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1.
PLoS Negl Trop Dis ; 14(4): e0008097, 2020 04.
Article in English | MEDLINE | ID: mdl-32275653

ABSTRACT

Dengue is one of the most important vector-borne diseases, resulting in an estimated hundreds of millions of infections annually throughout the tropics. Control of dengue is heavily dependent upon control of its primary mosquito vector, Aedes aegypti. Innovative interventions that are effective at targeting the adult stage of the mosquito are needed to increase the options for effective control. The use of insecticide-treated curtains (ITCs) has previously been shown to significantly reduce the abundance of Ae. aegypti in and around homes, but the impact of ITCs on dengue virus (DENV) transmission has not been rigorously quantified. A parallel arm cluster-randomized controlled trial was conducted in Iquitos, Peru to quantify the impact of ITCs on DENV seroconversion as measured through plaque-reduction neutralization tests. Seroconversion data showed that individuals living in the clusters that received ITCs were at greater risk to seroconverting to DENV, with an average seroconversion rate of 50.6 per 100 person-years (PY) (CI: 29.9-71.9), while those in the control arm had an average seroconversion rate of 37.4 per 100 PY (CI: 15.2-51.7). ITCs lost their insecticidal efficacy within 6 months of deployment, necessitating re-treatment with insecticide. Entomological indicators did not show statistically significant differences between ITC and non-ITC clusters. It's unclear how the lack of protective efficacy reported here is attributable to simple failure of the intervention to protect against Ae. aegypti bites, or the presence of a faulty intervention during much of the follow-up period. The higher risk of dengue seroconversion that was detected in the ITC clusters may have arisen due to a false sense of security that inadvertently led to less routine protective behaviors on the part of households that received the ITCs. Our study provides important lessons learned for conducting cluster randomized trials for vector control interventions against Aedes-transmitted virus infections.


Subject(s)
Dengue/prevention & control , Dengue/transmission , Disease Transmission, Infectious/prevention & control , Insecticide-Treated Bednets , Mosquito Control/methods , Adolescent , Adult , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Child , Child, Preschool , Dengue Virus/immunology , Female , Humans , Male , Middle Aged , Neutralization Tests , Peru , Seroconversion , Treatment Outcome , Young Adult
2.
PLoS One ; 13(7): e0200576, 2018.
Article in English | MEDLINE | ID: mdl-30024910

ABSTRACT

Group C orthobunyaviruses (GRCVs) are a complex of viruses in the genus Orthobunyavirus and are associated with human febrile disease in tropical and subtropical areas of South and Central America. While numerous GRCVs have been isolated from mosquitoes, animals, and humans, genetic analysis of these viruses is limited. In this study, we characterized 65 GRCV isolates from febrile patients identified through clinic-based surveillance in the northern and southern Peruvian Amazon. A 500 base pair region of the S segment and 750 base pair regions of the M and L segments were sequenced. Pairwise sequence analysis of the clinical isolates showed nucleotide identities ranging from 68% to 100% and deduced amino acid sequence identities ranging from 72% to 100%. Sequences were compared with reference strains of the following GRCVs: Caraparu virus (CARV), Murutucu virus (MURV), Oriboca virus (ORIV), Marituba virus (MTBV), Itaqui virus (ITQV), Apeu virus (APEUV), and Madrid virus (MADV). Sequence comparison of clinical isolates with the prototype strains based on the S and L segments identified two clades; clade I included isolates with high genetic association with CARV-MADV, and clade II included isolates with high genetic association with MURV, ORIV, APEUV, and MTBV. Genetic relationships based on the M segment were at time inconsistent with those based on the S and L segments. However, clade groupings based on the M segment were highly consistent with relationships based on microneutralization assays. These results advance our understanding of the genetic and serologic relationships of GRCVs circulating in the Peruvian Amazon.


Subject(s)
Genome, Viral/genetics , High-Throughput Nucleotide Sequencing/methods , Orthobunyavirus/genetics , RNA, Viral/genetics , Adolescent , Adult , Bunyaviridae Infections/virology , Child , Female , Genome, Viral/immunology , Geography , Humans , Male , Middle Aged , Neutralization Tests , Orthobunyavirus/classification , Orthobunyavirus/physiology , Peru , Phylogeny , RNA, Viral/immunology , Species Specificity , Young Adult
3.
Am J Trop Med Hyg ; 99(2): 266-274, 2018 08.
Article in English | MEDLINE | ID: mdl-29943710

ABSTRACT

Leptospirosis is a neglected zoonotic disease with worldwide endemicity and continues to be a significant public health burden on resource-limited populations. Previously, we produced three highly purified recombinant antigens (rLipL32, rLipL41, and rLigA-Rep) and evaluated their performance of detecting Leptospira-specific antibodies in enzyme-linked immunosorbent assay (ELISA) as compared with the microscopic agglutination test (MAT). The overall sensitivity of this assay approached 90%. Recently, another recombinant antigen (rLigB-Rep) was prepared. We tested each individual antigen and a 1:1:1:1 mixture of these four antigens for the detection of Leptospira-specific antibodies in ELISA. The performance of these recombinant antigens was evaluated with a much larger febrile patient panel (337 MAT-confirmed positive sera and 92 MAT-negative sera from febrile patients). Combining the detection results of immunoglobulin M and immunoglobulin G from these four individual antigens, the overall sensitivity was close to 90% but the specificity was only 66%, based on the MAT reference method. The overall sensitivity and specificity of the four-antigen mixture were 82% and 86%, respectively. The mixture of four antigens also exhibited a broader reactivity with MAT-positive samples of 18 serovars from six major pathogenic Leptospira species. Given the limitations of MAT, the data were further analyzed by Bayesian latent class model, showing that ELISA using a 1:1:1:1 mixture still maintained high sensitivity (79%) and specificity (88%) as compared with the sensitivity (90%) and specificity (83%) of MAT. Therefore, ELISA using a mixture of these four antigens could be a very useful test for seroprevalence studies.


Subject(s)
Antibodies, Bacterial/immunology , Enzyme-Linked Immunosorbent Assay/methods , Leptospira/immunology , Leptospirosis/diagnosis , Serologic Tests/methods , Zoonoses/diagnosis , Animals , Antigens, Bacterial/genetics , Antigens, Bacterial/immunology , Bayes Theorem , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Leptospirosis/immunology , Recombinant Proteins/immunology , Sensitivity and Specificity , Zoonoses/immunology
4.
Genome Announc ; 4(6)2016 Nov 10.
Article in English | MEDLINE | ID: mdl-27834712

ABSTRACT

A novel orthobunyavirus, Bellavista virus, was isolated from Culex (Melanoconion) portesi mosquitoes in the Bellavista neighborhood of Iquitos, Peru, in 2009. The assembled segment L, M, and S sequences of strain PRD0552 are 6,950, 4,469, and 1,256 bases in length, respectively, comprising complete protein-coding sequences and partial terminal untranslated sequences.

5.
Cell Host Microbe ; 20(3): 357-367, 2016 Sep 14.
Article in English | MEDLINE | ID: mdl-27569558

ABSTRACT

RNA viruses exhibit a variety of genome organization strategies, including multicomponent genomes in which each segment is packaged separately. Although multicomponent genomes are common among viruses infecting plants and fungi, their prevalence among those infecting animals remains unclear. We characterize a multicomponent RNA virus isolated from mosquitoes, designated Guaico Culex virus (GCXV). GCXV belongs to a diverse clade of segmented viruses (Jingmenvirus) related to the prototypically unsegmented Flaviviridae. The GCXV genome comprises five segments, each of which appears to be separately packaged. The smallest segment is not required for replication, and its presence is variable in natural infections. We also describe a variant of Jingmen tick virus, another Jingmenvirus, sequenced from a Ugandan red colobus monkey, thus expanding the host range of this segmented and likely multicomponent virus group. Collectively, this study provides evidence for the existence of multicomponent animal viruses and their potential relevance for animal and human health.


Subject(s)
Colobus/virology , Culicidae/virology , RNA Viruses/isolation & purification , RNA Viruses/ultrastructure , Viruses/isolation & purification , Viruses/ultrastructure , Animals , Microscopy, Fluorescence , Phylogeny , RNA Viruses/classification , RNA Viruses/genetics , Viruses/classification , Viruses/genetics
6.
Proc Biol Sci ; 283(1834)2016 Jul 13.
Article in English | MEDLINE | ID: mdl-27412286

ABSTRACT

Pathogens inflict a wide variety of disease manifestations on their hosts, yet the impacts of disease on the behaviour of infected hosts are rarely studied empirically and are seldom accounted for in mathematical models of transmission dynamics. We explored the potential impacts of one of the most common disease manifestations, fever, on a key determinant of pathogen transmission, host mobility, in residents of the Amazonian city of Iquitos, Peru. We did so by comparing two groups of febrile individuals (dengue-positive and dengue-negative) with an afebrile control group. A retrospective, semi-structured interview allowed us to quantify multiple aspects of mobility during the two-week period preceding each interview. We fitted nested models of each aspect of mobility to data from interviews and compared models using likelihood ratio tests to determine whether there were statistically distinguishable differences in mobility attributable to fever or its aetiology. Compared with afebrile individuals, febrile study participants spent more time at home, visited fewer locations, and, in some cases, visited locations closer to home and spent less time at certain types of locations. These multifaceted impacts are consistent with the possibility that disease-mediated changes in host mobility generate dynamic and complex changes in host contact network structure.


Subject(s)
Fever/epidemiology , Travel , Case-Control Studies , Cities , Dengue/epidemiology , Humans , Likelihood Functions , Models, Theoretical , Peru/epidemiology , Retrospective Studies
7.
BMC Public Health ; 16: 582, 2016 07 16.
Article in English | MEDLINE | ID: mdl-27422403

ABSTRACT

BACKGROUND: Dengue is an arthropod-borne viral disease responsible for approximately 400 million infections annually; the only available method of prevention is vector control. It has been previously demonstrated that insecticide treated curtains (ITCs) can lower dengue vector infestations in and around houses. As part of a larger trial examining whether ITCs could reduce dengue transmission in Iquitos, Peru, the objective of this study was to characterize the participants' experience with the ITCs using qualitative methods. METHODS: Knowledge, attitudes, and practices (KAP) surveys (at baseline, and 9 and 27 months post-ITC distribution, with n = 593, 595 and 511, respectively), focus group discussions (at 6 and 12 months post-ITC distribution, with n = 18 and 33, respectively), and 11 one-on-one interviews (at 12 months post-distribution) were conducted with 605 participants who received ITCs as part of a cluster-randomized trial. RESULTS: Focus groups at 6 months post-ITC distribution revealed that individuals had observed their ITCs to function for approximately 3 months, after which they reported the ITCs were no longer working. Follow up revealed that the ITCs required re-treatment with insecticide at approximately 1 year post-distribution. Over half (55.3 %, n = 329) of participants at 9 months post-ITC distribution and over a third (34.8 %, n = 177) at 27 months post-ITC distribution reported perceiving a decrease in the number of mosquitoes in their home. The percentage of participants who would recommend ITCs to their family or friends in the future remained high throughout the study (94.3 %, n = 561 at 9 months and 94.6 %, n = 488 at 27 months post-distribution). When asked why, participants reported that ITCs were effective at reducing mosquitoes (81.6 and 37.8 %, at 9 and 27 months respectively), that they prevent dengue (5.7 and 51.2 %, at 9 and 27 months), that they are "beautiful" (5.9 and 3.1 %), as well as other reasons (6.9 and 2.5 %). CONCLUSION: ITCs have substantial potential for long term dengue vector control because they are liked by users, both for their perceived effectiveness and for aesthetic reasons, and because they require little proactive behavioral effort on the part of the users. Our results highlight the importance of gathering process (as opposed to outcome) data during vector control studies, without which researchers would not have become aware that the ITCs had lost effectiveness early in the trial.


Subject(s)
Aedes/drug effects , Dengue/prevention & control , Insecticide-Treated Bednets/statistics & numerical data , Mosquito Control/methods , Adult , Aged , Aged, 80 and over , Animals , Arthropod Vectors , Female , Focus Groups , Health Knowledge, Attitudes, Practice , Humans , Male , Middle Aged , Peru , Qualitative Research , Surveys and Questionnaires
8.
PLoS Negl Trop Dis ; 10(2): e0004398, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26848841

ABSTRACT

BACKGROUND: Nearly half of the world's population is at risk for dengue, yet no licensed vaccine or anti-viral drug is currently available. Dengue is caused by any of four dengue virus serotypes (DENV-1 through DENV-4), and infection by a DENV serotype is assumed to provide life-long protection against re-infection by that serotype. We investigated the validity of this fundamental assumption during a large dengue epidemic caused by DENV-2 in Iquitos, Peru, in 2010-2011, 15 years after the first outbreak of DENV-2 in the region. METHODOLOGY/PRINCIPAL FINDINGS: We estimated the age-dependent prevalence of serotype-specific DENV antibodies from longitudinal cohort studies conducted between 1993 and 2010. During the 2010-2011 epidemic, active dengue cases were identified through active community- and clinic-based febrile surveillance studies, and acute inapparent DENV infections were identified through contact tracing studies. Based on the age-specific prevalence of DENV-2 neutralizing antibodies, the age distribution of DENV-2 cases was markedly older than expected. Homologous protection was estimated at 35.1% (95% confidence interval: 0%-65.2%). At the individual level, pre-existing DENV-2 antibodies were associated with an incomplete reduction in the frequency of symptoms. Among dengue cases, 43% (26/66) exhibited elevated DENV-2 neutralizing antibody titers for years prior to infection, compared with 76% (13/17) of inapparent infections (age-adjusted odds ratio: 4.2; 95% confidence interval: 1.1-17.7). CONCLUSIONS/SIGNIFICANCE: Our data indicate that protection from homologous DENV re-infection may be incomplete in some circumstances, which provides context for the limited vaccine efficacy against DENV-2 in recent trials. Further studies are warranted to confirm this phenomenon and to evaluate the potential role of incomplete homologous protection in DENV transmission dynamics.


Subject(s)
Dengue Virus/immunology , Dengue/epidemiology , Dengue/prevention & control , Disease Outbreaks , Adolescent , Adult , Age Distribution , Aged , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , Child , Child, Preschool , Female , Humans , Longitudinal Studies , Male , Middle Aged , Peru/epidemiology , Prevalence , Prospective Studies , Recurrence , Young Adult
9.
Am J Trop Med Hyg ; 93(6): 1330-1337, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26503276

ABSTRACT

As part of a cluster-randomized trial to evaluate insecticide-treated curtains for dengue prevention in Iquitos, Peru, we surveyed 1,333 study participants to examine knowledge and reported practices associated with dengue and its prevention. Entomological data from 1,133 of these households were linked to the survey. Most participants knew that dengue was transmitted by mosquito bite (85.6%), but only few (18.6%) knew that dengue vectors bite during daytime. Most commonly recognized dengue symptoms were fever (86.6%), headache (76.4%), and muscle/joint pain (67.9%). Most commonly reported correct practices for mosquito control were cleaning homes (61.6%), using insecticide sprays (23%), and avoiding having standing water at home (12.3%). Higher education was associated with higher knowledge about dengue, including transmission and vector control. Higher socioeconomic status was associated with increased reported use of preventive practices requiring money expenditure. We were less likely to find Aedes aegypti eggs, larvae, or pupae in households that had < 5-year-old children at home. Although dengue has been transmitted in Iquitos since the 1990s and the Regional Health Authority routinely fumigates households, treats domestic water containers with larvicide, and issues health education messages through mass media, knowledge of dengue transmission and household practices for prevention could be improved.


Subject(s)
Dengue/prevention & control , Health Knowledge, Attitudes, Practice , Adolescent , Adult , Aedes/virology , Aged , Aged, 80 and over , Animals , Dengue/psychology , Dengue/transmission , Family Characteristics , Female , Humans , Insect Vectors/virology , Insecticides , Male , Middle Aged , Mosquito Control , Peru/epidemiology , Risk Factors , Socioeconomic Factors , Surveys and Questionnaires , Young Adult
10.
Emerg Infect Dis ; 21(10): 1742-50, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26401714

ABSTRACT

In 2010, an outbreak of febrile illness with arthralgic manifestations was detected at La Estación village, Portuguesa State, Venezuela. The etiologic agent was determined to be Mayaro virus (MAYV), a reemerging South American alphavirus. A total of 77 cases was reported and 19 were confirmed as seropositive. MAYV was isolated from acute-phase serum samples from 6 symptomatic patients. We sequenced 27 complete genomes representing the full spectrum of MAYV genetic diversity, which facilitated detection of a new genotype, designated N. Phylogenetic analysis of genomic sequences indicated that etiologic strains from Venezuela belong to genotype D. Results indicate that MAYV is highly conserved genetically, showing ≈17% nucleotide divergence across all 3 genotypes and 4% among genotype D strains in the most variable genes. Coalescent analyses suggested genotypes D and L diverged ≈150 years ago and genotype diverged N ≈250 years ago. This virus commonly infects persons residing near enzootic transmission foci because of anthropogenic incursions.


Subject(s)
Alphavirus Infections/epidemiology , Alphavirus/genetics , Biological Evolution , Biota/immunology , Disease Outbreaks , Alphavirus/growth & development , Female , Humans , Male , Phylogeny , Venezuela/epidemiology
11.
Diagn Microbiol Infect Dis ; 83(1): 30-6, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26032430

ABSTRACT

During dengue outbreaks, acute diagnosis at the patient's point of need followed by appropriate supportive therapy reduces morbidity and mortality. To facilitate needed diagnosis, we developed and optimized a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay that detects all 4 serotypes of dengue virus (DENV). We used a quencher to reduce nonspecific amplification. The assay does not require expensive thermocyclers, utilizing a simple water bath to maintain the reaction at 63 °C. Results can be visualized using UV fluorescence, handheld readers, or lateral flow immunochromatographic tests. We report a sensitivity of 86.3% (95% confidence interval [CI], 72.7-94.8%) and specificity of 93.0% (95% CI, 83.0-98.1%) using a panel of clinical specimens characterized by DENV quantitative reverse transcription-polymerase chain reaction. This pan-serotype DENV RT-LAMP can be adapted to field-expedient formats where it can provide actionable diagnosis near the patient's point of need.


Subject(s)
Dengue Virus/classification , Dengue Virus/isolation & purification , Dengue/diagnosis , Dengue/virology , Nucleic Acid Amplification Techniques/methods , Serogroup , Dengue Virus/genetics , Humans , RNA, Viral/metabolism , Reverse Transcription , Sensitivity and Specificity , Temperature
12.
Emerg Infect Dis ; 21(5): 781-8, 2015 May.
Article in English | MEDLINE | ID: mdl-25898901

ABSTRACT

Our genetic analyses of uncharacterized bunyaviruses isolated in Peru identified a possible reassortant virus containing small and large gene segment sequences closely related to the Caraparu virus and a medium gene segment sequence potentially derived from an unidentified group C orthobunyavirus. Neutralization tests confirmed serologic distinction among the newly identified virus and the prototype and Caraparu strains. This virus, named Itaya, was isolated in 1999 and 2006 from febrile patients in the cities of Iquitos and Yurimaguas in Peru. The geographic distance between the 2 cases suggests that the Itaya virus could be widely distributed throughout the Amazon basin in northeastern Peru. Identification of a new Orthobunyavirus species that causes febrile disease in humans reinforces the need to expand viral disease surveillance in tropical regions of South America.


Subject(s)
Bunyaviridae Infections/epidemiology , Bunyaviridae Infections/virology , Fever/epidemiology , Fever/virology , Orthobunyavirus/classification , Adult , Animals , Cell Line , Geography , Humans , Male , Neutralization Tests , Orthobunyavirus/genetics , Orthobunyavirus/isolation & purification , Peru/epidemiology , Phylogeny , Population Surveillance , RNA, Viral , Reassortant Viruses , Serotyping
13.
Emerg Infect Dis ; 21(3): 460-3, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25695188

ABSTRACT

We conducted phylogeographic modeling to determine the introduction and spread of Guaroa virus in South America. The results suggest a recent introduction of this virus into regions of Peru and Bolivia over the past 60-70 years and emphasize the need for increased surveillance in surrounding areas.


Subject(s)
Bunyaviridae Infections/epidemiology , Bunyaviridae Infections/virology , Evolution, Molecular , Orthobunyavirus/classification , Orthobunyavirus/genetics , Phylogeny , Phylogeography , Bunyaviridae Infections/transmission , Geography , Humans , Molecular Typing , South America/epidemiology , Spatio-Temporal Analysis
14.
J Clin Microbiol ; 53(4): 1092-102, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25588659

ABSTRACT

We evaluated four dengue diagnostic devices from Alere, including the SD Bioline Dengue Duo (nonstructural [NS] 1 Ag and IgG/IgM), the Panbio Dengue Duo Cassette (IgM/IgG) rapid diagnostic tests (RDTs), and the Panbio dengue IgM and IgG capture enzyme-linked immunosorbent assays (ELISAs) in a prospective, controlled, multicenter study in Peru, Venezuela, Cambodia, and the United States, using samples from 1,021 febrile individuals. Archived, well-characterized samples from an additional 135 febrile individuals from Thailand were also used. Reference testing was performed on all samples using an algorithm involving virus isolation, in-house IgM and IgG capture ELISAs, and plaque reduction neutralization tests (PRNT) to determine the infection status of the individual. The primary endpoints were the clinical sensitivities and specificities of these devices. The SD Bioline Dengue Duo had an overall sensitivity of 87.3% (95% confidence interval [CI], 84.1 to 90.2%) and specificity of 86.8% (95% CI, 83.9 to 89.3%) during the first 14 days post-symptom onset (p.s.o.). The Panbio Dengue Duo Cassette demonstrated a sensitivity of 92.1% (87.8 to 95.2%) and specificity of 62.2% (54.5 to 69.5%) during days 4 to 14 p.s.o. The Panbio IgM capture ELISA had a sensitivity of 87.6% (82.7 to 91.4%) and specificity of 88.1% (82.2 to 92.6%) during days 4 to 14 p.s.o. Finally, the Panbio IgG capture ELISA had a sensitivity of 69.6% (62.1 to 76.4%) and a specificity of 88.4% (82.6 to 92.8%) during days 4 to 14 p.s.o. for identification of secondary dengue infections. This multicountry prospective study resulted in reliable real-world performance data that will facilitate data-driven laboratory test choices for managing patient care during dengue outbreaks.


Subject(s)
Dengue/diagnosis , Enzyme-Linked Immunosorbent Assay/methods , Reagent Kits, Diagnostic/virology , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Viral/blood , Child , Child, Preschool , Dengue/epidemiology , Dengue/immunology , Dengue Virus/immunology , Female , Humans , Immunoglobulin G/blood , Immunoglobulin M/blood , Infant , Male , Middle Aged , Prospective Studies , Sensitivity and Specificity , Young Adult
15.
PLoS One ; 9(11): e113411, 2014.
Article in English | MEDLINE | ID: mdl-25412170

ABSTRACT

BACKGROUND: Early diagnosis of dengue virus (DENV) infection can improve clinical outcomes by ensuring close follow-up, initiating appropriate supportive therapies and raising awareness to the potential of hemorrhage or shock. Non-structural glycoprotein-1 (NS1) has proven to be a useful biomarker for early diagnosis of dengue. A number of rapid diagnostic tests (RDTs) and enzyme-linked immunosorbent assays (ELISAs) targeting NS1 antigen (Ag) are now commercially available. Here we evaluated these tests using a well-characterized panel of clinical samples to determine their effectiveness for early diagnosis. METHODOLOGY/PRINCIPAL FINDINGS: Retrospective samples from South America were used to evaluate the following tests: (i) "Dengue NS1 Ag STRIP" and (ii) "Platelia Dengue NS1 Ag ELISA" (Bio-Rad, France), (iii) "Dengue NS1 Detect Rapid Test (1st Generation)" and (iv) "DENV Detect NS1 ELISA" (InBios International, United States), (v) "Panbio Dengue Early Rapid (1st generation)" (vi) "Panbio Dengue Early ELISA (2nd generation)" and (vii) "SD Bioline Dengue NS1 Ag Rapid Test" (Alere, United States). Overall, the sensitivity of the RDTs ranged from 71.9%-79.1% while the sensitivity of the ELISAs varied between 85.6-95.9%, using virus isolation as the reference method. Most tests had lower sensitivity for DENV-4 relative to the other three serotypes, were less sensitive in detecting secondary infections, and appeared to be most sensitive on Day 3-4 post symptom onset. The specificity of all evaluated tests ranged from 95%-100%. CONCLUSIONS: ELISAs had greater overall sensitivity than RDTs. In conjunction with other parameters, the performance data can help determine which dengue diagnostics should be used during the first few days of illness, when the patients are most likely to present to a clinic seeking care.


Subject(s)
Antigens, Viral/analysis , Dengue Virus/metabolism , Dengue/diagnosis , Viral Nonstructural Proteins/analysis , Adolescent , Adult , Aged , Aged, 80 and over , Antigens, Viral/immunology , Child , Dengue/virology , Dengue Virus/isolation & purification , Enzyme-Linked Immunosorbent Assay , Female , Humans , Male , Middle Aged , Reagent Kits, Diagnostic , Retrospective Studies , Sensitivity and Specificity , Serotyping , Viral Nonstructural Proteins/immunology , Young Adult
16.
Viruses ; 6(9): 3663-82, 2014 Sep 26.
Article in English | MEDLINE | ID: mdl-25256396

ABSTRACT

Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information's (NCBI's) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.


Subject(s)
Databases, Nucleic Acid , Filoviridae/genetics , Evolution, Molecular , Filoviridae/classification , Humans , Selection, Genetic
17.
J R Soc Interface ; 11(99)2014 Oct 06.
Article in English | MEDLINE | ID: mdl-25142528

ABSTRACT

Individual-based models of infectious disease transmission depend on accurate quantification of fine-scale patterns of human movement. Existing models of movement either pertain to overly coarse scales, simulate some aspects of movement but not others, or were designed specifically for populations in developed countries. Here, we propose a generalizable framework for simulating the locations that an individual visits, time allocation across those locations, and population-level variation therein. As a case study, we fit alternative models for each of five aspects of movement (number, distance from home and types of locations visited; frequency and duration of visits) to interview data from 157 residents of the city of Iquitos, Peru. Comparison of alternative models showed that location type and distance from home were significant determinants of the locations that individuals visited and how much time they spent there. We also found that for most locations, residents of two neighbourhoods displayed indistinguishable preferences for visiting locations at various distances, despite differing distributions of locations around those neighbourhoods. Finally, simulated patterns of time allocation matched the interview data in a number of ways, suggesting that our framework constitutes a sound basis for simulating fine-scale movement and for investigating factors that influence it.


Subject(s)
Cities , Geographic Mapping , Models, Theoretical , Motor Activity/physiology , Spatial Behavior/physiology , Computer Simulation , Geographic Information Systems , Humans , Interviews as Topic , Peru , Time Factors
18.
PLoS Negl Trop Dis ; 8(7): e3003, 2014 Jul.
Article in English | MEDLINE | ID: mdl-25033412

ABSTRACT

INTRODUCTION: Long-term disease surveillance data provide a basis for studying drivers of pathogen transmission dynamics. Dengue is a mosquito-borne disease caused by four distinct, but related, viruses (DENV-1-4) that potentially affect over half the world's population. Dengue incidence varies seasonally and on longer time scales, presumably driven by the interaction of climate and host susceptibility. Precise understanding of dengue dynamics is constrained, however, by the relative paucity of laboratory-confirmed longitudinal data. METHODS: We studied 10 years (2000-2010) of laboratory-confirmed, clinic-based surveillance data collected in Iquitos, Peru. We characterized inter and intra-annual patterns of dengue dynamics on a weekly time scale using wavelet analysis. We explored the relationships of case counts to climatic variables with cross-correlation maps on annual and trimester bases. FINDINGS: Transmission was dominated by single serotypes, first DENV-3 (2001-2007) then DENV-4 (2008-2010). After 2003, incidence fluctuated inter-annually with outbreaks usually occurring between October and April. We detected a strong positive autocorrelation in case counts at a lag of ∼ 70 weeks, indicating a shift in the timing of peak incidence year-to-year. All climatic variables showed modest seasonality and correlated weakly with the number of reported dengue cases across a range of time lags. Cases were reduced after citywide insecticide fumigation if conducted early in the transmission season. CONCLUSIONS: Dengue case counts peaked seasonally despite limited intra-annual variation in climate conditions. Contrary to expectations for this mosquito-borne disease, no climatic variable considered exhibited a strong relationship with transmission. Vector control operations did, however, appear to have a significant impact on transmission some years. Our results indicate that a complicated interplay of factors underlie DENV transmission in contexts such as Iquitos.


Subject(s)
Dengue/epidemiology , Dengue/transmission , Dengue/virology , Animals , Culicidae , Dengue Virus , Humans , Incidence , Peru/epidemiology , Seasons , Weather
19.
PLoS Negl Trop Dis ; 8(6): e2888, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24922530

ABSTRACT

Quantifying human mobility has significant consequences for studying physical activity, exposure to pathogens, and generating more realistic infectious disease models. Location-aware technologies such as Global Positioning System (GPS)-enabled devices are used increasingly as a gold standard for mobility research. The main goal of this observational study was to compare and contrast the information obtained through GPS and semi-structured interviews (SSI) to assess issues affecting data quality and, ultimately, our ability to measure fine-scale human mobility. A total of 160 individuals, ages 7 to 74, from Iquitos, Peru, were tracked using GPS data-loggers for 14 days and later interviewed using the SSI about places they visited while tracked. A total of 2,047 and 886 places were reported in the SSI and identified by GPS, respectively. Differences in the concordance between methods occurred by location type, distance threshold (within a given radius to be considered a match) selected, GPS data collection frequency (i.e., 30, 90 or 150 seconds) and number of GPS points near the SSI place considered to define a match. Both methods had perfect concordance identifying each participant's house, followed by 80-100% concordance for identifying schools and lodgings, and 50-80% concordance for residences and commercial and religious locations. As the distance threshold selected increased, the concordance between SSI and raw GPS data increased (beyond 20 meters most locations reached their maximum concordance). Processing raw GPS data using a signal-clustering algorithm decreased overall concordance to 14.3%. The most common causes of discordance as described by a sub-sample (n=101) with whom we followed-up were GPS units being accidentally off (30%), forgetting or purposely not taking the units when leaving home (24.8%), possible barriers to the signal (4.7%) and leaving units home to recharge (4.6%). We provide a quantitative assessment of the strengths and weaknesses of both methods for capturing fine-scale human mobility.


Subject(s)
Epidemiologic Methods , Geographic Information Systems , Human Migration , Interviews as Topic , Adolescent , Adult , Aged , Child , Female , Humans , Male , Middle Aged , Peru , Spatio-Temporal Analysis , Young Adult
20.
PLoS One ; 9(6): e95002, 2014.
Article in English | MEDLINE | ID: mdl-24914538

ABSTRACT

Four distinct serotypes of dengue viruses (DENV) are the cause of re-emerging dengue fever (DF) and dengue hemorrhagic fever (DHF). Dengue circulation in the Caribbean has gone from none or single serotype to multiple serotypes co-circulating with reports of continuing cycles of progressively more severe disease in the region. Few studies have investigated dengue on Sint Eustatius. Blood samples were collected to determine the prevalence of antibodies against dengue in the Sint Eustatius population. Greater than 90% of the serum samples (184 of 204) were positive for anti-flavivirus antibodies by enzyme linked immunosorbance assay (ELISA). Plaque reduction neutralization test (PRNT), specific for dengue viruses, showed that 171 of these 184 flavivirus antibody positive sera had a neutralization titer against one or more DENV serotypes. A majority of the sera (62%) had neutralizing antibody to all four dengue serotypes. Only 26 PRNT positive sera (15%) had monotypic dengue virus neutralizing antibody, most of which (20 of 26) were against DENV2. Evidence of infection with all four serotypes was observed across all age groups except in the youngest age group (10-19 years) which contained only DENV2 positive individuals. In a multiple logistic regression model, only the length of residence on the island was a predictor of a positive dengue PRNT50 result. To our knowledge this is the first dengue serosurveillance study conducted on Sint Eustatius since the 1970s. The lack of antibodies to the DEN1, 3, and 4 in the samples collected from participants under 20 years of age suggests that only DEN2 has circulated on island since the early 1990s. The high prevalence of antibodies against dengue (83.8%) and the observation that the length of time on the island was the strongest predictor of infection suggests dengue is endemic on Sint Eustatius and a public health concern that warrants further investigation.


Subject(s)
Antibodies, Viral/blood , Dengue/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , Caribbean Region , Child , Dengue/blood , Dengue Virus/genetics , Dengue Virus/immunology , Female , Humans , Male , Middle Aged , Serogroup
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