Comparative evaluation of six nucleic acid amplification kits for SARS-CoV-2 RNA detection

Isothermal amplification technology (IAT) for rapid diagnosis of Rickettsioses: scope, overview, existing evidence, and the way forward

Rickettsioses, a category of zoonosis primarily caused by Rickettsia and Orientia, is a huge cause of public health concern worldwide. Diseases like murine typhus, scrub typhus, Mediterranean spotted fever and rocky mountain spotted fever are major contributors of Rickettsioses globally, with peculiar distributions in south-east Asia, Africa, Arabia and the Americas. With the innovations in molecular diagnostics, Isothermal Amplification Technology is gaining popularity for its fidelity, rapidity and cost-effectiveness. Compared to commercial assays, they are easily adaptable for point-of-care (PoC) settings. Due to nonspecific presentation as an acute undifferentiated febrile illness, diagnosis of Rickettsioses poses a great challenge. Certain isothermal amplification assays have proven to be highly efficient in diagnosing vector borne diseases like dengue, malaria, and chikungunya. The purpose of this review is to provide readers the current advancements, scope, challenges, and future prospects of isothermal amplification technologies in the detection of zoonotic pathogens like Rickettsia and Orientia.

The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies

BACKGROUND

The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process.

METHODOLOGY

A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes.

RESULTS

A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively.

CONCLUSIONS

NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.

Comparison of the performance of two real-time fluorescent quantitative PCR kits for the detection of SARS-CoV-2 nucleic acid: a study based on large real clinical samples

Background

The global pandemic of coronavirus disease 2019 (COVID-19) has led to the development of multiple detection kits by national manufacturers for severe acute respiratory syndrome coronavirus 2 viral nucleic acid testing. The purpose of this study is to evaluate the performance of different kits (i.e., Maccura kit and Sansure kit) in real clinical work using clinical samples, which will help with the optimization of the test kits.

Method

During the past three months (March–May 2022), 1399 pharyngeal swabs from suspected COVID-19 patients have been initially screened using the Maccura kit in Jilin, China, and the test results were verified using the Sansure kit. The cycle threshold (Ct) values generated by the two kits were compared at different viral load levels. Correlation and consistency of the Ct values were investigated using Spearman correlation, Deming regression, and Bland–Altman plots. The cut-off Ct values of the Maccura kit were recalculated by referencing the result of the Sansure kit as a standard. Furthermore, another 163 pharyngeal swabs from suspected COVID-19 patients were collected to verify the new cut-off values.

Results

As a result of the Maccura kit testing, 1192 positive cases and 207 suspected COVID-19 cases were verified. After re-examination by the Sansure kit, 1118 positive cases were confirmed. The difference between the Ct values provided by the two kits was statistically significant, except for the N gene at high viral load. The Ct values obtained from the two kits presented a linear positive correlation. The Maccura kit used new cut-off Ct values of 35.00 (ORF1ab gene) and 35.07 (N gene). Based on that, the validation pass rate for the new cut-off Ct values was 91.41%.

Conclusion

Since the Maccura kit is found to have false positives in actual clinical work, recalculation of the cut-off values can reduce this occurrence. In order to improve the accuracy of the testing, laboratories should use two kits for COVID-19 testing, and the adjusting and optimizing of the kits for their situation are needed.

The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk

Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.

Performance Evaluation of Developed Bangasure™ Multiplex rRT-PCR Assay for SARS-CoV-2 Detection in Bangladesh: A Blinded Observational Study at Two Different Sites

In this study, we evaluated the performance of the in-house developed rRT-PCR assay for SARS-CoV-2 RNA targeting the envelope (E) and nucleocapsid (N) genes with internal control as human RNase P. A total of 50 positive samples and 50 negative samples of SARS-CoV-2 were tested by a reference kit at site 1 and a subset (30 positives and 16 negatives) of these samples are tested blindly at site 2. The limit of detection (LoD) was calculated by using a replication-deficient complete SARS-CoV-2 genome and known copy numbers, where Pseudo-virus samples were used to evaluate accuracy. On site 1, among the 50 SARS-CoV-2 positive samples 24, 18, and eight samples showed high (Ct < 26), moderate (26 < Ct ≤ 32), and low (32 < Ct ≤ 38) viral load, respectively, whereas in site 2, out of 30 SARS-CoV-2 positive samples, high, moderate, and low viral loads were found in each of the 10 samples. However, SARS-CoV-2 was not detected in the negative sample. So, in-house assays at both sites showed 100% sensitivity and specificity with no difference observed between RT PCR machines. The Ct values of the in-house kit had a very good correlation with the reference kits. LoD was determined as 100 copies/mL. It also displayed 100% accuracy in mutant and wild-type SARS-CoV-2 virus. This Bangasure™ RT-PCR kit shows excellent performance in detecting SARS-CoV-2 viral RNA compared to commercially imported CE-IVD marked FDA authorized kits.

Research of childhood tuberculosis in suspected populations by molecular methods: A multicenter study in China

The research of childhood tuberculosis is inadequate in china. The cross-priming amplification (CPA) of specific DNA in clinical samples is increasingly adopted for the diagnosis of childhood tuberculosis. In this study, a multicenter research was performed to investigate the incidence and characteristics of childhood tuberculosis in suspected populations mainly by CPA method. 851 children suspected of tuberculosis were enrolled in seven centers across China. All samples were tested by a CPA method and 159 subjects were tested by Xpert MTB/RIF and liquid culture method in parallel to assess the reliability of the CPA method. A positive result in any one of the three methods provided a definitive diagnosis of Mycobacterium tuberculosis complex (MTBC) infection. The MTBC-positive rate was 9.5% (81/851) by the combined methods; 93.8% of the cases were detected by CPA technology (76/81). The rate of pulmonary infection was significantly higher than that of extrapulmonary infection (7.1%, 60/851 vs 2.5%, 21/851; P < 0.001). Scrofula was the predominant type of extrapulmonary tuberculosis. The MTBC positive rates in 12-18-year-old group (middle school), was 28.4% (23/81), higher than in those under-six-year-old (preschool; 39/525) and the 6~11-year-old (primary school; 18/235) groups combined (P < 0.001). The MTBC positive rate in patients with a clear history of tuberculosis exposure was significantly higher than in cases in which there was no history of tuberculosis contact(35.3%, 18/51 vs 7.8%, 61/782; P < 0.001). In conclusion, this multicenter investigation showed that pulmonary tuberculosis and extrapulmonary tuberculosis are not uncommon in children in China, with teenagers being particularly susceptible to infection. The incidence of pulmonary tuberculosis in children is higher than that of extrapulmonary tuberculosis. History of exposure to tuberculosis is a high risk factor for childhood tuberculosis.

A comparison of SARS-CoV-2 RNA extraction with the QuickGene-810 Nucleic Acid Isolation System compared to the EZ1 Advanced DSP Virus Kit

The QuickGene-810 Nucleic Acid Isolation System is a semi-automated extraction platform which may be used for RNA extraction. New methods were required to support the rapid increase in respiratory virus testing during the SARS-CoV-2 pandemic. The aim of this study was to assess SARS-CoV-2 RNA extraction using the QuickGene-810 kit compared to the EZ1 Advanced Extraction Platform for use on the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well RT-PCR assay. Qualitative results from all clinical samples were concordant between the QuickGene-810 and the EZ1 extraction methods, demonstrating that the QuickGene-810 kit is suitable for use in pathogen diagnostics. However, there was an average difference of approximately two cycles between the cycle threshold (Ct) values for both SARS-CoV-2 targets, suggesting that the EZ1 kit yields a higher concentration of nucleic acid extract, possibly related to its use of carrier RNA and/or smaller elution volume, which infers the possibility of false negative results for samples with very low viral loads.

Neutrophil-to-Lymphocyte Ratio and Absolute Lymphocyte Count as Early Diagnostic Tools for Corona Virus Disease 2019

Background and objectives

In comparison to real-time polymerase chain reaction (RT-PCR) testing, blood-related parameters including absolute lymphocyte count (ALC) and neutrophil-to-lymphocyte ratio (NLR) carry an indeterminate potential in the assessment of corona virus disease 2019 (COVID-19). Our main objective was to assess their efficacy in timely identification of COVID-19 patients and to determine whether these biomarkers can be employed as an early diagnostic tool in patients presenting with symptoms suggestive of COVID-19.

Methodology

This cross-sectional study was conducted at the Emergency Department of a Tertiary Care Hospital in Rawalpindi, Pakistan from November 2020 to March 2021. Patients suspected to have COVID-19 on a clinical basis (fever, cough or shortness of breath) were selected by using convenience non-probability sampling. RT-PCR was used to diagnose COVID-19 after evaluating NLR and ALC of the sample population. An NLR = 3.5 and ALC < 1 x 10³ cells/mm³ was considered as the cut-off value. Statistical analysis was conducted via SPSS 23.0 (IBM Corp., Armonk, NY). Chi-square and independent t-tests were used to correlate various data variables, while p-value <0.05 was considered significant.

Results

Out of the 172 subjects included in the study, the mean age was 40.6 ± 10.0 years, while 51% of individuals were males. Fever was found to be the most prevalent complaint (94%). Double RT-PCR testing showed that 51.2% of the population was RT-PCR positive, having a mean ALC of 1.4 ± 0.9 x 10³/mm³, significantly lower than RT-PCR negative cases (p < 0.001). In addition, NLR was drastically elevated for RT-PCR-positive individuals (p < 0.001) while it also had a distinctly high specificity of 91.7% among COVID-19 patients. Additionally, NLR did not correlate with any of the baseline patient-related parameters (presenting complaint, age, and gender).

Conclusion

NLR and ALC are potentially efficacious measures for an early diagnosis of COVID-19, and can be possibly utilized for an early diagnosis of COVID-19 suspects.