Vitality of Proteinase K in rRTPCR Detection of SARS-CoV2 Bypassing RNA Extraction

SARS-CoV-2 RT-LAMP in saliva: enhancing the results via a combination of cooling and specimen dilution procedure

Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a potential and relatively simple rapid diagnostics method for COVID-19 detection. This study aims to evaluate and optimize the RT-LAMP performance on saliva specimens based on a commercially available kit.Modifications on an established protocol (Protocol A) were used, including Proteinase K supplementation (Protocol B); pre-treatment using nuclease-free water and proteinase K (Protocol C); Saliva cooling (Protocol D); saliva dilution after pre-treatment (Protocol E); lastly a combination of saliva cooling and dilution (Protocol F). Protocol performances were evaluated by comparing success rates (SR), diagnostic accuracy (DA), sensitivity, specificity, and predictive values. Additionally, a correlation between the Ct value by RT-qPCR and RT-LAMP performance was analyzed.. A total of 106 specimens were used in this study. Protocols B and C showed 100% unreadable results, therefore were paused. Protocol F showed the highest SR (87.65%) compared to other protocols, with a slight compromise to DA (81.69%), sensitivity (57.14%), specificity (97.67%), PPV (94.12%), and NPV (77.78%). In the sub-analysis of the low Ct value group (Ct < 30), Protocol F demonstrated a higher success rate (86.57%) compared to protocol A (64.18%); increased 3.08% sensitivity and 2.42% NPV; comparable DA; minor reduction in specificity (A = 100%; F = 97.67%) and PPV (A = 100%; F = 92.31%). A combination of saliva cooling-dilution substantially increased the tested kit's success rate, despite a slight decrease in specificity and PPV. Findings confirmed the saliva cooling-dilution procedure was beneficial to the test's SR, sensitivity, and NPV in the low Ct value group.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00870-1.

A Comprehensive Comparison of Rapid RNA Extraction Methods for Detection of SARS-CoV-2 as the Infectious Agent of the Upper Respiratory Tract using Direct RT-LAMP Assay

Background

The current COVID-19 pandemic has highlighted the need for faster and more cost-effective diagnostic methods. The RNA extraction step in current diagnostic methods, such as real-time qPCR, increases the cost and time required for testing. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a promising technique for developing diagnostic tests with desired sensitivity and specificity without the need for RNA extraction.

Materials and Methods

An RT-LAMP assay was developed to detect SARS-CoV-2 with a sensitivity of 0.5 copies of positive control plasmid per microliter in 40 min. Several rapid RNA extraction protocols were evaluated using different reagents, including bovine serum albumin, Triton X-100, Tween 20, proteinase K, guanidine hydrochloride, guanidinium isothiocyanate (GITC), and thermal treatment. Finally, the sensitivity and specificity of the developed direct RT-LAMP were determined using 150 upper respiratory tract samples.

Results

Method 10 was selected as the most efficient protocol for the RNA extraction step. The sensitivity and specificity of the developed direct RT-LAMP assay with clinical samples were estimated at 98.4% and 88.8%, respectively.

Conclusion

These results suggest that the combination of GITC and Triton X-100 detergent is a highly efficient method for RNA extraction and direct RT-LAMP detection of SARS-CoV-2 in clinical samples, providing a valuable tool for the rapid and cost-effective diagnosis of COVID-19.

Critical evaluation of strategies to achieve direct real-time PCR detection of swine pathogens in oral fluids

Based on publications reporting improvements in real-time PCR (rtPCR) performance, we compared protocols based on heat treatment or dilution followed by direct rtPCR to standard extraction and amplification methods for the detection of porcine reproductive and respiratory syndrome virus (PRRSV), influenza A virus (IAV), porcine epidemic diarrhea virus (PEDV), or Mycoplasma hyopneumoniae (MHP) in swine oral fluids (OFs). In part A, we subjected aliquots of positive OF samples to 1 of 4 protocols: protocol 1: heat (95°C × 30 min) followed by direct rtPCR; protocol 2: heat and cool (25°C × 20 min) followed by direct rtPCR; protocol 3: heat, cool, extraction, and rtPCR; protocol 4 (control): extraction and then rtPCR. In part B, positive OF samples were split into 3, diluted (D1 = 1:2 with Tris-borate-EDTA (TBE); D2 = 1:2 with negative OF; D3 = not diluted), and then tested by rtPCR using the best-performing protocol from part A (protocol 4). In part A, with occasional exceptions, heat treatment resulted in marked reduction in the detection of target and internal sample control (ISC) nucleic acids. In part B, sample dilution with TBE or OF produced no improvement in the detection of targets and ISCs. Thus, standard extraction and amplification methods provided superior detection of PRRSV, IAV, PEDV, and MHP nucleic acids in OFs.