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1.
mSphere ; 6(5): e0075221, 2021 10 27.
Article in English | MEDLINE | ID: covidwho-1526451

ABSTRACT

During the progression of coronavirus disease 2019 (COVID-19), immune response and inflammation reactions are dynamic events that develop rapidly and are associated with the severity of disease. Here, we aimed to develop a predictive model based on the immune and inflammatory response to discriminate patients with severe COVID-19. COVID-19 patients were enrolled, and their demographic and immune inflammatory reaction indicators were collected and analyzed. Logistic regression analysis was performed to identify the independent predictors, which were further used to construct a predictive model. The predictive performance of the model was evaluated by receiver operating characteristic curve, and optimal diagnostic threshold was calculated; these were further validated by 5-fold cross-validation and external validation. We screened three key indicators, including neutrophils, eosinophils, and IgA, for predicting severe COVID-19 and obtained a combined neutrophil, eosinophil, and IgA ratio (NEAR) model (NEU [109/liter] - 150×EOS [109/liter] + 3×IgA [g/liter]). NEAR achieved an area under the curve (AUC) of 0.961, and when a threshold of 9 was applied, the sensitivity and specificity of the predicting model were 100% and 88.89%, respectively. Thus, NEAR is an effective index for predicting the severity of COVID-19 and can be used as a powerful tool for clinicians to make better clinical decisions. IMPORTANCE The immune inflammatory response changes rapidly with the progression of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and is responsible for clearance of the virus and further recovery from the infection. However, the intensified immune and inflammatory response in the development of the disease may lead to more serious and fatal consequences, which indicates that immune indicators have the potential to predict serious cases. Here, we identified both eosinophils and serum IgA as prognostic markers of COVID-19, which sheds light on new research directions and is worthy of further research in the scientific research field as well as clinical application. In this study, the combination of NEU count, EOS count, and IgA level was included in a new predictive model of the severity of COVID-19, which can be used as a powerful tool for better clinical decision-making.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/immunology , Clinical Decision Rules , Severity of Illness Index , Adult , Aged , Biomarkers/blood , COVID-19/blood , Clinical Decision-Making/methods , Disease Progression , Eosinophils/metabolism , Female , Humans , Immunoglobulin A/blood , Inflammation/blood , Inflammation/diagnosis , Inflammation/virology , Logistic Models , Male , Middle Aged , Neutrophils/metabolism , Predictive Value of Tests , Prognosis , Sensitivity and Specificity
2.
Analyst ; 146(22): 6917-6923, 2021 Nov 08.
Article in English | MEDLINE | ID: covidwho-1526109

ABSTRACT

Nucleic acid amplification is a widely used diagnostic tool, although it requires a relatively time-consuming and complicated extraction step. To address this issue outside the laboratory, we investigated a sample preparation system and determined that a silica membrane and silica-coated beads are powerful tools for the extraction from raw samples: nucleic acids are kept in the silica membrane, retained during a single wash step, and released at the elution step. The eluent is appropriate for the quantitative real-time polymerase chain reaction (qPCR) and loop-mediated amplification (LAMP) assay in terms of purity and quantity. We also built an innovative equipment-free nucleic acid extraction squeeze system which requires less than 20 min. The sample with improved purity augments the specificity and sensitivity. This system is simple, user-friendly, low-cost, and equipment-free, thus making nucleic acid extraction more accessible and affordable for researchers and untrained users. Furthermore, when combined with the reverse-transcription quantitative real-time polymerase chain reaction method, the method will accelerate the detection of diseases. The same goes when combined with the LAMP assay, especially in developing countries.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , Pathology, Molecular , RNA, Viral/genetics , Sensitivity and Specificity
3.
Pan Afr Med J ; 39: 228, 2021.
Article in French | MEDLINE | ID: covidwho-1524595

ABSTRACT

Introduction: the COVID-19 pandemic causes biological diagnostic problems that remain relevant in low-income countries in general and in Cameroon in particular. Rapids tests that reliably detect SARS-CoV-2 virus antigen present themselves as an important alternative in several contexts. The objective of our study was to evaluate the diagnostic performance of two rapid diagnostic tests BIOSYNEX® COVID-19 Ag BSS and BIOSYNEX® COVID-19 Ag + BSS, compared to each other and to the AmpliQuick® SARS-CoV-2 PCR test. Methods: a cross-sectional and comparative study was carried out from April 27 to May 29, 2021 in the city of Douala in Cameroon. The samples consisted of nasopharyngeal swabs received at the molecular biology laboratory of the Douala Gyneco-obstetric and pediatric hospital, whatever their origin. The socio-demographic parameters (age, profession, football players, travelers, others), marital status, nationality), comorbidity and known status of COVID-19, were recorded on the collection sites. The main collection sites were the Deïdo Health District and the Douala Gyneco-Obstetric and Pediatric Hospital. We performed the diagnosis of COVID-19 using the rapid diagnostic test (RDT) BIOSYNEX® COVID-19 Ag BSS and RDT BIOSYNEX® COVID-19 Ag + BSS compared to each other and to the AmpliQuick® SARS-CoV-2 polymerase chain reaction (PCR) test on each sample. Statistical analysis of the data was performed using Microsoft Excel and SPSS version 17 software. To determine the sensitivity of the two RDTs, the Bayesian latent class model was performed on the median with a 95% confidence interval with p<0.05 as the significant level. An ethical clearance was sought and obtained from the University of Douala Institutional Ethics Committee. Results: a total of 1813 participants were included in our study, with a predominance of men (1226, 68.68 %) and the most represented age group was that of 31 to 40 years (568, 31.33 %). Most of the participants were married (888, 53.46%) and only a few had a known COVID-19 status (75, 5.47%). The two rapid tests on our study population show much closed COVID-19 prevalence values, respectively 2.03 for BIOSYNEX® COVID-19 Ag BSS and 2.17 for BIOSYNEX® COVID-19 Ag + BSS. RDT BIOSYNEX® COVID-19 Ag + BSS showed higher sensitivity 94.1% vs. 87.5% for RDT BIOSYNEX® COVID-19 Ag BSS with almost identical specificity 98.9% for RDT BIOSYNEX® COVID-19 Ag + BSS vs. 98.7% for RDT BIOSYNEX® COVID-19 Ag BSS compared to AmpliQuick® SARS-CoV-2. BIOSYNEX® COVID-19 Ag + BSS RDT showed a negative predictive value of 99.9% compared to BIOSYNEX® COVID-19 Ag BSS RDT. There is a 99.9% agreement between the RDT BIOSYNEX® COVID-19 Ag BSS and the RDT BIOSYNEX® COVID-19 Ag + BSS. Conclusion: the RDT BIOSYNEX®COVID-19 Ag + BSS and RDT BIOSYNEX® COVID-19 Ag BSS can be used for the diagnosis of SARS-CoV-2 and can have an important contribution in the context of mass screenings and screening in remote areas.


Subject(s)
Antigens, Viral/analysis , COVID-19 Testing/methods , COVID-19/diagnosis , Polymerase Chain Reaction/methods , Adolescent , Adult , Aged , Cameroon , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Predictive Value of Tests , SARS-CoV-2 , Sensitivity and Specificity , Young Adult
4.
BMC Infect Dis ; 21(1): 1162, 2021 Nov 17.
Article in English | MEDLINE | ID: covidwho-1523285

ABSTRACT

BACKGROUND: Current assays for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on time consuming, costly and laboratory based methods for virus isolation, purification and removing inhibitors. To address this limitation, we propose a simple method for testing RNA from nasopharyngeal swab samples that bypasses the RNA purification step. METHODS: In the current project, we have described two extraction-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of SARS-CoV-2 by using E gene and RdRp gene as the targets. RESULTS: Here, results showed that reverse transcription loop-mediated isothermal amplification assays with 88.4% sensitive (95% CI: 74.9-96.1%) and 67.4% sensitive (95% CI: 51.5-80.9%) for E gene and RdRp gene, respectively. CONCLUSION: Without the need of RNA purification, our developed RT-LAMP assays for direct detection of SARS-CoV-2 from nasopharyngeal swab samples could be turned into alternatives to qRT-PCR for rapid screening.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , RNA, Viral/genetics , Reverse Transcription , Sensitivity and Specificity
5.
Am J Perinatol ; 38(12): 1236-1243, 2021 10.
Article in English | MEDLINE | ID: covidwho-1521902

ABSTRACT

OBJECTIVE: This study aimed to determine if laboratory inflammatory markers can predict critical disease in symptomatic COVID-19 pregnant women. STUDY DESIGN: Multicenter, retrospective cohort study of all pregnant women presenting to New York City Health + Hospitals emergency departments from March 1 to May 30, 2020. We assessed all symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive pregnant women with room air oxygen saturation <95% on presentation. Logistic regression modeled the relationship of inflammatory markers to outcomes. Area under receiver operating characteristic (ROC) curve and maximum Youden index determined prognostic ability and optimal predictive cut-off values. RESULTS: A total of 498 of 5,002 pregnant women were SARS-CoV-2 RT-PCR positive of which 77 presented with hypoxemia. The absolute lymphocyte count (ALC) and neutrophil to lymphocyte ratio (NLR) were highly sensitive for progression to severe illness. ROC curve analysis identified predictive cutoffs: ALC < 1.49 × 109/L (96% sensitivity, 52% specificity, area under the receiver operating characteristic curve [AUC] = 0.80 (95% confidence interval [CI]: 0.70-0.90) and NLR >8.1 (100% sensitivity, 70% specificity, AUC = 0.86 (95% CI: [0.76-0.96]). CONCLUSION: ALC and NLR on presentation are sensitive markers of progression to critical COVID-19 disease in symptomatic pregnant women. This finding provides a practical, rapid method for assessment and can assist clinicians with decision-making regarding triage, level of care, and patient management. KEY POINTS: · Few tools exist to gauge risk of severe COVID-19 disease in pregnancy.. · ALC and NLR are sensitive predictive markers of disease progression in symptomatic women.. · Cut-off values for ALC and NLR will help direct patient triage and management..


Subject(s)
COVID-19/complications , Lymphocyte Count , Lymphopenia/virology , Neutrophils/metabolism , Pregnancy Complications, Infectious/virology , Severity of Illness Index , Adult , Cohort Studies , Disease Progression , Female , Humans , Pregnancy , Retrospective Studies , Sensitivity and Specificity
6.
Int J Lab Hematol ; 43 Suppl 1: 137-141, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1526369

ABSTRACT

INTRODUCTION: Eosinopenia has been observed during infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. This study evaluated the role of eosinopenia as a diagnostic and prognostic indicator in COVID-19 infection. METHODS: Information on 429 patients with confirmed COVID-19, admitted to Apollo Hospitals, Chennai, India between 04 June 2020 to 15 August 2020, was retrospectively collected through electronic records and analysed. RESULTS: 79.25% of the patients included in the study had eosinopenia on admission. The median eosinophil count in COVID-19-positive patients was 0.015 × 109 /L, and in negative patients, it was 0.249 × 109 /L. Eighteen per cent of the positive patients presented with 0 eosinophil count. Eosinopenia for early diagnosis of COVID-19 had a sensitivity of 80.68% and specificity of 100% with an accuracy of 85.24. Role of eosinopenia in prognostication of COVID-19 was found to be insignificant. There was no statistically significant difference between the median eosinophil counts in survivors and nonsurvivors. Eosinophil trends during the course of disease were found to be similar between survivors and nonsurvivors. CONCLUSIONS: Eosinopenia on admission is a reliable and convenient early diagnostic marker for COVID-19 infection, helping in early identification, triaging and isolation of the patients till nucleic acid test results are available. Role of eosinopenia as a prognostic indicator is insignificant.


Subject(s)
COVID-19 Testing/methods , COVID-19/blood , Eosinophils , Leukocyte Count , Leukopenia/etiology , Area Under Curve , Biomarkers , COVID-19/diagnosis , COVID-19/mortality , Eosinophilia/blood , Eosinophilia/etiology , Humans , India , Leukopenia/blood , Prognosis , ROC Curve , Retrospective Studies , Selection Bias , Sensitivity and Specificity , Survival Analysis
7.
Euro Surveill ; 26(45)2021 11.
Article in English | MEDLINE | ID: covidwho-1515520

ABSTRACT

BackgroundReliable testing for SARS-CoV-2 is key for the management of the COVID-19 pandemic.AimWe estimate diagnostic accuracy for nucleic acid and antibody tests 5 months into the COVID-19 pandemic, and compare with manufacturer-reported accuracy.MethodsWe reviewed the clinical performance of SARS-CoV-2 nucleic acid and antibody tests based on 93,757 test results from 151 published studies and 20,205 new test results from 12 countries in the European Union and European Economic Area (EU/EEA).ResultsPooling the results and considering only results with 95% confidence interval width ≤ 5%, we found four nucleic acid tests, including one point-of-care test and three antibody tests, with a clinical sensitivity ≥ 95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Nine nucleic acid tests and 25 antibody tests, 12 of them point-of-care tests, had a clinical specificity of ≥ 98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid point-of-care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for eight of 14 sensitivity and 68 of 84 specificity results with confidence interval width ≤ 5%, and lower for nucleic acid tests than antibody tests. Manufacturer-reported clinical performance was significantly higher than independently assessed in 11 of 32 and four of 34 cases, respectively, for sensitivity and specificity, indicating a need for improvement in this area.ConclusionContinuous monitoring of clinical performance within more clearly defined target populations is needed.


Subject(s)
COVID-19 , Nucleic Acids , Humans , Pandemics , SARS-CoV-2 , Sensitivity and Specificity
8.
Sci Rep ; 11(1): 22013, 2021 11 10.
Article in English | MEDLINE | ID: covidwho-1510606

ABSTRACT

To meet the unprecedented requirement of diagnostic testing for SARS-CoV-2, a large number of diagnostic kits were authorized by concerned authorities for diagnostic use within a short period of time during the initial phases of the ongoing pandemic. We undertook this study to evaluate the inter-test agreement and other key operational features of 5 such commercial kits that have been extensively used in India for routine diagnostic testing for COVID-19. The five commercial kits were evaluated, using a panel of positive and negative respiratory samples, considering the kit provided by National Institute of Virology, Indian Council of Medical Research (2019-nCoV Kit) as the reference. The positive panel comprised of individuals who fulfilled the 3 criteria of being clinically symptomatic, having history of contact with diagnosed cases and testing positive in the reference kit. The negative panel included both healthy and disease controls, the latter being drawn from individuals diagnosed with other respiratory viral infections. The same protocol of sample collection, same RNA extraction kit and same RT-PCR instrument were used for all the kits. Clinical samples were collected from a panel of 92 cases and 60 control patients, who fulfilled our inclusion criteria. The control group included equal number of healthy individuals and patients infected with other respiratory viruses (n = 30, in each group). We observed varying sensitivity and specificity among the evaluated kits, with LabGun COVID-19 RT-PCR kit showing the highest sensitivity and specificity (94% and 100% respectively), followed by TaqPath COVID-19 Combo and Allplex 2019-nCoV assays. The extent of inter-test agreement was not associated with viral loads of the samples. Poor correlation was observed between Ct values of the same genes amplified using different kits. Our findings reveal the presence of wide heterogeneity and sub-optimal inter-test agreement in the diagnostic performance of the evaluated kits and hint at the need of adopting stringent standards for fulfilling the quality assurance requirements of the COVID-19 diagnostic process.


Subject(s)
COVID-19 Testing , COVID-19 , Humans , Pandemics , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
9.
Saudi Med J ; 42(4): 370-376, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1513257

ABSTRACT

OBJECTIVES: To assess the neutrophil-to-lymphocyte ratio (NLR) diagnostic and prognostic value in the context of Coronavirus disease-2019 (COVID-19) infection in Saudi Arabia. METHODS: A case-control study in which 701 confirmed COVID-19 patients (of which 41 were intensive care unit [ICU]-admitted) and 250 control subjects were enrolled. The study was conducted retrospectively in October on patients admitted to 3 separate hospitals in Saudi Arabia namely: King Abdullah Bin Abdulaziz University Hospital (Riyadh), Ohud Hospital (Madinah), and Nojood Medical Center (Madinah) between May and September 2020. Neutrophil-to-lymphocyte ratio was calculated based on absolute neutrophil and lymphocyte count. Institutional ethical approval was obtained prior to the study. RESULTS: Patients (median age 35 years), of which 54.8% were females, were younger than the control cohort (median age 48 years). Patients had significantly higher NLR compared to the control group. Intensive care unit admitted patients had significantly higher platelet, WBC and neutrophil counts. The ICU patients' NLR was almost twice as of the non-intensive patients. The NLR value of 5.5 was found to be of high specificity (96.4%) and positive predictive value (91.4%) in diagnosing COVID-19. Furthermore, it had a very good sensitivity (86.4%) in predicting severe forms of disease, such as, ICU admission. CONCLUSION: Neutrophil-to-lymphocyte ratio is an important tool in determining the COVID-19 clinical status. This study further confirms the prognostic value of NLR in detecting severe infection, and those patients with high NLR should be closely monitored and managed.


Subject(s)
COVID-19/diagnosis , Lymphocyte Count , Neutrophils , Adult , Blood Cell Count , COVID-19/blood , Case-Control Studies , Female , Hospitalization , Humans , Intensive Care Units , Leukocyte Count , Male , Middle Aged , Platelet Count , Predictive Value of Tests , Prognosis , Retrospective Studies , SARS-CoV-2 , Saudi Arabia , Sensitivity and Specificity , Severity of Illness Index
10.
Clin Lab ; 67(11)2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1513108

ABSTRACT

BACKGROUND: The objective of this study was to compare the validity of two different assays for the detection of SARS-CoV-2. METHODS: We collected 50 nasopharyngeal swabs in universal transport medium from the emergency department of Asia University Hospital for the detection of SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR). The samples for the Liat SARS-CoV-2 influenza A/B test were stored at -70℃ after SARS-CoV-2 testing using the RT-PCR in order to assess method comparison. RESULTS: In this study, the Limit of detection (LOD) of the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test is 12 copies/µL and the assay obtained 100% positive agreement and negative percent agreement with RT-PCR. CONCLUSIONS: In summary, a prefect agreement exists between the detection of SARS-CoV-2 conducted with the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test and the RT-PCR. The cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test is a reliable method for the detection of SARS-CoV-2, and it only requires 20 minutes to obtain the results. On the other hand, the cobas Liat SARS-CoV-2 and influenza A/B nucleic acid test is accurate, easy to use, and provides a faster turnaround time than testing performed in the high-throughput platform.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , Laboratories , Nasopharynx , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity
11.
Clin Lab ; 67(11)2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1513107

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) started to spread in Daegu beginning at the end of February 2020. IgG and IgM antibodies against SARS-CoV-2 were measured in hospitalized patients with COVID-19 with moderate to severe symptoms to improve the understanding of antibody responses. METHODS: We enrolled 312 patients with COVID-19 admitted to seven hospitals located in Daegu. Using serum (or plasma) samples from patients with polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infections, both IgG and IgM antibodies were measured using commercial enzyme-linked immunosorbent assay (R-FIND CO¬VID-19 ELISA, SG medical, Seoul, Korea). RESULTS: The median value from the initial diagnosis, confirmed by SARS-CoV-2 PCR, to the sampling date was 24 days (day 1 to 88). The total positive rate of IgG was 93.9% and the positive IgM rate was 39.4%, without considering the elapsed period after diagnosis. Positive IgG and IgM rates were highest at 100.0% and 59.0%, respectively, at 3 weeks (15 - 21 days). IgG showed a high positive rate of 79.3% even within 7 days after the initial diag-nosis of the disease and maintained a positive rate of 97.8% until after 8 weeks. CONCLUSIONS: Among hospitalized patients with COVID-19, IgG was detected from the beginning of the diagnosis and persisted for an extended time period.


Subject(s)
COVID-19 , Antibodies, Viral , Antibody Formation , Enzyme-Linked Immunosorbent Assay , Humans , Immunoglobulin G , Immunoglobulin M , Republic of Korea , SARS-CoV-2 , Sensitivity and Specificity
12.
Clin Lab ; 67(11)2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1513105

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that brings a significant public health challenge. A rapid and simple method is necessary for testing suspected samples and screening the population. METHODS: To better monitor sample effectiveness, this study described a method to detect nucleocapsid protein gene (N gene) of SARS-CoV-2 and human ACTB gene employing real-time duplex reverse transcription multienzyme isothermal rapid amplification (RT-MIRA) assays. RESULTS: The established real-time duplex RT-MIRA assays showed that no cross-reactions were observed to other pathogens and the detection limit was 100 copies/reaction. Using simulated clinical samples to test established assays further and the amplification process took no more than 20 minutes at 42°C. CONCLUSIONS: RT-MIRA assays are faster and easier than reverse transcription real-time polymerase chain reaction (RT-PCR). It is expected to be further optimized and evaluated in the detection of SARS-CoV-2 confirmed cases.


Subject(s)
COVID-19 , Reverse Transcription , Humans , Nucleic Acid Amplification Techniques , SARS-CoV-2 , Sensitivity and Specificity
13.
Clin Lab ; 67(11)2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1513104

ABSTRACT

BACKGROUND: The rapid spread of pneumonia caused by SARS-CoV-2 has seriously threatened people. In this study, we detected the expression of anti-SARS-CoV-2 IgG/IgM and respiratory tract SARS-CoV-2 RNA in patients with COVID-19 and explored the correlation and clinical significance between SARS-CoV-2 antibody and respiratory SARS-CoV-2 RNA. METHODS: From March 5, 2020 to April 28, 2020, 48 cases with COVID-19 diagnosed in Beijing Xiaotangshan Hospital were enrolled. SARS-CoV-2 RNAs were detected by real-time fluorescence RT-PCR method. Serum SARS-CoV-2 IgG/IgM antibodies were determined by colloidal gold immunochromatography. The statistical analysis was performed using chi-squared test. RESULTS: In all the patients, SARS-CoV-2 RNA among 270 upper respiratory tract (nasal or throat swabs) samples, 71 lower respiratory tract (sputum) samples, and anti-SARS-CoV-2 IgM/IgG antibodies in 123 serum samples were detected during the hospitalization period. The positive rate of anti-SARS-CoV-2 IgG was significantly higher than that of anti-SARS-CoV-2 IgM within the first week after symptom onset (p < 0.05). The positive rate of anti-SARS-CoV-2 IgG was also significantly higher than that of anti-SARS-CoV-2 IgM during day 8 - 30 after symptom onset (p < 0.01). The positive rate of SARS-CoV-2 RNA in the lower respiratory tract specimens (64.8%, 46/71) was significantly higher than that in the upper respiratory tract (46.7%, 126/270) (p < 0.05). The positive rate (100%, 4/4) of SARS-CoV-2 RNA detection in the lower respiratory tract specimens before IgG seroconversion was significantly higher than that of the positive rate (59.3%, 32/54) after IgG seroconversion (p < 0.01). The positive rate (72.2%, 57/79) of SARS-CoV-2 RNA detection in the upper respiratory tract specimens before IgG seroconversion was significantly higher than that of the positive rate (30.7%, 39/127) after IgG seroconversion (p < 0.01). CONCLUSIONS: Anti-SARS-CoV-2 IgG might be detected within the first week after symptom onset. The application of SARS-CoV-2 antibody (IgG/IgM) detection is important for the suspected cases of SARS-CoV-2 infection with negative SARS-CoV-2 RNA results. The positive rate of SARS-CoV-2 RNA detection in the lower respiratory tract specimens was significantly higher than that in the upper respiratory tract. Sputum detection is recommended for the detection of SARS-CoV-2 RNA. Using lower respiratory tract specimens may reduce the false negative PCR tests. The detection of SARS-CoV-2 RNA can be improved by investigating follow-up specimens over time.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Humans , Immunoglobulin G , Immunoglobulin M , RNA, Viral/genetics , Respiratory System , Sensitivity and Specificity
14.
Front Cell Infect Microbiol ; 11: 741147, 2021.
Article in English | MEDLINE | ID: covidwho-1512020

ABSTRACT

The coronavirus disease 2019 (COVID-19) has caused and is still causing tremendous damage to the global economy and human health. Qualitative reverse transcription-PCR (RT-qPCR) is the golden standard for COVID-19 test. However, the SARS-CoV-2 variants may not only make vaccine less effective but also evade RT-qPCR test. Here we suggest an innovative primer design strategy for the RT-qPCR test of SARS-CoV-2. The principle is that the primers should be designed based on both the nucleic acid sequence and the structure of the protein encoded. The three nucleotides closest to the 3' end of the primer should be the codon which encodes the tryptophan in the structure core. Based on this principle, we designed a pair of primers targeting the nucleocapsid (N) gene. Since tryptophan is encoded by only one codon, any mutation that occurs at this position would change the amino acid residue, resulting in an unstable N protein. This means that this kind of SARS-CoV-2 variant could not survive. In addition, both our data and previous reports all indicate that the mutations occurring at other places in the primers do not significantly affect the RT-qPCR result. Consequently, no SARS-CoV-2 variant can escape detection by the RT-qPCR kit containing the primers designed based on our strategy.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Mutation , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity
15.
Med Oncol ; 39(1): 6, 2021 Nov 08.
Article in English | MEDLINE | ID: covidwho-1506526

ABSTRACT

To assess the prognostic role of different inflammatory indices on the outcome of cancer patients with COVID-19. Sixty-two adults and 22 pediatric cancer patients with COVID-19 infection were assessed for the prognostic value of certain inflammatory indices including the neutrophil to lymphocyte ratio (NLR), monocyte to lymphocyte ratio (MLR), platelet to lymphocyte ratio (PLR), derived NLR (dNLR), systemic inflammation index (SII), mean platelet volume to platelet ratio (MPR), C-reactive protein to lymphocyte ratio (CRP/L), aggregate index of systemic inflammation (AISI), systemic inflammation response index (SIRI), and neutrophil to lymphocyte, platelet ratio (NLPR). Data were correlated to patients' outcome regarding ICU admission, and incidence of mortality. Increased CRP/L ratio in adult COVID-19 cancer patients was significantly associated with inferior survival [152 (19-2253) in non-survivors, compared to 27.4 (0.8-681) in survivors (P = 0.033)]. It achieved a sensitivity (60%) and a specificity (90.2%) at a cut-off 152, while it achieved a sensitivity of 60% and specificity 95.1% at a cut-off 252 (AUC 0.795, P = 0.033). When combining both CRP/L and NLPR for the prediction of poor outcome in adult cancer patients with COVID19, the sensitivity increased to 80% and the specificity was 70.7% (AUC 0.805, P = 0.027). Increased incidence of ICU admission in pediatric cancer patients associated significantly with the severity of covid19 infection, decreased mean corpuscular hemoglobin (MCH) < 28.3, increased red cell distribution width (RDW) > 16, lymphopenia < 1.04, pseudo Pelger-Huet appearance, and PLR < 196.4 (P = 0.004, P = 0.040, P = 0.029, P = 0. 0.039, P = 0.050, and P = 0.040; respectively). The mean corpuscular volume (MCV), MCH, and RDW could be useful prognostic markers for poor outcome in COVID-19 pediatric cancer patients (P < 0.05 for all). Increased both CRP/L and NLPR associated significantly with poor survival in adult COVID-19 cancer patients, while PLR associated significantly with ICU admission in pediatric COVID-19 cancer patients.


Subject(s)
COVID-19/pathology , Inflammation/pathology , Neoplasms/pathology , Adolescent , Adult , Aged , Blood Platelets/pathology , Child , Child, Preschool , Female , Humans , Inflammation/virology , Leukocyte Count/methods , Lymphocytes/pathology , Male , Middle Aged , Neoplasms/virology , Neutrophils/pathology , Prognosis , Retrospective Studies , SARS-CoV-2/pathogenicity , Sensitivity and Specificity , Young Adult
16.
Euro Surveill ; 26(44)2021 Nov.
Article in English | MEDLINE | ID: covidwho-1504717

ABSTRACT

IntroductionNumerous CE-marked SARS-CoV-2 antigen rapid diagnostic tests (Ag RDT) are offered in Europe, several of them with unconfirmed quality claims.AimWe performed an independent head-to-head evaluation of the sensitivity of SARS-CoV-2 Ag RDT offered in Germany.MethodsWe addressed the sensitivity of 122 Ag RDT in direct comparison using a common evaluation panel comprised of 50 specimens. Minimum sensitivity of 75% for panel specimens with a PCR quantification cycle (Cq) ≤ 25 was used to identify Ag RDT eligible for reimbursement in the German healthcare system.ResultsThe sensitivity of different SARS-CoV-2 Ag RDT varied over a wide range. The sensitivity limit of 75% for panel members with Cq ≤ 25 was met by 96 of the 122 tests evaluated; 26 tests exhibited lower sensitivity, few of which failed completely. Some RDT exhibited high sensitivity, e.g. 97.5 % for Cq < 30.ConclusionsThis comparative evaluation succeeded in distinguishing less sensitive from better performing Ag RDT. Most of the evaluated Ag RDT appeared to be suitable for fast identification of acute infections associated with high viral loads. Market access of SARS-CoV-2 Ag RDT should be based on minimal requirements for sensitivity and specificity.


Subject(s)
COVID-19 , SARS-CoV-2 , Antigens, Viral , Diagnostic Tests, Routine , Germany , Humans , Sensitivity and Specificity
17.
Euro Surveill ; 26(44)2021 11.
Article in English | MEDLINE | ID: covidwho-1504591

ABSTRACT

IntroductionThe detection of SARS-CoV-2 with rapid diagnostic tests (RDT) has become an important tool to identify infected people and break infection chains. These RDT are usually based on antigen detection in a lateral flow approach.AimWe aimed to establish a comprehensive specimen panel for the decentralised technical evaluation of SARS-CoV-2 antigen rapid diagnostic tests.MethodsWhile for PCR diagnostics the validation of a PCR assay is well established, there is no common validation strategy for antigen tests, including RDT. In this proof-of-principle study we present the establishment of a panel of 50 pooled clinical specimens that cover a SARS-CoV-2 concentration range from 1.1 × 109 to 420 genome copies per mL of specimen. The panel was used to evaluate 31 RDT in up to six laboratories.ResultsOur results show that there is considerable variation in the detection limits and the clinical sensitivity of different RDT. We show that the best RDT can be applied to reliably identify infectious individuals who present with SARS-CoV-2 loads down to 106 genome copies per mL of specimen. For the identification of infected individuals with SARS-CoV-2 loads corresponding to less than 106 genome copies per mL, only three RDT showed a clinical sensitivity of more than 60%.ConclusionsSensitive RDT can be applied to identify infectious individuals with high viral loads but not to identify all infected individuals.


Subject(s)
COVID-19 , SARS-CoV-2 , Antigens, Viral , Diagnostic Tests, Routine , Humans , Sensitivity and Specificity , Serologic Tests
18.
BMJ Glob Health ; 6(8)2021 08.
Article in English | MEDLINE | ID: covidwho-1504484

ABSTRACT

BACKGROUND: Early access to diagnosis is crucial for effective management of any disease including tuberculosis (TB). We investigated the barriers and opportunities to maximise uptake and utilisation of molecular diagnostics in routine healthcare settings. METHODS: Using the implementation of WHO approved TB diagnostics, Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) and Line Probe Assay (LPA) as a benchmark, we evaluated the barriers and how they could be unlocked to maximise uptake and utilisation of molecular diagnostics. RESULTS: Health officers representing 190 districts/counties participated in the survey across Kenya, Tanzania and Uganda. The survey findings were corroborated by 145 healthcare facility (HCF) audits and 11 policy-maker engagement workshops. Xpert MTB/RIF coverage was 66%, falling behind microscopy and clinical diagnosis by 33% and 1%, respectively. Stratified by HCF type, Xpert MTB/RIF implementation was 56%, 96% and 95% at district, regional and national referral hospital levels. LPA coverage was 4%, 3% below culture across the three countries. Out of 111 HCFs with Xpert MTB/RIF, 37 (33%) used it to full capacity, performing ≥8 tests per day of which 51% of these were level five (zonal consultant and national referral) HCFs. Likewise, 75% of LPA was available at level five HCFs. Underutilisation of Xpert MTB/RIF and LPA was mainly attributed to inadequate-utilities, 26% and human resource, 22%. Underfinancing was the main reason underlying failure to acquire molecular diagnostics. Second to underfinancing was lack of awareness with 33% healthcare administrators and 49% practitioners were unaware of LPA as TB diagnostic. Creation of a national health tax and decentralising its management was proposed by policy-makers as a booster of domestic financing needed to increase access to diagnostics. CONCLUSION: Our findings suggest higher uptake and utilisation of molecular diagnostics at tertiary level HCFs contrary to the WHO recommendation. Country-led solutions are crucial for unlocking barriers to increase access to diagnostics.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis, Pulmonary , Humans , Mycobacterium tuberculosis/genetics , Pathology, Molecular , Rifampin , Sensitivity and Specificity
19.
Sci Rep ; 11(1): 21658, 2021 11 04.
Article in English | MEDLINE | ID: covidwho-1503936

ABSTRACT

More than one year since Coronavirus disease 2019 (COVID-19) pandemic outbreak, the gold standard technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is still the RT-qPCR. This is a limitation to increase testing capacities, particularly at developing countries, as expensive reagents and equipment are required. We developed a two steps end point RT-PCR reaction with SARS-CoV-2 Nucleocapsid (N) gene and Ribonuclease P (RNase P) specific primers where viral amplicons were verified by agarose gel electrophoresis. We carried out a clinical performance and analytical sensitivity evaluation for this two-steps end point RT-PCR method with 242 nasopharyngeal samples using the CDC RT-qPCR protocol as a gold standard technique. With a specificity of 95.8%, a sensitivity of 95.1%, and a limit of detection of 20 viral RNA copies/uL, this two steps end point RT-PCR assay is an affordable and reliable method for SARS-CoV-2 detection. This protocol would allow to extend COVID-19 diagnosis to basic molecular biology laboratories with a potential positive impact in surveillance programs at developing countries.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/genetics , COVID-19/genetics , COVID-19 Nucleic Acid Testing/economics , COVID-19 Testing/methods , Coronavirus Nucleocapsid Proteins/genetics , DNA Primers , Electrophoresis, Agar Gel/methods , Humans , Laboratories , Nasopharynx/virology , RNA, Viral/genetics , Ribonuclease P/genetics , Ribonuclease P/metabolism , SARS-CoV-2/pathogenicity , Sensitivity and Specificity
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