Variantes do vírus SARS-COV-2 causadoras da COVID-19 no Brasil / Variants of the SARS-COV-2 virus that cause COVID-19 in Brazil / Variantes del virus SARS-COV-2 que causan COVID-19 en Brasil

Objetivo: Analisar as variantes do vírus SARS-COV-2 causadoras da COVID-19 no Brasil, identificadas até fevereiro de 2021. Método: Estudo exploratório, descritivo, comparativo e quantitativo. Os dados foram adquiridos no Ministério da Saúde (MS). Resultados: Foram identificadas as variantes "VOC B.1.1.7, VOC202012/01 ou 201/501Y.V1" do Reino Unido, a "VOC B.1.351 ou VOC202012/02 ou 20H/501Y.V2" da África do Sul e a "VOC B.1.1.28.1 ou P.1 ou 20J/501Y.V3" do Brasil/Japão. As variantes VOV P.1 e a VOC B.1.1.7 foram as mais preponderantes do Brasil, com o universo de 334 casos, onde a primeira registrou 89,5% (n=299) e a segunda 10,5% (n=35). A região Nordeste (NE) registrou a maior preponderância das duas variantes contabilizando 32,6% (n=109) e o estado da Paraíba (PB) a maior preponderância da variante VOV P.1 com 23,1% (n=69). Considerações finais: As mutações do vírus SARS-CoV-2, causador da COVID-19, podem ter causado o surgimento de nova linhagem do vírus em circulação no Brasil.

To analyze the variants of the SARS-COV-2 virus that causes COVID-19 in Brazil, identified until february 2021. Method: Exploratory, descriptive, comparative and quantitative study. The data were acquired at the Ministry of Health (MS). Results: The variants "VOC B.1.1.7, VOC202012/01 or 201/501Y.V1" from the United Kingdom, "VOC B.1.351 or VOC202012/02 or 20H/501Y.V2" from South Africa and the "VOC B.1.1.28.1 or P.1 or 20J/501Y.V3" from Brazil/Japan. The VOV P.1 and VOC B.1.1.7 variants were the most prevalent in Brazil, with a universe of 334 cases, where the first registered 89.5% (n=299) and the second 10.5% (n=35). The Northeast region (NE) registered the highest preponderance of the two variants accounting for 32.6% (n=109) and the state of Paraíba (PB) the highest preponderance of the VOV P.1 variant with 23.1% (n=69) . Final considerations: Mutations of the SARS-CoV-2 virus, which causes COVID-19, may have caused the emergence of a new strain of the virus in circulation in Brazil.

Objetivo: Analizar las variantes del virus SARS-COV-2 que causa COVID-19 en Brasil, identificadas hasta febrero de 2021. Método: Estudio exploratorio, descriptivo, comparativo y cuantitativo. Los datos se obtuvieron del Ministerio de Salud (MS). Resultados: las variantes "VOC B.1.1.7, VOC202012/01 o 201/501Y.V1" del Reino Unido, "VOC B.1.351 o VOC202012/02 o 20H/501Y.V2" de Sudáfrica y el "VOC B.1.1.28.1 o P.1 o 20J/501Y.V3" de Brasil/Japón. Las variantes VOV P.1 y VOC B.1.1.7 fueron las más prevalentes en Brasil, con un universo de 334 casos, donde la primera registró 89,5% (n=299) y la segunda 10,5% (n=35). La región Nordeste (NE) registró la mayor preponderancia de las dos variantes con 32,6% (n=109) y el estado de Paraíba (PB) la mayor preponderancia de la variante VOV P.1 con 23,1% (n=69). Consideraciones finales: Las mutaciones del virus SARS-CoV-2, que causa COVID-19, pueden haber causado la aparición de una nueva cepa del virus en circulación en Brasil.

Saliva as a promising biofluid for SARS-CoV-2 detection during the early stages of infection / La saliva como biofluido promisorio para la detección del SARS-CoV-2 durante las primeras etapas de la infección

Abstract Background: Diagnostic testing for coronavirus disease (COVID)-19 is performed using nasopharyngeal swabs. This type of sampling is uncomfortable for the patient, dangerous for health workers, and its high demand has led to a global shortage of swabs. One of the alternative specimens is saliva. However, the optimal conditions for the test have not been established. Methods: Reverse transcription-polymerase chain reaction was used to detect the viral genome in saliva samples kept at room temperature, in the fridge or frozen for 2 days. In addition, the influence of brushing teeth and feeding on the detection of the virus in saliva was addressed. Finally, the efficiency of saliva in revealing the presence of the virus during the hospitalization period was determined in children. Results: The viral genome was consistently detected regardless of the storage conditions of saliva samples. Brushing teeth and feeding did not influence the sensitivity of the test. In hospitalized children, positive results were obtained only during the early days. Conclusions: These results support the idea of the use of saliva as an alternative specimen for diagnostic testing for COVID-19. The viral genome is stable and endures perturbations in the oral cavity. However, clearance of the virus from the mouth during the infection may limit the use of the test only to the early stages of the disease.

Resumen Introducción: El diagnóstico de COVID-19 (enfermedad por coronavirus 2019) se realiza con un hisopado nasofaríngeo. El procedimiento de toma de muestra es molesto para el paciente y peligroso para el personal de salud, y la alta demanda de análisis ha conducido a la escasez de hisopos. Una alternativa es el uso de saliva, pero las condiciones óptimas para realizar el estudio no han sido establecidas. Métodos: Se usó la reacción en cadena de la polimerasa con transcriptasa reversa para detectar el genoma viral en muestras de saliva mantenidas a temperatura ambiente, en refrigeración o congeladas. Además, se evaluó la influencia del aseo bucal y de la ingesta de alimento en la detección del virus. Finalmente, se determinó el desempeño de la saliva para reportar la presencia del virus durante el periodo de hospitalización en niños. Resultados: El genoma viral fue estable durante 2 días a las diferentes temperaturas ensayadas. El aseo bucal y la ingesta de alimento no influyeron en la detección del virus. En los niños hospitalizados solo se obtuvieron resultados positivos durante los primeros días. Conclusiones: Los resultados coinciden con la idea del uso de la saliva como biofluido alternativo para el diagnóstico de COVID-19. El genoma viral es estable y no se ve afectado por perturbaciones en la cavidad oral; sin embargo, la dinámica de la infección puede provocar que el ensayo solo sea útil durante las primeras etapas de la enfermedad.

Alfabetización en salud pública ante la emergencia de la pandemia por Covid-19 / Public health literacy in the face of the Covid-19 pandemic emergency

Resumen: La alfabetización en salud es el proceso centrado en la obtención del conocimiento, la motivación y las competencias individuales para entender y acceder a información, expresar opiniones y tomar decisiones relacionadas con la promoción y el mantenimiento de la salud, lo que es aplicable en diferentes contextos, entornos y a lo largo de toda la vida. Esta perspectiva conceptual es muy necesaria ante la emergencia del virus SARS-CoV-2 que produce la enfermedad Covid-19, la cual ha producido una pandemia con efectos devastadores, no sólo desde el punto de vista de la salud, sino también, de manera muy importante, desde el económico, político y social. En este ensayo se tratan de establecer los elementos basados en la evidencia científica que orientan las políticas públicas de prevención y control, entre los que destacan: a) la inteligencia epidemiológica, la cual incluye no sólo la estrategia de vigilancia poblacional sino, ante la imposibilidad real de identificación de todos los casos positivos, la puesta en práctica de estrategias de vigilancia centinela y la vigilancia basada en eventos; b) las medidas de mitigación de la propagación de la epidemia, tales como distanciamiento social e higiene, lavado de manos, cuarentena, restricción de movimiento y utilización de cubrebocas, entre otras; c) medidas de supresión de la transmisión cuando el número de casos es muy elevado, como el endurecimiento de medidas drásticas de encierro en casa; d) fortalecimiento de la capacidad de atención médica en los sistemas de salud e incremento de la capacidad de prevención de la transmisión en los servicios de salud, incluyendo la utilidad de las pruebas diagnósticas; y e) el desarrollo de vacunas profilácticas contra Covid-19, así como la generación de agentes terapéuticos. Todas estas acciones no sólo deben implementarse rápidamente desde la perspectiva multidisciplinaria y multisectorial de la salud pública para contener, prevenir y controlar la epidemia, sino que necesitan obligatoriamente del concurso de la comunidad como responsabilidad compartida. Debido a todo esto, es necesaria la alfabetización en salud pública.

Abstract: Health literacy is the process of obtaining knowledge, motivation and individual competencies to understand and access information, express opinions and make decisions with respect to health promotion and maintenance. This applies in different contexts, environments, and throughout life. This conceptual perspective is very necessary in the face of the SARS-CoV-2 virus emergency. This virus produces the Covid-19 disease, which has become a pandemic of devastating effects not only healthwise, but also, importantly, from an economic, political and social point of view. This essay seeks to establish the scientific evidence-based elements that guide public policies for prevention and control. Some of these elements are: a) epidemiologic intelligence. This includes not only the strategy of public surveillance, but also sentinel and event-based surveillance, as it is impossible to actually identify all positive cases; b) Mitigating measures against the spread of the epidemic, such as social distancing and hygiene, washing hands, quarantine, restricting movement and using masks, among others; c) Measures to suppress transmission when the number of cases is very high, such as strict measures to stay at home; d) strengthening health services 'capacity for medical attention and improving health services' ability to prevent transmission, including the use of diagnostic tests; e) the development of prophylactic vaccines against Covid-19, as well as the development of therapeutic agents. All of these actions must be rapidly implemented, from a multidisciplinary and multisectorial public health perspective, and they absolutely must also be taken with the community's participation as shared responsibility. Therefore, public health literacy is needed.

Clínica y diagnóstico SARS-COV-2 / Clinic and diagnosis SARS-COV-2

SARS-CoV-2 virus infection behaves differently in children versus adults, a significant percentage of children are asymptomatic or present mild symptoms. That situation makes diagnostic tests more important in this group. To date, pediatric patients behave less severely compared to adult patients. Among the diagnostic methods, the most important is the detection of RNA through PCR, which is the gold standard. Other tests can be used in a complementary way, especially in cases of uncertain diagnostic or in seriously ill patients.

La infección por virus SARS-CoV-2 se comporta de manera distinta en niños versus adultos, un porcentaje importante de los niños son asintomáticos o presentan síntomas leves, por lo que las pruebas diagnósticas cobran mayor importancia en este grupo. Hasta la fecha los pacientes pediátricos se comportan con menor severidad en comparación con pacientes adultos. Dentro de los métodos diagnósticos el más importante es la detección de RNA a través de PCR que constituye el estándar. Otros exámenes pueden ser utilizados en forma complementaria, especialmente en casos de duda diagnostica o en pacientes graves.

Atualização epidemiológica: ocorrência de variantes de SARS-CoV-2 nas Américas (11 de janeiro de 2021) / Ocurrencia de variantes de SARS-CoV-2 en las Américas. Información preliminar / Occurrence of variants of SARS-CoV-2 in the Americas (11 January 2021)

Por meio deste documento, a Organização Pan-Americana da Saúde / Organização Mundial da Saúde (OPAS/OMS) comunica aos Estados Membros informações preliminares sobre a detecção, nas Américas, de duas variantes de interesse de SARS-CoV-2 associadas ao aumento de transmissão no Reino Unido e na República da África do Sul. A OPAS/OMS recomenda que os Estados Membros continuem o sequenciamento de amostras, conforme as diretrizes da rede regional de vigilância genômica, e monitorem as mudanças repentinas na incidência de COVID-19, à luz das medidas de saúde pública e de distanciamento social implementadas e cumpridas pela população.

A través de este documento, la Organización Panamericana de la Salud / Organización Mundial de la Salud (OPS/OMS) comunica a los Estados Miembros información preliminar sobre la detección en las Américas de dos variantes de interés de SARS-CoV-2 que han sido asociadas al incremento de transmisión en el Reino Unido y en la República de Sudáfrica. OPS/OMS recomienda a los Estados Miembros continuar con la secuenciación de muestras, según las pautas de la red regional de vigilancia genómica y monitorear los cambios repentinos en la incidencia de la COVID-19, a la luz de las medidas de salud pública y de distanciamiento social implementadas y cumplidas por la población.

Through this document, the Pan American Health Organization / World Health Organization (PAHO/WHO) communicates to the Member States preliminary information on the detection in the Americas of two variants of interest of SARS-CoV-2 that have been associated with increased transmission in the United Kingdom and in the Republic of South Africa. PAHO / WHO recommends that Member States continue with the sequencing of samples according to the guidelines of the regional genomic surveillance network and monitor sudden changes in the incidence of COVID-19, which occur in light of public health measures and of social distancing implemented and fulfilled by the population.

In silico analysis of mismatches in RT-qPCR assays of 177 SARS-CoV-2 sequences from Brazil

Abstract INTRODUCTION: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) can detect the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) in a highly specific manner. However, a decrease in the specificity of PCR assays for their targets may lead to false negative results. METHODS: Here, 177 high-coverage complete SARS-CoV-2 genome sequences from 13 Brazilian states were aligned with 15 WHO recommended PCR assays. RESULTS: Only 3 of the 15 completely aligned to all Brazilian sequences. Ten assays had mismatches in up to 3 sequences and two in many sequences. CONCLUSION: These results should be taken into consideration when using PCR-based diagnostics in Brazil.

A novel Betacoronavirus characterised in collared peccaries from the Rio de Janeiro Zoo (Brazil) killed by unknown disease

In an enclosure with nine collared peccaries (Pecari tajacu) from the Rio de Janeiro city Zoo, Brazil, one specimen was found dead and two others developed prostration, apathy and dehydration, resulting on its death. Necropsy of two animals pointed to pulmonary and renal damage. Histological examination revealed vasculitis in spleen from both P. tajacu, suggesting a systemic viral infection. Lungs from one specimen showed fibrinoid vasculitis, alveolar damage with hyaline membrane, and interstitial lymphocytes infiltration. Virome analysis in anal wash samples from the latter two animals revealed a new type of Betacoronavirus, lineage A, provisionally named Ptajacu-CoV.

Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil

A new coronavirus [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] is currently causing a life-threatening pandemic. In this study, we report the complete genome sequencing and genetic characterisation of a SARS-CoV-2 detected in Manaus, Amazonas, Brazil, and the protocol we designed to generate high-quality SARS-CoV-2 full genome data. The isolate was obtained from an asymptomatic carrier returning from Madrid, Spain. Nucleotide sequence analysis showed a total of nine mutations in comparison with the original human case in Wuhan, China, and support this case as belonging to the recently proposed lineage A.2. Phylogeographic analysis further confirmed the likely European origin of this case. To our knowledge, this is the first SARS-CoV-2 genome obtained from the North Brazilian Region. We believe that the information generated in this study may contribute to the ongoing efforts toward the SARS-CoV-2 emergence.

SARS-CoV-2 diagnostic diary: from rumors to the first case. Early reports of molecular tests from the military research and diagnostic institute of Rio de Janeiro

Corona virus disease (COVID-19) presents a serious threat to global health. A historical timeline of early molecular diagnostics from government alert (January 22) (D) was presented. After in silico analysis, Brazilian Army Institute of Biology (IBEx-RJ) tested samples in house using real-time reverse transcriptase polymerase chain reaction (RT-PCR) (fast mode) based on Centers for Disease Control and Prevention (CDC) recommendations. First cases from Brazil, Rio de Janeiro, IBEx, and diagnosis team were reported in D36, D44, D66, and D74 respectively. Therefore, after 1300 tests, we recommend N1/N2 primer sets (CDC) for preliminary and Charité protocol confirmation in case of positive results. Moreover, every professional should be tested before starting work, in addition to weekly tests for everyone involved.

Detección de COVID -19 (SARS-CoV-2) mediante la saliva: una alternativa diagnóstica poco invasiva / Detection of COVID-19 (SARS-CoV-2) by saliva: a low-invasive diagnostic alternative

La nueva enfermedad por coronavirus, también denominada COVID 19 es la última enfermedad infecciosa de preocupación internacional. Originada en Wuhan, China, se extendió a nivel mundial, resultando en la pandemia 2019-2020 y una Emergencia de Salud Pública de Preocupación Internacional (ESPII) según lo declarado por la Organización Mundial de la Salud (OMS). Esta enfermedad suele cursar con fiebre, tos, dolor de garganta, dificultad respiratoria, fatiga y malestar general, sin embargo, también se han presentado casos asintomáticos. Su diagnóstico se realiza con una combinación tanto de exámenes clínicos, radiológicos y moleculares, donde la prueba de reacción en cadena de la polimerasa con transcriptasa inversa (RT-PCR) ha sido el examen de elección para el análisis de material genético viral de muestras extraídas del tracto respiratorio superior. Se ha reportado que COVID-19 se transmite persona a persona o por contacto indirecto por gotas, lo que tiene fundamental importancia en procedimientos clínicos dentales y donde la saliva tendría una función crítica en la transmisión de SARS-CoV-2 en la población. Es por esto, que los diagnósticos salivales no invasivos podrían proporcionar una plataforma de detección rápida, temprana y poco invasiva de la infección por COVID-19. El objetivo de esta revisión es determinar los beneficios de la saliva como muestra no invasiva para el diagnóstico de COVID-19.

The new coronavirus disease, also called COVID 19, is the latest infectious disease of international concern. Originating in Wuhan, China, it spread globally, resulting in the 2019-2020 pandemic and a Public Health Emergency of International Concern (ESPII) as declared by the World Health Organization (WHO). This disease usually presents with fever, cough, sore throat, respiratory distress, fatigue and general discomfort; however, asymptomatic cases have been reported. The diagnosis is made with a combination of clinical, radiological and laboratory molecular tests, where the reverse transcriptase polymerase chain reaction (RT-PCR) test has been the alternative of choice for the analysis of viral genetic material from samples taken of upper respiratory tract. COVID-19 has been reported to be transmitted person-to-person or by indirect fluids drop contact, which is of fundamental importance for clinical dental procedures and where saliva would play a critical role in the transmission of SARS-CoV-2 from human to human. For this reason, non-invasive salivary diagnoses could provide a platform for rapid, early and non-invasive detection of COVID19 infection. The objective of this review is to determine the benefits of saliva as a non-invasive sample for the diagnosis of COVID-19.

Bases genéticas y moleculares del COVID-19 (SARS-CoV-2): mecanismos de patogénesis y de respuesta inmune / Genetic and molecular basis of COVID-19 (SARS-CoV-2) mechanisms of pathogenesis and imnune

A fines de diciembre de 2019, un nuevo coronavirus (SARS-CoV-2) fue identificado como el agente causal de una nueva enfermedad respiratoria llamada COVID-19 por la OMS. Sus síntomas incluyen fiebre, tos seca y dificultad respiratoria. Estos síntomas en general son leves, aunque, pueden ser fatales en adultos mayores y pacientes con comorbilidades. Se realizó búsqueda bibliográfica en Pubmed y Clinical Key donde se seleccionaron 22 artículos de acuerdo con los criterios de inclusión. SARS-CoV-2 pertenece al género de los Betacoronavirus y tiene similitudes genómicas con SARS-CoV y MERS-CoV. El virión de SARS-CoV-2 consta de una nucleocápside y de una envoltura externa compuesta por proteínas estructurales principales y accesorias. Su material genético consiste en una cadena de RNA monocatenario de polaridad positiva, en el que, se codifican proteínas importantes para su transcripción y replicación. El mecanismo de infección de SARS-CoV-2 comienza con la unión del virión a un receptor (ACE2) de la célula huésped y su posterior entrada por endocitosis. El genoma RNA viral se libera al citoplasma donde se transcriben y se traducen las proteínas necesarias para la producción de las proteínas estructurales y para la replicación de su material genético. Posteriormente, el RNA replicado se asocia con la nucleocápside y se ensambla junto con las proteínas estructurales para conformar las partículas víricas que serán liberadas de la célula infectada. El sistema inmune hace frente a la infección viral mediante el reconocimiento de patrones moleculares asociados a patógenos (PAMPs) por parte de la inmunidad innata y por la acción de los linfocitos T y B por parte de la inmunidad humoral. El conocimiento de las bases genéticas y moleculares de SARS-CoV-2 permite visualizar la posibilidad de establecer tratamientos farmacológicos o desarrollo de vacunas para controlar y disminuir los efectos patogénicos de la enfermedad.

In late December 2019, a new coronavirus (SARS-CoV-2) was identified as a causative agent of a new respiratory disease called COVID-19 by WHO. Its symptoms include fever, dry cough, and shortness of breath. Generally, these symptoms are mild, although, can be fatal in older adults and patients with comorbidities. A bibliographic search was carried out in Pubmed and Clinical Key. 22 articles were selected according to inclusion criteria. SARS-CoV-2 belongs to the genus of Betacoronaviruses and has genomic similarities to SARS-CoV and MERS-CoV. SARS-CoV-2 virion is made up of a nucleocapsid and external envelope composed of main structural and accesory proteins. Its genetic is a positive sense single stranded RNA in which important proteins are encoded for their transcription and replication. The mechanism of SARS-CoV-2 infection begins with the binding of the virion to (ACE2) receptor of the host cell and subsequent entry by endocytosis. This RNA genome is released into cytoplasm and the necessary proteins for the production of structural proteins and the replication of genetic material are transcribed and translated. Then, the replicated RNA associates with the nucleocapsid and assembles together with the structural proteins to form the viral particles that will be released from the infected cell. The immune system faces viral infection through the recognition of molecular patterns associated with pathogens (PAMPs) by innate immunity and the action of T cells and B cells by humoral immunity. Knowledge of the genetic and molecular basis of SARS-CoV-2 allows us to visualize the possibility of establishing pharmacological or vaccine treatments to control and reduce the pathogenic effects of the disease.

Standardized sputum collection increases sputum sample collection rate for novel coronavirus nucleic acid detection / 浙江大学学报·医学版

OBJECTIVE@#To evaluate the effect of standardized health education on the sputum specimen collection rate for nucleic acid detection of coronavirus disease 2019 (COVID-19).@*METHODS@#Two hundred and twenty-seven patients in fever clinics and isolation wards of Sir Run Run Shaw Hospital of Zhejiang University and 307 migrant workers returning to 5 enterprises in Shanghai from February 3 to March 14, 2020 were enrolled in the study. Through clarifying the procedures of collecting sputum specimens, making graphic/video health education materials, standardizing the contents and methods of health education, we conducted education to the subjects. The subject expectorated spontaneously or with medical assistance. For patients, the number of sampling attempts and sputum acquisition times were documented before and after the implementation of the standardized expectoration method; for the returning migrant employees in the enterprises, only the number of collected samples after the implementation of the standardized expectoration method were recorded.@*RESULTS@#A total of 378 sputum samples were collected from 227 patients. The sputum sampling rates before and after the implementation of health education were 40.9%and 58.4%, respectively (@*CONCLUSIONS@#The education for standardized sputum sample collection method can effectively increase the sputum collection rate.