Developing a temperature-driven map of the basic reproductive number of the emerging tick vector of Lyme disease Ixodes scapularis in Canada. J Theor Biol. 2013; 319: 50–61. doi: 10.1016/j.jtbi.2012.11.014 PMID: 23206385

c A deterministic model of the Lyme disease vector, I. scapularis, was developed. c The model was used to estimate R 0 for I scapularis under different climatic conditions. c A map of R 0 was developed for I scapularis in Canada, where this tick is emerging. c Estimation of R 0 for I. scapularis will assist public health responses to emerging Lyme disease. a r t i c l e i n f o a b s t r a c t A mechanistic model of the tick vector of Lyme disease, Ixodes scapularis, was adapted to a deterministic structure. Using temperature normals smoothed by Fourier analysis to generate seasonal temperaturedriven development rates and host biting rates, and a next generation matrix approach, the model was used to obtain values for the basic reproduction number (R 0 ) for I. scapularis at locations in southern Canada where the tick is established and emerging. The R 0 at Long Point, Point Pelee and Chatham sites where I. scapularis are established, was estimated at 1.5, 3.19 and 3.65, respectively. The threshold temperature conditions for tick population survival (R 0 ¼ 1) were shown to be the same as those identified using the mechanistic model (2800-3100 cumulative annual degree days 4 0 1C), and a map of R 0 for I. scapularis, the first such map for an arthropod vector, was drawn for Canada east of the Rocky Mountains. This map supports current risk assessments for Lyme disease risk emergence in Canada. Sensitivity analysis identified host abundance, tick development rates and summer temperatures as highly influential variables in the model, which is consistent with our current knowledge of the biology of this tick. The development of a deterministic model for I. scapularis that is capable of providing values for R 0 is a key step in our evolving ability to develop tools for assessment of Lyme disease risk emergence and for development of public health policies on surveillance, prevention and control

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Additional file 2: of Environmental and social determinants of population vulnerability to Zika virus emergence at the local scale

Methodology. 2.1 Data cleaning. Table S2.1.a. Number of observations and percentage of missing data. Table S2.1.b. Model parameter estimates, standard error and t-value. Table S2.1.c. Model parameter estimates, standard error and t-value. Table S2.1.d. Correlation between existing and imputed data. 2.2 Explanatory variables. 2.2.1 Environmental. 2.2.2 Social. 2.2.3 Neighbourhood disease intensity. Table S2.2.3.a. Summary statistics for explanatory variables. 2.3 Model formulation for a binary longitudinal response variable. 2.3.1 Logistic regression. 2.3.2 Accelerated failure time model. 2.4 References. (DOCX 56 kb

Evidence for increasing densities and geographic ranges of tick species of public health significance other than Ixodes scapularis in Québec, Canada.

Climate change is driving emergence and establishment of Ixodes scapularis, the main vector of Lyme disease in Québec, Canada. As for the black-legged tick, I. scapularis Say, global warming may also favor northward expansion of other species of medically important ticks. The aims of this study were to determine (1) current diversity and abundance of ticks of public health significance other than I. scapularis, (2) sex and age of the human population bitten by these ticks (3), and the seasonal and geographic pattern of their occurrence. From 2007 to 2015, twelve tick species other than I. scapularis were submitted in the Québec passive tick surveillance program. Of these 9243 ticks, 91.2% were Ixodes cookei, 4.1% were Dermacentor variabilis, 4.0% were Rhipicephalus sanguineus and 0.7% were Amblyomma americanum. The combined annual proportion of submitted I. cookei, D. variabilis, R. sanguineus and A. americanum ticks in passive surveillance rose from 6.1% in 2007 to 16.0% in 2015 and an annual growing trend was observed for each tick species. The number of municipalities where I. cookei ticks were acquired rose from 104 to 197 during the same period. Of the 862 people bitten by these ticks, 43.3% were I. cookei ticks removed from children aged < 10 years. These findings demonstrate the need for surveillance of all the tick species of medical importance in Québec, particularly because climate may increase their abundance and geographic ranges, increasing the risk to the public of the diseases they transmit

HIV-1 phylodynamic analysis among people who inject drugs in Pakistan correlates with trends in illicit opioid trade.

Pakistan is considered by the World Health Organization to currently have a "concentrated" HIV-1 epidemic due to a rapid rise in infections among people who inject drugs (PWID). Prevalence among the country's nearly 105,000 PWID is estimated to be 37.8% but has been shown to be higher in several large urban centers. A lack of public health resources, the common use of professional injectors and unsafe injection practices are believed to have fueled the outbreak. Here we evaluate the molecular characteristics of HIV-1 sequences (n = 290) from PWID in several Pakistani cities to examine transmission dynamics and the association between rates of HIV-1 transmission with regards to regional trends in opioid trafficking. Tip-to-tip (patristic) distance based phylogenetic cluster inferences and BEAST2 Bayesian phylodynamic analyses of time-stamped data were performed on HIV-1 pol sequences generated from dried blood spots collected from 1,453 PWID as part of a cross-sectional survey conducted in Pakistan during 2014/2015. Overall, subtype A1 strains were dominant (75.2%) followed by CRF02_AG (14.1%), recombinants/unassigned (7.2%), CRF35_AD (2.1%), G (1.0%) and C (0.3%). Nearly three quarters of the PWID HIV-1 sequences belonged to one of five distinct phylogenetic clusters. Just below half (44.4%) of individuals in the largest cluster (n = 118) did seek help injecting from professional injectors which was previously identified as a strong correlate of HIV-1 infection. Spikes in estimated HIV-1 effective population sizes coincided with increases in opium poppy cultivation in Afghanistan, Pakistan's western neighbor. Structured coalescent analysis was undertaken in order to investigate the spatial relationship of HIV-1 transmission among the various cities under study. In general terms, our analysis placed the city of Larkana at the center of the PWID HIV-1 epidemic in Pakistan which is consistent with previous epidemiological data

Different Ecological Niches for Ticks of Public Health Significance in Canada

<div><p>Tick-borne diseases are a growing public health concern as their incidence and range have increased in recent decades. Lyme disease is an emerging infectious disease in Canada due to northward expansion of the geographic range of <i>Ixodes scapularis</i>, the principal tick vector for the Lyme disease agent <i>Borrelia burgdorferi</i>, into central and eastern Canada. In this study the geographical distributions of Ixodid ticks, including <i>I</i>. <i>scapularis</i>, and environmental factors associated with their occurrence were investigated in New Brunswick, Canada, where few <i>I</i>. <i>scapularis</i> populations have been found to date. Density of host-seeking ticks was evaluated by drag sampling of woodland habitats in a total of 159 sites. <i>Ixodes scapularis</i> ticks (<i>n</i> = 5) were found on four sites, <i>Ixodes muris</i> (<i>n</i> = 1) on one site and <i>Haemaphysalis leporispalustris</i> (<i>n</i> = 243) on 41 sites. One of four adult <i>I</i>. <i>scapularis</i> ticks collected was PCR-positive for <i>B</i>. <i>burgdorferi</i>. No environmental variables were significantly associated with the presence of <i>I</i>. <i>scapularis</i> although comparisons with surveillance data in neighbouring provinces (Québec and Nova Scotia) suggested that temperature conditions may be too cold for <i>I</i>. <i>scapularis</i> (< 2800 annual degree days above 0°C [DD > 0°C]) across much of New Brunswick. In contrast, the presence of <i>H</i>. <i>leporispalustris</i>, which is a competent vector of tularaemia, was significantly (<i>P</i> < 0.05) associated with specific ranges of mean DD > 0°C, mean annual precipitation, percentage of clay in site soil, elevation and season in a multivariable logistic regression model. With the exception of some localized areas, temperature conditions and deer density may be too low for the establishment of <i>I</i>. <i>scapularis</i> and Lyme disease risk areas in New Brunswick, while environmental conditions were suitable for <i>H</i>. <i>leporispalustris</i> at many sites. These findings indicate differing ecological niches for two tick species of public health significance.</p></div

Final multivariable logistic regression model for predicting occurrence of <i>H</i>. <i>leporispalustris</i>.

<p>Hosmer and Lemeshow goodness-of-fit test χ² = 6.01, d.f. = 7, <i>P</i> = 0.54, AUC = 0.88.</p><p>Final multivariable logistic regression model for predicting occurrence of <i>H</i>. <i>leporispalustris</i>.</p

Detection of municipalities at-risk of Lyme disease using passive surveillance of Ixodes scapularis as an early signal: A province-specific indicator in Canada.

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

Distribution of sampling sites and tick-positive sites.

<p>Sites of occurrence of <i>I</i>. <i>scapularis</i> (green), <i>H</i>. <i>leporispalustris</i> (blue), <i>I</i>. <i>scapularis</i> and <i>H</i>. <i>leporispalustris</i> (pink) and <i>I</i>. <i>muris</i> and <i>H</i>. <i>leporispalustris</i> (yellow) are shown. The black circle indicates a significant cluster of sites where <i>H</i>. <i>leporispalustris</i> ticks were found. The two sites where <i>I</i>. <i>scapularis</i> were found in previous field studies are identified by red stars. The map was created in ArcGIS Version 10.2 (ESRI. Redlands, CA).</p

Descriptive statistics of explanatory variables and results from univariate analyses for occurrence of <i>I</i>. <i>scapularis</i> and <i>H</i>. <i>leporispalustris</i> at the 159 field sites visited during the study.

<p>^a Dominant tree species categorized as 0: woodlands of moist but well-drained fertile lowland soils—climax forest/closed canopy/shade tolerant, 1: woodlands of well drained sandy soils, 2: woodlands of wetlands/swamp or 3: woodlands comprising shade intolerant and/or pioneer species indicating disturbed woodlands</p><p>^b No tree species identified for 2 sites</p><p>^c No solution is provided because of degenerate estimates</p><p>^d Mean elevation inside a buffer zone with a radius of 200 m defined around the geographic position of each site.</p><p>^e Mean annual degree days above 0°C from 2009 to 2014.</p><p>^f Mean annual <i>R</i>₀ from 2009 to 2014.</p><p>^g Number of years where the annual degree days above 0°C was 2800 or higher from 2009 to 2014.</p><p>^h Mean annual precipitation data from 2009 to 2013.</p><p>ⁱ White-tailed deer population estimates for each wildlife management zone</p><p>^j Season when site was visited with ‘spring’ being May and June, ‘summer’ being July and August and ‘autumn’ being September.</p><p>Descriptive statistics of explanatory variables and results from univariate analyses for occurrence of <i>I</i>. <i>scapularis</i> and <i>H</i>. <i>leporispalustris</i> at the 159 field sites visited during the study.</p