Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks.

Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.

Understanding dengue virus evolution to support epidemic surveillance and counter-measure development.

Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.

Complete Genome Sequences of Zika Virus Strains Isolated from the Blood of Patients in Thailand in 2014 and the Philippines in 2012.

Here, we present the complete genome sequences of two Zika virus (ZIKV) strains, Zika virus/Homo sapiens-tc/THA/2014/SV0127-14 and Zika virus/H. sapiens-tc/PHL/2012/CPC-0740, isolated from the blood of patients collected in Thailand, 2014, and the Philippines, 2012, respectively. Sequencing and phylogenetic analysis showed that both strains belong to the Asian lineage.

A cross-sectional study of hepatitis E virus infection in healthy people directly exposed and unexposed to pigs in a rural community in northern Thailand.

A cross-sectional study of the association between occupational pig exposure and hepatitis E virus (HEV) infection in adult pig farmers and the general population who were not directly exposed to pigs was conducted in Nan Province, Thailand, from November 2010 to April 2011. All participants were interviewed to provide information on their job history, eating habits and other potential confounders. The prevalence of anti-HEV immunoglobulin G antibodies (IgG) among 513 subjects was 23.0%. Hand washing with water and soap was associated with a lower seroprevalence of HEV infection, whereas living in an area with frequent flooding (OR 1.64, 95% CI: 1.00-2.68) and consuming internal pig organs more than twice per week (OR 3.23, 95%CI: 1.15-9.01) were both associated with a higher seroprevalence of anti-HEV IgG. There was no association between HEV seroprevalence and frequent, direct occupational pig contact.

Evaluation of an epitope-blocking enzyme-linked immunosorbent assay for the diagnosis of West Nile virus infections in humans.

An epitope-blocking enzyme-linked immunosorbent assay (b-ELISA) was evaluated for the diagnosis of West Nile virus (WNV) infections in humans. Sera from patients diagnosed with WNV infections from an outbreak in 2003 in Colorado and from patients diagnosed with dengue virus infections from Mexico and Thailand were tested with the b-ELISA. The b-ELISAs were performed using the WNV-specific monoclonal antibody (MAb) 3.1112G and the flavivirus-specific MAb 6B6C-1. Although the WNV-specific b-ELISA was effective in diagnosing WNV infections in humans from Colorado, it was not efficacious for diagnosing WNV infections in serum specimens from Mexico and Thailand. In serum specimens from patients from Colorado, the WNV b-ELISA and the WNV plaque reduction neutralization test showed an overall agreement of 91%. The sensitivity and specificity of the WNV b-ELISA were 89% and 92%, respectively, with a false-positive rate of 5%, based on receiver operating characteristic analysis. In contrast, false-positive rate results in specimens from the countries of Mexico and Thailand, where flaviviruses are endemic, were 79% and 80%, presumably due to the presence of antibodies resulting from previous dengue virus infections in Mexico and/or Japanese encephalitis virus infections or vaccination in Thailand. Thus, in regions where people have experienced previous or multiple flavivirus infections, the use of the b-ELISA for WNV diagnosis is contraindicated.

LAT expression during an acute HSV infection in the mouse.

Previous studies using cell culture systems to evaluate LAT expression demonstrated that the LAT promoter expresses at much higher levels in neuroblastoma cell lines than fibroblast lines. The high level of LAT expression in neuronal-derived cell lines correlates with the high level of LAT accumulation observed in sensory ganglia neurons during a latent infection. We have found that using LAT promoters to express reporter genes from recombinant viruses in vivo produces high levels of LAT promoter activity in the epithelium of the mouse foot. An analysis of LAT promoter activity during an acute infection in the mouse clearly demonstrates that in contrast to studies performed with selected cell lines, the LAT promoter expresses similar levels of reporter gene product in peripheral cells and in neurons. In addition, the amount of reporter gene product is higher when the LAT promoter is located within the R(L) as compared to the U(L) region, and when expression is adjusted for copy number of the reporter construct, expression is roughly the same. These results suggest the activity of the LAT promoter varies greatly according to cell type and that high levels of expression is not limited solely to neurons, especially in the in vivo setting.

Generation and use of recombinant reporter viruses for study of herpes simplex virus infections in vivo.

It has become increasingly clear that the fate of herpes simplex virus (HSV) infections involves complex interactions between the virus and the specific cell types that comprise the tissues of the animal host. No reliable cell culture system for studying the establishment of latency and reactivation exists, and therefore these studies must be performed within animal models. One difficulty in elucidating the molecular regulation of these events is in determining the transcriptional activity of key viral genes during different stages of the infection in vivo. The heterogeneous cell types comprising infected tissues make PCR analysis of tissue homogenates difficult to interpret. The need to characterize expression of multiple transcriptional markers reliably and quantitatively at the level of individual cells is therefore key to determining the interplay between viral and cellular genes during latency and reactivation. Here we discuss the construction and evaluation of HSV reporter viruses that have been used in these analyses. HSV-1 recombinants have been engineered with representative viral promoters driving beta-galactosidase as a reporter. Methodology used to evaluate the levels of gene expression using (1) quantitative enzyme assays, (2) precipitatable substrate assays to localize the positive cells, and (3) immunohistochemistry and fluorescence assays to look at colocalization of markers during in vivo infection is presented. In addition to studying the molecular pathogenesis of HSV, the application of similar reporter viruses to evaluate promoters for targeting various differentiated tissues will be useful in developing these viruses as potential vectors for gene therapy.