Update on molecular techniques for diagnostic testing of infectious disease

An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection

SARS-CoV-2 variants surveillance is a worldwide task that has been approached with techniques such as Next Generation Sequencing (NGS); however, this technology is not widely available in developing countries because of the lack of equipment and limited funding in science. An option is to deploy a RT-qPCR screening test which aids in the analysis of a higher number of samples, in a shorter time and at a lower cost. In this study, variants present in samples positive for SARS-CoV-2 were identified with a RT-qPCR mutation screening kit and were later confirmed by NGS. A sample with an abnormal result was found with the screening test, suggesting the simultaneous presence of two viral populations with different mutations. The DRAGEN Lineage analysis identified the Delta variant, but there was no information about the other three mutations previously detected. When the sequenced data was deeply analyzed, there were reads with differential mutation patterns, that could be identified and classified in terms of relative abundance, whereas only the dominant population was reported by DRAGEN software. Since most of the software developed to analyze SARS-CoV-2 sequences was aimed at obtaining the consensus sequence quickly, the information about viral populations within a sample is scarce. Here, we present a faster and deeper SARS-CoV-2 surveillance method, from RT-qPCR screening to NGS analysis.

Standardization of BCR-ABL1 p210 Monitoring: From Nested to Digital PCR

The introduction of tyrosine kinase inhibitors in 2001 as a targeted anticancer therapy has significantly improved the quality of life and survival of patients with chronic myeloid leukemia. At the same time, with the introduction of tyrosine kinase inhibitors, the need for precise monitoring of the molecular response to therapy has emerged. Starting with a qualitative polymerase chain reaction, followed by the introduction of a quantitative polymerase chain reaction to determine the exact quantity of the transcript of interest-p210 BCR-ABL1, molecular monitoring in patients with chronic myeloid leukemia was internationally standardized. This enabled precise monitoring of the therapeutic response, unification of therapeutic protocols, and comparison of results between different laboratories. This review aims to summarize the steps in the diagnosis and molecular monitoring of p210 BCR-ABL1, as well as to consider the possible future application of a more sophisticated method such as digital polymerase chain reaction.

Aptamers, the bivalent agents as probes and therapies for coronavirus infections: A systematic review

The recently known coronavirus, SARS-CoV-2, has turn into the greatest global health challenge, affecting a large number of societies. The lack of specific treatment and gold-standard diagnostic system has made the situation more complicated. Efforts have led to production of several diagnostic kits that are associated with limitations such as inadequate sensitivity and accuracy. Aptamers as multipotent biological probes could be promising candidates to design sensitive and specific biosensors. Although few studies have introduced specific aptamer types of coronavirus, they may help us select the best approach to obtain specific aptamers for this virus. On the other hand, some of already-introduced aptamers have shown the inhibitory effects on coronavirus that could be applied as therapeutics. The present study has provided a systematic overview on use of aptamer-based biosensors and drugs to diagnose and treat coronavirus.

An update on the diagnosis and treatment of canine leishmaniosis caused by Leishmania infantum (syn. L. chagasi)

Canine leishmaniosis caused by Leishmania infantum is still a common disease in endemic areas, such as the Mediterranean countries, and has progressively expanded into non-endemic areas like Central and Northern Europe. The aim of this article is to critically review current knowledge on the diagnosis and treatment of this disease. In dogs with typical clinical signs and clinicopathological abnormalities, diagnosis is relatively easy based on the exclusion of major differentials, the demonstration of the parasite (e.g., with lymph node and/or skin cytology) and the presence of Leishmania-specific immunoglobulin G antibodies (quantitative serology). In less typical cases, these criteria together with the exclusion of possible differentials and the demonstration of compatible histological lesions in affected organs and tissues form the basis for a sound diagnosis. In clinically healthy dogs, molecular techniques are the most sensitive means for detecting L. infantum infection. Treatment of canine leishmaniosis should follow clinical staging and is usually based on meglumine antimonate or miltefosine administration for a few weeks in combination with allopurinol for several months. However, allopurinol monotherapy may be used in very mild cases as well as in dogs with end stage kidney disease. Aminosidine administered once daily at a revised dosage shows some promise but additional controlled studies are needed. Close attention to published guidelines regarding treatment and follow-up is necessary to achieve the best possible therapeutic outcome.

Beyond H&E: integration of nucleic acid-based analyses into diagnostic pathology

Veterinary pathology of infectious, particularly viral, and neoplastic diseases has advanced significantly with the advent of newer molecular methodologies that can detect nucleic acid of infectious agents within microscopic lesions, differentiate neoplastic from nonneoplastic cells, or determine the suitability of a targeted therapy by detecting specific mutations in certain cancers. Polymerase chain reaction-based amplification of DNA or RNA and in situ hybridization are currently the most commonly used methods for nucleic acid detection. In contrast, the main methodology used for protein detection within microscopic lesions is immunohistochemistry. Other methods that allow for analysis of nucleic acids within a particular cell type or individual cells, such as laser capture microdissection, are also available in some laboratories. This review gives an overview of the factors that influence the accurate analysis of nucleic acids in formalin-fixed tissues, as well as of different approaches to detect such targets.

Evaluation of different sampling methods and results of real-time PCR for detection of feline herpes virus-1, Chlamydophila felis and Mycoplasma felis in cats

OBJECTIVE

To investigate how different sampling techniques affect detection of DNA from feline herpes virus Type 1 (FHV-1), Chlamydophila felis and Mycoplasma felis and to study the correlation between positive test results and clinical signs in cats.

ANIMALS

Fifty-one cats; 24 with ocular signs and 27 healthy control cats.

PROCEDURES

Samples were collected from all cats using cotton swabs, conjunctival and corneal biopsies, and corneal scrapings. Samples were analyzed for presence of FHV-1, C. felis, M. felis, and feline DNA, defined by 28S rDNA, by using real-time PCR.

RESULTS

In affected cats, FHV-1 was detected in only one cat; C. felis and M. felis were not detected in any affected cats. None of the three organisms was detected in any control cats. Feline DNA was demonstrated in all conjunctival samples, in 82% of corneal swabs, 92% of corneal scrapings, and 100% of keratectomy samples.

CONCLUSIONS

Because of the generally low detection rate for FHV-1, C. felis, and M. felis DNA in this study, differences regarding sampling technique could not be determined and correlation between positive test results and degree of clinical signs could not be made. Detection of feline DNA in most samples irrespective of sampling technique, suggests a low prevalence of FHV-1, C. felis and M. felis in this population of cats.

Diagnostic investigation of emerging viruses of companion animals

In this article, the authors are specifically concerned with the timely and accurate detection of emerging diseases of small animals that are viral in origin. Veterinarians are bound to encounter emerging viruses in their practice. The problem is unavoidable, because viruses are highly mutagenic. Even the immune response dictates the nature of virus that evolves in a host. If the clinical signs and diagnostic methods fail to correlate, the veterinarian should work with the diagnostic laboratory to solve the diagnostic puzzle.

Molecular Biology for the Clinician: Understanding Current Methods

The basics of molecular biology involve the replication of deoxyribonucleic acid and its transcription and translation into proteins. Biochemical assays such as the Southern blot analysis, polymerase chain reaction (PCR), Northern blot analysis, reverse-transcriptase PCR, microarray technology, Western blot analysis, immunohistochemistry, enzyme-linked immunosorbent assay, and flow cytometry utilize various aspects of molecular biology. To understand these assays requires some basic understanding of the principles of molecular biology. This paper provides basic information on the methodology and techniques used in these assays.

Microarrays in veterinary diagnostics

Microarrays have numerous applications in the clinical setting, and these uses are not confined to the study of common human diseases. Indeed, the high-throughput technology affects clinical diagnostics in a variety of contexts, and this is reflected in the increasing use of microarray-based tools in the development of diagnostic and prognostic tests and in the identification of novel therapeutic targets. While much of the value of microarray-based experimentation has been derived from the study of human disease, there is equivalent potential for its role in veterinary medicine. Even though the resources devoted to the study of animal molecular diagnostics may be less than those available for human research, there is nonetheless a growing appreciation of the value of genome-wide information as it applies to animal disease. Therefore, this review focuses on the basics of microarray experimentation, and how this technology lends itself to a variety of diagnostic approaches in veterinary medicine.

Quantitative assessment of the effect of uracil-DNA glycosylase on amplicon DNA degradation and RNA amplification in reverse transcription-PCR

Although PCR and RT-PCR provided a valuable approach for detection of pathogens, the high level of sensitivity of these assays also makes them prone to false positive results. In addition to cross-contamination with true positive samples, false positive results are also possible due to "carry-over" contamination of samples with amplicon DNA generated by previous reactions. To reduce this source of false positives, amplicon generated by reactions in which dUTP was substituted for dTTP can be degraded by uracil DNA glycosylase (UNG). UNG does not degrade RNA but will cleave contaminating uracil-containing DNA while leaving thymine-containing DNA intact. The availability of heat-labile UNG makes use of this approach feasible for RT-PCR. In this study, real-time RT-PCR was used to quantify UNG degradation of amplicon DNA and the effect of UNG on RNA detection. Using the manufacturers' recommended conditions, complete degradation of DNA was not observed for samples containing 250 copies of amplicon DNA. Doubling the UNG concentration resulted in degradation of the two lowest concentrations of DNA tested, but also resulted in an increase of 1.94 cycles in the CT for RNA detection. To improve DNA degradation while minimizing the effect on RNA detection, a series of time, temperature and enzyme concentrations were evaluated. Optimal conditions were found to be 0.25 U UNG per 25 microl reaction with a 20 min, 30 degrees C incubation prior to RT-PCR. Under these conditions, high concentrations of amplicon DNA could be degraded while the CT for RNA detection was increased by 1.2 cycles.

Methodology in diagnostic virology

Selection of proper assays and appropriate interpretation of results can be a challenge to the veterinary clinician. Assays vary in methodology, sensitivity, and specificity. These assays can be invaluable in attaining the correct diagnosis, but a clear understanding of the assay and the results is essential. To this end, communication with the laboratory personnel is crucial. Optimal sample selection, shipping recommendations, assay selection, and interpretation should be discussed with the laboratory staff.