Correction: MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

[This corrects the article DOI: 10.1371/journal.pone.0151204.].

Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay

Ongoing evolution of viral pathogens is a significant issue in diagnostic virology employing TaqMan qPCR/RT-qPCR. Specific concerns are related to false negativity due to probe binding failure. One option for compensating for such deficiency is to integrate a second identically labelled probe in the assay. However, how this alteration influences the reaction parameters has not been comprehensively demonstrated. In the present study, we evaluate a TaqMan protocol using two identically labelled hydrolysis probes (simple, LNA (locked-nucleic-acid)) and MGB (minor-groove-binder) modified probes and combinations thereof in a single assay. Our results based on a synthetic amplicon suggest that the second probe does not compromise the TaqMan qPCR/RT-qPCR parameters, which repeatedly and reproducibly remained comparable to those of the corresponding single-probe assays, irrespective of the relative probe orientation, whether opposite or tandem, and probe modifications or combinations thereof. On the other hand, the second probe additively contributed to the overall fluorescence signal. The utility of the dual-probe approach was demonstrated on practical examples by using field specimens. We hope that the present study might serve as a theoretical basis for the development or improvement of TaqMan qPCR/RT-qPCR assays for the detection of highly variable nucleic acid templates.

MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence.

[Surveillance of West Nile fever in horses in the Czech Republic from 2011 to 2013]

STUDY AIM

The West Nile virus (WNV) is an important mosquito-borne flavivirus occurring around the world. Occasionally found in Central Europe, the virus spread massively through whole Hungary between 2008 and 2009. The aim of our study was to determine the recent prevalence of the WNV infection in horses in the Czech Republic.

MATERIAL AND METHODS

Overall, 2349 serum samples, collected from healthy unvaccinated adult horses in the Czech Republic between 2011 and 2013, were tested. A commercially available competitive ELISA kit (cELISA) was used for this purpose and positive samples were confirmed by virus neutralisation tests using WNV and tick-borne encephalitis virus (TBEV).

RESULTS

Altogether 271 of 2348 samples (11.5%) were positive by cELISA. Confirmatory VNT revealed 16 WNV positive samples, 11 of which had titres from 8 to 1024; VNTs with TBEV were negative. Three samples had antibodies against both viruses and the WNV antibody titres were less than or equal to the TBEV antibody titres. A cross reactivity of flaviviruses might have had an impact on the results, but in samples with similar WNV and TBEV titres, co-infection with both pathogens cannot be ruled out either. VNT antibody titres in two horses were inconclusive (cut-off titre 4). The place of birth and transfers (if any) were checked for each WNV seropositive horse. Five WNV positive/TBEV negative samples (0.2%) came from five administrative regions (South Bohemian, Karlovy Vary, Central Bohemian, South Moravian, and Moravian-Silesian) and the respective animals were never moved to a foreign country. Four of these horses never left the farm. Other six WNV positive/TBEV negative horses were imported to the Czech Republic from North America or Central and West Europe and therefore, it is not possible to tell unambiguously whether their infection is autochthonous or imported.

CONCLUSION

The results of the present study confirm that WNV antibodies occur sporadically in horses in the Czech Republic. WNV was found to circulate in different parts of the Czech Republic and not only in the South of Moravia.