Characterizing measles transmission in India: a dynamic modeling study using verbal autopsy data.
Ontology highlight
ABSTRACT:
SUBMITTER: Verguet S
PROVIDER: S-EPMC5550950 | biostudies-other | 2017 Aug
REPOSITORIES: biostudies-other
Similar Datasets
Project description:BackgroundThe most common method for determining cause of death is certification by physicians based either on available medical records, or where such data are not available, through verbal autopsy (VA). The physician-certification approach is costly and inconvenient; however, recent work shows the potential of a computer-based probabilistic model (InterVA) to interpret verbal autopsy data in a more convenient, consistent, and rapid way. In this study we validate separately both physician-certified verbal autopsy (PCVA) and the InterVA probabilistic model against hospital cause of death (HCOD) in adults dying in a district hospital on the coast of Kenya.MethodsBetween March 2007 and June 2010, VA interviews were conducted for 145 adult deaths that occurred at Kilifi District Hospital. The VA data were reviewed by a physician and the cause of death established. A range of indicators (including age, gender, physical signs and symptoms, pregnancy status, medical history, and the circumstances of death) from the VA forms were included in the InterVA for interpretation. Cause-specific mortality fractions (CSMF), Cohen's kappa (κ) statistic, receiver operating characteristic (ROC) curves, sensitivity, specificity, and positive predictive values were applied to compare agreement between PCVA, InterVA, and HCOD.ResultsHCOD, InterVA, and PCVA yielded the same top five underlying causes of adult deaths. The InterVA overestimated tuberculosis as a cause of death compared to the HCOD. On the other hand, PCVA overestimated diabetes. Overall, CSMF for the five major cause groups by the InterVA, PCVA, and HCOD were 70%, 65%, and 60%, respectively. PCVA versus HCOD yielded a higher kappa value (κ = 0.52, 95% confidence interval [CI]: 0.48, 0.54) than the InterVA versus HCOD which yielded a kappa (κ) value of 0.32 (95% CI: 0.30, 0.38). Overall, (κ) agreement across the three methods was 0.41 (95% CI: 0.37, 0.48). The areas under the ROC curves were 0.82 for InterVA and 0.88 for PCVA. The observed sensitivities and specificities across the five major causes of death varied from 43% to 100% and 87% to 99%, respectively, for the InterVA/PCVA against the HCOD.ConclusionBoth the InterVA and PCVA compared well with the HCOD at a population level and determined the top five underlying causes of death in the rural community of Kilifi. We hope that our study, albeit small, provides new and useful data that will stimulate further definitive work on methods of interpreting VA data.
| S-EPMC3160942 | biostudies-literature
Project description:BackgroundRegistration of the fact of death is almost complete in the city of Chennai and not so in the rural Villupuram district in Tamilnadu, India. The cause of death is often inadequately recorded on the death certificate in developing countries like India. A special verbal autopsy (VA) study of 48,000 adult (aged >or= 25 yrs) deaths in the city of Chennai (urban) during 1995-97 and 32,000 in rural Villupuram during 1997-98 was conducted to arrive at the probable underlying cause of death to estimate cause specific mortality.MethodsA ten day training on writing verbal autopsy (VA) report for adult deaths was given to non-medical graduates with at least 15 years of formal education. They interviewed surviving spouse/close associates of the deceased to write a verbal autopsy report in local language (Tamil) on the complaints, symptoms, signs, duration and treatment details of illness prior to death. Each report was reviewed centrally by two physicians independently. Random re-interviewing of 5% of the VA reports was done to check the reliability and reproducibility of the VA report. The validity of VA diagnosis was assessed only for cancer deaths.ResultsVerbal autopsy reduced the proportion of deaths attributed to unspecified and unknown causes from 54% to 23% (p < 0.0001) in urban and from 41% to 26% (p < 0.0001) in rural areas in Tamilnadu for adult deaths (>or= 25). The sensitivity of VA to identify cancer was 95% in the age group 25-69.ConclusionA ten day training programme to write verbal autopsy report with adequate feed back sessions and random sampling of 5% of the verbal autopsy reports for re-interview worked very well in Tamilnadu, to arrive at the probable underlying cause of death reliably for deaths in early adult life or middle age (25-69 years) and less reliably for older ages (70+). Thus VA is practicable for deaths in early adult life or middle age and is of more limited value in old age.
| S-EPMC535898 | biostudies-literature
Project description:BackgroundVerbal Autopsy (VA) is widely viewed as the only immediate strategy for registering cause of death in much of Africa and Asia, where routine physician certification of deaths is not widely practiced. VA involves a lay interview with family or friends after a death, to record essential details of the circumstances. These data can then be processed automatically to arrive at standardized cause of death information.MethodsThe Population Health Metrics Research Consortium (PHMRC) undertook a study at six tertiary hospitals in low- and middle-income countries which documented over 12,000 deaths clinically and subsequently undertook VA interviews. This dataset, now in the public domain, was compared with the WHO 2012 VA standard and the InterVA-4 interpretative model.ResultsThe PHMRC data covered 70% of the WHO 2012 VA input indicators, and categorized cause of death according to PHMRC definitions. After eliminating some problematic or incomplete records, 11,984 VAs were compared. Some of the PHMRC cause definitions, such as 'preterm delivery', differed substantially from the International Classification of Diseases, version 10 equivalent. There were some appreciable inconsistencies between the hospital and VA data, including 20% of the hospital maternal deaths being described as non-pregnant in the VA data. A high proportion of VA cases (66%) reported respiratory symptoms, but only 18% of assigned hospital causes were respiratory-related. Despite these issues, the concordance correlation coefficient between hospital and InterVA-4 cause of death categories was 0.61.ConclusionsThe PHMRC dataset is a valuable reference source for VA methods, but has to be interpreted with care. Inherently inconsistent cases should not be included when using these data to build other VA models. Conversely, models built from these data should be independently evaluated. It is important to distinguish between the internal and external validity of VA models. The effects of using tertiary hospital data, rather than the more usual application of VA to all-community deaths, are hard to evaluate. However, it would still be of value for VA method development to have further studies of population-based post-mortem examinations.
| S-EPMC3912496 | biostudies-literature
Project description:ObjectiveThis paper aims to determine the cost of establishing and sustaining a verbal-autopsy based mortality surveillance system in rural India.Materials and methodsDeaths occurring in 45 villages (population 185,629) were documented over a 4-year period from 2003-2007 by 45 non-physician healthcare workers (NPHWs) trained in data collection using a verbal autopsy tool. Causes of death were assigned by 2 physicians for the first year and by one physician for the subsequent years. Costs were calculated for training of interviewers and physicians, data collection, verbal autopsy analysis, project management and infrastructure. Costs were divided by the number of deaths and the population covered in the year.ResultsVerbal-autopsies were completed for 96.7% (5786) of all deaths (5895) recorded. The annual cost in year 1 was INR 1,133,491 (USD 24,943) and the total cost per death was INR 757 (USD 16.66). These costs included training of NPHWs and physician reviewers Rs 67,025 (USD 1474), data collection INR 248,400 (USD 5466), dual physician review for cause of death assignment INR 375,000 (USD 8252), and project management INR 341,724 (USD 7520). The average annual cost to run the system each year was INR 822,717 (USD18104) and the cost per death was INR 549 (USD 12) for the next 3 years. Costs were reduced by using single physician review and shortened re-training sessions. The annual cost of running a surveillance system was INR 900,410 (USD 19814).DiscussionThis study provides detailed empirical evidence of the costs involved in running a mortality surveillance site using verbal-autopsy.
| S-EPMC4425407 | biostudies-literature
Project description:IntroductionEach year, more than 10 million children younger than five years of age die. The large majority of these deaths occur in the developing world. The verbal autopsy (VA) is a tool designed to ascertain cause of death in such settings. While VA has been validated against hospital diagnosed cause of death, there has been no research conducted to better understand the factors that may influence individual physicians in determining cause of death from VA.Methodology/principal findingsThis study uses data from over 27,000 neonatal and childhood deaths from The Million Death Study in which 6.3 million people in India were monitored for vital status between 1998 and 2003. The main outcome variable was physician agreement or disagreement of category of death and the variables were assessed for association using the kappa statistic, univariate and multivariate logistic regression using a conceptual hierarchical model, and a sensitivity and specificity analysis using the final VA category of mortality as the gold standard. The main variables found to be significantly associated with increased physician agreement included older ages and male gender of the deceased. When taking into account confounding factors in the multivariate analysis, we did not find consistent significant differences in physician agreement based on the death being in a rural or urban area, at home or in a health care facility, registered or not, or the respondent's gender, religion, relationship to the deceased, or whether or not the respondent lived with the deceased.Conclusions/significanceFactors influencing physician agreement/disagreement to the greatest degree are the gender and age of the deceased; specifically, physicians tend to be less likely to agree on a common category of death in female children and in younger ages, particularly neonates. Additional training of physician reviewers and continued adaptation of the VA itself, with a focus on gender and age of the deceased, may be useful in increasing rates of physician agreement in these groups.
| S-EPMC2833201 | biostudies-literature
Project description:ObjectivesThis study was conducted to evaluate the performance of World Health Organisation (WHO) verbal autopsy tool in determining major causes of neonatal deaths.MethodsFrom a tertiary care hospital and a government multispecialty hospital, the attending paediatricians ascertained a clinical cause of death for 371 neonatal deaths. Trained field workers conducted verbal autopsy (VA) interviews. Two independent paediatricians, who had no access to the clinical information, assigned cause of death as per verbal autopsy. Analysis was based on 313 cases in which both clinical diagnosis and VA diagnosis was obtained.FindingsAs per the clinical diagnosis, four most common causes of neonatal deaths were sepsis (29.1%), preterm birth (27.8%), birth asphyxia (27.2%), and congenital anomalies (11.5%). Cause specific mortality fractions by VA diagnosis were statistically similar to those obtained by clinical diagnosis except for birth asphyxia (16.3%). Diagnostic accuracy of verbal autopsy diagnosis against clinical diagnosis ranged from 78% to 92% in ascertaining different underlying causes of death. Area under the Receiver-Operator Characteristics curve (95% confidence interval) was 0.75 (0.69-0.80) for sepsis, 0.74 (0.68-0.80) for preterm birth, 0.73 (0.65-0.82) for congenital anomaly and 0.70 (0.64-0.75) for birth asphyxia. Kappa for all four causes was moderate (0.46-0.55).InterpretationThe WHO verbal autopsy tools can provide reasonably good estimates of predominant causes of neonatal deaths in countries where neonatal mortality is high. Caution is required to interpret cause specific mortality fraction (CSMF) for birth asphyxia by VA because it is likely to be an underestimate.
| S-EPMC3555991 | biostudies-literature
Project description:Of patients with multidrug-resistant tuberculosis (MDR TB), <50% complete treatment. Most treatment failures for patients with MDR TB are due to death during TB treatment. We sought to determine the proportion of deaths during MDR TB treatment attributable to TB itself. We used a structured verbal autopsy tool to interview family members of patients who died during MDR TB treatment in India during January-December 2016. A committee triangulated information from verbal autopsy, death certificate, or other medical records available with the family members to ascertain the underlying cause of death. For 66% of patient deaths (47/71), TB was the underlying cause of death. We assigned TB as the underlying cause of death for an additional 6 patients who died of suicide and 2 of pulmonary embolism. Deaths during TB treatment signify program failure; accurately determining the cause of death is the first step to designing appropriate, timely interventions to prevent premature deaths.
| S-EPMC5823351 | biostudies-literature
Project description:In low-resource settings where vital registration of death is not routine it is often of critical interest to determine and study the cause of death (COD) for individuals and the cause-specific mortality fraction (CSMF) for populations. Post-mortem autopsies, considered the gold standard for COD assignment, are often difficult or impossible to implement due to deaths occurring outside the hospital, expense, and/or cultural norms. For this reason, Verbal Autopsies (VAs) are commonly conducted, consisting of a questionnaire administered to next of kin recording demographic information, known medical conditions, symptoms, and other factors for the decedent. This article proposes a novel class of hierarchical factor regression models that avoid restrictive assumptions of standard methods, allow both the mean and covariance to vary with COD category, and can include covariate information on the decedent, region, or events surrounding death. Taking a Bayesian approach to inference, this work develops an MCMC algorithm and validates the FActor Regression for Verbal Autopsy (FARVA) model in simulation experiments. An application of FARVA to real VA data shows improved goodness-of-fit and better predictive performance in inferring COD and CSMF over competing methods. Code and a user manual are made available at https://github.com/kelrenmor/farva.
| S-EPMC8320757 | biostudies-literature
Project description:BackgroundThe World Health Organization (WHO) aims to reduce tuberculosis (TB) deaths by 95% by 2035; tracking progress requires accurate measurement of TB mortality. International Classification of Diseases (ICD) codes do not differentiate between HIV-associated TB and HIV more generally. Verbal autopsy (VA) is used to estimate cause of death (CoD) patterns but has mostly been validated against a suboptimal gold standard for HIV and TB. This study, conducted among HIV-positive adults, aimed to estimate the accuracy of VA in ascertaining TB and HIV CoD when compared to a reference standard derived from a variety of clinical sources including, in some, minimally-invasive autopsy (MIA).Methods and findingsDecedents were enrolled into a trial of empirical TB treatment or a cohort exploring diagnostic algorithms for TB in South Africa. The WHO 2012 instrument was used; VA CoD were assigned using physician-certified VA (PCVA), InterVA-4, and SmartVA-Analyze. Reference CoD were assigned using MIA, research, and health facility data, as available. 259 VAs were completed: 147 (57%) decedents were female; median age was 39 (interquartile range [IQR] 33-47) years and CD4 count 51 (IQR 22-102) cells/μL. Compared to reference CoD that included MIA (n = 34), VA underestimated mortality due to HIV/AIDS (94% reference, 74% PCVA, 47% InterVA-4, and 41% SmartVA-Analyze; chance-corrected concordance [CCC] 0.71, 0.42, and 0.31, respectively) and HIV-associated TB (41% reference, 32% PCVA; CCC 0.23). For individual decedents, all VA methods agreed poorly with reference CoD that did not include MIA (n = 259; overall CCC 0.14, 0.06, and 0.15 for PCVA, InterVA-4, and SmartVA-Analyze); agreement was better at population level (cause-specific mortality fraction accuracy 0.78, 0.61, and 0.57, for the three methods, respectively).ConclusionsCurrent VA methods underestimate mortality due to HIV-associated TB. ICD and VA methods need modifications that allow for more specific evaluation of HIV-related deaths and direct estimation of mortality due to HIV-associated TB.
| S-EPMC5363862 | biostudies-literature
Project description:OBJECTIVE:To estimate and evaluate the cause-of-death structure and disease-specific mortality rates in a rural area of The Gambia as determined using the InterVA-4 model. DESIGN:Deaths and person-years of observation were determined by age group for the population of the Farafenni Health and Demographic Surveillance area from January 1998 to December 2007. Causes of death were determined by verbal autopsy (VA) using the InterVA-4 model and ICD-10 disease classification. Assigned causes of death were classified into six broad groups: infectious and parasitic diseases; cancers; other non-communicable diseases; neonatal; maternal; and external causes. Poisson regression was used to estimate age and disease-specific mortality rates, and likelihood ratio tests were used to determine statistical significance. RESULTS:A total of 3,203 deaths were recorded and VA administered for 2,275 (71%). All-age mortality declined from 15 per 1,000 person-years in 1998-2001 to 8 per 1,000 person-years in 2005-2007. Children aged 1-4 years registered the most marked (74%) decline from 27 to 7 per 1,000 person-years. Communicable diseases accounted for half (49.9%) of the deaths in all age groups, dominated by acute respiratory infections (ARI) (13.7%), malaria (12.9%) and pulmonary tuberculosis (10.2%). The leading causes of death among infants were ARI (5.59 per 1,000 person-years [95% CI: 4.38-7.15]) and malaria (4.11 per 1,000 person-years [95% CI: 3.09-5.47]). Mortality rates in children aged 1-4 years were 3.06 per 1,000 person-years (95% CI: 2.58-3.63) for malaria, and 1.05 per 1,000 person-years (95% CI: 0.79-1.41) for ARI. The HIV-related mortality rate in this age group was 1.17 per 1,000 person-years (95% CI: 0.89-1.54). Pulmonary tuberculosis and communicable diseases other than malaria, HIV/AIDS and ARI were the main killers of adults aged 15 years and over. Stroke-related mortality increased to become the leading cause of death among the elderly aged 60 years or more in 2005-2007. CONCLUSIONS:Mortality in the Farafenni HDSS area was dominated by communicable diseases. Malaria and ARI were the leading causes of death in the general population. In addition to these, diarrhoeal disease was a particularly important cause of death among children under 5 years of age, as was pulmonary tuberculosis among adults aged 15 years and above.
| S-EPMC4220164 | biostudies-literature