Your browser doesn't support javascript.
Шоу: 20 | 50 | 100
Результаты 1 - 20 de 7.487
Фильтр
Добавить фильтры

Годовой диапазон
1.
Biomedica ; 42(Sp. 2): 59-72, 2022 10 31.
Статья в английский, испанский | MEDLINE | ID: covidwho-2164147

Реферат

Introducción. Desde el primer reporte en la provincia de Wuhan (China) en el año 2019, el SARS-CoV-2 se ha diseminado por todo el mundo, provocando un enorme impacto en la salud pública. Para su diagnóstico, la Organización Mundial de la Salud ha incentivado el desarrollo de pruebas rápidas, de simple ejecución, sensibles y específicas, que complementan la RT-qPCR como prueba de referencia. La prueba RT-LAMP ha mostrado ser una excelente alternativa para la detección del SARS-CoV-2 en diferentes biofluidos. OBJETIVO: Validar la técnica RT-LAMP colorimétrica en muestras de hisopado nasofaríngeo previamente confirmadas por RT-qPCR, usando el protocolo Charité, Berlín, Alemania. Materiales y métodos. Un total de 153 muestras de hisopado nasofaríngeo de individuos con sospecha de COVID-19 se sometieron a RT-qPCR y RT-LAMP, usando un estuche comercial colorimétrico (NEB, Germany). La RT-LAMP se practicó con las muestras de ARN extraídas del hisopado nasofaríngeo y con muestras crudas sin previa extracción de ARN. El resultado fue evaluado por un simple cambio de color en la reacción. RESULTADOS: La sensibilidad y especificidad de la técnica RT-LAMP para detectar el gen N del SARS-CoV-2 mediante un set de cebadores previamente reportados (set de Broughton), arrojó valores de 0,97 (0,85-1,00) y 0,81 (0,65-0,92), respectivamente, con un intervalo de confianza del 95%. Otro set de cebadores dirigidos contra otra región del mismo gen (set de Lalli) arrojó valores de sensibilidad y especificidad de 0,96 (0,78-1,00) y 0,77 (0,55-0,92), respectivamente. Sin previa extracción de ARN, se encontró que la sensibilidad fue del 0,95 (0,74-1,00) y la especificidad del 0,88 (0,64-0,99). CONCLUSIONES: Estos resultados evidencian que la técnica RT-LAMP podría considerarse una prueba diagnóstica rápida, de fácil ejecución, libre de equipos sofisticados, sensible y específica, para el diagnóstico del SARS-CoV-2 en muestras de hisopados nasofaríngeos.


Introducción. Desde el primer reporte en la provincia de Wuhan (China) en el año 2019, el SARS-CoV-2 se ha diseminado por todo el mundo, provocando un enorme impacto en la salud pública. Para su diagnóstico, la Organización Mundial de la Salud ha incentivado el desarrollo de pruebas rápidas, de simple ejecución, sensibles y específicas, que complementan la RT-qPCR como prueba de referencia. La prueba RT-LAMP ha mostrado ser una excelente alternativa para la detección del SARS-CoV-2 en diferentes biofluidos. Objetivo. Validar la técnica RT-LAMP colorimétrica en muestras de hisopado nasofaríngeo previamente confirmadas por RT-qPCR, usando el protocolo Charité, Berlín, Alemania. Materiales y métodos. Un total de 153 muestras de hisopado nasofaríngeo de individuos con sospecha de COVID-19 se sometieron a RT-qPCR y RT-LAMP, usando un estuche comercial colorimétrico (NEB, Germany). La RT-LAMP se practicó con las muestras de ARN extraídas del hisopado nasofaríngeo y con muestras crudas sin previa extracción de ARN. El resultado fue evaluado por un simple cambio de color en la reacción. Resultados. La sensibilidad y especificidad de la técnica RT-LAMP para detectar el gen N del SARS-CoV-2 mediante un set de cebadores previamente reportados (set de Broughton), arrojó valores de 0,97 (0,85-1,00) y 0,81 (0,65-0,92), respectivamente, con un intervalo de confianza del 95%. Otro set de cebadores dirigidos contra otra región del mismo gen (set de Lalli) arrojó valores de sensibilidad y especificidad de 0,96 (0,78-1,00) y 0,77 (0,55-0,92), respectivamente. Sin previa extracción de ARN, se encontró que la sensibilidad fue del 0,95 (0,74-1,00) y la especificidad del 0,88 (0,64-0,99). Conclusiones. Estos resultados evidencian que la técnica RT-LAMP podría considerarse una prueba diagnóstica rápida, de fácil ejecución, libre de equipos sofisticados, sensible y específica, para el diagnóstico del SARS-CoV-2 en muestras de hisopados nasofaríngeos.


Тема - темы
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , China , Retrospective Studies
2.
Front Cell Infect Microbiol ; 12: 814782, 2022.
Статья в английский | MEDLINE | ID: covidwho-2162957

Реферат

Objective: To evaluate the necessity of Covid-19 vaccination in children aged < 12 y by comparing the clinical characteristics between unvaccinated children aged < 12 y and vaccinated patients aged ≥ 12y during the Delta surge (B.1.617.2) in Putian, Fujian, China. Methods: A total of 226 patients with SARS-Cov-2 Delta variant (B.1.167.2; confirmed by Real-time PCR positivity and sequencing) were enrolled from Sep 10th to Oct 20th, 2021, including 77 unvaccinated children (aged < 12y) and 149 people aged ≥ 12y, mostly vaccinated. The transmission route was explored and the clinical data of two groups were compared; The effect factors for the time of the nucleic acid negativization (NAN) were examined by R statistical analysis. Results: The Delta surge in Putian spread from children in schools to factories, mostly through family contact. Compared with those aged ≥ 12y, patients aged < 12y accounted for 34.07% of the total and showed milder fever, less cough and fatigue; they reported higher peripheral blood lymphocyte counts [1.84 (1.32, 2.71)×10^9/L vs. 1.31 (0.94, 1.85)×10^9/L; p<0.05), higher normal CRP rate (92.21% vs. 57.72%), lower IL-6 levels [5.28 (3.31, 8.13) vs. 9.10 (4.37, 15.14); p<0.05]. Upon admission, their COVID19 antibodies (IgM and IgG) and IgG in convalescence were lower [0.13 (0.00, 0.09) vs. 0.12 (0.03, 0.41), p<0.05; 0.02 (0.00, 0.14) vs. 1.94 (0.54, 6.40), p<0.05; 5.46 (2.41, 9.26) vs. 73.63 (54.63, 86.55), p<0.05, respectively], but longer NAN time (18 days vs. 16 days, p=0.13). Conclusion: Unvaccinated children may be an important link in the transmission of SARS-CoV-2 delta variant (B1.617.2), which indicated an urgent need of vaccination for this particular population.


Тема - темы
COVID-19 , SARS-CoV-2 , Aged , COVID-19 Vaccines , Child , Humans , Immunoglobulin M , SARS-CoV-2/genetics
3.
Front Cell Infect Microbiol ; 12: 960938, 2022.
Статья в английский | MEDLINE | ID: covidwho-2154694

Реферат

Coronavirus disease 2019 (COVID-19) is an extremely contagious illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Early disease recognition of COVID-19 is crucial not only for prompt diagnosis and treatment of the patients, but also for effective public health surveillance and response. The reverse transcription-polymerase chain reaction (RT-PCR) is the most common method for the detection of SARS-CoV-2 viral mRNA and is regarded as the gold standard test for COVID-19. However, this test and those for antibodies (IgM and IgG) and antigens have certain limitations (e.g., by yielding false-negative and false-positive results). We have developed an RNA fluorescence in situ hybridization (FISH) method for high-sensitivity detection of SARS-CoV-2 mRNAs in HEK 293T cell cultures as a model. After transfection of HEK 293T cells with plasmids, Spike (S)/envelope (E) proteins and their mRNAs were clearly detected inside the cells. In addition, hybridization time could be reduced to 2 hours for faster detection when probe concentration was increased. Our approach might thus significantly improve the sensitivity and specificity of SARS-CoV-2 detection and be widely applied for the high-sensitivity single-molecular detection of other RNA viruses (e.g., Middle East respiratory syndrome coronavirus (MERS-CoV), Hepatitis A virus, all influenza viruses, and human immunodeficiency virus (HIV)) in various types of samples including tissue, body fluid, blood, and water. RNA FISH can also be utilized for the detection of DNA viruses (e.g., Monkeypox virus, human papillomavirus (HPV), and cytomegalovirus (CMV)) by detection of their mRNAs inside cells or body fluid.


Тема - темы
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19 Testing , Clinical Laboratory Techniques/methods , RNA, Messenger/genetics , In Situ Hybridization, Fluorescence , HEK293 Cells , Immunoglobulin M , Immunoglobulin G , Water
4.
Front Cell Infect Microbiol ; 12: 902914, 2022.
Статья в английский | MEDLINE | ID: covidwho-2154670

Реферат

Identification of the main SARS-CoV-2 variants in real time is of interest to control the virus and to rapidly devise appropriate public health responses. The RT-qPCR is currently considered to be the reference method to screen SARS-CoV-2 mutations, but it has some limitations. The multiplexing capability is limited when the number of markers to detect increases. Moreover, the performance of this allele-specific method may be impacted in the presence of new mutations. Herein, we present a proof-of-concept study of a simple molecular assay to detect key SARS-CoV-2 mutations. The innovative features of the assay are the multiplex asymmetric one-step RT-PCR amplification covering different regions of SARS-CoV-2 S gene and the visual detection of mutations on a lateral flow DNA microarray. Three kits (Kit 1: N501Y, E484K; Kit 2: L452R, E484K/Q; Kit 3: K417N, L452R, E484K/Q/A) were developed to match recommendations for surveillance of SARS-CoV-2 variants between January and December 2021. The clinical performance was assessed using RNA extracts from 113 SARS-CoV-2-positive samples with cycle thresholds <30, and results demonstrated that our assay allows specific and sensitive detection of mutations, with a performance comparable to that of RT-qPCR. The VAR-CoV assay detected four SARS-CoV-2 targets and achieved specific and sensitive screening of spike mutations associated with the main variants of concern, with a performance comparable to that of RT-qPCR. With well-defined virus sequences, this assay can be rapidly adapted to other emerging mutations; it is a promising tool for variant surveillance.


Тема - темы
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Mutation , SARS-CoV-2/genetics
5.
Front Cell Infect Microbiol ; 12: 887754, 2022.
Статья в английский | MEDLINE | ID: covidwho-2154665

Реферат

Candida auris continues to be a global threat for infection and transmission in hospitals and long-term care facilities. The emergence of SARS-CoV-2 has rerouted attention and resources away from this silent pandemic to the frontlines of the ongoing COVID-19 disease. Cases of C. auris continue to rise, and clinical laboratories need a contingency plan to prevent a possible outbreak amid the COVID-19 pandemic. Here, we introduce a two-tier Candida auris surveillance program that includes, first, a rapid qualitative rt-PCR for the identification of high-risk patients and, second, a method to analyze the isolated C. auris for strain typing using the Fourier-Transform Infrared spectroscopy. We have performed this two-tier surveillance for over 700 at-risk patients being admitted into our hospital and have identified 28 positive specimens (4%) over a 1-year period. Strain typing analysis by the IR spectrum acquisition typing method, supplemented by whole genome sequencing, has shown grouping of two significant clusters. The majority of our isolates belong to circulating African lineage associated with C. auris Clade III and an isolated strain grouping differently belonging to South Asian lineage C. auris Clade I. Low numbers of genomic variation point to local and ongoing transmission within the Los Angeles area not specifically within the hospital setting. Collectively, clinical laboratories having the ability to rapidly screen high-risk patients for C. auris and to participate in outbreak investigations by offering strain typing will greatly assist in the control of C. auris transmission within the hospital setting.


Тема - темы
COVID-19 , Candidiasis , Algorithms , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Candida , Humans , Pandemics , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics
6.
Euro Surveill ; 27(43)2022 10.
Статья в английский | MEDLINE | ID: covidwho-2154580

Реферат

BackgroundTracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective.AimWe demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters.MethodsGenomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021.ResultsCluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf.ConclusionIGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.


Тема - темы
COVID-19 , Communicable Diseases, Imported , Humans , SARS-CoV-2/genetics , Travel , Communicable Diseases, Imported/epidemiology , COVID-19/epidemiology , Phylogeny , Contact Tracing , Germany/epidemiology , Genomics
7.
Lancet Glob Health ; 10(12): e1855-e1859, 2022 Dec.
Статья в английский | MEDLINE | ID: covidwho-2150878

Реферат

Data sharing in research is fraught with controversy. Academic success is premised on competitive advantage, with research teams protecting their research findings until publication. Research funders, by contrast, often require data sharing. Beyond traditional research and funding requirements, surveillance data have become contentious. Public health emergencies involving pathogens require intense genomic surveillance efforts and call for the rapid sharing of data on the basis of public interest. Under these circumstances, timely sharing of data becomes a matter of scientific integrity. During the COVID-19 pandemic, the transformative potential of genomic pathogen data sharing became obvious and advanced the debate on data sharing. However, when the genomic sequencing data of the omicron (B.1.1.529) variant was shared and announced by scientists in southern Africa, various challenges arose, including travel bans. The scientific, economic, and moral impact was catastrophic. Yet, travel restrictions failed to mitigate the spread of the variant already present in countries outside Africa. Public perceptions of the negative effect of data sharing are detrimental to the willingness of research participants to consent to sharing data in postpandemic research and future pandemics. Global health governance organisations have an important role in developing guidance on responsible sharing of genomic pathogen data in public health emergencies.


Тема - темы
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Pandemics , COVID-19/epidemiology , Emergencies , Information Dissemination , Genomics , Africa, Southern
9.
N Z Med J ; 135(1559): 53-58, 2022 Aug 05.
Статья в английский | MEDLINE | ID: covidwho-2147482

Реферат

AIM: To compare detection of SARS-CoV-2 from paired nasopharyngeal swabs (NPS) and saliva using molecular methods in common use for testing swabs in New Zealand. METHOD: Samples from individuals testing positive for SARS-CoV-2 in Auckland, Wellington and Dunedin were tested at the local laboratories using methods previously established for these sample types. RESULTS: One hundred and ninety-six paired samples from unique individuals were tested, with 46 (23%) positive from either sample type, of which 43/46 (93%) tested positive from NPS, and 42/46 (91%) from saliva, indicating no significant difference in performance between sample types (p=0.69). The average Δ Ct between saliva and nasopharyngeal swabs overall across the sample set was 0.22 cycles, indicating excellent concordance; however, the difference between NPS and saliva collected from the same individual was quite variable with up to 19 cycles difference between the sample types. CONCLUSION: We found that saliva is an equivalent sample type to nasopharyngeal swab for the detection of SARS-CoV-2 in our laboratories using multiple assay combinations and is suitable for use as a diagnostic and surveillance test for selected groups of individuals.


Тема - темы
COVID-19 , Nucleic Acids , COVID-19/diagnosis , Clinical Laboratory Techniques/methods , Humans , Nasopharynx , New Zealand , SARS-CoV-2/genetics , Saliva , Specimen Handling/methods
10.
Klin Lab Diagn ; 67(11): 678-684, 2022 Nov 14.
Статья в английский | MEDLINE | ID: covidwho-2146786

Реферат

The issues of laboratory diagnostics have been relevant since the first days of the SARS-CoV-2 pandemic and play a key role in the fight against the spread of a new coronavirus infection. A direct method for the etiological diagnosis of the causative agent of COVID-19 is the detection of SARS-CoV-2 RNA using the nucleic acid amplification method. In the context of a pandemic and the mass appeal of patients for medical care, the issues of ensuring the quality of ongoing molecular biological studies at all stages (preanalytical, analytical, postanalytical) become the most relevant. the results and timing of the study not only affect the diagnosis and treatment tactics of a particular patient, but are also the basis for the introduction of anti-epidemic measures, the adoption of organizational measures. The study is to summarize the experience in creating an effective and reliable system for managing the quality of molecular biological research in a pandemic using the example of a federal budgetary healthcare institution. The experience of the laboratory of a federal healthcare institution in the context of the COVID-19 pandemic was analyzed, errors were analyzed at the preanalytical, analytical and postanalytical stages of PCR studies with the identification of quality criteria, the impact on which significantly leads to quality improvement. The quality control system for PCR studies is based on the development of regulatory documents and instructions for the patient and laboratory staff, registration of all documents in a single information system with access to information from all structural divisions, with the possibility of uploading data to the patient's personal account on the institution's website. Quality indicators of all stages of PCR studies and measures that significantly affect the quality of laboratory studies were identified; Measures have been identified to reduce the turnaround time of a PCR test: distribution of biomaterial flows, optimization of operators' work, purchase of additional equipment, a patient feedback system, and an infection control information system. The obtained results make it possible to create a reliable quality control system, minimize the risk of obtaining erroneous research results, optimizing the work of the clinical diagnostic laboratory and increasing its productivity.


Тема - темы
COVID-19 , Humans , COVID-19/diagnosis , COVID-19/epidemiology , Pandemics , RNA, Viral , SARS-CoV-2/genetics , Polymerase Chain Reaction
11.
Klin Lab Diagn ; 67(11): 672-677, 2022 Nov 14.
Статья в английский | MEDLINE | ID: covidwho-2146783

Реферат

COVID-19 is a disease caused by the new coronavirus SARS-CoV-2. Outbreaks were first reported in China on December 31, 2019. Exactly one month later, the WHO declared the outbreak a public health emergency of international concern, and on March 11, it was declared a pandemic. In February, the infection began to spread rapidly to various countries, with Europe declared the center. By April 17, 2020, cases had been confirmed in all subjects of the Russian Federation. At the beginning of September 2020, the number of cases exceeded one million; at November 19, two million; at December 26, three million. At February 10, 2021, four million; at May 23, five million; at July 20, six million; at September 5, seven million; at October 18, eight million; at November 13, nine million; and at December 12, 2021, ten million. The rapid spread of the virus, accompanied by a significant increase in the number of infections and deaths. A total of about 18.6 million cases were recorded at the end of the first half of 2022. The total number of deaths from coronavirus in Russia at that time was 382,313 (2.06% of all cases). The number of tests performed by various analytical methods amounted to over 274, 5 million, i.e. 1.9 million per 1 million population. The rapid spread and the increase in new infections caused by SARS-CoV-2 made it necessary to use new epidemiological and diagnostic approaches based on fast, accurate and reliable technology for detecting the infectious agent. One such virus detection method is polymerase chain reaction with reverse transcription and real-time detection of the results. The review presents the domestic market offerings of PCR diagnostic kits and provides their comparative consumer characteristics.


Тема - темы
COVID-19 , Reverse Transcription , Humans , COVID-19/diagnosis , COVID-19/epidemiology , SARS-CoV-2/genetics , Reverse Transcriptase Polymerase Chain Reaction , Real-Time Polymerase Chain Reaction
12.
Klin Lab Diagn ; 67(11): 663-667, 2022 Nov 14.
Статья в английский | MEDLINE | ID: covidwho-2146780

Реферат

The coronavirus infection continues to spread around the world. In this regard, the purpose of this work was: to develop a set of reagents for the qualitative detection of SARS-CoV-2 virus RNA. The set was developed by CJSC «Ecolab¼, 20 positive samples were used to develop the kit. The research method consisted of several stages: isolation of SARS-CoV-2 RNA, RNA reverse transcription reaction and PCR amplification of cDNA with simultaneous detection of the result in real time. The main characteristics of the kit: analytical sensitivity - 100%, specificity - 100%, accuracy - 100%. Thus, our method for diagnosing a new coronavirus infection based on real-time RT-PCR makes it possible to qualitatively and quickly detect betacoronavirus RNA in clinical material from patients and healthy individuals with suspected coronavirus infection and other symptoms of SARS.


Тема - темы
COVID-19 , SARS-CoV-2 , Humans , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/genetics , RNA, Viral/analysis , Indicators and Reagents , Sensitivity and Specificity , COVID-19/diagnosis , Real-Time Polymerase Chain Reaction
13.
MEDICC Rev ; 24(3-4): 18-23, 2022 Oct 31.
Статья в английский | MEDLINE | ID: covidwho-2146581

Реферат

INTRODUCTION: In November 2021, omicron-a new SARS-CoV-2 variant-was identified in South Africa and almost immediately, WHO declared it a 'variant of concern'. In view of its rapid worldwide spread and its imminent introduction in Cuba, genomic surveillance was strengthened. OBJECTIVE: Describe cases during the first eight epidemiological weeks (epiweeks) of SARS-CoV-2 infection attributable to omicron variant in Cuba by clinical and epidemiological variables. METHODS: From epiweek 48, 2021 to epiweek 4, 2022, 288 nasopharyngeal swabs were processed for sequencing of a 1836 bp fragment of the S gene. Variants were identified according to GISAID database and confirmed by phylogenetic analysis. Variants' association with clinical and epidemiological outcomes was assessed. RESULTS: The first cases of omicron variant were imported, mostly from African countries and the United States. During the period studied, omicron was detected in 83.0% (239/288) of cases processed, while the delta variant was found in 17.0% (49/288). Most persons infected with omicron were symptomatic (63.2%; 151/239) and fully vaccinated (65.3%; 156/239); severe cases and deaths occurred mainly among patients aged ≥65 years (92.9%; 13/14), and 12 of these deaths occurred in fully vaccinated persons (92.3%; 12/13). Omicron spread rapidly throughout the country (from 10% of cases in epiweek 48, 2021, to 100% by epiweek 4, 2022), displacing the formerly predominant delta variant. CONCLUSIONS: Omicron's rapid expansion in Cuba was associated with increased incidence but not with a higher case fatality rate. The relatively milder disease in those infected with this variant could be influenced by the high vaccination coverage, along with the natural immunity acquired as a consequence of previous virus infection.


Тема - темы
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Phylogeny , Cuba/epidemiology , COVID-19/epidemiology
14.
Elife ; 112022 11 23.
Статья в английский | MEDLINE | ID: covidwho-2145048

Реферат

Transmission of SARS-CoV-2 from humans to other species threatens wildlife conservation and may create novel sources of viral diversity for future zoonotic transmission. A variety of computational heuristics have been developed to pre-emptively identify susceptible host species based on variation in the angiotensin-converting enzyme 2 (ACE2) receptor used for viral entry. However, the predictive performance of these heuristics remains unknown. Using a newly compiled database of 96 species, we show that, while variation in ACE2 can be used by machine learning models to accurately predict animal susceptibility to sarbecoviruses (accuracy = 80.2%, binomial confidence interval [CI]: 70.8-87.6%), the sites informing predictions have no known involvement in virus binding and instead recapitulate host phylogeny. Models trained on host phylogeny alone performed equally well (accuracy = 84.4%, CI: 75.5-91.0%) and at a level equivalent to retrospective assessments of accuracy for previously published models. These results suggest that the predictive power of ACE2-based models derives from strong correlations with host phylogeny rather than processes which can be mechanistically linked to infection biology. Further, biased availability of ACE2 sequences misleads projections of the number and geographic distribution of at-risk species. Models based on host phylogeny reduce this bias, but identify a very large number of susceptible species, implying that model predictions must be combined with local knowledge of exposure risk to practically guide surveillance. Identifying barriers to viral infection or onward transmission beyond receptor binding and incorporating data which are independent of host phylogeny will be necessary to manage the ongoing risk of establishment of novel animal reservoirs of SARS-CoV-2.


The COVID-19 pandemic affects humans, but also many of the animals we interact with. So far, humans have transmitted the SARS-CoV-2 virus to pet dogs and cats, a wide range of zoo animals, and even wildlife. Transmission of SARS-CoV-2 from humans to animals can lead to outbreaks amongst certain species, which can endanger animal populations and create new sources of human infections. Thus, careful monitoring of animal infections may help protect both animals and humans. Identifying which animals are susceptible to SARS-CoV-2 would help scientists monitor these species for outbreaks and viral circulation. Unfortunately, testing whether SARS-CoV-2 can infect different species in the laboratory is both time-consuming and expensive. To overcome this obstacle, researchers have used computational methods and existing data about the structure and genetic sequences of ACE2 receptors ­ the proteins on the cell surface that SARS-CoV-2 uses to enter the cell ­ to predict SARS-COV-2 susceptibility in different species. However, it remained unclear how accurate this approach was at predicting susceptibility in different animals, or whether their correct predictions indicated causal links between ACE2 variability and SARS-CoV-2 susceptibility. To assess the usefulness of this approach, Mollentze et al. started by using data on the ACE2 receptors from 96 different species and building a machine learning model to predict how susceptible those species might be to SARS-CoV-2. The susceptibility of these species had either been observed in natural infections ­ in zoos, for example ­ or had been assessed in the laboratory, so Mollentze et al. were able to use this information to determine how good both their model and previous approaches based on the sequence of ACE2 receptors were. The results showed that while the model was quite accurate (it correctly predicted susceptibility to SARS-CoV-2 about 80% of the time), its predictions were based on regions of the ACE2 receptors that were not known to interact with the virus. Instead, the regions that the machine learning model relied on were ones that tend to vary more the more distantly related two species are. This indicates that existing computational approaches are likely not relying on information about how ACE2 receptors interact with SARS-CoV-2 to predict susceptibility. Instead, they are simply using information on how closely related the different animal species are, which is much easier to source than data about ACE2 receptors. Indeed, the sequences of the ACE2 receptors in many species are unknown and the species for which this information is available come only from a few geographic areas. Mollentze et al. also showed that limiting the predictions about susceptibility to these species could mislead scientists when deciding which species and geographic areas to surveil for possible viral circulation. Instead, it may be more effective and cost-efficient to use animal relatedness to predict susceptibility to SARS-CoV-2. This makes it possible to make predictions for nearly all mammals, while being just as accurate as models based on ACE2 receptor data. However, Mollentze et al. point out that this approach would still fail to narrow down the number of animals that need to be monitored enough for it to be practical. Considering additional factors like how often the animals interact with humans or how prone they are to transmit the virus among themselves may help narrow it down more. Further research is therefore needed to identify the best multifactor approaches to identifying which animal populations should be monitored.


Тема - темы
Angiotensin-Converting Enzyme 2 , COVID-19 , Animals , Humans , Angiotensin-Converting Enzyme 2/genetics , COVID-19/diagnosis , COVID-19/genetics , Retrospective Studies , SARS-CoV-2/genetics , Disease Susceptibility
16.
Indian J Public Health ; 66(Supplement): S36-S40, 2022 Nov.
Статья в английский | MEDLINE | ID: covidwho-2144164

Реферат

Background: The incidence of breakthrough infection with the emergence of new variants of concern of SARS-CoV-2 is posing a threat, and it is pertinent to understand the role of vaccines in protecting the elderly and people with comorbidities. Objective: The present study was undertaken to understand the natural history of SARS-CoV-2 infection in a closed cohort of the elderly population in an old-age home who have received two doses of COVID-19 vaccination. The study has also undertaken genomic sequencing to identify SARS-CoV-2 variants of concern from an academic perspective. Materials and Methods: A prospective observational study was conducted from March to August 2021 among residents of 11 old-age homes in Kerala who were vaccinated with 2 doses of the COVID-19 vaccine, from 2 weeks following vaccination. Samples with a threshold cycle value of <25 were subjected to targeted sequencing of the spike protein receptor-binding domain coding region. Results: Among the 479 vaccinated individuals, 86 (17.95%) turned positive during the follow-up period. The mean duration of symptoms was 3-5 days, and no hospitalization was required. A phylogenetic analysis of the nucleotide sequences from the samples indicated B.1.617.2 lineage representing the Delta strain. Conclusion: The evidence supports maximizing the vaccine coverage among vulnerable groups to prevent hospitalization and death rate on the verge of the emergence of new variants of SARS-CoV-2.


Тема - темы
COVID-19 , SARS-CoV-2 , Aged , Humans , Infant, Newborn , SARS-CoV-2/genetics , COVID-19 Vaccines , Phylogeny , India/epidemiology
17.
J Microbiol Biotechnol ; 32(9): 1073-1085, 2022 Sep 28.
Статья в английский | MEDLINE | ID: covidwho-2144004

Реферат

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has continued for over 2 years, following the outbreak of coronavirus-19 (COVID-19) in 2019. It has resulted in enormous casualties and severe economic crises. The rapid development of vaccines and therapeutics against SARS-CoV-2 has helped slow the spread. In the meantime, various mutations in the SARS-CoV-2 have emerged to evade current vaccines and therapeutics. A better understanding of SARS-CoV-2 pathogenesis is a prerequisite for developing efficient, advanced vaccines and therapeutics. Since the outbreak of COVID-19, a tremendous amount of research has been conducted to unveil SARSCoV-2 pathogenesis, from clinical observations to biochemical analysis at the molecular level upon viral infection. In this review, we discuss the molecular mechanisms of SARS-CoV-2 propagation and pathogenesis, with an update on recent advances.


Тема - темы
COVID-19 , Vaccines , Humans , Pandemics/prevention & control , SARS-CoV-2/genetics
18.
Viruses ; 14(11)2022 Nov 12.
Статья в английский | MEDLINE | ID: covidwho-2143711

Реферат

SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April-December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy.


Тема - темы
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/epidemiology , Italy/epidemiology
19.
Viruses ; 14(9)2022 09 14.
Статья в английский | MEDLINE | ID: covidwho-2143631

Реферат

In this retrospective, single-center study, we conducted an analysis of 13,699 samples from different individuals obtained from the Federal Research Center of Fundamental and Translational Medicine, from 1 April to 30 May 2020 in Novosibirsk region (population 2.8 million people). We identified 6.49% positive for SARS-CoV-2 cases out of the total number of diagnostic tests, and 42% of them were from asymptomatic people. We also detected two asymptomatic people, who had no confirmed contact with patients with COVID-19. The highest percentage of positive samples was observed in the 80+ group (16.3%), while among the children and adults it did not exceed 8%. Among all the people tested, 2423 came from a total of 80 different destinations and only 27 of them were positive for SARS-CoV-2. Out of all the positive samples, 15 were taken for SARS-CoV-2 sequencing. According to the analysis of the genome sequences, the SARS-CoV-2 variants isolated in the Novosibirsk region at the beginning of the pandemic belonged to three phylogenetic lineages according to the Pangolin classification: B.1, B.1.1, and B.1.1.129. All Novosibirsk isolates contained the D614G substitution in the Spike protein, two isolates werecharacterized by an additional M153T mutation, and one isolate wascharacterized by the L5F mutation.


Тема - темы
COVID-19 , SARS-CoV-2 , Adult , COVID-19/epidemiology , Child , Genome, Viral , Genomics , Humans , Mutation , Pandemics , Phylogeny , Retrospective Studies , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
20.
Front Immunol ; 13: 1001070, 2022.
Статья в английский | MEDLINE | ID: covidwho-2142020

Реферат

Severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) is the causative virus of the pandemic coronavirus disease 2019 (COVID-19). Evaluating the immunological factors and other implicated processes underlying the progression of COVID-19 is essential for the recognition and then the design of efficacious therapies. Therefore, we analyzed RNAseq data obtained from PBMCs of the COVID-19 patients to explore coding and non-coding RNA diagnostic immunological panels. For this purpose, we integrated multiple RNAseq data and analyzed them overall as well as by considering the state of disease including severe and non-severe conditions. Afterward, we utilized a co-expressed-based machine learning procedure comprising weighted-gene co-expression analysis and differential expression gene as filter phase and recursive feature elimination-support vector machine as wrapper phase. This procedure led to the identification of two modules containing 5 and 84 genes which are mostly involved in cell dysregulation and innate immune suppression, respectively. Moreover, the role of vitamin D in regulating some classifiers was highlighted. Further analysis disclosed the role of discriminant miRNAs including miR-197-3p, miR-150-5p, miR-340-5p, miR-122-5p, miR-1307-3p, miR-34a-5p, miR-98-5p and their target genes comprising GAN, VWC2, TNFRSF6B, and CHST3 in the metabolic pathways. These classifiers differentiate the final fate of infection toward severe or non-severe COVID-19. The identified classifier genes and miRNAs may help in the proper design of therapeutic procedures considering their involvement in the immune and metabolic pathways.


Тема - темы
COVID-19 , MicroRNAs , Humans , COVID-19/diagnosis , COVID-19/genetics , MicroRNAs/genetics , MicroRNAs/metabolism , SARS-CoV-2/genetics , Machine Learning
Критерии поиска