Detection and subtyping of dengue 1-4 and yellow fever viruses by means of a multiplex RT-nested-PCR using degenerated primers

Yellow Fever Virus: Diagnostics for a Persistent Arboviral Threat

Yellow fever (YF) is the prototypical hemorrhagic fever and results from infection with yellow fever virus (YFV), which is endemic to regions of Africa and South America. Despite the availability of an effective vaccine, YFV continues to cause disease throughout regions where it is endemic, including intermittent large outbreaks among undervaccinated populations. A number of diagnostic methods and assays have been described for the detection of YFV infection, including viral culture, molecular testing, serology, and antigen detection. Commercial diagnostics are not widely available, and testing is generally performed at a small number of reference laboratories. The goal of this article, therefore, is to review available clinical diagnostics for YFV, which may not be familiar to many practitioners outside areas where it is endemic. Additionally, we identify gaps in our current knowledge about YF that pertain to diagnosis and describe interventions that may improve YFV detection.

What Does the Future Hold for Yellow Fever Virus? (II)

As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas with low vaccination coverage but that are suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization's initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately viral dissemination, and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more yellow fever (YF) cases in the upcoming years. Hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of a two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.

Clinical diagnosis of early dengue infection by novel one-step multiplex real-time RT-PCR targeting NS1 gene

BACKGROUND

Dengue is a mosquito-borne disease that causes a public health problem in tropical and subtropical countries. Current immunological diagnostics based on IgM and/or nonstructural protein 1 (NS1) antigen are limited for acute dengue infection due to low sensitivity and accuracy.

OBJECTIVES

This study aimed to develop a one-step multiplex real-time RT-PCR assay showing higher sensitivity and accuracy than previous approaches.

STUDY DESIGN

Serotype-specific primers and probes were designed through the multiple alignment of NS1 gene. The linearity and limit of detection (LOD) of the assay were determined. The assay was clinically validated with an evaluation panel that was immunologically tested by WHO and Malaysian specimens.

RESULTS

The LOD of the assay was 3.0 log10 RNA copies for DENV-1, 2.0 for DENV-3, and 1.0 for DENV-2 and DENV-4. The assay showed 95.2% sensitivity (20/21) in an evaluation panel, whereas NS1 antigen- and anti-dengue IgM-based immunological assays exhibited 0% and 23.8-47.6% sensitivities, respectively. The assay showed 100% sensitivity both in NS1 antigen- and anti-dengue IgM-positive Malaysian specimens (26/26). The assay provided the information of viral loads and serotype with discrimination of heterotypic mixed infection.

CONCLUSIONS

The assay could be clinically applied to early dengue diagnosis, especially during the first 5 days of illness and approximately 14 days after infection showing an anti-dengue IgM-positive response.

Universal single-probe RT-PCR assay for diagnosis of dengue virus infections

BACKGROUND

Dengue is a mosquito-borne viral disease that has become more prevalent in the last few decades. Most patients are viremic when they present with symptoms, and early diagnosis of dengue is important in preventing severe clinical complications associated with this disease and also represents a key factor in differential diagnosis. Here, we designed and validated a hydrolysis-probe-based one-step real-time RT-PCR assay that targets the genomes of dengue virus serotypes 1-4.

METHODOLOGY/PRINCIPAL FINDINGS

The primers and probe used in our RT-PCR assay were designed to target the 3' untranslated region of all complete genome sequences of dengue virus available in GenBank (n = 3,305). Performance of the assay was evaluated using in vitro transcribed RNA, laboratory-adapted virus strains, external control panels, and clinical specimens. The linear dynamic range was found to be 104-1011 GCE/mL, and the detection limit was between 6.0×102 and 1.1×103 GCE/mL depending on target sequence. The assay did not cross-react with human RNA, nor did it produce false-positive results for other human pathogenic flaviviruses or clinically important etiological agents of febrile illnesses. We used clinical serum samples obtained from returning travelers with dengue-compatible symptomatology (n = 163) to evaluate the diagnostic relevance of our assay, and laboratory diagnosis performed by the RT-PCR assay had 100% positive agreement with diagnosis performed by NS1 antigen detection. In a retrospective evaluation including 60 archived serum samples collected from confirmed dengue cases 1-9 days after disease onset, the RT-PCR assay detected viral RNA up to 9 days after appearance of symptoms.

CONCLUSIONS/SIGNIFICANCE

The validation of the RT-PCR assay presented here indicates that this technique can be a reliable diagnostic tool, and hence we suggest that it be introduced as the method of choice during the first 5 days of dengue symptoms.

Yellow fever vaccine-associated adverse events following extensive immunization in Argentina

As a consequence of YF outbreaks that hit Brazil, Argentina, and Paraguay in 2008-2009, a significant demand for YF vaccination was subsequently observed in Argentina, a country where the usual vaccine recommendations are restricted to provinces that border Brazil, Paraguay, and Bolivia. The goal of this paper is to describe the adverse events following immunization (AEFI) against YF in Argentina during the outbreak in the northeastern province of Misiones, which occurred from January 2008 to January 2009. During this time, a total of nine cases were reported, almost two million doses of vaccine were administered, and a total of 165 AEFI were reported from different provinces. Case study analyses were performed using two AEFI classifications. Forty-nine events were classified as related to the YF vaccine (24 serious and 1 fatal case), and 12 events were classified as inconclusive. As the use of the YF 17D vaccine can be a challenge to health systems of countries with different endemicity patterns, a careful clinical and epidemiological evaluation should be performed before its prescription to minimize serious adverse events.

Polymerase chain displacement reaction

Quantitative PCR assays are now the standard method for viral diagnostics. These assays must be specific, as well as sensitive, to detect the potentially low starting copy number of viral genomic material. We describe a new technique, polymerase chain displacement reaction (PCDR), which uses multiple nested primers in a rapid, capped, one-tube reaction that increases the sensitivity of normal quantitative PCR (qPCR) assays. Sensitivity was increased by approximately 10-fold in a proof-of-principle test on dengue virus sequence. In PCDR, when extension occurs from the outer primer, it displaces the extension strand produced from the inner primer by utilizing a polymerase that has strand displacement activity. This allows a greater than 2-fold increase of amplification product for each amplification cycle and therefore increased sensitivity and speed over conventional PCR. Increased sensitivity in PCDR would be useful in nucleic acid detection for viral diagnostics.

Analytical and clinical performance of the CDC real time RT-PCR assay for detection and typing of dengue virus

Dengue is an acute illness caused by the positive-strand RNA dengue virus (DENV). There are four genetically distinct DENVs (DENV-1–4) that cause disease in tropical and subtropical countries. Most patients are viremic when they present with symptoms; therefore, RT-PCR has been increasingly used in dengue diagnosis. The CDC DENV-1–4 RT-PCR Assay has been developed as an in-vitro diagnostic platform and was recently approved by the US Food and Drug Administration (FDA) for detection of dengue in patients with signs or symptoms of mild or severe dengue. The primers and probes of this test have been designed to detect currently circulating strains of DENV-1–4 from around the world at comparable sensitivity. In a retrospective study with 102 dengue cases confirmed by IgM anti-DENV seroconversion in the convalescent sample, the RT-PCR Assay detected DENV RNA in 98.04% of the paired acute samples. Using sequencing as a positive indicator, the RT-PCR Assay had a 97.92% positive agreement in 86 suspected dengue patients with a single acute serum sample. After extensive validations, the RT-PCR Assay performance was highly reproducible when evaluated across three independent testing sites, did not produce false positive results for etiologic agents of other febrile illnesses, and was not affected by pathological levels of potentially interfering biomolecules. These results indicate that the CDC DENV-1–4 RT-PCR Assay provides a reliable diagnostic platform capable for confirming dengue in suspected cases.

Significant expansion of the four DENV serotypes (DENV-1, -2, -3 and -4) has been reported throughout tropical and sub-tropical regions of the world, with estimates of 390 million cases annually. The need has arisen for expanded diagnostic testing for DENV infections in the United States, as dengue infection has been added to the list of national notifiable diseases. Timely and accurate diagnosis of dengue is important for clinical care, disease surveillance, disease prevention, and control activities. However, current testing is performed with laboratory-developed research-based assays available only in a limited number of laboratories that have not been validated or approved for diagnostic testing in the United States. Here we report the development and evaluation of the CDC DENV-1–4 Real Time RT-PCR Assay, the first molecular test approved by the US Food and Drug Administration for the diagnosis and serotyping of DENV in human serum or plasma samples. This test was designed and validated for the detection of contemporary, clinically relevant DENV strains transmitted globally, facilitating the global deployment of the test and increase detection of traveler-associated dengue cases.

Alignment-free distance measure based on return time distribution for sequence analysis: applications to clustering, molecular phylogeny and subtyping

The data deluge in post-genomic era demands development of novel data mining tools. Existing molecular phylogeny analyses (MPAs) developed for individual gene/protein sequences are alignment-based. However, the size of genomic data and uncertainties associated with alignments, necessitate development of alignment-free methods for MPA. Derivation of distances between sequences is an important step in both, alignment-dependant and alignment-free methods. Various alignment-free distance measures based on oligo-nucleotide frequencies, information content, compression techniques, etc. have been proposed. However, these distance measures do not account for relative order of components viz. nucleotides or amino acids. A new distance measure, based on the concept of 'return time distribution' (RTD) of k-mers is proposed, which accounts for the sequence composition and their relative orders. Statistical parameters of RTDs are used to derive a distance function. The resultant distance matrix is used for clustering and phylogeny using Neighbor-joining. Its performance for MPA and subtyping was evaluated using simulated data generated by block-bootstrap, receiver operating characteristics and leave-one-out cross validation methods. The proposed method was successfully applied for MPA of family Flaviviridae and subtyping of Dengue viruses. It is observed that method retains resolution for classification and subtyping of viruses at varying levels of sequence similarity and taxonomic hierarchy.

Evaluation of two molecular methods for the detection of Yellow fever virus genome

Yellow fever virus (YFV), a member of the family Flaviviridae, genus Flavivirus is endemic to tropical areas of Africa and South America and is among the arboviruses that pose a threat to public health. Recent outbreaks in Brazil, Bolivia, and Paraguay and the observation that vectors capable of transmitting YFV are presenting in urban areas underscore the urgency of improving surveillance and diagnostic methods. Two novel methods (RT-hemi-nested-PCR and SYBR(®) Green qRT-PCR) for efficient detection of YFV strains circulating in South America have been developed. The methods were validated using samples obtained from golden hamsters infected experimentally with wild-type YFV strains as well as human serum and tissue samples with acute disease.

2nd International external quality control assessment for the molecular diagnosis of dengue infections

Background

Currently dengue viruses (DENV) pose an increasing threat to over 2.5 billion people in over 100 tropical and sub-tropical countries worldwide. International air travel is facilitating rapid global movement of DENV, increasing the risk of severe dengue epidemics by introducing different serotypes. Accurate diagnosis is critical for early initiation of preventive measures. Different reverse transcriptase PCR (RT-PCR) methods are available, which should be evaluated and standardized. Epidemiological and laboratory-based surveillance is required to monitor and guide dengue prevention and control programmes, i.e., by mosquito control or possible vaccination (as soon as an effective and safe vaccine becomes available).

Objective

The purpose of the external quality assurance (EQA) study described is to assess the efficiency and accuracy of dengue molecular diagnosis methods applied by expert laboratories.

Study Design

A panel of 12 human plasma samples was distributed and tested for DENV-specific RNA. The panel comprised 9 samples spiked with different DENV serotypes (DENV-1 to DENV-4), including 10-fold dilution series of DENV-1 and DENV-3. Two specificity controls consisted of a sample with a pool of 4 other flaviviruses and a sample with chikungunya virus. A negative control sample was also included.

Results

Thirty-seven laboratories (from Europe, Middle East Asia, Asia, the Americas/Caribbean, and Africa) participated in this EQA study, and reports including 46 sets of results were returned. Performance among laboratories varied according to methodologies used. Only 5 (10.9%) data sets met all criteria with optimal performance, and 4 (8.7%) with acceptable performance, while 37 (80.4%) reported results showed the need for improvement regarding accomplishment of dengue molecular diagnosis. Failures were mainly due to lack of sensitivity and the presence of false positives.

Conclusions

The EQA provides information on each laboratory's efficacy of RT-PCR techniques for dengue diagnosis and indicates for most laboratories an urgent need to improve sensitivity and specificity.

Dengue viruses (DENV) are the most widespread arthropod-borne viruses which have shown an unexpected geographic expansion, as well as an increase in the number and severity of outbreaks in the last decades. In this context, the accurate diagnosis and reliable surveillance of dengue infections are essential. The laboratory diagnosis of dengue relies on the use of several methods detecting markers of DENV infection present in patient serum. Molecular diagnosis methods are usually rapid, sensitive, and simple when correctly standardized. Moreover, PCR-based diagnosis techniques are able to readily detect DENV during the acute phase of the disease and may assume an important role in dengue diagnosis and surveillance. Different reverse transcriptase PCR (RT-PCR) methods have been developed and are currently available and should be standardized in each laboratory to maintain high quality performance. In this work an External quality assessment (EQA) activity has been carried out to evaluate the accuracy and quality of laboratory data for the molecular diagnosis and surveillance of dengue, which involved worldwide dengue reference laboratories. In conclusion, RT-PCR techniques for dengue diagnosis applied by the participating laboratories demonstrated the need of further improvement in most laboratories.