Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field.

Yashpal Singh Malik,Kumaragurubaran Karthik,Ruchi Tiwari,Maged Gomaa Hemida,Ahmed S Abdel-Moneim,Nobumichi Kobayashi,Krisztián Bányai,Atul Kumar Verma,Raj Kumar Singh,Nadia Touil,Souvik Ghosh,Kuldeep Dhama,Durlav Prasad Bora,Naveen Kumar,Anastasia N Vlasova

doi:10.3389/fmicb.2019.01957

Abstract

The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.

Highlights

Advances in the enteric microbiology research have improved the understanding of etiology of infectious gastroenteritis, as well as the involvement and transmission modes of enteric pathogens
This paper systematically describes and discusses the features, advantages and limitations primarily of advanced diagnostic tools devised for the sensitive and quick detection of enteric viruses worldwide (Figure 1)
immune-chromatography test (ICT)-based virus detection strips/kits are available in the market for the identification and direct detection of Norovirus, Rotavirus, and Astrovirus in fecal samples with good sensitivity and specificity ranging between 90–95% (Khamrin et al, 2009)

Summary

INTRODUCTION

Advances in the enteric microbiology research have improved the understanding of etiology of infectious gastroenteritis, as well as the involvement and transmission modes of enteric pathogens. Among different techniques used to explore new viruses, such as conventional and next-generation sequencing, metagenomics has been a promising approach to study the unrevealed viral genomes since more than a decade (Garza and Dutilh, 2015; Martinez-Hernandez et al, 2017) This allows researchers to study the genetic material directly from pooled samples and bypass the need for culturing the virus in vitro as well. For culturing gastrointestinal viruses in the laboratory, induced intestine-like human intestinal organoids (iHIOs) with differentiation of human embryonic or induced pluripotent stem cell lines have been used successfully for culturing rotavirus (McCracken et al, 2011; Spence et al, 2011) This increases the potential for successful isolation and propagation of other enteric viruses, there is still a need to develop better isolation or cultivation methods for enteric viruses. Hybridization (DIG) probe, surface enhanced raman spectroscopy, RT-LAMP, RT-PCR, novel enzyme immunoassay, paper-LAMP Pyrosequencing, RT-LAMP Metagenomics, sanger sequencing Metagenomics Metagenomics, digital RT-PCR Metagenomics, electrochemical biosensor, aptamer based in situ capture RT-qPCR Metagenomics RT-PCR and sanger sequencing RT-PCR and sanger sequencing RT-PCR and sanger sequencing, RT-LAMP RT-PCR and sanger sequencing RT-PCR and sanger sequencing TaqMan RT-qPCR Metagenomics RT-PCR and sanger sequencing RT-qPCR RT-PCR and sanger sequencing RT-qPCR RT-PCR and sanger sequencing

Serological Methods

Findings

CONCLUSION