Development and evaluation of serotype- and group-specific fluorogenic reverse transcriptase PCR (TaqMan) assays for dengue virus

Mosquito immune cells enhance dengue and Zika virus dissemination in Aedes aegypti

Mosquito-borne viruses cause more than 400 million annual infections and place over half of the world's population at risk. Despite this importance, the mechanisms by which arboviruses infect the mosquito host and disseminate to tissues required for transmission are not well understood. Here, we provide evidence that mosquito immune cells, known as hemocytes, play an integral role in the dissemination of dengue virus (DENV) and Zika virus (ZIKV) in the mosquito Aedes aegypti. We establish that phagocytic hemocytes are a focal point for virus infection and demonstrate that these immune cell populations facilitate virus dissemination to the ovaries and salivary glands. Additional transfer experiments confirm that virus-infected hemocytes confer a virus infection to non-infected mosquitoes more efficiently than free virus in acellular hemolymph, revealing that hemocytes are an important tropism to enhance virus dissemination in the mosquito host. These data support a "trojan horse" model of virus dissemination where infected hemocytes transport virus through the hemolymph to deliver virus to mosquito tissues required for transmission and parallels vertebrate systems where immune cell populations promote virus dissemination to secondary sites of infection. In summary, this study significantly advances our understanding of virus infection dynamics in mosquitoes and highlights conserved roles of immune cells in virus dissemination across vertebrate and invertebrate systems.

Investigating the dose-dependency of the midgut escape barrier using a mechanistic model of within-mosquito dengue virus population dynamics

Arboviruses can emerge rapidly and cause explosive epidemics of severe disease. Some of the most epidemiologically important arboviruses, including dengue virus (DENV), Zika virus (ZIKV), Chikungunya (CHIKV) and yellow fever virus (YFV), are transmitted by Aedes mosquitoes, most notably Aedes aegypti and Aedes albopictus. After a mosquito blood feeds on an infected host, virus enters the midgut and infects the midgut epithelium. The virus must then overcome a series of barriers before reaching the mosquito saliva and being transmitted to a new host. The virus must escape from the midgut (known as the midgut escape barrier; MEB), which is thought to be mediated by transient changes in the permeability of the midgut-surrounding basal lamina layer (BL) following blood feeding. Here, we present a mathematical model of the within-mosquito population dynamics of DENV (as a model system for mosquito-borne viruses more generally) that includes the interaction of the midgut and BL which can account for the MEB. Our results indicate a dose-dependency of midgut establishment of infection as well as rate of escape from the midgut: collectively, these suggest that the extrinsic incubation period (EIP)-the time taken for DENV virus to be transmissible after infection-is shortened when mosquitoes imbibe more virus. Additionally, our experimental data indicate that multiple blood feeding events, which more closely mimic mosquito-feeding behavior in the wild, can hasten the course of infections, and our model predicts that this effect is sensitive to the amount of virus imbibed. Our model indicates that mutations to the virus which impact its replication rate in the midgut could lead to even shorter EIPs when double-feeding occurs. Mechanistic models of within-vector viral infection dynamics provide a quantitative understanding of infection dynamics and could be used to evaluate novel interventions that target the mosquito stages of the infection.

Rapid detection of West Nile and Dengue viruses from mosquito saliva by loop-mediated isothermal amplification and displaced probes

Arthropod-borne viruses are major causes of human and animal disease, especially in endemic low- and middle-income countries. Mosquito-borne pathogen surveillance is essential for risk assessment and vector control responses. Sentinel chicken serosurveillance (antibody testing) and mosquito pool screening (by RT-qPCR or virus isolation) are currently used to monitor arbovirus transmission, however substantial time lags of seroconversion and/or laborious mosquito identification and RNA extraction steps sacrifice their early warning value. As a consequence, timely vector control responses are compromised. Here, we report on development of a rapid arbovirus detection system whereby adding sucrose to reagents of loop-mediated isothermal amplification with displaced probes (DP-LAMP) elicits infectious mosquitoes to feed directly upon the reagent mix and expectorate viruses into the reagents during feeding. We demonstrate that RNA from pathogenic arboviruses (West Nile and Dengue viruses) transmitted in the infectious mosquito saliva was detectable rapidly (within 45 minutes) without RNA extraction. Sucrose stabilized viral RNA at field temperatures for at least 48 hours, important for transition of this system to practical use. After thermal treatment, the DP-LAMP could be reliably visualized by a simple optical image sensor to distinguish between positive and negative samples based on fluorescence intensity. Field application of this technology could fundamentally change conventional arbovirus surveillance methods by eliminating laborious RNA extraction steps, permitting arbovirus monitoring from additional sites, and substantially reducing time needed to detect circulating pathogens.

Phylogenetics, Epidemiology and Temporal Patterns of Dengue Virus in Araraquara, São Paulo State

Dengue virus (DENV) is a prominent arbovirus with global spread, causing approximately 390 million infections each year. In Brazil, yearly epidemics follow a well-documented pattern of serotype replacement every three to four years on average. Araraquara, located in the state of São Paulo, has faced significant impacts from DENV epidemics since the emergence of DENV-1 in 2010. The municipality then transitioned from low to moderate endemicity in less than 10 years. Yet, there remains an insufficient understanding of virus circulation dynamics, particularly concerning DENV-1, in the region, as well as the genetic characteristics of the virus. To address this, we sequenced 37 complete or partial DENV-1 genomes sampled from 2015 to 2022 in Araraquara. Then, using also Brazilian and worldwide DENV-1 sequences we reconstructed the evolutionary history of DENV-1 in Araraquara and estimated the time to the most recent common ancestor (tMRCA) for serotype 1, for genotype V and its main lineages. Within the last ten years, there have been at least three introductions of genotype V in Araraquara, distributed in two main lineages (L Ia and L Ib, and L II). The tMRCA for the first sampled lineage (2015/2016 epidemics) was approximately 15 years ago (in 2008). Crucially, our analysis challenges existing assumptions regarding the emergence time of the DENV-1 genotypes, suggesting that genotype V might have diverged more recently than previously described. The presence of the two lineages of genotype V in the municipality might have contributed to the extended persistence of DENV-1 in the region.

Nutritional stress compromises mosquito fitness and antiviral immunity, while enhancing dengue virus infection susceptibility

Diet-induced nutritional stress can influence pathogen transmission potential in mosquitoes by impacting life history traits, infection susceptibility, and immunity. To investigate these effects, we manipulate mosquito diets at larval and adult stages, creating two nutritional levels (low and normal), and expose adults to dengue virus (DENV). We observe that egg number is reduced by nutritional stress at both stages and viral exposure separately and jointly, while the likelihood of laying eggs is exclusively influenced by adult nutritional stress. Adult nutritional stress alone shortens survival, while any pairwise combination between both-stage stress and viral exposure have a synergistic effect. Additionally, adult nutritional stress increases susceptibility to DENV infection, while larval nutritional stress likely has a similar effect operating via smaller body size. Furthermore, adult nutritional stress negatively impacts viral titers in infected mosquitoes; however, some survive and show increased titers over time. The immune response to DENV infection is overall suppressed by larval and adult nutritional stress, with specific genes related to Toll, JAK-STAT, and Imd immune signaling pathways, and antimicrobial peptides being downregulated. Our findings underscore the importance of nutritional stress in shaping mosquito traits, infection outcomes, and immune responses, all of which impact the vectorial capacity for DENV transmission.

Investigating the dose-dependency of the midgut escape barrier using a mechanistic model of within-mosquito dengue virus population dynamics

Flaviviruses are arthropod-borne (arbo)viruses which can emerge rapidly and cause explosive epidemics of severe disease. Some of the most epidemiologically important flaviviruses, including dengue virus (DENV), Zika virus (ZIKV) and yellow fever virus (YFV), are transmitted by Aedes mosquitoes, most notably Aedes aegypti and Aedes albopictus. After a mosquito blood feeds on an infected host, virus enters the midgut and infects the midgut epithelium. The virus must then overcome a series of barriers before reaching the mosquito saliva and being transmitted to a new host. The virus must escape from the midgut (known as the midgut escape barrier; MEB), which is thought to be mediated by transient changes in the permeability of the midgut-surrounding basal lamina layer (BL) following blood feeding. Here, we present a mathematical model of the within-mosquito population dynamics of flaviviruses that includes the interaction of the midgut and BL which can account for the MEB. Our results indicate a dose-dependency of midgut establishment of infection as well as rate of escape from the midgut: collectively, these suggest that the extrinsic incubation period (EIP) - the time taken for DENV virus to be transmissible after infection - is shortened when mosquitoes imbibe more virus. Additionally, our experimental data indicates that multiple blood feeding events, which more closely mimic mosquito-feeding behavior in the wild, can hasten the course of infections, and our model predicts that this effect is sensitive to the amount of virus imbibed. Our model indicates that mutations to the virus which impact its replication rate in the midgut could lead to even shorter EIPs when double-feeding occurs. Mechanistic models of within-vector viral infection dynamics provide a quantitative understanding of infection dynamics and could be used to evaluate novel interventions that target the mosquito stages of the infection.

Author summary

Aedes mosquitoes are the main vectors of dengue virus (DENV), Zika virus (ZIKV) and yellow fever virus (YFV), all of which can cause severe disease in humans with dengue alone infecting an estimated 100-400 million people each year. Understanding the processes that affect whether, and at which rate, mosquitoes may transmit such viruses is, hence, paramount. Here, we present a mathematical model of virus dynamics within infected mosquitoes. By combining the model with novel experimental data, we show that the course of infection is sensitive to the initial dose of virus ingested by the mosquito. The data also indicates that mosquitoes which blood feed subsequent to becoming infected may be able to transmit infection earlier, which is reproduced in the model. This is important as many mosquito species feed multiple times during their lifespan and, any reduction in time to dissemination will increase the number of days that a mosquito is infectious and so enhance the risk of transmission. Our study highlights the key and complementary roles played by mathematical models and experimental data for understanding within-mosquito virus dynamics.

Phylogenetic Investigations of Dengue 2019-2021 Outbreak in Guadeloupe and Martinique Caribbean Islands

Dengue fever has been a public health problem in the Caribbean region since 1981, when it first reappeared in Cuba. In 1989, it was reported in Martinique and Guadeloupe (two French islands 200 km apart); since then, DENV has caused several epidemics locally. In 2019-2021, DENV-1, DENV-2, and DENV-3 were detected. Serotype distribution was differentiated, with DENV-2 and DENV-3 predominating in Guadeloupe and Martinique, respectively. Complete genome sequencing was carried out on 32 specimens, and phylogenic analysis identified the circulation of genotype V for DENV-1, cosmopolitan genotype for DENV-2, and genotype III for DENV-3. However, two distinct circulating groups were identified for DENV-1 and DENV-3, suggesting independent introductions. Overall, despite the context of the COVID-19 pandemic and the associated travel restrictions, these results confirm the active circulation of DENV and specific epidemiological features on each of the two islands. Such differences may be linked to the founder effect of the various introduction events, and to local factors such as the population immunity and the transmission capacity of the vectors. Further genomic and epidemiological characterization of DENV strains remains essential to understand how dengue spreads in each specific geographical context and to prevent future epidemics.

Strategies in the optimization of DNA hybridization conditions and its role in electrochemical detection of dengue virus (DENV) using response surface methodology (RSM)

In recent years, limited research has been conducted on enhancing DNA hybridization-based biosensor approaches using statistical models. This study explores the application of response surface methodology (RSM) to improve the performance of a DNA hybridization biosensor for dengue virus (DENV) detection. The biosensor is based on silicon nanowires decorated with gold nanoparticles (SiNWs/AuNPs) and utilizes methylene blue as a redox indicator. The DNA hybridization process between the immobilized DNA probe and the target DENV gene was monitored using differential pulse voltammetry (DPV) based on the reduction of methylene blue. Fourier-transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS) were employed to confirm successful DNA hybridization events on the modified screen-printed gold electrode (SPGE) surface. Several parameters, including pH buffer, NaCl concentration, temperature, and hybridization time, were simultaneously optimized, with NaCl concentration having the most significant impact on DNA hybridization events. This study enhances the understanding of the role of each parameter in influencing DNA hybridization detection in electrochemical biosensors. The optimized biosensor demonstrated the ability to detect complementary oligonucleotide and amplified DENV gene concentrations as low as 0.0891 ng µL^-1 (10 pM) and 2.8 ng µL^-1, respectively. The developed biosensor shows promise for rapid clinical diagnosis of dengue virus infection.

Limited Capacity for Aedes aegypti to Mechanically Transmit Chikungunya Virus and Dengue Virus

Mechanical transmission is an understudied mode of arbovirus transmission that occurs when a biting insect transmits virus among hosts by the direct transfer of virus particles contaminating its mouthparts. Multiple arboviruses have been shown to be capable of utilizing this transmission route, but most studies were conducted 40 to 70 years ago using dated methodologies. To gain a better understanding of this phenomenon, we used molecular techniques to evaluate the efficiency of mechanical transmission by Aedes aegypti mosquitoes for two evolutionarily divergent arboviruses, chikungunya virus (CHIKV) and dengue virus (DENV). Viral RNA and/or infectious DENV could be detected on 13.8% of mosquito proboscises sampled immediately after an infectious bloodmeal, but positivity rates declined within hours. CHIKV RNA and/or infectious virus was detected on 38.8% of proboscises immediately after feeding but positivity rates dropped to 2.5% within 4 hours. RNA copy numbers were low for both viruses, and we were unable to demonstrate mechanical transmission of CHIKV using an established animal model, suggesting that this mode of transmission is unlikely under natural conditions.

Preparedness for the Dengue Epidemic: Vaccine as a Viable Approach

Dengue fever is one of the significant fatal mosquito-borne viral diseases and is considered to be a worldwide problem. Aedes mosquito is responsible for transmitting various serotypes of dengue viruses to humans. Dengue incidence has developed prominently throughout the world in the last ten years. The exact number of dengue cases is underestimated, whereas plenty of cases are misdiagnosed as alternative febrile sicknesses. There is an estimation that about 390 million dengue cases occur annually. Dengue fever encompasses a wide range of clinical presentations, usually with undefinable clinical progression and outcome. The diagnosis of dengue depends on serology tests, molecular diagnostic methods, and antigen detection tests. The therapeutic approach relies completely on supplemental drugs, which is far from the real approach. Vaccines for dengue disease are in various stages of development. The commercial formulation Dengvaxia (CYD-TDV) is accessible and developed by Sanofi Pasteur. The vaccine candidate Dengvaxia was inefficient in liberating a stabilized immune reaction toward different serotypes (1-4) of dengue fever. Numerous promising vaccine candidates are now being developed in preclinical and clinical stages even though different serotypes of DENV exist that worsen the situation for a vaccine to be equally effective for all serotypes. Thus, the development of an efficient dengue fever vaccine candidate requires time. Effective dengue fever management can be a multidisciplinary challenge, involving international cooperation from diverse perspectives and expertise to resolve this global concern.

Surveillance of Viral Encephalitis in the Context of COVID-19: A One-Year Observational Study among Hospitalized Patients in Dakar, Senegal

The burden of encephalitis and its associated viral etiology is poorly described in Africa. Moreover, neurological manifestations of COVID-19 are increasingly reported in many countries, but less so in Africa. Our prospective study aimed to characterize the main viral etiologies of patients hospitalized for encephalitis in two hospitals in Dakar. From January to December 2021, all adult patients that met the inclusion criteria for clinical infectious encephalitis were enrolled. Cerebrospinal fluids, blood, and nasopharyngeal swabs were taken and tested for 27 viruses. During the study period, 122 patients were enrolled. Viral etiology was confirmed or probable in 27 patients (22.1%), with SARS-CoV-2 (n = 8), HSV-1 (n = 7), HHV-7 (n = 5), and EBV (n = 4) being the most detected viruses. Age groups 40–49 was more likely to be positive for at least one virus with an odds ratio of 7.7. The mortality was high among infected patients, with 11 (41%) deaths notified during hospitalization. Interestingly, SARS-CoV-2 was the most prevalent virus in hospitalized patients presenting with encephalitis. Our results reveal the crucial need to establish a country-wide surveillance of encephalitis in Senegal to estimate the burden of this disease in our population and implement strategies to improve care and reduce mortality.

Zika virus and temperature modulate Elizabethkingia anophelis in Aedes albopictus

BACKGROUND

Vector-borne pathogens must survive and replicate in the hostile environment of an insect's midgut before successful dissemination. Midgut microbiota interfere with pathogen infection by activating the basal immunity of the mosquito and by synthesizing pathogen-inhibitory metabolites.

METHODS

The goal of this study was to assess the influence of Zika virus (ZIKV) infection and increased temperature on Aedes albopictus midgut microbiota. Aedes albopictus were reared at diurnal temperatures of day 28 °C/night 24 °C (L) or day 30 °C/night 26 °C (M). The mosquitoes were given infectious blood meals with 2.0 × 108 PFU/ml ZIKV, and 16S rRNA sequencing was performed on midguts at 7 days post-infectious blood meal exposure.

RESULTS

Our findings demonstrate that Elizabethkingia anophelis albopictus was associated with Ae. albopictus midguts exposed to ZIKV infectious blood meal. We observed a negative correlation between ZIKV and E. anophelis albopictus in the midguts of Ae. albopictus. Supplemental feeding of Ae. albopictus with E. anophelis aegypti and ZIKV resulted in reduced ZIKV infection rates. Reduced viral loads were detected in Vero cells that were sequentially infected with E. anophelis aegypti and ZIKV, dengue virus (DENV), or chikungunya virus (CHIKV).

CONCLUSIONS

Our findings demonstrate the influence of ZIKV infection and temperature on the Ae. albopictus microbiome along with a negative correlation between ZIKV and E. anophelis albopictus. Our results have important implications for controlling vector-borne pathogens.

Dengue RNA detection and seroprevalence in blood donors during an outbreak in the São Paulo State, Brazil, 2016

Most dengue virus (DENV) infections remain asymptomatic. This increases the risk of DENV transfusion transmission (TT-DENV) during outbreaks. We evaluated DENV viremia in 8475 blood donations assembled in minipools for the presence of DENV RNA. The tested samples were obtained between February and May, 2016, during a large DENV outbreak in Ribeirão Preto city, northeast region of the São Paulo State, Brazil. The DENV RNA + samples were serotyped and screened for DENV NS1. We also tested a significant number of plasma samples (n = 372) to estimate the DENV seroprevalence among blood donors in the region. We detected three DENV RNA + samples in the tested blood donations (n = 3/8475, 0.04%). From these, two samples were further serotyped as DENV-1 and one sample as DENV-2. All DENV RNA positive samples were negative for anti-DENV IgG, indicating the presence of primary acute infection. Moreover, two of the DENV RNA + samples were also NS1 antigen positive (antigenemia). The anti-DENV IgG seroprevalence among blood donor population was 50.8% (n = 189/372). Our results are in accordance with the presence of DENV primary infection in blood donors which can lead to transfusion transmission of the infection to recipients. Measures to exclude such donors should be adopted to prevent TT-DENV.

A systematic review on phytochemicals for the treatment of dengue

Dengue fever is prevalent in subtopic regions, producing mortality and morbidity worldwide, which have been of major concern to different governments and World Health Organization. The search of new anti-dengue agents from phytochemicals was assumed to be highly emergent in past. The phytochemicals have been used in wide distribution of vector ailments such as malaria. The demand of the phytochemicals is based on the medicines which are mostly considered to be safer, less harmful than synthetic drugs and nontoxic. This review mentions majorly about the phytochemicals potentially inhibiting dengue fever around the world. The phytochemicals have been isolated from different species, have potential for the treatment of dengue. Different crude extracts and essential oils obtained from different species showed a broad activity against different phytochemicals. The current studies showed that natural products represent a rich source of medicines toward the dengue fever. Furthermore, ethnobotanical surveys and laboratory investigation established identified natural plants species in the development of drug discovery to control the dengue fever.

Integrated Arbovirus Surveillance Improves the Detection Onset of Zika Virus in Panama

We tested 700 serum samples collected throughout Panama from 2015 to 2016 for detecting antibodies and RNA of arboviruses. In convalescent specimens, microsphere immunoassay detected an antibody prevalence of 59.3% for dengue virus (DENV) and 30.3% for Zika virus (ZIKV), which included samples that were collected before the Panamanian surveillance system reported the first case of Zika in the country. For acute sera, the most common arbovirus was DENV with 18 positive samples (6%), followed by four (1.3%) of ZIKV and one (0.6%) of chikungunya virus (CHIKV). Our results indicate a change in the chronology of when ZIKV was first detected in Panama and stress the importance of integrating various approaches to enable improved surveillance of both endemic and emerging arboviruses.

Data on dengue incidence in South-eastern Brazil, 2014-2018

Data from the routine surveillance systems have been extensively used to estimate the incidence of dengue. However, routine surveillance data frequently underestimate the diseases' incidence. Underreporting of dengue cases is related to the varying spectrum of its clinical presentation, with a large proportion of mild and asymptomatic infections, to its unspecific signs and symptoms, to the limitations of access to health care, and to the performance of the surveillance system itself [1-3]. In order to obtain accurate figures on dengue incidence, a cohort of children and adolescents was set up and followed during four years. The incidence of reported cases was used as a reference for the sample size calculation, which was stratified by age groups. A two-stage procedure was used to select the participants: census tracts were randomly selected, and within each one, a pre-determined number of children of each age group was randomly selected. The parents or legal guardians of the participating children and adolescents provided a written informed consent. In the first home visit, they responded to a questionnaire containing data on socio-demographic characteristics, housing, access to water, sewage, and garbage collection. Also, during the first visit a blood sample of the participating child/adolescent was collected for dengue baseline serology. Beginning in the week after the enrolment, the parent or legal guardian that was designated in the first visit received weekly phone calls for fever surveillance. If the child/adolescent had fever during the week, a nurse was dispatched to the family's home to collect more detailed data on the fever episode and collect a blood sample for dengue diagnosis (IgG, IgM, NS1 and PCR). If the dengue diagnosis was confirmed, a medical appointment was scheduled, and another blood sample for confirmatory tests was collected. It was also agreed that in every anniversary of their participation, they would receive another visit for a blood collection for dengue serology, regardless if they had a fever episode or a confirmed dengue diagnosis during the previous year. This article contains the description of the cohort's dataset. It is associated with the article published in Acta Tropica, under the title "A cohort study to assess the incidence of dengue, Brazil, 2014-2018" [4]. The associated article focused on the seroprevalence and incidence of dengue, and explored some associations between both outcomes and some explanatory variables.

A cohort study to assess the incidence of dengue, Brazil, 2014-2018

The present cohort study was set up with the aim of determining the incidence of dengue among children and adolescents, from 2 to 16 years of age, living in Araraquara, South-Eastern Brazil, a city classified as a mid-level endemicity location for dengue. Enrollment took place from September 2014 to March 2015. Baseline socio-demographic data were collected, and a blood sample from the participant was drawn, for dengue serology. Families were contacted weekly for fever surveillance. If the child developed fever, a nurse visited the household to collect a blood sample. PCR, NS1 and IgM were used for dengue diagnosis. Parents or legal guardians of participating children provided a written informed consent. 3,514 children and adolescents were enrolled in the cohort. Dengue baseline seroprevalence was 12.2% (95%CI: 11.1 - 13.3). The incidence density of symptomatic dengue was 8.94 per 100 person/years in the first year of follow-up, 0.58 in the second, and 0.19 in the fourth. No cases were confirmed in the third year. Incidence was associated with age, sex, baseline seroprevalence and with living in a house as opposed to an apartment. This study provides relevant information on the epidemiology of dengue in mid-level transmission settings that may be useful to policymakers in the evaluation of control strategies.

First report of Aedes albopictus infected by Dengue and Zika virus in a rural outbreak in Brazil

In Brazil, Dengue (DENV) and Zika (ZIKV) viruses are reported as being transmitted exclusively by Aedes aegypti in urban settings. This study established the vectors and viruses involved in an arbovirus outbreak that occurred in 2019 in a rural area of Espírito Santo state, Brazil. Mosquitoes collected were morphologically identified, sorted in samples, and submitted to molecular analysis for arboviruses detection. Phylogenetic reconstruction was performed for the viral sequence obtained. All 393 mosquitoes were identified as Aedes albopictus. DENV-1 genotype V was present in one sample and another sample was positive for ZIKV. The DENV-1 clustered with viruses that have circulated in previous years in large urban centers of different regions in Brazil. This is the first report of A. albopictus infected by DENV and ZIKV during an outbreak in a rural area in Brazil, indicating its involvement in arboviral transmission. The DENV-1 strain found in the A. albopictus was not new in Brazil, being involved previously in epidemics related to A. aegypti, suggesting the potential to A. albopictus in transmitting viruses already circulating in the Brazilian population. This finding also indicates the possibility of these viruses to disperse across urban and rural settings, imposing additional challenges for the control of the diseases.

Nine year trends of dengue virus infection in Mumbai, Western India

INTRODUCTION:

Dengue virus (DENV) causes a wide range of diseases in humans, from acute febrile illness Dengue fever (DF) to life-threatening Dengue hemorrhagic fever (DHF) or Dengue shock syndrome (DSS). Factors believed to be responsible for spread of Dengue virus infection include explosive population growth, unplanned urban overpopulation with inadequate public health systems, poor standing water and vector control, climate changes and increased international recreational, business, military travel to endemic areas. All of these factors must be addressed to control the spread of Dengue and other mosquito-borne infections. The detection of Dengue virus RNA by reverse transcriptase PCR (RT-PCR) in human serum or plasma samples is highly indicative of acute Dengue fever. Moreover, the method is able to identify the Dengue virus serotype by demonstrating defined sequence homologies in the viral genomic RNA.

METHODS AND RESULTS:

During the nine year period of this study analysis, 6767 strongly suspected cases were tested by RT-PCR. 1685 (24.9%) were Dengue PCR positive and confirmed as Dengue cases. Observations on the seasonality were based on the nine year's data as the intensity of sampling was at its maximum during monsoon season. Dengue typing was done on 100 positive samples after storage of Dengue RNA at – 80°C. Dengue serotypes were detected in 69 samples of which Dengue 2 was most predominant. 576 samples were processed for NS1 antigen and PCR simultaneously. 19/576 were positive (3.3 %) for NS1 as well as by PCR. 23/576 samples were negative for NS1 antigen, but were positive by RT-PCR. The remaining 534 samples which were negative for NS1 antigen were also negative by Dengue RT-PCR.

CONCLUSION:

In this study we sought to standardize rapid, sensitive, and specific fluorogenic probe-based RT-PCR assay to screen and serotype a representative range of Dengue viruses that are found in and around Mumbai. Qualitative Dengue virus TaqMan assays could have tremendous utility for the epidemiological investigation of Dengue illness and especially for the study of the viremic response with candidate live-attenuated dengue virus vaccines.

Chikungunya virus populations experience diversity- dependent attenuation and purifying intra-vector selection in Californian Aedes aegypti mosquitoes

Chikungunya virus (Togaviridae, Alphavirus; CHIKV) is a mosquito-borne global health threat that has been transmitted transiently in the southeastern United States. A primary CHIKV mosquito vector, Aedes aegypti, was recently established in the populous state of California, but the vector competence of Californian mosquitoes is unknown. Explosive CHIKV epidemics since 2004 have been associated with the acquisition of mosquito-adaptive mutations that enhance transmission by Ae. aegypti or Ae. albopictus. As a highly mutable RNA virus, CHIKV has the potential for extensive and rapid genetic diversification in vertebrate hosts and mosquito vectors. We previously demonstrated that expansion of CHIKV diversity in cell culture allows for greater adaptability to novel selection pressures, and that CHIKV fidelity variants are able to diversify more than wildtype (WT) CHIKV in mice. The evolution of intra-vector CHIKV populations and the correlation between CHIKV population diversity and infectivity and transmissibility in mosquitoes has not yet been studied. Here, we address these gaps in knowledge via experimental infection of Ae. aegypti from California with WT and fidelity variant CHIKV. We show that Ae. aegypti from California are highly competent vectors for CHIKV. We also report that CHIKV fidelity variants diversify more than WT in mosquitoes and exhibit attenuated infectivity at the level of the midgut. Furthermore, we demonstrate that intra-vector populations of CHIKV are subjected to purifying selection in mosquito bodies, and sequences of non-coding CHIKV regions are highly conserved. These findings will inform public health risk assessment for CHIKV in California and improve our understanding of constraints to CHIKV evolution in mosquitoes.

Chikungunya virus (CHIKV) is transmitted by Aedes aegypti mosquitoes and has caused explosive epidemics in Asia and the Americas since 2004. During mosquito infection, the CHIKV genome replicates with a high mutation rate to produce virus populations with high genetic diversity that facilitate virus evolution. With this study, we address three gaps in knowledge: 1) are Ae. aegypti mosquitoes from Los Angeles, California, capable of transmitting CHIKV, 2) what effect does increased CHIKV population diversity have on virus infection and transmission by mosquitoes, and 3) are there constraints to CHIKV evolution in mosquitoes? We use oral infection of Ae. aegypti mosquitoes originating from Los Angeles, California to demonstrate high laboratory transmission competence of CHIKV. We also show that oral infection of mosquitoes with CHIKV variants that produce more diverse populations are less able to infect mosquitoes than wildtype CHIKV populations. Lastly, our study provides evidence of genome-wide and regional constraints to CHIKV evolution within Ae. aegypti mosquitoes. Our results will inform public health risk assessments for potential CHIKV introduction in southern California and advance our understanding of the role of mosquitoes in CHIKV evolution.

Novel pan-serotype control RNA for dengue virus typing through real-time reverse transcription-polymerase chain reaction

Dengue virus (DENV) is the causative agent of one of the most important febrile illnesses worldwide. Four DENV serotypes are responsible for a broad clinical spectrum of the disease. Positive controls are costly and required for the validation of molecular test results of DENV serotyping. In this study, we describe the in silico design of the qDENV-Control plasmid with the target sequences to oligonucleotides and probes widely used for DENV serotyping, and the subsequent production of qDENV Control RNA by T7-driven run-off in vitro transcription. The qDENV Control RNA was successfully used to validate the positive and negative DENV serotyping results, allowing its incorporation in routine in-house protocols for virologic surveillance. This Control RNA allowed the absolute quantification of viral RNA copies from unknown samples as required in several fundamental studies.

Travel-Associated Zika Cases and Threat of Local Transmission during Global Outbreak, California, USA

Zika and associated microcephaly among newborns were reported in Brazil during 2015. Zika has since spread across the Americas, and travel-associated cases were reported throughout the United States. We reviewed travel-associated Zika cases in California to assess the potential threat of local Zika virus transmission, given the regional spread of Aedes aegypti and Ae. albopictus mosquitoes. During November 2015-September 2017, a total of 588 travel-associated Zika cases were reported in California, including 139 infections in pregnant women, 10 congenital infections, and 8 sexually transmitted infections. Most case-patients reported travel to Mexico and Central America, and many returned during a period when they could have been viremic. By September 2017, Ae. aegypti mosquitoes had spread to 124 locations in California, and Ae. albopictus mosquitoes had spread to 53 locations. Continued human and mosquito surveillance and public health education are valuable tools in preventing and detecting Zika virus infections and local transmission in California.

Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples

Background

Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing.

Results

This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage.

Conclusions

Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5543-2) contains supplementary material, which is available to authorized users.

Molecular characterization of viruses associated with encephalitis in São Paulo, Brazil

The objective of this study was to characterize the prevalence of viral encephalitis due to arbovirus infection of the Togaviridae and Flaviviridae families in São Paulo, Brazil. A total of 500 cerebrospinal fluid (CSF) samples collected between August 2012 and January 2013, from patients with symptoms of acute encephalitis were analyzed. Findings suggestive of viral encephalitis—elevations in cell concentration, glucose and total protein—were observed in 234 (46.8%) samples, designated as Group 1. The remaining 266 samples comprised Group 2. All samples were tested for Flaviviruses (dengue virus 1, 2, 3 and 4, yellow fever virus and West Nile virus), Alphavirus (NS5 region) and enterovirus by RT- PCR and for herpesviruses and enteroviruses using CLART^-Entherpex. A presumptive viral etiological agent was detected in 26 samples (5.2%), 18 (8.0%) in Group 1 and 8 (3.0%) in Group 2. In Group 1 human herpesviruses were detected in 9 cases, enteroviruses in 7 cases, dengue viruses (DENV) in 2 CSFs and St. Louis encephalitis virus (SLEV) in one case. In Group 2 there were 3 CSFs positive for human herpesviruses, 2 for enteroviruses, 2 for DENV and 1 for SLEV. Detection of arboviruses, even though present in a minority of infected patients, identifies these viruses as a probable etiological agent of encephalitis. This is of special concern in regions where this class of viruses is endemic and has been linked to other recent epidemics.

First Complete Genome Sequences of Dengue Virus Serotype 2 Strains from the Solomon Islands and Vanuatu

Isolates of dengue virus serotype 2 (DENV-2) were recovered from a female resident of the Solomon Islands in 2016 and another female patient who had traveled from Vanuatu to Australia in 2017. Here, we describe the first complete genome sequences of DENV-2 strains from Vanuatu and the Solomon Islands.

Isolates of dengue virus serotype 2 (DENV-2) were recovered from a female resident of the Solomon Islands in 2016 and another female patient who had traveled from Vanuatu to Australia in 2017. Here, we describe the first complete genome sequences of DENV-2 strains from Vanuatu and the Solomon Islands.

Induction of anti-viral genes mediated by humoral factors upon stimulation with Lactococcus lactis strain plasma results in repression of dengue virus replication in vitro

Dengue is a mosquito-borne disease caused by dengue virus (DENV) infection. There is currently no effective vaccine or antiviral treatment available against DENV. In previous studies, we showed that Lactococcus lactis strain Plasma (LC-Plasma) could activate plasmacytoid dendritic cells, which play an important role against virus infection. LC-Plasma administration ameliorated symptoms of viral diseases and its effect appeared to be associated with IFN-α induction. However the precise mechanism of LC-Plasma protection remained unclear. In this study, we investigated the effects of LC-Plasma-induced humoral factors on DENV replication using HepG2 cells as an in vitro infection model. When HepG2 cells were preincubated with supernatants of LC-Plasma-stimulated bone marrow-derived dendritic cells, the replication of DENV was significantly inhibited in a dose dependent manner and its activity was evident regardless of the DENV serotype. In addition, the expression of interferon-stimulated genes, including ISG15, IFITM-1, MxA, RSAD2, and RyDEN, was significantly upregulated by humoral factors. We also compared the effects of representative strains of lactic acid bacteria and found that the ability to prevent DENV replication was unique to LC-Plasma. In addition, it was revealed that both anti-DENV replication activity and ISG induction depended on type I IFN rather than type III IFN signaling. Taken together, since LC-Plasma induces, in a more natural form, potent anti-DENV replication activities irrespective of viral serotypes via induction of type I IFN, LC-Plasma could be safely used as a prophylactic anti-DENV option.

First Reported Complete Genome Sequence of a Dengue Virus Serotype 4 Strain from Papua New Guinea

A male patient in his 50s who traveled from Papua New Guinea (PNG) to Australia in 2016 was diagnosed with a dengue virus serotype 4 (DENV-4) infection, and the virus was isolated from his acute-phase serum. Here, we describe the first complete genome sequence of a DENV-4 strain from PNG.

A male patient in his 50s who traveled from Papua New Guinea (PNG) to Australia in 2016 was diagnosed with a dengue virus serotype 4 (DENV-4) infection, and the virus was isolated from his acute-phase serum. Here, we describe the first complete genome sequence of a DENV-4 strain from PNG.

Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study

Background

Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR) directed against genomic regions conserved between different isolates. Genetic variation can however result in mismatches of primers and probes with their targeted nucleic acid regions. Whole genome sequencing allows to characterize and track such changes, which in turn enables to evaluate, optimize, and (re-)design novel and existing RT-qPCR methods. The immense amount of available sequence data renders this however a labour-intensive and complex task.

Results

We present a bioinformatics approach that enables in silico evaluation of primers and probes intended for routinely employed RT-qPCR methods. This approach is based on analysing large amounts of publically available whole genome data, by first employing BLASTN to mine the genomic regions targeted by the RT-qPCR method(s), and afterwards using BLASTN-SHORT to evaluate whether primers and probes will anneal based on a set of simple in silico criteria. Using dengue virus as a case study, we evaluated 18 published RT-qPCR methods using more than 3000 publically available genomes in the NCBI Virus Variation Resource, and provide a systematic overview of method performance based on in silico sensitivity and specificity.

Conclusions

We provide a comprehensive overview of dengue virus RT-qPCR method performance that will aid appropriate method selection allowing to take specific measures that aim to contain and prevent viral spread in afflicted regions. Notably, we find that primer-template mismatches at their 3′ end may represent a general issue for dengue virus RT-qPCR detection methods that merits more attention in their development process. Our approach is also available as a public tool, and demonstrates how utilizing genomic data can provide meaningful insights in an applied public health setting such as the detection of viral species in human diagnostics.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2313-0) contains supplementary material, which is available to authorized users.

On the Home Front: Specialised Reference Testing for Dengue in the Australasian Region

Reference laboratories are vital for disease control and interpreting the complexities and impact of emerging pathogens. The role of these centralized facilities extends beyond routine screening capabilities to provide rapid, specific, and accurate diagnoses, advanced data analysis, consultation services, and sophisticated disease surveillance and monitoring. Within the Australasian region, the Public Health Virology Laboratory (PHV), Forensic and Scientific Services, Department of Health, Queensland Government, Australia, and the Institute of Environmental Science and Research Limited (ESR), New Zealand (NZ) perform specialised reference testing and surveillance for dengue viruses (DENVs) and other emerging arthropod-borne viruses (arboviruses), including chikungunya virus (CHIKV) and Zika virus (ZIKV). With a focus on DENV, we review the reference testing performed by PHV (2005 to 2017) and ESR (2008 to 2017). We also describe how the evolution and expansion of reference-based methodologies and the adoption of new technologies have provided the critical elements of preparedness and early detection that complement frontline public health control efforts and limit the spread of arboviruses within Australasia.

Parental and offspring larval diets interact to influence life-history traits and infection with dengue virus in Aedes aegypti

The environmental conditions experienced by parents can influence offspring phenotype along with the conditions experienced by offspring. These parental effects are clear in organisms that display parental care and are less clear in other organisms. Here, we consider effects of parental and offspring larval nutrition on offspring development time, survivorship and infection with dengue virus in Aedes aegypti, the mosquito vector of dengue, chikungunya, yellow fever and Zika. Parents were raised on either high or low larval detritus inputs with subsequent offspring being divided into two groups, one receiving high nutrients and the other low. Low nutrient females from low nutrient parents (LL) developed significantly slower than those from high nutrient parents (HL). Females from all parent by offspring nutrient treatment groups were equally likely to become infected with dengue virus at 24 h, 3 days and 14 days. After 14 days, high nutrient females from low nutrient parents (LH) had 11 times higher viral titres and more disseminated infections than high nutrient females from high nutrient parents (HH). These results suggest that carry-over environmental stress from the parental generation can influence life histories and arbovirus infection in Ae. aegypti females. We found males to be robust to the life-history parameters measured, suggesting sex-specific differences which may relate to their lower nutrient requirements for metamorphosis.

Enhanced surveillance during a public health emergency in a resource-limited setting: Experience from a large dengue outbreak in Solomon Islands, 2016-17

Between August-2016 and April-2017, Solomon Islands experienced the largest and longest-running dengue outbreak on record in the country, with 12,329 suspected cases, 877 hospitalisations and 16 deaths. We conducted a retrospective review of related data and documents, and conducted key informant interviews to characterise the event and investigate the adaptability of syndromic surveillance for enhanced and expanded data collection during a public health emergency in a low resource country setting. While the outbreak quickly consumed available public and clinical resources, we found that authorities were able to scale up the conventional national syndrome-based early warning surveillance system to support the increased information demands during the event demonstrating the flexibility of the system and syndromic surveillance more broadly. Challenges in scaling up included upskilling and assisting staff with no previous experience of the tasks required; managing large volumes of data; maintaining data quality for the duration of the outbreak; harmonising routine and enhanced surveillance data and maintaining surveillance for other diseases; producing information optimally useful for response planning; and managing staff fatigue. Solomon Islands, along with other countries of the region remains vulnerable to outbreaks of dengue and other communicable diseases. Ensuring surveillance systems are robust and able to adapt to changing demands during emergencies should be a health protection priority.

Infection rate of Aedes aegypti mosquitoes with dengue virus depends on the interaction between temperature and mosquito genotype

Dengue fever is the most prevalent arthropod-transmitted viral disease worldwide, with endemic transmission restricted to tropical and subtropical regions of different temperature profiles. Temperature is epidemiologically relevant because it affects dengue infection rates in Aedes aegypti mosquitoes, the major vector of the dengue virus (DENV). Aedes aegypti populations are also known to vary in competence for different DENV genotypes. We assessed the effects of mosquito and virus genotype on DENV infection in the context of temperature by challenging Ae. aegypti from two locations in Vietnam, which differ in temperature regimes, with two isolates of DENV-2 collected from the same two localities, followed by incubation at 25, 27 or 32°C for 10 days. Genotyping of the mosquito populations and virus isolates confirmed that each group was genetically distinct. Extrinsic incubation temperature (EIT) and DENV-2 genotype had a direct effect on the infection rate, consistent with previous studies. However, our results show that the EIT impacts the infection rate differently in each mosquito population, indicating a genotype by environment interaction. These results suggest that the magnitude of DENV epidemics may not only depend on the virus and mosquito genotypes present, but also on how they interact with local temperature. This information should be considered when estimating vector competence of local and introduced mosquito populations during disease risk evaluation.

Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype

BACKGROUND

4 one-step, real-time, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays were developed for the detection of dengue virus (DENV) serotypes by considering 2,056 full genome DENV sequences. DENV1 and DENV2 RT-LAMP assays were validated with 31 blood and 11 serum samples from Tanzania, Senegal, Sudan and Mauritania. DENV3 and DENV4 RT-LAMP assays were validated with 25 serum samples from Cambodia.

METHODOLOGY/PRINCIPAL FINDINGS

4 final reaction primer mixes were obtained by using a combination of Principal Component Analysis of the full DENV genome sequences, and LAMP primer design based on sequence alignments using the LAVA software. These mixes contained 14 (DENV1), 12 (DENV2), 8 (DENV3) and 3 (DENV4) LAMP primer sets. The assays were evaluated with an External Quality Assessment panel from Quality Control for Molecular Diagnostics. The assays were serotype-specific and did not cross-detect with other flaviviruses. The limits of detection, with 95% probability, were 22 (DENV1), 542 (DENV2), 197 (DENV3) and 641 (DENV4) RNA molecules, and 100% reproducibility in the assays was obtained with up to 102 (DENV1) and 103 RNA molecules (DENV2, DENV3 and DENV4). Validation of the DENV2 assay with blood samples from Tanzania resulted in 23 samples detected by RT-LAMP, demonstrating that the assay is 100% specific and 95.8% sensitive (positive predictive value of 100% and a negative predictive value of 85.7%). All serum samples from Senegal, Sudan and Mauritania were detected and 3 untyped as DENV1. The sensitivity of RT-LAMP for DENV4 samples from Cambodia did not quite match qRT-PCR.

CONCLUSIONS/SIGNIFICANCE

We have shown a novel approach to design LAMP primers that makes use of fast growing sequence databases. The DENV1 and DENV2 assays were validated with viral RNA extracted clinical samples, showing very good performance parameters.

A one-step TaqMan real-time qRT-PCR assay for the specific detection and quantitation of the Spanish goat encephalitis virus (SGEV)

Louping ill-like virus (LI) has been recently detected in two different locations in the north of Spain and separated by only around 400 km. Using molecular approaches, the viruses causing both outbreaks have been shown to be different to LI virus, but also different to each other. They have been called SSEV (Spanish sheep encephalitis virus) and SGEV (Spanish goat encephalitis virus) taking into account the species from which they were isolated. The aim of this paper was to design a quantitative TaqMan real-time RT-PCR protocol, for the specific diagnostic and quantitation of SGEV. Linearity, efficiency and dynamic range as well as reproducibility and specificity of the method has been tested and established. The method has proved to be valid for the specific detection and viral load quantitation of SGEV genome in virus isolates and tissue samples from infected animals. This assay will be a useful analytical tool in early diagnosis and epidemiological surveys.

Clinical Features and Laboratory Findings of Travelers Returning to South Australia with Dengue Virus Infection

Reported cases of dengue are rising in South Australia (SA) in travellers returning from dengue-endemic regions. We have undertaken a retrospective analysis to identify the clinical and laboratory characteristics of patients returning to SA with suspected dengue virus (DENV) infection. From 488 requests, 49 (10%) were defined by serology as acute dengue, with the majority of patients (75%) testing as non-structural protein 1 (NS1) and/or IgM positive. Dengue was most commonly acquired in Indonesia (42.9%) with clinical features of fever (95%), headache (41%) and myalgia/arthralgia (56%). The presence of rash (36%) and laboratory findings of neutropenia, leukopenia, thrombocytopenia, but not elevated C-reactive protein, were distinct from findings in DENV-seronegative patients. Available dengue seropositive samples were analysed by RT-PCR, with 14/32 (43.8%) positive by a serotype non-specific DENV assay, but 28/32 positive (87.5%) when also assessed by serotype-specific RT-PCR. Serotype analysis revealed the predominance of DENV-1 and DENV-2 and the presence of DENV-3, but not DENV-4 or Zika virus (ZIKV). Thus, dengue in returned travellers in SA presents in a manner consistent with World Health Organization (WHO) definitions, with symptoms, travel history and laboratory results useful in prioritising the likelihood of dengue. This definition will assist the future management in DENV-non-endemic regions, such as SA.

Rapid detection of a dengue virus RNA sequence with single molecule sensitivity using tandem toehold-mediated displacement reactions

Novel tandem toehold-mediated displacement reactions were developed to detect dengue virus RNA. As few as 6 copies of RNA per sample were detected.

Zika Virus Persistence and Higher Viral Loads in Cutaneous Capillaries Than in Venous Blood

We collected venous and capillary serum samples from 21 Zika virus‒infected patients on multiple days after symptom onset and found RNA load was higher and median duration of virus detection significantly longer in capillary than in venous blood. These findings raise questions about the role of the capillary compartment in virus transmission dynamics.

Characterization of type I interferon responses in dengue and severe dengue in children in Paraguay

BACKGROUND

Infection with dengue virus (DENV) produces a wide spectrum of clinical illness ranging from asymptomatic infection to mild febrile illness, and to severe forms of the disease. Type I interferons (IFNs) represent an initial and essential host defense response against viruses. DENV has been reported to trigger a robust type I IFN response; however, IFN-α/β profile in the progression of disease is not well characterized.

OBJECTIVES AND STUDY DESIGN

In this context, we conducted a retrospective study assessing the circulating serum levels of type I IFNs and related cytokines at different phases of illness in children during the 2011 outbreak of DENV in Paraguay. Demographic, clinical, laboratory and virological data were analyzed.

RESULTS

During defervescence, significantly higher levels of IFN-β, IL-6 and MIP-1β, were detected in severe vs. non-severe dengue patients. Additionally, a significant positive correlation between INF-α and viremia was detected in children with severe dengue. A significant positive correlation was also observed between IFN-β serum levels and hematocrit during the febrile phase, whereas IFN-α levels negatively correlated with white blood cells during defervescence in severe dengue patients. Furthermore, previous serologic status of patients to DENV did not influence type I IFN production.

CONCLUSIONS

The distinct type I IFN profile in children with dengue and severe dengue, as well as its association with viral load, cytokine production and laboratory manifestations indicate differences in innate and adaptive immune responses that should be investigated further in order to unveil the association of immunological and physiological pathways that underlie in DENV infection.

Isolation of serotype-specific antibodies against dengue virus non-structural protein 1 using phage display and application in a multiplexed serotyping assay

The multidimensional nature of dengue virus (DENV) infections, which can be caused by four distinct serotypes of the virus, complicates the sensitivity of assays designed for the diagnosis of infection. Different viral markers can be optimally detected at different stages of infection. Of particular clinical importance is the early identification of infection, which is pivotal for disease management and the development of blood screening assays. Non-structural protein 1 (NS1) is an early surrogate marker of infection and its detection in serum coincides with detectable viraemia. The aim of this work was to isolate and characterise serotype-specific monoclonal antibodies that bind to NS1 for each of the four DENV serotypes. This was achieved using phage display and a subtractive biopanning strategy to direct the antibody selection towards serotype-specific epitopes. This antibody isolation strategy has advantages over immunisation techniques where it is difficult to avoid antibody responses to cross-reactive, immunodominant epitopes. Serotype specificity to recombinant antigen for each of the antibodies was confirmed by Enzyme Linked Immunosorbent Assay (ELISA) and Surface Plasmon Resonance. Confirmation of binding to native DENV NS1 was achieved using ELISA and immunofluorescence assay on DENV infected Vero cells. No cross-reactivity with Zika or Kunjin viruses was observed. A previously isolated pan-reactive antibody that binds to an immunodominant epitope was able to pair with each of the serotype-specific antibodies in a sandwich ELISA, indicating that the serotype specific antibodies bind to epitopes which are all spatially distinct from the immunodominant epitope. These antibodies were suitable for use in a multiplexed assay for simultaneous detection and serotyping of DENV NS1 in human serum. This work demonstrates that phage display coupled with novel biopanning strategies is a valuable in vitro methodology for isolation of binders that can discern amongst antigens with high homology for diagnostic applicability.

Serological, molecular and clinical correlates of dengue from a tertiary care centre in Chennai, India

Dengue disease is caused by dengue viruses 1-4 and has been ranked by the World Health Organisation (WHO) as the fastest spreading vector-borne viral disease. Dengue is often underreported and misdiagnosed due to a wide spectrum of clinical manifestations. Diagnosis of dengue is based on clinical case definitions and laboratory methods. Newer case definitions of dengue have been formulated by clinical studies in order to improve case detection. Owing to its epidemic potential, mortality and morbidity, there is a need for a rapid and accurate diagnostic assay for dengue in order to help the clinician in the early detection of cases and to prevent disease progression. A duplex real time PCR targeting the 3'UTR region for rapid and simultaneous detection of all dengue viruses serotypes (1-4) was standardized based on published literature. About 150 patients with acute undifferentiated febrile illness classified based on the 2009 WHO dengue case definition were tested using the duplex real time dengue PCR. Sequencing based PCR was performed on selected PCR positive samples for partial nucleotide sequence of the CprM gene and a phylogenetic tree was constructed. Statistical analysis was done using the MedCalc software. Out of the 126 patients classified as dengue disease positive, according to the 2009 WHO dengue case definition, 54% had "probable dengue", 43% had "dengue with warning signs" and 3% had "severe dengue". The performance of the duplex real time PCR was assessed among the various clinical groups of dengue and it was found that in the "dengue with warning signs group" PCR had a positive predictive value of 85.29% (range - 68.94% to 95.05%) when compared with dengue NS1 ELISA. The average time for PCR positivity was found to be four days from the onset of illness. The cycling threshold values obtained from real time PCR were used as a semi quantitative measure of viremia. Accordingly, there was a relatively low CT value among the "warning signs dengue group" when compared to the "probable dengue group". The use of the duplex PCR is suggested in the early diagnosis of dengue, especially in the 'warning signs' group of patients as they showed a higher positivity rate. Also, the use of the resultant CT value as a semi-quantitative measure of viremia will assist the clinician in early diagnosis and prevention of disease development.

Simultaneous detection of chikungunya virus, dengue virus and human pathogenic Leptospira genomes using a multiplex TaqMan® assay

Background

In 2005–2006 a major epidemics of Chikungunya disease occurred in South-West Indian Ocean islands. In Reunion Island, the magnitude of Chikungunya infection related symptoms was high and with over 38% of serological prevalence in the population. This epidemics illustrated the potential threat of emerging arboviral diseases for inhabitants of Reunion Island and elsewhere since vectors are worldwide distributed. A sentinel surveillance network was set-up to detect emerging pathogens associated with fever over 38 °C and in the absence of known etiologic causes. Leptospirosis is caused by a pathogenic spirochete of the Leptospira genus and is an endemic and recurrent seasonal disease of great concern in Reunion Island. To accurately diagnose potentially infected patients and to advise Health authorities on the presence of emerging pathogens, a rapid diagnostic test was needed that could differentiate between these 3 pathogens.

Methods

A one-step multiplex real-time PCR assay was developed that can simultaneously detect RNA of Chikungunya and Dengue viruses and leptospiral DNA with good performance for a routine diagnostic use.

Results

Simplex protocols already published were used with key modifications to implement a triplex assay which was set-up with a small reaction volume to improve cost efficiency.

Conclusions

This approach has enabled greater diagnostic capacity in our laboratory. We established a multiplex approach validated and valuable for cost savings, and with the concurrent detection of 3 pathogens of public health concern.

Re-evaluation of routine dengue virus serology in travelers in the era of Zika virus emergence

BACKGROUND

Diagnostic requests for both Zika virus (ZIKV) and dengue virus (DENV) infections in returning travelers have significantly increased during the recent ZIKV outbreak in the Americás. These flaviviruses have overlapping clinical syndromes and geographical distribution, but diagnostic differentiation is important because of different clinical consequences. As flaviviruses are known to have a short viremic period, diagnostics often rely on serological methods, which are challenging due to extensive cross-reactive antibodies.

OBJECTIVE

To re-evaluate the performance of DENV serological assays in laboratory confirmed ZIKV-infected travelers.

STUDY DESIGN

The extent of cross-reactivity of the DENV NS1 antigen, IgM and IgG ELISA was analyzed in 152 clinical blood samples collected from 69 qRT-PCR and 24 virus neutralization titer (VNT) confirmed ZIKV-infected travelers.

RESULTS

The majority of travelers in the presented cohort returned to the Netherlands from Suriname and presented with symptoms of fever and rash. Twenty-three percent of the female travelers were pregnant. None of the 39 ZIKV RNA positive blood samples were cross-reactive in the DENV NS1 antigen ELISA. The rates of cross-reactivity of the DENV IgM and IgG ELISÁs were 31% and 54%, respectively, after excluding travelers with (potential) previous DENV exposure.

CONCLUSIONS

Although the DENV NS1 antigen assay was highly specific in this cohort of laboratory confirmed ZIKV-infected travelers, we demonstrate high percentages of cross-reactivity of DENV IgM and IgG ELISÁs of which diagnostic laboratories should be aware. In addition, the high rate of DENV IgG background of >25% complicates a proper serological diagnosis in this group.

The Role of Heterotypic DENV-specific CD8+T Lymphocytes in an Immunocompetent Mouse Model of Secondary Dengue Virus Infection

Dengue is the most prevalent arthropod-borne viral disease worldwide and is caused by the four dengue virus serotypes (DENV-1-4). Sequential heterologous DENV infections can be associated with severe disease manifestations. Here, we present an immunocompetent mouse model of secondary DENV infection using non mouse-adapted DENV strains to investigate the pathogenesis of severe dengue disease. C57BL/6 mice infected sequentially with DENV-1 (strain Puerto Rico/94) and DENV-2 (strain Tonga/74) developed low platelet counts, internal hemorrhages, and increase of liver enzymes. Cross-reactive CD8⁺ T lymphocytes were found to be necessary and sufficient for signs of severe disease by adoptively transferring of DENV-1-immune CD8⁺T lymphocytes before DENV-2 challenge. Disease signs were associated with production of tumor necrosis factor (TNF)-α and elevated cytotoxicity displayed by heterotypic anti-DENV-1 CD8⁺ T lymphocytes. These findings highlight the critical role of heterotypic anti-DENV CD8⁺ T lymphocytes in manifestations of severe dengue disease.

Zika Virus RNA Replication and Persistence in Brain and Placental Tissue

Zika virus is causally linked with congenital microcephaly and may be associated with pregnancy loss. However, the mechanisms of Zika virus intrauterine transmission and replication and its tropism and persistence in tissues are poorly understood. We tested tissues from 52 case-patients: 8 infants with microcephaly who died and 44 women suspected of being infected with Zika virus during pregnancy. By reverse transcription PCR, tissues from 32 (62%) case-patients (brains from 8 infants with microcephaly and placental/fetal tissues from 24 women) were positive for Zika virus. In situ hybridization localized replicative Zika virus RNA in brains of 7 infants and in placentas of 9 women who had pregnancy losses during the first or second trimester. These findings demonstrate that Zika virus replicates and persists in fetal brains and placentas, providing direct evidence of its association with microcephaly. Tissue-based reverse transcription PCR extends the time frame of Zika virus detection in congenital and pregnancy-associated infections.

Preparation of MS2-based nanoparticles as control and standard materials for the molecular detection of dengue virus serotypes

To quantify dengue virus (DENV) and evaluate the performance of clinical laboratories using quantitative real-time polymerase chain reaction (qRT-PCR) assays, we constructed high-efficiency expression systems to produce DENV-1 to 4 nanoparticles and assessed their suitability as standard and control materials in 20 laboratories across China. Targeted gene sequences of DENV-1 to 4 were synthesized and inserted into pACYC-Duet 1-MS2 recombinant plasmids to generate corresponding nanoparticle expression systems. After collection, verification, and quantification by digital PCR (dPCR), DENV-1 to 4 nanoparticles were prepared as control and standard materials. Five positive and three negative samples of each DENV serotype in every panel were used for assessing the performance of the participating laboratories across China, as well as standard materials for the quantitative detection of DENV using qRT-PCR assays. The accuracy, sensitivity, and specificity of qRT-PCR used by the 20 evaluated laboratories were 89.6 (569/635), 85.1 (336/395), and 97.1% (233/240), respectively. Overall, sixteen (80.0%) laboratories were qualified in detecting DENV, among which five (25.0%) were designated as "competent", eleven (55.0%) were defined as "acceptable", and four (20%) were considered to be "improvable". The results generated from the DENV standard samples were significantly positively correlated with those generated by dPCR (r²=0.8698, P<0.001). In summary, DENV nanoparticles could potentially be used as controls for improving the performance of laboratories and as standards for the quantitative detection of DENV.

Diagnosis of Viral Infections

Accurate diagnosis of viral infections enhances the ability of the clinician to make decisions on appropriate treatment of patients, evaluate disease progression and prevent misuse of antibiotics. Knowledge of the pathogen involved also allow implementation of infection control and monitoring of success of antiviral treatments that may affect the prognosis of patients. Epidemiological data collected through accurate diagnostics play an important role in public health through identification and control of outbreaks, implementation of appropriate diagnostic tests, vaccination programs and treatment but also to recognize common and emerging pathogens in a community. It is key that the clinician have an understanding of appropriate specimens to send to the laboratory and the value of specific nucleic acid and serological testing for different viral pathogens. Molecular techniques have revolutionized viral diagnoses over the past decade and enhanced both the sensitivity and specificity of tests and the speed by which a diagnosis can be made and new tests be developed. The continued use of serology for viruses with a short viremia, or for chronic infections should however complement these tests. This chapter aims to provide an overview of the available tests, the principles of testing and appropriate tests to select for different viruses and syndromes. Also provided is a glimpse of new developments in diagnostics that may further enhance the capacity to make a conclusive diagnosis in the near future.

Issues in contemporary and potential future molecular diagnostics for dengue

INTRODUCTION

Dengue has been the most common arbovirus infection worldwide with 2.5 billion people living in over 100 endemic tropical and subtropical regions. Due to the high number of asymptomatic cases and the signs and symptoms being rather unspecific, dengue cases are often under-reported and might influence dengue surveillance programs. Therefore, a rapid, easy to use, inexpensive, and highly sensitive and specific diagnostic tool is essential for early and accurate diagnosis to ease the clinical management of patients as well as for the development of new interventions. Areas covered: This report discusses the contemporary dengue diagnostic tool, mainly from the aspect of molecular diagnosis where an overview of several nuclei acid amplification tests has been included. Potential molecular diagnostic tools such as biosensor and microarray are also discussed in this report. Expert commentary: Rapidness and accuracy in terms of sensitivity and specificity is imperative in dengue diagnosis for both clinical management and surveillance of dengue to ensure early treatment and corrective control measures can be carried out. In the next five years it is expected that there will be newer tests developed using not only the lateral flow techniques but more specifically biosensors and nanotechnology. These new technologies will have to be validated with the appropriate number and category of samples and to address the issue of cross-reactivity.

Validation and Application of a Commercial Quantitative Real-Time Reverse Transcriptase-PCR Assay in Investigation of a Large Dengue Virus Outbreak in Southern Taiwan

Background

Accurate, rapid, and early diagnosis of dengue virus (DENV) infections is essential for optimal clinical care. Here, we evaluated the efficacy of the quantitative real-time PCR (qRT-PCR)-LightMix dengue virus EC kit for DENV detection using samples from a dengue outbreak in Taiwan in 2015.

Methods

Sera from patients with suspected DENV infection were analyzed and compared using the LightMix kit, a Dengue NS1 Ag + Ab Combo kit for detection of NS1 antigen and DENV-specific IgM and IgG antibodies, and an “in-house” qualitative DENV-specific RT-PCR assay.

Results

A total of 8,989, 8,954, and 1581 samples were subjected to NS1 antigen detection, IgM and IgG detection, and LightMix assays, respectively. The LightMix assay yielded a linear curve for viral loads (VL) between 10² and 10⁶ copies/reaction, and the minimum detection limits for DENV serotype 1 (DENV1) and DENV2, DENV3, and DENV4 were 1, 10, and 100 focus forming units (FFU)/mL, respectively. There was 88.9% concordance between the results obtained using the NS1 antigen combo kit and by LightMix analysis, and the diagnostic sensitivity and specificity of the two methods were 89.4 and 100%, and 84.7 and 100%, respectively. Notably, fatal cases were attributed to DENV2 infection, and 79.5% (27/34) of these cases occurred in patients ≥ 71 years of age. Among these older patients, 82.3% (14/17) were NS1/IgM/IgG (+/-/-), exhibiting VLs between 10⁶–10⁹ copies/mL, which was markedly higher than the rate observed in the other age groups.

Conclusions

The LightMix assay was effective for early diagnosis of DENV infection. Our data indicate that high VLs during primary infection in elderly patients may be a positive predictor for severe illness, and may contribute to high mortality rates.

The LightMix dengue virus EC qRT-PCR assay is effective for early diagnosis of DENV infection. High viral loads during primary infection in elderly patients may comprise a positive predictor for severe illness, and may contribute to high mortality rates.

Pathology of congenital Zika syndrome in Brazil: a case series

BACKGROUND

Zika virus is an arthropod-borne virus that is a member of the family Flaviviridae transmitted mainly by mosquitoes of the genus Aedes. Although usually asymptomatic, infection can result in a mild and self-limiting illness characterised by fever, rash, arthralgia, and conjunctivitis. An increase in the number of children born with microcephaly was noted in 2015 in regions of Brazil with high transmission of Zika virus. More recently, evidence has been accumulating supporting a link between Zika virus and microcephaly. Here, we describe findings from three fatal cases and two spontaneous abortions associated with Zika virus infection.

METHODS

In this case series, formalin-fixed paraffin-embedded tissue samples from five cases, including two newborn babies with microcephaly and severe arthrogryposis who died shortly after birth, one 2-month-old baby, and two placentas from spontaneous abortions, from Brazil were submitted to the Infectious Diseases Pathology Branch at the US Centers for Disease Control and Prevention (Atlanta, GA, USA) between December, 2015, and March, 2016. Specimens were assessed by histopathological examination, immunohistochemical assays using a mouse anti-Zika virus antibody, and RT-PCR assays targeting the NS5 and envelope genes. Amplicons of RT-PCR positive cases were sequenced for characterisation of strains.

FINDINGS

Viral antigens were localised to glial cells and neurons and associated with microcalcifications in all three fatal cases with microcephaly. Antigens were also seen in chorionic villi of one of the first trimester placentas. Tissues from all five cases were positive for Zika virus RNA by RT-PCR, and sequence analyses showed highest identities with Zika virus strains isolated from Brazil during 2015.

INTERPRETATION

These findings provide strong evidence of a link between Zika virus infection and different congenital central nervous system malformations, including microcephaly as well as arthrogryposis and spontaneous abortions.

FUNDING

None.