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Martyn C, Hayes BM, Lauko D, Midthun E, Castaneda G, Bosco-Lauth A, Salkeld DJ, Kistler A, Pollard KS, Chou S. Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements. mSystems 2024; 9:e0032124. [PMID: 38742892 DOI: 10.1128/msystems.00321-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. In addition to commonly found tick-associated microbes, we assembled 11 novel RNA virus genomes from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae and two highly divergent RNA virus genomes lacking sequence similarity to any known viral families. We experimentally verified the presence of these in I. pacificus ticks across several life stages. We also unexpectedly identified numerous virus-like transcripts that are likely encoded by tick genomic DNA, and which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Taken together, our work reveals that I. pacificus ticks carry a greater diversity of viruses than previously appreciated, in some cases resulting in evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick-virus interactions are, with major implications for both the fundamental biology and vectorial capacity of I. pacificus ticks. IMPORTANCE Ticks are increasingly important vectors of disease, particularly in the United States where expanding tick ranges and intrusion into previously wild areas has resulted in increasing human exposure to ticks. Emerging human pathogens have been identified in ticks at an increasing rate, and yet little is known about the full community of microbes circulating in various tick species, a crucial first step to understanding how they interact with each and their tick host, as well as their ability to cause disease in humans. We investigated the bacterial and viral communities of the Western blacklegged tick in California and found 11 previously uncharacterized viruses circulating in this population.
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Affiliation(s)
- Calla Martyn
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
- Gladstone Institute of Data Science & Biotechnology, San Francisco, California, USA
| | - Beth M Hayes
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
- One Health Institute, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Domokos Lauko
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
| | - Edward Midthun
- Department of Biomedical Sciences, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Gloria Castaneda
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
| | - Angela Bosco-Lauth
- Department of Biomedical Sciences, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Daniel J Salkeld
- Department of Biology, Colorado State University-Fort Collins, Fort Collins, Colorado, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science & Biotechnology, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Seemay Chou
- Department of Biochemistry & Biophysics, University of California-San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, San Francisco, California, USA
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Adhikari BN, Paskey AC, Frey KG, Bennett AJ, Long KA, Kuhn JH, Hamilton T, Glang L, Cer RZ, Goldberg TL, Bishop-Lilly KA. Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms. Virology 2024; 591:109992. [PMID: 38246037 PMCID: PMC10849055 DOI: 10.1016/j.virol.2024.109992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
We investigated the virome of agaonid fig wasps (Ceratosolen spp.) inside syconia ("fruits") of various Ficus trees fed upon by frugivores such as pteropodid bats in Sub-Saharan Africa. This virome includes representatives of viral families spanning four realms and includes near-complete genome sequences of three novel viruses and fragments of five additional potentially novel viruses evolutionarily associated with insects, fungi, plants, and vertebrates. Our study provides evidence that frugivorous animals are exposed to a plethora of viruses by coincidental consumption of fig wasps, which are obligate pollinators of figs worldwide.
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Affiliation(s)
- Bishwo N Adhikari
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Adrian C Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Kyle A Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Global Health Institute, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Zoology, Makerere University, Kampala, Uganda
| | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA.
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Antúnez MP, Marín Montesinos JC, Corduneanu A, Obregón D, Moutailler S, Cabezas-Cruz A. Tick-borne viruses and their risk to public health in the Caribbean: Spotlight on bats as reservoirs in Cuba. Heliyon 2024; 10:e26118. [PMID: 38375245 PMCID: PMC10875593 DOI: 10.1016/j.heliyon.2024.e26118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
In recent decades, tick-borne diseases (TBDs) have surged and expanded globally due to factors like changes in human activities, land use patterns, and climate change, and it have been associated with the emergence of zoonotic diseases. Cuba faces the impact of ticks on human health and the economy. Although Cuba has studied TBDs extensively for the past 50 years, focus on tick-borne viral pathogens affecting humans remains scant. Despite TBDs not currently being a major health concern in Cuba, factors like inadequate clinician awareness, climate conditions, global tick emergence, and evidence of zoonotic pathogens in ticks underscore the importance of enhanced TBD surveillance in the country. Here we revised the available information on ticks as vectors of pathogenic viruses to humans, spotlighting bats as potential reservoirs of tick-borne viruses (TBVs). Ticks on bats have gained interest as potential reservoirs of pathogenic viruses to humans in Cuba and worldwide. Understanding their role in maintaining viruses and their potential transmission to humans is crucial for the implementation of surveillance and control programs to reduce the risk of tick-borne viral diseases and public health management.
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Affiliation(s)
- Maritza Pupo Antúnez
- Laboratorio de Virología. Departamento de Microbiología y Virología. Facultad de Biología, Universidad de la Habana, C.P. 10400, Plaza de la Revolución, Cuba
| | - José Carlos Marín Montesinos
- Laboratorio de Virología. Departamento de Microbiología y Virología. Facultad de Biología, Universidad de la Habana, C.P. 10400, Plaza de la Revolución, Cuba
| | - Alexandra Corduneanu
- Department of Animal Breeding and Animal Production, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca-Napoca, Romania
| | - Dasiel Obregón
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sara Moutailler
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
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Lin Y, Pascall DJ. Characterisation of putative novel tick viruses and zoonotic risk prediction. Ecol Evol 2024; 14:e10814. [PMID: 38259958 PMCID: PMC10800298 DOI: 10.1002/ece3.10814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.
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Affiliation(s)
- Yuting Lin
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
- Royal Veterinary CollegeUniversity of LondonLondonUK
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Lourenço EC, Famadas KM, Gomes LAC, Bergallo HG. Ticks (Ixodida) associated with bats (Chiroptera): an updated list with new records for Brazil. Parasitol Res 2023; 122:2335-2352. [PMID: 37597061 DOI: 10.1007/s00436-023-07935-y] [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: 04/17/2023] [Accepted: 08/01/2023] [Indexed: 08/21/2023]
Abstract
Bats harbor diverse groups of ectoparasites, such as insects and mites like ticks (Ixodida). Some species of ticks with records for bats and humans have already been reported with the occurrence of pathogens. This research article aims to document new geographical and host records of ticks infesting bats in Rio de Janeiro state, Southeastern Brazil, and provides a list of tick species associated with bats in Brazil. We counted 12 argasid ticks and five ixodid ticks associated with six individuals of bats. Larvae of Amblyomma sp., Ixodes sp., Ornithodoros sp., and Ornithodoros hasei and one nymph of Amblyomma sculptum parasitizing Artibeus obscurus, Phyllostomus hastatus, Micronycteris sp., Molossus fluminensis, and Carollia perspicillata in different localities of Rio de Janeiro state were studied. We carried out a systematic review with the descriptors: tick bat Brazil. We considered data from 42 articles in the systematic review. We compiled eleven records of Ixodidae, and 160 records of Argasidae. Ornithodoros cavernicolous were the most recorded tick species. Overall, we registered 171 tick-bat or roost-bat associations with 85 records of these infesting bats. The review also shows the occurrence of tick species associated with bats, and we present new records on ticks parasitizing bats in Brazil.
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Affiliation(s)
- Elizabete Captivo Lourenço
- Mammal Ecology Laboratory, Ecology Department, Rio de Janeiro State University, Rio de Janeiro, Rio de Janeiro state, Brazil.
| | - Kátia Maria Famadas
- Hemoparasites and Vectors Laboratory, Parasitology Animal Department, Rio de Janeiro Rural Federal University, Rio de Janeiro state, Seropédica, Brazil
| | - Luiz Antonio Costa Gomes
- Institutional Platform Biodiversity and Wildlife Health, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro state, Brazil
| | - Helena Godoy Bergallo
- Mammal Ecology Laboratory, Ecology Department, Rio de Janeiro State University, Rio de Janeiro, Rio de Janeiro state, Brazil
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Ortiz-Baez AS, Jaenson TGT, Holmes EC, Pettersson JHO, Wilhelmsson P. Substantial viral and bacterial diversity at the bat-tick interface. Microb Genom 2023; 9. [PMID: 36862584 PMCID: PMC10132063 DOI: 10.1099/mgen.0.000942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Ticks harbour a high diversity of viruses, bacteria and protozoa. The soft tick Carios vespertilionis (Argasidae) is a common ectoparasite of bats in the Palearctic region and is suspected to be vector and reservoir of viruses and other microbial species in bat populations, some of which may act as zoonotic agents for human disease. The Soprano pipistrelle (Pipistrellus pygmaeus, Vespertilionidae) is widely distributed in Europe, where it can be found inside or close to human habitation. We used meta-transcriptomic sequencing to determine the RNA virome and common microbiota in blood-fed C. vespertilionis ticks collected from a Soprano pipistrelle bat roosting site in south-central Sweden. Our analyses identified 16 viruses from 11 virus families, of which 15 viruses were novel. For the first time in Sweden we identified Issuk-Kul virus, a zoonotic arthropod-borne virus previously associated with outbreaks of acute febrile illness in humans. Probable bat-associated and tick-borne viruses were classified within the families Nairoviridae, Caliciviridae and Hepeviridae, while other invertebrate-associated viruses included members of the Dicistroviridae, Iflaviridae, Nodaviridae, Partitiviridae, Permutotetraviridae, Polycipiviridae and Solemoviridae. Similarly, we found abundant bacteria in C. vespertilionis, including genera with known tick-borne bacteria, such as Coxiella spp. and Rickettsia spp. These findings demonstrate the remarkable diversity of RNA viruses and bacteria present in C. vespertilionis and highlight the importance of bat-associated ectoparasite surveillance as an effective and non-invasive means to track viruses and bacteria circulating in bats and ticks.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - Thomas G T Jaenson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - John H-O Pettersson
- Sydney Institute for Infectious Diseases, School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, SE-751 23 Uppsala, Sweden.,Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, 75237 Uppsala, Sweden
| | - Peter Wilhelmsson
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, SE-581 83 Linköping, Sweden.,Department of Clinical Microbiology, Region Jönköping County, SE-553 05 Jönköping, Sweden
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Sequence diversity and evolution of a group of iflaviruses associated with ticks. Arch Virol 2021; 166:1843-1852. [PMID: 33870470 PMCID: PMC8195936 DOI: 10.1007/s00705-021-05060-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/15/2021] [Indexed: 11/21/2022]
Abstract
We studied a group of tick-associated viruses with characteristics of members of the family Iflaviridae, a family of viruses frequently found in arthropods. Our aim was to gain insight into the evolutionary dynamics of this group of viruses, which may be linked to the biology of ticks. We explored assembled RNA-Seq data sets for different species of ticks. We identified members of five different iflavirus species, four of them novel, and discovered nine new genome sequences, including variants. Five variants represented a virus species associated with Ixodes ricinus. Unexpectedly, a sequence found in the Ixodes scapularis cell line ISE6 was nearly identical to the sequences of I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Analysing patterns of substitutions between these variants, we detected a strong excess of synonymous mutations, suggesting evolution under strong positive selection. The phylogenies of the viruses and of their tick hosts were not congruent, suggesting recurrent host changes across tick genera during their evolution. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.
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Barbier E, Bernard E, Dantas-Torres F. Ecology of Antricola ticks in a bat cave in north-eastern Brazil. EXPERIMENTAL & APPLIED ACAROLOGY 2020; 82:255-264. [PMID: 32920651 DOI: 10.1007/s10493-020-00544-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Argasid ticks are a diverse group of acarines that parasitize numerous vertebrate hosts. Along with birds, bats serve as hosts for several argasid ticks, which are commonly found in bat caves. Argasid ticks have regained attention from tick taxonomists in recent decades, with a number of new species described in various zoogeographical regions. Nonetheless, studies on their ecology are still scarce. We conducted a 1-year longitudinal study to assess the presence of argasid ticks in a bat cave in the drylands of north-eastern Brazil and evaluate their possible response to abiotic factors. From July 2014 to June 2015, 490 ticks were collected (272 nymphs, 169 males and 49 females) in a cave chamber hosting a large colony of Pteronotus spp. bats, being relatively more frequent from July to December 2014. Adults were identified as Antricola guglielmonei, whereas nymphs were assigned to the genus Antricola. Almost all ticks (98%) were collected on the cave walls. Only 2% were on the ceiling and, surprisingly, no specimens were found on the floor and/or guano. Adults were usually clustered in the crevices and little mobile, whereas nymphs were dispersed and more active, moving over the walls or ceiling of the cave. Although present in most of the studied period, there was a significantly negative correlation between tick abundance and relatively humidity, and A. guglielmonei was more frequent during the dry season. Moreover, there was no evident correlation between the abundance of ticks and bats. Further long-term studies will be able to verify whether this pattern is repeated over time, and even whether other variables can influence the population dynamics of A. guglielmonei.
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Affiliation(s)
- Eder Barbier
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Programa de Pós-graduação em Biologia Animal, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Enrico Bernard
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Programa de Pós-graduação em Biologia Animal, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Filipe Dantas-Torres
- Laboratório de Imunoparasitologia, Departamento de Imunologia, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (Fiocruz), Recife, PE, Brazil.
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Akello JO, Leib SL, Engler O, Beuret C. Evaluation of Viral RNA Recovery Methods in Vectors by Metagenomic Sequencing. Viruses 2020; 12:v12050562. [PMID: 32438629 PMCID: PMC7290855 DOI: 10.3390/v12050562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022] Open
Abstract
Identification and characterization of viral genomes in vectors including ticks and mosquitoes positive for pathogens of great public health concern using metagenomic next generation sequencing (mNGS) has challenges. One such challenge is the ability to efficiently recover viral RNA which is typically dependent on sample processing. We evaluated the quantitative effect of six different extraction methods in recovering viral RNA in vectors using negative tick homogenates spiked with serial dilutions of tick-borne encephalitis virus (TBEV) and surrogate Langat virus (LGTV). Evaluation was performed using qPCR and mNGS. Sensitivity and proof of concept of optimal method was tested using naturally positive TBEV tick homogenates and positive dengue, chikungunya, and Zika virus mosquito homogenates. The amount of observed viral genome copies, percentage of mapped reads, and genome coverage varied among different extractions methods. The developed Method 5 gave a 120.8-, 46-, 2.5-, 22.4-, and 9.9-fold increase in the number of viral reads mapping to the expected pathogen in comparison to Method 1, 2, 3, 4, and 6, respectively. Our developed Method 5 termed ROVIV (Recovery of Viruses in Vectors) greatly improved viral RNA recovery and identification in vectors using mNGS. Therefore, it may be a more sensitive method for use in arbovirus surveillance.
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Affiliation(s)
- Joyce Odeke Akello
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Hochschulstrasse 4, 3012 Bern, Switzerland
- Correspondence: (J.O.A.); (C.B.); Tel.: +41-316328646 (J.O.A.); +41-584681664 (C.B.)
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3001 Bern, Switzerland;
| | - Olivier Engler
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
| | - Christian Beuret
- Biology Division, Spiez Laboratory, Swiss Federal Office for Civil Protection, Austrasse, CH-3700 Spiez, Switzerland;
- Correspondence: (J.O.A.); (C.B.); Tel.: +41-316328646 (J.O.A.); +41-584681664 (C.B.)
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