Total RNA sequencing of Phlebotomus chinensis sandflies in China revealed viral, bacterial, and eukaryotic microbes potentially pathogenic to humans

References

• Mayer SV, Tesh RB, Vasilakis N. The emergence of arthropod-borne viral diseases: a global prospective on dengue, chikungunya and Zika fevers. Acta Trop. 2017 Feb;166:155–163.
   PubMed Web of Science ®Google Scholar
• Lloyd-Smith JO, George D, Pepin KM, et al. Epidemic dynamics at the human-animal interface. Science. 2009 Dec 4;326(5958):1362–1367.
   PubMed Web of Science ®Google Scholar
• Faria NR, Azevedo R, Kraemer MUG, et al. Zika virus in the americas: early epidemiological and genetic findings. Science. 2016 Apr 15;352(6283):345–349.
   PubMed Web of Science ®Google Scholar
• Liang G, Li X, Gao X, et al. Arboviruses and their related infections in China: a comprehensive field and laboratory investigation over the last 3 decades. Rev Med Virol. 2018 Jan;28(1):e1959.
   Web of Science ®Google Scholar
• Cecílio P, Cordeiro-da-Silva A, Oliveira F. Sand flies: basic information on the vectors of leishmaniasis and their interactions with leishmania parasites. Commun Biol. 2022;5(1):305.
   PubMed Web of Science ®Google Scholar
• Depaquit J, Grandadam M, Fouque F, et al. Arthropod-borne viruses transmitted by phlebotomine sandflies in Europe: a review. Euro Surveill. 2010 Mar 11;15(10):19507.
   PubMedGoogle Scholar
• Maran N, Gomes PS, Freire-de-Lima L, et al. Host resistance to visceral leishmaniasis: prevalence and prevention. Expert Rev Anti Infect Ther. 2016;14(4):435–442.
   PubMed Web of Science ®Google Scholar
• Li K, Chen H, Jiang J, et al. Diversity of bacteriome associated with Phlebotomus chinensis (Diptera: Psychodidae) sand flies in two wild populations from China. Sci Rep. 2016 Nov 7;6:36406.
   PubMed Web of Science ®Google Scholar
• Tesh RB. The genus Phlebovirus and its vectors. Annu Rev Entomol. 1988;33:169–181.
   PubMed Web of Science ®Google Scholar
• Wang J, Fu S, Xu Z, et al. Emerging sand fly-borne Phlebovirus in China. Emerg Infect Dis. 2020 Oct;26(10):2435–2438.
   PubMed Web of Science ®Google Scholar
• Wang J, Fan N, Fu S, et al. Isolation and characterization of Wuxiang Virus from sandflies collected in Yangquan County, Shanxi Province, China. Vector Borne Zoonotic Dis. 2021 Jun;21(6):446–457.
   PubMed Web of Science ®Google Scholar
• Xu Z, Fan N, Hou X, et al. Isolation and identification of a novel Phlebovirus, Hedi Virus, from sandflies collected in China. Viruses. 2021 Apr 27;13(5):772.
   PubMed Web of Science ®Google Scholar
• Xu X, Cheng J, Fu S, et al. Wuxiang virus Is a virus circulated naturally in Wuxiang County, China. Vector Borne Zoonotic Dis. 2021 Apr;21(4):289–300.
   PubMed Web of Science ®Google Scholar
• Shi M, Lin XD, Tian JH, et al. Redefining the invertebrate RNA virosphere. Nature. 2016 Dec 22;540(7634):539–543.
   PubMed Web of Science ®Google Scholar
• Li CX, Shi M, Tian JH, et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Elife. 2015 Jan 29;4:e05378.
   PubMed Web of Science ®Google Scholar
• Webster CL, Waldron FM, Robertson S, et al. The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster. PLoS Biol. 2015 Jul;13(7):e1002210.
   PubMed Web of Science ®Google Scholar
• He WT, Hou X, Zhao J, et al. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell. 2022 Mar 31;185(7):1117–1129 e8.
   PubMed Web of Science ®Google Scholar
• Shi M, Lin XD, Chen X, et al. The evolutionary history of vertebrate RNA viruses. Nature. 2018 Apr;556(7700):197–202.
   PubMed Web of Science ®Google Scholar
• Zayed AA, Wainaina JM, Dominguez-Huerta G, et al. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science. 2022 Apr 8;376(6589):156–162.
   PubMed Web of Science ®Google Scholar
• Feng Y, Gou QY, Yang WH, et al. A time-series meta-transcriptomic analysis reveals the seasonal, host, and gender structure of mosquito viromes. Virus Evol. 2022;8(1):veac006.
   PubMed Web of Science ®Google Scholar
• Shi M, White VL, Schlub T, et al. No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster. Proc Biol Sci. 2018 Jul 25;285(1883):20181165.
   PubMed Web of Science ®Google Scholar
• Batson J, Dudas G, Haas-Stapleton E, et al. Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay. Elife. 2021 Apr 27;10.
   PubMed Web of Science ®Google Scholar
• Shi M, Zhao S, Yu B, et al. Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China. PLoS Pathog. 2022 Feb;18(2):e1010259.
   PubMed Web of Science ®Google Scholar
• Fang C, Han-ming C, Hui-ying C, et al. Molecular characteristics of common sandflies species (Diptera: Psychodidae) in Hainan province. Chin J Vector Biol Control. 2018;29(1):15–19.
   Google Scholar
• Li D, Liu CM, Luo R, et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015 May 15;31(10):1674–1676.
   PubMed Web of Science ®Google Scholar
• Buchfink B, Reuter K, Drost HG. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021 Apr;18(4):366–368.
   PubMed Web of Science ®Google Scholar
• Clewley JP. Macintosh sequence analysis software. DNAStar's LaserGene. Mol Biotechnol. 1995 Jun;3(3):221–224.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4;9(4):357–359.
   PubMed Web of Science ®Google Scholar
• Kearse M, Moir R, Wilson A, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012 Jun 15;28(12):1647–1649.
   PubMed Web of Science ®Google Scholar
• Segata N, Waldron L, Ballarini A, et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012 Jun 10;9(8):811–814.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013 Apr;30(4):772–780.
   PubMed Web of Science ®Google Scholar
• Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009 Aug 1;25(15):1972–1973.
   PubMed Web of Science ®Google Scholar
• Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003 Oct;52(5):696–704.
   PubMed Web of Science ®Google Scholar
• Ringner M. What is principal component analysis? Nat Biotechnol. 2008 Mar;26(3):303–304.
   PubMed Web of Science ®Google Scholar
• Ni W, Zhang S, Jiang B, et al. Identification of cancer-related gene network in hepatocellular carcinoma by combined bioinformatic approach and experimental validation. Pathol Res Pract. 2019 Jun;215(6):152428.
   PubMed Web of Science ®Google Scholar
• Ito K, Murphy D. Application of ggplot2 to pharmacometric graphics. CPT Pharmacometrics Syst Pharmacol. 2013 Oct 16;2:e79.
   PubMedGoogle Scholar
• Kaur R, Shropshire JD, Cross KL, et al. Living in the endosymbiotic world of Wolbachia: A centennial review. Cell Host Microbe. 2021 Jun 9;29(6):879–893.
   PubMed Web of Science ®Google Scholar
• Kobayashi D, Watanabe M, Faizah AN, et al. Discovery of a novel flavivirus (Flaviviridae) from the horse fly, Tabanus rufidens (Diptera: Tabanidae): the possible coevolutionary relationships between the classical insect-specific flaviviruses and host dipteran insects. J Med Entomol. 2021 Mar 12;58(2):880–890.
   PubMed Web of Science ®Google Scholar
• Brown LD, Macaluso KR. Rickettsia felis, an emerging flea-borne rickettsiosis. Curr Trop Med Rep. 2016;3:27–39.
   PubMedGoogle Scholar
• Walker T, Johnson PH, Moreira LA, et al. The wMel Wolbachia strain blocks dengue and invades caged aedes aegypti populations. Nature. 2011 Aug 24;476(7361):450–453.
   PubMed Web of Science ®Google Scholar
• Shi M, Neville P, Nicholson J, et al. High-Resolution metatranscriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia. J Virol. 2017 Sep 1;91(17):e00680-17.
   PubMed Web of Science ®Google Scholar
• Hao Y, Hu X, Gong Y, et al. Spatio-temporal clustering of mountain-type zoonotic visceral Leishmaniasis in China between 2015 and 2019. PLoS Negl Trop Dis. 2021 Mar;15(3):e0009152.
   PubMed Web of Science ®Google Scholar
• Wei F, Shang L, Jin H, et al. Molecular detection and genetic diversity of Leishmania donovani in naturally infected Phlebotomus chinensi from southwestern China. Vector Borne Zoonotic Dis. 2011 Jul;11(7):849–852.
   PubMed Web of Science ®Google Scholar
• Travassos da Rosa AP, Tesh RB, Pinheiro FP, et al. Characterization of eight new phlebotomus fever serogroup arboviruses (Bunyaviridae: Phlebovirus) from the Amazon region of Brazil. Am J Trop Med Hyg. 1983 Sep;32(5):1164–1171.
   PubMed Web of Science ®Google Scholar
• Jia N, Zheng YC, Ma L, et al. Human infections with Rickettsia raoultii, China. Emerg Infect Dis. 2014 May;20(5):866–868.
   PubMed Web of Science ®Google Scholar
• Wang J. Isolation and identification of arbovirus in Shanxi Province, China—Sandfly-borne Phlebovirus is emerging in China. Qingdao University. 2020.
   Google Scholar
• Pettersson JH, Shi M, Bohlin J, et al. Characterizing the virome of Ixodes ricinus ticks from northern Europe. Sci Rep. 2017 Sep 7;7(1):10870.
   PubMed Web of Science ®Google Scholar
• Xu Z, Feng Y, Chen X, et al. Virome of Bat-infesting arthropods: highly divergent viruses in different vectors. J Virol. 2022 Feb 23;96(4):e0146421.
   PubMed Web of Science ®Google Scholar
• Beaurepaire A, Piot N, Doublet V, et al. Diversity and global distribution of viruses of the Western Honey bee, Apis mellifera. Insects. 2020 Apr 10;11(4):239.
   PubMed Web of Science ®Google Scholar
• Lay CL, Shi M, Bucek A, et al. Unmapped RNA virus diversity in termites and their symbionts. Viruses. 2020 Oct 9;12(10):1145.
   PubMed Web of Science ®Google Scholar
• Liu L, Shen Q, Li N, et al. Comparative viromes of Culicoides and mosquitoes reveal their consistency and diversity in viral profiles. Brief Bioinform. 2021 Jul;22(4):bbaa323.
   PubMed Web of Science ®Google Scholar
• Shi M, Zhang YZ, Holmes EC. Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Res. 2018 Jan 2;243:83–90.
   PubMed Web of Science ®Google Scholar
• Ye SH, Siddle KJ, Park DJ, et al. Benchmarking metagenomics tools for taxonomic classification. Cell. 2019 Aug 8;178(4):779–794.
   PubMed Web of Science ®Google Scholar
• McIntyre ABR, Ounit R, Afshinnekoo E, et al. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol. 2017 Sep 21;18(1):182.
   PubMed Web of Science ®Google Scholar
• Kim TG, Moon KE, Yun J, et al. Comparison of RNA- and DNA-based bacterial communities in a lab-scale methane-degrading biocover. Appl Microbiol Biotechnol. 2013 Apr;97(7):3171–3181.
   PubMed Web of Science ®Google Scholar
• Zheng X, Zhang D, Li Y, et al. Incompatible and sterile insect techniques combined eliminate mosquitoes. Nature. 2019 Aug;572(7767):56–61.
   PubMed Web of Science ®Google Scholar
• Dutra HL, Rocha MN, Dias FB, et al. Wolbachia blocks currently circulating Zika Virus Isolates in Brazilian Aedes aegypti mosquitoes. Cell Host Microbe. 2016 Jun 8;19(6):771–774.
   PubMed Web of Science ®Google Scholar
• Chrostek E, Marialva MS, Esteves SS, et al. Wolbachia variants induce differential protection to viruses in Drosophila melanogaster: a phenotypic and phylogenomic analysis. PLoS Genet. 2013;9(12):e1003896.
   PubMed Web of Science ®Google Scholar
• Martinez J, Longdon B, Bauer S, et al. Symbionts commonly provide broad spectrum resistance to viruses in insects: a comparative analysis of Wolbachia strains. PLoS Pathog. 2014 Sep;10(9):e1004369.
   PubMed Web of Science ®Google Scholar
• Wang A. Dissecting the molecular network of virus-plant interactions: the complex roles of host factors. Annu Rev Phytopathol. 2015;53:45–66.
   PubMed Web of Science ®Google Scholar