Rapid detection and genotyping of SARS-CoV-2 Omicron BA.4/5 variants using a RT-PCR and CRISPR-Cas12a-based assay / 南方医科大学学报

OBJECTIVE@#To establish a rapid detection and genotyping method for SARS-CoV-2 Omicron BA.4/5 variants using CRISPPR-Cas12a gene editing technology.@*METHODS@#We combined reverse transcription-polymerase chain reaction (RT-PCR) and CRISPR gene editing technology and designed a specific CRISPPR RNA (crRNA) with suboptimal protospacer adjacent motifs (PAM) for rapid detection and genotyping of SARS- CoV-2 Omicron BA.4/5 variants. The performance of this RT- PCR/ CRISPPR-Cas12a assay was evaluated using 43 clinical samples of patients infected by wild-type SARS-CoV-2 and the Alpha, Beta, Delta, Omicron BA. 1 and BA. 4/5 variants and 20 SARS- CoV- 2-negative clinical samples infected with 11 respiratory pathogens. With Sanger sequencing method as the gold standard, the specificity, sensitivity, concordance (Kappa) and area under the ROC curve (AUC) of RT-PCR/CRISPPR-Cas12a assay were calculated.@*RESULTS@#This assay was capable of rapid and specific detection of SARS- CoV-2 Omicron BA.4/5 variant within 30 min with the lowest detection limit of 10 copies/μL, and no cross-reaction was observed in SARS-CoV-2-negative clinical samples infected with 11 common respiratory pathogens. The two Omicron BA.4/5 specific crRNAs (crRNA-1 and crRNA-2) allowed the assay to accurately distinguish Omicron BA.4/5 from BA.1 sublineage and other major SARS-CoV-2 variants of concern. For detection of SARS-CoV-2 Omicron BA.4/5 variants, the sensitivity of the established assay using crRNA-1 and crRNA-2 was 97.83% and 100% with specificity of 100% and AUC of 0.998 and 1.000, respectively, and their concordance rate with Sanger sequencing method was 92.83% and 96.41%, respectively.@*CONCLUSION@#By combining RT-PCR and CRISPPR-Cas12a gene editing technology, we successfully developed a new method for rapid detection and identification of SARS-CoV-2 Omicron BA.4/5 variants with a high sensitivity, specificity and reproducibility, which allows rapid detection and genotyping of SARS- CoV-2 variants and monitoring of the emerging variants and their dissemination.

Plasma Targeted Metabolomics Analysis for Amino Acids and Acylcarnitines in Patients with Prediabetes, Type 2 Diabetes Mellitus, and Diabetic Vascular Complications

Background@#We hypothesized that specific amino acids or acylcarnitines would have benefits for the differential diagnosis of diabetes. Thus, a targeted metabolomics for amino acids and acylcarnitines in patients with diabetes and its complications was carried out. @*Methods@#A cohort of 54 normal individuals and 156 patients with type 2 diabetes mellitus and/or diabetic complications enrolled from the First Affiliated Hospital of Jinzhou Medical University was studied. The subjects were divided into five main groups: normal individuals, impaired fasting glucose, overt diabetes, diabetic microvascular complications, and diabetic peripheral vascular disease. The technique of tandem mass spectrometry was applied to obtain the plasma metabolite profiles. Metabolomics multivariate statistics were applied for the metabolic data analysis and the differential metabolites determination. @*Results@#A total of 10 cross-comparisons within diabetes and its complications were designed to explore the differential metabolites. The results demonstrated that eight comparisons existed and yielded significant metabolic differences. A total number of 24 differential metabolites were determined from six selected comparisons, including up-regulated amino acids, down-regulated medium-chain and long-chain acylcarnitines. Altered differential metabolites provided six panels of biomarkers, which were helpful in distinguishing diabetic patients. @*Conclusion@#Our results demonstrated that the biomarker panels consisted of specific amino acids and acylcarnitines which could reflect the metabolic variations among the different stages of diabetes and might be useful for the differential diagnosis of prediabetes, overt diabetes and diabetic complications.

Plasma Targeted Metabolomics Analysis for Amino Acids and Acylcarnitines in Patients with Prediabetes, Type 2 Diabetes Mellitus, and Diabetic Vascular Complications

Background@#We hypothesized that specific amino acids or acylcarnitines would have benefits for the differential diagnosis of diabetes. Thus, a targeted metabolomics for amino acids and acylcarnitines in patients with diabetes and its complications was carried out. @*Methods@#A cohort of 54 normal individuals and 156 patients with type 2 diabetes mellitus and/or diabetic complications enrolled from the First Affiliated Hospital of Jinzhou Medical University was studied. The subjects were divided into five main groups: normal individuals, impaired fasting glucose, overt diabetes, diabetic microvascular complications, and diabetic peripheral vascular disease. The technique of tandem mass spectrometry was applied to obtain the plasma metabolite profiles. Metabolomics multivariate statistics were applied for the metabolic data analysis and the differential metabolites determination. @*Results@#A total of 10 cross-comparisons within diabetes and its complications were designed to explore the differential metabolites. The results demonstrated that eight comparisons existed and yielded significant metabolic differences. A total number of 24 differential metabolites were determined from six selected comparisons, including up-regulated amino acids, down-regulated medium-chain and long-chain acylcarnitines. Altered differential metabolites provided six panels of biomarkers, which were helpful in distinguishing diabetic patients. @*Conclusion@#Our results demonstrated that the biomarker panels consisted of specific amino acids and acylcarnitines which could reflect the metabolic variations among the different stages of diabetes and might be useful for the differential diagnosis of prediabetes, overt diabetes and diabetic complications.

First-trimester ultrasound screening for prenatal diagnosis of fetal congenital heart disease / 中华围产医学杂志

Objective To investigate the value of standardized ultrasound screening in diagnosis of fetal congenital heart disease (CHD) during the first trimester. Methods This study retrospectively analyzed the clinical data of 8 383 fetuses who received ultrasound screening during the first trimester in the Dongguan Maternal and Child Health Hospital from September 2015 to December 2016. Standardized ultrasound was performed to observe fetal heart position, apical direction, apical four-chamber view, three vessels and trachea view and the thickness of nuchal translucency (NT). Fetuses with thickened NT or fetal CHD observed during the first and second trimester were followed up. Pregnancy outcomes and the growth of newborns within one year after birth were recorded and analyzed. Pathological results after the termination of pregnancy were compared with the results of routine karyotyping and chromosome microarray analysis (CMA). Results (1) A total of 27 cases of fetal CHD were identified during the first trimester giving a detection rate of 0.32% (27/8 383). These included ten (37.0%) of single atrium and/or single ventricle, seven (25.9%) of endocardial cushion defect (including two complicated by persistent arterial trunk), three (11.1%) of hypoplastic right heart syndrome, three (11.1%) of interventricular septal defect, two (7.4%) of hypoplastic left heart syndrome, one (3.7%) of mirror-image dextrocardia and one (3.7%) of right atrial enlargement and severe tricuspid regurgitation. Nineteen out of the 27 cases had NT thickening (NT≥3.0 mm) and 17 of them had a cystic hygroma (NT≥6.0 mm). Among the 27 cases, 22 were terminated in the first trimester which autopsy results were consistent with ultrasound and the other five were rescreened during the second trimester. Thirteen out of the 27 cases received chorionic villus sampling, and seven of them were found to have chromosomal abnormalities by karyotyping and CMA, among whom one was microdeletion of 22q11. (2) Twenty-one cases of CHD were detected in the second-trimester ultrasound screening, including five initially identified in the first trimester. These cases included four (19.0%) of complex cardiac malformations (with three or more malformations), four (19.0%) of interventricular septal defect, three (14.3%) of dextroaortic arch, left subclavian artery vagus and 'U' shaped vascular ring, three (14.3%) of hypoplastic right heart syndrome (including one complicated by coronary artery-right ventricular fistula and one by interventricular septal defect), two (9.5%) of transposition of the great arteries, two (9.5%) of tetralogy of Fallot, one (4.8%) of hypoplastic left heart syndrome, one (4.8%) of Taussig-Bing anomaly and one (4.8%) of coarctation of the aorta. Among the 16 cases first identified in the second trimester, eight had NT thickening, including one with cystic hygroma. Among the 21 cases, two were lost to follow-up after being transferred to another hospital; four with negative results in karyotype analysis and CMA were delivered vaginally at term (37-40 gestational weeks) with 1-min Apgar scores of ten points and postpartum ultrasound of the baby was consistent with the second-trimester ultrasound screening; 15 were terminated and the autopsy confirmed those findings in the second-trimester ultrasound screening. Eleven out of the 21 cases received amniocentesis and five of them were found to be abnormal according to karyotype analysis and CMA, including one of microdeletion of 22q11. Conclusions Standardized first-trimester ultrasound screening is important and of great clinical value in the diagnosis of fetal CHD. Increased NT thickness could be a key indicator of fetal CHD and chromosomal abnormalities in early pregnancy. CMA may facilitate detecting the abnormality of genetic material in fetuses with normal chromosome karyotype.

Ultrasonography-based diagnosis of fetal craniocerebral and neural tube malformation in early pregnancy / 实用医学杂志

Objective To evaluate the clinical effects of ultrasonography for structural examination in the diagnosis of fetal brain malformation and neural tube defects ( NTDs ) in early pregnancy . Methods A retrospective study was conducted to analyse 6 630 cases taking obstetric examination in Dongguan Maternal and Child Health Hospital from February 2014 to June 2015. The examination included a standardized ultrasound structural examination at 11-13 plus 6 weeks of pregnancy. The autopsied results of the induced fetus in early pregnancy from craniocerebral and neural tube structure malformation were investigated. All the cases were followed up concerning the outcomes and the malformation detection rate was calculated for analysis. Results The detection rates of exencephalus and anencephalus, holoprosencephaly, aphylly-holoprosencephaly, rachischisis, open spina bifida, and meningocele were 100%, 80%, 100%, 42.9%, 50% and 100%, respectively. The malformations which was missed in the early pregnancy but detected in the later gestational ages included:Dandy-Walker Syndrome, most of the non-open spina bifida, hypoplasia of the corpus callosum, foliaceous-holoprosencephaly and ventriculomegaly. Conclusions The structural examination using ultrasonography at early pregnancy is effective in the detection of severe open-neural tube defects. It′s worth generalizing in the cliical diagnosis but part of fetal malformations still need a further ultrasound examination in the mid-gestation or the later gestation.