Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review

ABSTRACT

Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).

Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).

Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.

KEYWORDS:

• Arbovirus
• Chikungunya
• Dengue
• diagnostics
• molecular techniques
• West Nile
• Zika

Article highlights

• Recent decades have been characterized by an increase in the emergence and the re-emergence of infections due to Arthropod-borne viruses

• This narrative review provides an overview of the main molecular methods offering new diagnostic strategies for West Nile, Dengue, Zika, and Chikungunya

• Direct molecular methods to detect viral genomes can be assembled in Target analysis (TA) including the nucleic acid amplification (NAA) and the no-amplified nucleic acid hybridization probes (T-nAHP); and in no Target analysis (nTA) such as NNext-GenerationSequencing (NGS)

• Sample type, sample preparation, and detection modalities are important considerations for a molecular assay design and choice

• Isothermal amplification (IA) method remains the most ideal tool for field-adaptable diagnostics in resource-limited settings with the possibility of performing direct amplification from crude samples without extraction

• For multiplexing detection and differential diagnosis, Real-Time PCR and Array-based are more powerful than IA but still not adaptable for field-usage and so is NGS for the identification of unknown strains

• An improved design of current assays along with more rigorous characterization and validation are necessary to improve their translation to the point of care

Declaration of interest

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This work was supported by the Italian Ministry of Health ‘Fondi Ricerca corrente – L1P2’ to IRCCS Ospedale Sacro Cuore – Don Calabria.