SARS-CoV-2 and the ocular surface: test accuracy and viral load / SARS-CoV-2 e a superfície ocular: acurácia dos testes e carga viral

ABSTRACT Purpose: This study aimed to evaluate the pre-sence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the ocular surface of individuals clinically suspected of coronavirus disease 2019 (COVID-19) and determine the accuracy of different approaches of molecular testing on the ocular surface based on the nasopharyngeal positivity status for COVID-19. Methods: A total of 152 individuals with suspected COVID-19 symptoms who simultaneously underwent nasopharyngeal and two different tear film collection techniques for quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) were included. Tears were collected and randomized: one eye had the filter strip for the Schirmer test and the contralateral eye had conjunctival swab/cytology in the inferior fornix. All patients underwent slit lamp biomicroscopy. The accuracy of various ocular surface collection techniques used for the detection of SARS-CoV-2 RNA was determined. Results: Of the 152 patients enrolled in the study, 86 (56.6%) had COVID-19 confirmed by nasopharyngeal PCR. Both tear film collection techniques detected viral particles: the Schirmer test was positive in 16.3% (14/86) and the conjunctival swab/cytology in 17.4% (15/86), with no statistically significant differences. No positive ocular tests were found among those with negative nasopharyngeal PCR tests. The overall agreement of the ocular tests was 92.7%, and in combination, the sensitivity would increase to 23.2%. The mean cycle threshold values in the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests were 18.2 ± 5.3, 35.6 ± 1.4, and 36.4 ± 3.9, respectively. Compared with the nasopharyngeal test, the Schirmer (p=0.001) and conjunctival swab/cytology (p<0.001) tests had significantly different Ct values. Conclusion: The Schirmer (16.3%) and conjunctival swab (17.4%) tests were comparably capable of detecting SARS-CoV-2 RNA in the ocular surface by RT-PCR accurately based on nasopharyngeal status and demonstrated indistinct sensitivity and specificity. Simultaneous specimen sampling and processing from the nasopharyngeal, Schirmer, and conjunctival swab/cytology tests demonstrated significantly lower viral load in both ocular surface approaches than in the nasopharyngeal test. Ocular manifestations detected by slit lamp biomicroscopy were not associated with ocular RT-PCR positivity.

RESUMO Objetivo: Avaliar a presença de RNA de coronavírus 2 causador de síndrome respiratória aguda grave (SARS-CoV-2) na superfície ocular de indivíduos clinicamente suspeitos com COVID-19 e determinar a precisão de diferentes abordagens de testes moleculares na superfície ocular com base no status de positividade do RT-qPCR de nasofaringe para COVID-19. Métodos: 152 indivíduos com sintomas suspeitos para a COVID-19 foram submetidos a coleta de reação em cadeia da polimerase de nasofaringe simultaneamente a duas técnicas diferentes de coleta de filme lacrimal para RT-qPCR: aleatoriamente, um olho com a tira filtro do teste de Schirmer e, o olho contralateral, com citologia (swab) conjuntival no fórnice inferior. Todos os indivíduos foram submetidos à biomicroscopia com lâmpada de fenda. Resultados: Dos 152 pacientes, 86 (56,6%) tiveram a COVID-19 confirmada por PCR de nasofaringe. Ambas as técnicas de coleta detectaram partículas virais: o teste de Schirmer foi positivo em 16,3% (14/86) e a citologia conjuntival em 17,4% (15/86), sem diferenças estatisticamente significativas. Não houve testes oculares positivos entre aqueles com reação em cadeia da polimerase de nasofaringe negativo. A concordância geral dos testes oculares foi de 92,7% e, em combinação, a sensibilidade aumentaria para 23,2%. Os valores médios do limiar de ciclo nos testes de nasofaringe, Schirmer e citologia conjuntival foram 18,2 ± 5,3, 35,6 ± 1,4 e 36,4 ± 3,9, respectivamente. Conclusão: Os testes de Schirmer (16,3%) e swab conjuntival (17,4%) foram igualmente capazes de detectar RNA de SARS-CoV-2 na superfície ocular por RT-PCR e demonstraram sensibilidade e especificidade indistintas. A coleta simultânea de amostras ao processamento dos testes de RT-PCR de nasofaringe, Schirmer e citologia (swab) conjuntival demonstraram carga viral significativamente menor em ambas as abordagens da superfície ocular em comparação com o teste de nasofaringe. As manifestações oculares detectadas pela biomicroscopia com lâmpada de fenda não foram claramente associadas à positividade do RT-PCR ocular.

Tumor markers expression levels in gastric cancer patient's peripheral blood by rt-pcr assessment / Avaliação por rt-pcr de expressão de marcadores tumorais em sangue periférico de pacientes com câncer gástrico

ABSTRACT BACKGROUND: Hematological recurrence is the second most frequent cause of failure in the treatment of gastric cancer. The detection of circulating tumor markers in peripheral blood by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) method may be a useful tool to predict recurrence and determine the patient's prognosis. However, no consensus has been reached regarding the association between the tumor markers level in peripheral blood and its impact on patient survival. AIMS: To evaluate the expression of the circulating tumor markers CK20 and MUC1 in peripheral blood samples from patients with gastric cancer by qRT-PCR, and to verify the association of their expression levels with clinicopathological characteristics and survival. METHODS: A total of 31 patients with gastric adenocarcinoma were prospectively included in this study. CK20 and MUC1 expression levels were analyzed from peripheral blood by the qRT-PCR technique. RESULTS: There was no statistically significant (p>0.05) association between CK20 expression levels and clinical, pathological, and surgical features. Higher MUC1 expression levels were associated with female patients (p=0.01). There was a correlation between both gene levels (R=0.81, p<0.001), and CK20 level and tumor size (R=0.39, p=0.034). CONCLUSIONS: CK20 and MUC1 expression levels could be assessed by qRT-PCR from total peripheral blood samples of patients with gastric cancer. CK20 levels were correlated to MUC1 levels as well as to tumor size. There was no difference in disease-free survival and overall survival regarding both genetic markers expression in this series.

RESUMO RACIONAL: A recorrência hematológica é a segunda causa mais frequente de falha no tratamento do câncer gástrico. A detecção de marcadores tumorais circulantes no sangue periférico, pelo método de reação em cadeia da polimerase de transcrição reversa quantitativa (qRT-PCR) pode ser uma ferramenta útil para prever a recorrência e determinar o prognóstico do paciente. No entanto, ainda não foi alcançado consenso em relação à associação entre o nível de marcadores tumorais circulantes no sangue periférico e seu impacto na sobrevida do paciente. OBJETIVOS: Avaliar a expressão de CK20 e MUC1 em amostras de sangue periférico de pacientes com câncer gástrico por meio de qRT-PCR e verificar a associação dos níveis de expressão com características clinicopatológicas e sobrevida. MÉTODOS: Trinta e um pacientes com adenocarcinoma gástrico foram incluídos, prospectivamente. Os níveis de expressão de CK20 e MUC1 foram analisados a partir de sangue periférico por meio de qRT-PCR. RESULTADOS: Não houve associação estatisticamente significativa (p>0,05) entre os níveis de expressão de CK20 com características clínicas, patológicas e cirúrgicas. Níveis mais elevados de expressão de MUC1 estavam associados a pacientes do sexo feminino (p=0,01). Houve correlação entre os níveis de ambos os genes (R=0,81, p<0,001), nível de CK20 e tamanho do tumor (R=0,39, p=0,034). CONCLUSÕES: Os níveis de CK20 e MUC1 podem ser avaliados por qRT-PCR a partir de amostras de sangue periférico total de pacientes com câncer gástrico, os níveis de CK20 estavam correlacionados com os de MUC1, assim como tamanho do tumor. Não houve diferença de sobrevida global ou livre de doença em relação à expressão de ambos marcadores genéticos nesta série.

Associations of SARS-CoV-2 cycle threshold values with age, gender, sample collection setting, and pandemic period

ABSTRACT Cycle threshold (Ct) values in COVID-19 reverse-transcription polymerase chain reaction (RT-PCR) tests estimate the viral load in biological samples. Studies have investigated variables associated with SARS-CoV-2 viral load, aiming to identify factors associated with higher transmissibility. Using the results from tests performed between May/2020-July/2022 obtained from the database of a referent hospital in Sao Paulo, Brazil, we investigated associations between Ct values and patient's age, gender, sample collection setting and pandemic period according to the predominant SARS-CoV-2 variant locally. We also examined variations in Ct values, COVID-19 incidence, mortality, and vaccination coverage over time. The study sample included 42,741 tests. Gender was not significantly associated with Ct values. Age, sample collection setting and the pandemic period were significantly associated with Ct values even after adjustment to the multivariable model. Results showed lower Ct values in older groups, during the Gamma and Delta periods, and in samples collected in emergency units; and higher Ct values in children under 10 years old, home-based tests, during the Omicron period. We found evidence of a linear trend in the association between age and Ct values, with Ct values decreasing as age increases. We found no clear temporal associations between Ct values and local indicators of COVID-19 incidence, mortality, or vaccination between February/2020-November/2022. Our findings suggest that SARS-CoV-2 Ct values, a proxy for viral load and transmissibility, can be influenced by demographic and epidemiological variables.

Caracterización epidemiológica, clínica y de laboratorio en pacientes positivos persistentes a COVID-19

Introducción: La COVID-19 es una preocupación mundial, requiere enfoque integral para reducir la transmisión, comenzando por la detección de casos, atención hospitalaria y seguimiento posterior. Objetivo: Caracterizar a pacientes positivos persistentes a COVID-19 en cuanto a epidemiología, clínica y datos de laboratorio. Métodos: Se realizó un estudio descriptivo transversal en 16 pacientes positivos persistentes a SARS-CoV-2 diagnosticados por RCP-TR en hisopado nasofaríngeo, en el Hospital Comandante Manuel Fajardo Rivero de Santa Clara en el período de septiembre 2020 a noviembre 2020. Resultados: Predominó el sexo femenino en un 75 %, el grupo de edad más representativo fue de 40-59 años de edad (68,75 %), el 37,50 % de los casos fueron asintomáticos y el síntoma más frecuente fue la fiebre menor de siete días 31,25 %. Existió linfopenia en el hemograma inicial con media en 27,49, índice neutrófilo leucocitario por encima de tres en cuatro pacientes con una media inicial 3,42. Estadía hospitalaria de 20,75 días de promedio. La mitad no tenía historia de enfermedad conocida, la comorbilidad más frecuente fue la hipertensión arterial 43,75 %. El índice neutrófilo leucocitario por encima de tres en pacientes con comorbilidades, evolutivo para todos menor de tres. Conclusiones: Predominó el sexo femenino, el grupo de edad más representativo fue de 40-59 años, es frecuente que se presenten asintomáticos y la fiebre fue el síntoma más usual. Existió linfopenia en el hemograma inicial. La mitad de los contagiados sin comorbilidades. El índice neutrófilo leucocitario evolutivo fue menor de tres para todos los pacientes.

Introduction: COVID-19 is a global concern, it requires a comprehensive approach to reduce transmission, starting with case detection, hospital care and subsequent follow-up. Objective: To characterize persistent COVID-19 positive patients in terms of epidemiology, clinical and laboratory data. Methods: A cross-sectional descriptive study was carried out in 16 persistent SARS-CoV-2 positive patients diagnosed by RT-CPR in nasopharyngeal swab, at Comandante Manuel Fajardo Rivero Hospital of Santa Clara in the period from September 2020 to November 2020. Results: The female sex predominated in 75%, the most representative age group was 40-59 years of age (68.75%), 37.50% of the cases were asymptomatic and the most frequent symptom was fever less than seven days 31.25%. There was lymphopenia in the initial hemogram with an average of 27.49, and a leukocyte neutrophil index above three in 4 patients with an initial average of 3.42. Hospital stay of 20.75 days on average. Half had no history of known disease, the most frequent comorbidity was arterial hypertension 43.75 %. The neutrophil leukocyte index above 3 in patients with comorbidities, evolutionary for all pariente was less than 3. Conclusions: The female sex predominates, the most representative age group is 40-59 years, it is frequent that they present asymptomatic and fever is the most usual symptom. There is lymphopenia on the initial blood count. Half of those infected without comorbidities. The evolutionary leukocyte neutrophil index was less than 3 for all patients.

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

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

Genetic variation characteristics of HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019 / 中国基层医药

Objective:To analyze the genetic variation characteristics of the HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019. Methods:Twenty strains of influenza A virus (H3N2) were randomly selected from 10 network laboratories in Guizhou province for RNA extraction. Reverse transcriptase-polymerase chain reaction and sequencing were performed. The products were analyzed using bioinformatics software.Results:The nucleotide homology of the HA gene of the 20 strains was 97.7%-100%, which was highly homologous to the vaccine strains A/Hong-Kong/4801/2014 recommended by WHO in 2017 and A/Singapore-INFIMH/16-0019/2016 recommended by WHO in 2018, but they were significantly different from the vaccine strain A/Kansas/14/2017 recommended by WHO in 2019. Genetic analysis showed that the 20 strains were divided into two branches, and the strains that were prevalent in 2019 were located in different branches, with marked genetic differences. Key site analysis showed mutations in antigenic determinants A, B, C, and E and mutations in the anterior and posterior walls of receptor binding sites. Key site analysis also showed that there was an increase in the number of glycosylation sites compared with the vaccine strains prevalent in the same year. Genetic distance, antigen sites, and glycosylation sites were slightly different between virus strains prevalent in 2017-2018 and virus strains prevalent in 2019. Conclusion:The HA gene of the influenza A virus subtype H3N2 in Guizhou province from 2017 to 2019 showed heterogeneity and gene mutation, especially in 2019. Therefore, close monitoring of the genetic evolution of the influenza A virus subtype H3N2 is necessary.

Comparison of two isothermal methods for SARS-COV-2 screening in Callao, Peru

Objective: To compare the isothermal molecular screening techniques CPA and RT-LAMP, against the gold standard test, reverse transcription quantitative polymerase chain reaction (RT-qPCR), and to determine its agreement. Materials and Methods: Paired comparative case-control study. For the evaluation of the CPA method, 70 cases and 130 controls were used, while for RT-LAMP, 30 cases and 70 controls were used. The sensitivity and specificity of both tests were calculated. Subsequently, the bias-corrected Kappa index was calculated by resampling. Results: Both techniques have adequate and equivalent values of sensitivity (RT-LAMP: 82.8%, CPA: 83%) and specificity (RT-LAMP and CPA: 91.5%), as well as a high concordance (88%), and Kappa-index (0.72). Conclusion: Both isothermal molecular screening techniques are suitable for SARS-CoV-2 screening, with a similar sensitivity and specificity.

Objetivo : Comparar las técnicas de cribado molecular isotérmico CPA y RT-LAMP, frente a la prueba de referencia, la reacción en cadena de la polimerasa cuantitativa de transcripción inversa (RT-qPCR), y determinar su concordancia. Materiales y métodos : Estudio comparativo de casos y controles emparejados. Para la evaluación del método CPA se utilizaron 70 casos y 130 controles, mientras que para la RT-LAMP se utilizaron 30 casos y 70 controles. Se calcularon la sensibilidad y la especificidad de ambas pruebas. Posteriormente, se calculó el índice Kappa corregido por sesgo mediante un nuevo muestreo. Resultados: Ambas técnicas presentan valores adecuados y equivalentes de sensibilidad (RT-LAMP: 82,8 %, CPA: 83 %) y especificidad (RT-LAMP y CPA: 91,5 %), así como una alta concordancia (88 %), y un índice Kappa (0,72). Conclusiones: Ambas técnicas de cribado molecular isotérmico son adecuadas para el cribado del SARS-CoV-2, con una sensibilidad y especificidad similares.

A Comparative Study on the Efficiency of Commercial Reverse Transcriptase–Polymerase Chain Reaction Kits for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 Infections

Background: Real?time reverse transcriptase–polymerase chain reaction (RT?PCR) kits have been reliably employed for the diagnosis of coronavirus disease 2019 (COVID?19) by the detection of the severe acute respiratory syndrome coronavirus 2 (SARS?CoV?2) RNA since the beginning of the disease outbreak. In consideration of reliable diagnosis, apart from RT?PCR, the isothermal nucleic acid amplification?based point-of-care automated kits have also been tagged as a simpler and rapid alternative to the conventional techniques. Currently, the availability of a better diagnostic method for COVID?19 when compared to RT?PCR is nil. The most important step in the detection of SARS?CoV?2 in a RT?PCR diagnostic laboratory is to identify and employ RT?PCR kits with higher sensitivity as well as specificity. Objectives: This study aimed to study commercially available RT?PCR kits for the detection of SARS?CoV?2 infections. Methods: The performance of seven different RT-PCR kits from different manufacturers used for diagnosis of COVID-19 in Govt Theni Medical College and Hospital, Theni, Tamil Nadu were analysed. Nasopharyngeal and oropharyngeal swabs were collected from patients and subjected to RT-PCR using these kits. Results and Conclusion: The sensitivities and batch effects of the assessed kits were slightly different for different targets, for SARS?CoV?2 detection in nasopharyngeal swab specimens. Examination of COVID-19 kits should be done using currently employed kits in routine diagnosis for better efficiency

Troponina de alta sensibilidade no prognóstico de pacientes internados em terapia intensiva por COVID-19: um estudo de coorte longitudinal latino-americano / High-sensitivity troponin in the prognosis of patients hospitalized in intensive care for COVID-19: a Latin American longitudinal cohort study

RESUMO Objetivo: O presente estudo avaliou a prevalência da elevação da troponina e sua capacidade de prever a mortalidade em 60 dias em pacientes com COVID-19 internados em unidade de terapia intensiva. Metódos: Um estudo longitudinal prospectivo e unicêntrico foi realizado em uma coorte de pacientes em terapia intensiva devido a diagnóstico de COVID-19 confirmado, usando teste de reação em cadeia da polimerase em tempo real de maio a dezembro de 2020. Uma curva Característica de Operação do Receptor foi construída para predizer o óbito de acordo com o nível de troponina, calculando a área sob a curva e seus intervalos de confiança. Um modelo de risco proporcional de Cox foi gerado para relatar as razões de risco com intervalo de confiança de 95% e o valor de p para sua associação com mortalidade em 60 dias. Resultados: Foram incluídos 296 pacientes com taxa de mortalidade em 60 dias de 51%. A troponina foi positiva em 39,9% (29,6% versus 49,7% em sobreviventes e não sobreviventes, respectivamente). Foi encontrada área sob a curva de 0,65 (IC95% 0,59 - 0,71) para prever a mortalidade. O modelo univariado de Cox demonstrou razão de risco de 1,94 (IC95% 1,41 - 2,67) e p < 0,001, mas essa relação não se manteve no modelo de análise multivariado, no qual a razão de risco foi de 1,387 (IC95% 0,21 - 1,56) e o valor de p foi de 0,12. Conclusão: A elevação da troponina é frequentemente encontrada em pacientes em terapia intensiva para COVID-19. Embora seus níveis sejam maiores em pacientes que vão a óbito, nenhuma relação foi encontrada em um modelo de análise multivariado, o que indica que a troponina não deve ser utilizada como único marcador prognóstico de mortalidade nessa população.

ABSTRACT Objective: The current study assessed the prevalence of troponin elevation and its capacity to predict 60day mortality in COVID-19 patients in intensive care. Methods: A longitudinal prospective single-center study was performed on a cohort of patients in intensive care due to a COVID-19 diagnosis confirmed using real-time test polymerase chain reaction from May to December 2020. A Receiver Operating Characteristic curve was constructed to predict death according to troponin level by calculating the area under the curve and its confidence intervals. A Cox proportional hazards model was generated to report the hazard ratios with confidence intervals of 95% and the p value for its association with 60day mortality. Results: A total of 296 patients were included with a 51% 60-day mortality rate. Troponin was positive in 39.9% (29.6% versus 49.7% in survivors and non-survivors, respectively). An area under the curve of 0.65 was found (95%CI: 0.59 - 0.71) to predict mortality. The Cox univariate model demonstrated a hazard ratio of 1.94 (95%CI: 1.41 - 2.67) and p < 0.001, but this relationship did not remain in the multivariate model, in which the hazard ratio was 1.387 (95%CI: 0.21 - 1.56) and the p value was 0.12. Conclusion: Troponin elevation is frequently found in patients in intensive care for COVID-19. Although its levels are higher in patients who die, no relationship was found in a multivariate model, which indicates that troponin should not be used as an only prognostic marker for mortality in this population.

Effect of lateral decubitus acquisition in accuracy and lung severity estimation of chest computed tomography in children with suspected COVID-19

ABSTRACT Objective To compare inter-rater reliability, diagnostic accuracy, and extension of pulmonary involvement in children with suspected COVID-19 submitted to supine or supine and lateral decubitus computed tomography imaging. Methods Retrospective study carried out between March 2020 and March 2021 with patients submitted to reverse transcription-polymerase chain reaction testing and chest computed tomography. Patients were divided into two groups: supine or supine and lateral decubitus imaging. Standardized reporting systems of computed tomographic findings in COVID-19 and chest computed tomography score were used. Results One hundred and seventeen patients were enrolled. Moderate to substantial inter-rater reliability was observed for standardized reporting systems (weighted kappa, 0.553-0.764; p<0.001). Inter-rater reliability for the chest computed tomography score was substantial (weighted kappa, 0.620-0.670; p<0.001). Standardized reporting systems failed to predict COVID-19 in children, regardless of additional lateral decubitus imaging (area under the receiver operating characteristic curve, 0.491-0.608). Chest computed tomography scores assigned to lateral decubitus images were significantly lower. Conclusion Additional lateral decubitus imaging does not improve the accuracy of standardized reporting systems of computed tomographic findings in COVID-19 but may provide a more accurate estimation of lung involvement in uncooperative patients.

Thorax computed tomography findings and anti-SARS-CoV-2 immunoglobulin G levels in polymerase chain reaction-negative probable COVID-19 cases

SUMMARY OBJECTIVE: This study aimed to evaluate the SARS-CoV-2 immunoglobulin G (IgG) levels after 6 months of polymerase chain reaction (PCR) negative but assumed to be COVID-19 positive cases to investigate the relationship between IgG levels and thoracic computed tomography (CT) findings. METHODS: This was a single-center study that included patients whose PCR test results were negative at least three times using nasopharyngeal swabs but had clinical findings of COVID-19 and thoracic CT findings compatible with viral pneumonia. Six months after discharge, the IgG antibodies were analyzed. The cutoff value for negative and positive serology was defined as <1.4 (index S/C) and ≥1.4 (index S/C), respectively. In addition, the patients were categorized according to their thoracic CT findings as high (typical) and low (atypical). Also, the patients were grouped into classes as <5% lung involvement versus ≥5% lung involvement. RESULTS: The patients' mean age was 49.78±12.96 years. PCR was negative, but patients with COVID-19 symptoms who had SARS-CoV-2 IgG positive were 81.9% (n=95). The antibody titer and lung involvement ≥5% were statistically significantly higher in SARS-CoV-2 IgG positive cases (p<0.001 and p=0.021). Age and chest CT findings were the risk factors for lung involvement (OR=1.08, p<0.001 and OR=2.19, p=0.010, respectively). CONCLUSION: This study is valuable because increasing severity (≥5%) of lung involvement appears to be associated with high and persistent IgG antibody titers. In probable cases of COVID-19, even if the PCR test is negative, high IgG titers 6 months after discharge can predict the rate of lung parenchymal involvement.

Chlamydia trachomatis, virus herpes simple-2 y Neisseria gonohrroeae: prevalência y factores de riesgo en estudiantes / Chlamydia trachomatis, herpes simplex virus-2 and Neisseria gonorrhoeae: Prevalence and risk factors in students

RESUMEN Objetivo Determinar la prevalencia de Chlamydia trachomatis (CT), virus herpes simple-2 (VHS-2) y N. gonorrhoeae (NG) y los factores de riesgo relacionados con la infección, en un grupo de estudiantes universitarios de la ciudad de Medellín. Metodología Se realizó un estudio descriptivo en un grupo de 323 estudiantes universitarios. A través de un formulario en línea, se realizó el reporte de los factores de riesgo y síntomas relacionados con infecciones de transmisión sexual (ITS) y luego se determinó la presencia de anticuerpos IgG y IgM para CT y VHS-2 y se realizó una prueba de PCR-RT para detectar NG y CT. Resultados La frecuencia de IgG para CT fue del 13% y la positividad para IgM fue del 11,9%. La frecuencia de IgG para VHS-2 fue del 11,8% y la frecuencia de CT y NG por la prueba PCR-RT fue del 1,5% y del 0%, respectivamente. Los factores de riesgo más frecuentes fueron: vida sexual activa en el 96,9%, uso algunas veces o nunca del condón en un 75,2%. Reportaron que tenían secreción genital el 13,6% de los estudiantes; úlceras, el 2,8%; verrugas, el 5,3%; ardor al orinar, el 15,5%; ampollas, el 4,6%, y diagnóstico previo de una ITS, el 18,9% de los estudiantes. Conclusión Se encontró CT y VHS-2 entre los jóvenes estudiados y además una alta frecuencia de factores de riesgo para la adquisición de ITS. Se recomienda mejorar las campañas de prevención y diagnóstico de las ITS en los jóvenes universitarios.

ABSTRACT Objective The aim of this study was to determine the prevalence of Chlamydia trachomatis (CT), Herpes Simple-2 virus (HSV-2) and N. gonorrhoeae (NG), and the risk factors related to the infection in a group of college students in the city of Medellín, Colombia. Methods A descriptive study was carried out in a group of 323 university students. Through an online form, the risk factors and symptoms related to sexually transmitted infection (STI) were reported, and then the presence of IgG and IgM antibodies for CT and HSV-2 was determined, and RT-PCR testing was performed to detect NG and CT. Results 13% was the IgG frequency for CT while 11.9% was for IgM. The frequency for IgG for VHS-2 was 11.8 while the frequencies determined by RT-PCR for CT and NG were 1.5% and 0.0% respectively. The risk factors most commonly associated were active sex life, 96.9%, and random use of condom, 75.2%. It was also found that 13.6% of the students had genital secretions, 2.8% had ulcers, 5.3% had genital warts, 4.6% had blisters, 15.5% had dysuria, and 18.9% had a previous STI diagnosis. Conclusions CT and HVS-2 were found among college students, besides a series of risk factors associated with STI. It is recomended to improve prevention and diagnosis campaigns among young college students.

Open-source real-time quantitative RT-PCR-based on a RNA standard for the assessment of SARS-CoV-2 viral load

BACKGROUND Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target genes by molecular methods has been chosen as the main approach to identify individuals with Coronavirus disease 2019 (COVID-19) infection. OBJECTIVES In this study, we developed an open-source RNA standard-based real-time quantitative RT-PCR (RT-qPCR) assay for quantitative diagnostics of SARS-CoV-2 from nasopharynx, oropharynx, saliva and plasma samples. METHODS AND FINDINGS We evaluated three SARS-CoV-2 target genes and selected the RNA-dependent RNA polymerase (RdRp) gene, given its better performance. To improve the efficiency of the assay, a primer gradient containing 25 primers forward and reverse concentration combinations was performed. The forward and reverse primer pairs with 400 nM and 500 nM concentrations, respectively, showed the highest sensitivity. The LOD95% was ~60 copies per reaction. From the four biological matrices tested, none of them interfered with the viral load measurement. Comparison with the AllplexTM 2019-nCoV assay (Seegene) demonstrated that our test presents 90% sensitivity and 100% specificity. MAIN CONCLUSIONS We developed an efficient molecular method able to measure absolute SARS-CoV-2 viral load with high replicability, sensitivity and specificity in different clinical samples.

Chest computed tomography in the diagnosis of COVID-19 in patients with false negative RT-PCR / Tomografia computadorizada de tórax no diagnóstico de COVID-19 em pacientes com resultado falso-negativo na RT-PCR

ABSTRACT Objective To evaluate the role of chest computed tomography in patients with COVID-19 who presented initial negative result in reverse transcriptase-polymerase chain reaction (RT-PCR). Methods A single-center, retrospective study that evaluated 39 patients with negative RT-PCR for COVID-19, who underwent chest computed tomography and had a final clinical or serological diagnosis of COVID-19. The visual tomographic classification was evaluated according to the Consensus of the Radiological Society of North America and software developed with artificial intelligence for automatic detection of findings and chance estimation of COVID-19. Results In the visual tomographic analysis, only one of them (3%) presented computed tomography classified as negative, 69% were classified as typical and 28% as indeterminate. In the evaluation using the software, only four (about 10%) had a probability of COVID-19 <25%. Conclusion Computed tomography can play an important role in management of suspected cases of COVID-19 with initial negative results in RT-PCR, especially considering those patients outside the ideal window for sample collection for RT-PCR.

RESUMO Objetivo Avaliar o papel da tomografia computadorizada de tórax em pacientes com COVID-19 que apresentaram reação em cadeia da polimerase via transcriptase reversa (RT-PCR) inicial falsamente negativa. Métodos Estudo retrospectivo de centro único que avaliou 39 pacientes com RT-PCR negativa para COVID-19, submetidos à tomografia computadorizada de tórax e que tiveram diagnóstico final clínico ou serológico de COVID-19. A classificação tomográfica visual foi avaliada de acordo com o Consenso da Radiological Society of North America e o software desenvolvido com inteligência artificial para detecção automática de achados e estimativa de probabilidade de COVID-19. Resultados Na análise tomográfica visual, somente um deles (3%) apresentou tomografia computadorizada classificada como tendo resultado negativo, 69% foram classificados como típicos e 28% como indeterminados. Na avaliação com uso de software, somente quatro (cerca de 10%) tiveram probabilidade de COVID-19 <25%. Conclusão A tomografia computadorizada pode desempenhar papel importante no manejo de casos suspeitos de COVID-19 com RT-PCR inicialmente negativa, principalmente levando-se em consideração os pacientes que estão fora da janela ideal para coleta de amostra para RT-PCR.

Hallazgos incidentales de COVID-19 en PET/CT 18F-FDG de pacientes asintomáticos con cáncer en dos instituciones de salud de Bogotá, Colombia / Incidental findings of COVID-19 in F18-FDG PET/CT from asymptomatic patients with cancer in two healthcare institutions in Bogotá, Colombia

La COVID-19 es la infección viral causada por el SARS-CoV-2 y declarada por la Organización Mundial de la Salud (OMS) como pandemia. Los pacientes con cáncer tienen un mayor riesgo de adquirir la infección y un peor pronóstico, ya que deben asistir a visitas médicas en diferentes centros hospitalarios, reciben tratamientos médicos y quirúrgicos y deben someterse a estudios diagnósticos como la PET/CT en servicios de medicina nuclear, lo que es ocasión para el hallazgo incidental de la infección. Se presentan las imágenes de tomografías computarizadas por emisión de positrones con 18-fluorodesoxiglucosa (F18) (Positron Emission Tomography and Computed Tomography with 2-deoxy-2-[fluorine-18]fluoro-D-glucose, PET/CT F18-FDG) en las que se evidenció la COVID-19 en pacientes con diversas enfermedades oncológicas, pero sin sintomatología respiratoria.

COVID-19 is the viral infection caused by SARS-CoV-2 declared by the World Health Organization (WHO) as a pandemic. Patients with cancer have a higher risk to acquire the infection and worse prognosis as they have to attend more medical visits in healthcare institutions, receive medical and surgical treatments, and be subjected to diagnostic studies such as PET/CT in nuclear medicine services where the infection may be an incidental finding. We present here F18-FDG PET/CT (Positron Emission Tomography and Computed Tomography with 2-deoxy-2-[fluorine-18]fluoro-D-glucose), images with findings of COVID-19 from patients with different oncological conditions but no respiratory symptoms.

SARS-CoV-2 y RT-PCR en pacientes asintomáticos: resultados de una cohorte de trabajadores del Aeropuerto Internacional El Dorado de Bogotá, 2020 / SARS-CoV-2 and RT-PCR in asymptomatic patients: Results of a cohort of workers at El Dorado International Airport in Bogotá, 2020

Introducción. La pandemia de COVID-19 ha ocasionado cerca de 25 millones de casos en el mundo. Se ha descrito que los pacientes asintomáticos pueden ser fuentes de transmisión. Sin embargo, es difícil detectarlos y no es claro su papel en la dinámica de transmisión del virus, lo que obstaculiza la implementación de estrategias para la prevención. Objetivo. Describir el comportamiento de la infección asintomática por SARS-CoV-2 en una cohorte de trabajadores del Aeropuerto Internacional El Dorado "Luis Carlos Galán Sarmiento" de Bogotá, Colombia. Materiales y métodos. Se diseñó una cohorte prospectiva de trabajadores del Aeropuerto El Dorado. El seguimiento se inició en junio de 2020 con una encuesta a cada trabajador para caracterizar sus condiciones de salud y trabajo. Cada 21 días se tomó una muestra de hisopado nasofaríngeo para detectar la presencia del SARS-CoV-2 mediante reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR). Se analizó el comportamiento del umbral del ciclo (cycle threshold) de los genes ORFlab y N según el día de seguimiento. Resultados. En los primeros tres seguimientos de la cohorte se encontró una incidencia de la infección por SARS-CoV-2 del 16,51 %. La proporción de contactos positivos fue del 14,08 %. La mediana del umbral del ciclo fue de 33,53. Conclusión. Se determinaron las características de la infección asintomática por el SARS-CoV-2 en una cohorte de trabajadores. La detección de infectados asintomáticos sigue siendo un reto para los sistemas de vigilancia epidemiológica.

Introduction: The 2019 coronavirus pandemic (COVID-19) has caused around 25 million cases worldwide. Asymptomatic patients have been described as potential sources of transmission. However, there are difficulties to detect them and to establish their role in the dynamics of virus transmission, which hinders the implementation of prevention strategies. Objective: To describe the behavior of asymptomatic SARS-CoV-2 virus infection in a cohort of workers at the El Dorado "Luis Carlos Galán Sarmiento" International Airport in Bogotá, Colombia. Materials and methods: A prospective cohort of 212 workers from the El Dorado airport was designed. The follow-up began in June, 2020. A survey was used to characterize health and work conditions. Every 21 day, a nasopharyngeal swab was taken to identify the presence of SARS-CoV-2 using RT-PCR. We analyzed the behavior of the cycle threshold (ORFlab and N genes) according to the day of follow-up. Results: In the first three follow-ups of the cohort, we found an incidence of SARS-CoV-2 infection of 16.51%. The proportion of positive contacts was 14.08%. The median threshold for cycle threshold was 33.53. Conclusion: We characterized the asymptomatic SARS-CoV-2 infection in a cohort of workers. The identification of asymptomatic infected persons continues to be a challenge for epidemiological surveillance systems.

COVID-19: clinical and laboratory manifestations in novel coronavirus infection / COVID-19: manifestações clínicas e laboratoriais na infecção pelo novo coronavírus

ABSTRACT COVID-19 is a highly contagious disease caused by the coronavirus of severe acute respiratory syndrome 2 (SARS-CoV-2). In 2020, due to the outbreak, it was considered by the World Health Organization (WHO) as a pandemic. The infection caused by the novel coronavirus has high mortality in a small portion of the infected population, especially in elderly, immunosuppressed, diabetic, cardiac, and hypertensive individuals. Many infected are asymptomatic (and may be carriers) or present mild or moderate flu-like symptoms. The most severe clinical picture of COVID-19 is characterized by an inflammatory cytokine storm, with hematological changes and coagulation dysfunction, which can lead to tissue damage and death. Nonspecific laboratory biomarkers may be either increased or decreased as the course of the disease progresses and are often useful in predicting complications of the disease, such as the use of D-dimer and platelet/lymphocyte ratio. Specific laboratory diagnosis is based on the detection of viral ribonucleic acid (RNA) by real-time polymerase chain reaction (RT-PCR) of nasal and oropharyngeal swab samples; it is more effective when performed in the first days after symptom onset. Serological tests are useful in detecting the immune response, since both class M (IgM) and class G (IgG) immunoglobulin antibodies can be detected seven days after the onset of clinical symptoms, and may extend for more than 25 days, although not exempting the individual from remaining infectious, depending on their viral load and clinical presentation. The rational use of specific laboratory markers must respect the disease chronology, and the correct interpretation may provide subsidies for a better management of affected patients, as well as identifying asymptomatic carriers or those with mild symptoms.

RESUMEN La COVID-19 es una enfermedad altamente contagiosa causada por el coronavirus del síndrome respiratorio agudo grave (SARS-CoV-2). En 2002, a causa del brote, fue reconocida como una pandemia por la Organización Mundial de la Salud (OMS). La infección por el nuevo coronavirus provoca alta mortalidad en una pequeña parcela de la población infectada, especialmente en ancianos, pacientes inmunodeprimidos, diabéticos, cardiópatas e hipertensos. Muchos infectados son asintomáticos (y pueden ser portadores) o presentan síntomas leves a moderados, como en un estado gripal. El cuadro clínico de la COVID-19 en la forma más grave es caracterizado por una tormenta inflamatoria de citoquinas, con cambios hematológicos y de la coagulación que pueden llevar a daño tisular y muerte. Pruebas de laboratorio inespecíficas pueden presentar tasas más altas o bajas según el curso de la enfermedad, y muchas veces son útiles en la predicción de complicaciones, como el uso del dímero D y la ratio plaquetas/linfocitos. El diagnóstico de laboratorio específico se basa en la detección del ácido ribonucleico (ARN) viral por reacción en cadena de la polimerasa (PCR) en tiempo real de muestras de hisopado nasal y orofaríngeo; es más efectiva en los primeros días tras el inicio de los síntomas. Pruebas serológicas son útiles para detectar la respuesta inmune, pues tanto los anticuerpos de la inmunoglobulina M (IgM) como de la G (IgG) pueden se detectar siete días después del inicio de los síntomas clínicos, y pueden permanecer por más de 25 días, aunque no eximen al individuo de seguir infeccioso, dependiendo de su carga viral y presentación clínica. El uso racional de los marcadores de laboratorio específicos debe respetar la cronología de la enfermedad, y la interpretación correcta puede proporcionar recursos para un mejor manejo de los pacientes afectados, así como identificar portadores asintomáticos o con pocos síntomas.

RESUMO COVID-19 é uma doença altamente contagiosa provocada pelo coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2). Em 2020, devido ao surto, foi caracterizada pela Organização Mundial da Saúde (OMS) como pandemia. A infecção causada pelo novo coronavírus tem alta mortalidade em uma pequena parcela da população infectada, especialmente em indivíduos idosos, imunodeprimidos, diabéticos, cardiopatas e hipertensos. Muitos infectados são assintomáticos (e podem ser portadores) ou apresentam sintomas leves a moderados, semelhantes ao estado gripal. O quadro clínico da COVID-19 na forma mais severa é caracterizado por uma tempestade inflamatória de citocinas, com alterações hematológicas e da coagulação que podem levar ao dano tecidual e morte. Exames laboratoriais inespecíficos podem apresentar-se mais elevados ou diminuídos conforme o curso da doença, e muitas vezes são úteis na predição de complicações, como o uso do D-dímero e a razão plaqueta/linfócitos. O diagnóstico laboratorial específico se baseia na detecção do ácido ribonucleico (RNA) viral por reação em cadeia da polimerase em tempo real (RT-PCR) de amostras de suabe nasal e orofaríngeo; é mais efetivo nos primeiros dias após o início dos sintomas. Testes sorológicos são úteis na detecção da resposta imune, pois tanto os anticorpos da imunoglobulina da classe M (IgM) quanto da classe G (IgG) podem ser detectados após sete dias do início dos sintomas clínicos, podendo se estender por mais de 25 dias, embora não isente o indivíduo de continuar infectante, dependendo de sua carga viral e apresentação clínica. O uso racional dos marcadores laboratoriais específicos deve respeitar a cronologia da doença, e a interpretação correta pode fornecer subsídios para um melhor manejo dos pacientes acometidos, bem como identificar portadores assintomáticos ou com pouco sintomas.

Analysis of 8 274 cases of new coronavirus nucleic acid detection and co-infection in Wuhan / 中华检验医学杂志

Objective@#To investigate the positive rate for 2019-nCoV tests and co-infections in Wuhan district.@*Methods@#A total of 8 274 cases in Wuhan were enrolled in this cross-sectional study during January 20 to February 9, 2020, and were tested for 2019-nCoV using fluorescence quantitative PCR. Both respiratory tract samples (nasopharynx, oropharynx, sputum and alveolar lavage fluid) and non-respiratory tract samples (urine, feces, anal swabs, blood and conjunctival sac swabs) were collected. If both orf1ab and N genes are positive, they are classified as nucleic acid test positive group; if both orf1ab and N genes are negative, they are classified as negative group; if single gene target is positive, they are classified as suspicious group. Individuals were divided into male group and female group according to sex. At the same time, 316 patients were tested for 13 respiratory pathogens by multiplex PCR.@*Results@#Among the 8 274 subjects, 2 745 (33.2%) were 2019-nCoV infected; 5 277 (63.8%) subjects showed negative results in the 2019-nCoV nucleic acid test; and 252 cases (3.05%) was not definitive (inconclusive result). The age of cases with COVID-19 patients and inconclusive cases was significantly higher than that of cases without 2019-nCoV infection (40 vs 56, t=27.569, P<0.001; 52 vs 56, t=6.774, P<0.001). The positive rate of 13 respiratory pathogens multiple tests was significantly lower in 104 subjects who were positive for 2019-nCoV compared with those in subjects who were negative for 2019-nCoV test (5.77% vs 18.39%, χ2=24.105, P=0.003). Four types of respiratory tract samples and five types of non-respiratory tract samples were found to be positive for 2019-nCoV nucleic acid test.@*Conclusion@#The 2019-nCoV nucleic acid positive rate in male is higher than in female. Co-infections should be pay close attention in COVID-19 patients. 2019-nCoV nucleic acid can be detected in non-respiratory tract samples.

Case of the Index Patient Who Caused Tertiary Transmission of COVID-19 Infection in Korea: the Application of Lopinavir/Ritonavir for the Treatment of COVID-19 Infected Pneumonia Monitored by Quantitative RT-PCR

Since mid-December of 2019, coronavirus disease 2019 (COVID-19) infection has been spreading from Wuhan, China. The confirmed COVID-19 patients in South Korea are those who came from or visited China. As secondary transmissions have occurred and the speed of transmission is accelerating, there are rising concerns about community infections. The 54-year old male is the third patient diagnosed with COVID-19 infection in Korea. He is a worker for a clothing business and had mild respiratory symptoms and intermittent fever in the beginning of hospitalization, and pneumonia symptoms on chest computerized tomography scan on day 6 of admission. This patient caused one case of secondary transmission and three cases of tertiary transmission. Hereby, we report the clinical findings of the index patient who was the first to cause tertiary transmission outside China. Interestingly, after lopinavir/ritonavir (Kaletra, AbbVie) was administered, β-coronavirus viral loads significantly decreased and no or little coronavirus titers were observed.

Xp11 neoplasma with melanocytic differentiation: a clinicopathological analysis / 中华病理学杂志

Objective@#To investigate the clinical, histologic and immunophenotypic features, genetic alterations and prognosis of the rare Xp11 neoplasm with melanocytic differentiation.@*Methods@#Twenty-one cases were selected from the Department of Pathology, Jingling Hospital, Nanjing University School of Medicine from May 2008 to May 2018. The clinicopathologic, immunohistochemical, molecular analysis and follow-up details were collected.@*Results@#There were 7 males and 14 females, with their ages ranging from 4 to 57 years (mean 32.8 years). The tumors were located in kidney (11 cases), pelvis (three cases), and in pancreas, retroperitoneum, adrenal gland, small intestine, prostate, cervix and appendix (one case each). Microscopically, most tumors shared similar morphology such as purely nested or sheet-like architectures separated by a delicate vascular network, purely epithelioid cells with clear to granular eosinophilic cytoplasm, lacks of papillary structures, spindle cell or fat components, uniform round to oval nuclei with small visible nucleoli, and in most of them (16/21) melanin pigment. Immunohistochemically, all cases showed moderately (2+) or strongly (3+) positive staining for TFE3 and Cathepsin K. HMB45 and Melan A were focally expressed in three of 21 cases, while the remaining cases showed typically moderate(2+) or strong (3+) expression. None of the cases were immunoreactive for SMA, desmin, CKpan, S-100 and PAX8. All cases showed TFE3 rearrangement using fluorescence in-situ hybridization (FISH). Fusion FISH assays detected SFPQ-TFE3 gene fusion in 16 cases, NONO-TFE3 gene fusion in two, ASPL-TFE3 and MED15-TFE3 gene fusions in one case each. Polymerase chain reaction and direct sequencing detected SFPQ-TFE3 gene fusion in nine cases, NONO-TFE3 and MED15-TFE3 gene fusions in one case each. Clinical follow-up was available for 15 patients for 12 to 74 months. Six patients died of the disease; and three had recurrences and/or metastases. Six patients were alive with no evidence of disease after initial resection.@*Conclusions@#Xp11 neoplasm with melanocytic differentiation has unique morphologic, immunophenotypic and genetic characteristics. The tumor is aggressive, and should be differentiated from Xp11 translocation RCC and perivascular epithelioid cell tumor.