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Significance Forecasts routinely provide critical information for dangerous weather events but not yet for epidemics. Researchers develop computational models that can be used for infectious disease forecasting, but forecasts have not been broadly compared or tested. We collaboratively compared forecasts from 16 teams for 8 y of dengue epidemics in Peru and Puerto Rico. The comparison highlighted components that forecasts did well (e.g., situational awareness late in the season) and those that need more work (e.g., early season forecasts). It also identified key facets to improve forecasts, including using multiple model ensemble approaches to improve overall forecast skill. Future infectious disease forecasting work can build on these findings and this framework to improve the skill and utility of forecasts., A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project—integration with public health needs, a common forecasting framework, shared and standardized data, and open participation—can help advance infectious disease forecasting beyond dengue.

Militaries around the world play an important but at times poorly defined and underappreciated role in global health security. They are often called upon to support civilian authorities in humanitarian crises and to provide routine healthcare for civilians. Military personnel are a unique population in a health security context, as they are highly mobile and often deploy to austere settings domestically and internationally, which may increase exposure to endemic and emerging infectious diseases. Despite the role of militaries, few studies have systematically evaluated their involvement in global health security activities including the Global Health Security Agenda. We analyzed Joint External Evaluation (JEE) mission reports (n = 94) and National Action Plan for Health Security plans (n = 12), published as of July 2020, to determine the extent to which military organizations were involved in the evaluation process, military involvement in health security activities were described, and specific recommendations were provided for the country's military. For JEE reports, descriptions of military involvement were highest in 3 of the 4 core areas: Respond (76%), Prevent (39%), and Detect (32%). Similarly, National Action Plan for Health Security plans mentioned military involvement in the same 3 core areas: Respond (58%), Prevent (33%), and Detect (33%). Only 28% of JEE reports provided recommendations for the military in any of the core areas. Our results indicate that military roles and contributions are incorporated into some aspects of country-level health security activities, but that more extensive involvement may be warranted to improve national capabilities to prevent, detect, and respond to infectious disease threats.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Militaries across the world play an important but at times poorly defined and underappreciated role in global health security. For example, they are often called upon to support civilian authorities in humanitarian crises and to provide routine healthcare for civilians. Furthermore, military personnel are a unique population in a health security context, as they are highly mobile and often deploy to austere settings domestically and internationally, which may increase exposure to infectious diseases. Despite the role of militaries, few studies have systematically evaluated the involvement of militaries in global health security activities, including the Global Health Security Agenda (GHSA). To address this shortcoming, we analyzed Joint External Evaluation (JEE) mission reports (n=91) and National Action Plans for Health Security (n=11) that had been completed as of October 2019 (n=91) to determine the extent to which military organizations have been involved in the evaluation process, country military contributions to health security are accounted for, and specific recommendations are provided for the country’s military. For JEE reports, military involvement was highest for the “Respond” core area (73%) but much lower for the Prevent (36%) and Detect (30%) core areas. Similarly, 73% of NAPHS documents mentioned military involvement in the Respond core area, compared to 27% and 36% for Prevent and Detect, respectively. Additionally, only 26% of JEE reports provide recommendations for the military in any of the core areas. Our results indicate the need to more fully incorporate military roles and contributions into the GHSA framework and other health security activities in order to improve national capabilities to prevent, detect, and respond to infectious disease threats.

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., Author summary Dengue is one of the most important mosquito-borne diseases affecting humans, resulting in an estimated hundreds of millions of infections annually throughout the tropics. To control dengue, most public health programs use a variety of methods to kill the primary mosquito vector, Aedes aegypti. Water holding containers that harbor larvae (and other immature stages) are treated or eliminated. During emergencies, large insecticide spray campaigns are deployed to kill infected adult mosquitoes. Innovative interventions that are effective at targeting adult mosquitoes in sustainable ways are needed to increase the options for control of dengue and other Aedes borne virus diseases. The use of insecticide-treated curtains (ITCs) has previously been shown to significantly reduce Ae. aegypti numbers in and around homes, but the impact of ITCs on dengue virus (DENV) transmission has not previously been quantified. Using a rigorous study design in which 10 clusters (~90 houses per cluster) were provided multiple ITCs to place in their homes was compared to 10 clusters of homes without ITCs. Assignment of which clusters received ITCs was randomized. Blood samples were obtained at 9-month intervals from residents living in all the clusters, so that people with serological evidence of a DENV infection could be identified by comparing paired samples. Seroconversion data showed that individuals living in the clusters that received ITCs were at greater risk to DENV seroconverting, with an average seroconversion rate of 50.6 per 100 person-years (PY) (CI: 29.9–71.9). Conversely, 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. Ae. aegypti populations did not show statistically significant differences between ITC and non-ITC clusters. The reason for higher transmission in the ITC treated clusters could be attributable to failure of the curtains (loss of efficacy) and/or that the curtains were not sufficiently effective at protecting against mosquito bites. The higher risk of DENV seroconversion in ITC clusters may be due to a false sense of security that inadvertently led to less routine protective behaviors on the part of households that received the ITC.

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of infectious disease morbidity and mortality. Previous studies have confirmed the presence of S. aureus, including MRSA, on raw meat products. We investigated the prevalence and molecular epidemiology of S. aureus and MRSA in commercially-distributed antibiotic-free and conventional raw meat products (n = 3290) purchased in 8 Iowa retail stores weekly for a period of one year. Isolates were characterized using spa typing, and PCR was used to detect the presence of the Panton-Valentine leukocidin (PVL) and mecA genes. Quantitation of S. aureus on meat products was carried out one week per month. The prevalence of S. aureus on meat samples was 27.8% (913/3290). Compared to antibiotic-free meat samples, higher prevalence of both MRSA and methicillin-susceptible S. aureus (MSSA) were found in conventional meat samples. Among the S. aureus isolates, 18 were PVL-positive (1.9%) and 41 (4.5%) carried mecA. Phenotypic oxacillin resistance was observed for 17.1% (41/239) of the isolates tested, while 23% (55/239) were multi-drug resistant. A total of 132 spa types were detected from 913 contaminated meat samples. Overall, t002 was the most common spa type identified (137; 15.0%). The number of colony-forming units (CFU) per 10 g meat ranged from 2 to 517 (median: 8 CFU per 10 g of meat; mean: 28) with the highest bacterial load observed on turkey samples. These data reinforce the need to consider meat products as potential vehicles of S. aureus transmission from farm into human households, and the potential need for public health intervention programs pre and post-slaughter in meat processing facilities.

Los estudios de filariasis podrían ayudarnos a identificar casos febriles de etiología desconocida en los establecimientos de Salud. Se realizó un estudio epidemiológico, descriptivo, observacional, transversal y prospectivo; determinando la prevalencia de microfilariasis, relacionándola con las características epidemiológicas como sexo, edad y fiebre. Se procesaron 755 muestras. La microfilariasis fue detectada mediante microscopia simple, la prueba de Knott y Gota Gruesa fueron modificados por los autores. Se determinó una prevalencia de 6,2 %, encontrándose Mansonella ozzardi (2,0%) y una especie atípica, designada como Microfilaria sp. (4,1%); y la confección por ambas especies (0,1%). Las personas infectadas por Microfilaria sp., desarrollaban actividades en zona urbana; encontrándose una frecuencia alta en mujeres de 4 a 12 años, procedentes de los distritos de San Juan, Iquitos y Punchana. Las infecciones por M. ozzardi fueron frecuentes en pacientes febriles del género masculino, de 22 a 39 años, procedentes del distrito de Belén, cuya actividad principal se desarrolla mayormente en el campo. Se encontró pobladores infectados con microfilarias en la ciudad de Iquitos y zonas peri urbanas; resultados que justifican investigaciones para determinar si el parásito Microfilaria sp., está causando síndromes clínicos y definir los ciclos de transmisión.

This report describes a cluster of 11 soldiers with vivax malaria among U.S. military personnel who trained at Dagmar North training area, near the demilitarized zone (DMZ), in the Republic of Korea (ROK) in 2015. Two cases were diagnosed in the ROK in 2015, one of whom subsequently experienced a relapse, and nine other cases were diagnosed in 2016, 8-11 months after the soldiers had returned to the U.S. Vivax malaria poses a health threat to U.S. Forces Korea operating near the DMZ in the ROK. Continuing and enhanced focus on force health protection measures in endemic zones is warranted.

The study objective was to determine the prevalence ofStaphylococcus aureuscolonisation in the nares and oropharynx of healthy persons and identify any risk factors associated with suchS. aureuscolonisation. In total 263 participants (177 adults and 86 minors) comprising 95 families were enrolled in a year-long prospective cohort study from one urban and one rural county in eastern Iowa, USA, through local newspaper advertisements and email lists and through the Keokuk Rural Health Study. Potential risk factors including demographic factors, medical history, farming and healthcare exposure were assessed. Among the participants, 25.4% of adults and 36.1% minors carriedS. aureusin their nares and 37.9% of adults carried it in their oropharynx. The overall prevalence was 44.1% among adults and 36.1% for minors. Having at least one positive environmental site forS. aureusin the family home was associated with colonisation (prevalence ratio: 1.34, 95% CI: 1.07–1.66). The sensitivity of the oropharyngeal cultures was greater than that of the nares cultures (86.1% compared with 58.2%, respectively). In conclusion, the nares and oropharynx are both important colonisation sites for healthy community members and the presence ofS. aureusin the home environment is associated with an increased probability of colonisation.

Interannual climate variability patterns associated with the El Niño-Southern Oscillation phenomenon result in climate and environmental anomaly conditions in specific regions worldwide that directly favor outbreaks and/or amplification of variety of diseases of public health concern including chikungunya, hantavirus, Rift Valley fever, cholera, plague, and Zika. We analyzed patterns of some disease outbreaks during the strong 2015–2016 El Niño event in relation to climate anomalies derived from satellite measurements. Disease outbreaks in multiple El Niño-connected regions worldwide (including Southeast Asia, Tanzania, western US, and Brazil) followed shifts in rainfall, temperature, and vegetation in which both drought and flooding occurred in excess (14–81% precipitation departures from normal). These shifts favored ecological conditions appropriate for pathogens and their vectors to emerge and propagate clusters of diseases activity in these regions. Our analysis indicates that intensity of disease activity in some ENSO-teleconnected regions were approximately 2.5–28% higher during years with El Niño events than those without. Plague in Colorado and New Mexico as well as cholera in Tanzania were significantly associated with above normal rainfall (p

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.

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.

Introduction Epidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016–2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was. Methods To improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers. Results 2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies. Conclusions Many ZIKV predictions were published during the 2016–2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics., Author summary Researchers published many studies which sought to predict and forecast important features of Zika virus (ZIKV) infections and their spread during the 2016–2017 ZIKV pandemic. We conducted a comprehensive review of such ZIKV prediction studies and evaluated their aims, the data sources they used, which methods were used, how timely they were published, and whether they provided sufficient information to be used or reproduced by others. Of the 73 studies evaluated, we found the accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied; indicating there is substantial room for improvement. We identified that the release of study findings before formal journal publication (‘pre-prints’) increased the timeliness of Zika prediction studies, but note they were infrequently used during this public health emergency. Addressing these areas can improve our understanding of Zika and other outbreaks and ensure forecasts can inform preparedness and response to future outbreaks, epidemics, and pandemics.

Evaluation of: Nguyen MN, Duong TH, Trung VT et al. Host and viral features of human dengue cases shape the population of infected and infectious Aedes aegypti mosquitoes. Proc. Natl Acad. Sci. USA 110(22), 9072–9077 (2013). Dengue virus (DENV) is a mosquito-borne virus of immense and growing global health importance. Despite decades of research, many fundamental components of DENV biology remain poorly understood. The Nguyen et al. study shines new light on one such component: the relationship between DENV blood viremia and infectiousness to mosquitoes. By directly feeding mosquitoes on infected people, the authors identified the viremia levels required for mosquitoes to become infected with each of the four DENV serotypes. Based on these results, the authors then indicated that ambulatory dengue cases who did not visit a hospital had viremia levels sufficient to infect mosquitoes. In avoiding laboratory surrogates, this study has significantly improved our understanding of DENV with implications for modeling and vaccine development.

During the past decade, countries in South America have reported dengue hemorrhagic fever (DHF) associated with American/Asian genotype of dengue virus serotype 2 (DENV-2). DENV-2 strains have been associated with large outbreaks of dengue fever and DHF in numerous regions of Peru since the mid-1990s, but studies to address the origins, distribution, and genetic diversity of DENV-2 strains have been limited. To address this knowledge gap, we sequenced the envelope gene region of DENV-2 isolates from Peru, Ecuador, Paraguay, and Bolivia. Sequences were aligned and compared to a global sample of DENV-2 viruses. Phylogenetic analysis confirmed the circulation of two DENV-2 genotypes in Peru: American (prior to 2001) and American/Asian (2000 to present). American/Asian genotype variants can be classified into two lineages, and these were introduced into Peru from the north (Ecuador, Colombia, and/or Venezuela) and the east (Brazil and Bolivia). American/Asian lineage II replaced lineage I after 2009. We estimate the time to the most recent common ancestor for American/Asian DENV-2 genotype in the Americas was in 1980, and 1984 and 1989 for lineages I and II, respectively. In light of evidence for increased virulence of lineage II of American/Asian DENV-2, our results support the need for continuous monitoring for the emergence of new DENV genotypes that may be associated with severe disease.

The tourniquet test (TT) is a physical examination maneuver often performed on patients suspected of having dengue. It has been incorporated into dengue diagnostic guidelines and is used in clinical studies. However, little is known about TT performance characteristics in different patient types or epidemiologic conditions. In the dengue-endemic city of Iquitos, Peru, we performed TTs and dengue laboratory assays on 13,548 persons with febrile disease, recruited through either active (n = 1,095) or passive (n = 12,453) surveillance. The sensitivity was 52% and 56%, the specificity was 58% and 68%, the positive predictive value was 45% and 55%, and the negative predictive value was 64% and 69% for persons enrolled in active and passive surveillance, respectively. We demonstrated that the TT was more sensitive identifying dengue disease in women and those of younger age and that sensitivity increased the later a person came to a medical clinic for care.

Dengue virus (DENV) is the most prevalent arthropod-transmitted virus among humans, with conservative estimates placing half of the world's population at risk for infection [1, 2]. Dengue can be caused by any of 4 viral serotypes (DENV-1–4), and infection can lead to a range of outcomes, from subclinical infection to death [3]. Infection outcomes are determined by a suite of factors, including host susceptibility, virus genetics, cell-mediated immune response, and cross-reactive antibodies [4, 5]. Cross-reaction between preexisting DENV antibodies and virus of a heterotypic infecting serotype is due to the conservation of some viral envelope proteins across serotypes, which results in antibody binding to the virus particles without fully neutralizing them [6]. There is epidemiologic and in vitro evidence that these cross-reactive antibodies can enhance infection and disease severity during secondary infections (referred to as antibody-dependent enhancement [7–9]). It has also been inferred from hospital admissions data that severe disease is rare during third and fourth infections [10], suggesting that there is a protective effect conferred by cumulative cross-reactive antibodies. Despite the uncertainties, a general lesson from multiple-strain DENV mathematical models is that the effects of preexisting antibodies, either enhancing or protective, can significantly influence projected virus transmission and disease dynamics [11–15]. Because of the possibility for disease potentiation from subneutralizing antibodies, vaccine design efforts have aimed for a tetravalent formulation that simultaneously protects against all 4 DENV serotypes [16, 17]. Recent results from phase 2b trials of the leading vaccine candidate showed partial efficacy against DENV-1, DENV-3, and DENV-4 but did not protect against febrile illness associated with DENV-2 infection [18]. An important unanswered question concerns the effect that neutralizing antibody to ≥2 serotypes will have on disease burden and virus transmission. There is, therefore, a need for empirical data characterizing population-level outcomes of serial DENV infections. In this study, we used data from a longitudinal cohort in Iquitos, Peru, where prospective seroepidemiology and febrile surveillance studies have been ongoing since 1999. For the same individuals, biannual serological results were used to determine the baseline serostatus of participants, and door-to-door febrile surveillance paired with laboratory confirmation was used to identify subsequent disease due to a DENV infection. Of special interest were disease outcomes during third and fourth infections, which were classified together as postsecondary infections. Our data indicate that the risk of developing febrile dengue illness was significantly reduced in individuals with a history of ≥2 prior DENV exposures, despite the absence of preexisting antibodies specific to the infecting serotype.

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.

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.

Background. Infection with any of the 4 related dengue virus serotypes (DENV-1–4) is thought to result in lifelong immunity to homotypic reinfection (ie, reinfection with the same serotype).

Recent studies have shown that livestock can carry Staphylococcus aureus and transmit it to human caretakers. We conducted a pilot study to determine the prevalence and molecular epidemiology of S. aureus among rural Iowans, including individuals with livestock contact. Nasal and throat swabs were collected and plated onto selective media to isolate methicillin-susceptible and methicillin-resistant S. aureus (MRSA), followed by antibiotic resistance testing and molecular analysis of the isolates. While no MRSA was detected, overall, 23.7% (31/131) of participants were found to harbor S. aureus in their nose, throat, or both. Fifteen isolates displayed resistance to one or more tested antibiotics, and the Panton-Valentine leukocidin (PVL) genes were present at a high level (29% [9/31] of S. aureus-positive participants). Younger age and tobacco use were associated with increased risk of S. aureus carriage. Our results suggest that carriage of PVL-positive S. aureus is common among rural Iowans, even in the absence of detectable MRSA colonization.

While human illness associated with hantavirus infection has been documented in many countries of South America, evidence for hantavirus transmission in Peru has been limited to the isolation of Rio Mamore virus from a pigmy mouse rat (Oligoryzomys microtis) in the Amazon city of Iquitos. To address the possibility of human hantavirus exposure in the region, we screened febrile patients reporting to health clinics in Iquitos from 2007 to 2010 for serological evidence of recent hantavirus infection. In addition, we conducted a serological survey for hantavirus-reactive IgG among healthy participants residing in Iquitos and rural areas surrounding the city. Through the febrile surveillance study, we identified 15 participants (0.3%; 15/5174) with IgM reactive to hantavirus (Andes virus) antigen, all with relatively mild, self-limited illness. From the cross-sectional serosurvey we found that 1.7% (36/2063) of residents of the Iquitos area had serum IgG reactive to one or more hantaviruses, with a higher prevalence in the urban population (2.2%, compared to 1.1% in rural areas). These results suggest that human infection with hantavirus has occurred in Peru.

Secondary dengue viral infection can produce capillary leakage associated with increased mortality known as dengue hemorrhagic fever (DHF). Because the mortality of DHF can be reduced by early detection and intensive support, improved methods for its detection are needed. We applied multidimensional protein profiling to predict outcomes in a prospective dengue surveillance study in South America. Plasma samples taken from initial clinical presentation of acute dengue infection were subjected to proteomics analyses using ELISA and a recently developed biofluid analysis platform. Demographics, clinical laboratory measurements, nine cytokines, and 419 plasma proteins collected at the time of initial presentation were compared between the DF and DHF outcomes. Here, the subject's gender, clinical parameters, two cytokines, and 42 proteins discriminated between the outcomes. These factors were reduced by multivariate adaptive regression splines (MARS) that a highly accurate classification model based on eight discriminant features with an area under the receiver operator curve (AUC) of 0.999. Model analysis indicated that the feature–outcome relationship were nonlinear. Although this DHF risk model will need validation in a larger cohort, we conclude that approaches to develop predictive biomarker models for disease outcome will need to incorporate nonparametric modeling approaches. Clin Trans Sci 2012; Volume #: 1–13

Please cite this paper as: Laguna-Torres et al. (2011) Influenza and other respiratory viruses in three Central American countries. Influenza and Other Respiratory Viruses 5(2), 123–134. Background Despite the disease burden imposed by respiratory diseases on children in Central America, there is a paucity of data describing the etiologic agents of the disease. Aims To analyze viral etiologic agents associated with influenza-like illness (ILI) in participants reporting to one outpatient health center, one pediatric hospital, and three general hospitals in El Salvador, Honduras, and Nicaragua Material & Methods Between August 2006 and April 2009, pharyngeal swabs were collected from outpatients and inpatients. Patient specimens were inoculated onto cultured cell monolayers, and viral antigens were detected by indirect and direct immunofluorescence staining. Results A total of 1,756 patients were enrolled, of whom 1,195 (68.3%) were under the age of 5; and 183 (10.4%) required hospitalization. One or more viral agents were identified in 434 (24.7%) cases, of which 17 (3.9%) were dual infections. The most common viruses isolated were influenza A virus (130; 7.4% of cases), respiratory syncytial virus (122; 6.9%), adenoviruses (63; 3.6%), parainfluenza viruses (57; 3.2%), influenza B virus (47; 2.7% of cases), and herpes simplex virus 1 (22; 1.3%). In addition, human metapneumovirus and enteroviruses (coxsackie and echovirus) were isolated from patient specimens. Discussion When compared to the rest of the population, viruses were isolated from a significantly higher percentage of patients age 5 or younger. The prevalence of influenza A virus or influenza B virus infections was similar between the younger and older age groups. RSV was the most commonly detected pathogen in infants age 5 and younger and was significantly associated with pneumonia (p

Please cite this paper as: Forshey et al. (2010) Epidemiology of influenza-like illness in the Amazon Basin of Peru, 2008–2009. Influenza and Other Respiratory Viruses 4(4), 235–243. Background Data addressing the incidence and epidemiology of influenza and influenza-like illness (ILI) in tropical regions of the world is scarce, particularly for the neotropics of South America. Methods We conducted active, population-based surveillance for ILI across 45 city blocks within the Amazon Basin city of Iquitos, Peru. Demographic data and household characteristics were collected for all participants, and participating households were visited three times weekly to inquire about ILI (fever plus cough or sore throat) among household residents. Nasal and oropharyngeal swabs were collected from participants with ILI and tested for influenza virus infection. Results Between May 1, 2008 and July 8, 2009, we monitored 10,341 participants for ILI for a total of 11 569·5 person-years. We detected 459 ILI episodes, with 252 (54·9%) of the participants providing specimens. Age-adjusted incidence of ILI was estimated to be 46·7 episodes/1000 person-years. Influenza A and B viruses were detected in 25 (9·9%) and 62 (24·6%) specimens of ILI patients, respectively, for an estimated age-adjusted incidence rate of 16·5 symptomatic influenza virus infections/1000 person-years. Risk factors for ILI included age, household crowding, and use of wood as cooking fuel. For influenza virus infection specifically, age and use of wood as a cooking fuel were also identified as risk factors, but no effect of household crowding was observed. Conclusions Our results represent the initial population-based description of the epidemiology of ILI in the Amazon region of Peru, which will be useful for developing region-specific strategies for reducing the burden of respiratory disease.

Endemic dengue transmission has been documented in the Amazonian city of Iquitos, Peru, since the early 1990s. To better understand the epidemiology of dengue transmission in Iquitos, we established multiple active surveillance systems to detect symptomatic infections. Here we compare the efficacy of distinct community-based (door to door) and school absenteeism-based febrile surveillance strategies in detecting active cases of dengue. Febrile episodes were detected by both systems with equal rapidity after disease onset. However, during the period that both programs were running simultaneously in 2004, a higher number of febrile cases in general (4.52/100 versus 1.64/100 person-years) and dengue cases specifically (2.35/100 versus 1.29/100 person-years) were detected in school-aged children through the community-based surveillance program. Similar results were obtained by direct comparison of 435 participants concurrently enrolled in both programs (P < 0.005). We conclude that, in Iquitos, community-based door-to-door surveillance is a more efficient and sensitive design for detecting active dengue cases than programs based on school absenteeism.

In 2008, dengue virus serotype 4 (DENV-4) emerged in northeastern Peru, causing a large outbreak and displacing DENV-3, which had predominated for the previous 6 years. Phylogenetic analysis of 2008 and 2009 isolates support their inclusion into DENV-4 genotype II, forming a lineage distinct from strains that had previously circulated in the region.

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., Author Summary Dengue is a mosquito-borne viral illness that imposes a tremendous public health burden on tropical and sub-tropical regions. An estimated 390 million infections occur globally each year, and up to 4 billion people are at risk. Dengue is caused by four dengue virus (DENV) serotypes (DENV-1 to DENV-4). Infection with any DENV can lead to a range of disease outcomes, from mild febrile illness to severe, hemorrhagic manifestations and death. Infection by one serotype has been assume to provide complete and lifelong protection against re-infection by the same serotype, and to our knowledge, instances of re-infection by the same serotype have not been rigorously documented. However, few long-term studies have been conducted in such a way that re-infection by the same serotype could be observed, if it did in fact occur. Our study provides evidence that re-infection may occur in certain circumstances. We draw from data collected during a 2010–2011 DENV-2 epidemic in northeastern Peru, 15 years after the initial DENV-2 outbreak in the region. This finding has significant implications for our understanding of dengue epidemiology and for dengue vaccine formulation, which may need to consider multiple genotypes of each serotype. Data from other long-term dengue epidemiology studies should be analyzed to determine if homologous re-infection is a more widespread phenomenon.

Background Nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA) is associated with increased infection risk, yet colonization and infection isolates are rarely compared within the same study. The objectives of this study were to compare colonization and infection isolates from a Veterans Administration hospital in Iowa, and to determine the prevalence of livestock-associated MRSA (LA-MRSA) colonization and infection in a state with high livestock density. Methods All patients with available MRSA isolates collected through routine nasal screening (73%; n = 397) and from infections (27%; n = 148) between December 2010 and August 2012 were included and tested for spa type and presence of PVL and mecA genes. Clinical isolates were tested for antibiotic resistance patterns. Paired colonization and infection isolates were compared for genetic and phenotypic congruity. Results The most common spa types were t002 (and other CC5-associated strains; 65%) and t008 (and other CC8-associated strains; 20%). No classic LA-MRSA spa types were identified. CC5-associated strains were less likely to be associated with infections (22%; 77/353) compared with CC8-associated strains (49%; 53/109). MRSA colonization was more common among patients with infections (71%) compared with the general screening population (7%). In most cases (82%; 28/34), paired colonization and infection isolates were genetically and phenotypically indistinguishable. Conclusions Our data demonstrate a direct link between antecedent nasal colonization and subsequent MRSA infection. Further, our data indicate variability in colonization and infection efficiency among MRSA genotypes, which points to the need to define the molecular determinants underlying emergence of S. aureus strains in the community and nosocomial setting.

The lack of antiviral compounds targeting flaviviruses represents a significant problem in the development of strategies for treating West Nile Virus (WNV), Dengue, and Yellow Fever infections. Using WNV high-throughput screening techniques developed in our laboratories, we report the identification of several small molecule anti-WNV compounds belonging to four different structural classes including pyrazolines, xanthanes, acridines, and quinolines. The initial set of "hits" was further refined using cell viability-cytotoxicity assays to two 1,3,5-triaryl pyrazoline compounds: 1-(4-chlorophenylacetyl)-5-(4-nitrophenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole and 1-benzoyl-5-(4-chlorophenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole. On the basis of their activity and favorable therapeutic indexes, these compounds were identified as viable leads and subjected to additional evaluation using an authentic viral titer reduction assay employing an epidemic strain of WNV. The compounds were further evaluated in a transient replicon reporting system to gain insight into the mechanism of action by identifying the step at which inhibition takes place during viral replication. The results indicate the pyrazolines inhibit RNA synthesis, pointing to viral RNA polymerase, RNA helicase, or other viral replication enzymes as potential targets. Progress was also made in understanding the structural requirements for activity by synthesizing a focused chemical library of substituted pyrazolines. Preliminary SAR data are presented that show the aryl-rings are required for activity against WNV. More importantly, the results indicate WNV activity is tolerant to aryl-substitutions paving the way for the design and development of much larger combinatorial libraries with varied physicochemical properties.

Despite the effectiveness of currently available human immunodeficiency virus type 1 (HIV-1) therapies, a continuing need exists for new drugs to treat HIV-1 infection. We investigated the mechanism by which 3- O -{3′,3′-dimethylsuccinyl}-betulinic acid (DSB) inhibits HIV-1 replication. DSB functions at a late stage of the virus life cycle but does not inhibit the HIV-1 protease in vitro or interfere with virus assembly or release. DSB specifically delays the cleavage of Gag between the capsid (CA) and p2, resulting in delayed formation of the mature viral core and reduced HIV-1 infectivity. Replication of simian immunodeficiency virus (SIV) was resistant to DSB; however, a chimeric SIV carrying CA-p2 sequences from HIV-1 was inhibited by the drug, indicating that susceptibility to DSB maps to the CA-p2 region of the HIV-1 Gag protein. A single point mutation at the CA-p2 cleavage site of HIV-1 conferred strong resistance to DSB, confirming the target of the drug. HIV-1 strains that are resistant to a variety of protease inhibitors were sensitive to DSB. These findings indicate that DSB specifically protects the CA-p2 cleavage site from processing by the viral protease during virion maturation, thereby revealing a novel mechanism for pharmacologic inhibition of HIV-1 replication.

Internet-based surveillance methods for vector-borne diseases (VBDs) using "big data" sources such as Google, Twitter, and internet newswire scraping have recently been developed, yet reviews on such "digital disease detection" methods have focused on respiratory pathogens, particularly in high-income regions. Here, we present a narrative review of the literature that has examined the performance of internet-based biosurveillance for diseases caused by vector-borne viruses, parasites, and other pathogens, including Zika, dengue, other arthropod-borne viruses, malaria, leishmaniasis, and Lyme disease across a range of settings, including low- and middle-income countries. The fundamental features, advantages, and drawbacks of each internet big data source are presented for those with varying familiarity of "digital epidemiology." We conclude with some of the challenges and future directions in using internet-based biosurveillance for the surveillance and control of VBD.

Staphylococcus aureus colonizes approximately 30% of Americans and causes a range of infections [1]. An estimated 1.5% of the US population is colonized with methicillin-resistant S. aureus (MRSA) [2, 3]; emergence of multidrug-resistant strains increases this burden [4]. Staphylococcus aureus epidemiology has changed considerably in recent decades. Livestock-associated S. aureus (LA-SA) strains, including sequence type (ST) 398 and ST9, are often associated with swine, cattle, and poultry exposure [5], but little is known regarding LA-SA carriage and infection in the United States [6, 7]. ST398 carriage has been reported in areas with a high density of swine [8–12]. ST398 is the dominant MRSA strain on European farms [6, 13] and has been documented in the United States [11, 14]. It is unknown if ST398 colonizes a broader population of livestock workers or if additional strains may be zoonotic and spreading on US farms. Common human strains of t002/ST5 and t008/ST8 have been found in live pigs in North America [15–19]. Invasive human disease caused by ST398 has been reported, even in those without animal contact, suggesting that bidirectional spread of these strains is possible [6]. Many studies have investigated S. aureus colonization and infection in the healthcare setting [20]. Fewer have assessed its ecology and transmission in the community [21], and most of these have been conducted in urban areas [22, 23]. In a rural state like Iowa, which ranks third nationally in overall livestock production and first in swine production, transmission of S. aureus between pigs and farmers and into the broader community could complicate efforts to control S. aureus transmission statewide, and could have effects nationally due to movement of colonized pigs or travel by colonized humans. In this study, we report the prevalence of S. aureus colonization and infection among a population of Iowans, along with molecular characteristics, antimicrobial resistance profiles, and risk factors for carriage. We identified potential transmission within households and associations between duration of livestock exposure and LA-SA carriage.