Spatiotemporal analysis of West Nile virus infection in the human population based on arboviral detection testing of blood donations

doi:10.21203/rs.3.rs-4714418/v1

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Spatiotemporal analysis of West Nile virus infection in the human population based on arboviral detection testing of blood donations

https://doi.org/10.21203/rs.3.rs-4714418/v1

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West Nile virus (WNV) is a mosquito-borne zoonotic flavivirus which often causes asymptomatic infection in humans but may develop into a deadly neuroinvasive disease. In this study, we aimed to investigate variables potentially associated with human WNV infection using human and mosquito WNV surveillance and monitoring datasets, established over 20 years, from 2003 to 2022, across the province of Ontario, Canada. We combined climatic and geographic data, mosquito surveillance data (n=3,010 sites), blood donation arboviral detection testing data in the human population, and demographic and socio-economic data from Canadian population censuses. We hypothesized that spatio-temporal indices related to mosquito vector habitat and phenology, in addition to human demographic and socio-economic factors, were associated with WNV infection in the human population. Our results show that habitat suitability of the main WNV vector in this region, Cx. pipiens/restuans (IRR = 2.0), and variables related to lower income (IRR = 2.8), and shelter infrastructure spending (IRR = 0.7), were key risk factors associated with WNV infection among blood donors from 2003 to 2022 across Ontario (R² = 0.67). These results may inform points of entry for practical intervention aimed at reducing risk of mosquito-borne pathogens in Canada.

Biological sciences/Ecology/Ecological epidemiology

Health sciences/Diseases/Infectious diseases/Viral infection

Human infections with West Nile virus (WNV; family Flaviviridae) are most frequently mild or asymptomatic. Symptomatic infections result in an illness referred to as ‘West Nile fever’, which, in rare cases, particularly in older age groups, may develop into severe and sometimes fatal neuroinvasive disease ¹. The virus, first introduced to North America in 1999, rapidly spread across the continent in the following years ^2,3, and is now considered an endemic mosquito-borne pathogen in much of North America ^4,5. In Canada, detection tests for WNV have been regularly conducted on most blood donations since 2003, to avoid transmission from donors to recipients ⁶. While the blood donor population isn’t absolutely synonymous with the general population, data from WNV detection tests on blood donations offer a representative snapshot of spatio-temporal variations in WNV infection risk in the human population⁷. Human case reporting in surveillance is also a useful source of information on WNV risk in North America ⁸, despite having some limitations, including underreporting due to asymptomatic infections, misdiagnoses, and uncertainty as to the precise size of the exposed population ^9,10. While such limitations may be avoided by using active pathogen surveillance data on in the human population ^11–13, data spanning a large area and timeframe are scarce.

Mosquito species of the genus Culex, such as Culex pipiens and Culex restuans, are recognized as important vectors maintaining the enzootic cycle of WNV among avian hosts in northeastern North America. Culex pipiens and Cx. restuans also occasionally feed on mammals, bridging transmission between birds and humans ^14–19. Aedes vexans is very common in northeastern North America, is competent for the transmission of WNV and is highly opportunistic in its blood feeding preferences, meaning they can also effectively bridge transmission between birds and humans ^20–23. Environmental factors that influence mosquito development and virus transmission are important for understanding the drivers of human WNV infection risk. Larval development time for Cx. pipiens and Cx. restuans mosquitoes is estimated to be 19 and 14 days on average, respectively, while their adult lifespan is approximately 30 and 27 days, respectively ²⁴. Development time for Ae. vexans is 10 days on average ²⁵, and lifespan is 20 days on average ²³. WNV infection can be detected using nucleic acid tests to detect viral RNA by polymerase chain reaction (PCR) during viremia from around Day 1 to Day 13 after bite by an infected mosquito, and using serological tests to detect IgM or IgG by enzyme-linked immunosorbent assay (or ELISA) from around Day 5 to 9 (respectively for IgM and IgG) after bite by an infected mosquito, for approximately 5 to 7 months on average (respectively for IgM and IgG) ²⁶. Exposure of humans, including blood donors, to infected mosquitoes depends on their abundance and infection prevalence. Mosquito abundance varies seasonally and from year-to-year according to longer term impacts of weather and climate affecting survival over winter and shorter-term effects of weather on mosquito reproduction and activity, and WNV replication in infected mosquitoes ^27–32. Inter-annual variations in cycles of transmission amongst avian reservoirs, and mosquitoes changing their behaviour to include mammals as sources of blood meals also impact seasonal and inter-annual variations ³³. Together, this means that weather over a period of weeks to months, combined with local environmental impacts on mosquito reproduction and WNV transmission, determine the risk of human infections, and of WNV outbreaks, each year.

Current effects of climate change and land use change in Canada and elsewhere may contribute to an increase in the risk of zoonotic diseases, including mosquito-borne pathogens, such as WNV ^4,34–40. Therefore, there is a pressing need for an enhanced understanding of the environmental hazard posed by WNV for public health. Comprehensive temporal and spatial databases of a large variety of climatic, geographic and ecological factors are needed to correctly characterize the distribution and dynamics of mosquito vector populations and mosquito-borne disease transmission. Additionally, certain demographic and socio-economic factors may contribute to both mosquito vector density and exposure to mosquito-borne disease risk ^41–47. Indeed, lower socio-economic status seem to be strongly associated with mosquito-borne disease risk, through variation in population density ⁴⁸, quality of household infrastructure ⁴⁴, and education, potentially associated with level of risk perception ⁴⁶. Occupation ⁴⁹, age and sex ⁵⁰ may also influence exposure to mosquitoes. Therefore, regularly updated population censuses offer invaluable information to combine with other data sources to identify modifiable risk factors and better target interventions to reduce mosquito-borne disease risk.

In this study, we aimed to investigate variables potentially associated with human WNV exposure and infection using a large data collection, established over 20 years, from 2003 to 2022, across most of the province of Ontario, Canada. We combined climatic data, geographic data, mosquito surveillance data, arbovirus testing data from human blood donations, and demographic and socio-economic data from Canadian population censuses. We hypothesized that a mixture of spatial and temporal variables, impacting mosquito habitat and phenology, and demographic and socio-economic variables, which are associated with increased mosquito habitat and also increased exposure to mosquitoes, are the main predictors of WNV infection in the human population.

Study area and duration

The study area in Ontario, Canada spanned more than 428,000 km² with a northern limit (latitude ~ 50–51° N) that matched the extent of most datasets used in this study (Fig. 1). Major urban population centers in our study area are situated in the southeastern section, where a warmer agricultural and residential landscape predominates, and which represents the most populated corridor in Canada from the cities of Windsor to Ottawa. The northern section is dominated by a mixture of forests, wild grasslands and wetlands, with colder temperatures, and ranging from dry in the west at the border with the province of Manitoba, to humid in the center and towards the border with the province of Québec in the east (Fig. 1).

Mosquito collection data

Based on the available mosquito surveillance data from all 34 Ontario public health units, sampling sites (n = 3,010) were visited at least once, and at most 876 times, from 2003 to 2022. On average, each site was visited 48 times across the study period (Table 1). Sampling sites were visited mostly from May to October when both Cx. pipiens/restuans and Ae. vexans were most likely to be observed in the study area. Out of a total of 145,102 sampling site visits, 99.9% were made from May to October. About twice as many Ae. vexans than Cx. pipiens/restuans individuals were collected, in total and on average per sampling site visit. Around 60% of sampling visits yielded each species on average (Table 1). Average abundance and occurrence per sampling site visit generally decreased across years for Ae. vexans, but not for Cx. pipiens/restuans (Fig. 2). Average abundance and occurrence per sampling site visit increased from May to August, and then decreased in the following months to October (Fig. 2). The number of mosquito pools tested for West Nile virus (WNV) was higher for Cx. pipiens/restuans due to higher priority of Cx. pipiens/restuans for WNV testing, and the total number of positive pools was also higher for Cx. pipiens/restuans (Table 1). However, the total number of Cx. pipiens/restuans individuals tested was lower, which is due to fewer collected Cx. pipiens/restuans individuals for that species on average compared to Ae. vexans, and minimum infection rate (MIR) was much higher for Cx. pipiens/restuans (Table 1). There was an overall higher MIR infection rate from 2013 to 2022 (1.9), compared to 2003 to 2012 (1.3), where 2012 was the year with the highest MIR (7.9; Fig. 2). The MIR was also much higher in August and September, compared to July and October (Fig. 2). No WNV-positive mosquito pools were observed from November to May of any year.

Land cover and climatic data

Land cover data collated from Agriculture Canada and United States Geological Survey consisted of a total of 10 classes, namely two classes of humid cover (open water and wetlands), three classes of open cover (natural and anthropogenic vegetated, and barren), one class of forested cover, and four classes of residential cover (containing varying degrees of vegetation cover), at a resolution of 120 meters. The predominance of each class varied considerably across the study area (Fig. 1). The four most common landscape classes containing a mosquito sampling site were the medium green residential, high green residential, agricultural cropland and forested classes, and the three least common were non-vegetated residential, exposed, and wetlands (Table S1; Fig. 1). The 20-year average total daily precipitation varied between 1.7 to 4.0 mm across the study area. The western part of the study area received less precipitation on average, while a few areas in the center and center-east received more precipitation on average (Fig. 1). The 20-year average mean daily temperature varied between 0.7 and 10.4°C, and the southern part of the study area was much warmer on average than the northern part, with the warmest area being the corridor from Windsor to Toronto in the extreme south near Lake Erie, and the coldest area being the center north and northeast of the study area (Fig. 1). Average total precipitation and mean temperature at cells containing a sampling site were 2.6 mm and 7.5°C, respectively (Table S1).

Ecological niche modeling analysis

The correlation coefficient of 20-year average total daily precipitation and 20-year average mean daily temperature was low (r < 0.1). Overall, the receiver operating characteristic’s area under the curve (AUC) values were lower for Ae. vexans models compared to Cx. pipiens/restuans and West Nile virus models. Out of 100 models, the best performing model had an AUC = 0.82 for Cx. pipiens/restuans, 0.79 for West Nile virus, and 0.72 for Ae. vexans (Table 2). The ensemble model contained 100, 100 and 8 models, respectively for WNV, Cx. pipiens/restuans, and Ae. vexans, with a mean AUC higher than 0.9 for mean habitat suitability index (HSI) values and committee averaging for all species (Table 2). Explanatory variable importance (on a scale of 0 to 1, obtained from 100 permutations of the ensemble niche model) of temperature in the ensemble model was higher than 0.6 and higher than the importance of the other two explanatory variables for both mosquito species and WNV. The importance of precipitation was nearly the same as that of temperature for Ae. vexans, but was low, at less than 0.2, for Cx. pipiens/restuans and moderate, at less than 0.4, for West Nile virus. Comparatively, land cover was of moderate importance for all species, at less than 0.4 (Table 2).

Projected HSI of the best performing model for all species led to an area of highest HSI value (100, 924 and 883, for WNV, Ae. vexans and Cx. pipiens/restuans, respectively, with highest possible maximum value of 1000) concentrated in the extreme southern part of the study area for all species. This was centered around the corridor from Windsor to Toronto near Lake Erie (Fig. 1) for both mosquito species, and was confined to major urban centers for WNV. Another area of high HSI was present for both mosquito species in the southeast around the cities of Kingston and Ottawa near Lake Ontario, where HSI was overall higher for Ae. vexans than for Cx. pipiens/restuans. Ae. vexans also displayed high HSI in areas where Cx. pipiens/restuans did not, particularly in the center and center-east of the study area north of Lake Huron, and in several areas in the extreme west of the study area west of Lake Superior (Fig. 1).

Mean HSI and committee averaging showed high suitability of wetlands and two residential land cover classes, low green and medium green, for both mosquito species and WNV (Fig. 3). Wild grasslands had high suitability for the two mosquito species, but low for WNV. High green residential showed high suitability only for Ae. vexans. Open water, forested, and exposed land cover classes showed low suitability for WNV (Fig. 3). Other land cover classes either showed low confidence, as displayed by values near 0.5, or conflict between mean HSI and committee averaging values (Fig. 3). Mid-range values of total daily precipitation, i.e. between roughly 2.5 and 3.0 mm, were associated with the highest suitability values for both mosquito species, and lowest values, below 2.5 mm, were associated with the highest suitability values for WNV, according to both mean HSI and committee averaging (Fig. 3). Higher mean daily temperature values, i.e. above roughly 6°C for both mosquito species and 9°C for WNV, were associated with the highest suitability values, according to both mean HSI and committee averaging (Fig. 3).

Socio-economic and demographic data

Using Statistics Canada census datasets from 2016, we identified a total of 14 demographic and socio-economic variables of interest in our analyses, at the level of the census subdivision. One variable captured information on the sex ratio (percent male residents); three variables on age structure (percent residents younger than 15, percent residents older than 64, and percent residents older than 84); two variables on ethnicity (percent residents self-identified as immigrant, percent residents self-identified as Indigenous); one variable on population density (number of residents per km²); two variables on income (mean income, and percent of population earning less than $20,000), two variables on shelter (percent shelters needing major repairs, percent residents spending 30% or more of their income on shelter); one variable on education (percent residents with no secondary education); and two variables on occupation (percent residents working in trades, and percent residents working with natural resources).

Blood donation arboviral testing data

A total of more than 6.5 million blood donations from more than 900,000 donors were tested by Canadian Blood Services across the province of Ontario, Canada, from 2003 to 2022 (Table 3). Many donations were coming from the same donor multiple times throughout the study period. We hereby refer use ‘donor’ to refer to each unique individual who donated blood either once or multiple times, and the term ‘donation’ to reflect each individual donation given. There were more donations from male than female donors, and more donations from donors aged 39 to 65 compared to younger and older (Table 3). However, there were slightly more individual female donors than males, and slightly more individual donors younger than 39 compared to 39 and older. Donors aged older than 65 represented the lowest number of individual donors, among all age groups (Table 3).

There was a total of 102 donations with a positive test result for WNV infection based on nucleic acid testing. The bulk of WNV-positive blood donations were from male donors and from donors aged 39 to 65. The cumulative WNV infection rate was slightly higher for male than female donors, and much higher for donors older than 65 than for other age groups (Table 3). The WNV infection rate was also much higher in some census subdivisions and some years compared to others. There was an overall higher WNV infection rate in southern Ontario (Fig. 4). There was also an overall higher WNV infection rate from 2013 to 2022 (2.7 per 100,000), compared to 2003 to 2012 (0.8 per 100,000), where 2018 was the year with the highest WNV infection rate (10.6 per 100,000; Fig. 2). The incidence of WNV infection amongst blood donors was also much higher in August and September, compared to July and October (Fig. 2). No positive WNV blood sample was observed from November to June of any year.

Spatiotemporal WNV infection analyses

At the analysis level of the census subdivision, we considered a total of 30 variables in negative binomial regression models to identify variables associated with WNV incidence: 14 demographic and socio-economic variables, 10 land cover variables, two climatic variables, two mosquito vector habitat suitability index variables, one WNV habitat suitability index variable, and census subdivision area (Table S2). Two groups of variables had r > 0.7. Population density and all residential land cover classes were highly correlated, and therefore we chose to only keep population density, and dropped the four residential land cover variables. Mean daily temperature and habitat suitability index of both Ae. vexans and Cx. pipiens/restuans were highly correlated, so we chose to keep only habitat suitability index of Cx. pipiens/restuans, and dropped the temperature variable and habitat suitability index of Ae. vexans. Six variables were dropped due to absence of significant association with WNV infection in univariable models (Table S2). We ran a multivariable model with the remaining 18 variables. After model selection, the final model contained thirteen variables, three of which had an IRR that was significantly different from 1 (Table 4). The proportion of households earning less than $20,000 (low income) had an IRR around 2.8 (Table 4), suggesting a strong positive association of this variable with human WNV infection. The proportion of residents spending 30% or more of their income on their shelter (high spending on shelter) had an IRR around 0.7 (Table 4), suggesting a strong negative association of this variable with WNV infection. Habitat suitability index of Cx. pipiens/restuans had an IRR value around 2.0 (Table 4), suggesting a strong positive association of this variable with WNV infection. All other variables did not display a significant association with WNV infection. The R² value of the final model was around 0.67, which suggests strong statistical power in the final model.

At the analysis level of the individual blood donation, we considered a total of 4 variables in logistic regression models to identify factors associated with WNV infection: donor age and sex, and year and month of detection test (Table S2). No pair of variables had r > 0.7. One variable was dropped due to absence of significant association with WNV infection in univariable models (Table S2). The final model contained three variables, all of which had a statistically significant IRR, with values very close to 1 (Table 4). Donor age, year of detection test and month of detection test had an IRR value between 1.002 and 1.003 (Table 4), suggesting a positive association of these variables with WNV infection. The R² value of the final model was lower than 0.001, which suggests poor statistical power in the final model, potentially stemming from extremely low variation in the outcome variable, i.e. small number of cases.

Our study on spatiotemporal effects of climatic, geographic, ecological, demographic and socio-economic variables on West Nile virus (WNV) infection in the human blood donor population identified multiple modifiable and non-modifiable risk factors that may be practically useful to inform disease prevention and control efforts. First, we identified most regions of Southern Ontario along Saint Lawrence River, Lake Ontario, Lake Erie and south of Lake Huron, to be the main habitat for both Cx. pipiens/restuans and Ae. vexans, which is also where climate is warmest, somewhat more humid and mostly agricultural and urban. Habitat for WNV itself was much narrower, being confined to the Greater Toronto Area and the Windsor region. Some regions in Northern Ontario were also suitable for Ae. vexans. Positive WNV cases in the human blood donor population were mostly detected in Southern Ontario, with very few cases in Northern Ontario. Across years, the abundance and occurrence of Ae. vexans tended to decrease, but remained mostly unchanged for Cx. pipiens/restuans. We observed a peak during the month of August in abundance and occurrence of Cx. pipiens/restuans and Ae. vexans, the two main WNV vectors in our study area, and mosquito vector WNV infection prevalence. Positive mosquito vector pools and infection cases in the blood donor population mostly occurred in the second half of the study period, during the months of August and September. These results mostly support previous literature ^40,51–57. However, our study sheds light on the spatiotemporal interplay in abundance and/or occurrence between the two main WNV vectors in northeastern North America, and how this affects WNV infection in the vector populations and in the human population, using longitudinal surveillance data over long timeframe and over a large study area. In addition, our study leverages blood donor testing data to provide spatiotemporally widespread arboviral detection in the Ontario population, which to date has not been investigated to such an extent in Canada, as opposed to other countries such as the United States ⁷.

The importance of climatic and geographic variables in the ecological niche modeling analyses for WNV vector species showed similar results from a recent study in eastern Ontario, which performed similar analyses at a smaller but overlapping spatial and temporal scale using mosquito surveillance data from 2011 to 2020 ⁵⁶. Whereas the previous study identified a mediocre to weak importance of all variables, our study herein suggests a strong effect of temperature for both mosquito vector species and for WNV, and a strong effect of precipitation for Ae. vexans. This is to be expected given the larger climatic variation across this study area compared to the previous study. In this study, the threshold of temperature on habitat suitability for WNV was higher compared to that of the two mosquito species. Optimal amounts of precipitation were also lower compared to those of the two mosquito species alone. Interestingly, land cover had a moderate relative importance for both species, despite land cover classes being all relatively well represented in terms of sampling sites in the present study. Associations between habitat suitability and specific land cover classes were mostly similar between Ae. vexans, Cx. pipiens/restuans and WNV, except for wild grasslands which were unsuitable for WNV, and high levels of vegetation in urban landscape are not suitable for Cx. pipiens/restuans and WNV. Finally, urban landscapes with low to moderate levels of vegetation and wetlands were suitable for both mosquito species and for WNV. These results are largely supported by previous literature, where high temperatures, and vegetated urban and wetland cover were predictors of both WNV vector habitat and WNV transmission ^{55,56,58–61}.

Our statistical models identified habitat suitability index for Cx. pipiens/restuans as a strong predictor of WNV infection in the human blood donor population. Due to their strong correlation with habitat suitability index for Cx. pipiens/restuans, habitat suitability index for Ae. vexans and averaged mean daily temperature couldn’t be included in multivariable statistical models at the level of the census subdivision. However, they are similarly strong predictors of WNV infection. Canada is currently experiencing effects of climate change on vector-borne disease risk, including WNV ^4,34–40. Given the strong effect of temperature on mosquito WNV vector habitat, which in turn affects WNV infection in the human population, rigorous surveillance of southerly locations is needed to effectively predict large upticks in human WNV cases across Canada.

Our statistical models identified habitat suitability index for Cx. pipiens/restuans as a strong predictor of WNV infection in the human blood donor population, which may also be expanded to two highly correlated variables: habitat suitability index for Ae. vexans and averaged mean daily temperature. Our statistical models also identified the proportion of low-income households and proportion of households where 30% or more of the residents’ income is spent on shelter being positively and negatively, respectively, associated with WNV infection in the human population. Household wealth is widely known to be associated with mosquito vector density, potentially through greater perception of risk and access to mosquito control methods ^44,46,62,63. In a previous analysis at a smaller but completely overlapping spatial and temporal scale in the city of Ottawa, Ontario, from 2007 to 2014, proportion of 60-years-old-and-older shelters was associated with higher WNV risk. A similar result was also observed in Chicago during a WNV outbreak in 2002 ⁶³. This variable is possibly linked to availability of suitable habitats, i.e. breeding sites in suboptimal drainage systems ⁶⁴, used by WNV vector species. Population density and an urban environment were previously associated with higher WNV risk in Ottawa, Ontario, from 2007–2014 ⁵⁵, and in Chicago and Detroit during a WNV outbreak in 2002 ⁵⁹. However, in our study here there was no significant effect of either population density or residential land cover on WNV infection in the human population, despite using extensive and high-resolution datasets of both types of variables. Certain residential land cover classes do seem to affect habitat suitability of the two mosquito WNV vector species and WNV itself, albeit with an importance moderate or low compared to weather variables, but this effect does not seem to translate to significantly higher WNV infection in humans, as demonstrated by our multivariable statistical models. These results either suggest limited power to identify an effect of population density or residential land cover by our multivariable statistical models, or that spurious associations in previous studies would have been better explained by alternative unmeasured variables that have been included in this study herein.

Our study has a few limitations. Nucleic acid tests we used have a possibility of cross-reacting with other members of the Japanese encephalitis serocomplex, such as Japanese encephalitis, Murray Valley encephalitis, Saint Louis encephalitis and Kunjin virus ^65–68 (leading to a modification to the “National case definition: West Nile virus – Canada.ca” in 2024), which is relevant for donors with a certain travel history or due to vaccination with Japanese encephalitic virus vaccine. Also, most data points in the mosquito sampling data and the human donor data are highly aggregated around urban and metropolitan areas of the study area. However, outcomes of these limitations on the main results of our analyses are likely to be minimal.

In conclusion, results from our study point to several modifiable risk factors that may be used as points of entry for practical intervention aimed at reducing risk of mosquito-borne pathogens in Canada, in a context of increasing mosquito-borne pathogen exposure and illness. For example, our study supports the need for government education campaigns and incentives facilitating renovations aimed at reducing mosquito habitat and/or exposure to mosquitoes, especially in areas with highly suitable habitat for Cx. pipiens/restuans in Southern Ontario, such as the “Prevention of West Nile virus – Canada.ca” program. Such programs and incentives would also be useful in practical intervention measures against Aedes albopictus, an invasive mosquito vector for several pathogens, including dengue virus, which is detected periodically in Southern Ontario. Our study is one of the few using arboviral detection tests over a large area and a large period in the human population to identify factors predictive of WNV infection. Such studies are not impeded by the same spatial, temporal and clinical (e.g., under reporting) biases as those using disease case reports, but are uncommon due to the sheer amount of work needed to produce representative databases.

Study area and duration

The study area is situated across most of the province of Ontario, in Canada, at and below latitudes 50–51° N (Fig. 1). The study spans the years 2003 to 2022.

Mosquito collection data

Since 2002, Public Health Ontario (PHO) has collected data on mosquito surveillance activities conducted by public health units in Ontario, which comprise mosquito capture and identification of 22 species/species groups. Capture is performed using the protocol as described in Talbot et al. (2023) ⁵⁶. Briefly, Culex pipiens/restuans are prioritized over all other species, and Ae. vexans is also of high priority. RNA is extracted from each pool using RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA extracts are tested by quantitative polymerase chain reaction (PCR) for arbovirus presence ⁶⁹. We used all mosquito capture data available across the entire province of Ontario, Canada, comprising data from all 34 public health units, for the years 2003 to 2022. For each mosquito pool, we calculated the WNV minimum infection rate (MIR), which is the test outcome (positive = 1; negative = 0), divided by the number of mosquitoes present in the pool, multiplied by 1000.

Land cover and climatic data

We followed the approach of Talbot et al. (2023) ⁵⁶ to process land cover and climate data for subsequent ecological niche models. Land cover data for the year 2013 were obtained from Agriculture and Agri-Food Canada (AAFC) and the United States Geological Survey (USGS) with a resolution of 30 meters across our study area. Land cover data for the year 2013 were chosen because it is approximately the mid-point of our study period from 2003 to 2022. Annual crop inventory data from AAFC ⁷⁰ comprise seven land cover classes: open water, wetlands, agricultural croplands, natural grasslands, forests, exposed surface and residential areas. Residential areas were subdivided into four categories, according to the normalized difference vegetation index (NDVI) from USGS, created using Landsat 8 data (collection 2, level 2, maximum 50% clouds) from May to October 2013, from USGS ^71,72. The goal of this procedure was to subdivide urban environments according to the presence of vegetation, which may affect habitat selection by the studied species. Residential areas with NDVI < = 0.15 were referred to as non-vegetated, with NDVI > 0.15 and < = 0.30 as low green, with NDVI > 0.30 and < = 0.60 as medium green and with NDVI > 0.60 as high green residential areas. Data from AAFC and USGS used the same resolution with matching cell frames, and therefore merging of the two datasets could be performed manually.

Therefore, we considered temperature and precipitation data across the entire study duration. Temperature and precipitation data were obtained from the National Aeronautics and Space Administration (NASA). Given their ease of access, we extracted data on annual total precipitation, and annual maximum and minimum temperature from the annual surface weather and climatological summaries from NASA ⁷³ with a resolution of 1,000 meters. These data were averaged across the 20 years of the study duration, and then divided by number of days in a year to obtain 20-year averaged mean daily temperature and 20-year averaged total daily precipitation for the total period across our study area.

Ecological niche modeling analysis

We followed the approach of Talbot et al. (2023)⁵⁶. The two studied mosquito species were observed at least once in the vast majority of the 3,010 sampling locations over the study period (2,783 for Ae. vexans, or 92%, and 2,686 for Cx. pipiens/restuans, or 90%). At least one mosquito vector species was present in a total of 2,810 sites, for which a WNV detection test could be performed, and lead to at least one positive outcome in a total of 650 sites. Therefore, the number of visits in which each species was observed at least once at each site was calculated, and divided by the total number of visits at each site over the study period. The resulting value is the frequency of observed presence, and is a form of aggregated performance measure often used in species distribution models ⁷⁴. Sites were then dichotomized into a 0/1 distribution for each mosquito species and for WNV, which is a requirement of the approach.: Sites with 50% or more species occurrence for both mosquito species were classified as ‘presence, and sites with less than 50% as ‘absence. Sites with at least one positive test outcome for WNV were classified as ‘presence’, and others as ‘absence’.

The random forest algorithm was considered suitable for our analyses because the presence and absence of a species in a given sampling site visit are likely to be affected by the same sampling bias ^75,76. This decision tree-based approach performs as well as the maximum entropy approach ^77,78, and better than traditional regression-based approaches when using large datasets sampled over a long duration and a large spatial scale ⁷⁹. We performed the analyses using the ‘biomod2’ package ⁸⁰ in R 4.2.1 (R Development Core Team, Vienna, Austria). We projected all land cover and climatic datasets to Albers Conic Equal Area, which was the original projection of the land cover dataset from Agriculture Canada. All explanatory variables were resampled to a cell size of 120 x 120 meters and set to be at the same cell frame to reduce spatial bias caused by unequal resolution with the mosquito dataset ⁷⁵. We computed the Pearson’s correlation coefficient among climatic variables at sampling sites in R 4.2.1. Potential collinearity problems were considered if r > 0.7. We set the prevalence parameter to 0.5 was specified, meaning “presence” and “absence” distributions are considered in equal proportions in the analysis ⁸¹. For each species, we trained 100 replicate models using 80% of data. To evaluate each model, we computed a receiver operating characteristic’s area under the curve (AUC) using the remaining 20% of data. Data was selected randomly in each model for training versus testing. We used the final model, trained by the 100 replicate models and using 100% of data, to generate a habitat suitability index (HSI) map in the study area. We kept all other parameters at default values. We used all models with AUC above 0.7 to generate an ensemble niche model ⁸⁰. We generated response plots of the mean HSI across models and committee averaging ⁸², for each explanatory variable. We calculated variable importance for each explanatory variable, which varies from 0 to 1, using a procedure of 100 permutations from the ensemble niche model. Lastly, we created a projected HSI map from the model with the highest AUC for each mosquito species and for WNV.

Socio-economic data

Statistics Canada collects data on a large variety of socio-economic variables during the Census of Population every five years across Canada. Data for the years 2011 and 2016 were initially considered because they are near the mid-point of our study period from 2003 to 2022. Given their easier access and processing, we chose data for the year 2016, which we extracted using the Beyond 20/20 Professional Browser software. We selected all variables that relate to either sex, age, ethnicity, population density, income, shelter infrastructure, education, and occupation, to be included in analyses on the determinants of WNV infection in the human population. We uploaded data at the level of the census subdivision, to match blood donation arboviral testing data structure.

Blood donation arboviral testing data

Across the study area, since 2003, Canadian Blood Services (CBS) have tested blood donations across Ontario. These tests were performed on all blood donations from 2003 to 2015. As of December 2015, all donations from June to November were tested, but only donations from travelers to certain destinations were tested from December to May. These months usually see much less mosquito activity, and therefore likelihood of exposure to an infected mosquito is negligible. Groups of six donations were tested in 6-unit minipools. Positive minipools were then retested separately for each donation from the corresponding minipool, along with all donations from surrounding areas for the next two weeks. From June 2003, testing was performed using TaqScreen WNV test IUO (F. Hoffmann-La Roche AG, Basel, Switzerland). From June 2007, testing was performed using the IND cobas TaqScreen WNV test for use with the cobas s 201 system. From June 2008, testing was performed using the licensed cobas TaqScreen WNV test for use with the cobas s 201 system. From December 2017, testing was performed using the cobas® WNV – Nucleic acid test for use on the cobas® 6800/8800 Systems. At donor registration, the donor’s date of birth, sex and residential address are recorded. For confidentiality purposes, we used only the donor’s reported sex; year of birth, to obtain approximative age of the blood donor at the time of donation; census subdivision of residence from the Canadian Census of Population boundaries for the year 2016; and unique donor identifier.

To avoid sampling biases leading to spurious associations in our analyses of determinants of WNV infection in the human population, we chose to exclude all data from census subdivisions where fewer than 1000 WNV tests on blood donations were available, which are mostly located in sparsely populated areas mostly in northeastern parts of the study area, and north of the northern limit of the study area. This exclusion step lead to the removal of 126 subdivisions out of the total of 417 (30%) where blood donor data is available. In the remaining 291 subdivisions, we chose to exclude 4 census subdivisions where total number of residents was lower than 500, because most socio-economic variables were missing for confidentiality reasons. The final dataset contained 287 census subdivisions. Two of these census subdivisions, named “Kenora, Unorganized” and “Thunder Bay, Unorganized” had boundaries above the northern limit of the study area. However, the large majority of blood donations in these subdivisions were conducted in the south, near the Kenora and Thunder Bay townships, respectively, which is also where the large majority of the residents of these subdivisions live. For these reasons, we considered only the portion in these two subdivisions that lie within our study area (Fig. 1, Fig. 4).

Spatiotemporal WNV infection analyses

To attain our main objective, we investigated the effect of a wide range of factors related to land cover, climate, mosquito habitat and socio-economic status of residents on WNV infection in the human population, using data from WNV tests on blood donations. These factors were carefully chosen a priori to include variables most likely affecting WNV risk in the human population, including aspects related to mosquito occurrence, mosquito activity, and characteristics of residents linked to higher exposure to mosquito bites. We conducted these analyses as two different levels: one at the census subdivision, and one at the individual blood donation.

For the first level of analysis, we gathered all arboviral testing data from blood donations, for which residence information is available, from 2003 to 2022, and grouped them within the respective census subdivision of residence of the blood donor. We conducted a simple generalized linear regression, using the ‘lme4’ package ⁸³ in R 4.2.1, for each variable separately, namely selected socio-economic variables, land cover variables (percent cover of each class in census subdivisions), climatic variables (20-year averaged daily total precipitations and 20-year averaged daily mean temperature, averaged across census subdivisions), habitat suitability index variables (for each mosquito vector species and for WNV, averaged across census subdivisions), and lastly, the census subdivision geographic area (in km²), which can be stochastically associated with number of positive cases. Prior to these analyses, we subtracted the mean and divided by the standard deviation of all values for numerical variables, namely test outcome, donor age, month of test, and year of test. We used the zero-inflated negative binomial modeling family, using the ‘pscl’ package ⁸⁴ in R 4.2.1, where we used the number of positive cases within census subdivisions as outcome variable, and number of donations tested within census subdivisions as offset variable.

For the second level of analysis, we gathered all WNV testing data from blood donations, for which residence information is available, from 2003 to 2022. We conducted a simple mixed-effects generalized linear regression, using the ‘lme4’ package ⁸³ in R 4.2.1, for each variable separately, namely donor sex, donor age, month of test, and year of test, against test outcome, where 1 is positive and 0 is negative. We used a hierarchical random-effects term, which is the unique donor number nested within the census subdivision of residence. Prior to these analyses, we subtracted the mean and divided by the standard deviation of all values for numerical variables, namely test outcome, donor age, month of test, and year of test. Given the data structure is binomial, the ‘binomial’ modeling family was most intuitive, but the extremely small number of positive cases compared to negative cases lead to numerous fitting errors. Therefore, we chose the more general ‘gaussian’ modeling family, for which no modelling problem occurred.

For both analysis levels, we used Pearson’s correlation coefficient in R 4.2.1, to identify correlation among all selected variables, and dropped one variable from each pair of variables displaying r > 0.7. Next, we selected all variables displaying a significant univariable association (P < 0.01), with WNV infection into a multivariable generalized linear regression analysis, using the same packages as previously in R 4.2.1. For the analysis at the level of the census subdivision, given the large number of variables included, we proceeded with a two-step model selection approach using the Bayesian Information Criterion (BIC), i.e. the Akaike Information Criterion using the logarithm of the number of observations as the k parameter. We computed a BIC value for the full model and for all combinations of the full model excluding one variable. A BIC value decrease of 2 or more is considered positive evidence for a variable displaying little effect on the response variable ⁸⁵. We ran a new multivariable regression model, but this time excluding all variables that, when dropped from the full model, caused a decrease of the BIC value of more than 2. We then reapplied the same model selection approach as a second step on this new model. Using this model selection approach, we ensured that only the most important variables were retained in the resulting final model. In both analysis levels, we ran the final model using the full dataset, and computed incidence rate ratio (IRR) values, i.e. the exponents of the slope coefficients, 95% confidence intervals for the IRR values, and P values for each variable. Finally, we computed the R² of the final model, using the ‘modelsummary’ package ⁸⁶ in R 4.2.1.

Acknowledgements

We thank Canadian Blood Services (in particular Bill Ferguson), Public Health Ontario (in particular Curtis Russell), Statistics Canada, Agriculture and Agri-Food Canada, United States Geological Survey National Aeronautics and Space Administration, for access to blood donor, mosquito capture, socio-economic, geographic and climatic data used in this study. We also thank Maxime Rioux-Rousseau for their help collecting and processing geographic and climatic data sources. This project was supported by grants from the Canadian Institutes of Health Research and Natural Science and Engineering Research Council of Canada to M.A.K.

Author contribution

B.T. contributed to the conception of the study, performed analyses, interpreted results, and wrote the manuscript draft. M.A.K. and A.L. contributed in the conception of the study, interpreted results and edited the manuscript draft. N.H.O., S.F.O. and S.J.D. contributed in the conception of the study and edited the manuscript draft.

Data availability statement

Blood donor data from Canadian Blood Services is not available due to privacy reasons according to our data sharing agreement between University of Ottawa and Canadian Blood Services. All other data are freely available on the webpage of the relevant authority: Public Health Ontario (https://www.publichealthontario.ca/en/Data-and-Analysis/Using-Data/Data-Requests) for mosquito capture data, Statistics Canada (https://www150.statcan.gc.ca/n1/en/type/data) for socio-economic data, Agriculture and Agri-Food Canada (https://www.agr.gc.ca/atlas/apps/aef/main/index_en.html?AGRIAPP=23) and United States Geological Survey (https://earthexplorer.usgs.gov/) for geographic data, and National Aeronautics and Space Administration (https://www.earthdata.nasa.gov/) for climatic data.

Additional Information

We declare no competing interests.

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Table 1. Descriptive statistics relating to the abundance (number of mosquitoes per sampling visit) and occurrence (proportion of presence across sampling visits) for adult mosquitoes from both studied species, Culex pipiens/restuans and Aedes vexans, collected across 3,010 sampling locations in Ontario, Canada, 2003-2022.

Species	Culex pipiens/restuans	Aedes vexans
Total sampled adult mosquitoes	934,951	1,778,876
Number of visits/site (mean ± standard deviation)	48 ± 80
Abundance/visit (mean ± standard deviation)	5 ± 8	12 ± 18
Occurrence/visit (mean ± standard deviation)	0.57 ± 0.32	0.65 ± 0.29
Total number of WNV detection tests	102,938	82,134
Number of positive pools [% of total for all species]	2,949 [88]	182 [5]
Total number of adult mosquitoes tested for West Nile virus	916,673	1,147,874
Number of adult mosquitoes tested/test (mean ± standard deviation)	9 ± 12	14 ± 15
Total minimum infection rate (positive pools/number tested x1000)	3.22	0.16

Table 2. Parameters used to generate ensemble niche models for both studied species, Culex pipiens/restuans and Aedes vexans, collected across 3,010 sampling locations in Ontario, Canada, 2003-2022. Number of models included out of the 100 random forest models generated, response operating curves for the best-performing model, for the mean habitat suitability index (HSI) averaged across models, and committee averaging of HSI across models and variable importance calculated with a 100-permutation procedure for the three explanatory variables are shown.

Species		Aedes vexans	Culex pipiens/restuans	WNV
Number of models		8	100	100
Area under the curve	Best-performing model	0.72	0.82	0.79
	Mean HSI values	0.93	0.91	0.93
	Committee averaging	0.92	0.90	0.92
Variable importance	Land cover	0.32	0.21	0.29
	Precipitations	0.62	0.19	0.39
	Temperature	0.64	0.78	0.62

Table 3. Descriptive statistics relating to the number of blood donors and donations to the Canadian Blood Services in Ontario, Canada, 2003-2022, tested for presence of West Nile virus (WNV).

Age / Sex	11 to 38	39 to 65	66 to 93	Female	Male	Total
Number of tests on blood donations	2,200,777	3,990,529	389,440	2,776,604	3,804,165	6,580,769
Number of unique blood donors	576,752	439,512	52,525	504,580	467,814	972,394
Mean number of donations per donor	3.8	9.1	2.5	5.5	8.1	6.8
Number of WNV-positive donations	16	77	9	38	64	102
WNV-positive rate (x100,000 donations)	0.7	1.9	2.3	1.4	1.7	1.6

Table 4. Regression incidence rate ratio (IRR) values, 95% confidence intervals [95% CI], the P value for each variable, and the R² for the model, for the multivariable modelling analyses on the WNV infection in the human donor population in Ontario from 2003 to 2022, at the analysis levels of the individual donor and the 2016 Census subdivision. HSI refers to habitat suitability index of the corresponding mosquito vector species.

Analysis level	Variable (units)	IRR [95% CI]	P	R²
Census subdivision	Low income (%)	2.829 [2.061, 3.885]	<0.001	0.677
	High spending on shelter (%)	0.702 [0.526, 0.939]	0.017
	Cx. pipiens/restuans (HSI)	1.950 [1.160, 3.280]	0.012
	West Nile virus (HSI)	1.179 [0.845, 1.645]	0.333
	Precipitations (mm)	0.872 [0.558, 1.363]	0.548
	Population density (residents/km²)	0.908 [0.720, 1.145]	0.414
	Mean income ($)	1.316 [0.941, 1.839]	0.108
	Residents older than 64 (%)	0.878 [0.584, 1.321]	0.533
	Occupation in trades (%)	0.807 [0.479, 1.357]	0.418
	Occupation in natural resources (%)	1.389 [0.927, 2.081]	0.111
	Land cover of wetlands (%)	0.654 [0.347, 1.234]	0.190
	Land cover of wild grasslands (%)	1.397 [0.909, 2.148]	0.127
	Land cover of forests (%)	1.332 [0.680, 2.612]	0.403
Individual donation	Donor age (years since birth)	1.002 [1.001, 1.003]	<0.001	<0.001
	Year of detection test (date)	1.003 [1.002, 1.003]	<0.001
	Month of detection test (date)	1.002 [1.001, 1.003]	<0.001

No competing interests reported.

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10 Jul, 2024
First submitted to journal
09 Jul, 2024

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Spatiotemporal analysis of West Nile virus infection in the human population based on arboviral detection testing of blood donations

Status:

Version 1

Abstract

Figures

Introduction

Results

Study area and duration

Mosquito collection data

Land cover and climatic data

Ecological niche modeling analysis

Socio-economic and demographic data

Blood donation arboviral testing data

Spatiotemporal WNV infection analyses

Discussion

Materials and Methods

Study area and duration

Mosquito collection data

Land cover and climatic data

Ecological niche modeling analysis

Socio-economic data

Blood donation arboviral testing data

Spatiotemporal WNV infection analyses

Declarations

References

Tables

Additional Declarations

Supplementary Files

Status:

Version 1