The effect of saliva specimen collection, handling and storage protocols on hepatitis C virus (HCV) RNA detection by PCR

Stabilization of Salivary Biomarkers

The use of saliva as a diagnostic biofluid has been increasing in recent years, thanks to the identification and validation of new biomarkers and improvements in test accuracy, sensitivity, and precision that enable the development of new noninvasive and cost-effective devices. However, the lack of standardized methods for sample collection, treatment, and storage contribute to the overall variability and lack of reproducibility across analytical evaluations. Furthermore, the instability of salivary biomarkers after sample collection hinders their translation into commercially available technologies for noninvasive monitoring of saliva in home settings. The present review aims to highlight the status of research on the challenges of collecting and using diagnostic salivary samples, emphasizing the methodologies used to preserve relevant proteins, hormones, genomic, and transcriptomic biomarkers during sample handling and analysis.

Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFY™) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS^® easyMAG^®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs. 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

Detection of Hepatitis C Virus-RNA in Saliva from Chronically HCV-Infected Patients

The possibility of the non-parenteral Hepatitis C Virus (HCV) transmission is supported by the demonstration that the actual virus is present in several body fluids, including saliva. From a review of the literature many investigators have found the presence of HCV-RNA in saliva, however, widely contrasting results emerge, with detection rates ranging from 0–100%. To further examine HCV salivary shedding, saliva samples were collected from 46 chronically HCV-infected patients and tested for HCV-RNA and occult blood. Quantification and genotyping of serum HCV-RNA were also carried out for each patient. HCV-RNA was detected in 39.13% of the saliva samples. The viral salivary shedding was significantly related to viraemia levels, serum viral genotype and the presence of salivary occult blood. Our findings indicate that the HCV salivary shedding occurs in about one third of HCV-infected patients, but seem to suggest that it is unlikely when the serum viral genotype is 3a. Moreover, blood leakage into the oral cavity is possibly the main source of the salivary HCV-RNA. Although the occurrence of the viral salivary shedding does not necessarily mean that HCV trasmission occurs by saliva, our results suggest the need for further investigations into the biological factors possibly involved in HCV mucosal transmission related to both the source and the exposed subjects.

Evaluation of viral load in saliva from patients with chronic hepatitis C infection

Hepatitis C virus can be detected in blood and other bodily fluids, such as saliva. The aim of this study was to detect and quantify the HCV-RNA in saliva and plasma from patients with chronic hepatitis C infections, as well as check the level of viral load in sex groups (age, ethnicity and virus subtypes). Whole saliva and blood from 70 patients with chronic hepatitis C infections attended at the department of gastroenterology from University Hospital. The HCV-RNA load was performed by qRT-PCR using Sybr Green I master mix. HCV-RNA was detected in 80% (56/70) of patients in saliva and 92.85% (65/70) in plasma. The median of the viral load in the plasma was of 4.87 log10, and in saliva, it was 3.32log10, (p = 0.0005). Female patients and black patients exhibited a negative correlation between the HCV-RNA load in saliva vs. the HCV-RNA load in plasma (r = -0.3172, CI95% -0.6240 to -0.03736, p = 0.0491) and (r = -0.3141; IC95% -0.6069 to -0.05926; p = 0.0209), respectively. HCV-RNA was detected and quantified in saliva samples, and according to the quantification levels, saliva may be a possible transmission source of HCV, particularly in women and people of black ethnicity who develop chronic HCV infections.

Effect of handling and storage conditions and stabilizing agent on the recovery of viral RNA from oral fluid of pigs

•

Inactivation of salivary enzymes by heating oral fluid for 15 min at 60 °C was detrimental to hepatitis E virus (HEV) RNA.

•

HEV, F-RNA coliphage and murine norovirus RNA are not degraded in oral fluid stored at 4 °C for ≤24 h.

•

Recovery of HEV RNA from oral fluid after 30 days at −20 °C was higher in the absence of RNA stabilizer.

•

RNeasy Protect Saliva Mini kit does not work well for viral RNA.

There is an increasing interest in using oral fluid to determine herd health and documenting the circulation of viruses in commercial swine populations but little is known about the stability of viruses in oral fluid. Hepatitis E virus (HEV) is a zoonotic virus which is widespread in swine herds. Information on optimal handling methods such as heat treatments, freezing and RNA stabilization agents is needed to prevent or minimize degradation of viral RNA by degradative enzymes. The objectives of the study were to determine optimum handling conditions of the oral fluid before RNA extraction and to compare the performance of the RNeasy Protect Saliva Mini kit, which contains a stabilizing agent, with that of the QIAamp Viral RNA Mini kit, which does not contain a stabilizing agent. Preliminary studies with oral fluid inoculated with HEV indicated that a heat treatment of 60 °C for 15 min was detrimental to HEV RNA. HEV was recovered from 25/25 and 24/25 samples of oral fluid when samples were incubated for ≤24 h at 4 °C and 30 days at −20 °C, respectively, without a stabilizing agent and extracted with the QiaAMP kit. In contrast, HEV RNA was detected in 16/25 and 11/25 samples when samples were incubated with a stabilizing agent for 24 h at 37 °C and 30 days at −20 °C, respectively, and extracted with the RNeasy Protect Saliva kit. Moreover, the mean number of genome copies/ml of HEV recovered from oral fluid stored at −20 °C without the stabilizing agent was 2.9 log units higher than oral fluid stored at −20 °C in the presence of the stabilizing agent. The recovery of RNA from HEV, F-RNA coliphage MS2 and murine norovirus (MNV), which are surrogates for norovirus, was significantly greater when oral fluid was incubated for 24 h at 4 °C than when oral fluid was stabilized with RNAprotect Saliva Reagent for 24 h at 37 °C, where the relative differences between the two processes were 1.4, 1.8, and 2.7 log genome copies/ml for MS2, MNV, and HEV, respectively. The findings suggest that it is unnecessary to stabilize oral fluid from swine for the detection of viral RNA, provided the samples are stored at 4 °C or frozen at −20 °C, and that the RNeasy Protect Saliva Mini kit did not perform well for the detection of viral RNA.

Comparison of salivary collection and processing methods for quantitative HHV-8 detection

OBJECTIVES

Saliva is a proved diagnostic fluid for the qualitative detection of infectious agents, but the accuracy of viral load determinations is unknown. Stabilising fluids impede nucleic acid degradation, compared with collection onto ice and then freezing, and we have shown that the DNA Genotek P-021 prototype kit (P-021) can produce high-quality DNA after 14 months of storage at room temperature. Here we evaluate the quantitative capability of 10 collection/processing methods.

METHODS

Unstimulated whole mouth fluid was spiked with a mixture of HHV-8 cloned constructs, 10-fold serial dilutions were produced, and samples were extracted and then examined with quantitative PCR (qPCR). Calibration curves were compared by linear regression and qPCR dynamics.

RESULTS

All methods extracted with commercial spin columns produced linear calibration curves with large dynamic range and gave accurate viral loads. Ethanol precipitation of the P-021 does not produce a linear standard curve, and virus is lost in the cell pellet. DNA extractions from the P-021 using commercial spin columns produced linear standard curves with wide dynamic range and excellent limit of detection.

CONCLUSION

When extracted with spin columns, the P-021 enables accurate viral loads down to 23 copies μl(-1) DNA. The quantitative and long-term storage capability of this system makes it ideal for study of salivary DNA viruses in resource-poor settings.

Saliva specimen sampling: a noninvasive method for diagnosis and basic investigation of viral hepatitis A, B and C

Saliva is a biological fluid that is easy to collect and manipulate. Collection of saliva samples is less expensive, noninvasive and painless compared with blood collection. Due to these advantages, saliva has been investigated as an alternative fluid to serum for diagnostic and epidemiological purposes. The aim of this article was to the review research on salivary biomarkers of viral hepatitis A, B and C, highlighting their current use, collection devices, and potential applications for diagnosis and epidemiological studies. This paper also explores recent findings of saliva as a possible source of viral hepatitis transmission.

Importance of collection methods and stability of oral fluid samples for hepatitis B surface antigen detection

BACKGROUND

Oral fluid (OF) sample collection and stability for HBsAg detection are not fully established. This study aims to investigate the applicability of OF collectors and sample stability for Hepatitis B virus surface antigen detection.

METHODS

Paired serum and OF samples were obtained from 191 individuals, and Chembio (Chembio Diagnostic System, USA) and Salivette (Sarstedt, Germany) devices were used for OF collection. Two HBsAg enzyme immunoassays (EIAs) were used (HBsAg One kit, Radim, Rome, Italy and ETI-MAK-4, DiaSorin, Vercelli, Italy) to determine the most efficient method according OF collector. Sample volume, incubation time, and cutoff (CO) value were evaluated. The stability of OF samples was determined under different environmental conditions.

RESULTS

Chembio samples analyzed using DiaSorin EIA without modification of the manufacturer's instructions, demonstrated a sensitivity of 95.24% and a specificity of 100%. Salivette samples analyzed with Radim EIA with receiver operating characteristic (ROC) curve for calculating the CO showed a sensitivity of 78.26% and a specificity of 89.88%. HBsAg was detected in Chembio and Salivette samples under different environmental conditions, but the Chembio samples were the most stable.

CONCLUSIONS

Both collectors can be used for HBsAg detection in OF samples, but some modifications of commercial EIAs should be incorporated for Salivette device. OF samples were reliably stable and could be stored for up to 90 days at 2-8°C.

Oral fluid and hepatitis A, B and C: a literature review

BACKGROUND AND AIMS

Viral hepatitis is a significant global health problem that, depending upon the virus, affects individuals of the developing and/or developed world. In recent years, there has been renewed interest in whether oral fluids can be considered as a source of viral hepatitis transmission and whether oral fluid, in particular, whole saliva, may be a useful source for viral detection as part of the diagnosis and monitoring of viral hepatitis. The aim of this article was to review current data concerning the possible carriage of the hepatitis A, B and C viruses within saliva and gingival crevicular fluid. Such knowledge will indicate if (i) oral fluid is a possible source of infection and (ii) whether oral fluid can be used for diagnosis and monitoring of viral hepatitis.

DATA AND SOURCES

A literature search was conducted using PubMed (Medline), EMBASE/Excerpta medica, the Cochrane database and Scopus. The results were limited to published material after 2000. Relevant material was evaluated and reviewed.

CONCLUSION

There is some evidence that hepatitis viruses A, B and C are present in oral fluids, particularly whole saliva and gingival crevicular fluid and may thus be possible sources of viral detection in clinical diagnosis and monitoring. However, the data are inconsistent and warrant the need for well-planned longitudinal studies to explore the precise frequency of oral carriage of such viruses and to determine the virological and host factors that may influence the oral presence of hepatitis A, B and C viruses.

Detection of Porcine reproductive and respiratory syndrome virus infection in porcine oral fluid samples: a longitudinal study under experimental conditions

Isolation of Porcine reproductive and respiratory syndrome virus (PRRSV) from oral fluids was first reported in 1997. The objective of the present study was to determine whether PRRSV and/or anti-PRRSV antibodies were present in oral fluids at diagnostic levels. The level and duration of PRRSV and anti-PRRSV antibodies in serum and oral fluids was evaluated in 3 age groups of pigs (4, 8, or 12 weeks of age) inoculated with a type 2 (North American) PRRSV isolate. Serum, buccal swabs, and pen-based oral fluid samples were collected for 63 days following inoculation. Specimens were assayed for PRRSV by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), and for anti-PRRSV antibodies by enzyme-linked immunosorbent assay (ELISA) and indirect fluorescent antibody test (IFAT). Porcine reproductive and respiratory syndrome virus was detected by real-time qRT-PCR in serum for approximately 5 weeks and in oral fluids for approximately 4 weeks postinoculation. Pig age at the time of inoculation had no effect on the quantity or duration of virus in oral fluid samples. Low levels of anti-PRRSV antibody were detected in oral fluid samples by ELISA and IFAT. Although the approach remains to be validated in the field, the results of this experiment suggest that pen-based oral fluid sampling could be an efficient, cost-effective approach to PRRSV surveillance in swine populations.

Proteomic Studies of Saliva: A Proposal for a Standardized Handling of Clinical Samples

Background

In recent years, differential analysis of proteins from human saliva, i.e., proteomic analysis, has received much attention mainly due to its unstressful sampling and its great potential for biomarker research. It is widely considered that saliva is a highly stable medium for proteins thanks to a large amount of antiprotease agents, even at ambient and physiological temperatures.

Objective

To find the best protocol for the handling of samples, we have investigated the stability of saliva proteins stored at different temperatures (from −80 to 20°C) by one- and two-dimensional electrophoresis.

Results

At 20°C, no major changes were observed on protein one-dimensional profiles following 1 day of storage; however, between 7 days and 30 days, the native alpha-amylase band decreased slightly to give several bands with molecular weight between 35 and 25 kDa. The same phenomenon appeared after 30 days of storage at 4°C. Two-dimensional analysis of salivary maps revealed degradation from day 7 of several protein groups for samples stored at 20°C.

Conclusion

All these findings have to be carefully considered when saliva is collected for clinical proteomic analysis. We can conclude that, to maintain the optimum stability of saliva proteins, saliva samples should be collected on ice followed by the addition of protease inhibitor cocktail, centrifuged to remove insoluble material, and stored at −20 or −80°C.

Detection of Ebola virus in oral fluid specimens during outbreaks of Ebola virus hemorrhagic fever in the Republic of Congo

BACKGROUND

Patients who have refused to provide blood samples has meant that there have been significant delays in confirming outbreaks of Ebola virus hemorrhagic fever (EVHF). During the 2 EVHF outbreaks in the Republic of Congo in 2003, we assessed the use of oral fluid specimens versus serum samples for laboratory confirmation of cases of EVHF.

METHODS

Serum and oral fluid specimens were obtained from 24 patients with suspected Ebola and 10 healthy control subjects. Specimens were analyzed for immunoglobulin G antibodies by enzyme-linked immunosorbent assay (ELISA) and for Ebola virus by antigen detection ELISA and reverse-transcriptase polymerase chain reaction (RT-PCR). Oral fluid specimens were collected with a commercially available collection device.

RESULTS

We failed to detect antibodies against Ebola in the oral fluid specimens obtained from patients whose serum samples were seropositive. All patients with positive serum RT-PCR results also had positive results for their oral fluid specimens.

CONCLUSIONS

This study demonstrates the usefulness of oral fluid samples for the investigation of Ebola outbreaks, but further development in antibodies and antigen detection in oral fluid specimens is needed before these samples are used for filovirus surveillance activities in Africa.

The IgG antibody profile to various antigen regions of hepatitis C virus differs in oral fluid and serum of patients with chronic hepatitis C

Antibodies to hepatitis C virus (HCV) can be detected not only in serum but also in oral fluid. The aim of the study was to determine IgG antibody reactivity directed to six antigen regions of HCV in oral fluid and to evaluate the significance of the antibody pattern in oral fluid compared to serum. Oral fluid and serum samples of 32 HCV viremic patients were collected to detect antibodies to six antigen regions incorporated as antigen bands into modified commercial updated third generation line immuno-assay. Compared to serum, a significantly lower cumulative antibody response and reactivity to five HCV antigens was found in oral fluid. The significantly highest prevalence of oral fluid reactivity was recorded with antigen C1 (78%), whereas in serum the most significantly frequent reactivity was detected with antigen NS3 (100%). The absence of antibody reactivity with antigen E2 was similar in both body fluids. The discrepancy in antibody pattern to HCV antigens between oral fluid and serum indicates the possible existence of local viral replication, viral mutants, viral inhibitors in oral cavity and, most probably, leakage of the muco-vascular barrier.

Use of versant TMA and bDNA 3.0 assays to detect and quantify hepatitis C virus in semen

Previous findings of hepatitis C virus (HCV) in human semen have been inconsistent. This study attempted to elucidate the presence of HCV in semen from 80 HCV RNA blood plasma positive homeless men using two novel non-PCR based techniques. Semen was frozen immediately upon ejaculation in order to preserve virus quantity. This study demonstrated that 36% of the study population had HCV in semen. Bayer's Versant HCV RNA Qualitative Assay (Bayer Diagnostics, Emeryville, CA) based on transcription mediated amplification (TMA) assay detected 29 positive semen samples and Versant HCV RNA 3.0 Assay (bDNA) (Bayer Diagnostics, Emeryville, CA) detected only six. This demonstrated that TMA was more sensitive than the bDNA in detecting HCV in semen (P<0.002). HCV blood plasma viral load was positively correlated with the presence of HCV in semen (Spearman's Rho=0.40, P<0.0002), while the presence of leukocytes in semen was not (Spearman's Rho=0.19, P<0.12). This supports the hypothesis that HCV is "leaked out" from the peripheral circulation into semen. Three semen samples had a viral load of >5000 IU/mL. The presence of a high viral load in semen in certain men suggests that sexual transmission of the virus is possible. Laboratory capability to accurately detect HCV positive semen is an important step in establishing the risk of sexual transmission and in identifying strategies for protecting uninfected partners.

Detection of HCV RNA in saliva of patients with hepatitis C virus infection by using a highly sensitive test

Hepatitis C virus (HCV) is transmitted primarily by direct percutaneous exposures to blood. Since HCV RNA has been found in saliva, it has been suggested that saliva might also be a source of infection. HCV RNA in saliva from plasma HCV RNA positive patients was tested by a highly sensitive PCR method. HCV RNA was detected in 32 out of 61 saliva specimens (52.4%). No correlation was found between the presence of HCV in saliva and age, sex, identified risk factors for HCV infection, time lapsed since the diagnosis, transaminases and alkaline phosphatase values and stimulated salivary flow. A statistically significant relation between plasma HCV RNA viral load and saliva HCV RNA detection was observed (P<0.001). In conclusion, HCV RNA is often present in saliva of HCV infected patients, with plasma viral load being the only known predictable factor. Further studies on salivary HCV RNA are needed.

Evaluation of hepatitis C antibody testing in saliva specimens collected by two different systems in comparison with HCV antibody and HCV RNA in serum

Two different ELISA assays, the Ortho HCV 3.0 ELISA (Ortho Diagnostics Systems) and the Mono-Lisa anti-HCV Plus (Sanofi Diagnostics Pasteur) were evaluated for the detection of hepatitis C virus (HCV) antibody in saliva samples. Specimens were collected from 152 individuals who participated in a longitudinal cohort study on HIV infection, and who used illicit drugs. Saliva specimens were collected using two different systems: Salivette (Sarstedt) and Omni-Sal (Saliva Diagnostic Systems). Saliva specimens were tested following modified protocols by both ELISAs, and the results were compared with serum specimens that were tested according to the instructions of the manufacturer. Serum samples of 102 (67%) participants were positive by both assays, and 50 persons were negative for HCV antibody. A total of 99 of the 102 serum specimens were confirmed as positive using Ortho Riba HCV 3.0 (Ortho Diagnostics System) and Deciscan HCV (Sanofi Diagnostics Pasteur), and 3 yielded discrepant results. As no cut-off level is known for testing saliva samples by ELISA, 3 different levels were chosen: mean (M) + 1 standard deviation (SD), M + 2 SD, and M + 3 SD of the optical densities of saliva tests of the 50 HCV serum antibody negative persons. At a level of M + 1 SD and M + 2 SD the Salivette/Mono-Lisa combination gave the greatest proportion of HCV antibody positive saliva specimens obtained from the 102 HCV serum antibody positive participants, 88% and 79%, respectively. Differences between the various collection systems and assay combinations were not significant statistically. In 76 of the 102 persons with HCV antibodies in serum, HCV RNA was detected in serum. Salivary presence of HCV RNA, however, could not be demonstrated. The results show that the assays compared are unsuitable for diagnostic use, but the sensitivities of the assays are acceptable for use in epidemiological studies.