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Kalmouni J, Will JB, Townsend J, Paaijmans KP. Temperature and time of host-seeking activity impact the efficacy of chemical control interventions targeting the West Nile virus vector, Culex tarsalis. PLoS Negl Trop Dis 2024; 18:e0012460. [PMID: 39213461 PMCID: PMC11392387 DOI: 10.1371/journal.pntd.0012460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 09/12/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
West Nile virus (WNV) is the leading mosquito-borne disease causing-pathogen in the United States. Concerningly, there are no prophylactics or drug treatments for WNV and public health programs rely heavily on vector control efforts to lessen disease incidence. Insecticides can be effective in reducing vector numbers if implemented strategically, but can diminish in efficacy and promote insecticide resistance otherwise. Vector control programs which employ mass-fogging applications of insecticides, often conduct these methods during the late-night hours, when diel temperatures are coldest, and without a-priori knowledge on daily mosquito activity patterns. This study's aims were to 1) quantify the effect of temperature on the toxicity of two conventional insecticides used in fogging applications (malathion and deltamethrin) to Culex tarsalis, an important WNV vector, and 2) quantify the time of host-seeking of Cx. tarsalis and other local mosquito species in Maricopa County, Arizona. The temperature-toxicity relationship of insecticides was assessed using the WHO tube bioassay, and adult Cx. tarsalis, collected as larvae, were exposed to three different insecticide doses at three temperature regimes (15, 25, and 35°C; 80% RH). Time of host-seeking was assessed using collection bottle rotators with encephalitis vector survey traps baited with dry ice, first at 3h intervals during a full day, followed by 1h intervals during the night-time. Malathion became less toxic at cooler temperatures at all doses, while deltamethrin was less toxic at cooler temperatures at the low dose. Regarding time of host-seeking, Cx. tarsalis, Aedes vexans, and Culex quinquefasciatus were the most abundant vectors captured. During the 3-hour interval surveillance over a full day, Cx. tarsalis were most-active during post-midnight biting (00:00-06:00), accounting for 69.0% of all Cx. tarsalis, while pre-midnight biting (18:00-24:00) accounted for 30.0% of Cx. tarsalis. During the 1-hour interval surveillance overnight, Cx. tarsalis were most-active during pre-midnight hours (18:00-24:00), accounting for 50.2% of Cx. tarsalis captures, while post-midnight biting (00:00-06:00) accounted for 49.8% of Cx. tarsalis. Our results suggest that programs employing large-scale applications of insecticidal fogging should consider temperature-toxicity relationships coupled with time of host-seeking data to maximize the efficacy of vector control interventions in reducing mosquito-borne disease burden.
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Affiliation(s)
- Joshua Kalmouni
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - James B Will
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, Arizona, United States of America
| | - John Townsend
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, Arizona, United States of America
| | - Krijn P Paaijmans
- The Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Simon A. Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, Arizona, United States of America
- WITS Research Institute for Malaria (WRIM), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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2
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Penha VADS, Manica LT, Barrand ZA, Hepp CM, McGraw KJ. Correlates of Co-Infection with Coccidiosis and Avian Malaria in House Finches (Haemorhous mexicanus). J Wildl Dis 2024; 60:634-646. [PMID: 38741368 DOI: 10.7589/jwd-d-23-00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/11/2024] [Indexed: 05/16/2024]
Abstract
Pathogens have traditionally been studied in isolation within host systems; yet in natural settings they frequently coexist. This raises questions about the dynamics of co-infections and how host life-history traits might predict co-infection versus single infection. To address these questions, we investigated the presence of two parasites, a gut parasite (Isospora coccidians) and a blood parasite (Plasmodium spp.), in House Finches (Haemorhous mexicanus), a common passerine bird in North America. We then correlated these parasitic infections with various health and condition metrics, including hematological parameters, plasma carotenoids, lipid-soluble vitamins, blood glucose concentration, body condition, and prior disease history. Our study, based on 48 birds captured in Tempe, Arizona, US, in October 2021, revealed that co-infected birds exhibited elevated circulating lutein levels and a higher heterophil:lymphocyte ratio (H/L ratio) compared to those solely infected with coccidia Isospora spp. This suggests that co-infected birds experience heightened stress and may use lutein to bolster immunity against both pathogens, and that there are potentially toxic effects of lutein in co-infected birds compared to those infected solely with coccidia Isospora sp. Our findings underscore the synergistic impact of coparasitism, emphasizing the need for more co-infection studies to enhance our understanding of disease dynamics in nature, as well as its implications for wildlife health and conservation efforts.
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Affiliation(s)
- Victor Aguiar de Souza Penha
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal do Paraná, Setor de Ciências Biológicas, 100 Cel. Francisco H. dos Santos Avenue, Curitiba, Paraná 81531-980, Brazil
- School of Life Sciences, Arizona State University, ASU Life Sciences Building E, 400 E Tyler Mal, Tempe, Arizona 85287, USA
- Organismal and Evolutionary Research Programme, University of Helsinki, Biokeskus 3, PL 65 (Viikinkaari 1), Helsinki 00014, Finland
| | - Lilian Tonelli Manica
- Departamento de Zoologia, Setor de Ciências Biológicas, Universidade Federal do Paraná, Avenida Cel. Francisco H. dos Santos Avenue, 100, Curitiba, Paraná 81531-980, Brazil
| | - Zachary A Barrand
- Pathogen and Microbiome Institute, Northern Arizona University, Building 56, 1395 South Knoles Drive, Flagstaff, Arizona 86011, USA
- Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, Arizona 86001, USA
| | - Crystal M Hepp
- Pathogen and Microbiome Institute, Northern Arizona University, Building 56, 1395 South Knoles Drive, Flagstaff, Arizona 86011, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Building 90, 1295 South Knoles Drive, Flagstaff, Arizona 86011, USA
| | - Kevin J McGraw
- School of Life Sciences, Arizona State University, ASU Life Sciences Building E, 400 E Tyler Mal, Tempe, Arizona 85287, USA
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3
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Jobe NB, Franz NM, Johnston MA, Malone AB, Ruberto I, Townsend J, Will JB, Yule KM, Paaijmans KP. The Mosquito Fauna of Arizona: Species Composition and Public Health Implications. INSECTS 2024; 15:432. [PMID: 38921147 PMCID: PMC11203593 DOI: 10.3390/insects15060432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
Arizona is home to many mosquito species, some of which are known vectors of infectious diseases that harm both humans and animals. Here, we provide an overview of the 56 mosquito species that have been identified in the State to date, but also discuss their known feeding preference and the diseases they can (potentially) transmit to humans and animals. This list is unlikely to be complete for several reasons: (i) Arizona's mosquitoes are not systematically surveyed in many areas, (ii) surveillance efforts often target specific species of interest, and (iii) doubts have been raised by one or more scientists about the accuracy of some collection records, which has been noted in this article. There needs to be an integrated and multifaceted surveillance approach that involves entomologists and epidemiologists, but also social scientists, wildlife ecologists, ornithologists, representatives from the agricultural department, and irrigation and drainage districts. This will allow public health officials to (i) monitor changes in current mosquito species diversity and abundance, (ii) monitor the introduction of new or invasive species, (iii) identify locations or specific populations that are more at risk for mosquito-borne diseases, and (iv) effectively guide vector control.
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Affiliation(s)
- Ndey Bassin Jobe
- The Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA; (N.B.J.); (A.B.M.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Nico M. Franz
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
| | - Murray A. Johnston
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA;
| | - Adele B. Malone
- The Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA; (N.B.J.); (A.B.M.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ 85009, USA; (J.T.); (J.B.W.)
| | - Irene Ruberto
- Arizona Department of Health Services, Phoenix, AZ 85007, USA;
| | - John Townsend
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ 85009, USA; (J.T.); (J.B.W.)
| | - James B. Will
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ 85009, USA; (J.T.); (J.B.W.)
| | - Kelsey M. Yule
- Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ 85281, USA;
| | - Krijn P. Paaijmans
- The Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA; (N.B.J.); (A.B.M.)
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA;
- Simon A. Levin Mathematical, Computational and Modeling Sciences Center, Arizona State University, Tempe, AZ 85281, USA
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4
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Ward MJ, Sorek‐Hamer M, Henke JA, Little E, Patel A, Shaman J, Vemuri K, DeFelice NB. A Spatially Resolved and Environmentally Informed Forecast Model of West Nile Virus in Coachella Valley, California. GEOHEALTH 2023; 7:e2023GH000855. [PMID: 38077289 PMCID: PMC10702611 DOI: 10.1029/2023gh000855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 01/11/2024]
Abstract
West Nile virus (WNV) is the most significant arbovirus in the United States in terms of both morbidity and mortality. West Nile exists in a complex transmission cycle between avian hosts and the arthropod vector, Culex spp. mosquitoes. Human spillover events occur when humans are bitten by an infected mosquito and predicting these rates of infection and therefore the risk to humans may be associated with fluctuations in environmental conditions. In this study, we evaluate the hydrological and meteorological drivers associated with mosquito biology and viral development to determine if these associations can be used to forecast seasonal mosquito infection rates with WNV in the Coachella Valley of California. We developed and tested a spatially resolved ensemble forecast model of the WNV mosquito infection rate in the Coachella Valley using 17 years of mosquito surveillance data and North American Land Data Assimilation System-2 environmental data. Our multi-model inference system indicated that the combination of a cooler and dryer winter, followed by a wetter and warmer spring, and a cooler than normal summer was most predictive of the prevalence of West Nile positive mosquitoes in the Coachella Valley. The ability to make accurate early season predictions of West Nile risk has the potential to allow local abatement districts and public health entities to implement early season interventions such as targeted adulticiding and public health messaging before human transmission occurs. Such early and targeted interventions could better mitigate the risk of WNV to humans.
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Affiliation(s)
- Matthew J. Ward
- Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Meytar Sorek‐Hamer
- Universities Space Research Association (USRA) at NASA Ames Research CenterMoffett FieldCAUSA
| | | | - Eliza Little
- Connecticut Department of Public HealthHartfordCTUSA
| | - Aman Patel
- Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Jeffery Shaman
- Columbia Climate SchoolNew YorkNYUSA
- Mailman School of Public HealthNew YorkNYUSA
| | - Krishna Vemuri
- Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Nicholas B. DeFelice
- Environmental Medicine and Public HealthIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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Tešović B, Nišavić J, Banović Đeri B, Petrović T, Radalj A, Šekler M, Matović K, Debeljak Z, Vasković N, Dmitrić M, Vidanović D. Development of multiplex PCR based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological samples using Oxford Nanopore platform. Diagn Microbiol Infect Dis 2023; 105:115852. [PMID: 36427437 DOI: 10.1016/j.diagmicrobio.2022.115852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 11/08/2022]
Abstract
West Nile virus (WNV) can affect humans, birds, horses and another mammals, causing asymptomatic infection, mild febrile disease, neurological and systematic disease and death. In order to gain insight into the prevalence of WNV, a monitoring program has been established in the Republic of Serbia. Whole genome sequencing is essential for the molecular epizootiological analysis of virus entry and transmission routes, especially in high-risk regions. This paper describes the development of a multiplex PCR based NGS protocol for whole genome sequencing of WNV lineage 2 directly from biological samples using Oxford Nanopore (ONT) platform. The results obtained using this platform, confirmed by Sanger sequencing, indicate that this protocol can be applied to obtain whole sequences of the WNV genome, even when the virus concentration in the sample is medium, Ct value is approximately 30. The use of this protocol does not require prior virus isolation on cell culture nor the depletion of host nucleic acids.
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Affiliation(s)
- Bojana Tešović
- Veterinary Specilaized Institute "Kraljevo", Kraljevo, Serbia.
| | - Jakov Nišavić
- Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Bojana Banović Đeri
- Institute of molecular genetic and genetic engineering, University of Belgrade, Belgrade, Serbia
| | - Tamaš Petrović
- Scientific Veterinary Institute Novi Sad, Novi Sad, Serbia
| | - Andrea Radalj
- Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Milanko Šekler
- Veterinary Specilaized Institute "Kraljevo", Kraljevo, Serbia
| | - Kazimir Matović
- Veterinary Specilaized Institute "Kraljevo", Kraljevo, Serbia
| | - Zoran Debeljak
- Veterinary Specilaized Institute "Kraljevo", Kraljevo, Serbia
| | - Nikola Vasković
- Veterinary Specilaized Institute "Kraljevo", Kraljevo, Serbia
| | - Marko Dmitrić
- Veterinary Specilaized Institute "Kraljevo", Kraljevo, Serbia
| | - Dejan Vidanović
- Veterinary Specilaized Institute "Kraljevo", Kraljevo, Serbia
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6
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Ridenour CL, Cocking J, Poidmore S, Erickson D, Brock B, Valentine M, Roe CC, Young SJ, Henke JA, Hung KY, Wittie J, Stefanakos E, Sumner C, Ruedas M, Raman V, Seaton N, Bendik W, Hornstra O’Neill HM, Sheridan K, Centner H, Lemmer D, Fofanov V, Smith K, Will J, Townsend J, Foster JT, Keim PS, Engelthaler DM, Hepp CM. St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event. Front Genet 2021; 12:667895. [PMID: 34168675 PMCID: PMC8217752 DOI: 10.3389/fgene.2021.667895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022] Open
Abstract
Since the reemergence of St. Louis Encephalitis (SLE) Virus (SLEV) in the Southwest United States, identified during the 2015 outbreak in Arizona, SLEV has been seasonally detected within Culex spp. populations throughout the Southwest United States. Previous work revealed the 2015 outbreak was caused by an importation of SLEV genotype III, which had only been detected previously in Argentina. However, little is known about when the importation occurred or the transmission and genetic dynamics since its arrival into the Southwest. In this study, we sought to determine whether the annual detection of SLEV in the Southwest is due to enzootic cycling or new importations. To address this question, we analyzed 174 SLEV genomes (142 sequenced as part of this study) using Bayesian phylogenetic analyses to estimate the date of arrival into the American Southwest and characterize the underlying population structure of SLEV. Phylogenetic clustering showed that SLEV variants circulating in Maricopa and Riverside counties form two distinct populations with little evidence of inter-county transmission since the onset of the outbreak. Alternatively, it appears that in 2019, Yuma and Clark counties experienced annual importations of SLEV that originated in Riverside and Maricopa counties. Finally, the earliest representatives of SLEV genotype III in the Southwest form a polytomy that includes both California and Arizona samples. We propose that the initial outbreak most likely resulted from the importation of a population of SLEV genotype III variants, perhaps in multiple birds, possibly multiple species, migrating north in 2013, rather than a single variant introduced by one bird.
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Affiliation(s)
- Chase L. Ridenour
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jill Cocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Samuel Poidmore
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Daryn Erickson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Breezy Brock
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Michael Valentine
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Chandler C. Roe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Steven J. Young
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jennifer A. Henke
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Kim Y. Hung
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Jeremy Wittie
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | | | - Chris Sumner
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Martha Ruedas
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Vivek Raman
- Southern Nevada Health District, Las Vegas, NV, United States
| | - Nicole Seaton
- Southern Nevada Health District, Las Vegas, NV, United States
| | - William Bendik
- Southern Nevada Health District, Las Vegas, NV, United States
| | | | - Krystal Sheridan
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Heather Centner
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Viacheslav Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Kirk Smith
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - James Will
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - John Townsend
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jeffrey T. Foster
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Crystal M. Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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Casimiro-Soriguer CS, Perez-Florido J, Fernandez-Rueda JL, Pedrosa-Corral I, Guillot-Sulay V, Lorusso N, Martinez-Gonzalez LJ, Navarro-Marí JM, Dopazo J, Sanbonmatsu-Gámez S. Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain). Viruses 2021; 13:836. [PMID: 34063166 PMCID: PMC8148183 DOI: 10.3390/v13050836] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 12/17/2022] Open
Abstract
During recent decades West Nile Virus (WNV) outbreaks have continuously occurred in the Mediterranean area. In August 2020 a new WNV outbreak affected 71 people with meningoencephalitis in Andalusia and six more cases were detected in Extremadura (south-west of Spain), causing a total of eight deaths. The whole genomes of four viruses were obtained and phylogenetically analyzed in the context of recent outbreaks. The Andalusian viral samples belonged to lineage 1 and were relatively similar to those of previous outbreaks which occurred in the Mediterranean region. Here we present a detailed analysis of the outbreak, including an extensive phylogenetic study. As part on this effort, we implemented a local Nextstrain server, which has become a constituent piece of regional epidemiological surveillance, wherein forthcoming genomes of environmental samples or, eventually, future outbreaks, will be included.
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Affiliation(s)
- Carlos S. Casimiro-Soriguer
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.S.C.-S.); (J.P.-F.); (J.L.F.-R.)
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Javier Perez-Florido
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.S.C.-S.); (J.P.-F.); (J.L.F.-R.)
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Jose L. Fernandez-Rueda
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.S.C.-S.); (J.P.-F.); (J.L.F.-R.)
| | - Irene Pedrosa-Corral
- Laboratorio de Referencia de Virus de Andalucía, Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain; (I.P.-C.); (V.G.-S.); (J.M.N.-M.)
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
| | - Vicente Guillot-Sulay
- Laboratorio de Referencia de Virus de Andalucía, Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain; (I.P.-C.); (V.G.-S.); (J.M.N.-M.)
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
| | - Nicola Lorusso
- Dirección General de Salud Pública y Ordenación Farmacéutica, Consejería de Salud y Familias, Junta de Andalucía, 41020, Sevilla, Spain;
| | - Luis Javier Martinez-Gonzalez
- GENYO, Centre for Genomics and Oncological Research: Pfizer—University of Granada—Andalusian Regional Government, 18016 Granada, Spain;
| | - Jose M. Navarro-Marí
- Laboratorio de Referencia de Virus de Andalucía, Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain; (I.P.-C.); (V.G.-S.); (J.M.N.-M.)
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
| | - Joaquin Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocio, 41013 Sevilla, Spain; (C.S.C.-S.); (J.P.-F.); (J.L.F.-R.)
- Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013 Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
- ELIXIR.ES/FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
| | - Sara Sanbonmatsu-Gámez
- Laboratorio de Referencia de Virus de Andalucía, Servicio de Microbiología, Hospital Virgen de las Nieves, 18014 Granada, Spain; (I.P.-C.); (V.G.-S.); (J.M.N.-M.)
- Instituto de Investigación Biosanitaria, ibs.GRANADA, 18012 Granada, Spain
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8
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Furstenau TN, Cocking JH, Hepp CM, Fofanov VY. Sample pooling methods for efficient pathogen screening: Practical implications. PLoS One 2020; 15:e0236849. [PMID: 33175841 PMCID: PMC7657563 DOI: 10.1371/journal.pone.0236849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/14/2020] [Indexed: 01/06/2023] Open
Abstract
Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.
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Affiliation(s)
- Tara N. Furstenau
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jill H. Cocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M. Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Viacheslav Y. Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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9
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Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P. Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. Nat Commun 2020; 11:5620. [PMID: 33159066 PMCID: PMC7648063 DOI: 10.1038/s41467-020-19122-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/30/2020] [Indexed: 01/05/2023] Open
Abstract
Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 Avenue FD Roosevelt, 1050, Bruxelles, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Sebastian Lequime
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Paul Bastide
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yi Tan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Infectious Diseases Group, J. Craig Venter Institute, Rockville, MD, USA
| | | | - Alexander A Fisher
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Martha I Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 Avenue FD Roosevelt, 1050, Bruxelles, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
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10
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Hadfield J, Brito AF, Swetnam DM, Vogels CBF, Tokarz RE, Andersen KG, Smith RC, Bedford T, Grubaugh ND. Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain. PLoS Pathog 2019; 15:e1008042. [PMID: 31671157 PMCID: PMC6822705 DOI: 10.1371/journal.ppat.1008042] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It has been 20 years since West Nile virus first emerged in the Americas, and since then, little progress has been made to control outbreaks caused by this virus. After its first detection in New York in 1999, West Nile virus quickly spread across the continent, causing an epidemic of human disease and massive bird die-offs. Now the virus has become endemic to the United States, where an estimated 7 million human infections have occurred, making it the leading mosquito-borne virus infection and the most common cause of viral encephalitis in the country. To bring new attention to one of the most important mosquito-borne viruses in the Americas, we provide an interactive review using Nextstrain: a visualization tool for real-time tracking of pathogen evolution (nextstrain.org/WNV/NA). Nextstrain utilizes a growing database of more than 2,000 West Nile virus genomes and harnesses the power of phylogenetics for students, educators, public health workers, and researchers to visualize key aspects of virus spread and evolution. Using Nextstrain, we use virus genomics to investigate the emergence of West Nile virus in the U S, followed by its rapid spread, evolution in a new environment, establishment of endemic transmission, and subsequent international spread. For each figure, we include a link to Nextstrain to allow the readers to directly interact with and explore the underlying data in new ways. We also provide a brief online narrative that parallels this review to further explain the data and highlight key epidemiological and evolutionary features (nextstrain.org/narratives/twenty-years-of-WNV). Mirroring the dynamic nature of outbreaks, the Nextstrain links provided within this paper are constantly updated as new West Nile virus genomes are shared publicly, helping to stay current with the research. Overall, our review showcases how genomics can track West Nile virus spread and evolution, as well as potentially uncover novel targeted control measures to help alleviate its public health burden.
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Affiliation(s)
- James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Anderson F. Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Daniele M. Swetnam
- Department of Pathology, Microbiology and Immunology, University of California, Davis, Davis, California, United States of America
| | - Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Ryan E. Tokarz
- Department of Entomology, Iowa State University, Ames, Iowa, United States of America
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, United States of America
- Scripps Research Translational Institute, La Jolla, California, United States of America
| | - Ryan C. Smith
- Department of Entomology, Iowa State University, Ames, Iowa, United States of America
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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11
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Hepp CM. Towards Translational Epidemiology: Next-Generation Sequencing and Phylogeography as Epidemiological Mainstays. mSystems 2019; 4:e00119-19. [PMID: 31186309 PMCID: PMC6584875 DOI: 10.1128/msystems.00119-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/24/2019] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing, coupled with the development of user-friendly software, has achieved a level of accessibility that is revolutionizing the way we approach epidemiological investigations. We can sequence pathogen genomes and conduct phylogenetic analyses to assess transmission, identify from which country or city a pathogen originated, or which contaminated potluck item resulted in widespread foodborne illness. However, until recently, these types of studies have been rarities, limited to specific investigations usually conducted over the short term. Given the feasibility and realized public health benefits of ascertaining pathogen relationships, federal, state, and county agencies are building their sequencing capacities, either through acquisition of equipment or collaborative activities. In this perspective, I detail research projects that our group collaborates on with county and state public health agencies, where the objective is to identify pathogen source locations with the longer-term goal of implementing proactive interventions.
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Affiliation(s)
- Crystal M Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, USA
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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12
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Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol 2019; 20:8. [PMID: 30621750 PMCID: PMC6325816 DOI: 10.1186/s13059-018-1618-7] [Citation(s) in RCA: 571] [Impact Index Per Article: 114.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 12/26/2018] [Indexed: 01/17/2023] Open
Abstract
How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. We demonstrate the utility of PrimalSeq by measuring Zika and West Nile virus diversity from varied sample types and show that the accumulation of genetic diversity is influenced by experimental and biological systems.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jaqueline Goes De Jesus
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
- Laboratory of Experimental Pathology, Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil
| | - Bradley J Main
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, 95616, USA
| | - Amanda L Tan
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA
| | - Doug E Brackney
- Department of Environmental Sciences, The Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Saran Grewal
- Department of Environmental Health, San Diego County Vector Control Program, San Diego, CA, 92123, USA
| | - Nikos Gurfield
- Department of Environmental Health, San Diego County Vector Control Program, San Diego, CA, 92123, USA
| | - Koen K A Van Rompay
- California National Primate Research Center and Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, 95616, USA
| | - Sharon Isern
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, 33965, USA
| | - Lark L Coffey
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, 95616, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
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