This review discusses the most important emerging viral pathogensresponsible for human infections in India. It also documents viraldiseases recognized in India along with the conventional diagnostictechniques and their limitations. Additionally, the review examinesthe priorities in viral diagnostics and briefly discusses the newstrategies of genomics and proteomics, such as next-generationsequencing, used for identifying known/unknown viral infections. Thepaper also explores the future of rapid viral diagnostic techniquesand the challenges posed in point-of-care diagnosis of viralinfections.
Emerging andre-emerging pathogens pose several challenges to diagnosis,treatment, and public health surveillance. The identification of anemerging pathogen by conventional methods is difficult andtime-consuming because of the “novel” nature of the agentand requires a large array of techniques, including cell cultures,animal inoculation, cultivation in artificial media,histopathological evaluation of tissues (if available), andserological techniques using surrogate antigens. Looking back at pastepidemics or outbreaks caused by previously unknown infectiousagents, it is clear that the identification and characterization of anew infectious agent can take years to decades or even centuries.Such time frames have been decreased to weeks or months by the use ofpowerful molecular techniques, as illustrated by the identificationof severe acute respiratory syndrome coronavirus (SARS-CoV) withinweeks of the first cases being reported and the discovery of a newhantavirus in North America in 1993.2,3 Molecular techniques offer several advantages over conventionalmethods, including high sensitivity and specificity, speed, ease ofstandardization, and automation. Other advantages include theidentification of novel, non-cultivable, or very slowly growingorganisms, strain typing in epidemiological studies, determination ofantimicrobial susceptibility, and monitoring treatment by measuringbacterial or viral loads. Each diagnostic method has the potential toinfluence patient health outcomes and facilitate informed clinicaldecisions. The significance of diagnostics is anticipated to increasewith advances in interventions and health information technology.
Emerging and futurediagnostics will have wide-ranging impacts on all aspects of healthcare; further, they will help advance new fundamental concepts ofcare and improve the quality of health services. This reviewdiscusses in detail the important viral diseases in India, diagnosticassays and their limitations, key priorities, new technologies inviral diagnostics, and the future of viral diagnostics.
In India, theprevalence of a number of viruses, including dengue virus (DV),Japanese encephalitis virus (JEV), Chandipura virus (CHP), West Nile(WN) virus, Kyasanur forest disease virus (KFDV), measles virus,Chikungunya virus (CHIKV), enterovirus, influenza virus, and herpesviruses, has been identified. Major outbreaks of JEV, CHPV, DV,CHIKV, influenza virus, enterovirus, and measles virus have beendocumented in various parts of the country.4-9 Focal outbreaks of KFDV and Nipah virus are restricted to areas nearthe deep forests of Karnataka and those near the Bangladesh boarderof India, respectively.
The influenzapandemic caused by the new H1N1 virus has by now affected all partsof India. However, the extent of spread and possible impact are stillunclear. Similar to seasonal flu, the illness is mild andself-limiting in the majority of cases, with only 1–2% ofpatients requiring hospitalization.5 In a few cases, the clinical course can deteriorate in a matter ofhours, leading to severe complications and eventually death.
The riskof complications is high among those who have preexisting diseases,such as asthma, heart disease, and kidney disease, and among pregnantwomen. Antiviral drugs are now available, and the most preferred oneis oseltamivir, with zanamivir being an alternative.10 Antiviral treatment is not necessary for those who are otherwisehealthy and have mild or uncomplicated illness. It is beneficial forpatients with progressive lower respiratory tract disease orpneumonia, those with underlying medical conditions, and thosepregnant. There is a limited supply of the pandemic influenza vaccinein a few countries, and efforts to produce it in India are currentlyunderway. The molecular diagnostic assays, such as qualitativereal-time reverse transcription-polymerase chain reaction (RT-PCR),are considered most effective in the early detection of the virus.Another diagnostic test used is heamagglutinin inhibition assay (HIA)for the detection of the antibody against the HA gene of theinfluenza virus.
JEV is one of themost prevalent causes of encephalitis epidemics in Southeast Asiancountries. JE is characterized by the encephalomyelitis syndromeassociated with various movement disorders, anterior horn cellinvolvement, and typical radiological changes (thalamic, basalganglia, and brainstem). In India, JE was first recognized in 1955 insouthern India, and since then, it has been documented in severalparts of the country.11 It has been found to be associated with a number of encephalitisoutbreaks in various parts of the country, and currently, it isendemic in most of the southern and northern states. The pediatricage group is the most affected, with a fatality rate of 35–40%.12 However, JEV infection has been increasingly noted in adults duringrecent outbreaks. Serological (immunoglobulin (Ig)M enzyme-linkedimmunosorbent assay [ELISA]) and genome-based diagnostic techniquesare routinely available for the detection of this disease.13
Chandipuraencephalitis is emerging as a major public health concern in India.Its association with several encephalitis outbreaks in the pediatricpopulation has been documented in the states of Andhra Pradesh (2003)and Gujarat (2004), with minimum mortality rates of 50%.4,14, 15 Since the window period between infection and acute clinical illnessis short, the diagnosis of CHP encephalitis by IgM ELISA is notpreferred. Molecular diagnostic techniques are well established forCHPV and are preferred for human clinical specimens.
CHIKV, amosquito-transmitted alphavirus, causes Chikungunya fever, which ischaracterized by fever, rash, and severe arthralgia. The associationof CHIKV with human infection in India was first documented duringhuman outbreaks in the 1960s.16 Until 2006, an estimated 1.3 million human cases of CHIKV infectionhas been documented in India.17-19 Neurological complications in pediatric CHIKV infections areincreasingly being documented, and the virus has been detected incerebrospinal fluid (CSF) samples collected from cases.20,21 Direct PCR detection is considered the most appropriate technique fordiagnosing CHIKV infection, rather than testing for IgM antibodies,which may persist for several months after infection and can reflectcoincidental infection rather than an acute infection.22
Measles is theleading killer among vaccine-preventable diseases, responsible for anestimated 44% of the 1.7 million vaccine-preventable deaths amongchildren annually.23 An increasing number of cases with neurological complications (fatalencephalopathy) are being documented in several measlesoutbreaks.24-26 Subacute sclerosing panencephalitis (SSPE), a rare progressivedegenerative disease, is caused by persistent infection with adefective measles virus.27 Mutations in matrix genes have been frequently documented in strainsassociated with SSPE.28 SSPE is characterized by progressive mental deterioration, motordecline, and myoclonus, leading to death within 1–3 years ofonset. SSPE is essentially a disease of childhood, and commonlyoccurs at the age of 5–15 years. Early diagnosis of measles mayhelp in selecting the appropriate medical interventions andadministering necessary counseling.