Development of a mobile laboratory system in hydrogen fuel cell buses and evaluation of the performance for COVID-19 RT-PCR testing.

We designed and developed two new types of hydrogen fuel cell (HFC) buses (motorcoach and minibus) with a mobile laboratory system. Feasibility studies have been performed for mobile laboratory testing, particularly for the laboratory performance of COVID-19 RT-PCR (PCR). We evaluated the driving range capability, PCR sample size capacity, turnaround time (TAT), and analytical performance for the detection of SARS-CoV-2. Saliva samples were used for the current study, and the analytical performance was compared with that of the reference PCR. The estimated driving range and sample size capacity of the HFC and HFC minibus were 432 km and 2847 samples, respectively, for the HFC motorcoach and 313 km and 1949 samples for the HFC minibus. For the TAT, the median time between sample submission and completion of PCR was 86 min for the motorcoach and 76 min for the minibus, and the median time between sample submission and electronic reporting of the result to each visitor was 182 min for the motorcoach and 194 min for the minibus. A secondary analysis of 1574 HFC mobile laboratory testing samples was conducted, and all negative samples were found to be negative by reference PCR. Furthermore, all samples were confirmed to be positive by reference PCR or other molecular examinations.

Comparison of the Diagnostic Performance of Deep Learning Algorithms for Reducing the Time Required for COVID-19 RT-PCR Testing.

(1) Background: Rapid and accurate negative discrimination enables efficient management of scarce isolated bed resources and adequate patient accommodation in the majority of areas experiencing an explosion of confirmed cases due to Omicron mutations. Until now, methods for artificial intelligence or deep learning to replace time-consuming RT-PCR have relied on CXR, chest CT, blood test results, or clinical information. (2) Methods: We proposed and compared five different types of deep learning algorithms (RNN, LSTM, Bi-LSTM, GRU, and transformer) for reducing the time required for RT-PCR diagnosis by learning the change in fluorescence value derived over time during the RT-PCR process. (3) Results: Among the five deep learning algorithms capable of training time series data, Bi-LSTM and GRU were shown to be able to decrease the time required for RT-PCR diagnosis by half or by 25% without significantly impairing the diagnostic performance of the COVID-19 RT-PCR test. (4) Conclusions: The diagnostic performance of the model developed in this study when 40 cycles of RT-PCR are used for diagnosis shows the possibility of nearly halving the time required for RT-PCR diagnosis.

Impact of COVID-19 RT-PCR testing of asymptomatic health care workers on absenteeism and hospital transmission during the pandemic.

BACKGROUND: Reducing the transmission of SARS-CoV-2 from asymptomatic and pre-symptomatic patients is critical in controlling the circulation of the virus. METHODS: This study evaluated the prevalence of Reverse transcription polymerase chain reaction (RT-PCR) positivity in serial tests in 429 asymptomatic health care workers (HCW) and its impact on absenteeism. HCW from a COVID-19 reference hospital were tested, screened, and placed on leave. A time-series segmented regression of weekly absenteeism rates was used, and cases of infection among hospitalized patients were analyzed. Viral gene sequencing and phylogenetic analysis were performed on samples from HCW who had a positive result. RESULTS: A significant decrease in absenteeism was detected 3-4 weeks after the intervention at a time of increased transmission within the city. The prevalence of RT-PCR positivity among asymptomatic professionals was 17.3%. Phylogenetic analyses (59 samples) detected nine clusters, two of them strongly suggestive of intrahospital transmission with strains (75% B.1.1.28) circulating in the region during this period. CONCLUSIONS: Testing and placing asymptomatic professionals on leave contributed to control strategy for COVID-19 transmission in the hospital environment, and in reducing positivity and absenteeism, which directly influences the quality of care and exposes professionals to an extra load of stress.

Saúde mental e atuação de psicólogos hospitalares brasileiros na pandemia da covid-19 / Health and works of brazilian hospital psychologists in the covid-19 pandemic / Salud mental y actuación de psicólogos en hospitales brasileños en la pandemia del covid-19

Em março de 2020 a situação causada pela covid-19 foi elevada à categoria de pandemia, impactando de inúmeras formas a vida em sociedade. O objetivo deste estudo foi compreender os impactos da pandemia na atuação e saúde mental do psicólogo hospitalar, profissional que atua nos espaços de saúde e tem experienciado mais de perto o sofrimento dos doentes e dos profissionais de saúde frente à covid-19. Trata-se de um estudo exploratório-descritivo com 131 psicólogos que atuam em hospitais. Os profissionais foram convidados a participar através de redes sociais e redes de contatos das pesquisadoras, utilizando-se a técnica Bola de Neve. Foram utilizados dois questionários, disponibilizados na plataforma Google Forms, um abordando os impactos da pandemia sentidos pelos profissionais e outro referente ao sofrimento psíquico. Os dados foram analisados a partir de estatísticas descritivas e inferenciais. Foram observados impactos na atuação de quase a totalidade dos participantes, constatada a necessidade de preparação dos profissionais para o novo cenário, a percepção de pouco apoio institucional e quase metade da população estudada referiu-se a sintomas de sofrimento psíquico considerável desde o início da pandemia. É fundamental dar atenção a sinais e sintomas de sofrimento psíquico, procurando evitar o adoecimento de uma categoria profissional que se encontra na linha de frente do combate aos danos psicológicos da pandemia e cuja própria saúde mental é pouco abordada na literatura.(AU)

In March 2020, the COVID-19 pandemic breakout hugely impacted life in society. This study analyzes how the pandemic impacted hospital psychologists' mental health and performance, professional who more closely experienced the suffering of patients and health professionals in this period. An exploratory and descriptive study was conducted with 131 hospital psychologists. Professionals were invited to participate through the researchers' social and contact networks using the Snowball technique. Data were collected by two questionnaires available on the Google Forms platform, one addressing the impacts felt by professionals and the other regarding psychic suffering, and analyzed by descriptive and inferential statistics. Results showed that almost all participants had their performance affected by the need to prepare for the new scenario, the perceived little institutional support. Almost half of the study sample reported considerable psychological distress symptoms since the beginning of the pandemic. Paying attention to signs and symptoms of psychic suffering is fundamental to avoid compromising a professional category that is on the front line of combating the psychological damage caused by the pandemic and whose own mental health is little addressed by the literature.(AU)

En marzo de 2020, la situación provocada por el COVID-19 se caracterizó como pandemia e impactó el mundo de diversas maneras. El objetivo de este estudio fue comprender los impactos de la pandemia en la salud mental y la actuación del psicólogo en los hospitales, uno de los profesionales que trabaja en espacios sanitarios y que ha experimentado más de cerca el sufrimiento de pacientes y profesionales sanitarios frente al COVID-19. Este es un estudio exploratorio descriptivo, realizado con 131 psicólogos que trabajan en hospitales. Los profesionales recibieron la invitación a participar a través de las redes sociales y redes de contactos de las investigadoras, mediante la técnica snowball. Se utilizaron dos cuestionarios disponibles en la plataforma Google Forms: uno sobre los impactos de la pandemia en los profesionales y el otro sobre el sufrimiento psíquico. Los datos se analizaron a partir de estadísticas descriptivas e inferenciales. Se observaron impactos en el trabajo de casi todos los participantes, la necesidad de preparación de los profesionales para este nuevo escenario, la percepción de poco apoyo institucional, y casi la mitad de la población estudiada reportaron sentir síntomas de considerable angustia psicológica desde el inicio de la pandemia. Es esencial prestar atención a los signos y síntomas del sufrimiento psíquico, buscando evitar la enfermedad de una categoría profesional que está a la vanguardia de la lucha contra el daño psicológico de la pandemia y cuya propia salud mental se aborda poco en la literatura.(AU)

Incidence and factors associated with pulmonary embolism among RT-PCR confirmed Covid-19 patients with upfront CT pulmonary angiography in Ethiopia: A nested case-control study

Introduction: Pulmonary embolism is one of the complications of COVID-19, with reported incidence ranging from 3 to 33 % in non-ICU patients to as high as 40% among ICU patients. Since the clinical presentations of COVID-19 and Pulmonary embolism overlap, it is difficult to differentiate between these cases. This study aimed to assess the incidence of pulmonary embolism and associated factors among confirmed Covid-19 Patients in Ethiopia. Methods: A nested case control study was conducted among 131 patients with COVID-19 (40 COVID-19 patients with Pulmonary embolism and 91 COVID-19 patients with no PE) who were on follow up from May, 2021 to May, 2022. Data was summarized using frequencies with percentages. A chi-square test/ Fisher's exact test was run to determine the presence of a significant difference between the exposure variables and the development of PE. To identify factors associated with the development of Pulmonary embolism, a multivariable Binary Logistic Regression model with sensitivity analysis was run. Results: The incidence of PE was 30.5% (95% CI, 22.9% - 37.4%) in the cohort of patients for whom upfront CTPA was performed. The Chi-square/ Fisher's exact test results showed a significantly higher proportion of patients with PE tend to present with shortness of breath, chest pain and anosmia/ageusia than those with no PE. However, in a subsequent regression analysis, only chest pain was found to be significantly associated with the development of PE in COVID-19 patients (AOR= 3.24, 95% CI= 1.10, 9.54, p-value=0.033). Conclusion: The incidence of PE among COVID-19 patients was found to be relatively lower than reports from other countries. Having chest pain was found to be a significant factor that indicates the development of PE, implying that in a setting where performing upfront CTPA is not practical, detailed symptom inquiry could serve as an important clinical criteria.

Delayed SARS-COV-2 clearance in infected persons in Ghana

Objective: This study aimed to determine the duration of SARS-CoV-2 clearance in persons in Ghana. The research question was whether the duration of virus clearance in Ghana matched the 14 days recommended by the World Health Organization (WHO); this had direct implications for transmission, which was key in managing the COVID-19 pandemic. Design: This was a retrospective analytical study. Setting: All facilities that submitted clinical specimens to Noguchi Memorial Institute for Medical Research (NMIMR) for SARS-CoV-2 diagnosis between March to June 2020 were included in the study. Interventions: Samples from 480 persons who tested positive for SARS-CoV-2 by RT-PCR from March to June 2020 at NMIMR and submitted at least two follow-up samples were retrospectively analysed. Individuals with two consecutive negative RT-PCR retesting results were considered to have cleared SARS-CoV-2. Results: The median time from the initial positive test to virus clearance was 20 days (IQR: 5-56 days). This was six days longer than the WHO-recommended 14 days, after which infected persons could be de-isolated. Sputum and nasopharyngeal swabs proved more sensitive for detecting viral RNA as the infection progressed. At a significance level of 0.05, age and sex did not seem to influence the time to SARS-CoV-2 clearance. Conclusions: The median time to SARS-CoV-2 clearance in this study was 20 days, suggesting that SARS-CoV-2 infected persons in Ghana take longer to clear the virus. This finding calls for further investigations into whether patients who remain PCR positive continue to be infectious and inform isolation practices in Ghana.

Resultados terapêuticos da homeopatia em pacientes suspeitos ou confirmados de COVID-19: um estudo longitudinal prospectivo / Therapeutic results of homeopathy in suspected or confirmed COVID-19 patients: a longitudinal study

A infecção humana causada pelo vírus SARS-CoV-2 (COVID-19), diagnosticada como pneumonia de causa desconhecida originalmente na cidade de Wuhan (China), foi considerada como pandemia pela Organização Mundial da Saúde. Com a inexistência inicial de uma vacina para proteção dos sadios, foi adotada a estratégia de isolamento social e tratamento com medidas de suporte geral e/ou avançado. Neste contexto, coube investigar a contribuição da terapêutica homeopática no enfrentamento da doença, notadamente no alívio dos sintomas desconfortáveis por ela provocados em sua fase inicial, com acompanhamento e registro dos resultados obtidos pelos médicos homeopatas. MÉTODO: Este estudo coletou, durante o período de maio a setembro de 2020 (após aprovação pelo CEP), informações de pacientes diagnosticados com a doença, tratados por médicos homeopatas com medicamentos homeopáticos escolhidos de acordo com a sintomatologia apresentada pelo paciente. Foram avaliados os efeitos no estado de saúde do paciente, por meio de escores e escalas clínicas, bem como aspectos relacionados à segurança do medicamento, variação na duração da doença e medicamentos mais associados a eventuais sucessos terapêuticos. Questionário padronizado e específico para a COVID-19 foi elaborado e e aplicado para preenchimento dos médicos colaboradores do estudo durante o acompanhamento dos pacientes. Os dados foram armazenados em planilhas eletrônicas e analisados com técnicas estatísticas descritivas e inferenciais. Os pacientes selecionados eram colaboradores do Hospital Santo Antônio - Obras Sociais Irmã Dulce (OSID) e foram submetidos a uma avaliação preliminar presencial no ambulatório de Otorrinolaringologia deste hospital. As consultas homeopáticas foram realizadas por plataforma de Telemedicina para seguimento e acompanhamento do caso. Foram avaliados 116 colaboradores, com faixa etária que variou entre 21 e 66 anos, sendo a média de idade 38 anos; destes, 84 (72%) eram do gênero feminino e 32 (16%) gênero masculino; 53 pacientes (70% dos colaboradores atendidos) eram profissionais da saúde (médicos, enfermeiros e técnicos de enfermagem); 63 (30%) eram colaboradores de áreas administrativas ou técnicas; 50 pacientes tinham critérios para inclusão no grupo de risco (43%). Quanto ao resultado do RT-PCR: 58 pacientes (50%) tiveram RT-PCR detectado (confirmados); 58 pacientes (50%) tiveram RT-PCR não-detectado - destes, 18 pacientes (31%) apresentaram anosmia em sua evolução. Dos 116 pacientes do critério de inclusão, 77 estavam incluídos na síndrome clássica da COVID19. Destes 77 colaboradores, 3 não usaram o medicamento homeopático (N=74). Os medicamentos homeopáticos mais indicados foram: Arsenicum album (42%); Bryonia (24%), Phosphorus (15%); Gelsemium (15%); Pulsatilla (2%); outros (4%). O Score médio de sintomas antes do tratamento foi 12,27 e após o tratamento foi 0,52 (p < xxxxx). Dos 57 pacientes que tiveram anosmia, houve recuperação total em 43 (75%) dos casos no momento da reavaliação. O tempo médio decorrido entre o uso da medicação homeopática e a recuperação dos sintomas foi de 9 dias. Apenas 3 pacientes (3,9%) necessitaram de internamento hospitalar sem necessidade de intubação, sendo 2 deles pertencentes ao grupo de risco. apesar destes resultados serem parciais (pois ainda existem sujeitos da pesquisa ainda em fase de avaliação), os resultados sugerem que o tratamento homeopático promoveu o restabelecimento do quadro infeccioso sem necessidade de internamento em 97% dos pacientes. A anosmia teve recuperação completa em 75% dos pacientes. Arsenicum album, Bryonia e Phosphorus foram os medicamentos predominantemente eleitos para o tratamento, o que corrobora com outros estudos homeopáticos.

The human infection caused by the SARS-CoV-2 virus (COVID-19), originally diagnosed as pneumonia of unknown cause in the city of Wuhan (China), was considered a pandemic by the World Health Organization. With the initial lack of a vaccine to protect healthy people, the strategy relating to social isolation and treatment with general and/or advanced support measures was adopted. In this context, it was necessary to investigate the contribution of homeopathic therapy in coping with the disease, particularly in terms of relieving the uncomfortable symptoms caused by it in its initial phase, with monitoring and recording of the results obtained by homeopathic physicians. METHOD: This study collected information from patients diagnosed with the disease, treated by homeopathic physicians with homeopathic medications chosen according to the symptoms manifested by the patient, from May to September 2020 (after approval by the REC). The effects on the health conditions of patients were assessed using clinical scores and scales, as well as aspects related to the safety of the medication, variations in the duration of the disease and the medications most associated with any therapeutic successes. A standardized questionnaire specific to COVID-19 was drawn up and filled in by the physicians who collaborated in the study during patient monitoring. The data was stored in electronic spreadsheets and analyzed using descriptive and inferential statistical techniques. The selected patients were employees of Hospital Santo Antônio - Obras Sociais Irmã Dulce (OSID) and underwent a preliminary in-person assessment at the otolaryngology outpatient clinic of this hospital. The homeopathic consultations were carried out via a telemedicine platform to follow-up and monitor the case. A total of 116 employees were assessed, ranging in age from 21 to 66, with the average age being 38; of these, 84 (72%) were females and 32 (16%) males; 53 patients (70% of the employees cared for) were health care professionals (physicians, nurses and nursing technicians); 63 (30%) were employees from administrative or technical areas; 50 patients met the criteria for inclusion in the risk group (43%). As for the RT-PCR result: 58 patients (50%) had RT-PCR detected (confirmed); 58 patients (50%) had RT-PCR not detected - of these, 18 patients (31%) had anosmia during their evolution. Of the 116 patients who met the inclusion criteria, 77 were included in the classic COVID-19 syndrome. Of these 77 collaborators, 3 did not use homeopathic medication (N=74). The most indicated homeopathic medications were: Arsenicum album (42%); Bryonia (24%), Phosphorus (15%); Gelsemium (15%); Pulsatilla (2%); others (4%). The average symptom score before treatment was 12.27 and after treatment was 0.52 (p < xxxxx). Of the 57 patients who had anosmia, there was full recovery in 43 (75%) of the cases at the time of reassessment. The average time elapsed between the use of homeopathic medication and the recovery of symptoms was 9 days. Only 3 patients (3.9%) required hospitalization without the need for intubation, 2 of whom belonged to the risk group. Although these results are partial (as there are still research subjects in the evaluation phase), the results suggest that homeopathic treatment promoted the re-establishment of the infectious condition without the need for hospitalization in 97% of the patients. Anosmia recovered completely in 75% of the patients. Arsenicum album, Bryonia and Phosphorus were the drugs predominantly chosen for treatment, which corroborates other homeopathic studies.

Uma análise dos principais diagnósticos de Sars-cov-2 disponíveis no Brasil: uma revisão de literatura / Diagnosis and main types of coronavirus in humans: a narrative review / Diagnóstico y principales tipos de coronavirus en humanos: una revisión narrativa

Introdução: Com a emergência do SARS-CoV-2 foi disponibilizado uma grande quantidade de ferramentas de diagnóstico. Neste contexto, a falta de vacina, de tratamento e o grande número de casos graves e morte, possibilitou a aprovação emergencial de diversos testes, que ainda necessitam de estudos populacionais para seu registro definitivo. Objetivo: Realizar uma revisão de literatura para avaliar as metodologias de diagnóstico disponíveis no Brasil, de acordo com a realidade local de saúde, explorando o momento epidemiológico a complexidade do teste e a finalidade da sua aplicação. Metodologia: Trata-se de um estudo bibliográfico, descritivo do tipo revisão de literatura. Foram utilizadas as seguintes bases de dados científicos para buscas: PUBMED, MEDLINE, LILACS E COCHRANE LIBRARY, através de descritores selecionados na plataforma DECS. Resultados: O cenário de diversos ensaios, baseados em diferentes metodologias, como os testes baseados em RNA viral, em detecção de antígenos virais ou de anticorpos, associados ao conhecimento da história natural do vírus, possibilita uma análise crítica do melhor diagnóstico de acordo com a clínica do paciente, os epidemiológicos, o objetivo do diagnóstico e a acurácia do ensaio. Atualmente, há mudança no padrão imunológico da população e a descrição de tipos e subtipos de SARS-CoV-2 com mudanças gênicas, que podem levar a mudanças na acurácia diagnóstica ou a re-emergência em surtos de doença grave. Conclusão: Ainda é incerto o caminho evolutivo da história natural da Covid-19 e os ensaios diagnósticos estão em diferentes estágios de desenvolvimento, validação e produção e cada tipo de teste tem suas próprias vantagens e desvantagens distintas inerentes a plataforma tecnológica de origem e uma combinação de tipos de testes usados em momentos diferentes pode ser útil para a condução clínica dos pacientes e no controle da pandemia por SARS-CoV-2.

Introduction: With the emergence of SARS-CoV-2, a large number of diagnostic tools were made available. In this context, the lack of vaccine, treatment and the large number of severe cases and death, allowed the emergency approval of several tests, which still require population studies for their definitive registration. Objective: To carry out a literature review to evaluate the diagnostic methodologies available in Brazil, according to the local health reality, exploring the epidemiological moment, the complexity of the test and the purpose of its application. Methodology: This is a bibliographic, descriptive study of the literature review type. The following scientific databases were used for searches: PUBMED, MEDLINE, LILACS AND COCHRANE LIBRARY, through selected descriptors on the DECS platform. Results: The scenario of several tests, based on different methodologies, such as tests based on viral RNA, on detection of viral antigens or antibodies, associated with knowledge of the natural history of the virus, allows a critical analysis of the best diagnosis according to the patient's clinical, epidemiological, diagnostic objective and assay accuracy. Currently, there is a change in the immune pattern of the population and the description of types and subtypes of SARS-CoV-2 with genetic changes, which can lead to changes in diagnostic accuracy or the re-emergence in outbreaks of severe disease. Conclusion: The evolutionary path of the natural history of Covid-19 is still uncertain and diagnostic assays are at different stages of development, validation and production and each type of test has its own distinct advantages and disadvantages inherent in the technology platform of origin and a combination of types of tests used at different times can be useful for the clinical management of patients and in the control of the SARS-CoV-2 pandemic.

Introducción: Con la aparición del SARS-CoV-2, se dispuso de un gran número de herramientas diagnósticas. En este contexto, la falta de vacuna, tratamiento y el gran número de casos graves y muerte, permitieron la aprobación de urgencia de varias pruebas, que aún requieren estudios poblacionales para su registro definitivo. Objetivo: Realizar una revisión bibliográfica para evaluar las metodologías diagnósticas disponibles en Brasil, de acuerdo con la realidad sanitaria local, explorando el momento epidemiológico, la complejidad de la prueba y la finalidad de su aplicación. Metodología: Se trata de un estudio bibliográfico, descriptivo, del tipo revisión de literatura. Para las búsquedas se utilizaron las siguientes bases de datos científicas PUBMED, MEDLINE, LILACS Y COCHRANE LIBRARY, a través de descriptores seleccionados en la plataforma DECS. Resultados: El escenario de varias pruebas, basadas en diferentes metodologías, como pruebas basadas en el ARN viral, en la detección de antígenos virales o anticuerpos, asociado al conocimiento de la historia natural del virus, permite un análisis crítico del mejor diagnóstico de acuerdo con la clínica del paciente, epidemiológica, objetivo diagnóstico y precisión de la prueba. Actualmente, hay un cambio en el patrón inmunológico de la población y la descripción de tipos y subtipos de SARS-CoV-2 con cambios genéticos, que pueden conducir a cambios en la precisión diagnóstica o la reaparición en brotes de enfermedad grave. Conclusiones: El camino evolutivo de la historia natural del Covid-19 es aún incierto y los ensayos de diagnóstico se encuentran en diferentes etapas de desarrollo, validación y producción y cada tipo de prueba tiene sus propias ventajas y desventajas distintas inherentes a la plataforma tecnológica de origen y una combinación de tipos de pruebas utilizadas en diferentes momentos puede ser útil para el manejo clínico de los pacientes y en el control de la pandemia de SARS- CoV-2.

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.

Estimation of R0 for the spread of SARS-CoV-2 in Germany from excess mortality.

For SARS-CoV-2, R0 calculations in the range of 2-3 dominate the literature, but much higher estimates have also been published. Because capacity for RT-PCR testing increased greatly in the early phase of the Covid-19 pandemic, R0 determinations based on these incidence values are subject to strong bias. We propose to use Covid-19-induced excess mortality to determine R0 regardless of RT-PCR testing capacity. We used data from the Robert Koch Institute (RKI) on the incidence of Covid cases, Covid-related deaths, number of RT-PCR tests performed, and excess mortality calculated from data from the Federal Statistical Office in Germany. We determined R0 using exponential growth estimates with a serial interval of 4.7 days. We used only datasets that were not yet under the influence of policy measures (e.g., lockdowns or school closures). The uncorrected R0 value for the spread of SARS-CoV-2 based on RT-PCR incidence data was 2.56 (95% CI 2.52-2.60) for Covid-19 cases and 2.03 (95% CI 1.96-2.10) for Covid-19-related deaths. However, because the number of RT-PCR tests increased by a growth factor of 1.381 during the same period, these R0 values must be corrected accordingly (R0corrected = R0uncorrected/1.381), yielding 1.86 for Covid-19 cases and 1.47 for Covid-19 deaths. The R0 value based on excess deaths was calculated to be 1.34 (95% CI 1.32-1.37). A sine-function-based adjustment for seasonal effects of 40% corresponds to a maximum value of R0January = 1.68 and a minimum value of R0July = 1.01. Our calculations show an R0 that is much lower than previously thought. This relatively low range of R0 fits very well with the observed seasonal pattern of infection across Europe in 2020 and 2021, including the emergence of more contagious escape variants such as delta or omicron. In general, our study shows that excess mortality can be used as a reliable surrogate to determine the R0 in pandemic situations.

El dilema en los laboratorios de Koch, ¿Cultivar o no Cultivar? / The Dilemma in Koch's Laboratories, To Cultivate or Not to Cultivate?

La nueva norma técnica para el control y la eliminación de la tuberculosis es un gran avance para el diagnóstico de este microorganismo en Chile. Actualmente la principal técnica microbiológica para el diagnóstico de laboratorio es la biología molecular, que reduce el tiempo del resultado a tan solo un par de horas. La normativa actual indica que en el paciente caso presuntivo de tuberculosis (CPT) la técnica exclusiva a realizar es Biología molecular. La literatura indica que la detección a través de amplificación de material genético de la micobacteria tiene un límite de detección de 15,6 UFC/ ml, por tanto, todas las muestras bajo ese límite umbral potencialmente podrían no ser diagnosticadas bajo esta estructura emanada por el ministerio de Salud en Chile. Nuestra recomendación es continuar con el estudio de cultivo en medios líquidos o sólidos para todas las muestras hasta obtener literatura que avale lo contrario

The new technical standard for the control and elimination of tuberculosis in Chile is a great advance for the diagnosis of this microorganism. Currently the main microbiological technique for laboratory diagnosis is PCR, which reduces the time to result to just a couple of hours. The current regulations indicate that in the patient with a presumptive case of tuberculosis (CPT) t he exclusive technique to be performed is PCR. The literature indicates that the detection through amplification of genetic material of the mycobacterium has a detection limit of 15.6 CFU/ml, therefore, all samples under this threshold limit could potentially not be diagnosed under this structure emanated by the Ministry of Health in Chile. Our recommendation is to continue with the study of culture in liquid or solid media for all samples until literature confirms otherwise

Validity of at-home rapid antigen lateral flow assay and artificial intelligence read to detect SARS-CoV-2.

BACKGROUND: The gold standard for COVID-19 diagnosis-reverse-transcriptase polymerase chain reaction (RT-PCR)- is expensive and often slow to yield results whereas lateral flow tests can lack sensitivity. METHODS: We tested a rapid, lateral flow antigen (LFA) assay with artificial intelligence read (LFAIR) in subjects from COVID-19 treatment trials (N = 37; daily tests for 5 days) and from a population-based study (N = 88; single test). LFAIR was compared to RT-PCR from same-day samples. RESULTS: Using each participant's first sample, LFAIR showed 86.2% sensitivity (95% CI 73.6%-98.8) and 94.3% specificity (88.8%-99.7%) compared to RT-PCR. Adjusting for days since symptom onset and repeat testing, sensitivity was 97.8% (89.9%-99.5%) on the first symptomatic day and decreased with each additional day. Sensitivity improved with artificial intelligence (AI) read (86.2%) compared to the human eye (71.4%). CONCLUSION: LFAIR showed improved accuracy compared to LFA alone. particularly early in infection.

Aportes de la biotecnología en el diagnóstico de COVID-19 / Biotechnology contributions in COVID-19 diagnosis

Introducción: en diciembre del año 2019 surgió en China una neumonía viral; el virus fue identificado como un coronavirus SARS-CoV-2, que se propagó rápidamente de tal manera que se convirtió en pandemia. La alta contagiosidad y la presencia de portadores asintomáticos dificultaron el diagnóstico de la infección y la toma de decisiones sanitarias. Objetivo: el objetivo de esta revisión bibliográfica es presentar y describir las principales técnicas utilizadas actualmente para el diagnóstico de COVID-19 y establecer su relación con los conocimientos de distintas disciplinas y tecnologías emergentes que confluyen en la Biotecnología bioquímico-farmacéutica orientada a la Salud humana. Metodología: se realizó una revisión de la bibliografía disponible en PubMed a partir de enero de 2020 sobre las pruebas diagnósticas que se encuentran actualmente en uso, en el ámbito sanitario, para la detección y seguimiento de la enfermedad COVID-19. También se realizaron búsquedas a través de Google y Google Académico para publicaciones de organismos de Salud en referencia a métodos diagnósticos. Resultados: se presenta una importante cantidad de pruebas diagnósticas, basadas en diferentes tecnologías, que desempeñan un papel clave en la pandemia de COVID-19. Algunas de ellas muy sofisticadas, como la secuenciación genómica de próxima generación, otras más estándar, pero igualmente robustas, como la reacción en cadena de la polimerasa (PCR). También otras adaptadas para el brote pandémico, como la amplificación isotérmica de ácidos nucleicos mediada por bucle. Todas las mencionadas se consideran de tipo molecular, pero también existen las pruebas serológicas, como ELISA, que incluyen ensayos en plasma o de tipo inmunológico. Estas sirven para detectar anticuerpos frente a la exposición al virus o antígenos en personas potencialmente infectadas. Conclusiones: los procesos de investigación y desarrollo biotecnológicos aplicados al diagnóstico y los conocimientos científicos previos permitieron una respuesta tanto nacional como internacional rápida y eficaz en medio de una inédita pandemia global. En esta revisión destacamos las principales técnicas, en qué estadio se deben usar y qué información nos aportan. (AU)

Introduction: in December 2019, a viral pneumonia emerged in China, identifying the virus as a SARS-CoV-2 coronavirus, which spread rapidly in such a way that it became a pandemic. The high contagiousness and the presence of asymptomatic carriers make difficulted to diagnose the infection and to make health decisions. Target: the objective of this review is to present and describe the main techniques currently used for the diagnosis of COVID-19, and to establish their relationship with the knowledge of different disciplines and emerging technologies that converge in biochemical-pharmaceutical biotechnology oriented to human health. Methodology: a review of the literature available in Pubmed from January 2020 on the diagnostic tests that are currently in use in the health field, for the detection and monitoring of COVID-19 disease, was carried out. Searches were also carried out through Google and Google Scholar for publications of Health organizations in reference to diagnostic methods. Results: a significant number of diagnostic tests are presented, based on different technologies, which play a key role in the COVID-19 pandemic. Some of them are very sophisticated, such as next-generation genomic sequencing, others more standard, but equally robust, such as polymerase chain reaction. Also others adapted for the pandemic outbreak such as loop-mediated isothermal amplification of nucleic acids. All of the aforementioned are considered molecular, but there are also serological tests, such as ELISA, which include plasma or immunological tests. These serve to detect antibodies against exposure to the virus or antigens in potentially infected people. Conclusions: biotechnological research and development processes applied to diagnosis and previous scientific knowledge allowed a rapid and effective national and international response in the midst of an unprecedented global pandemic. In this review we highlight the main techniques, at what stage they should be used and what information they provide us. (AU)

Swab [libras]

O vídeo explica o que é surto e o que é necessário para caracterizar o aumento de casos de uma doença como um. O aplicativo FioLibras é um projeto do Instituto de Comunicação e Informação Científica e Tecnológica em Saúde da Fundação Oswaldo Cruz (Icict/Fiocruz), em parceria com o Núcleo de Estudos em Diversidade e Inclusão de Surdos da Universidade Federal Fluminense (Nuedis/UFF), e conta com financiamento do Fundo de Inovação da Fiocruz e do Ministério da Saúde, por meio do Programa Fiocruz de Fomento à Inovação (Inova Fiocruz).

Teste PCR [libras]

O vídeo explica o que é o teste PCR e como ele é realizado para detecção do vírus causador da COVID-19. O aplicativo FioLibras é um projeto do Instituto de Comunicação e Informação Científica e Tecnológica em Saúde da Fundação Oswaldo Cruz (Icict/Fiocruz), em parceria com o Núcleo de Estudos em Diversidade e Inclusão de Surdos da Universidade Federal Fluminense (Nuedis/UFF), e conta com financiamento do Fundo de Inovação da Fiocruz e do Ministério da Saúde, por meio do Programa Fiocruz de Fomento à Inovação (Inova Fiocruz).

Teste rápido [libras]

O vídeo apresenta informações sobre kits para verificação de infecção por COVID-19. O aplicativo FioLibras é um projeto do Instituto de Comunicação e Informação Científica e Tecnológica em Saúde da Fundação Oswaldo Cruz (Icict/Fiocruz), em parceria com o Núcleo de Estudos em Diversidade e Inclusão de Surdos da Universidade Federal Fluminense (Nuedis/UFF), e conta com financiamento do Fundo de Inovação da Fiocruz e do Ministério da Saúde, por meio do Programa Fiocruz de Fomento à Inovação (Inova Fiocruz).

Petroleum jelly and COVID-19 prevention.

Since the ongoing pandemic of COVID-19, caused by SARS-CoV-2, has had a significant impact on public health and, also the clinical benefits of the medications are so limited, preventive measures may be able to help control its spread. Because the petroleum jelly compound could alter the physicochemical properties that affect adhesion, we investigated the preventive role of Petroleum jelly on covid-19 infection. Forty people with no sign and no history of covid-19 infection, were included in this study. They use petroleum jelly (Vaseline) nasally twice a day for about two months. After that time, participants tested by RT-qPCR to determine any infection with SARS-CoV-2 virus. There was a significant difference in terms of RT-qPCR results between the intervention and control groups. Petroleum jelly may be effective in preventing covid-19 infection (Tab. 2, Fig. 1, Ref. 13). Keywords: COVID-19, pandemic, reverse transcriptase polymerase chain reaction, public health.

Performance of the QIAprep& Viral RNA UM Kit assay (Qiagen), an automatable method for RT-qPCR detection of SARS-CoV-2 without RNA extraction.

We evaluated the performance of the QIAprep& Viral RNA UM Kit (Qiagen) for SARS-CoV-2 detection. It displayed specificity and sensitivity required for SARS-CoV-2 RNA detection from swab transport media without RNA extraction. This method identifies accurately patients at risk of transmission while saving time and cost of extraction.

Twin peaks: The Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England.

Rapid transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has led to record-breaking incidence rates around the world. The Real-time Assessment of Community Transmission-1 (REACT-1) study has tracked SARS-CoV-2 infection in England using reverse transcription polymerase chain reaction (RT-PCR) results from self-administered throat and nose swabs from randomly selected participants aged 5 years and older approximately monthly from May 2020 to March 2022. Weighted prevalence in March 2022 was the highest recorded in REACT-1 at 6.37% (N = 109,181), with the Omicron BA.2 variant largely replacing the BA.1 variant. Prevalence was increasing overall, with the greatest increase in those aged 65 to 74 years and 75 years and older. This was associated with increased hospitalizations and deaths, but at much lower levels than in previous waves against a backdrop of high levels of vaccination.

Large-Scale SARS-CoV-2 Antigen Testing With Real-World Specimens.

Real-world data are needed to establish SARS-CoV-2 rapid antigen testing (RAT) as an effective and reliable approach for SARS-CoV-2 screening. This study included 1,952,931 individuals who provided upper respiratory specimens during SARS-CoV-2 screening at CityMD urgent care locations in the New York metropolitan area from October 2020 to March 2021. Positive and negative results, as determined by the BD Veritor™ System for Rapid Detection of SARS-CoV-2 antigen (Veritor), were obtained for all individuals, with reflex reverse transcriptase-polymerase chain reaction (RT-PCR) testing performed on a case-by-case basis, per standard of care. Using verification bias adjustment, two alternative model assumptions were utilized for RAT results with missing reflex RT-PCR results. The worst antigen diagnostic performance estimates asserted that missing RT-PCR results would show a distribution similar to those RT-PCR results actually obtained, based on symptom category. The best antigen diagnostic performance estimates asserted that individuals without RT-PCR results had a clinical presentation consistent with RAT results, and, therefore, missing RT-PCR results would agree with RAT results. For patients with symptoms or high-risk exposure, 25.3% (n = 86,811/343,253) of RAT results were positive; vs. 3.4% (n = 53,046/1,559,733) positive for asymptomatic individuals without high-risk exposure. Reflex RT-PCR results were obtained from 46.3% (n = 158,836/343,253) and 13.8% (n = 215,708/1,559,733) of symptomatic and asymptomatic individuals, respectively. RT-PCR confirmed 94.4% (4,265/4,518) of positive and 90.6% (139,759/154,318) of negative RAT results in symptomatic individuals; and confirmed 83.4% (6,693/8,024) of positive and 95.3% (197,955/207,684) of negative RAT results in asymptomatic individuals. Applied assumptions for missing reflex RT-PCR results led to worst performance sensitivity estimates of 77.2 and 38.5% in the symptomatic and asymptomatic populations, respectively; assumptions for best performance estimates led to sensitivity values of 85.6 and 84.2%, respectively. Specificity values, regardless of assumptions or symptom category, ranged from 97.9-99.9%. At 10% SARS-CoV-2 prevalence, RAT positive predictive value was 86.9 and 99.0% for worst and best performance estimates across the total population, respectively; negative predictive values were >95% regardless of the applied assumption. Veritor test performance was consistent with that listed in the manufacturer instructions for use for symptomatic individuals. Real-world evidence should be gathered on RATs to support their efficacy as SARS-CoV-2 persists.