Development of an Integrated Disposable Device for SARSCoV-2 Nucleic Acid Extraction and Detection

Objective To develop a highly sensitive and rapid nucleic acid detection method for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Methods We designed,developed,and manufactured an integrated disposable device for SARS-CoV-2 nucleic acid extraction and detection.The precision of the liquid transfer and temperature control was tested.A comparison between our device and a commercial kit for SARS-Cov-2 nucleic acid extraction was performed using real-time fluorescence reverse transcription polymerase chain reaction(RT-PCR).The entire process,from SARS-CoV-2 nucleic acid extraction to amplification,was evaluated.Results The precision of the syringe transfer volume was 19.2±1.9μL(set value was 20),32.2±1.6(set value was 30),and 57.2±3.5(set value was 60).Temperature control in the amplification tube was measured at 60.0±0.0℃(set value was 60)and 95.1±0.2℃(set value was 95)respectively.SARS-Cov-2 nucleic acid extraction yield through the device was 7.10×10^(6) copies/mL,while a commercial kit yielded 2.98×10^(6) copies/mL.The mean time to complete the entire assay,from SARS-CoV-2 nucleic acid extraction to amplification detection,was 36 min and 45 s.The detection limit for SARS-CoV-2 nucleic acid was 250 copies/mL.Conclusion The integrated disposable devices may be used for SARS-CoV-2 Point-of-Care test(POCT).

Clinical application of combined detection of SARS-CoV-2-specific antibody and nucleic acid

BACKGROUND The global outbreak of human severe acute respiratory syndrome coronavirus(SARS-CoV)-2 infection represents an urgent need for readily available,accurate and rapid diagnostic tests.Nucleic acid testing of respiratory tract specimens for SARS-CoV-2 is the current gold standard for diagnosis of coronavirus disease 2019(COVID-19).However,the diagnostic accuracy of reverse transcription polymerase chain reaction(RT-PCR)tests for detecting SARS-CoV-2 nucleic acid may be lower than optimal.The detection of SARS-CoV-2-specific antibodies should be used as a serological non-invasive tool for the diagnosis and management of SARS-CoV-2 infection.AIM To investigate the diagnostic value of SARS-CoV-2 IgM/IgG and nucleic acid detection in COVID-19.METHODS We retrospectively analyzed 652 suspected COVID-19 patients,and 206 non-COVID-19 patients in Wuhan Integrated TCM and Western Medicine Hospital.Data on SARS-CoV-2 nucleic acid tests and serum antibody tests were collected to investigate the diagnostic value of nucleic acid RT-PCR test kits and immunoglobulin(Ig)M/IgG antibody test kits.The j2 test was used to compare differences between categorical variables.A 95%confidence interval(CI)was provided by the Wilson score method.All analyses were performed with IBM SPSS Statistics version 22.0(IBM Corp.,Armonk,NY,United States).RESULTS Of the 652 suspected COVID-19 patients,237(36.3%)had positive nucleic acid tests,311(47.7%)were positive for IgM,and 592(90.8%)were positive for IgG.There was a significant difference in the positive detection rate between the IgM and IgG test groups(P<0.001).Using the RT-PCR results as a reference,the specificity,sensitivity,and accuracy of IgM/IgG combined tests for SARS-CoV-2 infection were 98.5%,95.8%,and 97.1%,respectively.Of the 415 suspected COVID-19 patients with negative nucleic acid test results,366 had positive IgM/IgG tests with a positive detection rate of 88.2%.CONCLUSION Our data indicate that serological IgM/IgG antibody combined test had high sensitivity and specificity for the diagnosis of SARS-CoV-2 infection,and can be used in combination with RT-PCR for the diagnosis of SARS-CoV-2 infection.

Molecular detection of SARS-CoV-2 being challenged by virus variation and asymptomatic infection

Coronavirus disease 2019(COVID-19)has been a pandemic for more than a year.With the expanding second wave of the pandemic in winter,the continuous evolution of SARS-CoV-2 has brought new issues,including the significance of virus mutations in infection and the detection of asymptomatic infection.In this review,we first introduced several major SARS-CoV-2 mutations since the COVID-19 outbreak and then mentioned the widely used molecular detection techniques to diagnose COVID-19,primarily focusing on their strengths and limitations.We further discussed the effects of viral genetic variation and asymptomatic infection on the molecular detection of SARS-CoV-2 infection.The review finally summarized useful insights into the molecular diagnosis of COVID-19 under the special situation being challenged by virus mutation and asymptomatic infection.

Nanomechanical assay for ultrasensitive and rapid detection of SARS-CoV-2 based on peptide nucleic acid

The massive global spread of the COVID-19 pandemic makes the development of more effective and easily popularized assays critical.Here,we developed an ultrasensitive nanomechanical method based on microcantilever array and peptide nucleic acid(PNA)for the detection of severe acute respiratory syndrome-coronavirus-2(SARS-CoV-2)RNA.The method has an extremely low detection limit of 0.1 fM(105 copies/mL)for N-gene specific sequence(20 bp).Interestingly,it was further found that the detection limit of N gene(pharyngeal swab sample)was even lower,reaching 50 copies/mL.The large size of the N gene dramatically enhances the sensitivity of the nanomechanical sensor by up to three orders of magnitude.The detection limit of this amplification-free assay method is an order of magnitude lower than RT-PCR(500 copies/mL)that requires amplification.The non-specific signal in the assay is eliminated by the in-situ comparison of the array,reducing the false-positive misdiagnosis rate.The method is amplification-free and label-free,allowing for accurate diagnosis within 1 h.The strong specificity and ultrasensitivity allow single base mutations in viruses to be distinguished even at very low concentrations.Also,the method remains sensitive to fM magnitude lung cancer marker(miRNA-155).Therefore,this ultrasensitive,amplification-free and inexpensive assay is expected to be used for the early diagnosis of COVID-19 patients and to be extended as a broad detection tool.

Multicenter evaluation of a simple and sensitive nucleic acid self-testing for SARS-CoV-2

A rapid and accurate COVID-19 diagnosis is a prerequisite for blocking the source of infection as soon as possible and taking the appropriate medical action.Herein,we developed GeneClick,a device for nucleic acid self-testing of SARS-CoV-2,consisting of three modules:a sampling kit,a microfluidic chip-based disposable cartridge,and an amplification reader.In addition,we evaluated the clinical performance of GeneClick using 2162 nasal swabs collected at three medical institutions,using three commercial RT-qPCR kits and an antigen self-test as references.Compared to RT-qPCR,the sensitivity and specificity of the GeneClick assay were 97.93%and 99.72%,respectively,with a kappa value of 0.979(P<0.01).Of the 2162 samples,2076 were also tested for SARS-CoV-2 antigens.Among the 314 positive samples identified by GeneClick assay,63 samples were undetected by antigen tests.Overall,the GeneClick nucleic acid self-test demonstrated higher accuracy than the antigen-based detection.Based on the additional features,including simple operation,affordable price,portable device,and reliability of smartphone APP-driven sampling and result reporting,GeneClick offers a powerful tool for field-based SARS-CoV-2 detection in primary healthcare institutions or at-home use.

COVID-19 mortality paradox(United States vs Africa):Mass vaccination vs early treatment

The coronavirus disease 2019(COVID-19)mortality rate in 55 African countries is almost 4.5 times lower than in the coronavirus disease 2019(COVID-19)despite Africa having over 4.2 times more people.This mortality paradox is also evident when comparing Nigeria,a heavily populated,poorly vaccinated and weakly mandated country to Israel,a small,highly vaccinated and strictly mandated country.Nigeria has almost 4 times lower COVID mortality than Israel.In this Field of Vision perspective,I explain how this paradox has evolved drawing upon my academic,clinical and social experience.Since April 2020,I’ve developed and been using the Egyptian immune-modulatory Kelleni’s protocol to manage COVID-19 patients including pediatric,geriatric,pregnant,immune-compromised and other individuals suffering from multiple comorbidities.It’s unfortunate that severe acute respiratory syndrome coronavirus 2 is still evolving accompanied by more deaths.However in Africa,we’ve been able to live without anxiety or mandates throughout the pandemic because we trust science and adopted early treatment using safe,and effective repurposed drugs that have saved the majority of COVID-19 patients.This article represents an African and Egyptian tale of honor.

Evaluation of factors contributing to variability of qualitative and quantitative proficiency testing for SARS-CoV-2 nucleic acid detection

The pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has led to unprecedented social and economic disruption.Many nucleic acid testing(NAT)laboratories in China have been established to control the epidemic better.This proficiency testing(PT)aims to evaluate the participants’performance in qualitative and quantitative SARS-CoV-2 NAT and to explore the factors that contribute to differences in detection capabilities.Two different concentrations of RNA samples(A,B)were used for quantitative PT.Pseudovirus samples D,E(different concentrations)and negative sample(F)were used for qualitative PT.50 data sets were reported for qualitative PT,of which 74.00%were entirely correct for all samples.Fortytwo laboratories participated in the quantitative PT.37 submitted all gene results,of which only 56.76%were satisfactory.For qualitative detection,it is suggested that laboratories should strengthen personnel training,select qualified detection kits,and reduce cross-contamination to improve detection accuracy.For quantitative detection,the results of the reverse transcription digital PCR(RT-dPCR)method were more comparable and reliable than those of reverse transcription quantitative PCR(RT-qPCR).The copy number concentration of ORF1ab and N in samples A and B scattered in 85,223,50,and 106 folds,respectively.The differences in the quantitative result of RT-qPCR was mainly caused by the non-standard use of reference materials and the lack of personnel operating skills.Comparing the satisfaction of participants participating in both quantitative and qualitative proficiency testing,95.65%of the laboratories with satisfactory quantitative results also judged the qualitative results correctly,while 85.71%of the laboratories with unsatisfactory quantitative results were also unsatisfied with their qualitative judgments.Therefore,the quantitative ability is the basis of qualitative judgment.Overall,participants from hospitals reported more satisfactory results than those from enterprises and universities.Therefore,surveillance,daily qualitiy control and standardized operating procedures should be strengthened to improve the capability of SARS-CoV-2 NAT.

An automated nucleic acid detection platform using digital microfluidics with an optimized Cas12a system

Outbreaks of both influenza virus and the novel coronavirus SARS-CoV-2 are serious threats to human health and life. It is very important to establish a rapid, accurate test with large-scale detection potential to prevent the further spread of the epidemic. An optimized RPA-Cas12a-based platform combined with digital microfluidics(DMF), the RCD platform, was established to achieve the automated, rapid detection of influenza viruses and SARS-CoV-2. The probe in the RPA-Cas12a system was optimized to produce maximal fluorescence to increase the amplification signal. The reaction droplets in the platform were all at the microliter level and the detection could be accomplished within 30 min due to the effective mixing of droplets by digital microfluidic technology. The whole process from amplification to recognition is completed in the chip, which reduces the risk of aerosol contamination. One chip can contain multiple detection reaction areas, offering the potential for customized detection.The RCD platform demonstrated a high level of sensitivity, specificity(no false positives or negatives), speed(≤30 min),automation and multiplexing. We also used the RCD platform to detect nucleic acids from influenza patients and COVID-19 patients. The results were consistent with the findings of q PCR. The RCD platform is a one-step, rapid, highly sensitive and specific method with the advantages of digital microfluidic technology, which circumvents the shortcomings of manual operation. The development of the RCD platform provides potential for the isothermal automatic detection of nucleic acids during epidemics.

中药治疗对新型冠状病毒肺炎新型冠状病毒核酸长期未转阴患者核酸转阴率的影响

目的探索中药治疗与新型冠状病毒肺炎新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARSCoV-2)核酸长期未转阴患者核酸转阴率的关系。方法回顾性分析163例病程>30 d的新型冠状病毒肺炎轻型及普通型患者,采集患者治疗策略(中药、胸腺肽、干扰素等),以及人口学资料、伴随疾病、SARS-CoV-2核酸转阴时间等信息,以40 d转阴为因变量,其它变量为调整变量,采用Logistic回归模型,探索多因素下中药治疗对SARS-CoV-2核酸转阴率的影响。结果未用中药治疗组患者平均转阴时间为49 d,长于用中药组患者平均转阴时间(40 d)(P<0.05)。单因素分析结果显示,与40 d转阴相关的因素有总蛋白(total protein,TP)、白蛋白(albumin,ALB)、ALB/球蛋白(globulin,GLO)比值(ALB/GLO,A/G)、使用胸腺肽、使用干扰素、使用中药(P均<0.05);Logistic回归分析结果显示,在调整其它因素后,中药治疗能够显著增加患者的SARS-CoV-2核酸转阴率(OR=1.725,P=0.000)。结论中药治疗能显著改善新型冠状病毒感染长期未转阴患者的SARS-CoV-2核酸转阴率。

系统免疫炎症指数对新型冠状病毒肺炎核酸转阴时间的影响

目的探讨系统免疫炎症指数(SII)对新型冠状病毒肺炎(COVID-19)核酸转阴时间的影响。方法选取接受住院治疗并康复出院的127例COVID-19患者为研究对象,通过电子病历系统收集患者临床资料及入院24 h内的实验室检查结果,根据血常规结果计算SII值并以其中位数将患者分为高SII组(≥393)和低SII组(<393),比较2组的临床资料及中性粒细胞与淋巴细胞比值(NLR)、血小板与淋巴细胞比值(PLR)、C反应蛋白(CRP)、白细胞介素(IL)-6、白蛋白(ALB)的差异。Cox回归分析确定影响核酸转阴时间的危险因素。Kaplan-Meier法比较不同组患者的核酸转阴曲线。结果高SII组的男性比例、NLR、PLR、CRP均高于低SII组(P<0.05)。Cox多因素回归分析显示,发病至入院时间>5 d、重症、高SII是影响核酸转阴的独立危险因素(P<0.05)。Kaplan-Meier曲线显示,高SII值、重症、发病至入院时间>5 d的患者核酸转阴中位时间分别长于低SII值、非重症、发病至入院时间≤5 d的患者,差异均有统计学意义(P<0.05)。结论SII是反映机体炎症及免疫状态的综合指标,简单易得,高SII值为COVID-19患者核酸转阴时间延长的独立危险因素。