Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

ObjectivesGenotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of the input material, the technology, and laboratory-specific implementation. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in genomic epidemiology studies. We aimed to establish clear and broadly applicable recommendations for reliable virus genotyping.MethodsWe established and used a sequencing data analysis workflow that reliably identifies and removes technical artefacts; such artefacts can result in miscalls when using alternative pipelines to process clinical samples and synthetic viral genomes with an amplicon-based genotyping approach. We evaluated the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination.ResultsWe found that at least 1000 viral genomes are necessary to confidently detect variants in the SARS-CoV-2 genome at frequencies of ≥10%. The broad applicability of our recommendations was validated in over 200 clinical samples from six independent laboratories. The genotypes we determined for clinical isolates with sufficient quality cluster by sampling location and period. Our analysis also supports the rise in frequencies of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was facilitated by travel during the summer of 2020.ConclusionsWe present much-needed recommendations for the reliable determination of SARS-CoV-2 genome sequences and demonstrate their broad applicability in a large cohort of clinical samples.     

Quantity and quality of complementary and alternative medicine recommendations in clinical practice guidelines for type 2 diabetes mellitus: A systematic review

AimsApproximately 70% of Americans with diabetes have used complementary and alternative medicine (CAM) in the past year. Healthcare providers often receive minimal training on these therapies and subsequently rely on clinical practice guidelines (CPGs) to supplement their knowledge about the safe and effective use of CAM for the treatment/management of type 2 diabetes mellitus (T2DM). The purpose of this systematic review is to determine the quantity and assess the quality of CAM recommendations in CPGs for the treatment and/or management of T2DM.Data synthesisMEDLINE, EMBASE, and CINAHL were systematically searched from 2009 to 2020, in addition to the Guidelines International Network and the National Center for Complementary and Integrative Health websites. CPGs containing treatment and/or management recommendations for T2DM were eligible; those with CAM recommendations were quality-assessed with the AGREE II instrument twice, once for the overall CPG and once for the CAM sections. Twenty-seven CPGs were deemed eligible, of which 7 made CAM recommendations. Mean scaled domain percentages were (overall, CAM): scope and purpose (89.7%, 79.8%), clarity of presentation (85.7%, 48.4%), stakeholder involvement (67.9%, 28.2%), applicability (54.8%, 20.2%), rigour of development (49.7%, 35.7%), and editorial independence (44.1%, 44.1%).ConclusionsQuality varied within and across CPGs; domain scores across CAM sections generally scored lower than the overall CPG. Given that CAM therapies for T2DM are only represented in one-quarter of eligible CPGs and are of lower quality, a knowledge gap exists for healthcare providers who seek evidence-based information on this topic in order to effectively counsel inquiring patients.     

The need for patient-focused therapy for children and teenagers with allergic rhinitis: a case-based review of current European practice

Allergic rhinitis is a common problem in childhood and adolescence, with a negative impact on the quality of life of patients and their families. The treatment modalities for allergic rhinitis include allergen avoidance, anti-inflammatory symptomatic treatment and allergen specific immunotherapy. In this review, four cases of children with allergic rhinitis are presented to illustrate how the recently published EAACI Guidelines on Pediatric Allergic Rhinitis can be implemented in clinical practice.     

Japanese guidelines for food allergy 2020

Five years have passed since the Japanese Pediatric Guideline for Food Allergy (JPGFA) was first revised in 2011 from its original version. As many scientific papers related to food allergy have been published during the last 5 years, the second major revision of the JPGFA was carried out in 2016. In this guideline, food allergies are generally classified into four clinical types: (1) neonatal and infantile gastrointestinal allergy, (2) infantile atopic dermatitis associated with food allergy, (3) immediate-type of food allergy (urticaria, anaphylaxis, etc.), and (4) special forms of immediate-type of food allergy such as food-dependent exercise-induced anaphylaxis and oral allergy syndrome (OAS). Much of this guideline covers the immediate-type of food allergy that is seen during childhood to adolescence. Infantile atopic dermatitis associated with food allergy type is especially important as the onset of most food allergies occurs during infancy. We have discussed the neonatal and infantile gastrointestinal allergy and special forms of immediate type food allergy types separately. Diagnostic procedures are highlighted, such as probability curves and component-resolved diagnosis, including the recent advancement utilizing antigen-specific IgE. The oral food challenge using a stepwise approach is recommended to avoid complete elimination of causative foods. Although oral immunotherapy (OIT) has not been approved as a routine treatment by nationwide insurance, we included a chapter for OIT, focusing on efficacy and problems. Prevention of food allergy is currently the focus of interest, and many changes were made based on recent evidence. Finally, the contraindication between adrenaline and antipsychotic drugs in Japan was discussed among related medical societies, and we reached an agreement that the use of adrenaline can be allowed based on the physician's discretion. In conclusion, this guideline encourages physicians to follow the principle to let patients consume causative foods in any way and as early as possible.     

Implementation of pregnancy weight management and obesity guidelines: a meta‐synthesis of healthcare professionals' barriers and facilitators using the Theoretical Domains Framework

Obesity in pregnancy is rising and is associated with severe health consequences for both the mother and the child. There is an increasing international focus on guidelines to manage the clinical risks of maternal obesity, and for pregnancy weight management. However, passive dissemination of guidelines is not effective and more active strategies are required for effective guideline implementation into practice. Implementation of guidelines is a form of healthcare professional behaviour change, and therefore implementation strategies should be based on appropriate behaviour change theory. This systematic review aimed to identify the determinants of healthcare professionals' behaviours in relation to maternal obesity and weight management. Twenty‐five studies were included. Data synthesis of the existing international qualitative and quantitative evidence base used the Theoretical Domains Framework to identify the barriers and facilitators to healthcare professionals' maternal obesity and weight management practice. The domains most frequently identified included ‘knowledge’, ‘beliefs about consequences’ and ‘environmental context and resources’. Healthcare professionals' weight management practice had the most barriers compared with any other area of maternal obesity practice. The results of this review will be used to inform the development of an intervention to support healthcare professional behaviour change.     

Comparison of Korean COPD Guideline and GOLD Initiative Report in Term of Acute Exacerbation: A Validation Study for Korean COPD Guideline

The purpose of this study was to compare the Korean COPD guideline to GOLD consensus report in terms of acute exacerbation. A total of 361 patients were enrolled in this study, and 16.9% of them experienced acute exacerbation during the follow-up. A total of 6.3% of patients in GOLD A, 9.5% in GOLD B, 7.7% in GOLD C and 17.0% of GOLD D experienced exacerbation during the first year of follow-up, respectively (P=0.09). There was no one who experienced exacerbation during the first year of follow-up in the Korean group ''ga''. The 12-month exacerbation rates of Korean group ''na'' and ''da'' were 4.5% and 16.0%, respectively (P<0.001). We explore the experience of exacerbation in patients with change of their risk group after applying Korean COPD guideline. A total of 16.0% of the patients who were reclassified from GOLD A to Korean group ''da'' experienced acute exacerbation,and 15.3% from GOLD B to Korean group ''da'' experienced acute exacerbation. In summary, the Korean COPD guideline is useful to differentiate the high risk from low risk for exacerbation in terms of spirometry. This indicates that application of Korean COPD guideline is appropriate to treat Korean COPD patients.     

2019年 NICE《成人原发性高血压管理指南》解读

高血压是脑卒中、心脏病、慢性肾衰竭等疾病的主要危险因素,高血压的及时治疗和综合管理具有重要意义。2019年8月英国国家卫生与临床优化研究所（NICE）发布了成人高血压诊断和管理指南,这是距2004年NICE高血压诊断和管理指南发布后的第３次更新,既沿用了以往的一些理念,又补充了许多新的内容,新版高血压管理指南在血压测量、高血压诊断、心血管风险、靶器官损害评估、降压治疗、血压监测及哪些患者需要专科医生诊治等方面均进行了全面而详细的阐述,尤其在高血压药物治疗的启动时机、治疗方案的选择及综合管理的治疗理念方面,值得临床医生借鉴与学习。