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1.
Talanta ; 236: 122847, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34635237

RESUMEN

Nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV2 and is highly conserved, and there are no homologous proteins in the human body, making it an ideal biomarker for the early diagnosis of SARS-CoV2. However, early detection of clinical specimens for SARS-CoV2 remains a challenge due to false-negative results with viral RNA and host antibodies based testing. In this manuscript, a microfluidic chip with femtoliter-sized wells was fabricated for the sensitive digital detection of N protein. Briefly, ß-galactosidase (ß-Gal)-linked antibody/N protein/aptamer immunocomplexes were formed on magnetic beads (MBs). Afterwards, the MBs and ß-Gal substrate fluorescein-di-ß-d-galactopyranoside (FDG) were injected into the chip together. Each well of the chip would only hold one MB as confined by the diameter of the wells. The MBs in the wells were sealed by fluorocarbon oil, which confines the fluorescent (FL) product generated from the reaction between ß-Gal and FDG in the individual femtoliter-sized well and creates a locally high concentration of the FL product. The FL images of the wells were acquired using a conventional inverted FL microscope. The number of FL wells with MBs (FL wells number) and the number of wells with MBs (MBs wells number) were counted, respectively. The percentage of FL wells was calculated by dividing (FL wells number) by (MBs wells number). The higher the percentage of FL wells, the higher the N protein concentration. The detection limit of this digital method for N protein was 33.28 pg/mL, which was 300 times lower than traditional double-antibody sandwich based enzyme-linked immunosorbent assay (ELISA).


Asunto(s)
Inmunoensayo/métodos , Proteínas de la Nucleocápside , SARS-CoV-2 , Anticuerpos , COVID-19/diagnóstico , Humanos , Proteínas de la Nucleocápside/aislamiento & purificación , ARN Viral
2.
Talanta ; 236: 122868, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34635250

RESUMEN

Early diagnosis and timely management of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are the keys to preventing the spread of the epidemic and controlling new infection clues. Therefore, strengthening the surveillance of the epidemic and timely screening and confirming SARS-CoV-2 infection is the primary task. In this work, we first proposed the idea of activating CRISPR-Cas12a activity using double-stranded DNA amplified by a three-dimensional (3D) DNA walker. We applied it to the design of an electrochemiluminescent (ECL) biosensor to detect the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) gene. We first activated the cleavage activity of CRISPR-Cas12a by amplifying the target DNA into a segment of double-stranded DNA through the amplification effect of a 3D DNA walker. At the same time, we designed an MXene based ECL material: PEI-Ru@Ti3C2@AuNPs, and constructed an ECL biosensor to detect the RdRp gene based on this ECL material as a framework. Activated CRISPR-Cas12a cleaves the single-stranded DNA on the surface of this sensor and causes the ferrocene modified at one end of the DNA to move away from the electrode surface, increasing the ECL signal. The extent of the change in electrochemiluminescence reflects the concentration of the gene to be measured. Using this system, we detected the SARS-CoV-2 RdRp gene with a detection limit of 12.8 aM. This strategy contributes to the rapid and convenient detection of SARS-CoV-2-associated nucleic acids and promotes the clinical application of ECL biosensors based on CRISPR-Cas12a and novel composite materials.


Asunto(s)
Sistemas CRISPR-Cas , ARN Polimerasa Dependiente del ARN/aislamiento & purificación , SARS-CoV-2 , COVID-19 , ADN , Oro , Humanos , Nanopartículas del Metal , ARN Viral
3.
Ocul Immunol Inflamm ; 29(4): 629-630, 2021 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-34596492
4.
Front Cell Infect Microbiol ; 11: 716436, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34604108

RESUMEN

Rapid and demonstrable inactivation of SARS-CoV-2 is crucial to ensure operator safety during high-throughput testing of clinical samples. The inactivation efficacy of SARS-CoV-2 was evaluated using commercially available lysis buffers from three viral RNA extraction kits used on two high-throughput (96-well) RNA extraction platforms (Qiagen QIAcube HT and the Thermo Fisher KingFisher Flex) in combination with thermal treatment. Buffer volumes and sample ratios were chosen for their optimised suitability for RNA extraction rather than inactivation efficacy and tested against a representative sample type: SARS-CoV-2 spiked into viral transport medium (VTM). A lysis buffer mix from the MagMAX Pathogen RNA/DNA kit (Thermo Fisher), used on the KingFisher Flex, which included guanidinium isothiocyanate (GITC), a detergent, and isopropanol, demonstrated a minimum inactivation efficacy of 1 × 105 tissue culture infectious dose (TCID)50/ml. Alternative lysis buffer mixes from the MagMAX Viral/Pathogen Nucleic Acid kit (Thermo Fisher) also used on the KingFisher Flex and from the QIAamp 96 Virus QIAcube HT Kit (Qiagen) used on the QIAcube HT (both of which contained GITC and a detergent) reduced titres by 1 × 104 TCID50/ml but did not completely inactivate the virus. Heat treatment alone (15 min, 68°C) did not completely inactivate the virus, demonstrating a reduction of 1 × 103 TCID50/ml. When inactivation methods included both heat treatment and addition of lysis buffer, all methods were shown to completely inactivate SARS-CoV-2 inactivation against the viral titres tested. Results are discussed in the context of the operation of a high-throughput diagnostic laboratory.


Asunto(s)
COVID-19 , SARS-CoV-2 , Humanos , ARN Viral , Manejo de Especímenes , Inactivación de Virus
5.
Elife ; 102021 10 07.
Artículo en Inglés | MEDLINE | ID: mdl-34617885

RESUMEN

The absence of 'shovel-ready' anti-coronavirus drugs during vaccine development has exceedingly worsened the SARS-CoV-2 pandemic. Furthermore, new vaccine-resistant variants and coronavirus outbreaks may occur in the near future, and we must be ready to face this possibility. However, efficient antiviral drugs are still lacking to this day, due to our poor understanding of the mode of incorporation and mechanism of action of nucleotides analogs that target the coronavirus polymerase to impair its essential activity. Here, we characterize the impact of remdesivir (RDV, the only FDA-approved anti-coronavirus drug) and other nucleotide analogs (NAs) on RNA synthesis by the coronavirus polymerase using a high-throughput, single-molecule, magnetic-tweezers platform. We reveal that the location of the modification in the ribose or in the base dictates the catalytic pathway(s) used for its incorporation. We show that RDV incorporation does not terminate viral RNA synthesis, but leads the polymerase into backtrack as far as 30 nt, which may appear as termination in traditional ensemble assays. SARS-CoV-2 is able to evade the endogenously synthesized product of the viperin antiviral protein, ddhCTP, though the polymerase incorporates this NA well. This experimental paradigm is essential to the discovery and development of therapeutics targeting viral polymerases.


Asunto(s)
Antivirales/farmacología , COVID-19/tratamiento farmacológico , ARN Polimerasa Dependiente de ARN de Coronavirus/antagonistas & inhibidores , Nucleótidos/farmacología , SARS-CoV-2/efectos de los fármacos , Adenosina Monofosfato/análogos & derivados , Adenosina Monofosfato/farmacología , Alanina/análogos & derivados , Alanina/farmacología , Línea Celular , ARN Polimerasa Dependiente de ARN de Coronavirus/metabolismo , Inhibidores Enzimáticos/farmacología , Ensayos Analíticos de Alto Rendimiento/métodos , Humanos , Modelos Teóricos , Nucleótidos/metabolismo , ARN Viral , SARS-CoV-2/enzimología , Procesos Estocásticos , Replicación Viral/efectos de los fármacos
7.
Zhonghua Yu Fang Yi Xue Za Zhi ; 55(2): 219-225, 2021 Feb 06.
Artículo en Chino | MEDLINE | ID: mdl-34645183

RESUMEN

Objective: To evaluate the performance and application of a fast nucleic acid detection system for testing severe acute respiratory syndrome virus 2 (SARS-COV-2). Methods: Clinical samples were collected from February to July 2020 from Beijing Center for Diseases Prevention and Control and the Laboratory Department of China-Japan Friendship Hospital, to evaluate the sensitivity, specificity, anti-interference ability, precision and clinical sample coincidence rate of fast nucleic acid detection system for SARS-CoV-2. The analytical sensitivity was determined by a dilution series of 20 replications for each concentration. Analytical specificity study was performed by testing organisms whose infection produces symptoms similar to those observed at the onset of corona virus disease 2019 (COVID-19), and of the normal or pathogenic microflora that may be present in specimens collected. Potential interference substances were evaluated with different concentration in the interference study. Precision study was conducted by estimating intra-and inter-batch variability. Clinical evaluation was performed by testing 230 oropharyngeal swab specimens and 95 sputum specimens in fast nucleic acid detection system, comparing with conventional real-time fluorescent quantitative PCR (RT-qPCR) and clinical diagnostic results. Results: The analytical sensitivity of SARS-CoV-2 using fast nucleic acid detection system was 400 copies/ml. The result is negative for testing with the organisms that may likely in the circulating area or causing similar symptoms with SARS-CoV-2 and human nucleic acid, indicating that no cross reactivity with organisms. The results of precision test showed that the Coefficient of variation of Ct value of high, medium and low concentration samples was 1.90%-3.92%, and all of them were less than 5% in intra-and inter-batch testing. The results of the samples were still positive after adding the potential interfering substances, indicating that the possible interfering substances in the samples had no effect on the results. 98.46% and 97.85% diagnosis results of fast nucleic acid detection system were consistent with RT-qPCR and clinical diagnostic results, respectively. Conclusion: The fast nucleic acid detection system based on molecular parallel reaction can be used as a selection method for SARS-CoV-2 testing.


Asunto(s)
COVID-19 , Ácidos Nucleicos , Prueba de COVID-19 , Humanos , ARN Viral , Reacción en Cadena en Tiempo Real de la Polimerasa , SARS-CoV-2 , Sensibilidad y Especificidad
8.
Sci Rep ; 11(1): 19456, 2021 09 30.
Artículo en Inglés | MEDLINE | ID: mdl-34593871

RESUMEN

Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerges to scientific research and monitoring of wastewaters to predict the spread of the virus in the community. Our study investigated the COVID-19 disease in Bratislava, based on wastewater monitoring from September 2020 until March 2021. Samples were analyzed from two wastewater treatment plants of the city with reaching 0.6 million monitored inhabitants. Obtained results from the wastewater analysis suggest significant statistical dependence. High correlations between the number of viral particles in wastewater and the number of reported positive nasopharyngeal RT-qPCR tests of infected individuals with a time lag of 2 weeks/12 days (R2 = 83.78%/R2 = 52.65%) as well as with a reported number of death cases with a time lag of 4 weeks/27 days (R2 = 83.21%/R2 = 61.89%) was observed. The obtained results and subsequent mathematical modeling will serve in the future as an early warning system for the occurrence of a local site of infection and, at the same time, predict the load on the health system up to two weeks in advance.


Asunto(s)
COVID-19/epidemiología , SARS-CoV-2/genética , Aguas Residuales/análisis , Aguas Residuales/virología , COVID-19/mortalidad , Brotes de Enfermedades/prevención & control , Humanos , Modelos Teóricos , ARN Viral/aislamiento & purificación , Reacción en Cadena en Tiempo Real de la Polimerasa , Eslovaquia/epidemiología , Aguas Residuales/química , Monitoreo Epidemiológico Basado en Aguas Residuales , Purificación del Agua
9.
Nat Commun ; 12(1): 5753, 2021 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-34599164

RESUMEN

Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.


Asunto(s)
Prueba de Ácido Nucleico para COVID-19/normas , Heces/virología , SARS-CoV-2/aislamiento & purificación , COVID-19/diagnóstico , Proteínas de la Nucleocápside de Coronavirus/genética , Humanos , Fosfoproteínas/genética , Preservación Biológica/normas , ARN Viral/análisis , ARN Viral/genética , Juego de Reactivos para Diagnóstico , Estándares de Referencia , SARS-CoV-2/genética , Manejo de Especímenes/normas , Carga Viral/normas
10.
Front Immunol ; 12: 705646, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34603282

RESUMEN

COVID-19 is a disease with a spectrum of clinical responses ranging from moderate to critical. To study and control its effects, a large number of researchers are focused on two substantial aims. On the one hand, the discovery of diverse biomarkers to classify and potentially anticipate the disease severity of patients. These biomarkers could serve as a medical criterion to prioritize attention to those patients with higher prone to severe responses. On the other hand, understanding how the immune system orchestrates its responses in this spectrum of disease severities is a fundamental issue required to design new and optimized therapeutic strategies. In this work, using single-cell RNAseq of bronchoalveolar lavage fluid of nine patients with COVID-19 and three healthy controls, we contribute to both aspects. First, we presented computational supervised machine-learning models with high accuracy in classifying the disease severity (moderate and severe) in patients with COVID-19 starting from single-cell data from bronchoalveolar lavage fluid. Second, we identified regulatory mechanisms from the heterogeneous cell populations in the lungs microenvironment that correlated with different clinical responses. Given the results, patients with moderate COVID-19 symptoms showed an activation/inactivation profile for their analyzed cells leading to a sequential and innocuous immune response. In comparison, severe patients might be promoting cytotoxic and pro-inflammatory responses in a systemic fashion involving epithelial and immune cells without the possibility to develop viral clearance and immune memory. Consequently, we present an in-depth landscape analysis of how transcriptional factors and pathways from these heterogeneous populations can regulate their expression to promote or restrain an effective immune response directly linked to the patients prognosis.


Asunto(s)
Líquido del Lavado Bronquioalveolar/citología , Líquido del Lavado Bronquioalveolar/inmunología , COVID-19/patología , Pulmón/citología , SARS-CoV-2/inmunología , Linfocitos B/inmunología , Biomarcadores , Líquido del Lavado Bronquioalveolar/química , Células Dendríticas/inmunología , Células Epiteliales/citología , Células Epiteliales/virología , Humanos , Células Asesinas Naturales/inmunología , Pulmón/química , Aprendizaje Automático , Macrófagos/inmunología , Monocitos/inmunología , Neutrófilos/inmunología , ARN Viral/genética , Análisis de Secuencia de ARN , Índice de Severidad de la Enfermedad , Análisis de la Célula Individual , Linfocitos T/inmunología
11.
BMJ Case Rep ; 14(10)2021 Oct 04.
Artículo en Inglés | MEDLINE | ID: mdl-34607818

RESUMEN

SARS-COV-2 predominantly results in a respiratory illness. However, it has also been associated with a wide range of neurological disorders including a broad range of immune neuropathies. These immune neuropathies associated with SARS-COV2 infection include Guillain-Barré syndrome (GBS), recurrent GBS and exacerbation of pre-existing chronic inflammatory demyelinating polyneuropathy (CIDP). We describe a case with acute-onset CIDP presenting with three relapses of demyelinating polyradiculoneuropathy, the third relapse occurring in the 8 week of illness following a previous COVID-19 infection and a recent COVID-19 vaccination with ChAdOx1 nCoV-19 and high COVID-19 antibody level. In our knowledge, this is the ever reported case of acute-onset CIDP associated with COVID-19 vaccine and high COVID-19 antibody level.


Asunto(s)
COVID-19 , Síndrome de Guillain-Barré , Polirradiculoneuropatía Crónica Inflamatoria Desmielinizante , Vacunas contra la COVID-19 , Síndrome de Guillain-Barré/etiología , Humanos , Polirradiculoneuropatía Crónica Inflamatoria Desmielinizante/tratamiento farmacológico , ARN Viral , SARS-CoV-2 , Vacunación/efectos adversos
12.
Sci Rep ; 11(1): 19579, 2021 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-34599242

RESUMEN

The increasing risk from viral outbreaks such as the ongoing COVID-19 pandemic exacerbates the need for rapid, affordable and sensitive methods for virus detection, identification and quantification; however, existing methods for detecting virus particles in biological samples usually depend on multistep protocols that take considerable time to yield a result. Here, we introduce a rapid fluorescence in situ hybridization (FISH) protocol capable of detecting influenza virus, avian infectious bronchitis virus and SARS-CoV-2 specifically and quantitatively in approximately 20 min, in virus cultures, combined nasal and throat swabs with added virus and likely patient samples without previous purification. This fast and facile workflow can be adapted both as a lab technique and a future diagnostic tool in enveloped viruses with an accessible genome.


Asunto(s)
Hibridación Fluorescente in Situ/métodos , ARN Viral/aislamiento & purificación , Virus/aislamiento & purificación , Virus/genética
13.
Sci Rep ; 11(1): 19713, 2021 10 05.
Artículo en Inglés | MEDLINE | ID: mdl-34611200

RESUMEN

The novel coronavirus disease 2019 (COVID-19) presents with non-specific clinical features. This may result in misdiagnosis or delayed diagnosis, and lead to further transmission in the community. We aimed to derive early predictors to differentiate COVID-19 from influenza and dengue. The study comprised 126 patients with COVID-19, 171 with influenza and 180 with dengue, who presented within 5 days of symptom onset. All cases were confirmed by reverse transcriptase polymerase chain reaction tests. We used logistic regression models to identify demographics, clinical characteristics and laboratory markers in classifying COVID-19 versus influenza, and COVID-19 versus dengue. The performance of each model was evaluated using receiver operating characteristic (ROC) curves. Shortness of breath was the strongest predictor in the models for differentiating between COVID-19 and influenza, followed by diarrhoea. Higher lymphocyte count was predictive of COVID-19 versus influenza and versus dengue. In the model for differentiating between COVID-19 and dengue, patients with cough and higher platelet count were at increased odds of COVID-19, while headache, joint pain, skin rash and vomiting/nausea were indicative of dengue. The cross-validated area under the ROC curve for all four models was above 0.85. Clinical features and simple laboratory markers for differentiating COVID-19 from influenza and dengue are identified in this study which can be used by primary care physicians in resource limited settings to determine if further investigations or referrals would be required.


Asunto(s)
COVID-19/patología , Dengue/patología , Gripe Humana/patología , Adulto , Área Bajo la Curva , COVID-19/complicaciones , COVID-19/virología , Estudios de Cohortes , Dengue/complicaciones , Dengue/virología , Diagnóstico Diferencial , Diarrea/etiología , Femenino , Fiebre/etiología , Humanos , Gripe Humana/complicaciones , Gripe Humana/virología , Recuento de Linfocitos , Masculino , Persona de Mediana Edad , Recuento de Plaquetas , ARN Viral/análisis , ARN Viral/metabolismo , Curva ROC , SARS-CoV-2/genética , SARS-CoV-2/aislamiento & purificación , Vómitos/etiología , Adulto Joven
14.
Euro Surveill ; 26(40)2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-34622759

RESUMEN

We evaluated routine testing with SARS-CoV-2 Delta variant-specific RT-PCR in regional hospital laboratories in addition to centralised national genomic surveillance in the Netherlands during June and July 2021. The increase of the Delta variant detected by RT-PCR correlated well with data from genomic surveillance and was available ca 2 weeks earlier. This rapid identification of the relative abundance and increase of SARS-CoV-2 variants of concern may have important benefits for implementation of local public health measures.


Asunto(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiología , COVID-19/virología , Genómica , Humanos , Países Bajos/epidemiología , Reacción en Cadena de la Polimerasa , ARN Viral/genética , SARS-CoV-2/genética
15.
Front Immunol ; 12: 739037, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34594341

RESUMEN

Background: Transfusion of COVID-19 convalescent plasma (CCP) containing high titers of anti-SARS-CoV-2 antibodies serves as therapy for COVID-19 patients. Transfusions early during disease course was found to be beneficial. Lessons from the SARS-CoV-2 pandemic could inform early responses to future pandemics and may continue to be relevant in lower resource settings. We sought to identify factors correlating to high antibody titers in convalescent plasma donors and understand the magnitude and pharmacokinetic time course of both transfused antibody titers and the endogenous antibody titers in transfused recipients. Methods: Plasma samples were collected up to 174 days after convalescence from 93 CCP donors with mild disease, and from 16 COVID-19 patients before and after transfusion. Using ELISA, anti-SARS-CoV-2 Spike RBD, S1, and N-protein antibodies, as well as capacity of antibodies to block ACE2 from binding to RBD was measured in an in vitro assay. As an estimate for viral load, viral RNA and N-protein plasma levels were assessed in COVID-19 patients. Results: Anti-SARS-CoV-2 antibody levels and RBD-ACE2 blocking capacity were highest within the first 60 days after symptom resolution and markedly decreased after 120 days. Highest antibody titers were found in CCP donors that experienced fever. Effect of transfused CCP was detectable in COVID-19 patients who received high-titer CCP and had not seroconverted at the time of transfusion. Decrease in viral RNA was seen in two of these patients. Conclusion: Our results suggest that high titer CCP should be collected within 60 days after recovery from donors with past fever. The much lower titers conferred by transfused antibodies compared to endogenous production in the patient underscore the importance of providing CCP prior to endogenous seroconversion.


Asunto(s)
COVID-19/terapia , Convalecencia , SARS-CoV-2/inmunología , Seroconversión , Adulto , Anticuerpos Neutralizantes/sangre , Anticuerpos Neutralizantes/inmunología , Anticuerpos Antivirales/sangre , Anticuerpos Antivirales/inmunología , Antígenos Virales/sangre , Donantes de Sangre , COVID-19/sangre , COVID-19/inmunología , Femenino , Humanos , Inmunización Pasiva , Cinética , Masculino , Persona de Mediana Edad , Pacientes Ambulatorios , ARN Viral/sangre
16.
Sci Rep ; 11(1): 20121, 2021 10 11.
Artículo en Inglés | MEDLINE | ID: mdl-34635707

RESUMEN

The Brazilian strategy to overcome the spread of COVID-19 has been particularly criticized due to the lack of a national coordinating effort and an appropriate testing program. Here, a successful approach to control the spread of COVID-19 transmission is described by the engagement of public (university and governance) and private sectors (hospitals and oil companies) in Macaé, state of Rio de Janeiro, Brazil, a city known as the National Oil Capital. In 2020 between the 17th and 38th epidemiological week, over two percent of the 206,728 citizens were subjected to symptom analysis and RT-qPCR testing by the Federal University of Rio de Janeiro, with positive individuals being notified up to 48 h after swab collection. Geocodification and spatial cluster analysis were used to limit COVID-19 spreading in Macaé. Within the first semester after the outbreak of COVID-19 in Brazil, Macaé recorded 1.8% of fatalities associated with COVID-19 up to the 38th epidemiological week, which was at least five times lower than the state capital (10.6%). Overall, considering the successful experience of this joint effort of private and public engagement in Macaé, our data suggest that the development of a similar strategy countrywise could have contributed to a better control of the COVID-19 spread in Brazil. Quarantine decree by the local administration, comprehensive molecular testing coupled to scientific analysis of COVID-19 spreading, prevented the catastrophic consequences of the pandemic as seen in other populous cities within the state of Rio de Janeiro and elsewhere in Brazil.


Asunto(s)
Prueba de Ácido Nucleico para COVID-19/estadística & datos numéricos , COVID-19/epidemiología , Pandemias/estadística & datos numéricos , SARS-CoV-2/aislamiento & purificación , Adolescente , Adulto , Anciano , Brasil/epidemiología , COVID-19/diagnóstico , COVID-19/transmisión , COVID-19/virología , Ciudades/epidemiología , Ciudades/estadística & datos numéricos , Femenino , Humanos , Masculino , Persona de Mediana Edad , ARN Viral/aislamiento & purificación , SARS-CoV-2/genética , Adulto Joven
17.
Life Sci Alliance ; 4(12)2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34593555

RESUMEN

The continued resurgence of the COVID-19 pandemic with multiple variants underlines the need for diagnostics that are adaptable to the virus. We have developed toehold RNA-based sensors across the SARS-CoV-2 genome for direct and ultrasensitive detection of the virus and its prominent variants. Here, isothermal amplification of a fragment of SARS-CoV-2 RNA coupled with activation of our biosensors leads to a conformational switch in the sensor. This leads to translation of a reporter protein, for example, LacZ or nano-lantern that is easily detected using color/luminescence. By optimizing RNA amplification and biosensor design, we have generated a highly sensitive diagnostic assay that is capable of detecting as low as 100 copies of viral RNA with development of bright color. This is easily visualized by the human eye and quantifiable using spectrophotometry. Finally, this PHAsed NASBA-Translation Optical Method (PHANTOM) using our engineered RNA biosensors efficiently detects viral RNA in patient samples. This work presents a powerful and universally accessible strategy for detecting COVID-19 and variants. This strategy is adaptable to further viral evolution and brings RNA bioengineering center-stage.


Asunto(s)
COVID-19/virología , ARN Viral/análisis , SARS-CoV-2/aislamiento & purificación , Técnicas Biosensibles , COVID-19/diagnóstico , Humanos , Luminiscencia , Técnicas de Amplificación de Ácido Nucleico/métodos , ARN/genética , ARN Viral/genética , SARS-CoV-2/genética
18.
J Glob Health ; 11: 05022, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34671463

RESUMEN

Background: This study sought to determine the presence of SARS-CoV-2 virus on surfaces that trainees and faculty of an academic eye clinic came into contact with during daily life at the time of the COVID-19 pandemic in New York City. Methods: This cross-sectional analysis involved collection of at least two samples by teams on four different days (November 9, 2020 - December 18, 2020) using sterile swabs (Puritan HydraFlock, Garden Grove, CA). Collection sites were grouped into four zones depending on proximity and amount of time personnel spent there. Samples were transported to the laboratory in transport medium and RNA was extracted using the QIAamp DSP Viral RNA Mini Kit (Qiagen, Germantown, MD). Presence of viral RNA was investigated using the Luna Universal Probe One-step RT-qPCR kit (New England Biolabs, Ipwsich, MA). Results: 834 samples were submitted. Two were positive for SARS-CoV-2 RNA. The first was a sample from a patient bathroom sink handle in the main emergency department. The second was a nasal swab sample from a staff member who had been assigned to collect samples. Prior to this positive result, this asymptomatic staff member had tested positive for COVID-19, had quarantined for two weeks, and had received a negative test. Conclusion: Though COVID-19 is currently widespread in the United States, this study shows that health care personnel working in New York City at the Columbia University Irving Medical Center have a low chance of encountering viral RNA on surfaces they are in close contact with during daily life.


Asunto(s)
COVID-19 , ARN Viral , Estudios Transversales , Humanos , Ciudad de Nueva York/epidemiología , Pandemias , SARS-CoV-2
19.
BMC Infect Dis ; 21(1): 1076, 2021 Oct 18.
Artículo en Inglés | MEDLINE | ID: mdl-34663257

RESUMEN

BACKGROUND: The ongoing coronavirus disease 2019 (COVID-19) global pandemic caused by the SARS-CoV-2 virus remains a major threat to public health. At present, it is recommended that patients with known or suspected COVID-19 undergo quarantine or medical observation for 14 days. However, recurrent SARS-CoV-2 RNA positivity and prolonged viral shedding have been documented in convalescent COVID-19 patients, complicating efforts to control viral spread and ensure patient recovery. CASE PRESENTATION: We report the case of a patient who experienced two recurrent episodes of SARS-CoV-2 RNA and IgM positivity and viral shedding over 60 days during hospitalization. CONCLUSIONS: This case report demonstrates that relapses of SARS-CoV-2 RNA and IgM positivity may occur even after COVID-19 symptoms have resolved, possibly as a consequence of prolonged viral shedding rather than re-infection.


Asunto(s)
COVID-19 , ARN Viral , Humanos , ARN Viral/genética , SARS-CoV-2 , Esparcimiento de Virus
20.
Clin Lab ; 67(10)2021 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-34655184

RESUMEN

BACKGROUND: As an emerging infectious disease, coronavirus disease 2019 (COVID-19) exhibits occult infection, which might cause difficulties in controlling disease spread. The possibility of aerosol transmission in a relatively closed environment contributes to the high infectivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in hospitals. This study presents an environmental surveillance system for SARS-CoV-2 that is suitable for a clinical laboratory and may also lead to further assessment of infection prevention programs in different departments in hospitals. METHODS: The study was performed in a SARS-CoV-2 RNA laboratory involved in the diagnosis of COVID-19 in China. Reverse transcription-polymerase chain reaction (RT-PCR) assays were used to detect viral pathogens. Standard operating procedures (SOPs) for monitoring infectious pathogens were developed in this study. RESULTS: In total, more than 180 air and surface samples were tested for SARS-CoV-2 to determine whether the virus was present at the airborne and particle level. The employed molecular method effectively identified environmental contamination. CONCLUSIONS: Our study suggests that regular environmental surveillance is critical in a clinical PCR laboratory. The presented strategy could also be used for monitoring and surveillance in negative pressure wards and clinics in hospitals to prevent hospital-acquired infections.


Asunto(s)
COVID-19 , SARS-CoV-2 , Hospitales , Humanos , Laboratorios , ARN Viral/genética
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