首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 12 毫秒
1.
    
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.

High mutation rates of RNA viruses enable adaptation to hosts at a staggering pace (14). Nevertheless, robust sequence conservation indicates that purifying selection is the principal force shaping the evolution of virus populations, with positive selection affecting only relatively small subsets of sites directly involved in virus−host coevolution (58). The fate of a novel zoonotic virus is, in part, determined by the race between public health intervention and virus diversification. Even intermittent periods of positive selection can result in lasting immune evasion, leading to oscillations in the size of the susceptible population and, ultimately, a regular pattern of repeating epidemics, as has been amply demonstrated for influenza (911).During the current coronavirus pandemic (COVID-19), understanding the degree and dynamics of the diversification of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) and identification of sites subject to positive selection are essential for establishing practicable, proportionate public health responses, from guidelines on isolation and quarantine to vaccination (12). To investigate the evolution of SARS-CoV-2, we collected all available SARS-Cov-2 genomes as of January 8, 2021, and constructed a global phylogenetic tree using a “divide and conquer” approach. Patterns of repeated mutations fixed along the tree were analyzed in order to identify the sites subject to positive selection. These sites form a network of potential epistatic interactions. Analysis of the putative adaptive mutations provides for the identification of signatures of evolutionary partitions of SARS-CoV-2. The dynamics of these partitions over the course of the pandemic reveals alternating periods of globalization and regional diversification.  相似文献   

2.
    
Italy’s second wave of SARS-CoV-2 has hit hard, with more than three million cases and over 100,000 deaths, representing an almost ten-fold increase in the numbers reported by August 2020. Herein, we present an analysis of 6515 SARS-CoV-2 sequences sampled in Italy between 29 January 2020 and 1 March 2021 and show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became the dominant variant in November 2020, when cases peaked at 40,000 a day, but since January 2021 this is being replaced by the B.1.1.7 ‘variant of concern’. In addition, we report a sudden increase in another documented variant of concern—lineage P.1—from December 2020 onwards, most likely caused by a single introduction into Italy. We again highlight how international importations drive the emergence of new lineages and that genome sequencing should remain a top priority for ongoing surveillance in Italy.  相似文献   

3.
4.
    
The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolved into a worldwide outbreak, with the first Polish cases in February/March 2020. This study aimed to investigate the molecular epidemiology of the circulating virus lineages between March 2020 and February 2021. We performed variant identification, spike mutation pattern analysis, and phylogenetic and evolutionary analyses for 1106 high-coverage whole-genome sequences, implementing maximum likelihood, multiple continuous-time Markov chain, and Bayesian birth–death skyline models. For time trends, logistic regression was used. In the dataset, virus B.1.221 lineage was predominant (15.37%), followed by B.1.258 (15.01%) and B.1.1.29 (11.48%) strains. Three clades were identified, being responsible for 74.41% of infections over the analyzed period. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. In population dynamics inferences, three periods with exponential increase in infection were observed, beginning in March, July, and September 2020, respectively, and were driven by different virus clades. Additionally, a notable increase in infections caused by the B.1.1.7 lineage since February 2021 was noted. Over time, the virus accumulated mutations related to optimized transmissibility; therefore, faster dissemination is reflected by the second wave of epidemics in Poland.  相似文献   

5.
糖尿病是一种慢性代谢性疾病,其特征为多种代谢及血管异常,会影响机体对病原体的反应,大多数现有证据表明,无论是1型糖尿病(T1DM)还是2型糖尿病(T2DM)患者,新冠肺炎的严重程度和死亡率都有显著增加,新型冠状病毒肺炎(COVID-19)的存在也对糖尿病的治疗产生了一定的影响。本文对COVID-19及糖尿病的相互作用机...  相似文献   

6.
We introduce a conceptual bridge between the previously unlinked fields of phylogenetics and mathematical spatial ecology, which enables the spatial parameters of an emerging epidemic to be directly estimated from sampled pathogen genome sequences. By using phylogenetic history to correct for spatial autocorrelation, we illustrate how a fundamental spatial variable, the diffusion coefficient, can be estimated using robust nonparametric statistics, and how heterogeneity in dispersal can be readily quantified. We apply this framework to the spread of the West Nile virus across North America, an important recent instance of spatial invasion by an emerging infectious disease. We demonstrate that the dispersal of West Nile virus is greater and far more variable than previously measured, such that its dissemination was critically determined by rare, long-range movements that are unlikely to be discerned during field observations. Our results indicate that, by ignoring this heterogeneity, previous models of the epidemic have substantially overestimated its basic reproductive number. More generally, our approach demonstrates that easily obtainable genetic data can be used to measure the spatial dynamics of natural populations that are otherwise difficult or costly to quantify.  相似文献   

7.
    
Blocking IL-6 pathways with sarilumab, a fully human anti–IL-6R antagonist may potentially curb the inflammatory storm of SARS-CoV2. In the present emergency scenario, we used “off-label” sarilumab in 5 elderly patients in life-threatening condition not candidates to further active measures. We suggest that sarilumab can modulate severe COVID-19-associated Cytokine Release Syndrome.  相似文献   

8.
    
Complete heart block (CHB) is a serious health condition, and polyarteritis nodosa (PAN) is an important autoimmune disease. In the COVID-19 pandemy, several vaccines were developed for the COVID-19 disease that shown several side effects, and some of these complications are still unknown. This is the first report of CHB in a patient with history of PAN after COVID-19 vaccination. A 68-year-old man with a history of PAN referred to our hospital, complaining of presyncope episodes and dizziness after receiving a COVID-19 vaccine. Physical examination, laboratory tests, and transthoracic echocardiography were normal. In his electrocardiogram, a narrow QRS complex, AV dissociation, and junctional escape rhythm were seen. Coronary angiography showed a mild coronary artery disease. The patient, suffering from PAN for years, was hypothesized due to CHB a few days after COVID-19 vaccination. This case report suggests that COVID-19 vaccines may interrupt the conduction system of the heart and the fact that underlying PAN may predispose to CHB following COVID-19 vaccination. Further studies are needed to accurately assess a possible association between PAN, CHB, and COVID-19 vaccines.  相似文献   

9.
[摘要]?新型冠状病毒肺炎(新冠肺炎)疫情自2019年12月暴发以来,已形成全球大流行,严重危害人类生命安全。新型冠状病毒核酸检测阳性是确诊感染的首要诊断标准,核酸检测是有效排查、精准防控的重要手段。医疗机构作为保障人民生命安全的重要场所、疫情防控的前线,建设相对固定的核酸采样站是开展正常诊疗的重要保障。随着我国新冠肺炎疫情防控从应急状态转为常态化“后疫情时代”,大规模核酸采集已不再常规开展,但类似传染病仍有暴发可能,诸如批量检测抗原等类似的生物样本采集应对模式,亦有相应的应用空间。本文结合解放军总医院第五医学中心在新型冠状病毒流行期间建设核酸采样站的实践经验,分析核酸采样站的建设要点与注意事项,从核酸采样站的功能分区、器材配备、配套设施、运行保障等方面提出建设性意见,并在流程、布局等方面与其他集中采样站点建设模式进行比较,分析优劣,以期在应对类似突发公共卫生事件时为建设科学合理的采样站提供有益参考。  相似文献   

10.
    
To clarify the effect of aspirin on mortality and viral duration in adults infected with respiratory syndrome coronavirus 2 (SARS-Cov-2).After propensity score-matched (PSM) case-control analyses 24 pairs of patients were enrolled and followed up for 2 months. Both 30-day and 60-day mortality in the aspirin group were significantly lower than that in the non-aspirin group (P = .021 and P = .030, respectively). The viral duration time between the 2 groups was not significantly different (P = .942).Among adults (with hypertension, cardiovascular diseases) infected with SARS-Cov-2, low-dose aspirin medication (100 mg/day) was associated with lower risk of mortality compared with non-aspirin users.  相似文献   

11.
Since December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pathogen of coronavirus disease 2019 (COVID-19), has posed a serious threat to global health and is currently causing a major pandemic. While patients typically present with fever and a respiratory illness, mounting evidence indicates that patients might also report extra-pulmonary manifestations, including those affecting the liver and gastrointestinal tract. This involvement may have important implications to the disease management, transmission, and prognosis, especially in patients with pre-existing hepatic or digestive co-morbidities.In this review, the characteristics and possible explanations of hepatic and gastrointestinal involvement caused by SARS-CoV-2 infection are summarized, adding to our knowledge of the spectrum of COVID-19. In addition, preventive measures implemented in endoscopy departments to prevent further dissemination of SARS-CoV-2 infection are proposed.  相似文献   

12.
Background and aimsProbiotics can support the body’s systems in fighting viral infections. This review is aimed to focus current knowledge about the use of probiotics as adjuvant therapy for COVID-19 patients.MethodsWe performed an extensive research using the PubMed-LitCovid, Cochrane Library, Embase databases, and conducting manual searches on Google Scholar, Elsevier Connect, Web of Science about this issue.ResultsWe have found several papers reporting data about the potential role of probiotics as well as contrasting experimental data about it.ConclusionsMost data show good results demonstrating that probiotics can play a significant role in fighting SARS-CoV-2 infection, also compared with their use in the past for various diseases. They seem effective in lowering inflammatory status, moreover in patients with chronic comorbidities such as cancer and diabetes, improving clinical outcomes.  相似文献   

13.
    
BackgroundAnalyses of diagnostic performance of SARS-CoV-2 antigen rapid diagnostic tests (AG-RDTs) based on long-term data, population subgroups and many AG-RDT types are scarce.AimWe aimed to analyse sensitivity and specificity of AG-RDTs for subgroups based on age, incidence, sample type, reason for test, symptoms, vaccination status and the AG-RDT’s presence on approved lists.MethodsWe included AG-RDT results registered in Czechia’s Information System for Infectious Diseases between August and November 2021. Subpopulations were analysed based on 346,000 test results for which a confirmatory PCR test was recorded ≤ 3 days after the AG-RDT; 38 AG-RDTs with more than 100 PCR-positive and 300 PCR-negative samples were individually evaluated.ResultsAverage sensitivity and specificity were 72.4% and 96.7%, respectively. We recorded lower sensitivity for age groups 0–12 (65.5%) and 13–18 years (65.3%). The sensitivity level rose with increasing SARS-CoV-2 incidence from 66.0% to 76.7%. Nasopharyngeal samples had the highest sensitivity and saliva the lowest. Sensitivity for preventive reasons was 63.6% vs 86.1% when testing for suspected infection. Sensitivity was 84.8% when one or more symptoms were reported compared with 57.1% for no symptoms. Vaccination was associated with a 4.2% higher sensitivity. Significantly higher sensitivity levels pertained to AG-RDTs on the World Health Organization Emergency Use List (WHO EUL), European Union Common List and the list of the United Kingdom’s Department of Health and Social Care.ConclusionAG-RDTs from approved lists should be considered, especially in situations associated with lower viral load. Results are limited to SARS-CoV-2 delta variant.  相似文献   

14.
15.
    
Evaluation of population‐based COVID‐19 control measures informs strategies to quell the current pandemic and reduce the impact of those yet to come. Effective COVID‐19 control measures may simultaneously reduce the incidence of other acute respiratory infections (ARIs) due to shared transmission modalities. To assess the impact of stay‐at‐home orders and other physical distancing measures on the prevalence of ARI‐related symptoms, we compared symptoms reported by prospective college cohorts enrolled during two consecutive academic years. ARI‐related symptoms declined following campus closure and implementation of stay‐at‐home orders, demonstrating the impact of population‐based physical distancing measures on control of a broad range of respiratory infections.  相似文献   

16.
新型冠状病毒(2019 severe acute respiratory syndrome coronavirus 2,SARS-Cov-2)感染引发的新型冠状病毒病(coronavirus disease 2019,COVID-19)患者的血液学改变很常见。研究发现感染初期可见外周血白细胞和淋巴细胞减少,CD4+T及CD8+T淋巴细胞显著减少,也可见血小板减少及血红蛋白下降。随着病情加重,淋巴细胞持续严重减少。中性粒细胞数增高、中性粒细胞/淋巴细胞比值升高及血红蛋白水平下降与疾病进展和预后不良关联。单核-巨噬细胞系统活化加重了肺和其他组织免疫损伤,导致D-二聚体升高、凝血酶原时间延长及血小板消耗增加。文章对COVID-19引起的造血异常及其可能机制进行综述。  相似文献   

17.
    
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has a major impact on transplant recipients, with mortality rates up to 20%. Therefore, the effect of established messenger RNA (mRNA)-based SARS-CoV-2 vaccines have to be evaluated for solid organ transplant patients (SOT) since they are known to have poor responses after vaccination. We investigated the SARS-CoV-2 immune response via SARS-CoV-2 IgG detection in 23 renal transplant recipients after two doses of the mRNA-based SARS-CoV-2 vaccine BNT162b2 following the standard protocol. The antibody response was evaluated once with an anti-SARS-CoV-2 IgG CLIA 15.8 +/− 3.0 days after the second dose. As a control, SARS-CoV-2 IgG was determined in 23 healthcare workers (HCW) and compared to the patient cohort. Only 5 of 23 (22%) renal transplant recipients were tested positive for SARS-CoV-2 IgG antibodies after the second dose of vaccine. In contrast, all 23 (100%) HCWs were tested positive for antibodies after the second dose. Thus, the humoral response of renal transplant recipients after two doses of the mRNA-based vaccine BNT162b2 (Pfizer-BioNTech, Kronach, Germany) is impaired and significantly lower compared to healthy controls (22% vs. 100%; p = 0.0001). Individual vaccination strategies might be beneficial in these vulnerable patients.  相似文献   

18.
    
IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease (COVID-19). People infected with SARS-CoV-2 may exhibit no or mild non-specific symptoms; thus, they may contribute to silent circulation of the virus among humans. Since SARS-CoV-2 RNA can be detected in stool samples, monitoring SARS-CoV-2 RNA in waste water (WW) has been proposed as a complementary tool to investigate virus circulation in human populations.AimTo test if the quantification of SARS-CoV-2 genomes in WW correlates with the number of symptomatic or non-symptomatic carriers.MethodWe performed a time-course quantitative analysis of SARS-CoV-2 by RT-qPCR in raw WW samples collected from several major WW treatment plants in Greater Paris. The study period was 5 March to 23 April 2020, including the lockdown period in France (from 17 March).ResultsWe showed that the increase of genome units in raw WW accurately followed the increase of human COVID-19 cases observed at the regional level. Of note, the viral genome could be detected before the epidemic grew massively (around 8 March). Equally importantly, a marked decrease in the quantities of genome units was observed concomitantly with the reduction in the number of new COVID-19 cases, 29 days following the lockdown.ConclusionThis work suggests that a quantitative monitoring of SARS-CoV-2 genomes in WW could generate important additional information for improved monitoring of SARS-CoV-2 circulation at local or regional levels and emphasises the role of WW-based epidemiology.  相似文献   

19.
    
To analyze the clinical characteristics and outcomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with sarcoidosis from a large multicenter cohort from Southern Europe and to identify the risk factors associated with a more complicated infection. We searched for patients with sarcoidosis presenting with SARS-CoV-2 infection (defined according to the European Centre for Disease Prevention and Control guidelines) among those included in the SarcoGEAS Registry, a nationwide, multicenter registry of patients fulfilling the American Thoracic Society/European Respiratory Society/World Association of Sarcoidosis and Other Granulomatous Disorders 1999 classification criteria for sarcoidosis. A 2:1 age-sex-matched subset of patients with sarcoidosis without SARS-CoV-2 infection was selected as control population. Forty-five patients with SARS-CoV-2 infection were identified (28 women, mean age 55 years). Thirty-six patients presented a symptomatic SARS-CoV-2 infection and 14 were hospitalized (12 required supplemental oxygen, 2 intensive care unit admission and 1 mechanical ventilation). Four patients died due to progressive respiratory failure. Patients who required hospital admission had an older mean age (64.9 vs. 51.0 years, p = 0.006), a higher frequency of baseline comorbidities including cardiovascular disease (64% vs. 23%, p = 0.016), diabetes mellitus (43% vs. 13%, p = 0.049) and chronic liver/kidney diseases (36% vs. 0%, p = 0.002) and presented more frequently fever (79% vs. 35%, p = 0.011) and dyspnea (50% vs. 3%, p = 0.001) in comparison with patients managed at home. Age- and sex-adjusted multivariate analysis identified the age at diagnosis of SARS-Cov-2 infection as the only independent variable associated with hospitalization (adjusted odds ratio 1.18, 95% conficence interval 1.04–1.35). A baseline moderate/severe pulmonary impairment in function tests was associated with a higher rate of hospitalization but the difference was not statistically significant (50% vs. 23%, p = 0.219). A close monitoring of SARS-CoV-2 infection in elderly patients with sarcoidosis, especially in those with baseline cardiopulmonary diseases and chronic liver or renal failure, is recommended. The low frequency of severe pulmonary involvement in patients with sarcoidosis from Southern Europe may explain the weak prognostic role of baseline lung impairment in our study, in contrast to studies from other geographical areas.  相似文献   

20.
    
New tools have been developed to distinguish the COVID-19 diagnosis from other viral infections presenting similar symptomatology and mitigate the lack of sensitivity of molecular testing. We previously identified a specific “sandglass” aspect on the white blood cells (WBC) scattergram of COVID-19 patients, as a highly reliable COVID-19 screening test (sensitivity: 85.9%, specificity: 83.5% and positive predictive value: 94.3%). We then decided to validate our previous data in a multicentric study.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号