SARS-CoV-2 RT-PCR as a universal screening on planned admission in asymptomatic patients.

Universal screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on admission is reportedly beneficial in preventing nosocomial infections. However, some issues remain, including low positivity rate, cost, and time required for testing. We describe SARS-CoV-2 reverse transcription polymerase chain reaction (PCR) for universal screening in asymptomatic patients on planned admissions. In total, 14,574 patients were included between October 12, 2020, and June 23, 2022. The PCR-positive rate for the period was 0.44 % (64/14,574). The PCR positivity for the epidemic period by strain was 0.28 % (95 % confidence interval [CI] 0.12-0.56 %), 0.16 % (95 % CI 0.05-0.37 %), 0.21 % (95 % CI 0.09-0.41 %), and 0.9 % (95 % CI 0.65-1.2 %) for the wild-type strain, Alpha, Delta, and Omicron variants, respectively. The proportion of Ct values < 30 was higher in the first half of the epidemic (first vs. second, 29.4 % [95 % CI 16.9-44.8 %] vs. 16.7 % [95 % CI 6.0-28.5 %]), whereas that of Ct values ≥ 35 increased significantly in the second half (first vs. second, 32.4 % [95 % CI 19.3-47.8 %] vs. 70.0 % [95 % CI 53.5-83.4 %]). Of all positives, 50 % (32/64) had a coronavirus disease (COVID-19) history before PCR screening, with a median of 28 days (10-105) from COVID-19 onset or positive to PCR screening. PCR screening may help detect positives with high viral loads early in the epidemic for each mutant strain, with an increasing proportion of positives with low viral loads later in the epidemic. PCR testing may be unnecessary for recently diagnosed cases and patients in whom reinfection is unlikely.

Consecutive positive nucleic acid tests in COVID-19 patients: a retrospective cohort study in Fangcang hospitals, Shanghai.

INTRODUCTION: The coronavirus disease 2019 (COVID-19) spread rapidly in Shanghai in February 2022. Patients with asymptomatic and mild symptoms were admitted to Fangcang shelter hospitals for centralized quarantine. METHODOLOGY: A total of 5,217 non-severe patients hospitalized in the Longyao Fangcang and Shilong Fangcang hospitals were included in the study. Demographic and clinical characteristics, comorbidity, exposure history, treatment and disease duration were analyzed. Univariate analysis and binomial logistic regression analysis were performed to identify the factors influencing nucleic acid change from positive to negative over 14 days. RESULTS: Consecutive positive nucleic acid test results (days) were significantly associated with advanced age (OR = 1.343, 95% CI 1.143 to 1.578, p < 0.001), smoking (OR = 0.510, 95% CI 0.327 to 0.796, p = 0.003) and vaccination (OR = 0.728, 95% CI 0.641 to 0.827, p < 0.001). However, there was no significant difference between asymptomatic and mild symptomatic patients (p = 0.187). In univariate analysis, comorbidities including diabetes, hypertension, cardiovascular system, malignant tumors, autoimmune diseases and cerebral apoplexy were associated with consecutive positive nucleic acid test results, but there was no significant difference in binomial logistics regression analysis. CONCLUSIONS: Aging and comorbid conditions lead to the prolongation of positive nucleic acid test results for several days. Improving vaccination coverage is beneficial for prevention and control of the epidemic. The management and treatment methods of Shanghai Fangcang shelter hospitals had important referential significance, which can provide valuable guidance for the prevention and control of the COVID-19 epidemic in the future.

Effect of testing criteria for infectious disease surveillance: The case of COVID-19 in Norway.

During the COVID-19 pandemic in Norway, the testing criteria and capacity changed numerous times. In this study, we aim to assess consequences of changes in testing criteria for infectious disease surveillance. We plotted the proportion of positive PCR tests and the total number of PCR tests for different periods of the pandemic in Norway. We fitted regression models for the total number of PCR tests and the probability of positive PCR tests, with time and weekday as explanatory variables. The regression analysis focuses on the time period until 2021, i.e. before Norway started vaccination. There were clear changes in testing criteria and capacity over time. In particular, there was a marked difference in the testing regime before and after the introduction of self-testing, with a drastic increase in the proportion of positive PCR tests after the introduction of self-tests. The probability of a PCR test being positive was higher for weekends and public holidays than for Mondays-Fridays. The probability for a positive PCR test was lowest on Mondays. This implies that there were different testing criteria and/or different test-seeking behaviour on different weekdays. Though the probability of testing positive clearly changed over time, we cannot in general conclude that this occurred as a direct consequence of changes in testing policies. It is natural for the testing criteria to change during a pandemic. Though smaller changes in testing criteria do not seem to have large, abrupt consequences for the disease surveillance, larger changes like the introduction and massive use of self-tests makes the test data less useful for surveillance.

Maternal and neonatal outcomes of French prospective multicenter cohort study COVIPREG during the first two COVID-19 waves.

BACKGROUND: SARS-CoV-2 infection on pregnant women was the subject of many questions since the COVID-19 pandemic. METHODS: We aim to assess maternal and neonatal outcomes of SARS-CoV-2 infection contracted during 2nd and 3rd trimesters of pregnancy during the first two COVID-19 waves across a prospective French multicenter cohort study. Patients were included between April 2020 and January 2021 in 10 maternity hospitals in Paris area with two groups (i) pregnant women with a positive SARS-CoV-2 nasopharyngeal RT-PCR between [14WG; 37WG[(symptomatic infection), (ii) pregnant women with a negative serology (or equivocal) at delivery and without a positive SARS-CoV-2 nasopharyngeal RT-PCR at any time during pregnancy (G2 group) MAIN FINDINGS: 2410 pregnant women were included, of whom 310 had a positive SARS-CoV-2 nasopharyngeal RT-PCR and 217 between [14WG; 37WG[. Most infections occurred between 28 and 37 weeks of gestation (56 %). Most patients could be managed as outpatients, while 23 % had to be hospitalized. Among women with a positive RT-PCR, multiparous women were over-represented (OR = 2.45[1.52;3.87]); were more likely to deliver before 37 weeks of gestation (OR = 2.19[1.44;3.24]) and overall cesarean deliveries were significantly increased (OR = 1.53[1.09;2.13]). CONCLUSIONS: This study highlights the maternal, obstetrical, and neonatal burden associated with SARS-CoV-2 infections during the first two pandemic waves before availability of vaccines. TRIAL REGISTRATION: NCT04355234 (registration date: 21/04/2020).

Factores asociados a la positividad de la PCR para SARS-CoV-2 en menores de 15 años / Related PCR positivity factors for SARS-CoV-2 in children under 15 years of age / Fatores associados à positividade da PCR para SARS-CoV-2 em crianças menores de 15 anos de idade

Introducción: la infección por SARS-CoV-2 en niños representa un porcentaje menor en la incidencia global de pacientes infectados por este virus. La prueba de reacción en cadena de polimerasa (PCR) para SARS-CoV-2 en muestra de secreciones nasofaríngeas es considerada como estándar de referencia, con niveles de sensibilidad y especificidad superiores a otras técnicas. Objetivo: describir las características de los pacientes menores de 15 años a los que se realizó PCR para SARS-CoV-2 en un prestador privado de salud del interior del país entre el 1° julio 2020 y el 30 de abril 2021. Analizar posibles factores asociados a la positividad de la prueba. Describir las características de los casos con PCR positiva Metodología: estudio observacional prospectivo con un análisis retrospectivo de tipo caso-control, a partir del seguimiento de una cohorte de menores de 15 años a los que se les realizó una prueba de PCR para SARS-CoV-2 en el período analizado, en un prestador integral de salud privado del interior del país. Se recabaron datos durante el seguimiento de los pacientes de acuerdo a un protocolo institucional que incluye: datos patronímicos, causa de la solicitud de la PCR, características del contacto, resultado de PCR y umbral de ciclo (CT), manifestaciones clínicas y evolución. Resultados: se solicitaron 2.361 PCR a menores de 15 años (15% del total de las PCR de la institución). Promedio de edad: 8,6 años (rango 7 días-14 años y 11 meses); 49% niñas y 51% varones. Motivo de solicitud de la prueba: 78,4% para estudio de contacto, 14,3% por síntomas sin noción de contacto y 7,3% previo a ingreso hospitalario (de urgencia o coordinación). Porcentaje de positividad de todo el período: 14,7%, con una importante variabilidad mensual (5,6% en diciembre y 27% en abril). La PCR fue positiva en 346 casos, con CT promedio de 27, y rango entre 16,8 y 37,3. No se encontraron diferencias estadísticas en relación a la edad y sexo entre casos positivos y negativos. Solo un caso fue PCR positivo previo al ingreso hospitalario (OR 0,03; IC 95% 0,004-0,22) y 20 de las 611 PCR solicitadas por contacto institucional (escolar, deportivo, etc.), siendo la diferencia estadísticamente significativa cuando el caso era mayor de 15 años (p 0,029). Del estudio retrospectivo de casos (PCR positiva) y controles (PCR negativa) surge una asociación estadísticamente significativa (p<0,000001) con la causa de solicitud por contacto en comparación con otra causa (OR 5,2; IC 95% 3,28-8,26), que el caso índice sea mayor de 15 años (OR 4,57 IC 95% 2,95 - 7,10) y que sea conviviente (OR 5,28 IC 95% 3,97 - 7,04). No hubo hospitalizaciones ni fallecimientos por COVID en la población analizada. Conclusiones: el testeo de niños y adolescentes en busca de COVID 19 continúa siendo una estrategia válida cuando existen síntomas sugestivos o contacto con un caso confirmado. En este estudio, los niños con antecedente de contacto con conviviente positivo, y mayor de 15 años, mostraron una mayor proporción de resultados positivos de PCR para SARS-CoV-2.

Introduction: the SARS-CoV-2 infection has shown a lower percentage in children compared to the global incidence of patients infected by this virus. The Polymerase Chain Reaction (PCR) test for SARS-CoV-2 in a sample of nasopharyngeal secretions is considered the reference standard test, and it has shown higher sensitivity and specificity levels than other techniques. Objective: describe the characteristics of patients under 15 years of age who underwent PCR for SARS-CoV-2 in a private health provider in the interior of the country between July 1, 2020 and April 30, 2021. Analyze possible factors linked to test positivity. Describe the characteristics of cases with positive PCR Methodology: prospective observational study with a retrospective case-control analysis based on the follow-up of a cohort of children under 15 years of age who underwent a PCR test for SARS-CoV-2 in the period analyzed, at a private health provider in the interior of Uruguay. Data were collected during patients' follow-up according to the institutional protocol that includes: personal data, reason for requesting the PCR, contact data, PCR result and cycle threshold (CT), clinical manifestations and evolution. Results: 2,361 PCRs were performed to children of under 15 years of age (15% of all PCRs in the institution). Average age 8.6 years (range 7 days - 14 years and 11 months); 49% girls and 51% boys. Reason for requesting the test: 78.4% due to previous contact, 14.3% due to symptoms without knowledge of contact and 7.3% prior to hospital admission (emergency or scheduled). Positivity percentage for the entire period 14.7% with significant monthly variability (5.6% in December and 27% in April). The PCR was positive in 346 cases, with a mean CT of 27, and a range between 16.8 and 37.3. No statistical differences were found regarding age and sex between positive and negative cases. Only 1 case was positive PCR prior to hospital admission (OR 0.03 95% CI 0.004 - 0.22) and 20 out of the 611 PCR were requested due to prior institutional contact (school, sports centers, etc.), the difference being statistically significant when the patient was older than 15 years (p 0.029). From the retrospective study of cases (PCR positive) and controls (PCR negative), a statistically significant link (p<0.000001) arose regarding: when the request resulted from a prior contact compared to other causes (OR 5.2 CI 95% 3.28-8.26), when the index case was older than 15 years of age (OR 4.57 95% CI 2.95-7.10) and when the patient and the contact had cohabited (OR 5.28 95% CI 3.97-7.04). There were no hospitalizations or deaths from COVID in the population analyzed. Conclusions: testing children and adolescents for COVID 19 continues to be a valid strategy in case of suggestive symptoms or contact with a confirmed positive case. In this study, children with a history of contact with a positive case, and older than 15 years, showed a higher proportion of positive PCR results for SARS-CoV-2.

Introdução: a infecção por SARS-CoV-2 em crianças representa um percentual menor do que na incidência global de pacientes infectados por esse vírus. O teste de reação em cadeia da polimerase (PCR) para SARS-CoV-2 em uma amostra de secreções nasofaríngeas é considerado o padrão de referência, com níveis de sensibilidade e especificidade mais elevados do que outras técnicas. Objetivo: descrever as características dos pacientes menores de 15 anos de idade que realizaram PCR para SARS-CoV-2 em uma prestadora de saúde privada do interior do país entre 1º de julho de 2020 e 30 de abril de 2021. Analisar possíveis fatores associados à positividade do teste. Descrever as características dos casos com PCR positivo. Metodologia: estudo observacional prospectivo com análise retrospectiva caso-controle a partir do acompanhamento de uma coorte de crianças menores de 15 anos que realizaram teste de PCR para SARS-CoV 2 no período analisado, em uma assistência médica de saúde no interior do país. Os dados foram coletados durante o acompanhamento dos pacientes de acordo com o protocolo institucional e incluíram: informação pessoal, motivo da solicitação do PCR, características do contato, resultado do PCR e limiar de ciclo (CT), manifestações clínicas e evolução. Resultados: foram solicitados 2.361 PCRs de menores de 15 anos (15% do total de PCRs da instituição). Idade média 8,6 anos (variação 7 dias - 14 anos e 11 meses); 49% meninas e 51% meninos. Motivo do pedido do exame: 78,4% por estudo de contato, 14,3% por sintomas sem conhecimento de contato e 7,3% antes da internação (por emergência ou coordenação). Porcentagem de positividade para todo o período 14,7% com significativa variabilidade mensal (5,6% em dezembro e 27% em abril). O PCR foi positivo em 346 casos, com média de TC de 27 e variação entre 16,8 e 37,3. Não foram encontradas diferenças estatísticas em relação à idade e sexo entre os casos positivos e negativos. Apenas 1 caso foi PCR positivo antes da admissão hospitalar (OR 0,03 IC 95% 0,004 - 0,22) e 20 dos 611 PCR solicitados por contato institucional (escola, centros de esportes, etc.), sendo a diferença estatisticamente significativa para os casos que tinham mais de 15 anos de idade (p 0,029). Do estudo retrospectivo de casos (PCR positivo) e controles (PCR negativo), emergiu uma associação estatisticamente significativa (p <0,000001) quando: a causa da solicitação do teste tinha sido um contato positivo prévio em relação a outra causa (OR 5,2 IC 95% 3,28 - 8,26), e quando o caso índice era mais velho do que 15 anos (OR 4,57 IC 95% 2,95 - 7,10) ou coabitava com o paciente (OR 5,28 IC 95% 3,97 - 7,04). Não houve internações ou óbitos por COVID na população analisada. Conclusões: a testagem de crianças e adolescentes em busca de COVID-19 continua sendo uma estratégia válida quando há sintomas sugestivos ou contato com um caso positivo confirmado. Neste estudo, crianças com histórico de contato com casos positivos na mesma casa e mais velhos do que 15 anos de idade apresentaram maior proporção de resultados positivos de PCR para SARS-CoV-2.

O efeito da testagem laboratorial nos indicadores de acompanhamento da COVID-19: uma análise dos 50 países com maior número de casos / El efecto de las pruebas de laboratorio en los indicadores de seguimiento de COVID-19: un análisis de los 50 países con el mayor número de casos / The effect of laboratory testing on COVID-19 monitoring indicators: an analysis of the 50 countries with the highest number of cases

Objetivo: Analisar como a testagem da população influencia os indicadores de saúde usados para monitorar a pandemia de COVID-19 nos 50 países com maior número de casos diagnosticados. Métodos: Estudo ecológico sobre dados secundários, extraídos em 19/08/2020. Foram calculadas incidência acumulada, taxa de mortalidade, letalidade e proporção de testes positivos. Os dados foram descritos e apresentados graficamente, com o respectivo coeficiente de correlação de Spearman. Resultados: A taxa de testagem variou enormemente entre os países. A incidência acumulada e a proporção de testes positivos foram correlacionadas ao número de testes, enquanto a taxa de mortalidade e a letalidade apresentaram correlação baixa com esse indicador. Conclusão: A maioria dos países não testa o suficiente para garantir adequado monitoramento da pandemia, com reflexo na qualidade dos indicadores. A ampliação do número de testes é fundamental; porém, ela deve ser acompanhada de outras medidas, como isolamento de casos diagnosticados e rastreamento de contatos.

Objetivo: Analizar cómo el testeo poblacional influye en los indicadores de salud utilizados para monitorear la pandemia de COVID-19 en los 50 países con mayor número de casos diagnosticados. Métodos: Estudio ecológico, con datos secundarios, recogidos el 19/8/2020. Se calcularon la incidencia acumulada, la tasa de mortalidad, la letalidad y la proporción de pruebas positivas. Los datos fueron descritos y presentados gráficamente, con el respectivo Coeficiente de Correlación de Spearman. Resultados: La tasa de testeo varió enormemente entre los países. La incidencia acumulada y la proporción de pruebas positivas se correlacionaron con el número de pruebas, mientras que la tasa de mortalidad y de letalidad mostraron una baja correlación con este indicador. Conclusión: La mayoría de los países no realizan suficientes pruebas para garantizar un seguimiento adecuado de la pandemia, lo que se refleja en la calidad de los indicadores. La ampliación del número de pruebas es fundamental, y debe ir acompañada de aislamiento de casos y seguimiento de contactos.

Objective: To analyse how testing the population influences the health indicators used to monitor the COVID-19 pandemic in the 50 countries with the highest number of diagnosed cases. Methods:This was an ecological study using secondary data retrieved on 8/19/2020. Cumulative incidence, mortality rate, case-fatality rate, and proportion of positive tests were calculated. The data were described and presented graphically, with their respective Spearman Correlation Coefficients. Results: The testing rate varied enormously between countries. Cumulative incidence and the proportion of positive tests were correlated with the number of tests, while the mortality rate and case-fatality rate showed low correlation with this indicator. Conclusion: Most countries do not test enough to ensure adequate monitoring of the pandemic, and this is reflected in the quality of the indicators. Expanding the number of tests is essential, but it needs to be accompanied by other measures, such as isolation of diagnosed cases and contact tracing.

Afinidad entre las pruebas PCR y Antígeno, y su positivad para COVID-19 en Colombia / Affinity between the PCR and antigen tests and their positivity for COVID-19 in Colombia

Introducción: : El síndrome respiratorio agudo severo por coronavirus (SARS-CoV-2), el virus que origina la enfermedad 2019 (COVID-19) se ha diseminado con rapidez por todo el mundo desde que surgió en Wuhan, China, a finales de 2019. Objetivo: describir el comportamiento de positividad de muestras tomadas para SARS-CoV-2. Metodología: esta investigación se centró en las muestras de PCR y antígeno procesadas para COVID-19, con la información proveniente del Instituto Nacional de Salud en el periodo comprendido entre el 1 de enero a 31 de marzo 2021. Resultados: para la prueba de PCR en cada uno de los meses de enero a marzo 2021 en Colombia, se detalló que los días con mayor porcentaje de casos positivos fueron 12 de enero 56,3%, 7 de enero 44,9%, 6 de enero 45,1%, 5 de enero 43,7%, 2 de enero 38,1%, 24 de marzo 35,2%, y 26 de marzo con 31,3%. Para la prueba de antígeno en cada uno de los meses de enero a marzo 2021 en Colombia, se anota que los días con mayor porcentaje de casos positivos fueron 11 de enero 32,7%, 4 de enero 31,0%, 15 de enero 28,9%, 18 de enero 22,4%, 22 de marzo 21,1%, 28 de marzo 20,7%, y 17 de febrero 20,1%. Conclusión: hay que continuar la búsqueda activa de contagiados a través de la práctica de mayor número de pruebas de PCR, antígeno viral y molecular, la última con un alto nivel de precisión por parte de las EPS, y que a su vez aceleren el proceso de entrega de resultados.

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19) has spread rapidly around the world since it emerged in Wuhan, China, in late 2019. Objective: to describe the positivity rates of samples tested for SARS-CoV-2. Methodology: the research focused on PCR and antigen tests processed for COVID-19, using the information released by the National Institute of Health between January 1 and March 31 2021. Results: the highest positivity rate for PCR testing for each month between January to March 2021 in Colombia was found on the following days: January 12: 56.3%, January 7: 44.9%, January 6: 45.1%, January 5: 43.7%, January 2: 38.1%, March 24: 35.2% and March 26: (31.3%. The days with the highest percentage of positive cases found by antigen testing for each month from January to March 2021 in Colombia, were January 11: 32.7%, January 4: 31.0%, January 15: 28.9%, January 18: 22.4%, March 22: 21.1%, March 28: 20.7% and February 17: 20.1%. Conclusion: an active search of infected people must be continued through the practice of a greater number of PCR and viral antigen and molecular tests. The latter has been reported by the EPS to show very high accuracy, which accelerates the result delivery process.

Antigen-detection in the diagnosis of SARS-CoV-2 infection: interim guidance, 6 October 2021

Diagnostic testing for SARS-CoV-2 is a critical component to the overall prevention and control strategy for COVID-19. Countries should have a national testing strategy in place with clear objectives that can be adapted according to changes in the epidemiological situation, available resources and tools, and country-specific context. It is critical that all SARSCoV-2 testing is linked to public health actions to ensure appropriate clinical care and support and to carry out contact tracing to break chains of transmission. Since the early days of the SARS-CoV-2 pandemic, laboratories have been using nucleic acid amplification tests (NAATs), such as real time reverse transcription polymerase chain reaction (rRT-PCR) assays, to detect SARS-CoV-2, the virus that causes COVID-19. Since mid-2020, less expensive and faster diagnostic tests that detect antigens specific for SARS-CoV-2 infection have become commercially available, and several have achieved WHO Emergency use listing. Antigen-detecting diagnostic tests are designed to directly identify SARS-CoV-2 proteins produced by replicating virus in respiratory secretions (or oral fluid/saliva) and have been developed as both laboratory-based tests and rapid diagnostic tests (RDTs) intended for near-patient use. The diagnostic development landscape is dynamic, with over two hundred tests for SARS-CoV-2 antigen detection on the market, of which 85% can be delivered at the point of care and the other 15% for use on high throughput machines in laboratory-based settings.