ResearchPad - infectious-disease-surveillance https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[A systematic review of alternative surveillance approaches for lymphatic filariasis in low prevalence settings: Implications for post-validation settings]]> https://www.researchpad.co/article/elastic_article_13802 Lymphatic filariasis (LF) is a mosquito-borne disease, which can result in complications including swelling affecting the limbs (lymphoedema) or scrotum (hydrocele). LF can be eliminated by mass drug administration (MDA) which involves whole communities taking drug treatment at regular intervals. After MDA programmes, country programmes conduct the Transmission Assessment Survey (TAS), which tests school children for LF. It is important to continue testing for LF after elimination because there can be a 10-year period between becoming infected and developing symptoms, but it is thought that the use of TAS in such settings is likely to be too expensive and also not sensitive enough to detect low-level infections. Our study assesses the results from 44 studies in areas of low LF prevalence that have investigated methods of surveillance for LF which differ from the standardised TAS approach. These include both human and mosquito studies. Results show that there is currently no standardised approach to testing, but that surveillance can be made more sensitive through the use of new diagnostic tests, such as antibody testing, and also by targeting higher risk populations. However, further research is needed to understand whether these approaches work in a range of settings and whether they are affordable on the ground.

]]>
<![CDATA[epiDMS: Data Management and Analytics for Decision-Making From Epidemic Spread Simulation Ensembles]]> https://www.researchpad.co/article/N72c55080-2a92-441e-b06a-1ef616b4a36d

Background

Carefully calibrated large-scale computational models of epidemic spread represent a powerful tool to support the decision-making process during epidemic emergencies. Epidemic models are being increasingly used for generating forecasts of the spatial-temporal progression of epidemics at different spatial scales and for assessing the likely impact of different intervention strategies. However, the management and analysis of simulation ensembles stemming from large-scale computational models pose challenges, particularly when dealing with multiple interdependent parameters, spanning multiple layers and geospatial frames, affected by complex dynamic processes operating at different resolutions.

Methods

We describe and illustrate with examples a novel epidemic simulation data management system, epiDMS, that was developed to address the challenges that arise from the need to generate, search, visualize, and analyze, in a scalable manner, large volumes of epidemic simulation ensembles and observations during the progression of an epidemic.

Results and conclusions

epiDMS is a publicly available system that facilitates management and analysis of large epidemic simulation ensembles. epiDMS aims to fill an important hole in decision-making during healthcare emergencies by enabling critical services with significant economic and health impact.

]]>
<![CDATA[Surveillance for Respiratory Infections in Low- and Middle-Income Countries: Experience From the Centers for Disease Control and Prevention's Global Disease Detection International Emerging Infections Program]]> https://www.researchpad.co/article/N2e9d597e-2032-41b6-aaeb-2e5430628503 ]]> <![CDATA[Optimization of tissue sampling for Borrelia burgdorferi in white-footed mice (Peromyscus leucopus)]]> https://www.researchpad.co/article/Nff220985-8630-4822-8507-6b577103a931

Peromyscus leucopus (the white-footed mouse) is a known reservoir of the Lyme disease spirochete Borrelia burgdorferi. Sampling of white-footed mice allows for year-round B. burgdorferi surveillance as well as opportunities to establish the diversity of the different variants in a geographic region. This study explores the prevalence of B. burgdorferi infections in the tissues of white-footed mice, investigates the correlations between B. burgdorferi infected tissues, and determines the optimum field methods for surveillance of B. burgdorferi in P. leucopus. A total of 90 mice and 573 tissues (spleen, liver, ear, tongue, tail, heart, and kidney) were screened via nested PCR for B. burgdorferi infections. A large number of infections were found in the 90 mice as well as multiple infections within individual mice. Infections in a single mouse tissue (spleen, liver, ear, tongue and tail) were predictive of concurrent infection in other tissues of the same mouse at a statistically significant level. Ear tissue accounted for 68.4% of detected infections, which increased to 78.9% of the infected mice with the inclusion of tail samples. The use of ear punch or tail snip samples (used individually or in tandem) have multiple advantages over current Lyme disease ecological studies and surveillance methodologies, including lower associated costs, minimization of delays, year-round B. burgdorferi testing opportunities, as well as longitudinal monitoring of B. burgdorferi in defined geographic regions. In the absence of an effective vaccine, personal prevention measures are currently the most effective way to reduce Lyme disease transmission to humans. Thus, the identification and monitoring of environmental reservoirs to inform at-risk populations remains a priority. The sampling methods proposed in this study provide a reasonable estimate of B. burgdorferi in white-footed mice in a timely and cost-effective manner.

]]>
<![CDATA[Diversity of A(H5N1) clade 2.3.2.1c avian influenza viruses with evidence of reassortment in Cambodia, 2014-2016]]> https://www.researchpad.co/article/Nf51e501a-7d3b-493b-bbd9-bf4dbc27c932

In Cambodia, highly pathogenic avian influenza A(H5N1) subtype viruses circulate endemically causing poultry outbreaks and zoonotic human cases. To investigate the genomic diversity and development of endemicity of the predominantly circulating clade 2.3.2.1c A(H5N1) viruses, we characterised 68 AIVs detected in poultry, the environment and from a single human A(H5N1) case from January 2014 to December 2016. Full genomes were generated for 42 A(H5N1) viruses. Phylogenetic analysis shows that five clade 2.3.2.1c genotypes, designated KH1 to KH5, were circulating in Cambodia during this period. The genotypes arose through multiple reassortment events with the neuraminidase (NA) and internal genes belonging to H5N1 clade 2.3.2.1a, clade 2.3.2.1b or A(H9N2) lineages. Phylogenies suggest that the Cambodian AIVs were derived from viruses circulating between Cambodian and Vietnamese poultry. Molecular analyses show that these viruses contained the hemagglutinin (HA) gene substitutions D94N, S133A, S155N, T156A, T188I and K189R known to increase binding to the human-type α2,6-linked sialic acid receptors. Two A(H5N1) viruses displayed the M2 gene S31N or A30T substitutions indicative of adamantane resistance, however, susceptibility testing towards neuraminidase inhibitors (oseltamivir, zanamivir, lananmivir and peramivir) of a subset of thirty clade 2.3.2.1c viruses showed susceptibility to all four drugs. This study shows that A(H5N1) viruses continue to reassort with other A(H5N1) and A(H9N2) viruses that are endemic in the region, highlighting the risk of introduction and emergence of novel A(H5N1) genotypes in Cambodia.

]]>
<![CDATA[The burden of Staphylococcus aureus among Native Americans on the Navajo Nation]]> https://www.researchpad.co/article/5c8823e9d5eed0c4846392b2

Introduction

Native Americans in the southwestern United States have a higher risk for many infectious diseases and may be at higher risk for Staphylococcus aureus due to the high prevalence of risk factors for S. aureus. Recent data on invasive S. aureus infections among Native Americans are limited.

Methods

Active population- and laboratory-based surveillance was conducted in 2016–2017 on the Navajo Nation to document the rate of invasive S. aureus. A case of invasive S.aureus infection was defined as a Native American individual with S. aureus isolated from a normally sterile body site whose reported community of residence was on or around the Navajo Nation.

Results

One hundred and fifty-nine cases of invasive S. aureus from 152 individuals were identified. The median age of cases was 56.3 years and 35% were female. Thirty-five percent of cases had community-acquired infections. Ninety-three percent of cases had underlying medical conditions, including diabetes (60%) and obesity (42%), 28% of cases had a documented prior S. aureus infection, and 33% were infected with methicillin-resistant S. aureus. The annual incidence of invasive S. aureus and of invasive methicillin-resistant S. aureus was 64.9/100,000 persons and 21.2/100,000 persons, respectively.

Conclusions

This community has a high burden of invasive S. aureus infections. Further research is needed to identify prevention strategies and opportunities for intervention.

]]>
<![CDATA[Epidemiological and clinical features of invasive pneumococcal disease caused by serotype 12F in adults, Japan]]> https://www.researchpad.co/article/5c78501ad5eed0c484007c91

Enhanced surveillance of invasive pneumococcal disease (IPD) in adults was conducted during April 2013–March 2018 in 10 of 47 prefectures in Japan, and a total of 1277 IPD patients were enrolled. An emergence of IPD caused by serotype 12F was identified during May 2015–March 2018 through this surveillance. 12F isolates were composed of four related sequence types. In total, 120 patients with 12F IPD were reported during this period. To characterize the clinical features of 12F IPD, the disease characteristics of these patients were compared with those of 1157 patients with non-12F IPD. Compared with the non-12F IPD patients, a significantly lower proportion of 12F IPD patients was aged 65 years or older (55% vs. 70%), vaccinated with 23-valent pneumococcal polysaccharide (4% vs. 14%), had comorbid illness (65% vs. 77%), or were immunocompromised (19% vs. 30%; all P < 0.05). No significant difference in the proportion of case fatalities was found between the two groups. The proportions of those aged 65 years or older (53% vs. 69%) and with bacteremic pneumonia (35% vs. 69%) were significantly lower in 17 patients who died from 12F IPD than in 205 patients who died from non-12F IPD (all P < 0.05). Differences in clinical features were similarly found between 12F IPD patients and patients in low- or intermediate-level invasive potential serogroups. Our data demonstrated that serotype 12F was associated with IPD in younger adults and a lower proportion of comorbid illness, including immunocompromised conditions, in adult IPD, suggesting the high invasive potential of the serotype 12F. In addition, patients who died from 12F IPD were younger and had proportionately more bacteremia without focus. These findings may provide new insight into the pathogenesis of IPD in adults caused by 12F serotype with a high invasive potential.

]]>
<![CDATA[Detection of municipalities at-risk of Lyme disease using passive surveillance of Ixodes scapularis as an early signal: A province-specific indicator in Canada]]> https://www.researchpad.co/article/5c75ac66d5eed0c484d086db

Lyme disease, the most commonly reported vector-borne disease in North America, is caused by the spirochete Borrelia burgdorferi sensu stricto, which is transmitted by Ixodes scapularis in eastern Canada and Ixodes pacificus in western Canada. Recently, the northward range expansion of I. scapularis ticks, in south-eastern Canada, has resulted in a dramatic increase in the incidence of human Lyme disease. Detecting emerging areas of Lyme disease risk allows public health to target disease prevention efforts. We analysed passive tick surveillance data from Ontario and Manitoba to i) assess the relationship between the total numbers of I. scapularis submissions in passive surveillance from humans, and the number of human Lyme disease cases, and ii) develop province-specific acarological indicators of risk that can be used to generate surveillance-based risk maps. We also assessed associations between numbers of nymphal I. scapularis tick submissions only and Lyme disease case incidence. Using General Estimating Equation regression, the relationship between I. scapularis submissions (total numbers and numbers of nymphs only) in each census sub-division (CSD) and the number of reported Lyme disease cases was positively correlated and highly significant in the two provinces (P ≤ 0.001). The numbers of I. scapularis submissions over five years discriminated CSDs with ≥ 3 Lyme disease cases from those with < 3 cases with high accuracy when using total numbers of tick submission (Receiver Operating Characteristics area under the curve [AUC] = 0.89) and moderate accuracy (AUC = 0.78) when using nymphal tick submissions only. In Ontario the optimal cut-off point was a total 12 tick submissions from a CSD over five years (Sensitivity = 0.82, Specificity = 0.84), while in Manitoba the cut-off point was five ticks (Sensitivity = 0.71, Specificity = 0.79) suggesting regional variability of the risk of acquiring Lyme disease from an I. scapularis bite. The performances of the acarological indicators developed in this study for Ontario and Manitoba support the ability of passive tick surveillance to provide an early signal of the existence Lyme disease risk areas in regions where ticks and the pathogens they transmit are expanding their range.

]]>
<![CDATA[The successful containment of a hospital outbreak caused by NDM-1-producing Klebsiella pneumoniae ST307 using active surveillance]]> https://www.researchpad.co/article/5c6dc9abd5eed0c484529fbf

The worldwide dissemination of high-risk carbapenemase-producing Klebsiella pneumoniae clones has become a major threat to healthcare facilities. This study describes the successful containment of a hospital outbreak caused by NDM-1-producing K. pneumoniae Sequence Type (ST) 307 using active surveillance. The outbreak began when a patient was transferred from a local hospital. After 48 hours in our hospital, a tracheal aspirate was positive for a meropenem resistant and carbapenemase-producing K. pneumoniae. All patients in the medical intensive care unit (ICU) and the neurology wards were subject to contact precautions. The hospital surfaces and devices, healthcare workers, and patients from these wards were screened by cultures. Fecal swabs were placed into broth and PCR for blaKPC, blaOXA-48, blaIMP, blaVIM, and blaNDM, which were performed directly from the broth after 12 hours. PCRs were also performed on DNA extracted from carbapenemase-producing species from subcultured broths. Five and nine days later, two more patients’ rectal swabs tested positive. Molecular assays identified K. pneumoniae blaNDM-1 onto a 130-kb conjugative plasmid (IncY, IncFIIs, and IncFIIY), ST307. After the three patients were discharged, monitoring continued, and after three weeks with negative results, rectal swabbing ended. In conclusion, it was possible to contain a hospital outbreak caused by NDM-1-producing K. pneumoniae ST307 through epidemiological and microbiological surveillance. With the methodology used, the detection of NDM-type genes in fecal samples was obtained in approximately 15 hours after obtaining the fecal sample.

]]>
<![CDATA[The growing importance of lone star ticks in a Lyme disease endemic county: Passive tick surveillance in Monmouth County, NJ, 2006 – 2016]]> https://www.researchpad.co/article/5c6c75cbd5eed0c4843d01e0

As human cases of tick-borne disease continue to increase, there is a heightened imperative to collect data on human-tick encounters to inform disease prevention. Passive tick surveillance programs that encourage members of the public to submit ticks they have encountered can provide a relatively low-cost means of collecting such data. We report the results of 11 years of tick submissions (2006–2016) collected in Monmouth County, New Jersey, an Atlantic coastal county long endemic for Lyme disease. A total of 8,608 ticks acquired in 22 U.S. states were submitted, 89.7% of which were acquired in Monmouth County, from 52 of the County’s 53 municipalities. Seasonal submission rates reflected known phenology of common human-biting ticks, but annual submissions of both Amblyomma americanum and Dermacentor variabilis increased significantly over time while numbers of Ixodes scapularis remained static. By 2016, A. americanum had expanded northward in the county and now accounted for nearly half (48.1%) of submissions, far outpacing encounters with I. scapularis (28.2% of submissions). Across all tick species and stages the greatest number of ticks were removed from children (ages 0–9, 40.8%) and older adults (ages 50+, 23.8%) and these age groups were also more likely to submit partially or fully engorged ticks, suggesting increased risk of tick-borne disease transmission to these vulnerable age groups. Significantly more people (43.2%) reported acquiring ticks at their place of residence than in a park or natural area (17.9%). This pattern was more pronounced for residents over 60 years of age (72.7% acquired at home). Education that stresses frequent tick checks should target older age groups engaged in activity around the home. Our results strongly suggest that encounter rates with ticks other than I. scapularis are substantial and increasing and that their role in causing human illness should be carefully investigated.

]]>
<![CDATA[Zika virus: Epidemiological surveillance of the Mexican Institute of Social Security]]> https://www.researchpad.co/article/5c6b2665d5eed0c484289993

Introduction

At the end of 2015, the first cases of Zika were identified in southern Mexico. During 2016, Zika spread as an outbreak to a large part of the country's coastal zones.

Methodology

The Zika epidemiological surveillance system records cases with clinical symptoms of Zika virus disease (ZVD) and those confirmed by means of a reverse polymerase chain reaction (RT-PCR) assay. This report includes the suspected and confirmed cases from 2016. Incidence rates were estimated by region and in pregnant women based on the proportion of confirmed cases.

Results

In total, 43,725 suspected cases of ZVD were reported. The overall incidence of suspected cases of ZVD was 82.0 per 100,000 individuals and 25.3 per 100,000 Zika cases. There were 4,168 pregnant women with suspected symptoms of ZVD, of which infection was confirmed in 1,082 (26%). The estimated incidence rate of ZVD for pregnant women nationwide was 186.1 positive Zika cases per 100,000 pregnant women.

Conclusions

The incidence of Zika in Mexico is higher than that reported previously in the National System of Epidemiological Surveillance. Positive cases of Zika must be estimated and reported.

]]>
<![CDATA[The fight to keep resistance at bay, epidemiology of carbapenemase producing organisms (CPOs), vancomycin resistant enterococci (VRE) and methicillin resistant Staphylococcus aureus (MRSA) in Norway, 2006 - 2017]]> https://www.researchpad.co/article/5c61e8bad5eed0c48496f045

Introduction

Scandinavian countries have traditionally had a low prevalence of resistant organisms, but have in recent years experienced a change in their epidemiology. We aim to describe the epidemiology of carbapenemase-producing organisms (CPOs), vancomycin-resistant enterococci (VRE) and methicillin-resistant S. aureus (MRSA) in Norway, measure the importance of infections contracted abroad, and assess the morbidity and mortality associated with these resistant bacteria in Norway.

Methods and materials

We used data from the Norwegian surveillance system for communicable diseases covering all findings of the selected resistant bacteria including both infections and colonisation, in the period 2006–2017. Annual trends were assessed using negative binomial regression. For MRSA, we were able to calculate the Morisita-Horn index and transmission numbers following importation in order to assess the effect this had on further domestic transmission.

Results

The incidence rates (per 100,000 personyears) of the three groups of resistant bacteria have increased during the period. In 2017 the incidence rates were 0.82 for CPOs, 7.09 for VRE and 43.8 for MRSA. 81% of CPO cases were diagnosed in hospitals, but 73% were infected abroad. Most VRE cases were infected in Norwegian hospitals, 85% were associated with hospitals outbreaks. MRSA was predominantly diagnosed in the community, only 21% were diagnosed in hospitals. Of all MRSA cases, 35% were infected in other countries. Most MRSA spa-types were not identified again after introduction, resulting in a transmission of MRSA equivalent to a mean of 0.30 persons infected from each spa-type identified (range: 0–22). The proportion of infections among all notified cases within each diagnose was 44% for MRSA, 9% for VRE and 45% for CPOs. Among persons notified with bacteraemia, the 30 days all-cause mortality were 20%, 16% and 50% for MRSA, VRE and CPOs respectively.

Discussion

The incidence rates of CPOs, VRE and MRSA in Norway are low, but increasing. The continuing increase of notified resistant bacteria highlights the need for a revision of existing infection prevention and control guidelines.

]]>
<![CDATA[Metagenomic analysis of viruses in toilet waste from long distance flights—A new procedure for global infectious disease surveillance]]> https://www.researchpad.co/article/5c466576d5eed0c4845194b7

Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.

]]>
<![CDATA[Molecular detection of dengue virus in patients suspected of Ebola virus disease in Ghana]]> https://www.researchpad.co/article/5c23f270d5eed0c484046ac0

Dengue fever is known to be one of the most common arthropod-borne viral infectious diseases of public health importance. The disease is now endemic in more than 100 countries in Africa, the Americas, the Eastern Mediterranean, Southeast Asia and the Western Pacific with an estimated two fifths of the world's population being at risk. The notable endemic viral hemorrhagic fevers (VHFs) found in West Africa, including yellow fever, Lassa fever, Rift Valley fever, dengue fever and until recently Ebola have been responsible for most outbreaks with fatal consequences. These VHFs usually produce unclear acute febrile illness, especially in the acute phase of infection. In this study we detected the presence of 2 different serotypes (DENV-2 and DENV-3) of Dengue virus in 4 sera of 150 patients clinically suspected of Ebola virus disease during the Ebola Virus Disease (EVD) outbreak in West Africa with the use of serological and molecular test assays. Sequence data was successfully generated for DENV-3 and phylogenetic analysis of the envelope gene showed that the DENV-3 sequences had close homology with DENV-3 sequences from Senegal and India. This study documents molecular evidence of an indigenous Dengue fever viral infection in Ghana and therefore necessitates the need to have an efficient surveillance system to rapidly detect and control the dissemination of the different serotypes in the population which has the potential to cause outbreaks of dengue hemorrhagic fevers.

]]>
<![CDATA[Population based hospitalization burden of laboratory-confirmed hand, foot and mouth disease caused by multiple enterovirus serotypes in Southern China]]> https://www.researchpad.co/article/5c1c0a8bd5eed0c48442636c

Background

Hand, foot and mouth disease (HFMD) is spread widely across Asia, and the hospitalization burden is currently not well understood. Here, we estimated serotype-specific and age-specific hospitalization rates of HFMD in Southern China.

Methods

We enrolled pediatric HFMD patients admitted to 3/3 county-level hospitals, and 3/23 township-level hospitals in Anhua county, Hunan (CN). Samples were collected to identify enterovirus serotypes by RT-PCRs between October 2013 and September 2016. Information on other eligible, but un-enrolled, patients were retrospectively collected from the same six hospitals. Monthly numbers of all-cause hospitalizations were collected from each of the 23 township-level hospitals to extrapolate hospitalizations associated with HFMD among these.

Results

During the three years, an estimated 3,236 pediatric patients were hospitalized with lab-confirmed HFMD, and among these only one case was severe. The mean hospitalization rate was 660 (95% CI: 638–684) per 100,000 person-years for lab-confirmed HFMD, with higher rates among CV-A16 and CV-A6 associated HFMD (213 vs 209 per 100,000 person-years), and lower among EV-A71, CV-A10 and other enterovirus associated HFMD (134, 39 and 66 per 100,000 person-years respectively, p<0.001). Children aged 12–23 months had the highest hospitalization rates (3,594/100,000 person-years), followed by those aged 24–35 months (1,828/100,000 person-years) and 6–11 months (1,572/100,000 person-years). Compared with other serotypes, CV-A6-associated hospitalizations were evident at younger ages.

Conclusions

Our study indicates a substantial hospitalization burden associated with non-severe HFMD in a rural county in southern China. Future mitigation policies should take into account the disease burden identified, and optimize interventions for HFMD.

]]>
<![CDATA[Prioritizing surveillance activities for certification of yaws eradication based on a review and model of historical case reporting]]> https://www.researchpad.co/article/5c1028d5d5eed0c484248342

Background

The World Health Organization (WHO) has targeted yaws for global eradication. Eradication requires certification that all countries are yaws-free. While only 14 Member States currently report cases to WHO, many more are known to have a history of yaws and some of them may have ongoing transmission. We reviewed the literature and developed a model of case reports to identify countries in which passive surveillance is likely to find and report cases if transmission is still occurring, with the goal of reducing the number of countries in which more costly active surveillance will be required.

Methods

We reviewed published and unpublished documents to extract data on the number of yaws cases reported to WHO or appearing in other literature in any year between 1945 and 2015. We classified countries as: a) having interrupted transmission; b) being currently endemic; c) being previously endemic (current status unknown); or d) having no history of yaws. We constructed a panel dataset for the years 1945–2015 and ran a regression model to identify factors associated with some countries not reporting cases during periods when there was ongoing (and documented) transmission. For previously endemic countries whose current status is unknown, we then estimated the probability that countries would have reported cases if there had in fact been transmission in the last three years (2013–2015).

Results

Yaws has been reported in 103 of the 237 countries and areas considered. 14 Member States and 1 territory (Wallis and Futuna Islands) are currently endemic. 2 countries are believed to have interrupted transmission. 86 countries and areas are previously endemic (current status unknown). Reported cases peaked in the 1950s, with 55 countries reporting at least one case in 1950 and a total of 2.35 million cases reported in 1954. Our regression model suggests that case reporting during periods of ongoing transmission is positively associated with socioeconomic development and, in the short-term, negatively associated with independence. We estimated that for 66 out of the 86 previously endemic countries whose current status is unknown, the probability of reporting cases in the absence of active surveillance is less than 50%.

Discussion

Countries with a history of yaws need to be prioritized so that international resources for global yaws eradication may be deployed efficiently. Heretofore, the focus has been on mass treatment in countries currently reporting cases. It is also important to undertake surveillance in the 86 previously endemic countries for which the current status is unknown. Within this large and diverse group, we have identified a group of 20 countries with more than a 50% probability of reporting cases in the absence of active surveillance. For the other 66 countries, international support for active surveillance will likely be required.

]]>
<![CDATA[Identifying residual transmission of lymphatic filariasis after mass drug administration: Comparing school-based versus community-based surveillance - American Samoa, 2016]]> https://www.researchpad.co/article/5b600753463d7e39c5526206

Introduction

Under the Global Programme to Eliminate Lymphatic Filariasis (LF), American Samoa conducted seven rounds of mass drug administration (MDA) from 2000–2006. The World Health Organization recommends systematic post-MDA surveillance using Transmission Assessment Surveys (TAS) for epidemiological assessment of recent LF transmission. We compared the effectiveness of two survey designs for post-MDA surveillance: a school-based survey of children aged 6–7 years, and a community-based survey targeting people aged ≥8 years.

Methods

In 2016, we conducted a systematic school-based TAS in all elementary schools (N = 29) and a cluster survey in 28 villages on the two main islands of American Samoa. We collected information on demographics and risk factors for infection using electronic questionnaires, and recorded geo-locations of schools and households. Blood samples were collected to test for circulating filarial antigen (CFA) using the Alere Filariasis Test Strip. For those who tested positive, we prepared slides for microscopic examination of microfilaria and provided treatment. Descriptive statistics were performed for questionnaire variables. Data were weighted and adjusted to account for sampling design and sex for both surveys, and for age in the community survey.

Results

The school-based TAS (n = 1143) identified nine antigen-positive children and found an overall adjusted CFA prevalence of 0.7% (95% CI: 0.3–1.8). Of the nine positive children, we identified one microfilariaemic 7-year-old child. The community-based survey (n = 2507, 711 households) identified 102 antigen-positive people, and estimated an overall adjusted CFA prevalence of 6.2% (95% CI: 4.5–8.6). Adjusted village-level prevalence ranged from 0–47.1%. CFA prevalence increased with age and was higher in males. Of 86 antigen-positive community members from whom slides were prepared, 22 (25.6%) were microfilaraemic. School-based TAS had limited sensitivity (range 0–23.8%) and negative predictive value (range 25–83.3%) but had high specificity (range 83.3–100%) and positive predictive value (range 0–100%) for identifying villages with ongoing transmission.

Conclusions

American Samoa failed the school-based TAS in 2016, and the community-based survey identified higher than expected numbers of antigen-positive people. School-based TAS was logistically simpler and enabled sampling of a larger proportion of the target population, but the results did not provide a good indication of the overall CFA prevalence in older age groups and was not sensitive at identifying foci of ongoing transmission. The community-based survey, although operationally more challenging, identified antigen-positive individuals of all ages, and foci of high antigen prevalence. Both surveys confirmed recrudescence of LF transmission.

]]>
<![CDATA[Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions]]> https://www.researchpad.co/article/5b30b251463d7e0b2827fd22

Accurate and reliable forecasts of seasonal epidemics of infectious disease can assist in the design of countermeasures and increase public awareness and preparedness. This article describes two main contributions we made recently toward this goal: a novel approach to probabilistic modeling of surveillance time series based on “delta densities”, and an optimization scheme for combining output from multiple forecasting methods into an adaptively weighted ensemble. Delta densities describe the probability distribution of the change between one observation and the next, conditioned on available data; chaining together nonparametric estimates of these distributions yields a model for an entire trajectory. Corresponding distributional forecasts cover more observed events than alternatives that treat the whole season as a unit, and improve upon multiple evaluation metrics when extracting key targets of interest to public health officials. Adaptively weighted ensembles integrate the results of multiple forecasting methods, such as delta density, using weights that can change from situation to situation. We treat selection of optimal weightings across forecasting methods as a separate estimation task, and describe an estimation procedure based on optimizing cross-validation performance. We consider some details of the data generation process, including data revisions and holiday effects, both in the construction of these forecasting methods and when performing retrospective evaluation. The delta density method and an adaptively weighted ensemble of other forecasting methods each improve significantly on the next best ensemble component when applied separately, and achieve even better cross-validated performance when used in conjunction. We submitted real-time forecasts based on these contributions as part of CDC’s 2015/2016 FluSight Collaborative Comparison. Among the fourteen submissions that season, this system was ranked by CDC as the most accurate.

]]>
<![CDATA[Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape]]> https://www.researchpad.co/article/5af106d0463d7e336df9e544

Characterising the spatio-temporal dynamics of pathogens in natura is key to ensuring their efficient prevention and control. However, it is notoriously difficult to estimate dispersal parameters at scales that are relevant to real epidemics. Epidemiological surveys can provide informative data, but parameter estimation can be hampered when the timing of the epidemiological events is uncertain, and in the presence of interactions between disease spread, surveillance, and control. Further complications arise from imperfect detection of disease and from the huge number of data on individual hosts arising from landscape-level surveys. Here, we present a Bayesian framework that overcomes these barriers by integrating over associated uncertainties in a model explicitly combining the processes of disease dispersal, surveillance and control. Using a novel computationally efficient approach to account for patch geometry, we demonstrate that disease dispersal distances can be estimated accurately in a patchy (i.e. fragmented) landscape when disease control is ongoing. Applying this model to data for an aphid-borne virus (Plum pox virus) surveyed for 15 years in 605 orchards, we obtain the first estimate of the distribution of flight distances of infectious aphids at the landscape scale. About 50% of aphid flights terminate beyond 90 m, which implies that most infectious aphids leaving a tree land outside the bounds of a 1-ha orchard. Moreover, long-distance flights are not rare–10% of flights exceed 1 km. By their impact on our quantitative understanding of winged aphid dispersal, these results can inform the design of management strategies for plant viruses, which are mainly aphid-borne.

]]>
<![CDATA[Dengue and the World Football Cup: A Matter of Timing]]> https://www.researchpad.co/article/5989daddab0ee8fa60bba7a8 ]]>