Effects of chemical & biological warfare agent decontaminants on trace survival: Impact on DNA profiling from blood and saliva

Forensic investigations following incidents involving chemical or biological agents present considerable challenges. Understanding the possibilities and limitations can aid in determining the most suitable procedures and enhancing the recovery of useful traces in these complex situations. This work complements previously published results on the effects of decontaminants on fingermarks deposited on glass. Identifying the perpetrators can be crucial, and DNA analysis remains a cornerstone in this regard. In this study, we investigated the ability to obtain usable DNA profiles from blood and saliva (pure and diluted) exposed to 16 different decontamination methods. Both DNA quantitation and DNA profiling were considered to assess the outcomes. The results revealed considerable variability but indicated that biological agents' decontaminants hindered DNA profiling post-decontamination to a greater extent than decontaminants aimed for chemical agents. Chlorine-based decontaminants also globally had a deleterious impact on DNA profiling. Powder decontaminants such as Fast-Act, CHpowder, and the liquid decontaminants GDS2000 did not affect DNA profiling.

The Effectiveness of ddPCR for Detection of Point Mutations in Poor-Quality Saliva Samples

Background: The noninvasive collection of saliva samples for DNA analyses is simple, and its potential for research and diagnostic purposes is great. However, DNA isolates from such samples are often of inferior quality to those from blood. Aim: The aim of this study was to investigate the robustness and sensitivity of the ddPCR instrument for genetic analyses from saliva samples of poor quality by comparing their results to those obtained using an established method from blood samples. Methods: Blood and saliva were collected from 47 university students, which was followed by manual isolation of DNA and analysis on droplet digital PCR (ddPCR). Results of analyses were supplemented with values of fractional abundances. Results: ddPCR proved to be highly suitable for analysis of even low-quality saliva samples (concentrations as low as 0.79 ng/µL), especially when augmented by fractional abundance data. This combination yielded 100% agreement with results obtained from blood samples. Conclusion: This study verified the applicability of ddPCR as a sensitive and robust method of genetic diagnostic testing even from low-quality saliva isolates. This makes it potentially suitable for a wide range of applications and facilitates the performance of large epidemiological studies, even if sampling or sample processing is suboptimal.

[A non-invasive method for detecting mitochondrial tRNAThr15927G>A mutation]

OBJECTIVE

To explore the feasibility of detecting maternal hereditary mitochondrial tRNA^Thr15927G>A (m.15927G>A) mutation using buccal swabs.

METHODS

We performed sequence analysis of mitochondrial DNA in blood samples from 2070 cases of maternal hereditary mitochondrial disease in the First Affiliated Hospital of Wenzhou Medical University, and identified 3 patients with m.15927G>A mutation.Buccal swabs and blood samples were obtained from the 3 patients (mutation group) and 3 normal volunteers (control group).After extracting whole genomic DNA from all the samples, the DNA concentration and purity were analyzed.The PCR products were subjected to dot blot hybridization, Southern blot hybridization, and DNA sequencing analysis to verify the feasibility of detecting m.15927G>A mutation using buccal swabs.

RESULTS

There was no significant difference in DNA concentration extracted from buccal swabs and blood samples in either the mutation group or the control group (P > 0.05), but the purity of manually extracted oral mucosa DNA was significantly lower than that of whole blood and oral mucosa DNA extracted using commercial kits (P < 0.05).Dot blot hybridization and Southern blot hybridization both yielded positive results in the control group but negative results in the mutation group.DNA sequencing identified m.15927G>A mutation in all the samples from the mutation group.

CONCLUSIONS

Buccal swabs collection accurate is an accurate and sensitive method for the detection of m.15927G>A mutation.

Loop-mediated isothermal amplification for the detection of SARS-CoV-2 in saliva

In the fight against the recent COVID-19 pandemics, testing is crucial. Nasopharyngeal swabs and real-time RT-PCR are used for the detection of the viral RNA. The collection of saliva is non-invasive, pain-free and does not require trained personnel. An alternative to RT-PCR is loop-mediated isothermal amplification coupled with reverse transcription (RT-LAMP) that is easy to perform, quick and does not require a thermal cycler. The aim of this study was to test whether SARS-CoV-2 RNA can be detected directly in saliva using RT-LAMP. We have tested 16 primer mixes from the available literature in three rounds of sensitivity assays. The selected RT-LAMP primer mix has a limit of detection of 6 copies of viral RNA per reaction in comparison with RT-PCR with 1 copy per reaction. Whole saliva, as well as saliva collected using Salivette collection tubes, interfered with the RT-LAMP analysis. Neither Chelex-100 nor protease treatment of saliva prevented the inhibitory effect of saliva. With the addition of the ribonuclease inhibitor, the sensitivity of the RT-LAMP assay was 12 copies per reaction of RNA in Salivette® saliva samples and 6 copies per reaction of RNA in whole saliva samples. This study shows that it is possible to combine the use of saliva and RT-LAMP for SARS-CoV-2 RNA detection without RNA extraction which was confirmed on a small set of correctly diagnosed clinical samples. Further studies should prove whether this protocol is suitable for point of care testing in the clinical setting.

Salivary creatinine and urea are higher in an experimental model of acute but not chronic renal disease

Plasma creatinine and urea are commonly used markers of kidney function in both acute and chronic renal failure. The needed repeated blood collection is associated with pain, stress and might lead to infections. Saliva has the potential to be a non-invasive alternative diagnostic fluid. The use of saliva in clinical practice is limited, since many factors affect the concentration of salivary biomarkers. The aim of our study was to analyze salivary creatinine and urea in the animal models of acute and chronic renal disease. Bilateral nephrectomy and adenine nephropathy were induced in adult male mice. Both, plasma creatinine and urea were higher in animals with renal failure compared to controls. Salivary creatinine was higher by 81% and salivary urea by 43% in comparison to the control group, but only in animals with bilateral nephrectomy and not in adenine nephropathy. Our results indicate that the increase of salivary creatinine and urea depends on the experimental model of renal failure and its severity. Further studies are needed to monitor the dynamics of salivary markers of renal function and to reveal determinants of their variability.

Effect of preparation method and storage period on the stability of saliva DNA

Saliva is an attractive source for oral microbial detection and quantification since sampling is non-invasive and rapid.

OBJECTIVES

To determine whether different saliva preparation methods or preservation time periods affect DNA stability.

METHODS

Saliva samples from 4 healthy adult volunteers were processed to obtain 3 different preparations: whole saliva, and after centrifugation pellet and supernatant. Purified DNA (MasterPure™) from each sample was divided into 4 aliquots, one for immediate analysis and 3 (stored at -80°C) for later analyses after 1 week and 2 and 6 months. DNA concentrations and qPCR based quantities of Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, Fusobacterium nucleatum, Filifactor alocis and Streptococcus mutans were determined.

RESULTS

DNA concentration did not decrease (P>0.05) during the 6-month period in any sample. Mean (SE) DNA concentrations (ng/μl) in whole saliva were 152.2 (51.2) and 147.8 (50) at day 0 and 6 months, respectively. Similarly, the values for pellet were 134.9 (42.5) and 133.6 (42.9), and for supernatant, 11 (1.9) and 8.9 (2.3), the difference being significant (P<0.001) between supernatant and whole saliva or pellet. The quantities of most bacterial species found at day 0 remained stable over the 6-month period in all saliva preparations. In supernatant, species quantities were lower (P<0.05) than in whole saliva or pellet.

CONCLUSIONS

DNA concentrations were comparable between whole saliva and pellet, suggesting that either of them can be used for DNA-based analyses. Our results also demonstrated that DNA extracted from saliva can be preserved at -80°C for at least 6 months without decrease in DNA concentration.

Saliva DNA quality and genotyping efficiency in a predominantly elderly population

BACKGROUND

The question of whether DNA obtained from saliva is an acceptable alternative to DNA from blood is a topic of considerable interest for large genetics studies. We compared the yields, quality and performance of DNAs from saliva and blood from a mostly elderly study population.

METHODS

Two thousand nine hundred ten DNAs from primarily elderly subjects (mean age ± standard deviation (SD): 65 ± 12 years), collected for the Primary Open-Angle African-American Glaucoma Genetics (POAAGG) study, were evaluated by fluorometry and/or spectroscopy. These included 566 DNAs from blood and 2344 from saliva. Subsets of these were evaluated by Sanger sequencing (n = 1555), and by microarray SNP genotyping (n = 94) on an Illumina OmniExpress bead chip platform.

RESULTS

The mean age of subjects was 65, and 68 % were female in both the blood and saliva groups. The mean ± SD of DNA yield per ml of requested specimen was significantly higher for saliva (17.6 ± 17.8 μg/ml) than blood (13.2 ± 8.5 μg/ml), but the mean ± SD of total DNA yield obtained per saliva specimen (35 ± 36 μg from 2 ml maximum specimen volume) was approximately three-fold lower than from blood (106 ± 68 μg from 8 ml maximum specimen volume). The average genotyping call rates were >99 % for 43 of 44 saliva DNAs and >99 % for 50 of 50 for blood DNAs. For 22 of 23 paired blood and saliva samples from the same individuals, the average genotyping concordance rate was 99.996 %. High quality PCR Sanger sequencing was obtained from ≥ 98 % of blood (n = 297) and saliva (n = 1258) DNAs. DNA concentrations ≥10 ng/μl, corresponding to total yields ≥ 2 μg, were obtained for 94 % of the saliva specimens (n = 2344).

CONCLUSIONS

In spite of inferior purity, the performance of saliva DNAs for microarray genotyping was excellent. Our results agree with other studies concluding that saliva collection is a viable alternative to blood. The potential to boost study enrollments and reduce subject discomfort is not necessarily offset by a reduction in genotyping efficiency. Saliva DNAs performed comparably to blood DNAs for PCR Sanger sequencing.

Salivary markers of kidney function - Potentials and limitations

Saliva can be collected non-invasively, repeatedly and without trained personnel. It is a promising diagnostic body fluid with clinical use in endocrinology and dentistry. For decades, it is known that saliva contains also urea, creatinine and other markers of renal function. Clinical studies have shown that the salivary concentrations of these markers could be useful for the assessment of kidney function without the need of blood collection. This article summarizes the clinical and experimental data on the use of saliva as a diagnostic fluid in nephrology and points out the advantages, pitfalls, technical requirements and future perspective for the use of saliva as a novel potential diagnostic biofluid.

Organization, barrier function and antimicrobial lipids of the oral mucosa

As one moves from the skin across the vermilion region of the lip and into the oral cavity, the oral mucosa is encountered. The oral mucosa consists of connective tissue known as the lamina propria covered by a stratified squamous epithelium. In the regions of the hard palate and gingiva, the epithelium is keratinized like the epidermis. In the buccal region, the floor of the mouth and the underside of the tongue, the epithelium is non-keratinized. The epithelium on the dorsum of the tongue is a specialized epithelium, but can be approximated as a mosaic of keratinized and non-keratinized epithelia. The non-keratinized epithelial regions do not produce a stratum corneum. Nuclei with intact DNA are retained in the superficial cells. In all regions, the outer portions of the epithelium provide a protective permeability barrier, which varies regionally. Antimicrobial lipids at the surfaces of the oral mucosa are an integral part of innate immunity.

Comparative evaluation of saliva collection methods for proteome analysis

BACKGROUND

Saliva collection devices are widely used for large-scale screening approaches. This study was designed to compare the suitability of three different whole-saliva collection approaches for subsequent proteome analyses.

METHODS

From 9 young healthy volunteers (4 women and 5 men) saliva samples were collected either unstimulated by passive drooling or stimulated using a paraffin gum or Salivette® (cotton swab). Saliva volume, protein concentration and salivary protein patterns were analyzed comparatively.

RESULTS

Samples collected using paraffin gum showed the highest saliva volume (4.1±1.5 ml) followed by Salivette® collection (1.8±0.4 ml) and drooling (1.0±0.4 ml). Saliva protein concentrations (average 1145 μg/ml) showed no significant differences between the three sampling schemes. Each collection approach facilitated the identification of about 160 proteins (≥2 distinct peptides) per subject, but collection-method dependent variations in protein composition were observed.

CONCLUSION

Passive drooling, paraffin gum and Salivette® each allows similar coverage of the whole saliva proteome, but the specific proteins observed depended on the collection approach. Thus, only one type of collection device should be used for quantitative proteome analysis in one experiment, especially when performing large-scale cross-sectional or multi-centric studies.

A comparison of molecular methods for hepatitis B virus (HBV) DNA detection from oral fluid samples

The objective of the present study was to evaluate four commercial DNA extraction methods and three PCR protocols for hepatitis B virus (HBV) detection in artificially contaminated oral fluid samples. The extraction protocols were selected based on ease of use and cost, and were also compared with respect to sensitivity and cost. Prior PCR optimization was conducted, in which the sample volume for DNA extraction and the concentrations of DNA and Taq DNA polymerase in the PCR were adjusted. One-round PCR, used to amplify the core region of the HBV genome, achieved high levels of sensitivity in comparison with nested and semi-nested PCR experiments that were designed for the amplification of HBV surface protein genes. Of the four extraction protocols evaluated, the RTP DNA/RNA Virus Mini kit and the QIAamp DNA Mini kit gave the highest recovery rates, presenting 20 copies of HBV DNA ml(-1) as the limit of detection. These results suggest that HBV DNA can be detected from oral fluid samples but that the optimization of the PCR assays and the choice of extraction methods must be determined by laboratories before the implementation of this method in routine diagnostics.