Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 45
Filter
1.
Ieee Access ; 10:98633-98648, 2022.
Article in English | Web of Science | ID: covidwho-2070264

ABSTRACT

COVID-19 caused by the transmission of SARS-CoV-2 virus taking a huge toll on global health and caused life-threatening medical complications and elevated mortality rates, especially among older adults and people with existing morbidity. Current evidence suggests that the virus spreads primarily through respiratory droplets emitted by infected persons when breathing, coughing, sneezing, or speaking. These droplets can reach another person through their mouth, nose, or eyes, resulting in infection. The "gold standard" for clinical diagnosis of SARS-CoV-2 is the laboratory-based nucleic acid amplification test, which includes the reverse transcription-polymerase chain reaction (RT-PCR) test on nasopharyngeal swab samples. The main concerns with this type of test are the relatively high cost, long processing time, and considerable false-positive or false-negative results. Alternative approaches have been suggested to detect the SARS-CoV-2 virus so that those infected and the people they have been in contact with can be quickly isolated to break the transmission chains and hopefully, control the pandemic. These alternative approaches include electrochemical biosensing and deep learning. In this review, we discuss the current state-of-the-art technology used in both fields for public health surveillance of SARS-CoV-2 and present a comparison of both methods in terms of cost, sampling, timing, accuracy, instrument complexity, global accessibility, feasibility, and adaptability to mutations. Finally, we discuss the issues and potential future research approaches for detecting the SARS-CoV-2 virus utilizing electrochemical biosensing and deep learning.

2.
Infect Chemother ; 54(3): 517-528, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2055543

ABSTRACT

BACKGROUND: Self-sampling procedures to detect severe acute respiratory syndrome coronavirus 2 is important for patients who have difficulty visiting the hospital and may decrease the burden for health care workers (HCWs). The objective of this study was to evaluate the diagnostic performance, stability and usability of self-collected nasal and oral combo swabs and saliva specimens. MATERIALS AND METHODS: We conducted a case-control study with 50 patients with coronavirus disease 2019 (COVID-19) and 50 healthy volunteers from March, 2021 to June, 2021. We performed real-time reverse-transcription polymerase chain reaction to compare the diagnostic performance of self-collected specimens using positive percent agreements (PPAs). RESULTS: The PPAs between self-collected and HCW-collected specimens were 77.3 - 81.0% and 80.5 -86.7% for the combo swabs and saliva specimens, respectively. The PPAs increased to 88.9 - 89.2% and 81.2 - 82.1% with a cycle threshold value ≤30. CONCLUSION: The diagnostic performance of self sampling was comparable to that of HCW sampling in patients with high viral loads and may thus assist in the early diagnosis of COVID-19.

3.
Saudi J Biol Sci ; 29(11): 103465, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2042138

ABSTRACT

The ongoing novel COVID-19 has remained the center of attention, since its declaration as a pandemic in March 2020, due to its rapid and uncontrollable worldwide spread. Diagnostic tests are the first line of defense against the transmission of this infectious disease among individuals, with reverse-transcription quantitative polymerase chain reaction (RT-qPCR) being the approved gold standard for showing high sensitivity and specificity in detecting SARS-CoV-2. However, alternative tests are being invested due to the global demand for facilities, reagents, and healthcare workers needed for rapid population-based testing. Also, the rapid evolution of the viral genome and the emergence of new variants necessitates updating the existing methods. Scientists are aiming to improve tests to be affordable, simple, fast, and at the same time accurate, and efficient, as well as friendly user testing. The current diagnostic methods are either molecular-based that detect nucleic acids abundance, like RT-qPCR and reverse-transcription loop-mediated isothermal amplification (RT-LAMP); or immunologically based that detect the presence of antigens or antibodies in patients' specimens, like enzyme-linked immunosorbent assay (ELISA), lateral flow assay (LFA), chemiluminescent immunoassay (CLIA), and neutralization assay. In addition to these strategies, sensor-based or CRISPR applications are promising tools for the rapid detection of SARS-CoV-2. This review summarizes the most recent updates on the SARS-CoV-2 detection methods with their limitations. It will guide researchers, epidemiologists, and clinicians in identifying a more rapid, reliable, and sensitive method of diagnosing SARS-CoV-2 including the most recent variant of concern Omicron.

4.
Pathologie (Heidelb) ; 2022 Sep 16.
Article in German | MEDLINE | ID: covidwho-2035037

ABSTRACT

BACKGROUND: Autopsies are a valuable tool for understanding disease, including COVID-19. MATERIALS AND METHODS: The German Registry of COVID-19 Autopsies (DeRegCOVID), established in April 2020, serves as the electronic backbone of the National Autopsy Network (NATON), launched in early 2022 following DEFEAT PANDEMIcs. RESULTS: The NATON consortium's interconnected, collaborative autopsy research is enabled by an unprecedented collaboration of 138 individuals at more than 35 German university and non-university autopsy centers through which pathology, neuropathology, and forensic medicine autopsy data including data on biomaterials are collected in DeRegCOVID and tissue-based research and methods development are conducted. More than 145 publications have now emerged from participating autopsy centers, highlighting various basic science and clinical aspects of COVID-19, such as thromboembolic events, organ tropism, SARS-CoV­2 detection methods, and infectivity of SARS-CoV-2 at autopsy. CONCLUSIONS: Participating centers have demonstrated the high value of autopsy and autopsy-derived data and biomaterials to modern medicine. The planned long-term continuation and further development of the registry and network, as well as the open and participatory design, will allow the involvement of all interested partners.

5.
Frontiers in Ecology and Evolution ; 10, 2022.
Article in English | Web of Science | ID: covidwho-2022693

ABSTRACT

Animal specimens in natural history collections are invaluable resources in examining the historical context of pathogen dynamics in wildlife and spillovers to humans. For example, natural history specimens may reveal new associations between bat species and coronaviruses. However, RNA viruses are difficult to study in historical specimens because protocols for extracting RNA from these specimens have not been optimized. Advances have been made in our ability to recover nucleic acids from formalin-fixed paraffin-embedded samples (FFPE) commonly used in human clinical studies, yet other types of formalin preserved samples have received less attention. Here, we optimize the recovery of RNA from formalin-fixed ethanol-preserved museum specimens in order to improve the usability of these specimens in surveys for zoonotic diseases. We provide RNA quality and quantity measures for replicate tissues subsamples of 22 bat specimens from five bat genera (Rhinolophus, Hipposideros, Megareops, Cynopterus, and Nyctalus) collected in China and Myanmar from 1886 to 2003. As tissues from a single bat specimen were preserved in a variety of ways, including formalin-fixed (8 bats), ethanol-preserved and frozen (13 bats), and flash frozen (2 bats), we were able to compare RNA quality and yield across different preservation methods. RNA extracted from historical museum specimens is highly fragmented, but usable for short-read sequencing and targeted amplification. Incubation of formalin-fixed samples with Proteinase-K following thorough homogenization improves RNA yield. This optimized protocol extends the types of data that can be derived from existing museum specimens and facilitates future examinations of host and pathogen RNA from specimens.

6.
Diagn Microbiol Infect Dis ; 105(1): 115800, 2022 Aug 26.
Article in English | MEDLINE | ID: covidwho-2004017

ABSTRACT

Molecular testing of SARS-CoV-2 RNA is essential during the pandemic. Here, we compared the results of different respiratory specimens including anterior nasal swabs, pharyngeal swabs, saliva swabs, and gargle lavage samples to nasopharyngeal swabs on two automated SARS-CoV-2 test systems. Samples were collected and tested simultaneously from a total of 36 hospitalized symptomatic COVID-19 patients. Detection and quantification of SARS-CoV-2 was performed on cobas®6800 (Roche) and NeuMoDx™ (Qiagen) systems. Both assays showed reliable detection and quantification of SARS-CoV-2 RNA, with nasopharyngeal swabs showing the highest sensitivity. SARS-CoV-2 RNA concentrations in other respiratory specimens were lower (mean 2.5 log10 copies/ml) or even undetectable in up to 20%. These data clearly indicate that not all respiratory materials are equally suitable for the management of hospitalized patients, especially, in the late phase of COVID-19, when the viral phase subsides and inflammation becomes the predominant factor, making detection of even lower viral loads increasingly important.

7.
Journal of the Botanical Research Institute of Texas ; 16(1):343-356, 2022.
Article in English | Academic Search Complete | ID: covidwho-1975513

ABSTRACT

Alaska is relatively isolated from the rest of the United States, due to its distance, size and widespread population. Online course delivery is a valuable alternative to on-campus enrollment for many of the rural students in our state. Introduction to the Flora of Alaska and Systematic Botany are now being offered as fully online courses with a lab component. These courses taught both online, and in the classroom (COVID-19 depending), are versions of the first author's own experiences taking these same classes taught by Don Pinkava at Arizona State University. His legacy as an intrepid botanist and inspiring educator influenced how I (Steffi Ickert-Bond) approached developing my own teaching style. The course design presented reflects some of Don Pinkava's rigorous detailed and challenging course content and innovative labs. The devoted teacher he was, Dr. Pinkava left for us a comprehensive statement outlining his teaching principles he had acquired over many years (Appendix 1). As a student of Don's, I have applied those teaching principles to my own courses. To create a lab experience like Don's classes, I have carefully chosen technology that will allow students from all over the state (and even outside Alaska) to have a hands-on learning experience. Using cutting-edge virtual herbaria they collect data, and perform plant dissections within the flora's native environment. Instead of traditional course materials like textbooks, students use an inexpensive wide-angle macro lens to take high-resolution, detailed photos of flora on the go. The technology not only lets students mimic lab spaces in their own areas but also expands their digital networks through the submission of images to iNaturalist, enabling them to share and collaborate with enthusiasts around the world. Students must get outside, touch with their hands and share what they discover. In combining traditional methods with modern technologies such as virtual, streaming dissections students develop skills and confidence with the microscope and dissection techniques just as much as I did in Don's in person Flora of Arizona class in 1993. Today the Introduction to the Flora of Alaska (BIOL190), and Systematic Botany (BIOL331) are both exciting intersections highlighting a curiosity for wild plants, an exploration of Alaska's plant communities as well as a great introduction to the science of botany. Don's Flora of Arizona took us students to those same crossroads. Together with my colleague Dr. Ute Kaden who teaches STEM methodology at the School of Education, UAF we describe effective course design elements for online delivery of a biology course and the challenges that come with it. Some student feedback after the first semester running will be presented here as well. (English) [ FROM AUTHOR] Alaska está relativamente aislada del resto de los Estados Unidos, debido a su distancia, tamaño y población extendida. La entrega de cursos en línea es una alternativa valiosa a la inscripción en el campus para muchos de los estudiantes rurales de nuestro estado. Introducción a la Flora de Alaska y Botánica Sistemática ahora se ofrecen como cursos completamente en línea con un componente de laboratorio. Estos cursos impartidos tanto en línea como en el aula (dependiendo de COVID-19), son versiones de las propias experiencias del primer autor al tomar estas mismas clases impartidas por Don Pinkava en la Universidad Estatal de Arizona. Su legado como botánico intrépido y educador inspirador influyó en cómo yo (Steffi Ickert-Bond) abordé el desarrollo de mi propio estilo de enseñanza. El diseño del curso presentado refleja algunos de los contenidos rigurosos, detallados y desafiantes del curso y los laboratorios innovadores de Don Pinkava. El devoto maestro que fue, el Dr. Pinkava nos dejó una declaración completa que describe los principios de enseñanza que había adquirido durante muchos años (Apéndice 1). Como estudiante de Don, he aplicado esos principios de enseñanza a mis propios cursos. Para crear una experiencia de laboratorio como las clases de Don, he elegido cuidadosamente la tecnología que permitirá a los estudiantes de todo el estado (e incluso fuera de Alaska) tener una experiencia de aprendizaje práctica. Utilizando herbarios virtuales de última generación, recopilan datos y realizan disecciones de plantas dentro del entorno nativo de la flora. En lugar de los materiales tradicionales del curso, como los libros de texto, los estudiantes usan una lente macro gran angular económica para tomar fotografías detalladas de alta resolución de la flora sobre la marcha. La tecnología no solo permite a los estudiantes imitar espacios de laboratorio en sus propias áreas, sino que también expande sus redes digitales mediante el envío de imágenes a iNaturalist, lo que les permite compartir y colaborar con entusiastas de todo el mundo. Los estudiantes deben salir, tocar con las manos y compartir lo que descubren. Al combinar métodos tradicionales con tecnologías modernas, como disecciones virtuales, los estudiantes desarrollan habilidades y confianza con el microscopio y las técnicas de disección tanto como lo hice en la clase presencial de Flora de Arizona de Don en 1993. Hoy en día, la Introducción a la Flora de Alaska (BIOL190) y Systematic Botany (BIOL331) son interesantes intersecciones que destacan la curiosidad por las plantas silvestres, una exploración de las comunidades de plantas de Alaska y una gran introducción a la ciencia de la botánica. Don's Flora of Arizona nos llevó a los estudiantes a esa misma encrucijada. Junto con mi colega, la Dra. Ute Kaden, quien enseña metodología STEM en la Facultad de Educación de la UAF, describimos elementos de diseño de cursos efectivos para la entrega en línea de un curso de biología y los desafíos que conlleva. Aquí también se presentarán algunos comentarios de los estudiantes después del primer semestre. (Spanish) [ FROM AUTHOR] Copyright of Journal of the Botanical Research Institute of Texas is the property of Journal of the Botanical Research Institute of Texas and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

8.
11th Mediterranean Conference on Embedded Computing, MECO 2022 ; 2022.
Article in English | Scopus | ID: covidwho-1948828

ABSTRACT

The virus SARS-Co V -2 that has caused a pandemic of COVID-19 in 2019 is still a major concern for health care systems. The reason for this is the fact that the outcome of the disease is difficult to predict, as deadly complications can occur in all people. Diagnosing COVID-19 relies on polymerase chain reaction (PCR) testing and antigen testing, both of which require special referral. The aim of this study was to develop artificial intelligence (AI) expert system which will facilitate COVID-19 diagnosis based on parameters that can be readily collected from blood specimens. The database contains 1000 samples, divided into 2 categories: (1) healthy and (2) sick subjects The following parameters were used: CRP, LDH, SE, AST, ALT, D-dimer and IL-6. The sensitivity of the developed system was 100%, specificity 98.33%, and accuracy 99.67%, on the basis of which we can conclude that the use of AI in the diagnosis of COVID19 has a significant potential. © 2022 IEEE.

9.
Ann Anat ; 244: 151973, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1894715

ABSTRACT

BACKGROUND: In the field of medicine, anatomy is considered one of the most important subjects to be studied in college, even for clinicians. Learning from cadaveric specimens is considered an important part of the medical experience. The current study consisted of a questionnaire given to Year 1 and Year 2 medical students. This study was performed to assess using a questionnaire whether students were capable of continuing studying Anatomy during the COVID-19 period. METHODS: The study consisted of 102 students in Years 1 and 2 of the Faculty of Medicine of Alexandria University in Egypt. It included Year 1 Students (mean age 18.6 ± 1.1 years old; 21 males and 36 females), and Year 2 Students (mean age 20.4 ± 1.0 years old; 22 males and 23 females). The survey consisted of three sections. The first section consisted of four questions on the demographic data of the participating students. The second section consisted of 10 questions concerning their satisfaction with the tutorials and presented by the Department of Anatomy. Answers to the questionnaire were in the form of a Likert scale (with 1 = strongly disagree to 5 = strongly agree). RESULTS: The students disagreed with the fact that they found difficulty in time management, represented by a mean score of 2.23 ± 1.14. That is to say, the students were capable of managing their time well. Here also, the difference between Year 1 and Year 2 students was significant (p = 0.028), which is an indicator that Year 2 students found more difficulty in time management. Most students agreed (mean score of 3.48 ± 1.07) that they were able to handle online learning and the transition between the systems was acceptable. Students were also convinced and agreed that the methods used by the college limited the spread of COVID-19 (mean score of 3.81 ± 1.04). Allowing assignments and projects increased the interaction between the students and the staff members. CONCLUSIONS: Education must continue during the COVID-19 period, based on their responses and opinions in the questionnaire. Online learning proved to be effective in teaching medical students during the COVID-19 pandemic.


Subject(s)
Anatomy , COVID-19 , Education, Distance , Education, Medical, Undergraduate , Students, Medical , Male , Female , Humans , Adolescent , Young Adult , Adult , Education, Distance/methods , Education, Medical, Undergraduate/methods , Pandemics , Anatomy/education
10.
Taxon ; : 14, 2022.
Article in English | Web of Science | ID: covidwho-1894631

ABSTRACT

In response to the worldwide coronavirus outbreak, which effectively shut down fieldwork, laboratory and herbarium-based studies, an evaluation was made of the effectiveness and limitations of undertaking a virtual taxonomic study using only online herbarium specimen resources related to the genus Madhuca (Sapotaceae) for the Flora of Singapore. The study demonstrated the immense value of digital images to basic taxonomic research but also found that diagnostic micro-morphological characters, often critical in defining species boundaries, cannot be seen in many digital images, even at high resolution. Several recommendations are made on how to maximise the utility of online herbarium specimen images to help facilitate future taxonomic research, though it is clear that physical access to herbarium specimens remains essential.

11.
New Microbiol ; 45(2): 115-123, 2022 04.
Article in English | MEDLINE | ID: covidwho-1887517

ABSTRACT

Infectious diseases still register significant morbidity and mortality worldwide. Surveillance through a mandatory notification system allows the continuous analysis of the situation even at a local level and its importance has been highlighted by the recent COVID-19 pandemic. This paper aimed to outline the importance of the mandatory notification system as a Public Health tool in the continuous monitoring of infectious diseases. To this aim, we carried out a cross-sectional study examining the notifications reported in the Italian territory of Messina, Sicily, in the period 2001-2020. The institutional websites were examined and the notification data were used to obtain the incidences. Overall, a significant reduction of the incidence notification trend was observed. Chickenpox was by far the most notified infectious disease, followed by scabies, pediculosis, and brucellosis. Outbreaks of brucellosis, measles and hepatitis A occurred. All the diseases decreased over time, except syphilis, for which a significant increase was observed. Surveillance of infectious diseases through a mandatory notification system remains a bulwark of public health despite underreporting. Our study reflects the situation of a typical high-income area, although some unexpected criticisms are highlighted. Continuous information about correct behaviors through education campaigns are crucial in order to improve the situation. Keywords: mandatory notifications, infectious diseases, surveillance, public health Corresponding author: Alessio Facciolà, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Italy. Email: afacciola@unime.it.


Subject(s)
Brucellosis , COVID-19 , Communicable Diseases , Brucellosis/epidemiology , Communicable Diseases/diagnosis , Communicable Diseases/epidemiology , Cross-Sectional Studies , Disease Notification , Humans , Pandemics , Population Surveillance/methods , Sicily
12.
Microbiol Spectr ; 10(3): e0103322, 2022 Jun 29.
Article in English | MEDLINE | ID: covidwho-1879118

ABSTRACT

Respiratory specimen collection materials shortages hampers severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We compared specimen alternatives and evaluated SARS-CoV-2 RNA stability under simulated shipping conditions. We compared concordance of RT-PCR detection of SARS-CoV-2 from flocked midturbinate swabs (MTS) in viral transport media (VTM), foam MTS without VTM, and saliva. Specimens were collected between August 2020 and April 2021 from three prospective cohorts. We compared RT-PCR cycle quantification (Cq) for Spike (S), Nucleocapsid (N), and the Open Reading Frame 1ab (ORF) genes for flocked MTS and saliva specimens tested before and after exposure to a range of storage temperatures (4-30°C) and times (2, 3, and 7 days). Of 1,900 illnesses with ≥2 specimen types tested, 335 (18%) had SARS-CoV-2 detected in ≥1 specimen; 304 (91%) were concordant across specimen types. Among illnesses with SARS-CoV-2 detection, 97% (95% confidence interval [CI]: 94-98%) were positive on flocked MTS, 99% (95% CI: 97-100%) on saliva, and 89% (95% CI: 84-93%) on foam MTS. SARS-CoV-2 RNA was detected in flocked MTS and saliva stored up to 30°C for 7 days. All specimen types provided highly concordant SARS-CoV-2 results. These findings support a range of viable options for specimen types, collection, and transport methods that may facilitate SARS-CoV-2 testing during supply and personnel shortages. IMPORTANCE Findings from this analysis indicate that (1) self-collection of flocked and foam MTS and saliva samples is feasible in both adults and children, (2) foam MTS with VTM and saliva are both viable and reasonable alternatives to traditional flocked MTS in VTM for SARS-CoV-2 detection, and (3) these sample types may be stored and transported at ambient temperatures for up to 7 days without compromising sample quality. These findings support methods of sample collection for SARS-CoV-2 detection that may facilitate widespread community testing in the setting of supply and personnel shortages during the current pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , COVID-19/diagnosis , COVID-19 Testing , Child , Humans , Prospective Studies , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , Saliva , Specimen Handling/methods
13.
Comput Electr Eng ; 101: 108055, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1814286

ABSTRACT

As people all over the world are vulnerable to be affected by the COVID-19 virus, the automatic detection of such a virus is an important concern. The paper aims to detect and classify corona virus using machine learning. To spot and identify corona virus in CT-Lung screening and Computer-Aided diagnosis (CAD) system is projected to distinguish and classifies the COVID-19. By utilizing the clinical specimens obtained from the corona-infected patients with the help of some machine learning techniques like Decision Tree, Support Vector Machine, K-means clustering, and Radial Basis Function. While some specialists believe that the RT-PCR test is the best option for diagnosing Covid-19 patients, others believe that CT scans of the lungs can be more accurate in diagnosing corona virus infection, as well as being less expensive than the PCR test. The clinical specimens include serum specimens, respiratory secretions, and whole blood specimens. Overall, 15 factors are measured from these specimens as the result of the previous clinical examinations. The proposed CAD system consists of four phases starting with the CT lungs screening collection, followed by a pre-processing stage to enhance the appearance of the ground glass opacities (GGOs) nodules as they originally lock hazy with fainting contrast. A modified K-means algorithm will be used to detect and segment these regions. Finally, the use of detected, infected areas that obtained in the detection phase with a scale of 50×50 and perform segmentation of the solid false positives that seem to be GGOs as inputs and targets for the machine learning classifiers, here a support vector machine (SVM) and Radial basis function (RBF) has been utilized. Moreover, a GUI application is developed which avoids the confusion of the doctors for getting the exact results by giving the 15 input factors obtained from the clinical specimens.

14.
Talanta ; 243: 123356, 2022 Jun 01.
Article in English | MEDLINE | ID: covidwho-1778464

ABSTRACT

The increasing mutation frequency of the SARS-CoV-2 virus and the emergence of successive variants have made correct diagnosis hard to perform. Developing efficient and accurate methods to diagnose infected patients is crucial to effectively mitigate the pandemic. Here, we developed an electrochemical immunosensor based on SARS-CoV-2 antibody cocktail-conjugated magnetic nanoparticles for the sensitive and accurate detection of the SARS-CoV-2 virus and its variants in nasopharyngeal swabs. The application of the antibody cocktail was compared with commercially available anti-SARS-CoV-2 S1 (anti-S1) and anti-S2 monoclonal antibodies. After optimization and calibration, the limit of detection (LOD) determination demonstrated a LOD = 0.53-0.75 ng/mL for the antibody cocktail-based sensor compared with 0.93 ng/mL and 0.99 ng/mL for the platforms using anti-S1 and anti-S2, respectively. The platforms were tested with human nasopharyngeal swab samples pre-diagnosed with RT-PCR (10 negatives and 40 positive samples). The positive samples include the original, alpha, beta, and delta variants (n = 10, for each). The polyclonal antibody cocktail performed better than commercial anti-S1 and anti-S2 antibodies for all samples reaching 100% overall sensitivity, specificity, and accuracy. It also showed a wide range of variants detection compared to monoclonal antibody-based platforms. The present work proposes a versatile electrochemical biosensor for the indiscriminate detection of the different variants of SARS-CoV-2 using a polyclonal antibody cocktail. Such diagnostic tools allowing the detection of variants can be of great efficiency and economic value in the fight against the ever-changing SARS-CoV-2 virus.


Subject(s)
Biosensing Techniques , COVID-19 , Magnetite Nanoparticles , COVID-19/diagnosis , Humans , Immunoassay , SARS-CoV-2/genetics
15.
Front Cell Infect Microbiol ; 12: 824578, 2022.
Article in English | MEDLINE | ID: covidwho-1775646

ABSTRACT

Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.


Subject(s)
COVID-19 , Microbiota , Humans , Oropharynx/microbiology , RNA, Ribosomal, 16S/genetics , SARS-CoV-2
16.
Biosens Bioelectron ; 200: 113909, 2022 Mar 15.
Article in English | MEDLINE | ID: covidwho-1670212

ABSTRACT

Coronavirus disease 2019 (COVID-19) has been recognized as a global pandemic outbreak, opening the most severe socio-economic crisis since World War II. Different scientific activities have been emerged in this global scenario, including the development of innovative analytical tools to measure nucleic acid, antibodies, and antigens in the nasopharyngeal swab, serum, and saliva for prompt identification of COVID-19 patients and to evaluate the immune response to the vaccine. The detection of SARS-CoV-2 in saliva remains a challenge for the lack of sufficient sensitivity. To address this issue, we developed a novel paper-based immunoassay using magnetic beads to support the immunological chain and 96-well wax-printed paper plate as a platform for color visualization by using a smartphone combined with Spotxel free-charge app. To assess the reliability of the measurement of SARS-CoV-2 in saliva, untreated saliva was used as a specimen and the calibration curve demonstrated a dynamic range up to 10 µg/mL, with a detection limit equal to 0.1 µg/mL. The effectiveness of this sustainable analytical tool in saliva was evaluated by comparing the data with the nasopharyngeal swab specimens sampled by the same patients and tested with Real-Time PCR reference method, founding 100% of agreement, even in the case of high Cycle Threshold (CT) numbers (low viral load). Furthermore, the positive saliva samples were characterized by the next-generation sequencing method, demonstrating the capability to detect the Delta variant, which is actually (July 2021) the most relevant variant of concern.


Subject(s)
Biosensing Techniques , COVID-19 , Colorimetry , Humans , Immunoassay , Magnetic Phenomena , Nasopharynx , Reproducibility of Results , SARS-CoV-2 , Saliva , Smartphone , Specimen Handling
17.
Emerg Microbes Infect ; 11(1): 629-638, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1665837

ABSTRACT

Mounting evidence indicates that SARS-CoV-2 can infect multiple systemic tissues, but few studies have evaluated SARS-CoV-2 RNA dynamics in multiple specimen types due to their reduced accessibility and diminished performance of RT-qPCR with non-respiratory specimens. Here, we employed an ultrasensitive CRISPR-RT-PCR assay to analyze longitudinal mucosal (nasal, buccal, pharyngeal, and rectal), plasma, and breath samples from SARS-CoV-2-infected non-human primates (NHPs) to detect dynamic changes in SARS-CoV-2 RNA level and distribution among these specimens. We observed that CRISPR-RT-PCR results consistently detected SARS-CoV-2 RNA in all sample types at most time points post-infection, and that SARS-CoV-2 infection dose and administration route did not markedly affect the CRISPR-RT-PCR signal detected in most specimen types. However, consistent RT-qPCR positive results were restricted to nasal, pharyngeal, and rectal swab samples, and tended to decrease earlier than CRISPR-RT-PCR results, reflecting lower assay sensitivity. SARS-CoV-2 RNA was detectable in both pulmonary and extrapulmonary specimens from early to late infection by CRISPR-RT-PCR, albeit with different abundance and kinetics, with SARS-CoV-2 RNA increases detected in plasma and rectal samples trailing those detected in upper respiratory tract samples. CRISPR-RT-PCR assays for SARS-CoV-2 RNA in non-respiratory specimens may thus permit direct diagnosis of suspected COVID-19 cases missed by RT-PCR, while tracking SARS-CoV-2 RNA in minimally invasive alternate specimens may better evaluate the progression and resolution of SARS-CoV-2 infections.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Humans , Primates , RNA, Viral/analysis , Sensitivity and Specificity , Serologic Tests
18.
Chemical Biology Letters ; 8(3):106-116, 2021.
Article in English | Scopus | ID: covidwho-1589837

ABSTRACT

COVID-19, caused by the novel coronavirus SARS-CoV-2, has put most of the world under lockdown. Despite approved vaccines, COVID-19 cases, hospitalizations, and deaths have remained on the rise. Rapid diagnosis and necessary public health measures are still key parts to contain the pandemic. Here, the colorimetric isothermal nucleic acid amplification tests (iNAATs) for SARS-CoV-2 detection based on loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and polymerase spiral reaction (PSR) were designed and compared in performance for the first time. The findings showed that, for the detection of SARS-CoV-2 genomic-RNA, LAMP outperformed both CPA and PSR, exhibiting the limit of detection (LOD) of roughly 43.14 copies/reaction. The results can be read with the naked eye within 45 minutes, without cross-reactivity to closely related coronaviruses. The direct detection of SARS-CoV-2 RNA in simulated specimens by iNAATs was also successful. Additionally, the lyophilized reagents for LAMP reactions maintained the sensitivity and LOD of the liquid assays. The colorimetric LAMP assay was validated using clinical samples, showing 98.1% sensitivity and 100% specificity upon using extracted samples and 82.4% sensitivity and 86.2% specificity upon using unextracted specimens. The results indicate that the direct colorimetric LAMP assay developed is highly suitable for detecting SARS-CoV-2 at point-of-care. © ScienceIn Publishing.

19.
Infect Drug Resist ; 14: 5395-5401, 2021.
Article in English | MEDLINE | ID: covidwho-1581593

ABSTRACT

PURPOSE: This study detects SARS-CoV-2 in the ocular surface through one-step reverse-transcription droplet digital PCR (one-step RT-ddPCR) and evaluates the possibility of the ocular surface as a possible transmission route. METHODS: A single-center prospective observational study was designed to investigate the viral loads in ocular surface. Specimens including the conjunctival swabs, nasopharyngeal swabs and blood were synchronously collected at a single time point for all COVID-19 patients. SARS-CoV-2 loads in nasopharyngeal swabs were tested by real-time polymerase chain reaction (PCR); the blood samples and conjunctival swabs were tested by real-time PCR and one-step RT-ddPCR. RESULTS: Sixty-eight COVID-19 patients confirmed by nasopharyngeal real-time PCR were recruited. In the single time point test, 40 cases showed positive SARS-CoV-2 detection in either the blood, tears, or nasopharynx, of which four cases were triple-positive, 10 were dual-positive, and 26 were single-positive. The positive rate of nasopharyngeal swab real-time PCR test was 22.1% (15/68). The positive rate of blood and conjunctival swabs by one-step RT-ddPCR was 38.2% (26/68) and 25% (17/68), respectively, whereas real-time PCR was all negative. Positive conjunctival swabs were significantly correlated with positive nasopharyngeal swabs (P = 0.028). The sampling lags from illness onset to sampling day in 3 out of 4 triple-positive patients and in 9 out of 10 dual-positive patients were respectively less than 9 days and less than 20 days. CONCLUSION: Our results indicate that the positive rate of SARS-CoV-2 on the ocular surface is much higher than expected. Transmission possibility through the ocular surface may be greatly underestimated.

20.
Journal of pathology informatics ; 12, 2021.
Article in English | EuropePMC | ID: covidwho-1560088
SELECTION OF CITATIONS
SEARCH DETAIL