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1.
Article in Chinese | WPRIM | ID: wpr-935355

ABSTRACT

Objective: To evaluate the application of real-time RT-PCR and semi-nested RT-PCR in the detection of norovirus in oysters and analyzing the genetic characteristics of the isolates. Methods: Real-time fluorescent RT-PCR and semi-nested RT-PCR were used to detect norovirus GⅠ/GⅡ in fresh oysters collected from the markets in Beijing from November 2014 to October 2015. The detection rate of the parallel test was also analyzed. In addition, the reliability of semi-nested RT-PCR was evaluated by agreement rate and consistency test (Kappa value). The positive products of norovirus GⅠ/GⅡ capsid protein region gene by semi-nested RT-PCR were sequenced. Software BioEdit 7.0.9.0 was used for sequence alignment, and software Mega 6.0 was used to construct the evolutionary tree. Results: In 72 samples, the detection rate of norovirus was 31.94% (23/72) by real-time RT-PCR, 38.89% (28/72) by semi-nested RT-PCR and 48.61% (35/72) by parallel test. The coincidence rate of the two methods was 73.61%, a moderate degree (Kappa value =0.43). A total of 13 norovirus strains were successfully sequenced, and 11 strains (7 GⅡ.17 strains, 2 GⅡ. 4 Sydney_ 2012 strains, 1 GⅡ. 1 strain and 1 GⅡ. 21 strain) were obtained from norovirus positive samples by two RT-PCR methods, two strains (1 GⅡ. 17 strain and 1 GⅡ. 3 strain) were obtained from real-time RT-PCR negative samples which were positive for norovirus by semi-nested RT-PCR. The similarity between these strains and reference strains from diarrhea patients, environmental sewage, and shellfish products were 84.4% - 100.0%. Conclusions: The parallel test of norovirus in oysters by two RT-PCR methods can improve the detection rate and detect more genotypes. Norovirus strains in oysters were highly homologous with reference strains from diarrheal patients, environmental sewage, and shellfish products. Therefore, surveillance, prevention and control for norovirus should be carried out in people who have frequent contacts with oysters and related environments.


Subject(s)
Animals , Beijing , Humans , Norovirus/genetics , Ostreidae , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction
2.
Protein & Cell ; (12): 120-140, 2022.
Article in English | WPRIM | ID: wpr-929156

ABSTRACT

Ebola virus (EBOV) is an enveloped negative-sense RNA virus and a member of the filovirus family. Nucleoprotein (NP) expression alone leads to the formation of inclusion bodies (IBs), which are critical for viral RNA synthesis. The matrix protein, VP40, not only plays a critical role in virus assembly/budding, but also can regulate transcription and replication of the viral genome. However, the molecular mechanism by which VP40 regulates viral RNA synthesis and virion assembly/budding is unknown. Here, we show that within IBs the N-terminus of NP recruits VP40 and is required for VLP-containing NP release. Furthermore, we find four point mutations (L692A, P697A, P698A and W699A) within the C-terminal hydrophobic core of NP result in a stronger VP40-NP interaction within IBs, sequestering VP40 within IBs, reducing VP40-VLP egress, abolishing the incorporation of NC-like structures into VP40-VLP, and inhibiting viral RNA synthesis, suggesting that the interaction of N-terminus of NP with VP40 induces a conformational change in the C-terminus of NP. Consequently, the C-terminal hydrophobic core of NP is exposed and binds VP40, thereby inhibiting RNA synthesis and initiating virion assembly/budding.


Subject(s)
Ebolavirus/physiology , HEK293 Cells , HeLa Cells , Humans , Nucleocapsid Proteins/metabolism , RNA, Viral/metabolism , Viral Matrix Proteins/metabolism , Virion/metabolism , Virus Assembly
3.
Asian Journal of Andrology ; (6): 135-138, 2022.
Article in English | WPRIM | ID: wpr-928550

ABSTRACT

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) receptor, angiotensin-converting enzyme 2 (ACE2), has been identified in the human testis, but the risk of transmission of SARS-CoV-2 through sexual intercourse still needs to be defined. The goal of our study was to determine if SARS-CoV-2 is detectable in the semen of patients suffering or recovering from coronavirus disease-19 (COVID-19), still testing positive at nasopharyngeal swabs but showing mild or no symptoms at the time of sampling. Detection of SARS-CoV-2 RNA in semen was performed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR targeting open reading frame (ORF) 1ab. Medical history of the enrolled patients was taken, including COVID-19-correlated symptoms, both at the time of diagnosis and at the time of interview. Results of real-time RT-PCR and nested PCR in semen showed no evidence of SARS-CoV-2 RNA in the 36 patients suffering or recovering from COVID-19 but still positive in a nasopharyngeal swab, from over 116 patients enrolled in the study. SARS-CoV-2 detection and persistence in semen would have an impact on both clinical practice and public health strategies, but our results would suggest that SARS-CoV-2 is not present in the semen of men recovering from COVID-19.


Subject(s)
COVID-19/epidemiology , Humans , Male , Pandemics , RNA, Viral/genetics , SARS-CoV-2/genetics , Semen
4.
Medicina (B.Aires) ; 81(supl.2): 1-32, dic. 2021. graf
Article in Spanish | LILACS | ID: biblio-1351083

ABSTRACT

Resumen En las últimas décadas ha habido un importante desarrollo de dispositivos inhalados (DI) que permiten aumentar la eficacia de las drogas y disminuir los eventos adversos. Su correcto uso es de fundamental importancia para el control de las enfermedades respiratorias obstructivas. En la Argentina no existen recomendaciones locales sobre el uso de los DI. Se revisó la base biofísica, indicación, ventajas y limitaciones, técnica de correcto uso, errores frecuentes, mantenimiento y limpieza de cada DI. El uso de nebulizaciones ha quedado restringido a la administración de drogas que no están disponibles en otros DI (ejemplo: tratamiento de fibrosis quística), o ante la falla de los otros DI. No deben ser usados durante la pandemia de SARS-CoV2. Los inhaladores de dosis medida (aerosol) deben ser indicados siempre con aerocámaras (AC), las que reducen la incidencia de eventos adversos y aumentan el depósito de la droga en el pulmón. Son los dispositivos de elección junto a los inhaladores de polvo seco. Los aerosoles se deben usar en pacientes que no generan flujos inspiratorios altos. Los inhaladores de polvo seco deben recomendarse en aquellos que pueden realizar flujos inspiratorios enérgicos. Se revisaron los diferentes DI en fibrosis quística y en pacientes con asistencia respiratoria mecánica. La elección del DI dependerá de varios factores: situación clínica, edad, experiencia previa, preferencia del paciente, disponibilidad de la droga y entrenamiento alcanzado con el correcto uso.


Abstract Last decades, a broad spectrum of inhaled devices (ID) had been developed to enhance efficacy and reduce adverse events. The correct use of IDs is a critical issue for controlling obstructive respiratory diseases. There is no recommendation on inhalation therapy in Argentina. This document aims to issue local recommendations about the prescription of IDs. Each device was reviewed regarding biophysical laws, indication, strength, limitations, correct technique of use, frequent mistakes, and device cleaning and maintenance. Nebulization should be restricted to drugs that are not available in other IDs (for example, for treatment of cystic fibrosis) or where other devices fail. Nebulization is not recommended during the SARS-CoV2 pandemic. A metered-dose inhaler must always be used with an aerochamber. Aerochambers reduce the incidence of adverse events and improve lung deposition. Metered-dose inhalers must be prescribed to patients who cannot generate a high inspiratory flow and dry powders to those who can generate an energetic inspiratory flow. We reviewed the use of different IDs in patients with cystic fibrosis and under mechanical ventilation. The individual choice of an ID will be based on several variables like clinical status, age, previous experience, patient preference, drug availability, and correct use of the device.


Subject(s)
Humans , Asthma , COVID-19 , Argentina , RNA, Viral , Pulmonary Disease, Chronic Obstructive , SARS-CoV-2
5.
Rev. ADM ; 78(5): 275-279, sept.-oct. 2021.
Article in Spanish | LILACS | ID: biblio-1348224

ABSTRACT

El SARS-CoV-2, causante de que estemos viviendo una pandemia mundial, tuvo sus orígenes en China, desde donde ha traspasado fronteras rápidamente, llegando a todos los rincones del mundo. Muchos han sido los equipos de investigación que se enfrentan el reto de conseguir una vacuna que logre combatir este mortal virus. Es por este motivo que en esta investigación se pretendió analizar la bibliografía referida a la vacuna Johnson & Johnson (J&J) contra COVID-19: distribución mundial de la vacuna, mecanismo de acción, indicaciones, contraindicaciones y efectos secundarios. Varios estudios demuestran que su eficacia varía de acuerdo con la edad y género de cada individuo; sin embargo, esta vacuna alcanzó un grado de certeza moderada. Los efectos adversos en su mayoría son leves y se resolvieron al cabo de dos días, siendo excepción algunos casos, ya que se registró un efecto adverso poco común denominado trombocitopenia prevalente en mujeres de 18 a 40 años, por este motivo, la FDA (Administración de Alimentos y Medicamentos de EE.UU.) recomienda la precaución en el uso de la vacuna con respecto a este efecto adverso que en algunos casos podría ser mortal (AU)


The SARS-CoV-2, which caused us to be experiencing a global pandemic, had its origins in China, from where it has crossed borders rapidly, reaching all corners of the world. Many research teams have faced the challenge of getting a vaccine to fight this deadly virus. For this reason, this research aimed to analyze the literature on the Johnson & Johnson COVID-19 vaccine: global distribution of the vaccine, mechanism of action, indications, contraindications and side effects. Several studies show that its effectiveness varies according to the age and gender of each individual, but this vaccine reached a moderate degree of certainty. The adverse effects are mostly mild and resolved within two days, with some exceptions being a rare adverse effect called prevalent thrombocytopenia in women aged 18 to 40 years. For this reason, the FDA recommends caution in the use of the vaccine with respect to this potentially fatal adverse effect in some cases (AU)


Subject(s)
Humans , Male , Female , Contraindications, Drug , COVID-19 Vaccines/adverse effects , COVID-19 Vaccines/supply & distribution , COVID-19 Vaccines/therapeutic use , COVID-19 Vaccines/pharmacology , SARS-CoV-2 , COVID-19/prevention & control , United States Food and Drug Administration , Viral Proteins , Effectiveness , RNA, Viral , Sex Factors , Age Factors , Virus Inactivation
6.
Medicina (B.Aires) ; 81(2): 135-142, June 2021. graf
Article in English | LILACS | ID: biblio-1287262

ABSTRACT

Abstract Most countries in Latin America have already reported thousands of confirmed cases and vulnerable populations are the most affected by the coronavirus disease 2019 (COVID-19) pandemic. Preventive measures such as hygiene, social distancing, and isolation, essential to stop the spread of coronavirus, are difficult to accomplish for vulnerable populations due to their living conditions. Seroepidemiological surveys are assets to measure the transmission for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Until July 1st, the incidence rate of SARS-CoV-2 infection in Barrio Padre Mugica, one of the largest slums in Buenos Aires City, was 5.9%. This study aimed to establish the prevalence of SARS-CoV-2 antibodies immunoglobulin G (IgG) immediately after the outbreak, and to identify neighbourhood, household and individual factors associated with seroconversion. The prevalence based on IgG was 53.4% (95% CI 52.8% to 54.1%). For each polymerase chain reaction (RT-qPCR) confirmed case, nine people tested IgG positive, indicating a high rate of undetected (probably asymptomatic) infections. Hence, the high rate of undiagnosed people suggests that clinical criteria and epidemiological nexus should be considered. The high seroprevalence observed in the context of an intense epidemic in a vulnerable area might serve as a reference to other countries. This study contributes to future decision making by understanding population immunity against SARS-CoV2 and its relation to living conditions and foccus that comprehensive biosocial, household-level interventions are needed.


Resumen Muchos países de América Latina han informado miles de casos confirmados y las poblaciones vulnerables son las más afectadas por la pandemia de la enfermedad por coronavirus 2019 (COVID-19). Las medidas preventivas como la higiene, el distanciamiento social y el aislamiento, fundamentales para frenar la propagación del coronavirus, son difíciles de lograr en estas poblaciones debido a sus condiciones de vida. Los estudios seroepidemiológicos son de gran utilidad para medir la transmisión del síndrome respiratorio agudo severo coronavirus 2 (SARS-CoV-2). Hasta el 1 de julio, la tasa de incidencia de la infección por SARS-CoV-2 en el Barrio Padre Mugica, uno de los barrios marginales más grandes de la ciudad de Buenos Aires, era del 5.9%. Este estudio tuvo como objetivo estimar la prevalencia de anticuerpos inmunoglobulina G (IgG) para SARS-CoV-2 inmediatamente después del brote, e identificar factores del barrio, hogar e individuales asociados con la seroconversión. La prevalencia basada en IgG fue del 53.4% (IC del 95%: 52.8% a 54.1%). Para cada caso confirmado por reacción en cadena de la polimerasa (RT-qPCR), nueve personas dieron positivo en IgG, lo que indica una alta tasa de infecciones no detectadas y probablemente asintomáticas. La alta tasa de personas no diagnosticadas sugiere que se deben considerar los criterios clínicos y el nexo epidemiológico. La alta seroprevalencia observada en el contexto de una intensa epidemia en una zona vulnerable podría servir de referencia a otros países. Este estudio contribuye a la toma de decisiones futuras al comprender la inmunidad de la población contra el SARS-CoV2 en su relación con las condiciones de vida y por su enfoque en la necesidad de intervenciones integrales a nivel del hogar.


Subject(s)
Humans , Poverty Areas , COVID-19 , RNA, Viral , Seroepidemiologic Studies , SARS-CoV-2 , Antibodies, Viral
7.
Arq. gastroenterol ; 58(1): 1-4, Jan.-Mar. 2021. tab
Article in English | LILACS | ID: biblio-1248991

ABSTRACT

ABSTRACT Mass vaccination offers the best strategy to fight against COVID-19 pandemic, and SARS-CoV2 vaccines are being approved in several countries for emergency use. In Brazil, vaccine approval is expected in the next few days, however potential concerns exist regarding vaccine recommendations for specific populations, such as patients with inflammatory bowel disease (IBD). To address these questions, the Brazilian IBD Study Group (GEDIIB) provides this practical advice with key recommendations about the COVID-19 vaccines in IBD population.


RESUMO A vacinação em massa oferece a melhor estratégia para enfrentamento da pandemia de COVID-19, e as vacinas contra SARS-CoV2 estão sendo aprovadas em vários países para uso emergencial. No Brasil, a aprovação da vacina é esperada em breve, no entanto, existem potenciais preocupações em relação às recomendações de vacinas para populações específicas, como pacientes com doença inflamatória intestinal (DII). Para responder essas questões, o Grupo Brasileiro de Estudos IBD (GEDIIB) fornece conselhos práticos com recomendações importantes sobre as vacinas para COVID-19 na população com DII.


Subject(s)
Humans , Inflammatory Bowel Diseases , COVID-19 , Brazil , RNA, Viral , Vaccination , Pandemics , COVID-19 Vaccines , SARS-CoV-2
8.
An. bras. dermatol ; 96(2): 184-187, Mar.-Apr. 2021. graf
Article in English | LILACS | ID: biblio-1248747

ABSTRACT

Abstract Epstein Barr virus-associated smooth muscle tumors are an uncommon neoplasm that occurs in immunosuppressed patients of any age. Usually, it presents as multifocal tumors mainly in the spinal cord, epidural region, gastrointestinal tract and liver, upper respiratory tract and skin, the latest with few cases reported in the literature and related with human immunodeficiency virus infection and acquired immune deficiency syndrome. The authors present the first case of a Colombian adult patient with human immunodeficiency virus infection and multifocal Epstein Barr virus-associated smooth muscle tumors in the skin and epidural region, confirmed by histopathology, immunohistochemistry and in situ hybridization studies.


Subject(s)
Humans , Adult , HIV Infections/complications , Smooth Muscle Tumor , Epstein-Barr Virus Infections/complications , RNA, Viral , Herpesvirus 4, Human/genetics
9.
Chinese Journal of Biotechnology ; (12): 1237-1248, 2021.
Article in Chinese | WPRIM | ID: wpr-878627

ABSTRACT

RNA interference (RNAi) is one of the important mechanisms to regulate gene expression in eukaryotes. One of the original functions of RNAi is to facilitate the antiviral strategy of host. Early studies reveal that invertebrates can use RNAi to resist viruses. However, if this mechanism exists in mammals is still controversial. The latest studies confirm that mammals do have the RNAi-based immunity, and researchers believe that RNAi-based antiviral immunity is a brand-new immunological mechanism that was neglected in the past. It is worthy to note that virus can also use RNAi to enhance its infectivity and immune escape in host cells. This review introduces the research history of RNAi-based antiviral immunity in animals and summarizes the main findings in this field. Last but not least, we indicate a series of unresolved questions about RNAi-based antiviral immunity, and explore the relationship between RNAi-based antiviral immunity and other innate immunological pathways. The virus-mediated RNAi pathway in animal is not only an interesting basic biology question, but also has important guiding roles in the development of antiviral drugs.


Subject(s)
Animals , Antiviral Agents , Immunity, Innate/genetics , Mammals , RNA Interference , RNA, Small Interfering/genetics , RNA, Viral
10.
Article in English | WPRIM | ID: wpr-878357

ABSTRACT

Objective@#The aim of the present study was to evaluate the performance of the simultaneous detection of HIV-1 RNA, HIV-1 DNA, and HCV RNA using one dried blood spot (DBS) as an alternative sample to plasma.@*Method@#A total of 571 paired DBS/plasma samples were collected from men who have sex with men (MSM) and injection drug users (IDUs), and serological and molecular assays were performed. Using plasma results as the reference standard, the performance of DBS tests for HIV-1 RNA, HIV-1 DNA, and HCV RNA was evaluated. Pearson's correlation coefficients and Bland-Altman analysis were performed to assess the correlation and concordance between DBS and plasma.@*Results@#Among paired plasma/DBS samples with detectable HIV-1 RNA and HCV RNA, five samples (5/32) were not detectable in DBS, while measurable HIV-1 RNA levels were present in plasma (1.44 to 3.99 log @*Conclusion@#The performance of the simultaneous detection of HIV-1 RNA, HIV-1 DNA, and HCV RNA using one DBS was acceptable. DBS, as an alternative sample to plasma, may be a viable option for the simultaneous detection of HIV-1 RNA, HIV-1 DNA, and HCV RNA in resource-limited settings or for individuals living in areas that are difficult to access.


Subject(s)
DNA, Viral/analysis , Diagnostic Tests, Routine/methods , Dried Blood Spot Testing/methods , HIV Infections/diagnosis , HIV-1/isolation & purification , Hepacivirus/isolation & purification , Hepatitis C/diagnosis , RNA, Viral/analysis , Sensitivity and Specificity , Specimen Handling/methods , Syphilis/diagnosis , Treponema pallidum/isolation & purification
11.
Article in English | WPRIM | ID: wpr-922209

ABSTRACT

BACKGROUND@#We investigated factors associated with prolonged viral clearance of SARS-CoV-2 among non-severe adult patients in Osaka, Japan. A total of 706 laboratory-confirmed COVID-19 patients were enrolled in this longitudinal observational study between 29 January 2020 and 31 May 2020, across 62 hospitals and three non-hospital recuperation facilities.@*METHODS@#Logistic regression analysis was performed to investigate the factors associated with prolonged (29 days: upper 25% in duration) viral clearance of SARS-CoV-2. Linear regression analysis was conducted to assess these factors 14 days after symptom onset.@*RESULTS@#The median duration of viral clearance was 22 days from symptom onset. After adjustment for sex, age, symptoms, comorbidity, and location of recuperation, comorbidities were associated with prolonged duration: (OR, 1.77 [95% CI, 1.11-2.82]) for one, (OR, 2.47 [95% CI, 1.32-4.61]) for two or more comorbidities. Viral clearance 14 days after symptom onset was 3 days longer for one comorbidity and 4 days longer for two or more comorbidities compared to clearance when there was no comorbidity.@*CONCLUSION@#The presence of comorbidity was a robust factor associated with a longer duration of viral clearance, extending by 3 to 4 days compared to patients with no comorbidity.


Subject(s)
Adult , COVID-19 , Humans , Japan/epidemiology , RNA, Viral , SARS-CoV-2 , Virus Shedding
12.
Article in Chinese | WPRIM | ID: wpr-877518

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA detection is the key link for the precise epidemic prevention and control, and the urban detection bases have been proved to be achieved great successes in increasing the regional nucleic acid detection ability and efficiency. This expert advice contains ten aspects: environment and facilities management, personnel management and training, equipment management, materials management, quality management, bio-safety management, medical waste management, information system management, result report, supervision and continuous improvement. This manual aims to provide standards and suggestions for the SARS-CoV-2 RNA detection base management for ensuring the standardized, safe and orderly operation of the base to complete large-scale nucleic acid screening with high efficiency and quality. It also could be used by other SARS-CoV-2 RNA detection laboratory as reference.


Subject(s)
COVID-19 , Humans , Mass Screening , RNA, Viral , Reference Standards , SARS-CoV-2
13.
Protein & Cell ; (12): 717-733, 2021.
Article in English | WPRIM | ID: wpr-888715

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic is caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is spread primary via respiratory droplets and infects the lungs. Currently widely used cell lines and animals are unable to accurately mimic human physiological conditions because of the abnormal status of cell lines (transformed or cancer cells) and species differences between animals and humans. Organoids are stem cell-derived self-organized three-dimensional culture in vitro and model the physiological conditions of natural organs. Here we showed that SARS-CoV-2 infected and extensively replicated in human embryonic stem cells (hESCs)-derived lung organoids, including airway and alveolar organoids which covered the complete infection and spread route for SARS-CoV-2 within lungs. The infected cells were ciliated, club, and alveolar type 2 (AT2) cells, which were sequentially located from the proximal to the distal airway and terminal alveoli, respectively. Additionally, RNA-seq revealed early cell response to virus infection including an unexpected downregulation of the metabolic processes, especially lipid metabolism, in addition to the well-known upregulation of immune response. Further, Remdesivir and a human neutralizing antibody potently inhibited SARS-CoV-2 replication in lung organoids. Therefore, human lung organoids can serve as a pathophysiological model to investigate the underlying mechanism of SARS-CoV-2 infection and to discover and test therapeutic drugs for COVID-19.


Subject(s)
Adenosine Monophosphate/therapeutic use , Alanine/therapeutic use , Alveolar Epithelial Cells/virology , Antibodies, Neutralizing/therapeutic use , COVID-19/virology , Down-Regulation , Drug Discovery , Human Embryonic Stem Cells/metabolism , Humans , Immunity , Lipid Metabolism , Lung/virology , RNA, Viral/metabolism , SARS-CoV-2/physiology , Virus Replication/drug effects
14.
Chinese Medical Journal ; (24): 2048-2053, 2021.
Article in English | WPRIM | ID: wpr-887657

ABSTRACT

BACKGROUND@#With the ongoing worldwide coronavirus disease 2019 (COVID-19) pandemic, an increasing number of viral variants are being identified, which poses a challenge for nucleic acid-based diagnostic tests. Rapid tests, such as real-time reverse transcription-polymerase chain reaction (rRT-PCR), play an important role in monitoring COVID-19 infection and controlling its spread. However, the changes in the genotypes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may result in decreased sensitivity of the rRT-PCR assay and it is necessary to monitor the mutations in primers and probes of SARS-CoV-2 detection over time.@*METHODS@#We developed two rRT-PCR assays to detect the RNA-dependent RNA polymerase (RdRp) and nucleocapsid (N) genes of SARS-CoV-2. We evaluated these assays together with our previously published assays targeting the ORF1ab and N genes for the detection and confirmation of SARS-CoV-2 and its variants of concern (VOCs). In addition, we also developed two rRT-PCR assays (S484K and S501Y) targeting the spike gene, which when combined with the open reading frames (ORF)1ab assay, respectively, to form duplex rRT-PCR assays, were able to detect SARS-CoV-2 VOCs (lineages B.1.351 and B.1.1.7).@*RESULTS@#Using a SARS-CoV-2 stock with predetermined genomic copies as a standard, the detection limit of both assays targeting RdRp and N was five copies/reaction. Furthermore, no cross-reactions with six others human CoVs (229E, OC43, NL63, HKU1, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus) were observed using these assays. In addition, the S484K and S501Y assays were combined with the ORF1ab assay, respectively.@*CONCLUSIONS@#Four rRT-PCR assays (RdRp, N, S484K, and S501Y) were used to detect SARS-CoV-2 variants, and these assays were shown to be effective in screening for multiple virus strains.


Subject(s)
COVID-19 , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcription , SARS-CoV-2 , Sensitivity and Specificity
15.
Einstein (Säo Paulo) ; 19: eAO5800, 2021. tab, graf
Article in English | LILACS | ID: biblio-1350699

ABSTRACT

ABSTRACT Objective: To characterize the sociodemographic profile of the population undergoing antiretroviral treatment in the state of Paraná, Brazil, to investigate the proportion of people undergoing treatment among all those diagnosed, and to analyze the proportion of patients with suppressed viral load in different regions of the state. Methods: Observational descriptive and analytical study carried out with information referring to the period from January 2018 to January 2019. Data were obtained from the Sistema Informatizado de Monitoramento Clínico das Pessoas Vivendo com HIV/AIDS [Computerized System for Clinical Monitoring of People Living with HIV/AIDS] and Sistema de Controle Logístico de Medicamentos[Drug Supply Control System]. The proportion of people on antiretroviral treatment in the state and the proportion of patients with viral load ≤1,000 copies/mL and ≤50 copies/mL were calculated. The results were compared with the corresponding parameters of the World Health Organization goal 90-90-90. Results: The state of Paraná managed to reach the second and third parameters of the 90-90-90 goal of the World Health Organization. Among those diagnosed, 93.12% were on antiretroviral treatment, and 90.0% of them had a viral load below 50 copies of viral RNA/mL of blood, indicating virologic success. Conclusion: The health policy aimed at the population living with HIV/AIDS, and the health services available in Paraná have been successful in parameters relevant to the control of the epidemic. However, it is necessary to ensure the diagnosis of people infected with HIV in the population.


RESUMO Objetivo: Caracterizar o perfil sociodemográfico da população em tratamento antirretroviral no estado do Paraná, investigar a proporção de pessoas em tratamento entre todos os diagnosticados e analisar a proporção de pacientes com carga viral suprimida nas diferentes regiões do estado. Métodos: Estudo observacional descritivo e analítico realizado com informações referentes ao período de janeiro de 2018 a janeiro de 2019. Os dados foram obtidos do Sistema Informatizado de Monitoramento Clínico das Pessoas Vivendo com HIV/AIDS e do Sistema de Controle Logístico de Medicamentos. Foram calculadas as proporções de pessoas em tratamento antirretroviral no estado e de pacientes com carga viral ≤1.000 cópias/mL e ≤50 cópias/mL. Os resultados foram comparados com os parâmetros correspondentes da meta 90-90-90 da Organização Mundial da Saúde. Resultados: O estado do Paraná alcançou o segundo e o terceiro parâmetros da meta 90-90-90 da Organização Mundial da Saúde. Entre os diagnosticados, 93,12% encontravam-se em tratamento antirretroviral, e 90,0% destes apresentavam carga viral abaixo 50 cópias do RNA viral/mL de sangue, indicando sucesso virológico. Conclusão: A política de saúde voltada à população vivendo com HIV/AIDS e os serviços de saúde disponibilizados no Paraná têm obtido êxito em parâmetros relevantes para o controle da epidemia. Entretanto, é necessário assegurar o diagnóstico das pessoas infectadas por HIV na população.


Subject(s)
Humans , HIV Infections/drug therapy , Anti-HIV Agents/therapeutic use , Brazil , RNA, Viral , Viral Load , Antiretroviral Therapy, Highly Active , Anti-Retroviral Agents/therapeutic use
16.
Rev. Soc. Bras. Med. Trop ; 54: e02702021, 2021. tab, graf
Article in English | LILACS | ID: biblio-1347092

ABSTRACT

Abstract INTRODUCTION Herein, the authors describe a simple enhancement to a commercial rapid DNA extraction kit based on simple viral lysis for detecting COVID-19 via RT-qPCR. METHODS After testing several different modifications, the adapted protocol with the best results in preliminary experiments was statistically evaluated in comparison with an automated robotic protocol. RESULTS Processing and testing of 119 nasopharyngeal samples ultimately yielded near-perfect agreement with the automated protocol (κ = 0.981 [95% confidence interval 0.943-1.000]). CONCLUSIONS The low cost and rapidity of the enhanced protocol makes it suitable for adoption in laboratories diagnosing COVID-19, especially those with high demand for examinations.


Subject(s)
Humans , SARS-CoV-2 , COVID-19 , DNA , RNA, Viral , Sensitivity and Specificity
17.
Rev. Soc. Bras. Med. Trop ; 54: e10622021, 2021. graf
Article in English | LILACS | ID: biblio-1288110

ABSTRACT

Abstract INTRODUCTION: Considering the persistent positivity on RT-qPCR tests, the results of SARS-CoV-2 were monitored to evaluate the viral RNA shedding period. METHODS: Between March and June 2020, the sequential results of 29 healthcare workers' were monitored using RT-qPCR. RESULTS: More than 50% of the individuals remained RT-qPCR positive after 14 days. Furthermore, this is the first study to describe positive RT-qPCR for SARS-CoV-2 in a healthcare worker with mild symptoms 95 days after the first positive test. CONCLUSIONS: Sequential RT-qPCR results were heterogeneous, and the viral RNA shedding period is unique for each person.


Subject(s)
Humans , Nucleic Acids , COVID-19 , RNA, Viral/genetics , Virus Shedding , Real-Time Polymerase Chain Reaction , SARS-CoV-2
18.
Braz. j. infect. dis ; 25(5): 101632, 2021. tab, graf
Article in English | LILACS | ID: biblio-1350317

ABSTRACT

ABSTRACT Emerging human coronaviruses, including the recently identified SARS-CoV-2, are relevant respiratory pathogens due to their potential to cause epidemics with high case fatality rates, although endemic coronaviruses are also important for immunocompromised patients. Long-term coronavirus infections had been described mainly in experimental models, but it is currently evident that SARS-CoV-2 genomic-RNA can persist for many weeks in the respiratory tract of some individuals clinically recovered from coronavirus infectious disease-19 (COVID-19), despite a lack of isolation of infectious virus. It is still not clear whether persistence of such viral RNA may be pathogenic for the host and related to long-term sequelae. In this review, we summarize evidence of SARS-CoV-2 RNA persistence in respiratory samples besides results obtained from cell culture and histopathology describing long-term coronavirus infection. We also comment on potential mechanisms of coronavirus persistence and relevance for pathogenesis.


Subject(s)
Humans , RNA, Viral/genetics , COVID-19 , Respiratory System , Cell Culture Techniques , SARS-CoV-2
19.
Braz. j. infect. dis ; 25(4): 101606, 2021. tab, graf
Article in English | LILACS | ID: biblio-1339442

ABSTRACT

ABSTRACT Since the first described human infection with SARS-CoV-2 in December of 2019 many subunit protein vaccines have been proposed for use in humans. Subunit vaccines use one or more antigens suitable for eliciting a robust immune response. However, the major concern is the efficacy of subunit vaccines and elicited antibodies to neutralize the variants of SARS-CoV-2 like B.1.1.7 (Alpha), B.1.351 (Beta) and P1 (Gamma), B.1.617 (Delta) and C.37 (Lambda). The Spike protein (S) is a potential fragment for use as an antigen in vaccine development. This protein plays a crucial role in the first step of the infection process, as it binds to Angiotensin-Converting Enzyme 2 (ACE2) receptor and enters the host cell after binding. Immunization-induced specific antibodies against the receptor binding domain (RBD) may block and effectively prevent virus invasion. The focus of this review is the impact of spike mutated variants of SARS-CoV2 (Alpha, Beta, Gamma, Delta, and Lambda) on the efficacy of subunit recombinant vaccines. To date, a low or no significant impact on vaccine efficacy against Alpha and Delta variants has been reported. Such an impact on vaccine efficacy for Beta, Delta, Gamma, and Lambda variants may be even greater compared to the Alpha variant. Nonetheless, more comprehensive analyses are needed to assess the real impact on vaccine efficacy brought about by SARS-CoV-2 variants.


Subject(s)
Humans , Spike Glycoprotein, Coronavirus/genetics , COVID-19 , RNA, Viral , Vaccines, Synthetic , Vaccines, Subunit , SARS-CoV-2 , Antibodies, Viral
20.
Braz. j. infect. dis ; 25(3): 101587, 2021. tab
Article in English | LILACS | ID: biblio-1339426

ABSTRACT

ABSTRACT Hepatitis E Virus (HEV) is an infection known worldwide for its asymptomatic and self-limited course in most cases. Some cases progressing to chronicity have been described in immunosuppressed patients, especially in recipients of solid organ transplants. We evaluated laboratory parameters of HEV infection (HEV RNA, anti-HEV IgM and anti-HEV IgG) through enzyme-linked immunosorbent assay (Elisa), confirmed by immunoblotting, in a cohort of 294 patients who received liver transplants at the HCFMUSP (Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo). Laboratory and demographic data were collected from the entirety of the transplanted population. Hepatic biopsies of 122 patients transplanted due liver failure secondary to hepatitis C (HCV), with or without serological or molecular markers of HEV, were analyzed according to METAVIR score. Out of 24 (8.2%) patients tested positive for anti-HEV IgG, six (2%) were positive for anti-HEV IgM and 17 (5.8%) for HEV RNA. Of the patients transplanted because of HCV infection, 95 (77.8%) had received treatment including ribavirin for at least six months before blood sample collection. Among patients transplanted due to HCV cirrhosis who tested positive for anti-HEV IgG, only three (37.5%) showed fibrosis beyond stage 2, while five (41.7%) of the HEV RNA-positive patients had liver fibrosis beyond stage 2. Overall, the prevalence of HEV in the post-hepatic transplant scenario appears to be low, and, at least histologically, seemingly not harmful. We conclude that, although some studies reported a risk of HEV chronification, patients who had their livers transplanted due to HCV and showed serological or molecular markers of HEV did not have higher levels of fibrosis compared to patients who showed no indications of HEV infection at the time of the analysis.


Subject(s)
Humans , Liver Transplantation , Hepatitis E virus , Hepatitis E , Hepatitis C , Brazil , Immunoglobulin M , RNA, Viral , Hepatitis C Antibodies , Liver Cirrhosis
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