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bioRxiv2018

Exploring how generation intervals link strength and speed of epidemics

Infectious-disease outbreaks are often characterized by the reproductive number and exponential rate of growth r. provides information about out-break control and predicted final size. Directly estimating is difficult, while r can often be estimated from incidence data. These quantities are linked by the generation interval - the time between when an individual is infected by an infector, and when that infector was infected. It is often infeasible to ob-tain the exact shape of a generation-interval distribution, and to understand how this shape affects estimates of . We show that estimating generation interval mean and variance provides insight into the relationship between and r. We use examples based on Ebola, rabies and measles to explore approximations based on gamma-distributed generation intervals, and find that use of these simple approximations are often sufficient to capture the r- relationship and provide robust estimates of .

epidemiology↗

bioRxiv2018

A direct comparison of four high risk human papilloma virus tests versus the cobas test for detecting cervical intraepithelial neoplasia and cervical cancer

This study is to evaluate performances and genotyping capabilities of four human papilloma virus (HR-HPV) tests based on real-time polymerase chain reaction (PCR) technology platforms compared with the cobas test. Discordant results were further analyzed using INNO-LiPA HPV genotyping test, the gold standard laboratory test to determine presence and type of HPV infection. Over 200 samples from Hospital patients were collected and analyzed using five HR-HPV tests. Women with positive test results were referred directly to colposcopy. If a positive result was returned, biopsies were administered for pathological classification. Clinical performances and genotyping capabilities between the four HR-HPV and cobas tests were compared and contrasted. High levels of agreement were observed, though all HR-HPV tests presented discrepancies compared with the cobas test. Cervical intraepithelial neoplasia Grade 2 or higher lesions (CIN2+) was set as the threshold, and all five tests performed with equally high sensitivity. Lower levels of specificity were observed across all five tests. Results suggest the four HR-HPV tests analyzed are as effective as the cobas test in genotyping capacities and diagnosing CIN. Therefore, these test kits should be used for HPV screening, especially in developing nations because they are cost effective and reliable. Minor discrepancies between tests are generally unavoidable though this may add complexity to the clinical decision-making process. As such, we recommend that efforts be made to standardize HPV genotyping tests as well as to optimize clinical sensitivity and specificity. Focusing on these issues will drive the development of HPV detection techniques, therefore save lives.

epidemiology↗

bioRxiv2018

Heuristic optimisation of the management strategy of a plant epidemic using sequential sensitivity analyses

O_LIOptimisation of management strategies of epidemics is often limited by constraints on experiments at large spatiotemporal scales. A promising approach consists in modelling the biological epidemic process and human interventions, which both impact disease spread. However, few methods enable the simultaneous optimisation of the numerous parameters of sophisticated control strategies. To do so, we propose a heuristic approach based on sequential use of sensitivity analysis. This work is motivated by sharka (caused by Plum pox virus), a vector-borne disease of prunus trees (especially apricot, peach and plum), and its management in orchards, mainly based on surveillance and tree removal.\nC_LIO_LIOur approach is based on three sensitivity analyses which respectively aim to: i) identify the key parameters of a spatiotemporal model simulating disease spread and control; ii) approach optimal values for the key parameters; iii) refine the optimisation.\nC_LIO_LIWe highlight the importance of carefully designing the removal procedure, and propose improved strategies with regard to an economic criterion accounting for both the cost of the different control measures and the benefit generated by productive trees.\nC_LIO_LIWe expect that our general approach will help policymakers to design sustainable and cost-effective strategies for the management of infectious diseases.\nC_LI

epidemiology↗

bioRxiv2018

Spatial gene-by-environment mapping for schizophrenia reveals locale of upbringing effects beyond urban-rural differences

Identification of mechanisms underlying the incidence of psychiatric disorders has been hampered by the difficulty in discovering highly-predictive environmental risk factors. For example, prior efforts have failed to establish environmental effects predicting geospatial clustering of schizophrenia incidence beyond urban-rural differences. Here, we employ a novel statistical framework for decomposing the geospatial risk for schizophrenia based on locale of upbringing (place of residence, ages 0-7 years) and its synergistic effects with genetic liabilities (polygenic risk for schizophrenia). We use this statistical framework to analyze unprecedented geolocation and genotyping data in a case-cohort study of n=24,028 subjects, drawn from the 1.47 million Danish persons born between 1981 and 2005. Using this framework we estimate the effects of upbringing locale (E) and gene-by-locale interactions (GxE). After controlling for potential confounding variables, upbringing at high-risk locales increases the risk for schizophrenia on average by 122%, while GxE modulates genetic risk for schizophrenia on average by 78%. Within the boundaries of Copenhagen (the largest and most densely populated city of Denmark) specific locales vary substantially in their E and GxE effects, with hazard ratios ranging from 0.26 to 9.26 for E and from 0.20 to 5.95 for GxE. This study provides insight into the degree of geospatial clustering of schizophrenia risk, and our novel analytic procedure provides a framework for decomposing variation in geospatial risk into G, E, and GxE components.

epidemiology↗

bioRxiv2018

Iodine status of children and Knowledge, Attitude, Practice of Iodised salt use in a remote community in Kerema district, Gulf province, Papua New Guinea

Iodine deficiency is the single most common cause of preventable mental impairment in communities with suboptimal iodine intake. Objective of the present study was to assess in more detail the iodine status and knowledge, attitudes and practice (KAP) relating to use of iodised salt in a remote community in Kotidanga area, Kerema district, Gulf province, Papua New Guinea. This prospective school and community based cross-sectional study was carried out in 2017. Simple random sampling was used to select schools. Multistage sampling was used to randomly select 291 children aged 6 to 12 years. Salt samples were collected for analysis from childrens households as well as a single urine sample of selected children. Salt iodine content and Urinary iodine concentration (UIC) were analysed. A semi-structured FAO questionnaire was used to assess KAP of three different community groups. Only 64% of households had salt on the day of data collection. Mean iodine content in household salt samples was 29.0 {+/-} 19.1 ppm. Iodine content was below 30.0 ppm in 54.8% and below 15.0 ppm in 31.2% of salt samples. Mean per capita discretionary intake of household salt was 2.9 {+/-} 1.8 g/day. Median UIC was 25.5 g/L and Interquartile Range was 15.0 to 47.5 g/L; 75.9% (221/291) of the children had UIC below 50.0 g/L, indicating moderate status iodine nutrition. Median UIC was 34.3g/L for children in households with salt, compared to 15.5 g/L for children in households without salt, indicating severe iodine deficiency in the latter group. The three community groups had limited knowledge about importance of using iodised salt and consequences of iodine deficiency on health outcomes. This remote community has limited access to adequately iodised household salt due to high cost, inappropriate packaging, storage and food preparation, resulting in iodine deficiency. Strategies to increase iodine intake are needed.

epidemiology↗

bioRxiv2018

Facility ownership and mortality among older adults residing in care homes

Background and ObjectivesNursing or care home characteristics may have a long-term impact on the residents mortality risks that has not been studied previously. The studys main objective was to assess the association between facility ownership and long-term, all-cause mortality. Research Design and Methods. We conducted a mortality follow-up study on a cohort of 611 nursing-home residents in the city Madrid, Spain, from their 1998-1999 baseline interviews up to September 2013. Residents lived in three types of facilities: public, subsidized and private, which were also sub-classified according to size (number of beds). Residents information was collected by interviewing the residents themselves, their caregivers and facility physicians. We used time-to-event multivariable models and inverse probability weighting to estimate standardized mortality risk differences.\n\nResultsAfter a 3728 person-year follow-up (median/maximum of 4.8/15.2 years), 519 participants had died. In fully-adjusted models, the standardized mortality risk difference at 5 years of follow-up between large-sized public facilities and medium-sized private facilities was 18.9% (95% confidence interval [CI]: -33.4 to -4.5%), with a median survival (95% CI) of 3.6 (0.5 to 6.8) additional years. The fully-standardized 5-year mortality difference (95% CIs) comparing for-profit private facilities with not-for-profit public institutions was -15.1% (-31.1% to 0.9%), and the fully-standardized median survival difference (95% CIs) was 3.0 (-1.7 to 7.7) years.\n\nDiscussion and ImplicationsThese results are highly compatible with an effect on the long-term mortality risk for residents due to factors associated with the ownership of their facilities.

epidemiology↗

bioRxiv2018

Telomeres as integrative markers of exposure to stress and adversity: A systematic review and meta-analysis

Telomeres have been proposed as a biomarker that integrates the impacts of different kinds of stress and adversity into a common currency. There has as yet been no overall comparison of how different classes of exposure associate with telomeres. We present a meta-analysis of the literature relating telomere measures to stresses and adversities in humans. The analysed dataset contained 543 associations from 138 studies involving 402,116 people. Overall, there was a weak association between telomere variables and exposures (greater adversity, shorter telomeres: r = -0.15, 95% CI - 0.18 to -0.11). This was not driven by any one type of exposure, since significant associations were found separately for physical diseases, environmental hazards, nutrition, psychiatric illness, smoking, physical activity, psychosocial and socioeconomic exposures. Methodological features of the studies did not explain any substantial proportion of the heterogeneity in association strength. There was, however, evidence consistent with publication bias, with unexpectedly strong negative associations reported by studies with small samples. Restricting analysis to sample sizes greater than 100 attenuated the overall association substantially (r = -0.09, 95% CI -0.13 to -0.05). Most studies were underpowered to detect the typical association magnitude. The literature is dominated by cross-sectional and correlational studies which makes causal interpretation problematic.

epidemiology↗

bioRxiv2018

Examining food intake and eating out of home patterns among university students

Eating out of home (OH) is increasingly popular in Balkan countries, among them Albania. To date there is only anecdotal evidence regarding nutritional quality of food consumed OH and the contribution to diet. This study assessed intake of foods and drinks consumed OH and at home (AH), as well as their nutritional contribution to the daily diet of university students in Tirana, Albania. Using a single day Automated Multiple Pass Method (AMPM) 24-hour dietary recall, we examined food intake among 289 students aged 18-24 years old, from three major universities in Albania. Contribution of eating OH to total energy intake per day, as well as to daily consumption of macronutrients by eating OH intensity tertiles were assessed. Foods and drinks consumed OH contributed 46.9% [95%CI:41.4-52.8] of total daily energy intake, representing, on average, 1169.1kcal [95%CI:1088.3-1249.9]. Sweets, soft drinks and meat products were more frequently consumed OH, while fruits and vegetables consumption was extremely low. The average quantity of sugars and dietary fats per day was higher AH, 76.9g [95%CI:70.3-83.5] and 173.7g [95%CI:163.2-184.2] respectively, compared to OH, 33.7g [95%CI:30.4-37.0] and 142.0g [95%CI:131.5-152.5] respectively. Dietary composition of AH intake was richer in sugars, total fats and proteins, while OH intake was richer in saturated fats. The overall diet appeared unhealthy, when nutrients were assessed as energy percentage against WHO proposed nutrient standards for sugar and saturated fats. Eating OH, even though was associated with lower fruits and vegetables intake, was not clearly associated with poor diet quality, as AH foods were also characterized by increased saturated fats and sugars intake as energy percentage. This study provides data on the first assessment of current dietary patterns of the studied population and can be used as baseline for designing and conducting future studies and interventions targeting malnutrition in all its forms.

epidemiology↗

bioRxiv2018

Barriers and incentives for conducting research amongst the Ophthalmologists in Sub- Sahara Africa

BackgroundResearch is a critical component amongst the strategies to improve health outcomes of any country. The role of research assumes greater importance in Africa as it carries a larger share of global burden of diseases, blindness and low vision. \"Vision 2020- the Right to Sight\" is a WHO-IAPB collaborated initiative aiming to eliminate preventable blindness by the year 2020. High quality research in eye care is imperative for the initiative to succeed, however, there is a dearth of research in eye care in sub Saharan Africa in general and specifically in the Eastern, Central and Southern African (ECSA) region. Identifying the barriers that hamper research in this region is an important step towards elimination of preventable blindness.\n\nMethodsA structured questionnaire using the SurveyMonkey program was sent to ophthalmologists in the ECSA region and South Africa through their respective regional professional bodies. Data was analyzed using the SPSS program version.\n\nResultsLack of funding, inadequate time and poor research knowledge were the main research barriers while ability to improve eye health care through research was the main incentive for conducting research.\n\nConclusionThe barriers mainly center on financial, human and administrative infrastructure and resources. In spite of the barriers, ophthalmologists in the study region are enthusiastic in research aiming to increase evidence based knowledge to improve eye health care in line with the goals of \"Vision 2020- the Right to Sight\" initiative.

epidemiology↗

bioRxiv2018

Epigenetic selection and the DNA methylation signatures of adverse prenatal environments

Maternal adversity is associated with long-term physiological changes in offspring. These are believed to be mediated through epigenetic mechanisms, including DNA methylation (DNAm). Changes in DNAm are often interpreted as damage or as part of plastic responses of the embryo. We propose that selection on stochastic DNAm differences generated during epigenetic reprogramming after fertilization contributes to the effects of maternal adversity on DNAm. Using a mathematical model of epigenetic reprogramming in the early embryo we predict that this \"epigenetic selection\" will generate a characteristic reduction in variance of DNAm at selected loci in populations exposed to maternal adversity. We tested this prediction using DNAm data from a human cohort prenatally exposed to the Dutch Famine and confirmed the reduction in DNAm variance, suggesting that epigenetic selection may have occurred. Epigenetic selection should be considered as a possible mechanism linking adversity in pregnancy to offspring health and may have implications for the likely effectiveness of intervention strategies.

epidemiology↗

bioRxiv2018

Coronary artery disease risk and lipidomic profiles are similar in familial and population-ascertained hyperlipidemias

Aims: To characterize and compare coronary artery disease (CAD) risk and detailed lipidomic profiles of individuals with familial and population-ascertained hyperlipidemias.\n\nMethods and Results: We determined incident CAD risk for 760 members of 66 hyperlipidemic families ([≥] 2 first degree relatives with the same hyperlipidemia) and 19,644 Finnish FINRISK population study participants. We also quantified 151 lipid species in plasma or serum samples from 550 members of 73 hyperlipidemic pedigrees and 897 FINRISK participants using a mass spectrometric shotgun lipidomics platform. Hyperlipidemias (LDL-C or triacylglycerides over 90th population percentile) were associated with increased CAD risk (high LDL-C: HR 1.74, 95% CI 1.48-2.04; high triacylglycerides: HR 1.38, 95% CI 1.09-1.74) and the risk estimates were very similar between the family and population samples. High LDL-C was associated with altered levels of 105 lipid species in families (p-value range 0.033-7.3*10-20 at 5% false discovery rate) and 51 species in the population samples (p-value range 0.017-6.8*10-21). Hypertriglyceridemia was associated with altered levels of 117 lipid species in families (p-value range 0.035-1.8*10-49) and 119 species in the population sample (p-value range 0.038-2.3*10-56). The lipidomics profiles of hyperlipidemias were highly similar in families and population samples.\n\nConclusion: We identified distinct lipidomic profiles associated with high LDL-C and triacylglyceride levels. CAD risk, lipidomic profiles and genetic profiles are highly similar between familial and population-ascertained hyperlipidemias, providing evidence of similar and overlapping underlying mechanisms. Our results do not support different screening and treatment for such hyperlipidemias.

epidemiology↗

bioRxiv2018

Estimates for quality of life loss due to RSV

A number of vaccines against Respiratory Syncytial Virus (RSV) infection are approaching licensure. Deciding which RSV vaccine strategy, if any, to introduce, will partly depend on cost-effectiveness analyses, which compares the relative costs and health benefits of a potential vaccination programme. Health benefits are usually measured in Quality Adjusted Life Year (QALY) loss, however, there are no QALY loss estimates for RSV that have been determined using standardised instruments. Moreover, in children under the age of five years in whom severe RSV episodes predominantly occur, there are no appropriate standardised instruments to estimate QALY loss. We estimated the QALY loss due to RSV across all ages by developing a novel regression model which predicts the QALY loss without the use of standardised instruments. To do this, we conducted a surveillance study which targeted confirmed episodes in children under the age of five years (confirmed cases) and their household members who experienced symptoms of RSV during the same time (suspected cases.) All participants were asked to complete questions regarding their health during the infection, with the suspected cases aged 5-14 and 15+ years old additionally providing Health-Related Quality of Life (HR-QoL) loss estimates through completing EQ-5D-3L-Y and EQ-5D-3L instruments respectively. The questionnaire responses from the suspected cases were used to calibrate the regression model. The calibrated regression model then used other questionnaire responses to predict the HR-QoL loss without the use of EQ-5D instruments. The age-specific QALY loss was then calculated by multiplying the HR-QoL loss on the worst day predicted from the regression model, with estimates for the duration of infection from the questionnaires and a scaling factoring for disease severity. Our regression model for predicting HR-QoL loss estimates that for the worst day of infection, suspected RSV cases in persons five years and older who do and do not seek healthcare have an HR-QoL loss of 0{middle dot}616 (95% CI 0{middle dot}155-1{middle dot}371) and 0{middle dot}405 (95% CI 0{middle dot}111-1{middle dot}137) respectively. This leads to a QALY loss per RSV episode of 1{middle dot}950 x 10-3 (95% CI 0{middle dot}185 x 10-3 -9{middle dot}578 x 10-3) and 1{middle dot}543 x 10-3 (95% CI 0{middle dot}136 x 10-3 -6{middle dot}406 x 10-3) respectively. For confirmed cases in a child under the age of five years who sought healthcare, our model predicted a HR-QoL loss on the worst day of infection of 0{middle dot}820 (95% CI 0{middle dot}222-1{middle dot}450) resulting in a QALY loss per RSV episode of 3{middle dot}823 x 10-3 (95% CI 0{middle dot}492 x 10-3 -12{middle dot}766 x 10-3). Combing these results with previous estimates of RSV burden in the UK, we estimate the annual QALY loss of healthcare seeking RSV episodes as 1,199 for individuals aged five years and over and 1,441 for individuals under five years old. The QALY loss due to an RSV episode is less than the QALY loss due to an Influenza episode. These results have important implications for potential RSV vaccination programmes, which has so far focused on preventing infections in infants--where the highest reported disease burden lies. Future potential RSV vaccination programmes should also evaluate their impact on older children and adults, where there is a substantial but unsurveilled QALY loss.

epidemiology↗

bioRxiv2018

Prevalence and factors associated with Skilled Birth Attendants use among post-partum women in Arusha Tanzania

IntroductionDeath related to pregnancy complications and delivery remains a public health problem in developing countries including Tanzania where majority of women and newborns die each year due to preventable causes. Delivery with a skilled birth attendant (SBA) is an important intervention to avert maternal and newborn mortality. This study aimed to determine factors influencing skilled birth attendants use among postpartum women in Arusha city and Arumeru district in Arusha region.\n\nMethodsThis was a cross-sectional study which was conducted from April to July 2017. The study utilized secondary data from the parent study which was conducted in Arusha city and Arumeru district in Arusha region. The parent study aimed to assess knowledge of danger signs in obstetric complication, birth preparedness and utilization of skilled birth attendants among post-partum women in urban and rural Arusha region in Tanzania. Data analysis was performed using SPSS version 20. Chi square statistics was used to determine the association between a set of independent variables and utilization of skilled birth attendance in bivariate analysis. Odds ratios with 95% confidence interval for factors influencing skilled birth attendants use were estimated in a multivariable logistic regression models. A p-value of less than 0.05 was considered statistically significant.\n\nResultsA total of 1218 post-partum women were studied. Their mean age was 26.2 (SD 5.9) years. Of these, 1020 used skilled birth attendants during delivery; this corresponds to prevalence of 83.7%. Mothers education level, area of residence, distance from health facility, frequency of antenatal care and parity were significantly associated utilization of skilled birth attendants during delivery.\n\nConclusionThe prevalence of skilled birth attendants use among postpartum women is high in the studied population compared to the national level. Strategies to create community awareness on important of skilled birth attendants use will increase its uptake and my help to reduce both mother and child mortality.

epidemiology↗

bioRxiv2018

Structure and consistency of self-reported social contact networks in British secondary schools

Self-reported social mixing patterns are commonly used in mathematical models of infectious diseases. It is particularly important to quantify patterns for school-age children given their disproportionate role in transmission, but it remains unclear how the structure of such social interactions changes over time. By integrating data collection into a public engagement programme, we examined self-reported contact networks in year 7 groups in four UK secondary schools. We collected data from 460 unique participants across four rounds of data collection conducted between January and June 2015, with 7,315 identifiable contacts reported in total. Although individual-level contacts varied over the study period, we were able to obtain out-of-sample accuracies of more than 90% and F-scores of 0.49-0.84 when predicting the presence or absence of social contacts between specific individuals across rounds of data collection. Network properties such as clustering and number of communities were broadly consistent within schools between survey rounds, but varied significantly between schools. Networks were assortative according to gender, and to a lesser extent school class, with the estimated clustering coefficient larger among males in all surveyed co-educational schools. Our results demonstrate that it is feasible to collect longitudinal self-reported social contact data from school children and that key properties of these data are consistent between rounds of data collection.

epidemiology↗

bioRxiv2018

A dynamic power-law sexual network model of gonorrhoea outbreaks

Human networks of sexual contacts are dynamic by nature, with partnerships forming and breaking continuously over time. Sexual behaviours are also highly heterogeneous, so that the number of partners reported by individuals over a given period of time is typically distributed as a power-law. Both the dynamism and heterogeneity of sexual partnerships are likely to have an effect in the patterns of spread of sexually transmitted diseases. To represent these two fundamental properties of sexual networks, we developed a stochastic process of dynamic partnership formation and dissolution, which results in power-law numbers of partners over time. Model parameters can be set to produce realistic conditions in terms of the exponent of the power-law distribution, of the number of individuals without relationships and of the average duration of relationships. Using an outbreak of antibiotic resistant gonorrhoea amongst men have sex with men as a case study, we show that our realistic dynamic network exhibits different properties compared to the frequently used static networks or homogeneous mixing models. We also consider an approximation to our dynamic network model in terms of a much simpler branching process. We estimate the parameters of the generation time distribution and offspring distribution which can be used for example in the context of outbreak reconstruction based on genomic data. Finally, we investigate the impact of a range of interventions against gonorrhoea, including increased condom use, more frequent screening and immunisation, concluding that the latter shows great promise to reduce the burden of gonorrhoea, even if the vaccine was only partially effective or applied to only a random subset of the population.

epidemiology↗

bioRxiv2018

The Roles of Neighborhood Composition and Autism Prevalence on Vaccination Exemption Pockets: A Population-wide Study

The number of children entering schools without mandated vaccinations has increased in high-income countries due to the rise of nonmedical exemptions from school vaccination requirements. Herd immunity is threatened when unvaccinated children are concentrated in spatial pockets. It is often assumed that these exemption clusters are merely the result of population composition. On the other hand, despite the role of vaccine-autism controversy to the current wave of anti-vaccine movement, we do not know if exemption clusters are associated with local autism rates. Our spatial analysis of California shows that while racial/ethnic composition is associated with the locations of large exemption pockets, other sociodemographic factors and access to health care resources have limited geographical span. We decouple the race/ethnicity effect from that of unobserved socioeconomic status by examining families in poverty. Using unique address-level data on the locations of the majority of children with an autism diagnosis, we show that the prevalence of autism is not associated with the locations of large pockets of vaccination exemptions. In addition, we find charter schools in most exemption clusters; potential spillovers from charter schools to neighboring public schools are evaluated. Exemption pockets are not merely the result of population composition and community-level interventions are needed to maintain herd immunity.\n\nHighlightsO_LIAutism prevalence rates are not associated with the locations of large exemption pockets.\nC_LIO_LIThe average exemption rate in charter schools (7.5%) was higher than private schools.\nC_LIO_LIProportion non-Hispanic white has the strongest association with large exemption clusters.\nC_LIO_LIPopulation composition cannot fully explain the exemption clusters.\nC_LI

epidemiology↗

bioRxiv2018

Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis

Background Zika virus (ZIKV) emerged in Latin America & the Caribbean (LAC) region in 2013, and has had serious implications for population health in the region. In 2016, the World Health Organization declared the ZIKV outbreak a Public Health Emergency of International Concern following a cluster of associated neurological disorders and neonatal malformations. In 2017, Zika cases declined, but future incidence in LAC remains uncertain due to gaps in our understanding, considerable variation in surveillance and a lack of a comprehensive collation of data from affected countries.\n\nMethods Our analysis combines information on confirmed and suspected Zika cases across LAC countries and a spatio-temporal dynamic transmission model for ZIKV infection to determine key transmission parameters and projected incidence in 91 major cities within 35 countries. Seasonality was determined by spatio-temporal estimates of Aedes aegypti vector capacity. We used country and state-level data from 2015 to mid-2017 to infer key model parameters, country-specific disease reporting rates, and the 2018 projected incidence. A 10-fold cross-validation approach was used to validate parameter estimates to out-of-sample epidemic trajectories.\n\nResults There was limited transmission in 2015, but in 2016 and 2017 there was sufficient opportunity for wide-spread ZIKV transmission in most cities, resulting in the depletion of susceptible individuals. We predict that the highest number of cases in 2018 within some Brazilian States (Sao Paulo and Rio de Janeiro), Colombia and French Guiana, but the estimated number of cases were no more than a few hundred. Model estimates of the timing of the peak in incidence were correlated (p<0.05) with the reported peak in incidence. The reporting rate varied across countries, with lower reporting rates for those with only confirmed cases compared to those who reported both confirmed and suspected cases.\n\nConclusions The findings suggest that the ZIKV epidemic is by and large over, with incidence projected to be low in most cities in LAC in 2018. Local low levels of transmission are probable but the estimated rate of infection suggests that most cities have a population with high levels of herd immunity.

epidemiology↗

bioRxiv2018

Are you suppressed? Viral load test coverage for people living with HIV in Mutare District, Manicaland Province, Zimbabwe, 2015-2017

BackgroundThe third 90-90-90 UNAIDS goal require that 90% of people living with HIV (PLHIV) on antiretroviral treatment (ART) achieve viral load (VL) suppression. This study assessed the proportion of VL suppression and related factors among PLHIV on 1st and 2nd line ART in Mutare District, Manicaland Province, Zimbabwe between 2015-2017.\n\nMethodsA retrospective study using routine HIV programme data from the electronic monitoring system for nine health facilities in Mutare District. VL suppression was defined as < 1,000 copies/ml.\n\nResultsOf 16,590 registered patients, 15,566(94%) were on first-line and 1024(6%) on second-line ART. Of those on 1st-line ART, 2856(18%) had a VL test result documented, while 367(36%) of 2nd-line ART patients had VL results. VL suppression rates were 86% among those on 1st-line and 45% in 2nd-line ART. Independent risk factors associated with VL non-suppression for those on 1st-line ART were age 0-9 years (adjusted relative risk, aRR=2.9; 95% confidence interval, CI=1.7-4.8;P<0.001), 10-19 years (aRR=2.2;95%CI=1.4-3.2,P<0.001) compared to those 20-49 years, concurrent TB (aRR=9; CI=3.0-29.7,P<0.001) and male gender (aRR=1.5,95%CI=1.1-2.1;P=0.02). There were no significant risk factors associated with VL non-suppression for 2nd-line ART patients.\n\nConclusionFor PLHIV on 1st-line ART in Mutare district, Manicaland, Zimbabwe, the frequency of reported VL results were only 18% among those on 1st-line ART, while the rate of VL suppression was near 90%. Viral Load testing coverage appears to be lagging behind current Zimbabwe goals and increased support is needed to improve the quality of HIV care and help reduce the threat of possible HIV drug resistance in the future.

epidemiology↗