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1.  16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles 
Microbiome  2014;2:31.
Sample storage conditions, extraction methods, PCR primers, and parameters are major factors that affect metagenomics analysis based on microbial 16S rRNA gene sequencing. Most published studies were limited to the comparison of only one or two types of these factors. Systematic multi-factor explorations are needed to evaluate the conditions that may impact validity of a microbiome analysis. This study was aimed to improve methodological options to facilitate the best technical approaches in the design of a microbiome study. Three readily available mock bacterial community materials and two commercial extraction techniques, Qiagen DNeasy and MO BIO PowerSoil DNA purification methods, were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing-based analysis. Primers were chosen for 16S rDNA quantitative PCR and amplification of region V3 to V1. Swabs spiked with mock bacterial community cells and clinical oropharyngeal swabs were incubated at respective temperatures of -80°C, -20°C, 4°C, and 37°C for 4 weeks, then extracted with the two methods, and subjected to pyrosequencing and taxonomic and statistical analyses to investigate microbiome profile stability.
The bacterial compositions for the mock community DNA samples determined in this study were consistent with the projected levels and agreed with the literature. The quantitation accuracy of abundances for several genera was improved with changes made to the standard Human Microbiome Project (HMP) procedure. The data for the samples purified with DNeasy and PowerSoil methods were statistically distinct; however, both results were reproducible and in good agreement with each other. The temperature effect on storage stability was investigated by using mock community cells and showed that the microbial community profiles were altered with the increase in incubation temperature. However, this phenomenon was not detected when clinical oropharyngeal swabs were used in the experiment.
Mock community materials originated from the HMP study are valuable controls in developing 16S metagenomics analysis procedures. Long-term exposure to a high temperature may introduce variation into analysis for oropharyngeal swabs, suggestive of storage at 4°C or lower. The observed variations due to sample storage temperature are in a similar range as the intrapersonal variability among different clinical oropharyngeal swab samples.
PMCID: PMC4165438  PMID: 25228989
2.  Kinetics of Chikungunya Infections during an Outbreak in Southern Thailand, 2008–2009 
The Indian Ocean chikungunya epidemic re-emerged in Thailand in August 2008. Forty-five adults with laboratory-confirmed chikungunya in Songkhla province, Thailand were clinically assessed and serially bled throughout the acute and convalescent phase of the disease. Patient symptoms, antibody responses, and viral kinetics were evaluated using observational assessments, polymerase chain reaction (PCR), and serological assays. All subjects experienced joint pain with 42 (93%) involving multiple joints; the interphalangeal most commonly affected in 91% of the subjects. The mean duration of joint pain was 5.8 days, 11 (25%) experiencing discomfort through the duration of the study. Rash was observed in 37 (82%) subjects a mean 3.5 days post onset of symptoms. Patents were positive by PCR for a mean of 5.9 days with sustained peak viral load through Day 5. The IgM antibodies appeared on Day 4 and peaked at Day 7 and IgG antibodies first appeared at Day 5 and rose steadily through Day 24.
PMCID: PMC3945684  PMID: 24493674
3.  An Adjuvanted, Tetravalent Dengue Virus Purified Inactivated Vaccine Candidate Induces Long-Lasting and Protective Antibody Responses Against Dengue Challenge in Rhesus Macaques 
The immunogenicity and protective efficacy of a candidate tetravalent dengue virus purified inactivated vaccine (TDENV PIV) formulated with alum or an Adjuvant System (AS01, AS03 tested at three different dose levels, or AS04) was evaluated in a 0, 1-month vaccination schedule in rhesus macaques. One month after dose 2, all adjuvanted formulations elicited robust and persisting neutralizing antibody titers against all four dengue virus serotypes. Most of the formulations tested prevented viremia after challenge, with the dengue serotype 1 and 2 virus strains administered at 40 and 32 weeks post-dose 2, respectively. This study shows that inactivated dengue vaccines, when formulated with alum or an Adjuvant System, are candidates for further development.
PMCID: PMC4385761  PMID: 25646261
4.  Whole-Genome Sequence of “Candidatus Rickettsia asemboensis” Strain NMRCii, Isolated from Fleas of Western Kenya 
Genome Announcements  2015;3(2):e00018-15.
Herein we present the draft genome sequence and annotation of “Candidatus Rickettsia asemboensis” strain NMRCii. “Ca. Rickettsia asemboensis” is phylogenetically related to but distinct from the flea-borne spotted fever pathogen Rickettsia felis. “Ca. Rickettsia asemboensis” was initially identified in and subsequently isolated from Ctenocephalides cat and dog fleas from Kenya.
PMCID: PMC4357741  PMID: 25767219
5.  Characteristics of Mild Dengue Virus Infection in Thai Children 
A four-year longitudinal cohort and geographic cluster study in rural Thailand was conducted to characterize the clinical spectrum of dengue virus (DENV) infection. Symptomatic DENV infections in the cohort were detected by active school absence–based surveillance that triggered cluster investigations around ill cohort children. Data from 189 cohort children with symptomatic DENV infection and 126 contact children in the clusters with DENV infection were analyzed. Of infected contacts, only 19% were asymptomatic; 81% were symptomatic, but only 65.9% reported fever. Symptom-based case definitions were unreliable for diagnosis. Symptomatic infections in contacts were milder with lower DENV RNA levels than the cohort. Infections in contacts with fever history were more likely to have detectable DENV RNA than infections without fever history. Mild infections identified by cluster investigations account for a major proportion of all DENV infections. These findings are relevant for disease burden assessments, transmission modeling, and determination of vaccine impact.
PMCID: PMC3854884  PMID: 24127167
6.  Dengue Virus Neutralizing Antibody Levels Associated with Protection from Infection in Thai Cluster Studies 
Long-term homologous and temporary heterologous protection from dengue virus (DENV) infection may be mediated by neutralizing antibodies. However, neutralizing antibody titers (NTs) have not been clearly associated with protection from infection.
Methodology/Principal Findings
Data from two geographic cluster studies conducted in Kamphaeng Phet, Thailand were used for this analysis. In the first study (2004–2007), cluster investigations of 100-meter radius were triggered by DENV-infected index cases from a concurrent prospective cohort. Subjects between 6 months and 15 years old were evaluated for DENV infection at days 0 and 15 by DENV PCR and IgM ELISA. In the second study (2009–2012), clusters of 200-meter radius were triggered by DENV-infected index cases admitted to the provincial hospital. Subjects of any age ≥6 months were evaluated for DENV infection at days 0 and 14. In both studies, subjects who were DENV PCR positive at day 14/15 were considered to have been “susceptible” on day 0. Comparison subjects from houses in which someone had documented DENV infection, but the subject remained DENV negative at days 0 and 14/15, were considered “non-susceptible.” Day 0 samples were presumed to be from just before virus exposure, and underwent plaque reduction neutralization testing (PRNT). Seventeen “susceptible” (six DENV-1, five DENV-2, and six DENV-4), and 32 “non-susceptible” (13 exposed to DENV-1, 10 DENV-2, and 9 DENV-4) subjects were evaluated. Comparing subjects exposed to the same serotype, receiver operating characteristic (ROC) curves identified homotypic PRNT titers of 11, 323 and 16 for DENV-1, -2 and -4, respectively, to differentiate “susceptible” from “non-susceptible” subjects.
PRNT titers were associated with protection from infection by DENV-1, -2 and -4. Protective NTs appeared to be serotype-dependent and may be higher for DENV-2 than other serotypes. These findings are relevant for both dengue epidemiology studies and vaccine development efforts.
Author Summary
Dengue is caused by four different dengue virus serotypes (DENV-1, -2, -3, -4). Infection induces long-term protection against the same serotype, but only short-term protection, and possible enhancement, from different serotypes. DENV neutralizing antibody titers (NTs) are thought to mediate protection or modify disease. Association of NTs with protection from infection has not, however, been clearly demonstrated. We analyzed data from two geographic clusters studies conducted in Kamphaeng Phet, Thailand, in which DENV NTs just before virus exposure were compared between DENV-infected “susceptible” and non-infected “non-susceptible” subjects. NTs appeared to be associated with protection against DENV-1, -2, and -4, but at different NT cutoff levels, with the cutoff for DENV-2 appearing to be the highest. These findings are relevant for ongoing efforts to investigate dengue epidemiology and develop dengue vaccine candidates.
PMCID: PMC4199527  PMID: 25329173
7.  Evaluation of a Dengue NS1 Antigen Detection Assay Sensitivity and Specificity for the Diagnosis of Acute Dengue Virus Infection 
Currently, no dengue NS1 detection kit has regulatory approval for the diagnosis of acute dengue fever. Here we report the sensitivity and specificity of the InBios DEN Detect NS1 ELISA using a panel of well characterized human acute fever serum specimens.
Methodology/Principal Findings
The InBios DENV Detect NS1 ELISA was tested using a panel composed of 334 serum specimens collected from acute febrile patients seeking care in a Bangkok hospital in 2010 and 2011. Of these patients, 314 were found to have acute dengue by either RT-PCR and/or anti-dengue IgM/IgG ELISA. Alongside the InBios NS1 ELISA kit, we compared the performance characteristics of the BioRad Platelia NS1 antigen kit. The InBios NS1 ELISA Ag kit had a higher overall sensitivity (86% vs 72.8%) but equal specificity (100%) compared to the BioRad Platelia kit. The serological status of the patient significantly influenced the outcome. In primary infections, the InBios NS1 kit demonstrated a higher sensitivity (98.8%) than in secondary infections (83.5%). We found significant variation in the sensitivity of the InBios NS1 ELISA kit depending on the serotype of the dengue virus and also found decreasing sensitivity the longer after the onset of illness, showing 100% sensitivity early during illness, but dropping below 50% by Day 7.
The InBios NS1 ELISA kit demonstrated high accuracy when compared to the initial clinical diagnosis with greater than 85% agreement when patients were clinically diagnosed with dengue illness. Results presented here suggest the accurate detection of circulating dengue NS1 by the InBios DENV Detect NS1 ELISA can provide clinicians with a useful tool for diagnosis of early dengue infections.
Author Summary
Infections by the mosquito-transmitted dengue virus continue to increase, threatening the health of people in over a hundred countries worldwide. The lack of effective mosquito control, licensed dengue vaccines or specific therapeutics to treat dengue infections presents challenges to reduce the burden of this disease. Rapid and accurate diagnosis of dengue infections is critical for the reduction of patients' morbidity and mortality. We present data that support the use of the InBios DENV Detect NS1 ELISA for the detection of dengue NS1 in patient serum. The InBios NS1 ELISA kit was tested against sera collected from acute fever patients seeking medical care in a Bangkok, Thailand hospital during 2010 and 2011. The data demonstrate the InBios DENV Detect NS1 ELISA accurately detects circulating dengue NS1 in the tested specimens, demonstrating high sensitivity and specificity. Nonetheless, the sensitivity of the NS1 ELISA kits was found to vary depending on the serological status of the patient (primary versus secondary dengue infection), time of specimen collection and dengue serotype. Further, the performance characteristics of the InBios DENV Detect NS1 ELISA were found to meet and exceed those of the commonly used Platelia Dengue NS1 Ag kit.
PMCID: PMC4183466  PMID: 25275493
8.  Factors Influencing Dengue Virus Isolation by C6/36 Cell Culture and Mosquito Inoculation of Nested PCR-Positive Clinical Samples 
Dengue viral isolation is necessary for definitive diagnosis, pathogenesis and evolutionary research, vaccine candidates, and diagnostic materials. Using standardized techniques, we analyzed isolation rates of 1,544 randomly selected polymerase chain reaction (PCR)-positive samples, representing all four dengue serotypes, from patients with serologically confirmed dengue infections and evaluated whether clinical and laboratory results could be predictive of isolation using standard and mosquito isolation techniques. Viruses were isolated from 62.5% of the samples by direct application to C6/36 cells and increased to 79.4% when amplifying C6/36 negative samples by intrathorasic inoculation in Toxyrhynchites splendens mosquitoes. High viremia, measured by reverse transcriptase (RT)-PCR, was a strong predictor for viral isolation by either method. Isolation was most successful in samples collected early in the disease, had low antibody levels, temperatures greater than 38°C, and had a final clinical diagnosis of dengue fever. Dengue serotypes also played a role in the success of viral isolation.
PMCID: PMC3029170  PMID: 21292887
9.  Neuropathogenesis of Japanese Encephalitis in a Primate Model 
Japanese encephalitis (JE) is a major cause of mortality and morbidity for which there is no treatment. In addition to direct viral cytopathology, the inflammatory response is postulated to contribute to the pathogenesis. Our goal was to determine the contribution of bystander effects and inflammatory mediators to neuronal cell death.
Methodology/Principal Findings
Material from a macaque model was used to characterize the inflammatory response and cytopathic effects of JE virus (JEV). Intranasal JEV infection induced a non-suppurative encephalitis, dominated by perivascular, infiltrates of mostly T cells, alongside endothelial cell activation, vascular damage and blood brain barrier (BBB) leakage; in the adjacent parenchyma there was macrophage infiltration, astrocyte and microglia activation. JEV antigen was mostly in neurons, but there was no correlation between intensity of viral infection and degree of inflammatory response. Apoptotic cell death occurred in both infected and non-infected neurons. Interferon-α, which is a microglial activator, was also expressed by both. Tumour Necrosis Factor-α, inducible nitric oxide synthase and nitrotyrosine were expressed by microglial cells, astrocytes and macrophages. The same cells expressed matrix metalloproteinase (MMP)-2 whilst MMP-9 was expressed by neurons.
The results are consistent with JEV inducing neuronal apoptotic death and release of cytokines that initiate microglial activation and release of pro-inflammatory and apoptotic mediators with subsequent apoptotic death of both infected and uninfected neurons. Activation of astrocytes, microglial and endothelial cells likely contributes to inflammatory cell recruitment and BBB breakdown. It appears that neuronal apoptotic death and activation of microglial cells and astrocytes play a crucial role in the pathogenesis of JE.
Author Summary
Japanese encephalitis (JE) is one of the most important causes of viral encephalitis worldwide, with no specific antiviral treatment available. Despite some recent successes with widespread vaccination, JE will likely remain an important public health problem; because the virus is mosquito-borne and has natural animal hosts, it will never be eradicated. We have little understanding of what determines the severity and outcome of infection. Data from human post mortem studies is very limited because of cultural constraints on autopsies in areas where JE occurs. Circumstantial evidence suggests that in addition to cytopathology caused directly by infection of neurons, there may be bystander cell death of non-infected neurons, caused by an excessive inflammatory response. Our study used archived brain samples from a prior challenge study in a validated macaque model of JE. We stained for the presence of JEV antigen, apoptosis, and pro-inflammatory markers in affected areas, such as the thalamus and brainstem. We show that bystander neuronal cell death is important, and elucidate the inflammatory and apoptotic mechanisms underlying it. Currently there is no proven efficacious therapy for most viral infections of the central nervous system, including JE. Novel strategies for treating such infections are urgently needed. Our findings suggest new anti-inflammatory and anti-apoptotic therapeutic approaches may be useful in treating this debilitating disease.
PMCID: PMC4125110  PMID: 25102067
10.  Space-time analysis of hospitalized dengue patients in rural Thailand reveals important temporal intervals in the pattern of dengue virus transmission 
This study uses space-time analysis to determine the temporal intervals at which spatial clustering of dengue hospitalizations occurs.
Analysis of 262 people hospitalized and serologically confirmed with dengue virus infections in Kamphaeng Phet, Thailand was performed. The cases were observed between January 1, 2009 and May 6, 2011. Spatial coordinates of each patient’s home were captured using the Global Positioning System. A novel methodology based on the Knox test was used to determine the temporal intervals between cases at which spatial clustering occured. These intervals are indicative of the length of time between successive illnesses in the chain of dengue virus transmission.
The strongest spatial clustering occurred at the 15–17 day interval. Therewas also significant spatial clustering over short time intervals (2–5 days). The highest excess risk was observed within 200m of a previous hospitalized case and significantly elevated risk persisted within this distance for as long as 32–34 days.
The analyses indicate that 15–17 days is the most likely serial interval between successive dengue illnesses. This novel methodology relies only on passively-detected, hospitalized case data with household locations and provides a useful tool for understanding region-specific and outbreak-specific dengue virus transmission dynamics.
PMCID: PMC4099473  PMID: 22808917
dengue; transmission; serial interval; space-time; clustering; Thailand
11.  Safety and Immunogenicity of a Rederived, Live-Attenuated Dengue Virus Vaccine in Healthy Adults Living in Thailand: A Randomized Trial 
Safety and immunogenicity of two formulations of a live-attenuated tetravalent dengue virus (TDEN) vaccine produced using rederived master seeds from a precursor vaccine were tested against a placebo control in a phase II, randomized, double blind trial (NCT00370682). Two doses were administered 6 months apart to 120 healthy, predominantly flavivirus-primed adults (87.5% and 97.5% in the two vaccine groups and 92.5% in the placebo group). Symptoms and signs reported after vaccination were mild to moderate and transient. There were no vaccine-related serious adverse events or dengue cases reported. Asymptomatic, low-level viremia (dengue virus type 2 [DENV-2], DENV-3, or DENV-4) was detected in 5 of 80 vaccine recipients. One placebo recipient developed a subclinical natural DENV-1 infection. All flavivirus-unprimed subjects and at least 97.1% of flavivirus-primed subjects were seropositive to antibodies against all four DENV types 1 and 3 months post-TDEN dose 2. The TDEN vaccine was immunogenic with an acceptable safety profile in flavivirus-primed adults.
PMCID: PMC4080550  PMID: 24865677
12.  Variability in Dengue Titer Estimates from Plaque Reduction Neutralization Tests Poses a Challenge to Epidemiological Studies and Vaccine Development 
Accurate determination of neutralization antibody titers supports epidemiological studies of dengue virus transmission and vaccine trials. Neutralization titers measured using the plaque reduction neutralization test (PRNT) are believed to provide a key measure of immunity to dengue viruses, however, the assay's variability is poorly understood, making it difficult to interpret the significance of any assay reading. In addition there is limited standardization of the neutralization evaluation point or statistical model used to estimate titers across laboratories, with little understanding of the optimum approach.
Methodology/Principal Findings
We used repeated assays on the same two pools of serum using five different viruses (2,319 assays) to characterize the variability in the technique under identical experimental conditions. We also assessed the performance of multiple statistical models to interpolate continuous values of neutralization titer from discrete measurements from serial dilutions. We found that the variance in plaque reductions for individual dilutions was 0.016, equivalent to a 95% confidence interval of 0.45–0.95 for an observed plaque reduction of 0.7. We identified PRNT75 as the optimum evaluation point with a variance of 0.025 (log10 scale), indicating a titer reading of 1∶500 had 95% confidence intervals of 1∶240–1∶1000 (2.70±0.31 on a log10 scale). The choice of statistical model was not important for the calculation of relative titers, however, cloglog regression out-performed alternatives where absolute titers are of interest. Finally, we estimated that only 0.7% of assays would falsely detect a four-fold difference in titers between acute and convalescent sera where no true difference exists.
Estimating and reporting assay uncertainty will aid the interpretation of individual titers. Laboratories should perform a small number of repeat assays to generate their own variability estimates. These could be used to calculate confidence intervals for all reported titers and allow benchmarking of assay performance.
Author Summary
Plaque Reduction Neutralization Tests (PRNTs) remain the most popular approach to characterize an individual's ability to neutralize dengue viruses and are widely used in both epidemiological studies and vaccine trials. However, the underlying variability in the assay is poorly understood, hindering the interpretation of PRNT titer estimates. Further, there is little standardization of its use across laboratories limiting our ability to compare results across settings. Here we used many repeated experiments on the same serum under identical laboratory conditions to estimate the variance in titer measurements. We also identified both the optimum PRNT evaluation point and statistical model to calculate titers. By providing an estimate of the variability in the assay, laboratories will be able to provide a confidence bound on individual PRNT readings. In addition by providing recommended statistical approaches that could be used across laboratories, our findings will help the standardization of the assay across settings.
PMCID: PMC4072537  PMID: 24967885
13.  The Serial Intervals of Seasonal and Pandemic Influenza Viruses in Households in Bangkok, Thailand 
American Journal of Epidemiology  2013;177(12):1443-1451.
The serial interval (SI) of human influenza virus infections is often described by a single distribution. Understanding sources of variation in the SI could provide valuable information for understanding influenza transmission dynamics. Using data from a randomized household study of nonpharmaceutical interventions to prevent influenza transmission in Bangkok, Thailand, over 34 months between 2008 and 2011, we estimated the influence of influenza virus type/subtype and other characteristics of 251 pediatric index cases and their 315 infected household contacts on estimates of household SI. The mean SI for all households was 3.3 days. Relative to influenza A(H1N1)pdm09 (3.1 days), the SI for influenza B (3.7 days) was 22% longer (95% confidence interval: 4, 43), or about half a day. The SIs for influenza viruses A(H1N1) and A(H3N2) were similar to that for A(H1N1)pdm09. SIs were shortest for older index cases (age 11–14 years) and for younger infected household contacts (age ≤15 years). Greater time spent in proximity to the index child was associated with shorter SIs. Differences in the SI might reflect differences in incubation period, viral shedding, contact, or susceptibility. These findings could improve parameterization of mathematical models to better predict the impact of epidemic or pandemic influenza mitigation strategies.
PMCID: PMC3676150  PMID: 23629874
human; influenza; Thailand
14.  Differential Susceptibility of Two Field Aedes aegypti Populations to a Low Infectious Dose of Dengue Virus 
PLoS ONE  2014;9(3):e92971.
The infectious dose required to infect mosquito vectors when they take a blood meal from a viremic person is a critical parameter underlying the probability of dengue virus (DENV) transmission. Because experimental vector competence studies typically examine the proportion of mosquitoes that become infected at intermediate or high DENV infectious doses in the blood meal, the minimum blood meal titer required to infect mosquitoes is poorly documented. Understanding the factors influencing the lower infectiousness threshold is epidemiologically significant because it determines the transmission potential of humans with a low DENV viremia, possibly including inapparent infections, and during the onset and resolution of the viremic period of acutely infected individuals.
Methodology/Principal Findings
We compared the susceptibility of two field-derived Aedes aegypti populations from Kamphaeng Phet, Thailand when they were orally exposed to low titers of six DENV-2 isolates derived from the serum of naturally infected humans living in the same region. The infectious dose, time-point post-blood feeding, viral isolate and mosquito population, were significant predictors of the proportion of mosquitoes that became infected. Importantly, the dose-response profile differed significantly between the two Ae. aegypti populations. Although both mosquito populations had a similar 50% oral infectious dose (OID50), the slope of the dose-response was shallower in one population, resulting in a markedly higher susceptibility at low blood meal titers.
Our results indicate that mosquitoes in nature vary in their infectious dose-response to DENV. Thus, different mosquito populations have a differential ability to acquire DENV infection at low viremia levels. Future studies on human-to-mosquito DENV transmission should not be limited to OID50 values, but rather they should be expanded to account for the shape of the dose-response profile across a range of virus titers.
PMCID: PMC3963970  PMID: 24664142
15.  Genomic Characterization of Group C Orthobunyavirus Reference Strains and Recent South American Clinical Isolates 
PLoS ONE  2014;9(3):e92114.
Group C orthobunyaviruses (family Bunyaviridae, genus Orthobunyavirus), discovered in the 1950s, are vector-borne human pathogens in the Americas. Currently there is a gap in genomic information for group C viruses. In this study, we obtained complete coding region sequences of reference strains of Caraparu (CARV), Oriboca (ORIV), Marituba (MTBV) and Madrid (MADV) viruses, and five clinical isolates from Peru and Bolivia, using an unbiased de novo approach consisting of random reverse transcription, random anchored PCR amplification, and high throughput pyrosequencing. The small, medium, and large segments encode for a 235 amino acid nucleocapsid protein, an approximately 1430 amino acid surface glycoprotein polyprotein precursor, and a 2248 amino acid RNA-dependent RNA polymerase, respectively. Additionally, the S segment encodes for an 83 amino acid non-structural protein, although this protein is truncated or silenced in some isolates. Phylogenetically, three clinical isolates clustered with CARV, one clustered with MTBV, and one isolate appeared to be a reassortant or a genetic drift resulted from the high variability of the medium segment which was also seen in a few other orthobunyaviruses. These data represent the first complete coding region sequences for this serocomplex of pathogenic orthobunyaviruses. The genome-wide phylogeny of reference strains is consistent with the antigenic properties of the viruses reported in the original serological studies conducted in the 1960s. Comparative analysis of conserved protein regions across group C virus strains and the other orthobunyavirus groups revealed that these group C viruses contain characteristic domains of potential structural and functional significance. Our results provide the basis for the developments of diagnostics, further genetic analyses, and future epidemiologic studies of group C viruses.
PMCID: PMC3954874  PMID: 24633174
16.  Diversity and Origin of Dengue Virus Serotypes 1, 2, and 3, Bhutan 
Emerging Infectious Diseases  2009;15(10):1630-1632.
To determine the serotype and genotype of dengue virus (DENV) in Bhutan, we conducted phylogenetic analyses of complete envelope gene sequences. DENV-2 (Cosmopolitan genotype) predominated in 2004, and DENV-3 (genotype III) predominated in 2005–2006; these viruses were imported from India. Primary dengue infections outnumbered secondary infections, suggesting recent emergence.
PMCID: PMC2866390  PMID: 19861059
Dengue; Bhutan; Nepal; phylogeny; emergence; serotypes; viruses; dispatch
17.  Specificity of resistance to dengue virus isolates is associated with genotypes of the mosquito antiviral gene Dicer-2 
In contrast to the prevailing view that invertebrate immunity relies on broad-spectrum recognition and effector mechanisms, intrinsic genetic compatibility between invertebrate hosts and their pathogens is often highly specific in nature. Solving this puzzle requires a better understanding of the molecular basis underlying observed patterns of invertebrate host–pathogen genetic specificity, broadly referred to as genotype-by-genotype interactions. Here, we identify an invertebrate immune gene in which natural polymorphism is associated with isolate-specific resistance to an RNA virus. Dicer-2 (dcr2) encodes a key protein upstream of the RNA interference (RNAi) pathway, a major antiviral component of innate immunity in invertebrates. We surveyed allelic polymorphism at the dcr2 locus in a wild-type outbred population and in three derived isofemale families of the mosquito Aedes aegypti that were experimentally exposed to several, genetically distinct isolates of dengue virus. We found that dcr2 genotype was associated with resistance to dengue virus in a virus isolate-specific manner. By contrast, no such association was found for genotypes at two control loci flanking dcr2, making it likely that dcr2 contains the yet-unidentified causal polymorphism(s). This result supports the idea that host–pathogen compatibility in this system depends, in part, on a genotype-by-genotype interaction between dcr2 and the viral genome, and points to the RNAi pathway as a potentially important determinant of intrinsic insect-virus genetic specificity.
PMCID: PMC3574411  PMID: 23193131
Aedes aegypti; dengue virus; genotype-by-genotype interaction; Dicer-2; RNAi
18.  Increased hand washing reduces influenza virus surface contamination in Bangkok households, 2009–2010 
Within a hand-washing clinical trial, we evaluated factors associated with fomite contamination in households with an influenza-infected child. Influenza virus RNA contamination was higher in households with low absolute humidity and in control households, suggesting that hand washing reduces surface contamination.
PMCID: PMC4177792  PMID: 24373290
Human; influenza; Thailand; transmission
19.  Molecular Typing of “Candidatus Bartonella ancashi,” a New Human Pathogen Causing Verruga Peruana 
Journal of Clinical Microbiology  2013;51(11):3865-3868.
A recently described clinical isolate, “Candidatus Bartonella ancashi,” was obtained from a blood sample of a patient presenting with verruga peruana in the Ancash region of Peru. This sample and a second isolate obtained 60 days later from the same patient were molecularly typed using multilocus sequence typing (MLST) and multispacer sequence typing (MST). The isolates were 100% indistinguishable from each other but phylogenetically distant from Bartonella bacilliformis and considerably divergent from other known Bartonella species, confirming their novelty.
PMCID: PMC3889784  PMID: 23985925
20.  Underrecognized Mildly Symptomatic Viremic Dengue Virus Infections in Rural Thai Schools and Villages 
The Journal of Infectious Diseases  2012;206(3):389-398.
Background. The understanding of dengue virus (DENV) transmission dynamics and the clinical spectrum of infection are critical to informing surveillance and control measures. Geographic cluster studies can elucidate these features in greater detail than cohort studies alone.
Methods. A 4-year longitudinal cohort and geographic cluster study was undertaken in rural Thailand. Cohort children underwent pre-/postseason serology and active school absence–based surveillance to detect inapparent and symptomatic dengue. Cluster investigations were triggered by cohort dengue and non-dengue febrile illnesses (positive and negative clusters, respectively).
Results. The annual cohort incidence of symptomatic dengue ranged from 1.3% to 4.4%. DENV-4 predominated in the first 2 years, DENV-1 in the second 2 years. The inapparent-to-symptomatic infection ratio ranged from 1.1:1 to 2.9:1. Positive clusters had a 16.0% infection rate, negative clusters 1.1%. Of 119 infections in positive clusters, 59.7% were febrile, 20.2% were afebrile with other symptoms, and 20.2% were asymptomatic. Of 16 febrile children detected during cluster investigations who continued to attend school, 9 had detectable viremia.
Conclusions. Dengue transmission risk was high near viremic children in both high- and low-incidence years. Inapparent infections in the cohort overestimated the rate of asymptomatic infections. Ambulatory children with mild febrile viremic infections could represent an important component of dengue transmission.
PMCID: PMC3490697  PMID: 22615312
21.  Genetic Mapping of Specific Interactions between Aedes aegypti Mosquitoes and Dengue Viruses 
PLoS Genetics  2013;9(8):e1003621.
Specific interactions between host genotypes and pathogen genotypes (G×G interactions) are commonly observed in invertebrate systems. Such specificity challenges our current understanding of invertebrate defenses against pathogens because it contrasts the limited discriminatory power of known invertebrate immune responses. Lack of a mechanistic explanation, however, has questioned the nature of host factors underlying G×G interactions. In this study, we aimed to determine whether G×G interactions observed between dengue viruses and their Aedes aegypti vectors in nature can be mapped to discrete loci in the mosquito genome and to document their genetic architecture. We developed an innovative genetic mapping strategy to survey G×G interactions using outbred mosquito families that were experimentally exposed to genetically distinct isolates of two dengue virus serotypes derived from human patients. Genetic loci associated with vector competence indices were detected in multiple regions of the mosquito genome. Importantly, correlation between genotype and phenotype was virus isolate-specific at several of these loci, indicating G×G interactions. The relatively high percentage of phenotypic variation explained by the markers associated with G×G interactions (ranging from 7.8% to 16.5%) is consistent with large-effect host genetic factors. Our data demonstrate that G×G interactions between dengue viruses and mosquito vectors can be assigned to physical regions of the mosquito genome, some of which have a large effect on the phenotype. This finding establishes the existence of tangible host genetic factors underlying specific interactions between invertebrates and their pathogens in a natural system. Fine mapping of the uncovered genetic loci will elucidate the molecular mechanisms of mosquito-virus specificity.
Author Summary
The outcome of invertebrate host-pathogen interactions often depends on the specific pairing of host and pathogen genotypes. This genetic specificity challenges our current understanding of invertebrate resistance to pathogens because it contrasts the limited discriminatory power of known invertebrate defense mechanisms. However, genetic factors underlying this observed specificity have remained elusive, questioning their very existence. In this study, we developed an innovative strategy to localize factors in the genome of the mosquito Aedes aegypti that govern specific interactions with dengue viruses. We used large mosquito families derived from a natural population in Thailand that we experimentally challenged with virus isolates obtained from human patients living in the same area. We identified several regions of the mosquito genome that control specific interactions with dengue viruses and contribute significantly to the observed variation in vector competence. Our study establishes the existence of tangible host genetic factors underlying specific interactions between invertebrates and their pathogens in a natural system that is relevant to human health. This represents a critical step towards identification of mechanisms underlying the genetic specificity of insect-virus interactions.
PMCID: PMC3731226  PMID: 23935524
22.  Evaluation of In Vitro Cross-Reactivity to Avian H5N1 and Pandemic H1N1 2009 Influenza Following Prime Boost Regimens of Seasonal Influenza Vaccination in Healthy Human Subjects: A Randomised Trial 
PLoS ONE  2013;8(3):e59674.
Recent studies have demonstrated that inactivated seasonal influenza vaccines (IIV) may elicit production of heterosubtypic antibodies, which can neutralize avian H5N1 virus in a small proportion of subjects. We hypothesized that prime boost regimens of live and inactivated trivalent seasonal influenza vaccines (LAIV and IIV) would enhance production of heterosubtypic immunity and provide evidence of cross-protection against other influenza viruses.
In an open-label study, 26 adult volunteers were randomized to receive one of four vaccine regimens containing two doses of 2009-10 seasonal influenza vaccines administered 8 (±1) weeks apart: 2 doses of LAIV; 2 doses of IIV; LAIV then IIV; IIV then LAIV. Humoral immunity assays for avian H5N1, 2009 pandemic H1N1 (pH1N1), and seasonal vaccine strains were performed on blood collected pre-vaccine and 2 and 4 weeks later. The percentage of cytokine-producing T-cells was compared with baseline 14 days after each dose.
Subjects receiving IIV had prompt serological responses to vaccine strains. Two subjects receiving heterologous prime boost regimens had enhanced haemagglutination inhibition (HI) and neutralization (NT) titres against pH1N1, and one subject against avian H5N1; all three had pre-existing cross-reactive antibodies detected at baseline. Significantly elevated titres to H5N1 and pH1N1 by neuraminidase inhibition (NI) assay were observed following LAIV-IIV administration. Both vaccines elicited cross-reactive CD4+ T-cell responses to nucleoprotein of avian H5N1 and pH1N1. All regimens were safe and well tolerated.
Neither homologous nor heterologous prime boost immunization enhanced serum HI and NT titres to 2009 pH1N1 or avian H5N1 compared to single dose vaccine. However heterologous prime-boost vaccination did lead to in vitro evidence of cross-reactivity by NI; the significance of this finding is unclear. These data support the strategy of administering single dose trivalent seasonal influenza vaccine at the outset of an influenza pandemic while a specific vaccine is being developed.
Trial Registration NCT01044095
PMCID: PMC3608534  PMID: 23555741
23.  Frequent In-Migration and Highly Focal Transmission of Dengue Viruses among Children in Kamphaeng Phet, Thailand 
Revealing the patterns and determinants of the spread of dengue virus (DENV) at local scales is central to understanding the epidemiology and evolution of this major human pathogen. We performed a phylogenetic analysis of the envelope (E) genes of DENV-1, -2, -3, and -4 isolates (involving 97, 23, 5, and 74 newly collected sequences, respectively) sampled from school-based cohort and village-based cluster studies in Kamphaeng Phet, Thailand, between 2004 and 2007. With these data, we sought to describe the spatial and temporal patterns of DENV spread within a rural population where a future vaccine efficacy trial is planned. Our analysis revealed considerable genetic diversity within the study population, with multiple lineages within each serotype circulating for various lengths of time during the study period. These results suggest that DENV is frequently introduced into both semi-urban and rural areas in Kamphaeng Phet from other populations. In contrast, the persistence of viral lineages across sampling years was observed less frequently. Analysis of phylogenetic clustering indicated that DENV transmission was highly spatially and temporally focal, and that it occurred in homes rather than at school. Overall, the strength of temporal clustering suggests that seasonal bottlenecks in local DENV populations facilitate the invasion and establishment of viruses from outside of the study area, in turn reducing the extent of lineage persistence.
Author Summary
Long-term cohort studies of dengue virus (DENV), the most common vector-borne viral disease of humans, are essential to understand the epidemiology and evolution of this important human pathogen, and may assist in predicting the evolutionary response to vaccination. We utilized DENV gene sequences and information on the locations and timing of infected children within a primary school-based cohort in Kamphaeng Phet, Thailand to investigate the spatial and temporal relationships among viruses isolated from 2004 to 2007. We found that all four DENV serotypes circulated in the region during the study period, with the presence of multiple viral lineages within each serotype. Viruses sampled closely in time and space were generally very closely related. More genetic variation was observed across districts in a given year and within the same district across different years. The high genetic similarity among viruses during each season and the rare persistence of these lineages through multiple seasons suggest that seasonal reductions in the force of infection through changes in mosquito transmission and fluctuations in human population immunity are key factors shaping the genetic diversity of dengue virus diversity in this region. The importation of DENV by human movement from other populations is therefore an important generator of DENV diversity even in hyperendemic areas.
PMCID: PMC3547850  PMID: 23350000
24.  Safety and Immunogenicity of a Tetravalent Live-Attenuated Dengue Vaccine in Flavivirus-Naive Infants 
A Phase I/II observer-blind, randomized, controlled trial evaluated the safety and immunogenicity of a dengue virus (DENV) vaccine candidate in healthy Thai infants (aged 12–15 months) without measurable pre-vaccination neutralizing antibodies to DENV and Japanese encephalitis virus. Fifty-one subjects received two doses of either DENV (N = 34; four received 1/10th dose) or control vaccine (N = 17; dose 1, live varicella; dose 2, Haemophilus influenzae type b). After each vaccine dose, adverse events (AEs) were solicited for 21 days, and non-serious AEs were solicited for 30 days; serious AEs (SAEs) were recorded throughout the study. Laboratory safety assessments were performed at 10 and 30 days; neutralizing antibodies were measured at 30 days. The DENV vaccine was well-tolerated without any related SAEs. After the second dose, 85.7% of full-dose DENV vaccinees developed at least trivalent and 53.6% developed tetravalent neutralizing antibodies ≥ 1:10 to DENV (control group = 0%). This vaccine candidate, therefore, warrants continued development in this age group (NCT00322049;
PMCID: PMC3144835  PMID: 21813857
25.  Dengue-1 Virus Clade Replacement in Thailand Associated with Enhanced Mosquito Transmission 
Journal of Virology  2012;86(3):1853-1861.
Dengue viruses (DENV) are characterized by extensive genetic diversity and can be organized in multiple, genetically distinct lineages that arise and die out on a regular basis in regions where dengue is endemic. A fundamental question for understanding DENV evolution is the relative extent to which stochastic processes (genetic drift) and natural selection acting on fitness differences among lineages contribute to lineage diversity and turnover. Here, we used a set of recently collected and archived low-passage DENV-1 isolates from Thailand to examine the role of mosquito vector-virus interactions in DENV evolution. By comparing the ability of 23 viruses isolated on different dates between 1985 and 2009 to be transmitted by a present-day Aedes aegypti population from Thailand, we found that a major clade replacement event in the mid-1990s was associated with virus isolates exhibiting increased titers in the vector's hemocoel, which is predicted to result in a higher probability of transmission. This finding is consistent with the hypothesis that selection for enhanced transmission by mosquitoes is a possible mechanism underlying major DENV clade replacement events. There was significant variation in transmission potential among isolates within each clade, indicating that in addition to vector-driven selection, other evolutionary forces act to maintain viral genetic diversity. We conclude that occasional adaptive processes involving the mosquito vector can drive major DENV lineage replacement events.
PMCID: PMC3264336  PMID: 22130539

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