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.

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.

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.

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.

Design, synthesis and biological activity of DB02 amino acid derivatives as HIV-1 non-nucleoside reverse transcriptase inhibitors / 药学学报

To improve the stability of amino acid ester derivatives of DB02, a series of 24 amide derivatives of DB02 amino acids as non-nucleoside HIV-1 reverse transcriptase inhibitor were designed and synthesized based on bioisosterism by replacing amino acid ester scaffold with more stable amide bond. The anti-HIV-1 activity of these compounds was evaluated by MTT assay and counting the number of syncytia. Most of the target compounds showed a potential anti-HIV-1 activity, among which compounds 2d, 2i, 2l, 2s, and 2w had better antiviral effect than lead compound DB02, with a therapeutic index > 1 000.00. Finally, the structure-activity relationship of these compounds was discussed, which provided new ideas for the further development of DB02 derivatives.

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

Prevalence of molecular and serological tests of the new coronavirus (SARS-CoV-2) in Carlos Chagas laboratory - Sabin group in Cuiabá

SUMMARY BACKGROUND: Coronavirus disease 2019, which is caused by the new severe acute respiratory syndrome coronavirus 2, became a pandemic in 2020 with a mortality rate of 2% and high transmissibility, thus making studies with an epidemiological profile essential. OBJECTIVES: The aim of this study was to characterize the population that performed the severe acute respiratory syndrome coronavirus 2 molecular and serological tests in Carlos Chagas Laboratory - Sabin Group in Cuiabá. METHODS: A retrospective cross-sectional study was carried out with all the samples collected from nasal swab tested by RT-PCR and serological for severe acute respiratory syndrome coronavirus 2 IgM/IgG from the population served between April and December 2020. FINDINGS: In the analysis period, 23,631 PCR-coronavirus disease 2019 examinations were registered. Of this total number of cases, 7,649 (32.37%) tested positive, while 15,982 (66.31%) did not detect viral RNA and 374 of the results as undetermined. The peak of positive RT-PCR performed in July (n=5,878), with 35.65% (n=2,096). A total of 8,884 tests were performed on serological test SOROVID-19, with a peak of 1,169 (57.16%) of the positive tests for severe acute respiratory syndrome coronavirus 2 in July. MAIN CONCLUSIONS: Molecular positivity and serological tests, both peaked in July 2020, were mostly present in women aged 20-59 years, characterizing Cuiabá as the epicenter of the Midwest region in this period due to the high rate of transmissibility of severe acute respiratory syndrome coronavirus 2.

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.

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.

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.

Role of telomerase reverse transcriptase on cell apoptosis of neutrophils in rats with acute necrotizing pancreatitis / 中华胰腺病杂志

Objective:To investigate the effects of telomerase reverse transcriptase (TERT) on neutrophils apoptosis in rats with acute necrotizing pancreatitis (ANP).Methods:Twenty-four Sprague Dawley (SD) rats were randomly divided into three groups including control group, ANP (3h、6h) group and TERT inhibitor(BIBR1532)group using random number method with 6 in each group. ANP rats were induced by retrograde injection of 5% sodium taurocholate into the pancreaticcobiliary duct. After 3 and 6 hours, the fresh neutrophils were collected and isolated from peripheral blood of ANP rats. Rats were intraperitoneally injected with 2 mg/kg BIBR1532. After ANP modeling for 3 h, rats were killed and peripheral neutrophils were collected. Subsequently, the expression of TERT mRNA in neutrophils was tested by real-time quantitative PCR; the protein levels of TERT, BCL-xL and Bax were determined by Western blotting; neutrophil apoptosis was detected by flow cytometry; TNF-α and IL-6 were assayed by Elisa; the rat pancreatic tissue was pathologically examined.Results:In neutrophils from control group, ANP 3 h group, ANP 6 h group and BIBR1532 group, TERT mRNA was 1.03±0.26, 3.31±1.07, 5.21±0.78 and 1.95±0.49; TERT protein expression was 0.09±0.03, 0.43±0.12, 0.58±0.11 and 0.22±0.07; Bcl-xL protein expression was 0.19±0.05, 0.50±0.07, 0.85±0.04 and 0.40±0.11; Bax protein expression was 0.29±0.08, 0.23±0.03, 0.17±0.02 and 0.43±0.12; apoptosis rate was 10.03±0.74%, 7.99±0.27%, 6.65±0.36% and 22.98±2.86%. TERT mRNA and protein expression and Bcl-xL protein expression in ANP 3 h and 6 h group were higher than those in control group, but Bax preotein expression and apoptosis rate were lower than those in control group; TERT mRNA and protein expression and Bcl-xL protein expression in BIBR1532 group were lower than those in ANP 3 h group, but Bax protein expression and apoptosis rate in BIBR1532 group were higher than those in ANP 3 h group; and all the differences were statistically significant (all P value <0.05). The level of TNF-α was [(96.67±27.12)ng/L, (382.30±46.33)ng/L and (206.88±36.42)ng/L], IL-6 was [(43.34±14.50)ng/L, (134.21±16.13)ng/L and (88.06±13.05)ng/L in control, ANP 3 h and BIBR1532 group; those in ANP 3 h group were all higher than those in control group, but those in BIBR1532 group were lower than those in ANP 3 h group; all the differences were statistically significant (all P value <0.05). Compared with ANP group, the morphology of pancreatic tissue was obviously alleviated in BIBER1532 group. Conclusions:TERT expression is obviously increased in peripheral neutrophils in ANP rats, and apoptosis rate of neutrophils from ANP rats is greatly increased after TERT inhibitor treatment, demonstrating that TERT could inhibit the apoptosis of peripheral neutrophil in ANP rats.

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.

Dificultades en la detección de genomas del nuevo coronavirus 2 (SARS CoV-2) / Pandemic and social inequiality: the popular neighborhoods of the Buenos Aires suburbs in preventive social isolation

RESUMEN El manejo de las infecciones virales respiratorias, tanto a nivel nacional como a nivel mundial, requiere resultados científicos de calidad. La reacción en cadena de la polimerasa de transcriptasa inversa (rRT-PCR, por su sigla en inglés) es considerada el "patrón de oro" para detectar el genoma del nuevo coronavirus 2 (SARS-CoV-2), agente causal de la enfermedad por el nuevo coronavirus (COVID-19) sobre todo en la fase aguda de la infección. Su uso es controvertido fuera de un contexto de exposición viral. El objetivo del presente trabajo es analizar escollos encontrados durante la detección del genoma del SARS-CoV-2 que pueden producir resultados falsos. Los falsos negativos de rRT-PCR pueden deberse al momento y la eficacia de la toma de la muestra, la congelación, el almacenamiento y la descongelación, y a la inactivación térmica de la virulencia. Además, las señales retardadas de los controles internos invalidan la negatividad. Por otra parte, las muestras con escaso material biológico llevan a conclusiones negativas falsas, por lo que determinar un umbral (número mínimo de células epiteliales) contribuirá a reducirlas. Sin embargo, la mayoría de los kits detectan ADN humano, pero no fueron calibrados para cuantificar carga celular. Los ácidos ribonucleicos nucleares (ARN) virales adheridos a guantes, tubos y gorros, -entre otros elementos-, son fuente de falsos positivos. Las farmacopeas sugieren que la contaminación externa se controle en series de 100 muestras con al menos una representatividad del 10%. Si se extrapola esta aproximación al laboratorio de análisis clínicos, en lugar de uno se deberían procesar al menos 10 controles negativos contiguos a 10 positivos cada 100 pruebas. Mejorar la detección por rRT-PCR implica un aumento de al menos 20% en el costo de los reactivos, por lo que se necesitan recursos adicionales.

ABSTRACT Emerging respiratory viral infections like the severe coronavirus disease (CoVID 19) caused by novel coronavirus 2 (SARS-CoV-2) require quality results for science-based responses. The reverse transcriptase polymerase chain reaction (rRT-PCR) is considered the gold standard for detecting SARS-CoV-2 (particularly in the acute phase of infection). The aim of the present work was to analyze pitfalls during the search of viral genomes. False negative conclusions are result of sampling timing, performances of swabbing, storage, and thawing and heat-infectivity inactivation. Samples with low biologic material also lead to false negatives. Qualitative controls to detect the presence of human DNA are available in several kits but they were not calibrated for quantification of human cell loads. Moreover, negativity cannot be reported for samples with delayed signals for the internal control (due to deficiency in extraction and/or retro transcription and/or or to the presence of rRT-PCR inhibitors). The viral RNA that may have stick on gloves, on tubes, caps, etc. may produce false positives. The International Pharmacopoeias recommend for external contamination to test at least 10% of the samples. Couples of 10 negative contiguous to 10 positive controls randomly distributed should be therefore included in each series of 100 rRT-PCR tests. These improvements increase the cost of each determination (at least by 20% only for the reactants) and require additional resources.

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.