseline and to confirm cases during follow-up The incidence rate ratio was calculated according to the measured characteristics and the associated factors were calculated using logistic regression models. RESULTS: Out of 531 workers, 9.6% tested positive for SARS-CoV-2, Being male (RR: 2.07, 95% CI: 1.1-3.8, P = .02), performing administrative tasks (RR: 1.99, 95% CI: 1.0-3.9, P = .04), and having relatives also working at INCan (RR: 3.7, 95% CI: 1.4-9.5, P < .01) were associated with higher positivity rates. DISCUSSION: Incidence of positive cases in health workers were similar to that reported in non-COVID hospitals from other countries. CONCLUSIONS: Even though active surveillance helped to detect a significant number of asymptomatic infections, it is still necessary to reinforce preventive measures in non-medical staff to prevent nosocomial transmission.
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COVID-19 , Neoplasias , Estudos de Coortes , Pessoal de Saúde , Hospitais , Humanos , Masculino , México/epidemiologia , Neoplasias/epidemiologia , Encaminhamento e Consulta , SARS-CoV-2RESUMO
Introduction: The SARS-CoV-2 virus is a positive-strand RNA virus. The virus can also be detected in many different specimens as throat swabs, nasal swabs, sputum, saliva, blood, etc. Objective: The aim of this paper is to compare the reliability of different types of specimen collection, saliva and swabs samples for the detection of SARS-CoV-2. Material and Methods: A sample of 22 COVID-19 positive patients was selected. Paired samples from saliva, nasopharyngeal, oropharyngeal and nasopharyngeal + oropharyngeal swabs were collected on the 7th day after diagnosis. The hyssops and medium employed was IMPROSWAB and IMPROVIRAL NAT Medium, Germany. The sample evaluation was conducted through RT-PCR. The results were compared using Fisher's exact test and ROC curve. The gold standard proposed in this paper was the nasopharyngeal + oropharyngeal swabs specimen. Results: The gold standard method detected 10 true positive cases, of which oropharyngeal swabs, nasopharyngeal swabs and saliva only detected three positive cases. Significant differences (Fisher's exact test p = 0.003) were detected in the comparison between saliva and the gold standart proposed. The ROC curve analysis showed that saliva had an area under the curve of 0.650, with a 30 percent of sensibility. However, the nasopharyngeal and nasopharyngeal + oropharyngeal samples had an area under curve of 0.950 and 1.000, respectively, with a sensibility of 90 percent and 100 percent, respectively. Conclusion: Saliva samples are not a reliable specimen for SARS-CoV-2 RNA detection. In turn, the most reliable specimens are nasopharyngeal and nasopharyngeal + oropharyngeal samples collected by swabbing(AU)
Introducción: El SARS-CoV-2 es un virus ARN positivo. Este virus puede ser detectado en diferentes tipos de secreción como hisopada bucal, nasal, esputo, saliva, sangre, etc. Objetivo: El objetivo de este estudio es comparar la confiabilidad de diferentes tipos de muestras, saliva y exudado, en la detección de SARS-CoV-2. Material y Métodos: Una muestra de 22 pacientes con diagnóstico de Covid-19 fue estudiada. Se tomaron muestras pareadas de saliva y exudado nasofaríngeo y orofaríngeo en cada paciente. Se emplearon los hisopos y medios de la firma alemana IMPROVE®. Los resultados de las determinaciones por RT-PCR se compararon mediante test de Fisher (test de la probabilidad exacta de Fisher) y cada sets de muestras fue evaluada individualmente y luego comparadas por curvas ROC. El estándar de oro propuesto fue el doble hisopado nasofaríngeo/orofaríngeo. Resultados: El método de oro propuesto detectó 10 casos positivos. La coincidencia de detección entre todos los sets de muestras fue de 3 casos (30 por ciento). Se obtuvieron diferencias significativas (Fisher p = 0.003) en la comparación de los casos detectados en saliva vs el estándar de oro. El análisis de curvas ROC mostró un área bajo la curva de 0.650 (30 por ciento de sensibilidad) para la saliva. En el caso del hisopado nasofaríngeo y el estándar de oro mostraron un área bajo la curva de 0.95 y 1.00, respectivamente, con una sensibilidad del 90 (AU) por ciento y 100 por ciento, respectivamente. Conclusiones: La saliva no es una muestra confiable para la detección de SARS-CoV-2. La muestra más confiable para el diagnóstico fue el hisopado nasofaríngeo y el doble hisopado(AU)
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Humanos , Faringe/patologia , Saliva , Vírus de RNA de Cadeia Positiva/imunologia , SARS-CoV-2 , COVID-19/diagnóstico , Manejo de Espécimes/ética , Nasofaringe/virologiaRESUMO
Introducción: Los virus constituyen las causas más frecuentes de infección respiratoria aguda, aunque el diagnóstico causal suele ser empírico dada la complejidad de su aislamiento. Objetivo: Caracterizar a pacientes menores de 5 años de edad con infecciones respiratorias agudas, según variables epidemiológicas, clínicas e imagenológicas. Métodos: Se efectuó una investigación descriptiva y transversal de 171 pacientes con infecciones respiratorias agudas y aislamiento viral mediante exudado nasofaríngeo profundo, egresados del Servicio de Neonatología del Hospital Docente Infantil Sur Antonio María Béguez César de Santiago de Cuba, desde el 2014 hasta el 2016, para lo cual se realizaron cálculos de frecuencias y porcentajes. Resultados: Predominaron los lactantes (57,9 %), el sexo masculino y los afectados con diagnósticos de neumonía (40,9 %) y bronquiolitis (28,0 %) por virus sincitial respiratorio y rinovirus. La supresión precoz de lactancia materna y tabaquismo fueron los factores de riesgo prevalentes. Tanto la fiebre como la tos y las secreciones nasales resultaron preponderantes, e infrecuentes las complicaciones. La consolidación alveolar prevaleció en pacientes con neumonía. Conclusiones: Se caracterizó epidemiológica y clínicamente a los pacientes con virus respiratorios y se evidenció discordancia con el predominio del patrón de infiltrado alveolar descrito en la bibliografía médica consultada.
Introduction: Viruses constitute the most frequent causes in acute respiratory infection, although the causal diagnosis is usually empiric given the complexity of its isolation. Objective: To characterize patients under 5 years with acute respiratory infections, according to epidemiological, clinical and imaging variables. Methods: A descriptive and cross-sectional investigation of 171 patients with acute respiratory infections and viral isolation was carried out by means of deep nasopharyngeal swab. They were discharged from the Neonatology Service of Antonio María Béguez César Southern Children Teaching Hospital in Santiago de Cuba, from 2014 to 2016, for which calculations of frequencies and percentages were carried out. Results: There was a prevalence of infants (57.9 %), the male sex and those affected patients with diagnosis of pneumonia (40.9 %) and bronchiolitis (28.0 %) due to respiratory syncytial virus and rhinovirus. The early suppression of breast feeding and nicotine addiction were the prevalent risk factors. Both fever and cough and the nasal secretions were preponderant, and the complications were infrequent. The alveolar consolidation prevailed in patients with pneumonia. Conclusions: Patients with respiratory virus were clinically and epidemiologically characterized and conflict with the pattern prevalence of alveolar infiltrates described in the consulted medical literature was evidenced.
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Infecções Respiratórias/diagnóstico , Infecções Respiratórias/epidemiologia , Insuficiência Respiratória , Atenção Secundária à Saúde , Pré-EscolarRESUMO
One year into the coronavirus disease 2019 (COVID-19) pandemic, diagnostic strategies, although central for contact tracing and other preventive measures, are still limited. To meet the global demand, lower cost and faster antigen tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection are a convenient alternative to the gold standard reverse transcription-polymerase chain reaction (RT-PCR) assay. We tested laboratory-based RT-PCR RNA detection and two rapid antigen detection (RAD) tests, based on the immunochromatography test for nucleocapsid protein of SARS-CoV-2 (COVID-19 Ag ECO Test, ECO Diagnóstica, and Panbio COVID-19 Ag Rapid Test Abbott). Paired collection and testing were done in a small prospective open study in three clinical services in São Paulo, constituted of mostly symptomatic volunteers at collection (97%, 109/112) for a median of 4 days (interquartile range: 3-6), ranging from 1 to 30. Among the 108 paired RT-PCR/RAD tests, results were concordant in 96.4% (101/108). The test's performance was comparable, with an overall sensitivity of 87% and a specificity of 96%. These observations add to other data that suggest that antigen tests may provide reasonable sensitivity and specificity and deserve a role to improve testing strategies, especially in resource-limited settings.
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Antígenos Virais/análise , Teste de Ácido Nucleico para COVID-19/métodos , Teste Sorológico para COVID-19/métodos , COVID-19/diagnóstico , RNA Viral/análise , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Brasil , Criança , Pré-Escolar , Testes Diagnósticos de Rotina , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Estudos Prospectivos , SARS-CoV-2/genética , SARS-CoV-2/imunologia , Sensibilidade e Especificidade , Adulto JovemRESUMO
Current diagnostic standards involve severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in nasopharyngeal swabs (NPS), but saliva is an attractive and noninvasive option for diagnosis. The objectives were to determine the performance of saliva in comparison with NPS for detecting SARS-CoV-2 and to compare the optimized home brew reverse-transcription polymerase chain reaction (RT-PCR) with a commercial RT-PCR. Paired NPS and saliva specimens were prospectively collected and tested by RT-PCR from patients presenting at an emergency room with signs and symptoms compatible with coronavirus disease-2019. A total of 348 samples from 174 patients were tested by RT-PCR assays. Among 174 patients with symptoms, 63 (36%) were SARS-CoV-2 positive in NPS using the optimized home-brew PCR. Of these 63 patients, 61 (98%) were also positive in saliva. An additional positive SARS-CoV-2 saliva was detected in a patient with pneumonia. Kappa Cohen's coefficient agreement between NPS and saliva was 0.96 (95% confidence interval [CI], 0.90-0.99). Median Ct values in NPS versus saliva were 18.88 (interquartile range [IQR], 15.60-23.58; range, 11.97-38.10) versus 26.10 (IQR, 22.75-30.06; range, 13.78-39.22), respectively (p < .0001). The optimized home-brew RT-PCR demonstrated higher analytical and clinical sensitivity compared with the commercial RT-PCR assay. A high sensitivity (98%) and agreement (kappa 0.96) in saliva samples compared to NPS was demonstrated when using an optimized home-brew PCR even when the viral load in saliva was lower than in NPS. This noninvasive sample is easy to collect, requires less consumable and avoids discomfort to patients. Importantly, self-collection of saliva can diminish exposure to healthcare personnel.
Assuntos
COVID-19/diagnóstico , COVID-19/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , SARS-CoV-2/isolamento & purificação , Saliva/virologia , Manejo de Espécimes/métodos , Adulto , Idoso , Serviço Hospitalar de Emergência , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos ProspectivosRESUMO
RESUMEN: El coronavirus tipo 2, SARS-CoV-2, que causa la enfermedad denominada por la OMS como COVID-19, se ha expandido provocando una pandemia desde 2019, sin cura hasta la fecha. El mecanismo de transmisión del SARS-CoV-2 entre humanos es mediante las secreciones generadas durante la respiración y estornudos, presentándose con un período de incubación desde 1 a 14 días. Se describen fiebre, tos y astenia como los síntomas más habituales. El diagnóstico definitivo se logra a través de la correlación entre la presentación clínica y exámenes complementarios, pero en la actualidad, el método de muestreo de preferencia para el diagnóstico de SARS-CoV-2 es mediante una muestra de nasofaringe, en donde se analiza la presencia de material genético viral por medio de RT-PCR. Debido a las complicaciones en la obtención de la muestra, tanto para el personal sanitario como para el paciente, se ha implementado la muestra de saliva con finalidad diagnóstica, como un método que proporciona una detección rápida, simple y no invasiva de la infección viral. Esta alternativa diagnóstica podría entregar información respecto a la patogenia de la enfermedad, permitiendo el manejo y control de pacientes positivos. El siguiente artículo, tiene por objetivo realizar una comparación entre las tomas de muestra de saliva y de nasofaringe para el diagnóstico de SARS-CoV-2, mediante la prueba de reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR).
SUMMARY: The type 2 coronavirus, SARS-CoV-2, named by the WHO like COVID-19, has expanded causing a pandemic since 2019, with no cure to date. The mechanism of transmission of SARS-CoV-2 between humans is through secretions generated during breathing and sneezing, presenting with an incubation period range from 1 - 14 days. Fever, cough, and fatigue are described as the most common symptoms. The definitive diagnosis is achieved through the correlation between the clinical presentation and the complementary exams, but at present, the preferred sampling method for the diagnosis of SARS-CoV-2 is through a nasopharyngeal swab specimen, where it is analyzed the presence of viral genetic material by the RT-PCR. Due to the complications in obtaining the sample, both for health personnel and for the patient, the saliva sample has been implemented, as a method that provides rapid, simple and non-invasive detection of viral infection. This diagnostic alternative could provide information on the pathogenesis of the disease, the management and control of positive patients. The following article aims to make a comparison between the saliva and nasopharyngeal samples taken for the diagnosis of SARS-CoV-2, using the reverse transcription polymerase chain reaction test (RT-PCR).
Assuntos
Saliva/virologia , Infecções por Coronavirus/diagnóstico , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Betacoronavirus , Nasofaringe/virologia , Infecções por Coronavirus/epidemiologia , Técnicas de Laboratório ClínicoRESUMO
BACKGROUND: Noroviruses (NoVs) are an important cause of acute gastroenteritis (AGE), worldwide. OBJECTIVES: To evaluate the frequency, viral load and molecular profile of NoV in fecal and nasopharyngeal swab samples from hospitalized children, and to determine children's secretor status. STUDY DESIGN: From May 2014 to May 2015, 219 children were included in the study, 96 with gastroenteric symptoms and 123 without gastroenteric symptoms. All fecal and nasopharyngeal swab samples were screened by TaqMan RT-qPCR duplex (GI/GII NoV) and quality samples were characterized by genomic sequencing. RESULTS: Norovirus positivity rate in feces was 15.4% in asymptomatic and 18.8% in the symptomatic group. The median viral loads in feces were 2.69×108GC/g and 4.32×107GC/g from children with or without AGE symptoms, respectively. In nasopharyngeal swab samples, the NoV positivity was 11.4% in symptomatic children, with a median viral load of 2.20×107GC/mL and 6.5% in asymptomatic children, with an average viral load of 1.73×106GC/mL. In only two cases NoV was detected in both samples. A considerable genomic variability was observed in feces, with six genotypes being detected, as follows: GII.4, GII.6, GI.3 and GII.3, GI.2 and GI.5. Two GI.3 was detected in nasopharyngeal swab. CONCLUSIONS: Our data reveal considerable NoV frequencies in both nasopharyngeal and fecal samples from symptomatic and asymptomatic children. Higher viral loads were detected in samples from AGE symptomatic children, when compared to asymptomatic children. High genomic variability was observed, with this being the first report of GI.5 NoV in Brazil and of GI.3 in nasopharyngeal swab samples.
Assuntos
Infecções por Caliciviridae/virologia , Fezes/virologia , Genótipo , Nasofaringe/virologia , Norovirus/classificação , Norovirus/isolamento & purificação , Brasil/epidemiologia , Criança , Pré-Escolar , Estudos Transversais , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Norovirus/genética , Prevalência , RNA Viral/análise , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Sequência de DNA , Carga Viral , Eliminação de Partículas ViraisRESUMO
Introducción: las infecciones respiratorias agudas constituyen una de las principales causas de consulta en los servicios de salud. Objetivo: identificar las características epidemiológicas y clínicas de las infecciones producidas por los nuevos virus respiratorios emergentes. Método: se realizó un estudio epidemiológico descriptivo de serie de casos, en niños menores de 15 años ingresados en el Hospital Pediátrico Docente Luis Ángel Milanés Tamayo de Bayamo, Granma, desde el primero de diciembre de 2010 al 31 de diciembre de 2011. El universo estuvo constituido por 144 pacientes con el diagnóstico de infección respiratoria aguda, a los cuales se les realizó exudado nasofaríngeo. La muestra fue de 119 casos con aislamientos virales positivos. Resultados: predominó el grupo de edad uno a cuatro años (47,08 %) y el sexo masculino con 55,46 %. La desnutrición se presentó en 48 niños (40,33 %) y la exposición pasiva al cigarro en 59 pacientes (49,57 %). Los virus respiratorios emergentes encontrados fueron los metapneumovirus y el bocavirus con 12 casos respectivamente. Conclusiones: los niños menores de cinco años, con factores de riesgo como la desnutrición y exposición pasiva al humo del cigarro fueron los más afectados por estos agentes virales. Los rinovirus, el rincitial respiratorio y el virus de la influenza A H1N1 presentaron una circulación estacional.
Introduction: acute respiratory infections are a leading cause of consultation in health services. Objective: to identify the epidemiological characteristics and clinical infections caused by newly emerging respiratory virus. Method: a descriptive epidemiological study of case series was performed in children under 15 years admitted to the Luis Angel Milanés Tamayo Pediatric Teaching Hospital of Bayamo, Granma, from December 1st, 2010 to December 31st, 2011. The universe comprised 144 patients with the diagnosis of acute respiratory infection, with and nasopharyngeal sampling. The sample was composed of 119 cases with isolate positive virus. Results: the age group between 1-4 years (47.08 %) predominated as well as male sex (55.46 %). Malnutrition occurred in 48 children (40.33 %) and exposure to smoking in 59 patients (49.57 %). The emerging respiratory viruses found were metapneumovirus and bocavirus 12 cases respectively. Conclusions: children under 5 years with risk factors such as malnutrition and passive exposure to cigarette smoke were the most affected by these viral agents. Rhinovirus, respiratory and rincitial virus A H1N1 influenza showed a seasonal circulation.