Advances in Diagnosis, Surveillance, and Monitoring of Zika Virus: An Update

CRISPR/Cas13-assisted carbapenem-resistant Klebsiella pneumoniae detection

BACKGROUND/PURPOSE

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is capable of causing serious community and hospital-acquired infections. However, currently, the identification of CRKP is complex and inefficient. Hence, this study aimed to develop methods for the early and effective identification of CRKP to allow reasonable antimicrobial therapy in a timely manner.

METHODS

K. pneumoniae (KP)-, K. pneumoniae carbapenemase (KPC)- and New Delhi metallo-β-lactamase (NDM)- specific CRISPR RNAs (crRNAs), polymerase chain reaction (PCR) primers and recombinase-aided amplification (RAA) primers were designed and screened in conserved sequence regions. We established fluorescence and lateral flow strip assays based on CRISPR/Cas13a combined with PCR and RAA, respectively, to assist in the detection of CRKP. Sixty-one clinical strains (including 51 CRKP strains and 10 carbapenem-sensitive strains) were collected for clinical validation.

RESULTS

Using the PCR-CRISPR assay, the limit of detection (LOD) for KP and the blaKPC and blaNDM genes reached 1 copy/μL with the fluorescence signal readout. Using the RAA-CRISPR assay, the LOD could reach 101 copies/μL with both the fluorescence signal readout and the lateral flow strip readout. Additionally, the positivity rates of CRKP-positive samples detected by the PCR/RAA-CRISPR fluorescence and RAA-CRISPR lateral flow strip methods was 92.16% (47/51). The sensitivity and specificity reached 100% for KP and blaKPC and blaNDM gene detection. For detection in a simulated environmental sample, 1 CFU/cm2 KP could be detected.

CONCLUSION

We established PCR/RAA-CRISPR assays for the detection of blaKPC and blaNDM carbapenemase genes, as well as KP, to facilitate the detection of CRKP.

Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach

Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3pro (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.

Novel Therapeutic Nutrients Molecules That Protect against Zika Virus Infection with a Special Note on Palmitoleate

Zika virus (ZIKV) is a Flavivirus from the Flaviviridae family and a positive-sense single strand RNA virus. ZIKV infection can cause a mild infection to the mother but can be vertically transmitted to the developing fetus, causing congenital anomalies. The prevalence of ZIKV infections was relatively insignificant with sporadic outbreaks in the Asian and African continents until 2006. However, recent epidemic in the Caribbean showed significant increased incidence of Congenital Zika Syndrome. ZIKV infection results in placental pathology which plays a crucial role in disease transmission from mother to fetus. Currently, there is no Food and Drug Administration (FDA) approved vaccine or therapeutic drug against ZIKV. This review article summarizes the recent advances on ZIKV transmission and diagnosis and reviews nutraceuticals which can protect against the ZIKV infection. Further, we have reviewed recent advances related to the novel therapeutic nutrient molecules that have been shown to possess activity against Zika virus infected cells. We also review the mechanism of ZIKV-induced endoplasmic reticulum and apoptosis and the protective role of palmitoleate (nutrient molecule) against ZIKV-induced ER stress and apoptosis in the placental trophoblasts.

Molecular surveillance of arboviruses circulation and co-infection during a large chikungunya virus outbreak in Thailand, October 2018 to February 2020

A large national outbreak of chikungunya virus (CHIKV) was recently reported in Thailand. While dengue virus (DENV) infection tends to occur year-round with an upsurge in the rainy season, Zika virus (ZIKV) also circulates in the country. The overlap in the distribution of these viruses increased the probability of co-infections during the heightened CHIKV activity. By examining 1806 patient serum samples submitted for CHIKV diagnostics from October 2018-February 2020 (511 CHIKV-negatives and 1295 CHIKV-positives), we used real-time reverse transcription-polymerase chain reaction to identify DENV and ZIKV individually. A total of 29 ZIKV and 36 DENV single-infections were identified. Interestingly, 13 co-infection cases were observed, of which 8 were CHIKV/DENV, 3 were CHIKV/ZIKV, and 2 were DENV/ZIKV. There were six DENV genotypes (13 DENV-1 genotype I, 10 DENV-2 Asian I, 10 DENV-2 Cosmopolitan, 6 DENV-3 genotype I, 2 DENV-3 genotype III, and 5 DENV-4 genotype I). Additionally, ZIKV strains identified in this study either clustered with strains previously circulating in Thailand and Singapore, or with strains previously reported in China, French Polynesia, and the Americas. Our findings reveal the co-infection and genetic diversity patterns of mosquito-borne viruses circulating in Thailand.

Epigenetic paradigms/exemplars of the macrophage: inflammasome axis in Leishmaniasis

The infectious paradigms have recently led to the recognition interplay of complex phenomenon underpinning disease diagnosis and prognosis. Evidently, parasitic infection studies are depicting converging trends of the epigenetic, environmental, and microbiome contributions, assisting pathogen-directed modulations of host biological system. The molecular details of epigenetic variations and memory, along with the multi-omics data at the interface of the host-pathogen level becomes strong indicator of immune cell plasticity, differentiation, and pathogen survival. Despite being one of the most important aspects of the disease's etiopathology, the epigenetic regulation of host-pathogen interactions and evolutionary epigenetics have received little attention thus far. Recent evidence has focused on the growing need to link epigenetic and microbiome modulations on parasite phenotypic plasticity and pathogen-induced host phenotypic plasticity for designing futuristic therapeutic regimes. Leishmaniasis is a neglected tropical illness with varying degrees of disease severity that is linked to a trans-species and epigenetic heredity process, including the pathogen-induced host and strain-specific modulations. The review configures research findings aligning to the epigenetic epidemiology niche, involving co-evolutionary epigenetic inheritance and plasticity disease models. The epigenetic exemplars focus on the host-pathogen interactome expanse at the macrophage-inflammasome axis.

Therapeutic approaches and vaccination in fighting COVID-19 infections: A review

Coronavirus disease 2019 (COVID-19) is a remarkably contagious and pathogenic viral infection arising from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which first appeared in Wuhan, China. For the time being, COVID-19 is not treated with a specific therapy. The Food and Drug Administration (FDA) has approved Remdesivir as the first drug to treat COVID-19. However, many other therapeutic approaches are being investigated as possible treatments for COVID-19. As part of this review, we discussed the development of various drugs, their mechanism of action, and how they might be applied to different cases of COVID-19 patients. Furthermore, this review highlights an update in the emergence of new prophylactic or therapeutic vaccines against COVID-19. In addition to FDA or The World Health Organization (WHO) approved vaccines, we intended to incorporate the latest published data from phase III trials about different COVID-19 vaccines and provide clinical data released on the networks or peer-review journals.

Enhanced production of alkane hydroxylase from Penicillium chrysogenum SNP5 (MTCC13144) through feed-forward neural network and genetic algorithm

Alkane hydroxylase (AlkB), a membrane-bound enzyme has high industrial demand; however, its economical production remains challenging due to its intrinsic nature and co-factor dependency. In the current study, various critical process parameters for optimum production of AlkB have been optimized through feed forward neural network (FFNN) and genetic algorithm (GA) models using Penicillium chrysogenum SNP5 (MTCC13144). AlkB specific activity under preliminary un-optimized conditions i.e., 1% hexadecane, 7.4 pH, 11 days incubation time, 28 °C incubation temperature and 1 ml of inoculum size was 100 U/mg. ‘One variable at a time’ (OVAT) strategy was used to identify optimum physicochemical parameters and then its output data was fed to develop a model of FFNN with ‘6-12-1’ topology. Outputs of FFNN were further optimized through GA to minimize errors and intensify search level. This has provided superior predictive performances with 0.053 U/mg overall mean absolute percentage error (MAPE), 6.801 U/mg root mean square errors (RMSE), and 0.987 overall correlation coefficient (R). The AlkB specific activity improved by 3.5-fold, i.e., from 100 U/mg under preliminary un-optimized conditions to 351.32 U/mg under optimum physicochemical conditions obtained through FFNN-GA hybrid method, i.e., hexadecane (carbon source): 1.56% v/v, FeSO₄: 0.63 mM, incubation temperature: 27.40 °C, pH: 7.38, incubation time: 12.35 days and inoculums size: 1.33 ml. The developed process would be a stepping stone to fulfill the high industrial demands of  Alkane hydroxylase.

Evaluation of Two Serological Assays for Diagnosing Zika Virus Infection

Zika virus (ZIKV) emerged and spread rapidly in South American countries during 2015. Efforts to diagnose ZIKV infection using serological tools were challenging in dengue-endemic areas because of antigenic similarities between both viruses. Here, we assessed the performance of an in-house developed IgM antibody capture enzyme-linked immunosorbent assay (MAC-ELISA) and the plaque reduction neutralization test (PRNT) to diagnose ZIKV infection. Acute and convalescent paired serum samples from 51 patients who presented with clinical symptoms suggestive of an arbovirus illness in dengue-endemic areas of Honduras, Venezuela, Colombia and Peru were used in the assessment. Samples were tested for ZIKV, dengue and chikungunya virus using a variety of laboratory techniques. The results for the ZIKV-RNA screening and seroconversion detected by the microneutralization test were used to construct a composite reference standard. The overall sensitivity and specificity for the MAC-ELISA were 93.5% and 100.0%, respectively. Contrastingly, the overall sensitivity and specificity for the PRNT were 96.8% and 95.0%, respectively. Restricting the analysis according to IgM or neutralizing antibodies against dengue, the performances of both serological assays were adequate. The findings of this study reveal that the MAC-ELISA and PRNT would provide initial reliable laboratory diagnostic assays for ZIKV infection in dengue-endemic areas.

Role of plasmonics in detection of deadliest viruses: a review

Viruses have threatened animal and human lives since a long time ago all over the world. Some of these tiny particles have caused disastrous pandemics that killed a large number of people with subsequent economic downturns. In addition, the quarantine situation itself encounters the challenges like the deficiency in the online educational system, psychiatric problems and poor international relations. Although viruses have a rather simple protein structure, they have structural heterogeneity with a high tendency to mutation that impedes their study. On top of the breadth of such worldwide worrying issues, there are profound scientific gaps, and several unanswered questions, like lack of vaccines or antivirals to combat these pathogens. Various detection techniques like the nucleic acid test, immunoassay, and microscopy have been developed; however, there is a tradeoff between their advantages and disadvantages like safety in sample collecting, invasiveness, sensitivity, response time, etc. One of the highly resolved techniques that can provide early-stage detection with fast experiment duration is plasmonics. This optical technique has the capability to detect viral proteins and genomes at the early stage via highly sensitive interaction between the biological target and the plasmonic chip. The efficiency of this technique could be proved using commercialized techniques like reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA) techniques. In this study, we aim to review the role of plasmonic technique in the detection of 11 deadliest viruses besides 2 common genital viruses for the human being. This is a rapidly moving topic of research, and a review article that encompasses the current findings may be useful for guiding strategies to deal with the pandemics. By investigating the potential aspects of this technique, we hope that this study could open new avenues toward the application of point-of-care techniques for virus detection at early stage that may inhibit the progressively hygienic threats.

Non-Invasive versus Invasive Samples for Zika Virus Surveillance: A Comparative Study in New Caledonia and French Guiana in 2015-2016

Zika virus, an arbovirus responsible for major outbreaks, can cause serious health issues, such as neurological diseases. In the present study, different types of samples (serum, saliva, and urine), collected in 2015–2016 in New Caledonia and French Guiana from 53 patients presenting symptoms and clinical signs triggered by arbovirus infections, were analyzed using a recently developed, and in-house validated, 4-plex RT-qPCR TaqMan method for simultaneous detection and discrimination of the Zika and Chikungunya viruses. Subsequently, statistical analyses were performed in order to potentially establish recommendations regarding the choice of samples type to use for an efficient and early stage Zika infection diagnosis. On this basis, the use of only urine samples presented the highest probability to detect viral RNA from Zika virus. Moreover, such a probability was improved using both urine and saliva samples. Consequently, the added value of non-invasive samples, associated with a higher acceptance level for collection among patients, instead of serum samples, for the detection of Zika infections was illustrated.

Enlarging the Toolbox Against Antimicrobial Resistance: Aptamers and CRISPR-Cas

In the post-genomic era, molecular treatments and diagnostics have been envisioned as powerful techniques to tackle the antimicrobial resistance (AMR) crisis. Among the molecular approaches, aptamers and CRISPR-Cas have gained support due to their practicality, sensibility, and flexibility to interact with a variety of extra- and intracellular targets. Those characteristics enabled the development of quick and onsite diagnostic tools as well as alternative treatments for pan-resistant bacterial infections. Even with such potential, more studies are necessary to pave the way for their successful use against AMR. In this review, we highlight those two robust techniques and encourage researchers to refine them toward AMR. Also, we describe how aptamers and CRISPR-Cas can work together with the current diagnostic and treatment toolbox.

Recent progresses and remaining challenges for the detection of Zika virus

Zika virus (ZIKV) has emerged as a particularly notorious mosquito-borne flavivirus, which can lead to a devastating congenital syndrome in the fetuses of pregnant mothers (e.g., microcephaly, spasticity, craniofacial disproportion, miscarriage, and ocular abnormalities) and cause the autoimmune disorder Guillain-Barre' syndrome of adults. Due to its severity and rapid dispersal over several continents, ZIKV has been acknowledged to be a global health concern by the World Health Organization. Unfortunately, the ZIKV has recently resurged in India with the potential for devastating effects. Researchers from all around the world have worked tirelessly to develop effective detection strategies and vaccines for the prevention and control of ZIKV infection. In this review, we comprehensively summarize the most recent research into ZIKV, including the structural biology and evolution, historical overview, pathogenesis, symptoms, and transmission. We then focus on the detection strategies for ZIKV, including viral isolation, serological assays, molecular assays, sensing methods, reverse transcription loop mediated isothermal amplification, transcription-mediated amplification technology, reverse transcription strand invasion based amplification, bioplasmonic paper-based device, and reverse transcription isothermal recombinase polymerase amplification. To conclude, we examine the limitations of currently available strategies for the detection of ZIKV, and outline future opportunities and research challenges.

Zika Virus-Associated Birth Defects, Costa Rica, 2016-2018

Enhanced birth defect surveillance increased identification of virus-associated abnormalities, including microcephaly.

After Zika virus (ZIKV) infection in Costa Rica was confirmed in January 2016, the national surveillance system was enhanced to monitor associated birth defects. To characterize the ZIKV outbreak among live-born infants during March 2016–March 2018, we conducted a descriptive analysis. Prevalence of ZIKV-associated birth defects was 15.3 cases/100,000 live births. Among 22 infants with ZIKV-associated birth defects, 11 were designated as confirmed (positive for ZIKV) and 11 were designated as probable cases (negative for ZIKV or not tested, but mother was expsed to ZIKV during pregnancy). A total of 91% had microcephaly (head circumference >2 SDs below mean for age and sex), 64% severe microcephaly (head circumference > 3 SDs below mean for age and sex), 95% neurodevelopmental abnormalities, 82% brain anomalies, 41% eye abnormalities, and 9% hearing loss. Monitoring children for > 1 year can increase identification of ZIKV-associated abnormalities in addition to microcephaly.

Lab-on-a-Chip Zika Detection With Reverse Transcription Loop-Mediated Isothermal Amplification-Based Assay for Point-of-Care Settings

CONTEXT.—

Zika virus (ZIKV) infection, primarily transmitted by mosquitoes, causes various neurologic disorders. To differentiate ZIKV from other arboviruses, such as dengue, chikungunya, and yellow fever viruses, a highly specific, sensitive, and automated detection system is needed for point-of-care (POC) settings.

OBJECTIVE.—

To detect ZIKV at POC settings, we have developed a fully automated lab-on-a-chip microfluidic platform for rapid disease detection by using reverse transcription loop-mediated isothermal amplification.

DESIGN.—

The developed setup consists of a microfluidic chip, a platform for magnetic actuation, and a heater along with the sensor to precisely control the temperature for the target amplification. The platform accurately controls the movement of the magnetic beads that enable the isolation and purification of the target nucleotides adhered to their surface for the amplification and disease detection on the microfluidic chip.

RESULTS.—

Within 40 minutes, change in color due to the presence of ZIKV amplicons was visually observed with the spiked plasma samples in the end point analysis. Also, we have accurately and specifically identified ZIKV in a small number of de-identified clinical samples.

CONCLUSIONS.—

All-inclusive, the developed fully automated POC ZIKV diagnostic chip is rapid, simple, easy to use, inexpensive, and suitable for the areas where facilities are limited.

Highly sensitive SERS assay of DENV gene via a cascade signal amplification strategy of localized catalytic hairpin assembly and hybridization chain reaction

Pathogenic viruses with worldwide distribution, high incidence and great harm are significantly and increasingly threatening human health. However, there is still lack of sufficient, highly sensitive and specific detection methods for on-time and early diagnosis of virus infection. In this work, taking dengue virus (DENV) as an example, a highly sensitive SERS assay of DENV gene was proposed via a cascade signal amplification strategy of localized catalytic hairpin assembly (LCHA) and hybridization chain reaction (HCR). The SERS assay was performed by two steps, i.e., the operation of cascade signal amplification strategy and the following SERS measurements by transferring the products on SERS-active AgNRs arrays. The sensitivity of the cascade signal amplification strategy is significantly amplified, which is 4.5 times that of individual CHA, and the signal-to-noise ratio is also improved to 5.4 relative to 1.8 of the CHA. The SERS sensing possesses a linear calibration curve from 1 fM to 10 nM with the limit of detection low to 0.49 fM, and has good specificity, uniformity and recovery, which indicates that the highly sensitive SERS assay provides an attractive tool for reliable, early diagnosis of DENV gene and is worth to be popularized in a wide detection of other viruses.

CRISPR-based platform for carbapenemases and emerging viruses detection using Cas12a (Cpf1) effector nuclease

CRISPR-Cas12a (also called Cpf1) has been commonly used for genomic editing, based on its ability to generate precise double-stranded DNA (dsDNA) breaks. Recently, it was demonstrated that Cas12a exhibits unspecific ssDNAse activity upon target recognition. This feature allows CRISPR-Cas to be coupled with a ssDNA reporter and generate a fast, accurate and ultrasensitive molecular detection method. Here, we demonstrate that Cas12a was able to detect DNA target sequences corresponding to carbapenemases resistance genes such as KPC, NDM and OXA. Also, with the addition of a reverse-transcription step, we were able to detect viral RNA sequences from DENV, ZIKV and HANTV genomes. In all cases, assay run time was less than two hours. Additionally, we report attomolar levels of detection. This methodology was validated using clinical samples from patients infected with Dengue virus. Reactions were visualized by detection of a fluorescent signal, as well as by the use of a simple lateral flow strip. These results indicate that Cas12a is able to detect both DNA and RNA targets, making it an appropriate and convenient tool to detect all types of pathogens.

Field-deployable molecular diagnostic platform for arbovirus detection in Aedes aegypti

BACKGROUND

Surveillance of mosquito infection status is critical for planning and deployment of proper mosquito control initiatives. Point-of-care (POC) detection assays are necessary for monitoring the infection prevalence and geographical range of viruses in mosquito vector populations. We therefore assessed the novel real-time PCR (qPCR) bCUBE (Hyris, London, UK) molecular diagnostic system as a tool for virus detection.

METHODS

Aedes aegypti Rps17 was used to validate and determine correlation coefficient for the novel bCUBE qPCR system to a laboratory standard StepOnePlus real-time PCR system (Applied Biosystems, Waltham, MA, USA). Experimentally infected Ae. aegypti were quantified for Zika (ZIKV) and dengue virus serotype 2 (DENV2) viral genomic RNA. Infection prevalence was compared to plaque assay.

RESULTS

We developed and validated a novel qPCR system for the detection of ZIKV and DENV2 using the real-time qPCR system bCUBE. With bCUBE-based qRT-PCR, viral genomic RNA could be detected in individually infected Ae. aegypti mosquitoes and in pools of 5, 10 or 15 mosquitoes.

CONCLUSIONS

The portable qPCR bCUBE diagnostic system is capable of detecting Zika and dengue virus in mosquitoes and therefore has potential as a practical field-deployable diagnostic test for vector-borne disease surveillance programmes.

Evaluation of plant growth promotion properties and induction of antioxidative defense mechanism by tea rhizobacteria of Darjeeling, India

A total of 120 rhizobacteria were isolated from seven different tea estates of Darjeeling, West Bengal, India. Based on a functional screening of in vitro plant growth-promoting (PGP) activities, thirty potential rhizobacterial isolates were selected for in-planta evaluation of PGP activities in rice and maize crops. All the thirty rhizobacterial isolates were identified using partial 16S rRNA gene sequencing. Out of thirty rhizobacteria, sixteen (53.3%) isolates belong to genus Bacillus, five (16.6%) represent genus Staphylococcus, three (10%) represent genus Ochrobactrum, and one (3.3%) isolate each belongs to genera Pseudomonas, Lysinibacillus, Micrococcus, Leifsonia, Exiguobacterium, and Arthrobacter. Treatment of rice and maize seedlings with these thirty rhizobacterial isolates resulted in growth promotion. Besides, rhizobacterial treatment in rice triggered enzymatic [ascorbate peroxidase (APX), catalase (CAT), chitinase, and phenylalanine ammonia-lyase (PAL)], and non-enzymatic [proline and polyphenolics] antioxidative defense reactions indicating their possible role in the reduction of reactive oxygen species (ROS) burden and thereby priming of plants towards stress mitigation. To understand such a possibility, we tested the effect of rhizobacterial consortia on biotic stress tolerance of rice against necrotrophic fungi, Rhizoctonia solani AG1-IA. Our results indicated that the pretreatment with rhizobacterial consortia increased resistance of the rice plants towards the common foliar pathogen like R. solani AG1-IA. This study supports the idea of the application of plant growth-promoting rhizobacterial consortia in sustainable crop practice through the management of biotic stress under field conditions.

A recombinant platform for flavivirus vaccines and diagnostics using chimeras of a new insect-specific virus

Flaviviruses such as dengue, yellow fever, Zika, West Nile, and Japanese encephalitis virus present substantial global health burdens. New vaccines are being sought to address safety and manufacturing issues associated with current live attenuated vaccines. Here, we describe a new insect-specific flavivirus, Binjari virus, which was found to be remarkably tolerant for exchange of its structural protein genes (prME) with those of the aforementioned pathogenic vertebrate-infecting flaviviruses (VIFs). Chimeric BinJ/VIF-prME viruses remained replication defective in vertebrate cells but replicated with high efficiency in mosquito cells. Cryo-electron microscopy and monoclonal antibody binding studies illustrated that the chimeric BinJ/VIF-prME virus particles were structurally and immunologically similar to their parental VIFs. Pilot manufacturing in C6/36 cells suggests that high yields can be reached up to 10^9.5 cell culture infectious dose/ml or ≈7 mg/liter. BinJ/VIF-prME viruses showed utility in diagnostic (microsphere immunoassays and ELISAs using panels of human and equine sera) and vaccine applications (illustrating protection against Zika virus challenge in murine IFNAR^-/- mouse models). BinJ/VIF-prME viruses thus represent a versatile, noninfectious (for vertebrate cells), high-yield technology for generating chimeric flavivirus particles with low biocontainment requirements.

Performance of an Automated Zika IgG Immunoassay in the Detection of Zika IgG Specific Antibodies—A Validation Approach in Samples from Prevalence Areas and Non-Endemic Countries

The diagnosis of Zika virus infection is complicated and includes testing for nucleic acids and IgM and IgG antibodies, depending on the stage of infection. Zika IgG is an important marker of infection after the acute stage; however, IgG assays can lack specificity due to the similarities between Zika and other flaviviruses. In this study, the diagnostic sensitivity and specificity of the Elecsys^® Zika IgG assay were assessed in 496 samples from Zika endemic regions, and specificity only was assessed in 1685 blood screening and diagnostic samples from Zika non-endemic regions. Cross-reactivity was also assessed against a panel of 202 potentially cross-reacting samples. The performance of the Elecsys^® Zika IgG assay was compared with the anti-Zika virus ELISA IgG. In the samples from the Zika endemic regions, the Elecsys^® Zika IgG assay had 92.88% (95% confidence interval 89.42–95.48) sensitivity and 100% specificity and in the samples from Europe the Elecsys^® Zika IgG assay specificity was ≥99.62%. The Elecsys^® Zika IgG assay was highly specific in samples from both prevalent and non-endemic regions.

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.

Comparative specificity and sensitivity of NS1-based serological assays for the detection of flavivirus immune response

Flaviviruses are relevant animal and human pathogens of increasing importance worldwide. The similarities of the initial clinical symptoms and the serological cross-reactivity of viral structural antigens make a laboratory diagnosis of flavivirus infection problematic. The main aim of the present study was the comparative specificity and sensitivity analysis of the non-structural protein NS1 as an antigen to detect flavivirus antibodies in sera from exposed individuals. A strategy for the purification of native recombinant non-structural protein 1 of representative flaviviruses including tick-borne encephalitis, West Nile, Zika and dengue virus was developed. The immunological properties of the purified antigens were analyzed using sera of immunized mice and of infected individuals in comparison with standard commercial assays. Recombinant NS1 protein was confirmed as a valuable option for the detection of flavivirus antibodies with reduced cross-reactivity and high sensitivity offering additional advantages for the detection of vaccine breakthrough cases.

Comparing vector and human surveillance strategies to detect arbovirus transmission: A simulation study for Zika virus detection in Puerto Rico

Background

Detecting and monitoring the transmission of arboviruses such as Zika virus (ZIKV), dengue virus, and chikungunya virus is critical for prevention and control activities. Previous work has compared the ability of different human-focused surveillance strategies to detect ZIKV transmission in U.S. counties where no known transmission had occurred, but whether virological surveillance in mosquitoes could represent an effective surveillance system is unclear.

Objectives

We leveraged a unique set of data from human and virological surveillance in Ae. aegypti during the 2016 ZIKV epidemic in Caguas, Puerto Rico, to compare alternative strategies for detecting and monitoring ZIKV activity.

Methods

We developed a simulation model for mosquito and human surveillance strategies and simulated different transmission scenarios with varying infection rates and mosquito trap densities. We then calculated the expected weekly number of detected infections, the probability of detecting transmission, and the number of tests needed and compared the simulations with observed data from Caguas.

Results

In simulated high transmission scenarios (1 infection per 1,000 people per week), the models demonstrated that both approaches had estimated probabilities of detection of greater than 78%. In simulated low incidence scenarios, vector surveillance had higher sensitivity than human surveillance and sensitivity increased with more traps, more trapping effort, and testing. In contrast, the actual data from Caguas indicated that human virological surveillance was more sensitive than vector virological surveillance during periods of both high and low transmission.

Conclusion

In scenarios where human surveillance is not possible or when transmission intensity is very low, virological surveillance in Ae. aegypti may be able to detect and monitor ZIKV epidemic activity. However, surveillance for humans seeking care for Zika-like symptoms likely provides an equivalent or more sensitive indicator of transmission intensity in most circumstances.

Control of Zika virus and other mosquito-borne viruses is dependent on timely and accurate detection of viral activity. A previous assessment of surveillance strategies for U.S. counties where no known transmission had occurred, found that testing people seeking medical care with signs of Zika virus was a more effective strategy than testing blood donors or pregnant women. An alternative strategy to testing humans is to test the mosquitoes directly for viruses. In this study, we used data from human and mosquito surveillances during the Zika epidemic of 2016 in Caguas, Puerto Rico to compare these strategies for detecting and monitoring Zika virus activity. Using simulation models for human and mosquito surveillance strategies, we examined different transmission scenarios with varying Zika virus infection rates. The results suggest that in high Zika virus transmission scenarios, both approaches effectively identified transmission. In low transmission scenarios, routine mosquito surveillance had the potential for increased sensitivity compared to human-based surveillance. However, resource availability may also be an important factor when considering the most effective approach.

Serial real-time RT-PCR and serology measurements substantially improve Zika and Dengue virus infection classification in a co-circulation area

BACKGROUND

Real-time RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) is considered the gold standard for Zika virus (ZIKV) infection diagnosis, despite its low sensitivity. Diagnosis using recommended serologic cutoffs in co-circulating Flaviviruses areas maybe inadequate due to in-vitro cross-reactivities of Flaviviruses-specific antibodies. We evaluated Zika diagnosis in symptomatic patients using serial RT-PCR and develop a classification model using serial Dengue virus (DENV) and ZIKV serologies.

METHODS

A prospective longitudinal multicentric study in Southern Mexico (NCT02831699) enrolled symptomatic and non-symptomatic participants. In the classification model, true positives were symptomatic (using a modified World Health Organization/Pan American Health Organization definition) with RT-PCR positive for ZIKV or DENV. True negatives were non-symptomatic with negative RT-PCR. Serial serology measurements were used to predict disease status.

RESULTS

Analyzing ZIKV and DENV RT-PCR at 3 timepoints between days 3 and 13 of symptom onset detected 25% more cases than a single RT-PCR analysis between day 0 and 6. When considering sensitivity and specificity together, the serial serology model predicted all categories of disease and negatives better than manufactures cutoffs. Their cutoffs optimized sensitivity or specificity but not both.

CONCLUSIONS

We demonstrated the importance of serial RT-PCR and antibody measurements to diagnose arbovirus infection in symptomatic patients living in regions with co-circulating flaviviruses.

[Epidemic and emerging prone-infectious diseases: Lessons learned and ways forward]

Africa along side with south-east Asia are the epicentres of emerging and epidemic prone-infectious diseases and megacity biosecurity threat scenarios. Massive mobility and reluctance in the populations exposed to epidemic and emerging prone-infectious diseases coupled by a weak health system made disease alert and control measures difficult to implement. The investigation of virus detection and persistence in semen across a range of emerging viruses is useful for clinical and public health reasons, in particular for viruses that lead to high mortality or morbidity rates or to epidemics. Innovating built facility to safely treat patients with highly pathogenic infectious diseases is urgently need, not only to prevent the spread of infection from patients to healthcare workers but also to offer provision of relatively invasive organ support, whenever considered appropriate, without posing additional risk to staff. Despite multiple challenges, the need to conduct research during epidemics is inevitable, and candidate products must continue undergoing rigorous trials. Preparedness including management of complex humanitarian crises with community distrust is a cornerstone in response to high consequence emerging infectious disease outbreaks and imposes strengthening of the public health response infrastructure and emergency outbreak systems in high-risk regions.

Use of Monocyte-Derived Macrophage Culture Increases Zika Virus Isolation Rate from Human Plasma

Viral isolation is desirable for many reasons, including development of diagnostic assays and reference materials, and for virology basic research. Zika virus (ZIKV) isolation from clinical samples is challenging, but isolates are known to infect various cell lines. Here, we evaluated suitability of Vero, C6/36 and JEG-3 as host cells, for direct isolation of ZIKV from human plasma. We also assessed the use of primary monocyte-derived macrophages (MDMs) culture to enhance ZIKV isolation from human plasma samples followed by virus expansion in Vero, C6/36 and JEG-3 cultures. Direct inoculation of cell lines with 42 ZIKV-RNA positive samples resulted in isolation rates of 9.52% (4/42) in Vero and C6/36, and of 7.14% (3/42) in JEG-3 cells. Inoculation of plasma in MDMs followed by supernatant testing by TaqMan RT-PCR, resulted in 33/42 (78.57%) ZIKV-RNA-positive supernatants, which expansion in cell lines increased isolation rates to 24.24% (8/33) in Vero and to 27.27% (9/33) in C6/36 and JEG-3 regardless of the presence of ZIKV-antibody. Isolates generated in JEG-3 cells were also produced in Vero and C6/36 with similar viral titers. These results suggest that efficiency of ZIKV isolation from human plasma can be enhanced when MDM culture is used before viral expansion in cell lines.

Phylogenetic surveillance of travel-related Zika virus infections through whole-genome sequencing methods

In 2018, the World Health Organization identified the Zika virus (ZIKV) as a pathogen that should be prioritized for public health research due to its epidemic potential. In this study, whole-genome sequencing (WGS) of travel-acquired ZIKV infections was used to examine the limitations of phylogenetic analysis. WGS and phylogenetic analysis were performed to investigate geographic clustering of samples from five Canadians with travel-acquired ZIKV infections and to assess the limitations of phylogenetic analysis of ZIKV sequences using a phylogenetic cluster approach. Genomic variability of ZIKV samples was assessed and for context, compared with hepatitis C virus (HCV) samples. Phylogenetic analysis confirmed the suspected region of ZIKV infection for one of five samples and one sample failed to cluster with sequences from its suspected country of infection. Travel-acquired ZIKV samples depicted low genomic variability relative to HCV samples. A floating patristic distance threshold classified all pre-2000 ZIKV sequences into separate clusters, while only Cambodian, Peruvian, Malaysian, and South Korean sequences were similarly classifiable. While phylogenetic analysis of ZIKV data can identify the broad geographical region of ZIKV infection, ZIKV’s low genomic variability is likely to limit precise interpretations of phylogenetic analysis of the origins of travel-related cases.

Zika virus: A possible emerging threat for Bangladesh!

Zika virus, a member of Flaviviridae is the etiology of Zika or Zika fever or Zika virus (ZIKV) disease characterized by mild symptoms similar to very mild form of Dengue or Chikungunya. The virus transmits through Aedes mosquitoes, particularly by Aedes aegypti. The most dangerous effect of ZIKV infection is the ability of the virus to cause microcephaly and congenital malformation to the newborn baby if the mother is infected. The neurological disorders including Guillain-Barré syndrome might be associated with adults and children due to ZIKV infections. Zika has emerged as a serious global public health problem as it has been found in 87 countries, particularly in Africa, America, and Asia and has no vaccine and treatment so far. Bangladesh is at a high risk of ZIKV infection and we consider ZIKV as a possible emerging threat for Bangladesh. This short review summarizes the insights of ZIKV infection, present status of the disease in Bangladesh and its neighboring countries, and recommendations for necessary preparations and strategies to be taken for effective controlling of the ZIKV infection in Bangladesh before getting any havoc.

Performance of CDC Trioplex qPCR during a dengue outbreak in Brazil

BACKGROUND

In recent years real‑time reverse transcription polymerase chain reaction (real-time RT-PCR) has become a leading technique for nucleic acid detection and quantification of flaviviruses, including Dengue virus (DENV). Trioplex real-time RT-PCR has the advantages of providing the concurrent detection of Zika virus (ZIKV), DENV, and Chikungunya virus (CHIKV) RNA in human serum.

OBJECTIVE

This study sought to compare the sensitivity and specificity of the Trioplex real-time RT-PCR assay to those provided by CDC DENV TaqMan® RT-qPCR assay and conventional PCR when used for DENV detection in the context of a dengue epidemic.

STUDY DESIGN

We analyzed 1656 serum samples from symptomatic patients with acute febrile disease for 5 days less between December 2018 and May 2019. The samples were tested using the various PCR-based assays.

RESULTS

Of the 1656 serum samples analyzed, 713 (43%) were laboratory-confirmed as arboviruses: 99.86% (712/713) were confirmed as DENV and 0.14% (1/713) were confirmed as ZIKV. Next, 590 samples were selected, and of these, 331 samples (56.1%) were determined to be positive (Ct < 38) and 259 samples (43.9%) were determined to be negative (Ct > 38) using the Trioplex real-time RT-PCR assay. The multiplex method found that the test exhibits 95% sensitivity and 100% specificity.

CONCLUSION

This evaluation demonstrates the capacity of the Trioplex real-time RT-PCR assay to detect DENV at a high sensitivity and specificity in a geographic area with a current dengue outbreak and a lower co-circulation of other arboviruses - such as ZIKV and CHIKV, and the results prove it´s applicability as clinical screening test that can serve as a confirmatory test.

Environmental health effects attributed to toxic and infectious agents following hurricanes, cyclones, flash floods and major hydrometeorological events

Extreme hydrometeorological events such as hurricanes and cyclones are increasing in frequency and intensity due to climate change and often associated with flash floods in coastal, urbanized and industrial areas. Preparedness and response measures need to concentrate on toxicological and infectious hazards, the potential impact on environmental health, and threat to human lives. The recognition of the danger of flood water after hurricanes is critical. Effective health management needs to consider the likelihood and specific risks of toxic agents present in waters contaminated by chemical spills, bio-toxins, waste, sewage, and water-borne pathogens. Despite significant progress in the ability to rapidly detect and test water for a wide range of chemicals and pathogens, there has been a lack of implementation to adapt toxicity measurements in the context of flash and hurricane-induced flooding. The aim of this review was to highlight the need to collect and analyze data on toxicity of flood waters to understand the risks and prepare vulnerable communities and first responders. It is proposed that new and routinely used technologies be employed during disaster response to rapidly assess toxicity and infectious disease threats, and subsequently take necessary remedial actions.

Emerging infectious disease laboratory and diagnostic preparedness to accelerate vaccine development

Rapid vaccine development in response to an outbreak of a new emerging infectious disease (EID) is a goal targeted by public health agencies worldwide. This goal becomes more complicated when there are no standardized sets of viral and immunological assays, no accepted and well-characterized samples, standards or reagents, and no approved diagnostic tests for the EID pathogen. The diagnosis of infections is of critical importance to public health, but also in vaccine development in order to track incident infections during clinical trials, to differentiate natural infection responses from those that are vaccine-related and, if called for by study design, to exclude subjects with prior exposure from vaccine efficacy trials. Here we review emerging infectious disease biological standards development, vaccine clinical assay development and trial execution with the recent experiences of MERS-CoV and Zika virus as examples. There is great need to establish, in advance, the standardized reagents, sample panels, controls, and assays to support the rapid advancement of vaccine development efforts in response to EID outbreaks.

Infections in pregnancy

Infections in pregnancy represent a challenging and often underappreciated area of concern for many specialists and general practitioners and can cause serious sequelae. Antenatal status should be highlighted on pathology request forms, as this serves to alert the laboratory of the need to store serum for an extended period. Prior antenatal specimens can be forwarded to other laboratories to enable testing in parallel with the more recent sample. Women with a confirmed, potentially vertically transmissible infection should be referred to a specialist with expertise in the management of perinatal infections. Cytomegalovirus infection is the most common congenital infection. Women who care for young children are at greater risk of exposure to the virus. Preventive steps including hand hygiene and avoiding contact with children's urine, mucous and saliva are recommended for all pregnant women. The incidence of parvovirus B19 infection in pregnancy is unknown. This infection is highly contagious and may result in fetal loss; particularly in the first half of pregnancy, pregnant women should avoid contact with adults or children who may have an infection.

[A non-coated enzyme-linked immunosorbent assay for screening zika virus envelope protein]

OBJECTIVE

To establish a non-coated enzyme-linked immunosorbent assay (ELISA) based on zika virus envelope (E) protein for detecting the expression of E protein in infected cells.

METHODS

Adherent Vero-143 cells infected with zika virus in a 96-well plate were fixed, and the antibodies against zika virus E protein were added at an optimized concentration to establish the non-coated ELISA method for E protein. The antiviral activities of lignans compound C1 was evaluated using this method. The accuracy of this non-coated ELISA was verified by RT-PCR, and the cross reaction with dengue virus was assessed.

RESULTS

After optimization, the background absorbance at 450 nm of uninfected cells was reduced to about 0.20. The antiviral activities of lignans compound C1 detected by this method were basically consistent with the results of RT-PCR. No cross reaction with dengue virus was found in this assay.

CONCLUSIONS

A non- coated ELISA method based on zika virus E protein was established, which can be used for screening antiviral agents against zika virus.

Expression and purification of domain III proteins from Dengue and Zika viruses

The envelope (E) protein from Dengue and Zika viruses comprises three functional and structural domains (DI, DII, and DIII). Domain III induces most of the neutralizing antibodies and, as such, is considered as having the highest antigenic potential for the evaluation of population-level surveillance and for detecting past infections in both Dengue and Zika patients. The present study aimed to clone and express recombinant proteins of domain III from Dengue virus serotype 2 and from Zika virus in a prokaryotic system, as well as evaluate their immunogenicity and cross-reactivity. Both antigens were successfully purified and their antigenicity was assessed in mice. The antibodies elicited by domain III of Zika and Dengue virus antigens recognized specifically the native proteins in infected cells. Furthermore, the antigens showed a more specific immunogenic response than that of domain III proteins from Dengue virus. The generated recombinant proteins can be potentially used in subunit vaccines or for surveillance studies.

Scientific and technological contributions of Latin America and Caribbean countries to the Zika virus outbreak

Background

The recent Zika virus (ZIKAV) epidemics disclosed a major public health threat and a scientific and technological (S&T) challenge. The lessons learned from the S&T response of Latin America and the Caribbean (LAC) countries are critical to inform further research and guide scientific investments. The present study aimed to assess how new S&T knowledge produced and disseminated regionally can contribute to address global health challenges.

Methods

Scientometric and social network analysis methods were used to assess the LAC scientific contribution and potential technological development on ZIKAV up to December 2017. ZIKAV-related publications were retrieved from the Web of Science, Scopus, and PubMed databases. Regionally published articles were obtained from SciELO (Scientific Electronic Library Online) and LILACS (Literature in the Health Sciences in Latin America and the Caribbean) databases. Patent registries were retrieved using Orbit Intelligence and Derwent Innovation. Records from each database were individually downloaded, integrated, standardized and analyzed.

Results

We retrieved 5421 ZIKAV-related publications, revealing a sharp increase from 2015 onwards. LAC countries accounted for 20% of all publications and Brazil was among the top three most central countries in the global network for ZIKAV research. A total of 274 patent families backed up by experimental evidence were retrieved. Only 5% were filed by LAC assignees, all of them based in Brazil. The largest contribution of LAC research was on the clinical manifestations of the ZIKAV infection, along with vector control, which was also the main focus of patents.

Conclusions

Our analysis offered a comprehensive overview of ZIKAV’s research and development and showed that (i) LAC countries had a key role in generating and disseminating scientific knowledge on ZIKAV; (ii) LAC countries have expressively contributed to research on ZIKAV clinical manifestations; (iii) the Brazilian scientific community was potentially very effective in knowledge sharing and diffusion in the ZIKAV research network; (iv) Brazil was the single LAC country filing patents, mostly represented by independent inventors and low-tech patents. The paper advocates the need for a continued interdisciplinary approach to improve LAC countries ability to prevent, prepare for and control future outbreaks.

Electronic supplementary material

The online version of this article (10.1186/s12889-019-6842-x) contains supplementary material, which is available to authorized users.

Quantum dots-based fluoroimmunoassay for anti-Zika virus IgG antibodies detection

Zika virus (ZIKV) has been declared a public health emergency of international concern. ZIKV has been associated with some neurological disorders, and their long-term effects are not completely understood. The majority of the methods for ZIKV diagnosis are based on the detection of IgM antibodies, which are the first signs of immunological response. However, the detection of IgG antibodies can be an important approach for ZIKV past infection diagnosis, especially for pregnant women, helping the comprehension/treatment of this disease. There has been a growing interest in applying nanoparticles for efficient ZIKV or antibodies detection. Quantum dots (QD) are unique fluorescent semiconductor nanoparticles, highly versatile for biological applications. In the present study, we explored the special QD optical properties to develop an immunofluorescence assay for anti-ZIKV IgG antibodies detection. Anti-IgG antibodies were successfully conjugated with QDs and applied in a fluorescence sensing nanoplatform. After optimization using IgG antibodies, the conjugates were employed to detect anti-ZIKV IgG antibodies in polystyrene microplates sensitized with ZIKV envelope E protein. The nanoplatform was able to detect anti-ZIKV IgG antibodies in a concentration at least 100-fold lower than the amount expected for protein E immune response. Moreover, conjugates were able to detect the antibodies for at least 4 months. Thus, our results showed that this QDs-based fluoroimmunoplatform can be considered practical, simple and promising to detect Zika past infections and/or monitoring immune response in vaccine trials.

Comprehensive Evaluation of Differential Serodiagnosis between Zika and Dengue Viral Infections

Diagnostic testing for Zika virus (ZIKV) or dengue virus (DENV) infection can be accomplished by a nucleic acid detection method; however, a negative result does not exclude infection due to the low virus titer during infection depending on the timing of sample collection. Therefore, a ZIKV- or DENV-specific serological assay is essential for the accurate diagnosis of patients and to mitigate potential severe health outcomes. A retrospective study design with dual approaches of collecting human serum samples for testing was developed. All serum samples were extensively evaluated by using both noninfectious wild-type (wt) virus-like particles (VLPs) and soluble nonstructural protein 1 (NS1) in the standard immunoglobulin M (IgM) antibody-capture enzyme-linked immunosorbent assay (MAC-ELISA). Both ZIKV-derived wt-VLP- and NS1-MAC-ELISAs were found to have similar sensitivities for detecting anti-premembrane/envelope and NS1 antibodies from ZIKV-infected patient sera, although lower cross-reactivity to DENV2/3-NS1 was observed. Furthermore, group cross-reactive (GR)-antibody-ablated homologous fusion peptide-mutated (FP)-VLPs consistently showed higher positive-to-negative values than homologous wt-VLPs. Therefore, we used DENV-2/3 and ZIKV FP-VLPs to develop a novel, serological algorithm for differentiating ZIKV from DENV infection. Overall, the sensitivity and specificity of the FP-VLP-MAC-ELISA and the NS1-MAC-ELISA were each higher than 80%, with no statistical significance. The accuracy can reach up to 95% with the combination of FP-VLP and NS1 assays. In comparison to current guidelines using neutralization tests to measure ZIKV antibody, this approach can facilitate laboratory screening for ZIKV infection, especially in regions where DENV infection is endemic and capacity for neutralization testing does not exist.

Zika Virus Infection, Basic and Clinical Aspects: A Review Article

BACKGROUND

Zika virus infection has recently attracted the attention of medical community. While clinical manifestations of the infection in adult cases are not severe and disease is not associated with high mortality rates, Zika virus infection can have an impact on fetal development and lead to severe neurodevelopmental abnormalities.

METHODS

To gain insight into different aspects of Zika virus infection, a comprehensive literature review was performed. With regard to epidemiology and geographical distribution of Zika virus infection, relevant information was extracted from CDC and WHO websites.

RESULTS

In this review, we discuss different basic and clinical aspects of Zika virus infection including virology, epidemiology and pathogenesis of disease. Laboratory methods required for the diagnosis of disease together with ethical issues associated with Zika virus infection will also be discussed in detail.

CONCLUSION

Herein, we have tried to provide a multi-faceted view of Zika virus infection, with greater emphasis on disease status in Eastern Mediterranean Region.

Bioinformatics Applications in Advancing Animal Virus Research

Viruses serve as infectious agents for all living entities. There have been various research groups that focus on understanding the viruses in terms of their host-viral relationships, pathogenesis and immune evasion. However, with the current advances in the field of science, now the research field has widened up at the ‘omics’ level. Apparently, generation of viral sequence data has been increasing. There are numerous bioinformatics tools available that not only aid in analysing such sequence data but also aid in deducing useful information that can be exploited in developing preventive and therapeutic measures. This chapter elaborates on bioinformatics tools that are specifically designed for animal viruses as well as other generic tools that can be exploited to study animal viruses. The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame (ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc. Various databases that organize information on animal and human viruses have also been described. The chapter will converse on overview of the current advances, online and downloadable tools and databases in the field of bioinformatics that will enable the researchers to study animal viruses at gene level.

Epidemiological Perspective in Managing Viral Diseases in Animals

Since the first report of a viral disease associated with plants, the fascinating field of virology has evolved and aided mankind altogether. Viral infections are known for inflicting colossal economic losses worldwide in food/work/companion animals. During the last few decades, emergence of a number of new viral diseases in animals, humans and plants has been visualized. Animal disease surveillance and monitoring is essential for the sustainability of healthy livestock production systems internationally. Preparedness for combating the emerging, re-emerging, exotic and transboundary diseases requires comprehensive monitoring and precision detection systems that are pliable under the field situations. With collective and concerted scientific interventions, a few of the animal viral diseases have been stamped out globally or regionally. Rinderpest, popularly called cattle plague, was eradicated from India in 2006 and globally in 2011. Notably, India achieved the disease-free status by OIE in 2014 for African horse sickness (peste equine), a deadly viral disease of equines. Likewise, equine infectious anaemia (EIA) and equine influenza (EI) have been controlled to a greater extent in India by adopting surveillance and monitoring along with zoo sanitary measures. Overall, there is a need for developing the ‘One World, One Health’ concept using multidisciplinary, regional and international networking to control major economically important emerging/re-emerging infectious diseases of humans and animals. This chapter describes various strategies for combating viral diseases of livestock.

Assay Challenges for Emerging Infectious Diseases: The Zika Experience

From the perspective of vaccine development, it is imperative to accurately diagnose target infections in order to exclude subjects with prior exposure from evaluations of vaccine effectiveness, to track incident infection during the course of a clinical trial and to differentiate immune reactions due to natural infections from responses that are vaccine related. When vaccine development is accelerated to a rapid pace in response to emerging infectious disease threats, the challenges to develop such diagnostic tools is even greater. This was observed through the recent expansion of Zika virus infections into the Western Hemisphere in 2014⁻2017. When initial Zika vaccine clinical trials were being designed and launched in response to the outbreak, there were no standardized sets of viral and immunological assays, and no approved diagnostic tests for Zika virus infection. The diagnosis of Zika virus infection is still an area of active research and development on many fronts. Here we review emerging infectious disease vaccine clinical assay development and trial execution with a special focus on the state of Zika virus clinical assays and diagnostics.

Persistent detection of Zika virus RNA from an infant with severe microcephaly - a case report

BACKGROUND

Zika virus (ZIKV) is a recently emerged arbovirus, which infection during pregnancy is associated with a series of congenital malformations, collectively denominated Congenital Zika Syndrome (CZS). Following infection, ZIKV RNA has a median duration period of 10 days in plasma and up to 6 months in semen in immunocompetent adult individuals. Moreover, ZIKV is able to replicate and persist in fetal brains and placentas, consequently, infection is associated with pregnancy loss, albeit the pathogenic mechanisms are still unknown.

CASE PRESENTATION

Here we report a CZS case of an infant born during the ZIKV outbreak in northeast Brazil, the child presented recurrent episodes of seizures with prolonged presence of ZIKV RNA on the central nervous system (CNS) and blood. ZIKV RNA was identified and partially sequenced from a sample of cerebrospinal fluid (CSF) obtained from the infant with 6 months of life, and later from another sample after the infant completed 17 months of life. Commonly congenital infections were discarded based on STORCH (syphilis, toxoplasmosis, rubella, cytomegalovirus and herpes simplex virus) negative laboratory results. Presence of specific ZIKV antibodies on both mother and children confirmed the association of severe microcephaly and ZIKV infection, diagnosed after birth.

CONCLUSIONS

Altogether, our data raise the possibility that CZS cases may result in prolonged viral presence, these findings could be useful for therapy and diagnostic recommendations.

Prevention and Control Strategies to Counter Zika Virus, a Special Focus on Intervention Approaches against Vector Mosquitoes-Current Updates

Zika virus (ZIKV) is the most recent intruder that acquired the status of global threat creating panic and frightening situation to public owing to its rapid spread, attaining higher virulence and causing complex clinical manifestations including microcephaly in newborns and Guillain Barré Syndrome. Alike other flaviviruses, the principal mode of ZIKV transmission is by mosquitoes. Advances in research have provided reliable diagnostics for detecting ZIKV infection, while several drug/therapeutic targets and vaccine candidates have been identified recently. Despite these progresses, currently there is neither any effective drug nor any vaccine available against ZIKV. Under such circumstances and to tackle the problem at large, control measures of which mosquito population control need to be strengthened following appropriate mechanical, chemical, biological and genetic control measures. Apart from this, several other known modes of ZIKV transmission which have gained importance in recent past such as intrauterine, sexual intercourse, and blood-borne spread need to be checked and kept under control by adopting appropriate precautions and utmost care during sexual intercourse, blood transfusion and organ transplantation. The virus inactivation by pasteurization, detergents, chemicals, and filtration can effectively reduce viral load in plasma-derived medicinal products. Added to this, strengthening of the surveillance and monitoring of ZIKV as well as avoiding travel to Zika infected areas would aid in keeping viral infection under check. Here, we discuss the salient advances in the prevention and control strategies to combat ZIKV with a focus on highlighting various intervention approaches against the vector mosquitoes of this viral pathogen along with presenting an overview regarding human intervention measures to counter other modes of ZIKV transmission and spread. Additionally, owing to the success of vaccines for a number of infections globally, a separate section dealing with advances in ZIKV vaccines and transmission blocking vaccines has also been included.