SARS-CoV-2 antigen detection in deceased bodies: implications for infection prevention

Background & objectives: High transmissibility of the SARS-CoV-2 has significant implications on healthcare workers’ safety, preservation, handling, transportation and disposal of the deceased bodies. The objective of this study was to detect SARS-CoV-2 antigen in nasopharyngeal samples and its implications in handling and care of COVID-19 deceased bodies. Methods: A study was conducted at a dedicated COVID-19 centre on deceased individuals from April to December 2020. Rapid antigen test (RAT) and reverse transcription (RT)-PCR was compared on all the SARS-CoV-2 positive cadavers recruited in the study. Results: A total of 115 deceased individuals were included in the study. Of these, 79 (68.7%) were male and 36 (31.3%) were female and majority were in the age group of 51-60 yr [31 (27%)]. SARS-CoV-2 antigen test was positive in 32 (27.8%) and negative in 83 (72.1%) individuals. The mean time interval between deaths to the sample collection was 13.2 h with interquartile range of eight to 20 h. Reverse transcription (RT)-PCR was used as the reference test and 24 (20.9%) cases were true positive; 93.6 per cent [95% confidence interval (CI) 88.8-98.4%] sensitivity, 45.2 per cent (95% CI 35.5-55%) specificity, 60.2 per cent (95% CI 50.6-69.8%) positive predictive value and 88.8 per cent (95% CI 82.7-95%) negative predictive value of antigen test was computed. Interpretation & conclusions: SARS-CoV-2 antigen test was positive beyond 19 h in COVID-19 deceased individuals. Antigen test was found to be highly sensitive in the deceased. Patients, suspected of having died due to COVID-19, can be screened by this method. As infectiousness of the virus in the deceased bodies cannot be directly concluded from either the antigen or RT-PCR test, yet possible transmission cannot be completely ruled out. Strict infection control measures need to be followed during the handling and clearance of COVID-19 cadavers.

Diagnostic accuracy of saliva as a specimen for detection of SARS-CoV-2 by RT-PCR

Context: COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an emerging pandemic that is rapidly spreading with more than 114 million confirmed cases and 2.5 million deaths by far. Nasopharyngeal swab (NPS) in VTM has been used as the gold standard respiratory specimen for SARS-CoV-2 reverse-transcriptase real-time PCR (rRT-PCR) tests. But now the virus can also be detected in other clinical specimens like bronchoalveolar lavage, sputum, saliva, throat swab, blood, and stool specimens. Aims: The aim of this study was to determine the diagnostic potential of saliva as a sample in comparison to NPS for detection of SARS-CoV-2 by rRT-PCR. Settings and Design: A cross-sectional study was conducted among 256 paired samples (NPS and Saliva) received in the Department of Microbiology, SMS Medical College, Jaipur over a period of 2 months Methods and Material: NPS from individuals were collected in a sterile tube containing Viral Transport Medium™. Before swab collection, whole saliva was collected by spitting from the suspected patient into a sterile container. Both were stored at room temperature and transferred to the diagnostic laboratory within four hours of collection where extraction was done using Perkin Elmer chemagic extractor and rRT- PCR was performed using NIV, Pune mastermix. Results: Sensitivity, specificity, PPV, and NPV of RT-PCR for the diagnosis of COVID-19 in saliva were 84.26%, 100%, 100%, and 54.05%, respectively. The accuracy of detection of COVID-19 by saliva samples compared to the routinely used NPS samples (considered as the standard reference) for RT PCR was 86.72%. Conclusions: Our results show that saliva as a reliable sample type for SARS-CoV-2 detection.

SARS-COV-2 detection in saliva and nasopharyngeal swabs using RT-PCR was similar

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.

Reliability of CNEURO hyssops for sample collection in the SARS-CoV-2 diagnosis / Fiabilidad de los hisopos CNEURO para la recogida de muestras en el diagnóstico del SARS-CoV-2

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.

Estudio comparativo de la detección de SARS CoV-2 por RT-PCR en muestras de hisopado nasofaringeo y saliva un estudio piloto en Bolivia

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.

Detección del SARS-CoV-2 mediante RT-qPCR utilizando saliva en pacientes ambulatorios con estudio de COVID-19

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.

Complicações em testes para COVID-19 com swab nasal: relatos de caso / COVID-19 nasal swab testing complications: case reports

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]

Comparison between nasopharyngeal swabs and saliva as reliable specimens for the diagnosis of SARS-CoV-2 / Comparación de la confiabilidad del diagnóstico del SARS-CoV-2 entre muestras de hisopado y saliva

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)

Infecciones respiratorias agudas virales en pacientes menores de 5 años hospitalizados / Viral acute respiratory infections in hospitalized patients under 5 years

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.

Comparación de la Muestra Salival y de Nasofaringe en la Detección de SARS-CoV-2 mediante RT-PCR / Comparison Between Saliva and Nasopharyngeal Sample in Detection of SARS-CoV-2 by RT-PCR

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).

Effect of health seeking interval on outcome in swine flu cases attended a tertiary care hospital in southern Rajasthan region of India

Background: Swine flu influenza is an infection by H1N1 type of swine influenza virus. Swine influenza virus or swine-origin influenza virus (SIV or S-OIV) is a strain of the family of influenza viruses that’s endemic in swine (pigs). Early diagnosis and treatment is key approach to control the morbidity and mortality associated with swine flu which can be achieved by improving health seeking behaviour of community. Understanding of behaviour of community is essential for planning strategies for prevention and control. Aim of this study is to establish a relation between healthcare interval and outcome of swine flu.Methods: A complete data of all the patients visiting swine flu OPDs, swine flu wards and ICU were maintained for year 2015. Each patient visiting either the swine flu OPD or the swine flu ward, who was suspected clinically to be H1N1 positive were tested for real time PCR. Data was collected in a standardized pre-structured questionnaire.Results: Out of 1247 samples tested for rt-PCR, number of patients found to be swine positive was 491 (39.37%). Total 267 patients were admitted in swine flu ward and ICU, out of them 62 was expired. Clinical care intervals of more than 5 days from onset of symptoms to swab collection, diagnosis and admission were more in female and rural population. Mean duration between onset of symptom to hospitalization, swab collection and diagnosis was significantly higher in deceased patients than survived.Conclusions: Early presentation to healthcare facility is associated with better prognosis and outcome. After patient report to the health care setup, early sample collection and diagnosis help to reduce mortality.

Correlation of Bacterial Isolates from Middle Ear and Nasopharynx in Patients with Chronic Suppurative Otitis Media in Ilorin, Nigeria

Purpose: To determine the association between isolates in the middle ear (ME) and nasopharynx of patients with chronic otitis media in Ilorin, north-central Nigeria. Methods: An ethically approved case control study was carried out in the Ear, Nose, and Throat clinic amongst consenting cases using normal subjects as controls. A microbiology investigation form giving the results for otoscopy, aspirate and swabs was filled out for both the ME and nasopharynx. The experimental procedure was carried out and bacteria were identified according to colony characteristics, morphological appearance, Gram-staining, and standard biochemical testing. Data obtained were analysed with SPSS version 16.0 and Epi Info 3.5.1 using the mean, standard deviation and chi-square results. Results: A total of 140 cases and 70 controls, were recruited. The Gram stain reaction of the ME aspirates were positive in 28.6% and negative in 71.4% of cases. Nasopharyngeal swabs revealed 64.3% Gram positive and 35.7% negative organisms. Overall, there was no relationship between the ME and nasopharyngeal isolates amongst cases, with a P value of 0.000. However, there was a relationship amongst the isolate from the nasopharynx of cases and controls, with the exception of Klebsiella pneumoniae, at P < 0.009. Conclusion: There was no relationship amongst the bacterial isolate from the ME and nasopharyngeal specimen of patients with otitis media.

Nuevos virus respiratorios emergentes diagnosticados por exudado nasofaríngeo / New Emerging Respiratory Virus Diagnosed by Nasopharyngeal Swab

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.

Epidemiology of viral infection causing acute exacerbations of chronic obstructive pulmonary disease in the elderly patients during 2010-2012 in Minhang district of Shanghai / 中华急诊医学杂志

Objective To investigate the epidemiology of viral infection in elderly patients to contract acute exacerbations of chronic obstructive pulmonary disease (AECOPD)in Minhang district of Shanghai from 2010 to 2012,and to study the relationships between viral infection and clinical features.Methods The elderly patients (age >70 year old)with AECOPD admitted from September 2010 to November 2012 were enrolled for study.The patients who couldn't complete lung function test were excluded.The pharyngeal swabs (PS)were taken from each patient within the first 24 h after admission.Nine respiratory viruses and their subtypes from pharyngeal swabs were detected by the nested multiplex polymerase chain reaction (PCR)method,including influenza virus A (FluA),2009 influenza A (H1N1 )virus (09FluH1 ), influenza virus B (FluB),respiratory syncytial virus A (RSVA)and B (RSVB),human coronavirus-229E (hCOV-229E),human coronavirus-NL63 (hCOV-NL63 ),human coronavirus-OC43 (hCOV-OC43 ), human coronavirus-HKU1 (hCOV-HKU1),human parainfluenza virus 1-4 (hPIV1-4),human adenovirus (hAdV),human boca virus (hBoV),human metapneumo-virus (hMPV)and human rhinovirus (hRV). According to the PCR results,all patients were divided into positive viral infection group and negative viral infection group.The relationships between viral infection and clinical features were analyzed.Results Sixty patients were eligible for study.Of them,14 patients were found to be positive for virus infection including a triple infected patient (FluB,hRV and hROV)and 46 patients were negative for virus infection.The viral pathogens detected in the positive viral group were:9 cases of hRV (15.00%),2 cases of hPIV (3.33%),2 cases of hCOV (3.33%),2 cases of FluB (3.33%)and 1 cases of RSV (1.67%).The mortality in the positive viral group was higher than that in the negative viral group.However,the other clinical characteristics between the two groups had no significant differences. Conclusions Human rhinovirus was the most common viral pathogen in elderly patients with AECOPD.Viral infection might be associated with the prognosis.However,the patients with viral infection are lack of specific clinical characteristics,therefore,the prompt diagnosis before careful study would be difficult.

Comparison of Sputum and Nasopharyngeal Swab Specimens for Molecular Diagnosis of Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella pneumophila

BACKGROUND: Differentiation of atypical pathogens is important for community-acquired pneumonia (CAP). In this study, we compared sputum and nasopharyngeal swabs (NPS) for use in detection of Mycoplasma pneumoniae (MP), Chlamydophila pneumoniae (CP), and Legionella pneumophila (LP), using Seeplex PneumoBacter ACE Detection Assay (PneumoBacter; Seegene). METHODS: Sputum and NPS specimens were collected from patients in 15 hospitals. DNA was extracted from sputum using QIAamp DNA Stool Mini Kit (Qiagen) and from NPS using easyMAG (bioMerieux). Both types of specimens were evaluated by multiplex PCR using PneumoBacter. To determine the diagnostic performance of this assay, sputum samples were also tested using BD ProbeTec ET Atypical Pneumonia Assay (APA; Becton Dickinson). RESULTS: Among 217 sputum and NPS, 20 (9.2%), 2 (0.9%), and 0 sputum were positive for MP, LP, and CP, respectively, whereas 8 (3.7%) NPS were positive for MP. The sputum APA test yielded 186, 206, and 204 interpretable results for MP, LP, and CP, respectively. Of these, 21 (11.3%) were positive for MP, 2 (1.0%) were positive for LP, and 0 samples were positive for CP. Compared to APA, the sensitivity and specificity of the sputum assay for MP were 95.2% and 100.0%, respectively, whereas for the NPS assay, these were 38.1% and 93.9%. Sputum testing was more sensitive than NPS testing (P=0.002). For LP and CP diagnosis, PneumoBacter and APA tests agreed 100%. CONCLUSIONS: Specimen type is crucial and sputum is preferred over NPS for simultaneous detection of MP, LP, and CP using multiplex PCR in CAP.

Nasopharyngeal bacterial carriage and antimicrobial resistance in underfive children with community acquired pneumonia.

Pathogens in nasopharynx is a significant risk factor of pneumonia. According to WHO, isolates to be tested for antimicrobial resistance in the community should be obtained from nasopharyngeal (NP) swabs. The aim of this study is to know the bacterial patterns of the nasopharynx and cotrimoxazole resistance in under five-year old children with community acquired pneumonia. The study was carried out in 4 primary health clinic (Puskesmas) in Majalaya sub-district, Bandung, West Java, Indonesia. All underfive children with cough and/or difficult breathing and classified as having non-severe pneumonia (WHO guidelines) were placed in Amies transport medium and stored in a sterile jar, before taken to the laboratory for further examination, in the same day. During this nine month study, 698 children with clinical signs of non-severe pneumonia were enrolled. About 25.4% (177/698) of the nasopharyngeal specimens yielded bacterial isolates; i.e. 120 (67.8%) were positive for S pneumoniae, 21 for S epidermidis and alpha streptococcus, 6 for Hafnia alvei, 5 for S aureus, 2 for B catarrhalis, and 1(0.6%) for H influenza and Klebsiella, respectively. The antimicrobial resistance test to cotrimoxazole showed that 48.2% of S pneumoniae strain had full resistance and 32.7% showed intermediate resistance to cotrimoxazole. This result is almost similar to the other studies from Asian countries. It seems that H influenza is not a problem in the study area, however, a further study is needed.

Diagnostic Value of Gap-Ligase Chain Reaction Enzyme Linked Immunosorbent Assay for Chlamydia Trachomatis Pneumonia in Neonatal and Small Infants / 实用儿科临床杂志

Objective To explore the diagnostic value of Gap-ligase chain reaction(LCR)-enzyme linked immunosorbent assay(ELISA)for Chlamydia trachomatis(CT) pneumonia in infants(28 days-3 months old baby was 16.9%(27/160 cases),and the incidence in 3-6 months old baby was 8.1%(12/149 cases).The clinical symptoms included that 25 cases(51.0%) had fever,48 cases(98.0%) with paroxysmal cough,45 cases(91.8%) with rhinocleisis,45 cases(91.8%) with spitting foam,49 cases(100%) with tachypnea,28 cases(57.1%) with lips cyanosis,26 cases(53.1%) with medium and moist rales,24 cases(49.0%) with dry rales,18 cases(36.7%) with phlegm whimper,29 cases(59.2%) with rough breath sounds in both lungs and there were 13 cases(26.5%) with conjunctivitis.Chest film and paper capacitor showed that bilateral extensive interstitial and(or) alveolar infiltration,over-inflation 23 cases(46.9%) had no lobal consolidation or pleural effusion.The WBC counts were normal or slightly high.All children were treated with cephalothin or penicillin before confirmation with CT infection.Eleven cases were treated with azithromycin after diagnosis with CT pneumonia and were cured 9 days after treatment and the others were not treated with azithromycin so their course prolonged from 15 to 44 days,among them there were 11 out-patients who were treated many times because of repeated cough.Conclusions CT is important pathogenic organism to cause pneumonia in neonatal and small infants.It is important to pay attention to the possibility of pneumonia caused by CT and make the diagnosis in early period as soon as possible and treat them with sensitive drug to shorten the course.

Investigation methods of diagnosis of Chlamydia trachomatis by Gap ligase chain reaction / 重庆医科大学学报

Objective:To investigate the method with good sensitivity,specificity,reliability for diagnosis of Chlamydia trachomatis.Methods:Inoculate the nasopharyngeal swabs to detect the Chlamydia trachomatis(CT) with McCoy cell culture and plasmid gene probes labeled with biotin ligase-chain reaction.Then calculate the sensitivity,specificity,positive predicative value(PPV) and negative predicative value(NPV) of both TC and G-LCR respectively.Compare the difference of the two methods.Results:There were 49 positive specimens and 344 negative by enlarged gold standard.There was significant difference with cell culture,G-LCR-PAGE,G-LCR-ELISA by two-related-samples ? 2 tests( P