All Publications

  • Ecological drivers of dog heartworm transmission in California. Parasites & vectors Couper, L. I., Mordecai, E. A. 2022; 15 (1): 388


    BACKGROUND: Effectively controlling heartworm disease-a major parasitic disease threatening animal health in the US and globally-requires understanding the local ecology of mosquito vectors involved in transmission. However, the key vector species in a given region are often unknown and challenging to identify. Here we investigate (i) the key vector species associated with transmission of the parasite, Dirofilaria immitis, in California and (ii) the climate and land cover drivers of vector presence.METHODS: To identify key mosquito vectors involved in transmission, we incorporated long-term, finely resolved mosquito surveillance data and dog heartworm case data in a statistical modeling approach (fixed-effects regression) that rigorously controls for other unobserved drivers of heartworm cases. We then used a flexible machine learning approach (gradient boosted machines) to identify the climate and land cover variables associated with the presence of each species.RESULTS: We found significant, regionally specific, positive associations between dog heartworm cases and the abundance of four vector species: Aedes aegypti (Central California), Ae. albopictus (Southern California), Ae. sierrensis (Central California), and Culiseta incidens (Northern and Central California). The proportion of developed land cover was one of the most important ecological variables predicting the presence or absence of the putative vector species.CONCLUSION: Our results implicate three previously under-recognized vectors of dog heartworm transmission in California and indicate the land cover types in which each putative vector species is commonly found. Efforts to target these species could prioritize surveillance in these land cover types (e.g. near human dwellings in less urbanized settings for Ae. albopictus and Cs. incidens) but further investigation on the natural infection prevalence and host-biting rates of these species, as well as the other local vectors, is needed.

    View details for DOI 10.1186/s13071-022-05526-x

    View details for PubMedID 36274157

  • Host blood meal identity modifies vector gene expression and competency. Molecular ecology Ring, K., Couper, L. I., Sapiro, A. L., Yarza, F., Yang, X. F., Clay, K., Mateusiak, C., Chou, S., Swei, A. 2022

    View details for DOI 10.1111/mec.16413

    View details for PubMedID 35231145

  • How will mosquitoes adapt to climate warming? eLife Couper, L. I., Farner, J. E., Caldwell, J. M., Childs, M. L., Harris, M. J., Kirk, D. G., Nova, N., Shocket, M., Skinner, E. B., Uricchio, L. H., Exposito-Alonso, M., Mordecai, E. A. 2021; 10


    The potential for adaptive evolution to enable species persistence under a changing climate is one of the most important questions for understanding impacts of future climate change. Climate adaptation may be particularly likely for short-lived ectotherms, including many pest, pathogen, and vector species. For these taxa, estimating climate adaptive potential is critical for accurate predictive modeling and public health preparedness. Here, we demonstrate how a simple theoretical framework used in conservation biology-evolutionary rescue models-can be used to investigate the potential for climate adaptation in these taxa, using mosquito thermal adaptation as a focal case. Synthesizing current evidence, we find that short mosquito generation times, high population growth rates, and strong temperature-imposed selection favor thermal adaptation. However, knowledge gaps about the extent of phenotypic and genotypic variation in thermal tolerance within mosquito populations, the environmental sensitivity of selection, and the role of phenotypic plasticity constrain our ability to make more precise estimates. We describe how common garden and selection experiments can be used to fill these data gaps. Lastly, we investigate the consequences of mosquito climate adaptation on disease transmission using Aedes aegypti-transmitted dengue virus in Northern Brazil as a case study. The approach outlined here can be applied to any disease vector or pest species and type of environmental change.

    View details for DOI 10.7554/eLife.69630

    View details for PubMedID 34402424

  • Multi-year drought exacerbates long-term effects of climate on an invasive ant species. Ecology Couper, L. I., Sanders, N. J., Heller, N. E., Gordon, D. M. 2021: e03476


    Invasive species threaten biodiversity, ecosystem function, and human health, but the long-term drivers of invasion dynamics remain poorly understood. We use data from a 28-year ongoing survey of a Northern California ant community invaded by the Argentine ant (Linepithema humile) to investigate the influence of abiotic and biotic factors on invasion dynamics. We found that the distribution of L. humile retracted following an extreme drought that occurred in the region from 2012 - 2015. The distribution of several native ant species also contracted, but overall native ant diversity was higher after the drought and for some native ant species, distributions expanded over the 28-year survey period. Using structural equation models, we found the strongest impact on the distribution of L. humile was from direct effects of climate, namely cumulative precipitation and summer maximum temperatures, with only a negligible role for biotic resistance and indirect effects of climate mediated by native ants. The increasing drought and high temperature extremes projected for northern California due to anthropogenic driven climate change may limit the spread, and possibly the impact, of L. humile in invaded regions. The outcome will depend on the response of native ant communities to these climatic stressors.

    View details for DOI 10.1002/ecy.3476

    View details for PubMedID 34346070

  • The influence of vector-borne disease on human history: socio-ecological mechanisms. Ecology letters Athni, T. S., Shocket, M. S., Couper, L. I., Nova, N., Caldwell, I. R., Caldwell, J. M., Childress, J. N., Childs, M. L., De Leo, G. A., Kirk, D. G., MacDonald, A. J., Olivarius, K., Pickel, D. G., Roberts, S. O., Winokur, O. C., Young, H. S., Cheng, J., Grant, E. A., Kurzner, P. M., Kyaw, S., Lin, B. J., Lopez, R. C., Massihpour, D. S., Olsen, E. C., Roache, M., Ruiz, A., Schultz, E. A., Shafat, M., Spencer, R. L., Bharti, N., Mordecai, E. A. 2021


    Vector-borne diseases (VBDs) are embedded within complex socio-ecological systems. While research has traditionally focused on the direct effects of VBDs on human morbidity and mortality, it is increasingly clear that their impacts are much more pervasive. VBDs are dynamically linked to feedbacks between environmental conditions, vector ecology, disease burden, and societal responses that drive transmission. As a result, VBDs have had profound influence on human history. Mechanisms include: (1) killing or debilitating large numbers of people, with demographic and population-level impacts; (2) differentially affecting populations based on prior history of disease exposure, immunity, and resistance; (3) being weaponised to promote or justify hierarchies of power, colonialism, racism, classism and sexism; (4) catalysing changes in ideas, institutions, infrastructure, technologies and social practices in efforts to control disease outbreaks; and (5) changing human relationships with the land and environment. We use historical and archaeological evidence interpreted through an ecological lens to illustrate how VBDs have shaped society and culture, focusing on case studies from four pertinent VBDs: plague, malaria, yellow fever and trypanosomiasis. By comparing across diseases, time periods and geographies, we highlight the enormous scope and variety of mechanisms by which VBDs have influenced human history.

    View details for DOI 10.1111/ele.13675

    View details for PubMedID 33501751

  • The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models. Proceedings. Biological sciences Childs, M. L., Kain, M. P., Harris, M. J., Kirk, D., Couper, L., Nova, N., Delwel, I., Ritchie, J., Becker, A. D., Mordecai, E. A. 2021; 288 (1957): 20210811


    Mathematical models of epidemics are important tools for predicting epidemic dynamics and evaluating interventions. Yet, because early models are built on limited information, it is unclear how long they will accurately capture epidemic dynamics. Using a stochastic SEIR model of COVID-19 fitted to reported deaths, we estimated transmission parameters at different time points during the first wave of the epidemic (March-June, 2020) in Santa Clara County, California. Although our estimated basic reproduction number ([Formula: see text]) remained stable from early April to late June (with an overall median of 3.76), our estimated effective reproduction number ([Formula: see text]) varied from 0.18 to 1.02 in April before stabilizing at 0.64 on 27 May. Between 22 April and 27 May, our model accurately predicted dynamics through June; however, the model did not predict rising summer cases after shelter-in-place orders were relaxed in June, which, in early July, was reflected in cases but not yet in deaths. While models are critical for informing intervention policy early in an epidemic, their performance will be limited as epidemic dynamics evolve. This paper is one of the first to evaluate the accuracy of an early epidemiological compartment model over time to understand the value and limitations of models during unfolding epidemics.

    View details for DOI 10.1098/rspb.2021.0811

    View details for PubMedID 34428971

  • Environmental Drivers of Vector-Borne Diseases POPULATION BIOLOGY OF VECTOR-BORNE DISEASES Shocket, M. S., Anderson, C. B., Caldwell, J. M., Childs, M. L., Couper, L. I., Han, S., Harris, M. J., Howard, M. E., Kain, M. P., MacDonald, A. J., Nova, N., Mordecai, E. A., Drake, J. M., Bonsall, M. B., Strand, M. R. 2021: 85-118
  • Impact of prior and projected climate change on US Lyme disease incidence. Global change biology Couper, L. I., MacDonald, A. J., Mordecai, E. A. 2020


    Lyme disease is the most common vector-borne disease in temperate zones and a growing public health threat in the United States (US). The life cycles of the tick vectors and spirochete pathogen are highly sensitive to climate, but determining the impact of climate change on Lyme disease burden has been challenging due to the complex ecology of the disease and the presence of multiple, interacting drivers of transmission. Here we incorporated 18 years of annual, county-level Lyme disease case data in a panel data statistical model to investigate prior effects of climate variation on disease incidence while controlling for other putative drivers. We then used these climate-disease relationships to project Lyme disease cases using CMIP5 global climate models and two potential climate scenarios (RCP4.5 and RCP8.5). We find that interannual variation in Lyme disease incidence is associated with climate variation in all US regions encompassing the range of the primary vector species. In all regions, the climate predictors explained less of the variation in Lyme disease incidence than unobserved county-level heterogeneity, but the strongest climate-disease association detected was between warming annual temperatures and increasing incidence in the Northeast. Lyme disease projections indicate that cases in the Northeast will increase significantly by 2050 (23,619 ± 21,607 additional cases), but only under RCP8.5, and with large uncertainty around this projected increase. Significant case changes are not projected for any other region under either climate scenario. The results demonstrate a regionally variable and nuanced relationship between climate change and Lyme disease, indicating possible nonlinear responses of vector ticks and transmission dynamics to projected climate change. Moreover, our results highlight the need for improved preparedness and public health interventions in endemic regions to minimize the impact of further climate change-induced increases in Lyme disease burden.

    View details for DOI 10.1111/gcb.15435

    View details for PubMedID 33150704

  • The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control. medRxiv : the preprint server for health sciences Childs, M. L., Kain, M. P., Kirk, D., Harris, M., Couper, L., Nova, N., Delwel, I., Ritchie, J., Mordecai, E. A. 2020


    Non-pharmaceutical interventions to combat COVID-19 transmission have worked to slow the spread of the epidemic but can have high socio-economic costs. It is critical we understand the efficacy of non-pharmaceutical interventions to choose a safe exit strategy. Many current models are not suitable for assessing exit strategies because they do not account for epidemic resurgence when social distancing ends prematurely (e.g., statistical curve fits) nor permit scenario exploration in specific locations. We developed an SEIR-type mechanistic epidemiological model of COVID-19 dynamics to explore temporally variable non-pharmaceutical interventions. We provide an interactive tool and code to estimate the transmission parameter, β, and the effective reproduction number, R eff . We fit the model to Santa Clara County, California, where an early epidemic start date and early shelter-in-place orders could provide a model for other regions. As of April 22, 2020, we estimate an R eff of 0.982 (95% CI: 0.849 - 1.107) in Santa Clara County. After June 1 (the end-date for Santa Clara County shelter-in-place as of April 27), we estimate a shift to partial social distancing, combined with rigorous testing and isolation of symptomatic individuals, is a viable alternative to indefinitely maintaining shelter-in-place. We also estimate that if Santa Clara County had waited one week longer before issuing shelter-in-place orders, 95 additional people would have died by April 22 (95% CI: 7 - 283). Given early life-saving shelter-in-place orders in Santa Clara County, longer-term moderate social distancing and testing and isolation of symptomatic individuals have the potential to contain the size and toll of the COVID-19 pandemic in Santa Clara County, and may be effective in other locations.

    View details for DOI 10.1101/2020.05.03.20089078

    View details for PubMedID 32511583

    View details for PubMedCentralID PMC7276010

  • Comparative vector competence of North American Lyme disease vectors. Parasites & vectors Couper, L. I., Yang, Y., Yang, X. F., Swei, A. 2020; 13 (1): 29


    BACKGROUND: Understanding the drivers of Lyme disease incidence at broad spatial scales is critical for predicting and mitigating human disease risk. Previous studies have identified vector phenology and behavior, host community composition, and landscape features as drivers of variable Lyme disease risk. However, while the Lyme disease transmission cycles in the eastern and western USA involve different vector species (Ixodes scapularis and Ixodes pacificus, respectively), the role of vector-specific differences in transmission efficiency has not been directly examined. By comparing the performance of traits involved in vector competence between these two species, this study aims to identify how vector competence contributes to variable Lyme disease risk.METHODS: We used a suite of laboratory experiments to compare the performance of traits related to vector competence for the two USA Lyme disease vectors. For each species, we measured the rate of attachment to a common rodent host, the engorgement weight, and the efficiency of pathogen acquisition (host to tick) and pathogen transmission (tick to host) from laboratory mice. In measuring pathogen acquisition and transmission, we used two different pathogen strains, one sympatric with I. scapularis and one sympatric with I. pacificus, to assess the importance of vector-pathogen coevolutionary history in transmission dynamics.RESULTS: We found I. pacificus had significantly higher host attachment success and engorgement weights, but significantly lower pathogen transmission efficiency relative to I. scapularis. Molting success and pathogen acquisition did not differ between these two species. However, pathogen acquisition efficiency was significantly higher for both sympatric vector and pathogen strains than the allopatric pairings.CONCLUSIONS: This study identified species-specific vector traits as a potential driver of broad scale variation in Lyme disease risk in the USA. In particular, the exceedingly low rates of pathogen transmission from tick to host observed for I. pacificus may limit Lyme disease transmission efficiency in the western USA. Further, observed variation in pathogen acquisition between sympatric and allopatric vector-pathogen strains indicate that vector-pathogen coevolutionary history may play a key role in transmission dynamics. These findings underscore the need to consider vector traits and vector-pathogen coevolution as important factors governing regional Lyme disease risk.

    View details for DOI 10.1186/s13071-020-3893-x

    View details for PubMedID 31937369

  • Comparative Microbiome Profiles of Sympatric Tick Species from the Far-Western United States. Insects Chicana, B., Couper, L. I., Kwan, J. Y., Tahiraj, E., Swei, A. 2019; 10 (10)


    Insight into the composition and function of the tick microbiome has expanded considerably in recent years. Thus far, tick microbiome studies have focused on species and life stages that are responsible for transmitting disease. In this study we conducted extensive field sampling of six tick species in the far-western United States to comparatively examine the microbial composition of sympatric tick species: Ixodes pacificus, Ixodes angustus, Dermacentor variabilis, Dermacentor occidentalis, Dermacentor albipictus, and Haemaphysalis leporispalustris. These species represent both common vectors of disease and species that rarely encounter humans, exhibiting a range of host preferences and natural history. We found significant differences in microbial species diversity and composition by tick species and life stage. The microbiome of most species examined were dominated by a few primary endosymbionts. Across all species, the relative abundance of these endosymbionts increased with life stage while species richness and diversity decreased with development. Only one species, I. angustus, did not show the presence of a single dominant microbial species indicating the unique physiology of this species or its interaction with the surrounding environment. Tick species that specialize in a small number of host species or habitat ranges exhibited lower microbiome diversity, suggesting that exposure to environmental conditions or host blood meal diversity can affect the tick microbiome which in turn may affect pathogen transmission. These findings reveal important associations between ticks and their microbial community and improve our understanding of the function of non-pathogenic microbiomes in tick physiology and pathogen transmission.

    View details for DOI 10.3390/insects10100353

    View details for PubMedID 31635285

  • Patterns, Drivers, and Challenges of Vector-Borne Disease Emergence. Vector borne and zoonotic diseases (Larchmont, N.Y.) Swei, A. n., Couper, L. I., Coffey, L. L., Kapan, D. n., Bennett, S. n. 2019


    Vector-borne diseases are emerging at an increasing rate and comprise a disproportionate share of all emerging infectious diseases. Yet, the key ecological and evolutionary dimensions of vector-borne disease that facilitate their emergence have not been thoroughly explored. This study reviews and synthesizes the existing literature to explore global patterns of emerging vector-borne zoonotic diseases (VBZDs) under changing global conditions. We find that the vast majority of emerging VBZDs are transmitted by ticks (Ixodidae) and mosquitoes (Culicidae) and the pathogens transmitted are dominated by Rickettsiaceae bacteria and RNA viruses (Flaviviridae, Bunyaviridae, and Togaviridae). The most common potential driver of these emerging zoonoses is land use change, but for many diseases, the driver is unknown, revealing a critical research gap. While most reported VBZDs are emerging in the northern latitudes, after correcting for sampling bias, Africa is clearly a region with the greatest share of emerging VBZD. We highlight critical gaps in our understanding of VBZD emergence and emphasize the importance of interdisciplinary research and consideration of deeper evolutionary processes to improve our capacity for anticipating where and how such diseases have and will continue to emerge.

    View details for DOI 10.1089/vbz.2018.2432

    View details for PubMedID 31800374

  • Drivers and patterns of microbial community assembly in a Lyme disease vector. Ecology and evolution Couper, L. I., Kwan, J. Y., Ma, J. n., Swei, A. n. 2019; 9 (13): 7768–79


    Vector-borne diseases constitute a major global health burden and are increasing in geographic range and prevalence. Mounting evidence has demonstrated that the vector microbiome can impact pathogen dynamics, making the microbiome a focal point in vector-borne disease ecology. However, efforts to generalize preliminary findings across studies and systems and translate these findings into disease control strategies are hindered by a lack of fundamental understanding of the processes shaping the vector microbiome and the interactions therein. Here, we use 16S rRNA sequencing and apply a community ecology framework to analyze microbiome community assembly and interactions in Ixodes pacificus, the Lyme disease vector in the western United States. We find that vertical transmission routes drive population-level patterns in I. pacificus microbial diversity and composition, but that microbial function and overall abundance do not vary over time or between clutches. Further, we find that the I. pacificus microbiome is not strongly structured based on competition but assembles nonrandomly, potentially due to vector-specific filtering processes which largely eliminate all but the dominant endosymbiont, Rickettsia. At the scale of the individual I. pacificus, we find support for a highly limited internal microbial community, and hypothesize that the tick endosymbiont may be the most important component of the vector microbiome in influencing pathogen dynamics.

    View details for DOI 10.1002/ece3.5361

    View details for PubMedID 31346439

    View details for PubMedCentralID PMC6635933

  • Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing JOVE-JOURNAL OF VISUALIZED EXPERIMENTS Couper, L., Swei, A. 2018


    In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.

    View details for DOI 10.3791/58239

    View details for Web of Science ID 000444913100137

    View details for PubMedID 30199026

    View details for PubMedCentralID PMC6231894