Cycle threshold predicted mortality in a cohort of patients with hematologic malignancies infected with SARS-CoV-2 / El umbral de ciclado predijo la mortalidad en una cohorte de pacientes conneoplasias hematológicas infectados con SARS-CoV-2 / Microbiología clinica y enfermedades infecciosas

Abstract When a SARS-CoV-2 RT-qPCR test is performed, it may determine an indirect measureof viral load called cycle threshold (Ct). Respiratory samples with Ct <25.0 cycles are consideredto contain a high viral load. We aimed to determine whether SARS-CoV-2 Ct at diagnosis couldpredict mortality in patients with hematologic malignancies (lymphomas, leukemias, multiplemyeloma) who contracted COVID-19. We included 35 adults with COVID-19 confirmed by RT-qPCR performed at diagnosis. We evaluated mortality due to COVID-19 rather than mortalitydue to the hematologic neoplasm or all-cause mortality. Twenty-seven (27) patients survivedand 8 died. The global mean Ct was 22.8 cycles with a median of 21.7. Among the survivors,the mean Ct was 24.2, and the median Ct value was 22.9 cycles. In the deceased patients, themean Ct was 18.0 and the median Ct value was 17.0 cycles. Using the Wilcoxon Rank Sum test,we found a significant difference (p = 0.035). SARS-CoV-2 Ct measured in nasal swabs obtainedat diagnosis from patients with hematologic malignancies may be used to predict mortality.

Resumen Cuando se realiza una RT-qPCR para SARS-CoV-2, es posible determinar una medidaindirecta de la carga viral llamada umbral de ciclado (Ct). Las muestras respiratorias con Ct<25,0 ciclos se consideran de alta carga viral. Nos propusimos determinar si el Ct para SARS-CoV-2 al diagnóstico predice la mortalidad en pacientes con neoplasias hematológicas (linfomas,leucemias, mielomas) que contrajeron COVID-19. Incluimos 35 adultos con COVID-19 confirmadopor RT-qPCR al diagnóstico. Evaluamos la mortalidad por COVID-19, no la mortalidad por la neo-plasia hematológica o la mortalidad por cualquier causa. De los 35 pacientes, 27 sobrevivierony 8 fallecieron. El Ct global medio fue 22,8 ciclos con una mediana de 21,7 ciclos. Entre lossobrevivientes, el Ct medio fue 24,2 ciclos con una mediana de 22,9 ciclos. Entre los fallecidos,el Ct medio fue 18,0 y el Ct mediano fue 17,0 ciclos. Empleando la prueba de suma de rangosde Wilcoxon, encontramos una diferencia significative (p = 0,035). En pacientes con neoplasiashematológicas infectados con coronavirus, el Ct de SARS-CoV-2 medido en hisopados nasales almomento del diagnóstico podría ser utilizado para predecir la mortalidad.

Tiempo de ciclado y carga viral en pacientes infectados por SARS-CoV-2 en Sonora, México / Cycle threshold and viral load in SARS-CoV-2-infected patients in Sonora, Mexico

Resumen Antecedentes: La infección por SARS-CoV-2 se confirma con la prueba de reacción en cadena de la polimerasa. Su positividad se determina mediante el tiempo de ciclado (Ct, cycle threshold), el cual es inversamente proporcional a la carga viral. Objetivo: Describir las características clínicas y epidemiológicas de pacientes infectados por SARS-CoV-2 de acuerdo con su carga viral estimada mediante Ct. Material y métodos: Estudio transversal que incluyó 21 110 casos confirmados, los cuales fueron estratificados conforme a su carga viral: baja (Ct > 30), media (Ct 25-30) y alta (Ct < 25). Resultado: 53 % de los casos tuvo una carga viral alta, la hospitalización fue más frecuente en sujetos con carga viral media y las defunciones fueron más prevalentes en aquellos con carga viral alta. La mediana del Ct fue más baja durante los primeros cinco días y aumentó linealmente con los días de evolución clínica. Hubo una mayor prevalencia de defunciones, hospitalizaciones y apoyo ventilatorio en sujetos con infección confirmada por SARS-CoV-2 que presentaron carga viral media y alta. Conclusiones: El valor de Ct, correlacionado con otras características del paciente, puede orientar el pronóstico, así como al diseño de intervenciones que limiten la diseminación poblacional del virus.

Abstract Background: SARS-CoV-2 infection is confirmed with the polymerase chain reaction test. Its positivity is determined by the cycle threshold (Ct), which is inversely proportional to viral load. Objective: To describe clinical and epidemiological characteristics of SARS-CoV-2-infected patients according to their viral load estimated by Ct. Material and methods: Cross-sectional study that included 21,110 confirmed cases, which were stratified according to their viral load: low (Ct > 30), medium (Ct 25-30) and high (Ct < 25). Results: High viral load was identified in 53% of the cases, hospitalization was more common in subjects with medium viral load, and deaths were more prevalent in those with high viral load. Median Ct was lower during the first five days and linearly increased with the days of clinical evolution. There was a higher prevalence of deaths, hospitalizations and ventilatory support in subjects with confirmed SARS-CoV-2 infection who had a medium and high viral load. Conclusions: The Ct value, correlated with other patient characteristics, can guide the prognosis, as well as the design of interventions that limit the spread of the virus within the population.

SARS-CoV-2 RT-PCR Ct Value and Laboratory Tests: Clinicopathologic characteristics among adult Filipino Inpatients diagnosed with COVID-19 in a tertiary medical center

INTRODUCTION@# The role of the laboratory during the COVID-19 pandemic is not limited to just diagnosis of the disease, but also in clinical decision-making, by providing information on relevant laboratory biomarkers. Clinicians also use Ct value to guide patient management. There are limited studies available locally regarding the significance of Ct value and pertinent laboratory biomarkers in COVID-19 patients. This study aimed to assess the aforementioned laboratory data, along with the clinicopathologic characteristics of affected patients, and determined if this information may be useful for robust clinical decision-makin@*METHODOLOGY@#In this retrospective analytic study, we identified 325 out of 1,049 adult Filipino inpatients diagnosed with COVID-19 and analyzed their Ct values and pertinent laboratory biomarkers such as neutrophil and lymphocyte count, platelet count, LDH, ferritin, procalcitonin, CRP, AST/SGOT, ALT/SGPT, PT/ INR, and D-dimer, and correlated them with the severity of the disease.@*RESULTS@#Two hundred twenty (67.7%) patients had non-severe disease, while 105 (32.3%) had severe disease. Lower Ct values of ORF1ab (median = 26.4) and N (median = 24.8) genes were seen in the severe group compared to the non-severe group and were found to be significant (p<0.001). Laboratory markers (neutrophil, platelet counts, LDH, ferritin, procalcitonin, CRP, AST, PT/INR, and D-dimer) were associated with severe COVID-19. On the other hand, ALT was not associated with severe disease.@*CONCLUSION@#The laboratory biomarkers together with Ct value and overall clinical picture may provide valuable information to physicians for more robust clinical decision-making.

Trajectory and impact factors of cycle threshold values of virus load in respiratory tract in children infected with severe acute respiratory syndrome coronavirus 2 Omicron variants / 中华传染病杂志

Objective:To investigate the clinical characteristics of children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants, and the impact factors of duration of cycle threshold (Ct) values turning to ≥35 detected by nucleotide test.Methods:Children aged 0 to 14 years with clinical symptoms of Omicron variants infection who admitted to designated hospital in Shanghai City (Renji Hospital, South Branch, Shanghai Jiao Tong University School of Medicine) from April 7 to June 2, 2022 were enrolled. The daily nasopharyngeal swab specimens were used for SARS-CoV-2 nucleic acid detecting by polymerase chain reaction and the results were expressed as Ct values. The T Ct≥ x was defined as from the symptom onset or first positive nucleic acid test results (the earlier data) to Ct≥ x of the open reading frame 1ab ( ORF1 ab) gene, which was the time duration from the initial to a specific Ct value.Clinical data were collected, including age, sex, vaccination and comorbidities.Cox model was performed to analyzed the impact factors of T Ct≥35. Results:A total of 871 pediatric cases with a median age of two years (ranging from one month to 14 years old) were included. Among them, 474 cases (54.4%) were male, and 89 cases (10.2%) had underlying diseases including congenital heart disease, solid tumors and epilepsy. There were 572(65.7%) mild cases, 298(34.2%) common cases, one (0.1%) severe case and no critical cases or deaths. The T Ct≥35 was 12(10, 14) days. Cox model indicated that compared to children aged one to 12 months, children aged 37 to 84 months and 85 to 168 months had shorter T Ct≥35 (hazard ratio ( HR)=1.55 and 1.84, respectively, both P<0.001). After adjusted with age, comparing to unvaccinated patients, patients with one or two shots vaccine had shorter T Ct≥35 (adjected hazard ratio (a HR)=1.49, P=0.011), and common patients had longer T Ct≥35 than mild patients (a HR=0.78, P=0.002), and patients with comorbidities had longer T Ct≥35than patients without comorbidities (a HR=0.38, P<0.001).The duration of T Ct≥28, T Ct≥30, T Ct≥33 and T Ct≥35 in children without underlying diseases were 7(6, 9) d, 9(7, 10) d, 10(8, 11) d and 12(10, 14) d, respectively. Conclusions:Age, vaccination, disease severity and underlying diseases could affect the duration of SARS-CoV-2 nucleotide turning to negative (Ct value≥35) in children infected with Omicron variants.

Prevalence of COVID-19 at the Wahgnion-Gold mining site in Burkina Faso and use of RT-PCR initial cycle threshold to monitor the dynamics of SARS-CoV-2 load

Background: To control the spread of coronavirus disease-19 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), it is necessary to adequately identify and isolate infectious patients particularly at the work place. Real time polymerase chain reaction (RT-PCR) assay is the recommended confirmatory method for the diagnosis of SARS-CoV-2 infection. The aim of this study was to determine the prevalence of SARSCoV-2 infection in Burkina Faso and to use the initial cycle threshold (Ct) values of RT-PCR as a tool to monitor the dynamics of the viral load. Methodology: Between September 2021 and February 2022, oropharyngeal and/or nasopharyngeal swab samples of consecutively selected COVID-19 symptomatic and apparently healthy workers from the Wahgnion mining site in the South-western Burkina Faso who consented to the study were collected according to the two weeks shift program and tested for SARS-CoV-2 using RT-PCR assay. Patients positive for the virus were followed-up weekly until tests were negative. Association of the initial RT-PCR Ct values with disease duration was assessed by adjusted linear regression approach. Two-sided p value < 0.05 was considered statistically significant. Results: A total of 1506 (92.9% males) participants were recruited into the study, with mean age and age range of 37.18.7 and 18-68 years respectively. The overall prevalence of SARS-CoV-2 infection was 14.3% (216/1506). Of the 82 patients included in the follow-up study, the longest duration of positive RT-PCR test, from the first positive to the first of the two negative RT-PCR tests, was 33 days (mean 11.6 days, median 10 days, interquartile range 8- 14 days). The initial Ct values significantly correlated with the duration of RT-PCR positivity (with ß=-0.54, standard error=0.09 for N gene, and ß=-0.44, standard error=0.09 for ORF1ab gene, p<0.001). Participants with higher Ct values corresponding to lower viral loads had shorter viral clearance time than those of lower Ct values or higher viral loads. Conclusion: Approximately 1 out of 7 tested miners had SARS-CoV-2 infection and the duration of their RT-PCR tests positivity independently correlated with the initial viral load measured by initial Ct values. As participants with lower initial Ct values tended to have longer disease duration, initial RT-PCR Ct values could be used to guide COVID-19 patient quarantine duration particularly at the work place.

Contexte: Pour contrôler la propagation de la maladie à coronavirus 19 (COVID-19) causée par le syndrome respiratoire aigu sévère coronavirus-2 (SRAS-CoV-2), il est nécessaire d'identifier et d'isoler de manière adéquate les patients infectieux, en particulier sur le lieu de travail. Le test de réaction en chaîne par polymérase en temps réel (RT-PCR) est la méthode de confirmation recommandée pour le diagnostic de l'infection par le SRAS-CoV-2. Le but de cette étude était de déterminer la prévalence de l'infection par le SRAS-CoV-2 au Burkina Faso et d'utiliser les valeurs du seuil initial du cycle (Ct) de la RT-PCR comme outil de suivi de la dynamique de la charge virale. Méthodologie: Entre septembre 2021 et février 2022, des écouvillonnages oropharyngés et/ou nasopharyngés de travailleurs symptomatiques COVID-19 et apparemment en bonne santé sélectionnés consécutivement du site minier de Wahgnion dans le sud-ouest du Burkina Faso qui ont consenti à l'étude ont été prélevés selon les deux programme de quart de semaines et testé pour le SRAS-CoV-2 à l'aide d'un test RT-PCR. Les patients positifs pour le virus ont été suivis chaque semaine jusqu'à ce que les tests soient négatifs. L'association des valeurs Ct initiales de la RT-PCR avec la durée de la maladie a été évaluée par une approche de régression linéaire ajustée. Une valeur p bilatérale < 0,05 a été considérée comme statistiquement significative. Résultats: Un total de 1506 participants (92,9% d'hommes) ont été recrutés dans l'étude, avec un âge moyen et une tranche d'âge de 37,1 à 8,7 ans et de 18 à 68 ans, respectivement. La prévalence globale de l'infection par le SRAS-CoV-2 était de 14,3% (216/1506). Sur les 82 patients inclus dans l'étude de suivi, la plus longue durée de test RT-PCR positif, du premier test positif au premier des deux tests RT-PCR négatifs, était de 33 jours (moyenne 11,6 jours, médiane 10 jours, intervalle interquartile 8-14 jours). Les valeurs Ct initiales étaient significativement corrélées à la durée de positivité de la RT-PCR (avec ß=-0,54, erreur standard=0,09 pour le gène N et ß=-0,44, erreur standard=0,09 pour le gène ORF1ab, p<0,001). Les participants avec des valeurs de Ct plus élevées correspondant à des charges virales plus faibles avaient un temps de clairance virale plus court que ceux avec des valeurs de Ct plus basses ou des charges virales plus élevées. Conclusion: Environ 1 mineur testé sur 7 était infecté par le SRAS-CoV-2 et la durée de la positivité de ses tests RTPCR était indépendamment corrélée à la charge virale initiale mesurée par les valeurs Ct initiales. Comme les participants avec des valeurs Ct initiales inférieures avaient tendance à avoir une durée de maladie plus longue, les valeurs Ct initiales de la RT-PCR pourraient être utilisées pour guider la durée de la quarantaine des patients COVID19, en particulier sur le lieu de travail.

SARS-CoV-2 RT-PCR cycle threshold value and its association with disease severity and mortality among hospitalized pediatric COVID-19 patients

Objective@#This study determined the association of SARS-CoV-2 RT-PCR cycle threshold (Ct) value with disease severity and mortality among hospitalized pediatric COVID-19 patients.@*Methodology@#This is a retrospective cohort study of patients aged 0-18 years with SARS-CoV-2 RT-PCR-confirmed COVID-19 from 1-September-2020 to 31-August-2022. The cohort was divided into those with high (>30), medium (> 20) and low (</= 20) Ct values. Association between Ct values and disease severity was determined using Chi-square test and association between Ct values and mortality was determined using logistic regression.@*Results@#There were 236 patients included with male predominance. Median age was 7 years. Most belonged to the 0-5 years age group. Most were severe to critical COVID-19 cases. Median day of illness on swab collection was 4 days. Majority presented with symptoms such as fever (54%), cough (22%) and dyspnea (22%). Eighty-four percent had co-morbidities, of which majority were cancer and neurologic diseases. Median Ct value was 30.81. Fifty-four percent had high Ct values. The median age of patients with a high Ct value was significantly lower than other cohorts. The median day of illness of patients with low Ct value was significantly shorter than other cohorts. There was no significant difference across the terciles in terms of presence of co-morbidities. Majority of patients for each cohort had high Ct values. There was no significant association between Ct value and COVID-19 disease severity on admission. Nearly fifty percent had critical disease and the all-cause mortality rate was 21.61%. There was no significant association between Ct value and mortality.@*Conclusions@#Ct value was not associated with disease severity and all-cause mortality after controlling for confounders. A look into medical interventions, emergence of variants, and other factors that may affect the clinical presentation, disease course, severity and outcome are recommended in future studies.

Predictors of poor outcomes in young non-comorbid patients with COVID-19

ABSTRACT Background: Prognostic factors in previously healthy young patients with COVID-19 remained understudied. Objective: The objective of the study was to identify factors associated with in-hospital death or need for invasive mechanical ventilation (IMV) in young (aged ≤ 65 years) and previously healthy patients with COVID-19. Methods: We conducted a prospective cohort study that included patients admitted with COVID-19. The primary outcome was in-hospital death/need for IMV. Secondary outcomes included need for IMV during follow-up, days on IMV, length of stay (LOS), hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP), and pulmonary embolism (PE). Bivariate and multivariate analyses were performed. Results: Among 92 patients, primary outcome occurred in 16 (17%), death in 12 (13%), need for IMV in 16 (17%), HAP/VAP in 7 (8%), and PE in 2 (2%). Median LOS and IMV duration were 7 and 12 days, respectively. Independent associations were found between the primary outcome and male sex (Adjusted odds ratio [aOR] 7.1, 95%CI 1.1-46.0, p < 0.05), D-dimer levels > 1000ng/mL (aOR 9.0, 95%CI 1.6-49.1, p < 0.05), and RT-PCR Ct-value ≤ 24 on initial swab samples (aOR 14.3, 95%CI 2.0-101.5, p < 0.01). Conclusions: In young and non-comorbid COVID-19 patients, male sex, higher levels of D-dimer, and low SARS-CoV-2 RT-PCR Ct-value on an initial nasopharyngeal swab were independently associated with increased in-hospital mortality or need for IMV.

Asociación del umbral de ciclos (Ct) en prueba RT-PCR para SARS-CoV-2 y severidad de la COVID-19 en pacientes de un hospital de referencia en Paraguay

RESUMEN Algunos estudios han encontrado que la severidad de la COVID-19 se asocia con una alta carga viral determinada por los números de ciclos (Ct) de amplificación de ADN de SARS-CoV-2. El objetivo fue determinar la relación entre el umbral de ciclos de PCR de SARS-CoV-2 y la severidad de la infección por el virus SARS-COV-2 en pacientes internados y ambulatorios en un hospital de referencia entre marzo a junio del 2021. Estudio retrospectivo observacional analítico de corte trasverso de pacientes adultos con COVID-19, ambulatorios e internados en el Hospital Nacional. Se incluyeron los pacientes cuya infección fue confirmada por RT-PCR para SARS-CoV-2, se consideró un punto de corte para Ct60 años (36,6%), estuvieron hospitalizados (69,8%), internados en sala (57,1%), y admitidos en cuidados intensivos (12,8%), tiempo medio de enfermedad 8,48 ± 4,2 días. La mortalidad fue de 22,2%. Se encontró mayor riesgo de fallecer para los pacientes con Ct 60 años (OR: 3,69; IC95%: 2,39-5,68). Estos dos factores permanecieron asociados con el óbito en el análisis multivariado. Hubo mayor riesgo de hospitalizarse y fallecer en los pacientes con Ct<25. El valor Ct podría ser útil para la predicción del curso clínico y el pronóstico de los pacientes con COVID-19.

ABSTRACT Some studies have found that severity of COVID-19 is associated with a high viral load determined by the number of cycles (Ct) of SARS-CoV-2 DNA amplification. The objective was to determine the relationship between the Ct value and the severity of the SARS-COV-2 virus infection in inpatients and outpatients at a reference hospital in Paraguay between March and June 2021. Cross-sectional retrospective study of adult patients with COVID-19, ambulatory and hospitalized admitted to the National Hospital. Patients whose infection was confirmed by RT-PCR for SARS-CoV-2 were included, a cut off point of Ct 60 years (36.6%), hospitalized (69.8%), admitted to ward (57.1%), and admitted to intensive care (12.8%), mean time of illness 8.48 ± 4.2 days and mortality was 22.2%. A higher risk of death was found for patients with Ct 60 years (OR: 3.69; 95% CI: 2.39-5.68). These two factors remained associated with death in the multivariate analysis. There was a higher risk of hospitalization and death in patients with TC <25. Ct value could be useful for predicting clinical course and prognosis of COVID-19 patients.

Correlación entre el umbral de ciclo de la RPC en tiempo real y la clasificación clínica de la COVID-19 / Correlation between real-time PCR cycle threshold and clinical classification of COVID-19

INTRODUCCIÓN: El umbral de ciclo (en inglés cycle threshold-Ct) de la reacción de polimerasa en cadena en tiempo real con transcripción reversa (RT-qPCR) indica la concentración relativa de una secuencia de ARN; este valor se ha relacionado con la expresión de cuadros clínicos en infecciones virales. OBJETIVO: Determinar la correlación entre el valor Ct y la clasificación clínica de la COVID-19. MÉTODO: Se realizó un estudio transeccional correlacional; los valores Ct se obtuvieron mediante RT-qPCR dirigida al gen N del SARS-CoV-2 agrupándolos mediante un estimador robusto central y relacionándose con la clasificación clínica de la COVID-19. RESULTADOS: De los 718 casos incluidos en el estudio; 77,7% (558) fueron leves; 21,3% (153) moderados y 1% (7) graves. El valor Ct se agrupó en niveles: Ct bajo 18,83 - 30,10 y Ct alto > 30,10. Existió correlación significativa inversa débil (p = 0,002; rho de Spearman = -0,117) entre el valor Ct y la clasificación clínica. Las características: sexo, edad menor a 65 años, fiebre, escalofrío, diarrea, anosmia y sobrepeso-obesidad estuvieron asociadas al valor de Ct. CONCLUSIÓN: A menor valor Ct se espera una clasificación de mayor gravedad de la COVID-19; no obstante, debido a que la correlación es débil, su utilidad como predictor de gravedad es limitada.

BACKGROUND: The cycle threshold (Ct) of real-time reverse transcription PCR (RT-qPCR) indicates the relative concentration of an RNA sequence, this value has been related to clinical profile in viral infections. AIM: To determine the correlation between the Ct value and the clinical classification of COVID-19. METHOD: A correlational cross-sectional study was carried out, the Ct values were obtained by RT-qPCR directed to the N gene of SARS-CoV-2, grouping them by means of a central robust estimator and related to the clinical classification of COVID-19. RESULTS: Of the 718 cases included in the study; 77.7% (558) were mild; 21.3% (153) moderate and 1% (7) severe. The Ct value was grouped into levels: low Ct 18.83-30.10 and high Ct> 30.10. There was a weak inverse significant correlation (p = 0.002; Spearman's rho = -0.117) between the Ct value and the clinical classification. The characteristics: sex, age under 65 years, fever, chills, diarrhea, anosmia, and overweightobesity were associated with the Ct value. CONCLUSION: The lower the Ct value, a classification of greater severity of COVID-19 is expected, however, because the correlation is weak, its usefulness as a severity predictor is limited.

Características epidemiológicas y clínicas de los niños con COVID-19 asistidos en un prestador de salud privado de Uruguay / Epidemiological and clinical characteristics of children with COVID-19 cared for in a private health provider in Uruguay

INTRODUCCIÓN: Tras la detección de los primeros casos de SARS-CoV-2 y declararse la emergencia sanitaria en el país, la transmisión comunitaria del virus se mantuvo baja a moderada hasta noviembre de 2020 pasando luego a ser media y alta. Los niños bajo 15 años de edad constituyen el grupo menos afectado. El diagnóstico se confirma mediante RT-qPCR. La utilidad del CT (cycle threshold) es discutida. Objetivo: Describir las características epidemiológicas y clínicas de los niños infectados con SARS-CoV-2 y la relación entre el valor del CT y la presentación clínica. METODOLOGÍA: Se realizó un estudio descriptivo, retrospectivo, en pacientes bajo 16 años de edad con infección por SARS-CoV-2, asistidos en un prestador de salud de Montevideo entre la semana epidemiológica (S.E.) 3 del 2020 y la SE 9 del 2021. Se describieron variables clínicas, noción epidemiológica, gravedad y evolución. Se consignó el valor del CT al diagnóstico y se comparó con la presencia de síntomas. RESULTADOS: Los pacientes bajo 16 años representaron el 16,6% del total de infectados (794 en 4.792). El 70% de los casos ocurrió entre los meses de enero y febrero de 2021. El 67,6% presentó contacto intradomiciliario. La media de edad fue 7,5 ± 4,1 años, 51% de sexo masculino. Presentaron síntomas 55% y fueron asintomáticos 45%; no se observaron diferencias significativas en la media, moda y rango de edades de ambos grupos. Ninguno presentó comorbilidades. En el grupo de los 440 pacientes sintomáticos, 55% presentaron fiebre: 32% asociada con otros síntomas, principalmente respiratorios altos y 23% como único síntoma. El valor de CT se obtuvo en 536 de los 794 pacientes (67,5%). La media de CT fue 29,7 ± 5,8 en el grupo de sintomáticos vs. 31,5 ± 5,7 en asintomáticos (p > 0,05). Se hospitalizaron tres pacientes, ninguno requirió cuidados intensivos ni falleció. CONCLUSIONES: La prevalencia e incidencia de la infección por SARS-CoV-2 en niños acompañan a la de adultos y la mayoría cursó formas leves o asintomáticas, sin complicaciones. En esta serie, el valor de CT no fue diferente en niños sintomáticos y asintomáticos. El contacto estrecho intradomiciliario fue la principal fuente de infección.

BACKGROUND: After the detection of the first cases of SARS-CoV-2 and the declaration of a health emergency in the country, community transmission of the virus remained low to moderate until November 2020, later becoming medium and high. Children under 15 years of age constitute the least affected group. The diagnosis is confirmed by RT-qPCR. The usefulness of the CT (cycle threshold) is discussed. AIM: To describe the epidemiological and clinical characteristics of children infected with SARS-CoV-2 and the relationship between the CT value and clinical presentation. METHOD: A descriptive, retrospective study was carried out in patients under 16 years of age with SARS-CoV-2 infection, assisted by a health provider in Montevideo between epidemiological week (EW) 3 of2020 and EW 9 of2021. Clinical variables, epidemiological notion, severity and evolution were described. The CT value at diagnosis was recorded and compared with the presence of symptoms. RESULTS: Patients under 16 years of age represented 16.6% of the total infected (794 in 4,792). 70% of the cases occurred between the months of January and February 2021. 67.6% presented intradomiciliary contact. The mean age was 7.5 ± 4.1 years, 51% were male. 55% presented symptoms and 45% were asymptomatic; no significant differences were observed in the mean, mode and age range of both groups. None presented comorbidities. In the group of 440 symptomatic patients, 55% presented fever: 32% associated with other symptoms, mainly upper respiratory symptoms, and 23% as the only symptom. The CT value was obtained in 536 of the 794 patients (67.5%). The mean CT was 29.7+5.8 in the symptomatic group vs. 31.5 ± 5.7 in asymptomatic patients (p > 0.05). Three patients were hospitalized, none required intensive care and none died. CONCLUSIONS: The prevalence and incidence of SARS-CoV-2 infection in children accompany that of adults and the majority had mild or asymptomatic forms, without complications. In this series, the CT value was not different in symptomatic and asymptomatic children. Close household contact was the main source of infection.

A descriptive cross-sectional study on Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) cycle threshold level, mortality and pediatric acute respiratory distress syndrome among covid-19 patients admitted at PCMC

BACKGROUND@#Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is a novel pathogen that has rapidly caused a devastating pandemic of Coronavirus disease 2019 (COVID-19). The real time reverse transcriptase polymerase chain reaction cycle threshold values are inversely related to viral load and believed to have a role in terms of mortality and severity of the disease however, there is limited data in children. @*OBJECTIVES@#This study aims to determine the RT-PCR cycle threshold level in relation to mortality and pediatric acute respiratory distress syndrome (pARDS) among COVID-19 patients admitted at Philippine Children’s Medical Center.@*METHODS@#A cross sectional study was done on patients with RT-PCR confirmed covid-19 admitted at Philippine Children’s Medical Center from September 2020 to June 2021.@*RESULTS@#50 nasopharyngeal swab specimens from children admitted for COVID-19 were analyzed. 12 (24%) had acute respiratory distress syndrome. Among the 12 children who had pARDS, six (50%) expired; in those without pARDS, two (5.26%) expired. There was no difference in cycle threshold values between patients who died and who survived, as well as those with or without pARDS. @*CONCLUSIONS AND RECOMMENDATIONS@#We have no evidence to demonstrate a difference in Ct values alone between children who died or survived, or those who developed pARDS or those who did not. RT-PCR cycle threshold alone cannot predict mortality and development of pARDS, it can only indicate the presence of infection but not its severity. Cycle threshold and its significance may further be explored with a bigger population size in children in future studies.

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

Resumen Introducción: La pandemia de COVID-19 ha afectado a millones de personas en todo el mundo. La identificación de sujetos infectados ha sido importante para el control. Objetivo: Evaluar el rendimiento de una reacción de polimerasa en cadena (RPC) cuantitativa en tiempo real (en inglés: RT-qPCR) para SARS-CoV-2, utilizando saliva como matriz en comparación con un hisopado nasofaríngeo (HNF). Metodología: Se reclutaron adultos en atención ambulatoria, la mayoría sintomáticos. Fueron estudiadas 530 muestras pareadas de saliva e HNF con RT-qPCR. Resultados: Fueron positivas 59 muestras de HNF y 54 de saliva. La sensibilidad con saliva fue 91%, especificidad 100%, el valor predictor positivo (VPP) 100%, valor predictor negativo (VPN) 98%. El índice Kappa fue de 0,95 y LR-0,08. En promedio, el umbral de ciclo (en inglés cycle threshold-CT) de la saliva fue 3,99 puntos más alto que los de HNF (p < 0,0001) mostrando que la carga viral (CV) es menor en saliva. La carga viral en ambas disminuyó con el tiempo después del inicio de los síntomas. El muestreo de saliva fue preferido por los sujetos en lugar de HNF. Conclusión: Este estudio demuestra que la RPC para SARS-CoV-2 utilizando saliva, es adecuada para el diagnóstico de COVID-19 en adultos ambulatorios, especialmente en la etapa temprana de los síntomas.

Abstract Background: The COVID-19 pandemic has affected millions of people around the world. Part of control strategies is testing a large proportion of the population to identify and isolate the infected subjects. Aim: To evaluate the SARS-CoV-2 detection by the performance of a reverse transcription and quantitative polymerase chain reaction (RT-qPCR) against SARS-CoV-2, using saliva as a matrix compared to a nasopharyngeal swab (NPS) to simplify obtaining a diagnostic sample. Methods: Adults in outpatient care were recruited, 95% of them symptomatic. We studied 530 paired saliva and NPS samples by SARS-CoV-2 RT-qPCR. Results: Fifty-nine individuals tested positive in NPS and 54 in saliva samples. Sensitivity for saliva sample was 91%, specificity 100%, positive predictive value (PPV) 100%, negative predictive value (NPV) 98%. The Kappa index was 0.95 and LR-0.08. On average, the cycle threshold (CT) of saliva was 3.99 points higher than those of NPS (p < 0.0001) showing that viral load (VL) is lower in saliva than in NPS. Viral load in both decreased over the time after onset of symptoms. Saliva sampling was preferred by subjects instead of NPS. Conclusion: This study demonstrates that SARS-CoV-2 RT-qPCR using saliva, even with lower VL, is suitable for the diagnosis of COVID-19 in outpatient adults, especially at early stage of symptoms.

Persistently positive PCR SARS-CoV-2 at low cycle threshold in an immunosuppressed patient

ABSTRACT We describe the very prolonged course of the disease in an immunosuppressed patient with persistently positive PCR against SARS-CoV-2 with low cycle threshold for at least 114 days.

Prolonged SARS-CoV-2 RNA shedding in a young man recovering from traumatic pneumothorax

We describe a case of prolonged SARS-CoV-2 RNA shedding in an HIV-negative 21-year-old man recovering from abdominal and thoracic trauma. Nasopharyngeal (NP) swabs collected at 12 time points over a 95-day span all tested positive for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR). Genotyping revealed canonical beta-variant E484K and N501Y mutations at earlier time points. Human rhinovirus, coronavirus NL63 and respiratory syncytial virus B were detected at different time points by RT-PCR. Full blood analysis at time point 9 (day 82) showed leukopenia with lymphocytosis. The patient's NP swab tested negative for SARS-CoV-2 by RT-PCR 101 days after the first positive test. The prolonged duration of SARS-CoV-2 RNA shedding in the context of trauma presented here is unique and has important implications for COVID-19 diagnosis, management and policy guidelines

SARS CoV2 RT-PCR cycle threshold (Ct) values and the risk of developing acute respiratory distress syndrome in patients with Covid19

Background. SARS-CoV-2 viral loads may aid in the risk stratification of patients with COVID-19. Methods. 486 patients tested positive for SARS Cov2 by real time RT-PCR were included in this study. All the tests were performed on nasopharyngeal swabs during the first week after symptom onset using Sansure Biotech™ SARS Cov2 real time RT-PCR kits. Patient's condition was monitored over a period of one month after the onset of symptoms. Results. The mean Ct value in the group of patients who developed acute respiratory distress syndrome (ARDS +) was 18.27 (95% CI: 17.43-19.10) while for the ARDS group it was 33.06 (95% CI: 32.77-33.34). Discussion. The Ct values in the group of patients who developed ARDS (ARDS +) were significantly lower than those observed in the ARDS- group. By setting a cut-off value, the determination Ct values (on a qualitative technique) from nasopharyngeal swabs performed during the first week after symptom onset will assist clinicians in risk-stratifying patients. Conclusion. Our data show that the determination of SARS CoV2 RTPCR cycle threshold values from nasopharyngeal swabs performed during the first week after symptom onset may aid in the risk stratification of patients with COVID-19

Analysis on the difference of circulating threshold of polymerase chain reaction in blood screening of external quality assessment / 中国输血杂志

【Objective】 To analyze the difference of circulating threshold (Ct) of polymerase chain reaction (PCR) in blood station laboratories during the external quality assessment, and to put forward suggestions for the quality improvement of participating laboratories. 【Methods】 From 2018 to 2021, the blood station laboratories participated in the external laboratory quality assessment of CITIC including blood screening items with nucleic acid testing method. The data of Roche diagnostic reagent group were used as the source, and the detected Ct values of three groups of quality control samples of HBV A subtype (400 IU/mL), HCV 1b subtype (400 IU/mL) and HIV B genotype (500 IU/mL) were used as the objects. The data were grouped according to quality control (sample) batches, reagent batches and different laboratories. Using the statistical method of variance analysis (assuming P<0.05 as significant), the detected Ct value of each group was analyzed. 【Results】 For the three items (HBV/HCV/HIV), the grouping data involving 42 batches of quality control (13/12/17), 28 batches of reagent (11/8/9) and 57 laboratories (19/19/19) were selected. The grouping analysis of quality assessment batches shows that there was no significant difference between HBV and HCV quality assessment batches, and there was no significant difference between other HIV batches except the two batches of HIV quality assessment samples released in 2021. The grouping analysis of each reagent batch showed that there was no significant difference between each reagent batch for HCV and HIV detection, while there was significant difference between two batches of HBV reagents. After excluding the data groups with significant differences in the quality control batch groups and the reagent batch groups, the detected Ct value of each laboratory group had extremely significant differences in the three items of HBV, HCV and HIV. Through pairing analysis, it was found that four laboratories had significant differences with most other laboratories in the three items, mainly manifested in the high mean value of Ct. 【Conclusion】 For the blood station laboratories with correct test results of quality assessment samples, there are differences in Ct values detected by PCR, which may be mainly caused by the detection ability of the participating laboratories.

Stability of two internal control blood nucleic acid detection systems in plateau area / 中国输血杂志

【Objective】 To analyze the difference of the internal control (IC) Ct value of two sets of blood nucleic acid detection(NAT) systems for individual donation and explore the feasibility of the IC Ct value used as stability evaluation index of NAT system. 【Methods】 A total of 4342 blood samples were randomly selected from our center from June to November 2020, and the IC Ct values of NAT system were classified into three categories: 1) classified by detection items: HBV, HCV and HIV; 2) classified by sample type: negative control (NC), positive control (PC), internal quality control (QC), blood donor sample (S); 3) classified by different instruments: system A and system B, and the differences of IC Ct value were analyzed and compared. 【Results】 A total of 14 196 IC Ct values of NAT were collected, showing a non-normal distribution. 1) classified by detection items: there were differences in the median of overall IC Ct values of HBV, HCV and HIV (H=859.6, P0.05), except for HBV QC (Z=1 635)and S (Z=1 848 560), HCV S (Z=1 957 844), HIV S (Z= 2 217 855) (P<0.01). No difference in IC values (P<0.01) was noted for any detection items (NC, PC, QC and S) in the same set of detection system. 【Conclusion】 Although IC values trended to be different due to types of sample, the NC, PC, and QC samples that come with the original reagents were identical in the two detection systems. The change of IC Ct value may be used as an evaluation index for the stability of the detection system.

Study on the effects of hemolysis, fatty blood and various storage conditions on HBV DNA,HIV RNA nucleic acid screening / 天津医药

Objective To study the influences of hemolysis, fatty blood, storage temperature and storage time on blood HIV RNA and HBV DNA. Methods The HBV DNA and HIV RNA samples (the concentration was 12-30 times of limit of detection of reagent), which were stored for 4 h, 1 d, 3 d,1 w and 4 w under the conditions of 4℃, 25℃, 37℃and-30℃, were detected using Roche MPX V2.0 kit. The HBV DNA and HIV RNA samples (the concentration was 2-5 times of limit of detection of reagent) were detected by the 6 groups of hemolytic samples (the concentrations of hemoglobin were 97 g/L, 34 g/L,17 g/L, 8 g/L, 5 g/L and 3 g/L, respectively). NAT test was performed at 5-group lipid samples (the concentrations of triglyceride were 7.93 mmol/L, 3.80 mmol/L, 2.63 mmol/L, 1.83 mmol/L and 1.49 mmol/L, respectively) and the control group samples (the concentrations of hemoglobin and triglyceride were 0 g/L and 0.95 mmol/L respectively). Results There were no significant differences in Ct values of HIV RNA or HBV DNA between 4 h to 4 w at 25℃(P>0.05). There were significant differences in Ct values of HBV DNA after preservation for 3 d and 1 w under 37 ℃ compared with those of preservation for 4 h,1 d and 2 d (P<0.005). When Hb concentration was reached to 97 g/L, the results of HBV DNA and HIV RNA were negative. When the concentration of Hb was less than 34 g/L, compared with the control group, there were no significant differences in Ct values of HIV RNA and HBV DNA (P>0.05). When the TG concentration was≤7.93 mmol/L, there were no significant differences in Ct values between the control group and the TG group (P>0.05). Conclusion The samples of HIV RNA and HBV DNA detected by Roche MPX V2.0 kit can be stored at room temperature (25℃) for four weeks. When the concentrations of TG and Hb are less than 7.93 mmol/L and 34 g/L respectively, there are no effects on HIV RNA or HBV DNA samples detected by Roche MPX V2.0 kit.

Study on the effects of hemolysis, fatty blood and various storage conditions on HBV DNA,HIV RNA nucleic acid screening / 天津医药

Objective To study the influences of hemolysis, fatty blood, storage temperature and storage time on blood HIV RNA and HBV DNA. Methods The HBV DNA and HIV RNA samples (the concentration was 12-30 times of limit of detection of reagent), which were stored for 4 h, 1 d, 3 d,1 w and 4 w under the conditions of 4℃, 25℃, 37℃and-30℃, were detected using Roche MPX V2.0 kit. The HBV DNA and HIV RNA samples (the concentration was 2-5 times of limit of detection of reagent) were detected by the 6 groups of hemolytic samples (the concentrations of hemoglobin were 97 g/L, 34 g/L,17 g/L, 8 g/L, 5 g/L and 3 g/L, respectively). NAT test was performed at 5-group lipid samples (the concentrations of triglyceride were 7.93 mmol/L, 3.80 mmol/L, 2.63 mmol/L, 1.83 mmol/L and 1.49 mmol/L, respectively) and the control group samples (the concentrations of hemoglobin and triglyceride were 0 g/L and 0.95 mmol/L respectively). Results There were no significant differences in Ct values of HIV RNA or HBV DNA between 4 h to 4 w at 25℃(P>0.05). There were significant differences in Ct values of HBV DNA after preservation for 3 d and 1 w under 37 ℃ compared with those of preservation for 4 h,1 d and 2 d (P<0.005). When Hb concentration was reached to 97 g/L, the results of HBV DNA and HIV RNA were negative. When the concentration of Hb was less than 34 g/L, compared with the control group, there were no significant differences in Ct values of HIV RNA and HBV DNA (P>0.05). When the TG concentration was≤7.93 mmol/L, there were no significant differences in Ct values between the control group and the TG group (P>0.05). Conclusion The samples of HIV RNA and HBV DNA detected by Roche MPX V2.0 kit can be stored at room temperature (25℃) for four weeks. When the concentrations of TG and Hb are less than 7.93 mmol/L and 34 g/L respectively, there are no effects on HIV RNA or HBV DNA samples detected by Roche MPX V2.0 kit.

Modified low cost SNP genotyping technique using cycle threshold (Ct) & melting temperature (Tm) values in allele specific real-time PCR.

Background & objectives: Genotyping has now become one of the major diagnostic means for almost all diseases. Among the advanced techniques that are used to study single nucleotide polymorphisms (SNPs), only a few are applicable for routine disease diagnosis. Their applicability mainly depends on three factors: cost, time, and accuracy. The primary objective of this study was to propose allele-specific real-time PCR as a rapid, low cost and simple genotyping method for routine diagnostics. Methods: Two SNPs, rs3014866 and rs2149356 were analysed using allele-specific real-time PCR. The polymerase chain reaction was carried out using RealQ PCR master mix containing SYBR Green DNA I dye followed by melt curve analysis. The results were validated by agarose gel electrophoresis and DNA sequencing. Results: The allelic discrimination and zygosity of the two SNPs were assessed by combined cycle threshold (Ct) and melting temperature (Tm) values. Variations in Ct and Tm values among the two alleles were observed in both rs3014866 (Ct: C allele - 24±1, T allele - 27±1; Tm: C allele - 82.5±0.3, T allele - 86.3±0.2) and rs2149356 (Ct: C allele - 24±1, A allele - 26±1; Tm: C allele - 79.4±0.2, A allele - 80.4±0.3). Based on the variations, homozygous and heterozygous alleles were detected. Agarose gel electrophoresis and DNA sequencing also confirmed the allelic variation and zygosity observed in real-time PCR. Interpretation & conclusions: In diagnostic settings where a large number of samples are analysed daily, allele-specific real-time PCR assay may serve as a simple, low cost and efficient method of genotyping