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.

A cross-sectional study of enterovirus nucleic acid test with throat swabs for term late neonates during coronavirus disease 2019 / 中国当代儿科杂志

OBJECTIVES@#To investigate the positive rate of enterovirus (EV) nucleic acid in throat swabs of term late neonates hospitalized during the coronavirus disease 2019 (COVID-19) epidemic and the clinical characteristics of the neonates.@*METHODS@#A single-center cross-sectional study was performed on 611 term late infants who were hospitalized in the neonatal center from October 2020 to September 2021. Throat swabs were collected on admission for coxsackie A16 virus/EV71/EV universal nucleic acid testing. According to the results of EV nucleic acid test, the infants were divided into a positive EV nucleic acid group (8 infants) and a negative EV nucleic acid group (603 infants). Clinical features were compared between the two groups.@*RESULTS@#Among the 611 neonates, 8 tested positive for EV nucleic acid, with a positive rate of 13.1‰, among whom 7 were admitted from May to October. There was a significant difference in the proportion of infants contacting family members with respiratory infection symptoms before disease onset between the positive and negative EV nucleic acid groups (75.0% vs 10.9%, P<0.001). There were no significant differences between the two groups in demographic data, clinical symptoms, and laboratory test results (P>0.05).@*CONCLUSIONS@#There is a certain proportion of term late infants testing positive for EV nucleic acid in throat swabs during the COVID-19 epidemic, but the proportion is low. The clinical manifestations and laboratory test results of these infants are non-specific. Transmission among family members might be an important cause of neonatal EV infection.

The incidence of intestinal colonization of carbapenem-resistant Enterobacterales and its risk factors for bloodstream infection / 中华检验医学杂志

Objective:The aim of this study was to determine the colonization rate of carbapenem-resistant Enterobacterales (CRE) and identify the proportion and risk factors for bloodstream infection.Methods:This was a retrospective study conducted at the Department of Clinical Laboratory, Peking University People′s Hospital from January 2018 to December 2021. A total of 4 993 patients underwent rectal swab CRE screening for CRE, of which 137 were found to be positive. Clinical and laboratory data of the positive patients were collected, and the following parameters were analyzed: the positive rate of CRE screening in high-risk population, the species of colonized bacteria, antimicrobial resistance and the risk factors of CRE bloodstream infection in colonized patients. Statistical analysis was performed using SPSS 26.0 software. Univariate analysis was conducted using the chi-square (χ 2) test, while multivariate analysis was performed using binary logistic regression. The results were expressed as relative risk (odds ratio, OR) and 95% confidence interval ( CI). A significance level of 0.05 was considered statistically significant. The drug resistance rate of pathogen was analyzed by WHONET 5.6 software. Results:During the study period, a total of 4 991 patients who underwent rectal swab screening were eligible for inclusion, of which 137 patients were screened positive, resulting in a positive rate of 2.7% (137/4 991). The positive rates were higher in the intensive care ward and hematology ward, with rates of 5.5% (27/493) and 3.3% (109/3 321), respectively. A total of 145 colonization strains were isolated from patients with positive CRE screening, including 63 strains of Klebsiella pneumoniae (43.4%, 63/145), 52 strains of Escherichia coli (35.9%, 52/145), 16 strains of Enterobacter cloacae (11.0%, 16/145) and 14 strains of other Enterobacterales (9.7%, 14/145). The metal β-lactamase production type was the main component of CRE positive colonizing bacteria. The antimicrobial resistance of 145 strains to 22 antibacterial agents revealed that amikacin and tigacycline were the most sensitive. Among 137 CRE screening-positive patients, 14 (10.2%, 14/137) developed bloodstream infection. The isolated pathogenic bacteria included 10 Klebsiella pneumoniae strains and 4 Escherichia coli strains, with a predominant serine carbapenemase producing. Notably, the enzyme type and antimicrobial resistance of the bloodstream infection isolates in the same patient were highly consistent with those of the previous screening strains. Comparison was made between patients with positive CRE screening and those with CRE conversion to bloodstream infection. The unifactor analysis revealed significant differences in surgical history, neutropenia, hematopoietic stem cell transplantation, history of antibiotic use before rectal swab screening, screening within 48 hours after admission, and serine carbapenemase production by strains ( P<0.05). The multivariate analysis indicated that surgical history ( OR 24.659, 95% CI 2.540-239.411, P=0.006) and neutropenia ( OR 93.796, 95% CI 6.294-1 397.804, P=0.001) remained significantly associated with the risk of CRE bloodstream infection ( P<0.05). Conclusions:The CRE colonization rate was low in our hospital, but the proportion of patients with positive screening converted to bloodstream infection was high. Surgical history and neutropenia are risk factors for bloodstream infection transmission. Thus, it is essential to enhance monitoring in high-risk areas and susceptible patients.

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.

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]

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.

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.

Clinical characteristics in patients with persistent positive pharyngeal swab of omicron variant and analysis on nucleic acid testing of anal swabs / 中华危重病急救医学

Objective:To analyze the clinical characteristics in patients with persistent positive pharyngeal swab of 2019 novel coronavirus Omicron variant and results of nucleic acid testing of anal swabs to provide basis for prevention and control measures.Methods:This study included 93 patients whose pharyngeal swab nucleic acid test were persistent positive and admitted to the ward of Daping Hospital in the National Exhibition and Convention Center (Shanghai) Makeshift Hospital from May 1 to May 24, 2022. The gender, age, underlying diseases, vaccination status, clinical symptoms, interval between infection onset and anal sampling, length of hospital stay, the nucleic acid test result of pharyngeal swabs and anal swabs and the time turning negative were collected and analyzed.Results:The age of 93 patients ranged from 8 to 72 years old with a median of (46.0±16.0) years old. Among them, 30 cases (32.3%) were male and 63 cases (67.7%) were female. Sixty-five patients (69.9%) received 2-3 shots of vaccine, 2 patients (2.1%) received 1 shot, and 26 patients (28.0%) did not receive any vaccination. Twenty patients (21.5%) had underlying diseases, of which hypertension (13 cases, 14.0%) and type 2 diabetes mellitus (6 cases, 6.5%) were the most common. Twenty-four patients (25.8%) had asymptomatic infection and the rest (69 cases, 74.2%) had mild symptoms. Cough (50 cases, 53.8%) and sore throat (28 cases, 30.1%) were the most common clinical manifestations of the upper respiratory tract in these patients. Only 6 patients (6.5%) had gastrointestinal symptoms (including diarrhea in 5 patients and diarrhea with vomiting in 1 patient). Pharyngeal and anal swabs were collected simultaneously from all 93 patients at 8-16th days [(11.55±2.27) days] after 2019 novel coronavirus Omicron variant infection. The pharyngeal swabs were positive in 79 patients (85.0%) and the anal swabs were positive in 5 patients (5.4%). The time of pharyngeal swabs turning negative was (14.7±2.9) days, and that of anal swab turning positive was (14.2±1.9) days. The median length of hospital stay was (16.7±2.9) days.Conclusions:In patients with persistent positive nucleic acid of the 2019 novel coronavirus Omicron variant, there were more mild infection than asymptomatic. The upper respiratory tract symptoms such as cough and sore throat were the most. The likelihood of transmission of 2019 novel coronavirus Omicron variant through the digestive tract may be low. The correlation between gastrointestinal symptoms and 2019 novel coronavirus Omicron variant RNA in the digestive tract is uncertain.

Fístula de líquido cefalorraquídeo después de hisopado nasofaríngeo en pandemia COVID-19. A propósito de dos casos

Resumen Uno de los pilares fundamentales en el manejo de la pandemia por SARS-CoV2 es la detección temprana de la presencia del virus en pacientes. El método más utilizado es mediante hisopado nasofaríngeo para amplificar ácidos nucleicos mediante reacción en cadena de polimerasa (PCR). Las complicaciones asociadas a la técnica de hisopado aún no están completamente caracterizadas. Hasta ahora hay un caso reportado internacionalmente de fístula de líquido cefalorraquídeo poshisopado nasofaríngeo. Presentamos dos casos de fístula posterior a dicho examen: el primer caso un paciente de género femenino con sospecha de hipertensión intracraneal idiopática, cuya brecha se reparó quirúrgicamente; el segundo caso un paciente de género masculino con antecedente de hidrocefalia y meningitis neonatal que, al estudio por rinorraquia, se encuentra un meningoencefalocele en el receso frontal derecho, también reparado quirúrgicamente.

Abstract One of the cornerstones in the management of coronavirus pandemic is the early identification of virus presence in patients. The most used test is the nasopharyngeal swab, used to amplify nucleic acids through polymerase chain reaction. Complications with this test have not been completely characterized. Until now, only one international report of cerebrospinal fluid leak has been reported. We present two cases of leak after nasopharyngeal swab test: the first case corresponded to an adult feminine gender patient with suspected idiopathic intracranial hypertension, whose gap was surgically repaired; the second case adult male patient with medical history of hydrocephalus and neonatal meningitis who was further studied for rhinoliquorrhea that showed a meningoencephalocele occupying the right frontal recess.

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.

A non-invasive method for detecting mitochondrial tRNA / 南方医科大学学报

OBJECTIVE@#To explore the feasibility of detecting maternal hereditary mitochondrial tRNA@*METHODS@#We performed sequence analysis of mitochondrial DNA in blood samples from 2070 cases of maternal hereditary mitochondrial disease in the First Affiliated Hospital of Wenzhou Medical University, and identified 3 patients with m.15927G>A mutation.Buccal swabs and blood samples were obtained from the 3 patients (mutation group) and 3 normal volunteers (control group).After extracting whole genomic DNA from all the samples, the DNA concentration and purity were analyzed.The PCR products were subjected to dot blot hybridization, Southern blot hybridization, and DNA sequencing analysis to verify the feasibility of detecting m.15927G>A mutation using buccal swabs.@*RESULTS@#There was no significant difference in DNA concentration extracted from buccal swabs and blood samples in either the mutation group or the control group (@*CONCLUSIONS@#Buccal swabs collection accurate is an accurate and sensitive method for the detection of m.15927G>A mutation.

Detection of Chlamydia trachomatis DNA in urine and urethral/cervical swab samples: analysis of results from 1 475 outpatients attending sexually transmitted disease clinics / 中华皮肤科杂志

Objective:To compare the detection rate of genital Chlamydia trachomatis (CT) DNA between urine and urethral/cervical swab samples. Methods:From December 2018 to December 2019, a total of 1 475 outpatients were collected from sexually transmitted disease clinics in 7 medical institutions, such as Department of Venereology, Guangzhou Institute of Dermatology, including 1 118 males and 357 females. One urethral/cervical swab sample and one urine sample were collected successively from each patient. Real-time fluorescence-based PCR was performed to detect CT DNA in urine and urethral/cervical swab samples, and paired chi-square test was used to compare the positive rate of CT DNA between the 2 kinds of samples. Random- or fixed-effect meta-analysis was conducted for the test of heterogeneity and merging of positive rates of CT DNA in the urine and urethral/cervical swabs among 7 medical institutions.Results:The positive rate of CT DNA in the urine samples was significantly higher than that in the swab samples from 4 medical institutions (all P < 0.05) , while there was no significant difference in the positive rate of CT DNA between the 2 kinds of samples from 3 medical institutions (all P > 0.05) . The heterogeneity ( I2) estimates of the CT-DNA positive rate in urine and swab samples among different medical institutions were 78.6% (95% CI: 55.9% - 89.6%) and 73.7% (95% CI: 43.7% - 87.7%) , respectively; meta-analysis showed that the total merged positive rate of CT DNA in the urine samples was 10.8% (95% CI: 7.2% - 15.9%) , which was significantly higher than that in the swab samples (7.8%, 95% CI: 4.9% - 12.1%; χ2 = 39.2, P < 0.05) . Compared with the swab sample-based CT-DNA detection method, the sensitivity, specificity, positive predictive value, negative predictive value and consistency rate of the urine sample-based CT-DNA detection method were 97.0% (128/132) , 96.3% (1 293/1 343) , 71.9% (128/178) , 99.7% (1 293/1 297) , and 96.3% (1 421/1 475) , respectively. The positive rate of CT DNA in the urine samples from 1 118 male patients was 11.0% (95% CI: 7.2% - 16.5%) , which was significantly higher than that in the swab samples (7.6%, 95% CI: 4.9% - 11.8%; χ2 = 34.3, P < 0.05) . There was no significant difference in the positive rate of CT DNA between the urine (11.9%, 95% CI: 7.7% - 17.9%) and cervical swab samples from 357 female patients (10.4%, 95% CI: 7.6% - 14.0%; χ2 = 3.2, P > 0.05) . Conclusions:The positive rate of CT DNA in urine samples is higher than or similar to that in urethral/cervical swab samples. The urine sample-based CT-DNA detection method has characteristics of convenience, non-invasiveness, painlessness and low cost, and is worthy of clinical promotion.

Common microbes detected by conjunctival swab analysis and their antibiotic sensitivety / Шинэ санаа Шинэ нээлт

Background@#Bacterial ocular infection is a common problem.[1;6]. Microbiological investigation of the conjunctival swab is one of the broadly used method to study etiological agent of conjunctivitis[2]. Microbial culture techniques have shown that 80% of conjunctival swabs yield cultivable microbes.[3]. Conjunctival sac contains variety of pathogenic and non-pathogenic microbes. Normal microbes play a protective immunological role in preventing the proliferation of pathogenic species that can cause ocular infections whereas pathogenic microbes contribute to infectious and autoimmune diseases of the eye. [4;5]@*Purpose@#To investigate common microbes detected by conjunctival swab analysis and their antibiotic sensitivity.@*Methods@#In our descriptive study, 264 conjunctival swab samples that had been analyzed by MALDI-TOF technology using VITEX MS at Gyals Medical Center from July 2019 to November 2020 were evaluated.@*Results@#Cultivable microbes and fungus were detected in 71.56% of overall swabs. 28.44% were non cultivable. Fungus and 43 different types of microbes were found. 35% of all microbes were Staphylococcus including Methicillin -resistant Staphylococcus aureus, Staphylococcus aureus, Staphylococcus epidermidis. 28% of microbes were Streptococcus including Streptococcus mitis, Streptococcus pneumoniae, Streptococcus anginosus, Streptococcus parasanguinis, Streptococcus agalactiae, Streptococcus pyogenes, Streptococcus salivarius, Streptococcus spp. 20% of all microbes were miscellaneous bacterium including Enterococcus, Corynebacterium, Klebsiella, Acinetobacter, Escherichia, Candida parapsilosis and the remaining are others. Staphylococcus aureus is sensitive to Quinupristin/Dalfopristin, Linezolid, Vancomycin, Tigecycline, Nitrofurantoin whereas they are resistant to Benzylpenicillin, Ciprofloxacin, Amoxicillin, Amoxicillin/ Clavulanic Acid, Cefazolin that are widely used in Mongolia.@*Conclusion@#In 76.71% of overall conjunctival swab samples were found cultivable microbes. Methicillin -resistant Staphylococcus aureus, Staphylococcus aureus, Staphylococcus epidermidis are the most common microbes detected by conjunctival swab analysis. The common microbes are resistant to Benzylpenicillin, Ciprofloxacin, Amoxicillin, Amoxicillin/Clavulanic Acid, whereas they are sensitive to Quinupristin/Dalfopristin, Linezolid, Vancomycin, Tigecycline, Nitrofurantoin, Erythromycin, Clindamycin.

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).

An infant with a mild SARS-CoV-2 infection detected only by anal swabs: a case report

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China and has spread rapidly worldwide. We present a mild SARS-CoV-2 infection in a baby with non-productive cough and normal chest computed tomography, in whom only anal swabs tested positive by real-time PCR testing for SARS-CoV-2. She was given atomization inhalation therapy with recombinant human interferon alfa-1b for 10 days. Her anal swabs remained positive for eight days, whereas her throat swabs were persistently negative by real-time PCR testing. Mild and asymptomatic cases, especially in children, might present with PCR negative pharyngeal/nasal swabs and PCR positive anal swabs. Those patients are potential sources of infection via fecal-oral transmission for COVID-19.

A Study to Evaluate Clinical and Bacteriological Profile and the Effect of the Treatment to Diabetic Foot Ulcer Patients Both in Outpatient and Hospitalized Settings in a Newly Set Up Diabetic Foot Care Unit.

The problem of diabetes continues to explode in our country today. India now has the dubious distinction of being called, “the diabetic capital of the world”. Diabetic foot ulcerations & infections are one of the leading causes of mortality & morbidity from diabetes. It is the most expensive complication of diabetes & the leading cause of hospitalization when compared to other complication of diabetes. The number of cases & problems associated with diabetic foot infection have dramatically increased in the recent years. In rural Bengal, the problem is grave as detection and treatment initiation is very late.METHODSA prospective observational study was conducted in Medicine & Surgery OPD and IPD of Bankura Sammilani Medical College for twenty weeks. Baseline characteristic were noted, ulcer classification was done followed by swab culture, debridement and antimicrobial therapy. Then outcome was observed.RESULTSMaximum patients were aged between 38 to 58 years, were male and were Wagner 1-3 classification. From culture report S. aureus was predominant followed by Enterobacteriaceae group and anaerobes. Amoxicillin-clavulanic acid combination was the most effective antibiotic followed by amikacin. Treatment was satisfactory with dressing, debridement and appropriate antibiotic.CONCLUSIONSS. aureus, Enterococcus, Pseudomonas aeruginosa, E. coli & Anaerobes were the most common causes of diabetic foot infections in my study, and were sensitive to the conventional antibiotics indicating that there is no evidence to suggest significant resistance to these antibiotics. Hence, their empirical usage, either oral or injectable (depending on the type of foot ulcer) is justified. Proper education regarding footwear & foot care is strongly recommended in such patients.

Aetiological Factors and Foetomaternal Outcome in PROM.

Premature rupture of membrane (PROM) refers to the disruption of foetal membranes before the beginning of labour, resulting in spontaneous leakage of amniotic fluid.Homeyr, GJ et al in his study “Amnio infusion for third trimester preterm rupture of membranes”, march 2014 states that premature rupture of membranes (PROM), or pre-labour rupture of membranes, is a condition occurring in pregnancy and defined it as rupture of membranes (breakage of the amniotic sac), commonly called breaking of the mother's water (s), more than one hour before the onset of labour.METHODSThe present study was carried out in the Department of Obstetrics and Gynaecology of Rajendra Institute of Medical Sciences (RIMS), Ranchi, during from April 2017 to October 2018. A total 595 cases were studied. The cases were divided into two groups, Study Group-195 cases and Control Group- 400 cases.RESULTSVarious factors were studied and analysed. Incidence of PROM in the present study was 7.49%. Out of 195 cases 68% were term PROM and 32% were preterm PROM. Mean age in the study group was 23 yrs. Risk factors associated with PROM in most of the cases was unknown (52%). Other causes were anaemia 34%, cervicovaginal infections 16%, malpresentation 10%, multiple gestation 3.5%, prior cervical surgery 1%, history of fall 1% PROM following coitus was 1.5%. In the present study the correlation between CRP and clinical chorioamnionitis was significant. Caesarean section was done was done in 19% cases in study group. There were 3 % cases of chorioamnionitis in study group. Out of 10 patients in the study group, maximum patients had puerperal sepsis (4 patients- 40%) followed by UTI (30%), wound infection (20%) and breast engorgement (10%).CONCLUSIONSPremature infant puts immense burden on the economy and health care resources of the country. Therefore, management of PPROM requires accurate diagnosis and evaluation of the risks and benefits of continued pregnancy or expeditious delivery. Once PROM is diagnosed, it is important to weigh the risk of PROM and prematurity and make the right choice for conservative management or active interventions. Adequate antenatal care should be advocated so that appropriate risk assessment can be done, and intervention provided where applicable. Neonatal units should also be equipped to be able to render necessary care for these preterm neonates thereby reducing the morbidity and mortality associated with PPROM.