Abstract
The recent outbreak of Zika virus (ZIKV) in Brazil and other countries globally demonstrated the relevance of ZIKV studies. During and after this outbreak, there was an intense increase in scientific production on ZIKV infections, especially toward alterations promoted by the infection and related to clinical outcomes. Considering this massive amount of new data, mainly thousands of genes and proteins whose expression is impacted by ZIKV infection, the ZIKA Virus Infection Database (ZIKAVID) was created. ZIKAVID is an online database that comprises all genes or proteins, and associated information, for which expression was experimentally measured and found to be altered after ZIKV infection. The database, available at https://zikavid.org, contains 16,984 entries of gene expression measurements from a total of 7348 genes. It allows users to easily perform searches for different experimental hosts (cell lines, tissues, and animal models), ZIKV strains (African, Asian, and Brazilian), and target molecules (messenger RNA [mRNA] and protein), among others, used in differential expression studies regarding ZIKV infection. In this way, the ZIKAVID will serve as an additional and important resource to improve the characterization of the molecular impact and pathogenesis associated with ZIKV infection.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Adams Waldorf KM, Nelson BR, Stencel-Baerenwald JE, Studholme C, Kapur RP, Armistead B, Walker CL, Merillat S, Vornhagen J, Tisoncik-Go J, Baldessari A, Coleman M, Dighe MK, Shaw DWW, Roby JA, Santana-Ufret V, Boldenow E, Li J, Gao X, Davis MA, Swanstrom JA, Jensen K, Widman DG, Baric RS, Medwid JT, Hanley KA, Ogle J, Gough GM, Lee W, English C, Durning WM, Thiel J, Gatenby C, Dewey EC, Fairgrieve MR, Hodge RD, Grant RF, Kuller L, Dobyns WB, Hevner RF, Gale M, Rajagopal L (2018) Congenital Zika virus infection as a silent pathology with loss of neurogenic output in the fetal brain. Nat Med 24:368–374. https://doi.org/10.1038/nm.4485
Beaver JT, Lelutiu N, Habib R, Skountzou I (2018) Evolution of two major Zika virus lineages: implications for pathology, immune response, and vaccine development. Front Immunol 9:1640. https://doi.org/10.3389/fimmu.2018.01640
Beys-da-Silva WO, Rosa RL, Santi L, Berger M, Park SK, Campos AR, Terraciano P, Varela APM, Teixeira TF, Roehe PM, Quincozes-Santos A, Yates JR, Souza DO, Cirne-Lima EO, Guimarães JA (2018) Zika virus infection of human mesenchymal stem cells promotes differential expression of proteins linked to several neurological diseases. Mol Neurobiol 56:4708–4717. https://doi.org/10.1007/s12035-018-1417-x
Bowen JR, Quicke KM, Maddur MS, O’Neal JT, McDonald CE, Fedorova NB, Puri V, Shabman RS, Pulendran B, Suthar MS (2017) Zika virus antagonizes type i interferon responses during infection of human dendritic cells. PLoS Pathog 13:e1006164. https://doi.org/10.1371/journal.ppat.1006164
Buathong R, Hermann L, Thaisomboonsuk B, Rutvisuttinunt W, Klungthong C, Chinnawirotpisan P, Manasatienkij W, Nisalak A, Fernandez S, Yoon I-K, Akrasewi P, Plipat T (2015) Detection of Zika virus infection in Thailand, 2012–2014. Am J Trop Med Hyg 93:380–383. https://doi.org/10.4269/ajtmh.15-0022
Calvet G, Aguiar RS, Melo ASO, Sampaio SA, de Filippis I, Fabri A, Araujo ESM, de Sequeira PC, de Mendonça MCL, de Oliveira L, Tschoeke DA, Schrago CG, Thompson FL, Brasil P, dos Santos FB, Nogueira RMR, Tanuri A, de Filippis AMB (2016) Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect Dis 16:653–660. https://doi.org/10.1016/s1473-3099(16)00095-5
Chen J, Yang Y, Chen J, Zhou X, Dong Z, Chen T, Yang Y, Zou P, Jiang B, Hu Y, Lu L, Zhang X, Liu J, Xu J, Zhu T (2017) Zika virus infects renal proximal tubular epithelial cells with prolonged persistency and cytopathic effects. Emerg Microbes Infect 6:1–7. https://doi.org/10.1038/emi.2017.67
Dick GW, Kitchen S, Haddow A (1952) Zika virus (I). Isolations and serological specificity. Trans R Soc Trop Med Hyg 46:509–520. https://doi.org/10.1016/0035-9203(52)90042-4
Dowall SD, Graham VA, Rayner E, Hunter L, Atkinson B, Pearson G, Dennis M, Hewson R (2017) Lineage-dependent differences in the disease progression of Zika virus infection in type-I interferon receptor knockout (A129) mice. PLoS Negl Trop Dis 11:e0005704. https://doi.org/10.1371/journal.pntd.0005704
Duffy MR, Chen T-H, Hancock WT, Powers AM, Kool JL, Lanciotti RS, Pretrick M, Marfel M, Holzbauer S, Dubray C, Guillaumot L, Griggs A, Bel M, Lambert AJ, Laven J, Kosoy O, Panella A, Biggerstaff BJ, Fischer M, Hayes EB (2009) Zika virus outbreak on Yap island, Federated States of Micronesia. N Engl J Med 360:2536–2543. https://doi.org/10.1056/nejmoa0805715
Grant A, Ponia SS, Tripathi S, Balasubramaniam V, Miorin L, Sourisseau M, Schwarz MC, Sánchez-Seco MP, Evans MJ, Best SM, García-Sastre A (2016) Zika virus targets human STAT2 to inhibit type I interferon signaling. Cell Host Microbe 19:882–890. https://doi.org/10.1016/j.chom.2016.05.009
Guirimand T, Delmotte S, Navratil V (2014) VirHostNet 2.0: surfing on the web of virus/host molecular interactions data. Nucleic Acids Res 43:D583–D587. https://doi.org/10.1093/nar/gku1121
Gurumayum S, Brahma R, Naorem LD, Muthaiyan M, Gopal J, Venkatesan A (2018) ZikaBase: an integrated ZIKV- human interactome map database. Virology 514:203–210. https://doi.org/10.1016/j.virol.2017.11.007
Hamel R, Dejarnac O, Wichit S, Ekchariyawat P, Neyret A, Luplertlop N, Perera-Lecoin M, Surasombatpattana P, Talignani L, Thomas F, Cao-Lormeau V-M, Choumet V, Briant L, Desprès P, Amara A, Yssel H, Missé D (2015) Biology of Zika virus infection in human skin cells. J Virol 89:8880–8896. https://doi.org/10.1128/jvi.00354-15
Hastings AK, Yockey LJ, Jagger BW, Hwang J, Uraki R, Gaitsch HF, Parnell LA, Cao B, Mysorekar IU, Rothlin CV, Fikrig E, Diamond MS, Iwasaki A (2017) TAM receptors are not required for Zika virus infection in mice. Cell Rep 19:558–568. https://doi.org/10.1016/j.celrep.2017.03.058
Hu B, Huo Y, Yang L, Chen G, Luo M, Yang J, Zhou J (2017) ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells. Virol J 14:217. https://doi.org/10.1186/s12985-017-0882-6
Hu T, Li J, Carr MJ, Duchêne S, Shi W (2019) The asian lineage of Zika virus: transmission and evolution in asia and the americas. Virol Sin 34:1–8. https://doi.org/10.1007/s12250-018-0078-2
Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le Mercier P (2010) ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res 39:D576–D582. https://doi.org/10.1093/nar/gkq901
Jiang X, Dong X, Li S-H, Zhou Y-P, Rayner S, Xia H-M, Gao GF, Yuan H, Tang Y-P, Luo M-H (2018) Proteomic analysis of Zika virus infected primary human fetal neural progenitors suggests a role for doublecortin in the pathological consequences of infection in the cortex. Front Microbiol 9. https://doi.org/10.3389/fmicb.2018.01067
Lanciotti RS, Kosoy OL, Laven JJ, Velez JO, Lambert AJ, Johnson AJ, Stanfield SM, Duffy MR (2008) Genetic and serologic properties of Zika virus associated with an epidemic, Yap state, Micronesia, 2007. Emerg Infect Dis 14:1232–1239. https://doi.org/10.3201/eid1408.080287
Lindqvist R, Mundt F, Gilthorpe JD, Wölfel S, Gekara NO, Kröger A, Överby AK (2016) Fast type I interferon response protects astrocytes from flavivirus infection and virus-induced cytopathic effects. J Neuroinflammation 13:277. https://doi.org/10.1186/s12974-016-0748-7
McGrath EL, Rossi SL, Gao J, Widen SG, Grant AC, Dunn TJ, Azar SR, Roundy CM, Xiong Y, Prusak DJ, Loucas BD, Wood TG, Yu Y, Fernández-Salas I, Weaver SC, Vasilakis N, Wu P (2017) Differential responses of human fetal brain neural stem cells to Zika virus infection. Stem Cell Rep 8:715–727. https://doi.org/10.1016/j.stemcr.2017.01.008
Mishra A, Vijayakumar P, Raut AA (2017) Emerging avian influenza infections: current understanding of innate immune response and molecular pathogenesis. Int Rev Immunol 36:89–107. https://doi.org/10.1080/08830185.2017.1291640
Mitchell RD III, Wallace AD, Hodgson E, Roe RM (2017) Differential expression profile of lncRNAs from primary human hepatocytes following DEET and fipronil exposure. Int J Mol Sci 18:2104. https://doi.org/10.3390/ijms18102104
Mlakar J, Korva M, Tul N, Popović M, Poljšak-Prijatelj M, Mraz J, Kolenc M, Resman Rus K, Vesnaver Vipotnik T, Fabjan Vodušek V, Vizjak A, Pižem J, Petrovec M, Avšič Županc T (2016) Zika virus associated with microcephaly. N Engl J Med 374:951–958. https://doi.org/10.1056/nejmoa1600651
Musso D, Gubler DJ (2016) Zika virus. Clin Microbiol Rev 29:487–524. https://doi.org/10.1128/cmr.00072-15
Papanikolaou N, Pavlopoulos GA, Theodosiou T, Iliopoulos I (2015) Protein–protein interaction predictions using text mining methods. Methods 74:47–53. https://doi.org/10.1016/j.ymeth.2014.10.026
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, Zhou L, Larson CN, Dietrich J, Klem EB, Scheuermann RH (2011) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res 40:D593–D598. https://doi.org/10.1093/nar/gkr859
Przybyła P, Shardlow M, Aubin S, Bossy R, Eckart de Castilho R, Piperidis S, McNaught J, Ananiadou S (2016) Text mining resources for the life sciences. Database 2016. doi: https://doi.org/10.1093/database/baw145
Pylro VS, Oliveira FS, Morais DK, Cuadros-Orellana S, Pais FS-M, Medeiros JD, Geraldo JA, Gilbert J, Volpini AC, Fernandes GR (2016) ZIKV – CDB: a collaborative database to guide research linking sncrnas and Zika virus disease symptoms. PLoS Negl Trop Dis 10:e0004817. https://doi.org/10.1371/journal.pntd.0004817
Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmström J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO (2009) Comparative functional analysis of the caenorhabditis elegans and drosophila melanogaster proteomes. PLoS Biol 7:e1000048. https://doi.org/10.1371/journal.pbio.1000048
Schuler-Faccini L, Roehe P, Zimmer ER, Quincozes-Santos A, de Assis AM, Lima EOC, Guimarães JA, Victora C, Neto VM, Souza DO (2017) ZIKA virus and neuroscience: the need for a translational collaboration. Mol Neurobiol 55:1551–1555. https://doi.org/10.1007/s12035-017-0429-2
Sheridan MA, Balaraman V, Schust DJ, Ezashi T, Roberts RM, Franz AWE (2018) African and Asian strains of Zika virus differ in their ability to infect and lyse primitive human placental trophoblast. PLoS One 13:e0200086. https://doi.org/10.1371/journal.pone.0200086
Strange DP, Green R, Siemann DN, Gale M, Verma S (2018) Immunoprofiles of human sertoli cells infected with Zika virus reveals unique insights into host-pathogen crosstalk. Sci Rep 8:8702. https://doi.org/10.1038/s41598-018-27027-7
Tabata T, Petitt M, Puerta-Guardo H, Michlmayr D, Wang C, Fang-Hoover J, Harris E, Pereira L (2016) Zika virus targets different primary human placental cells, suggesting two routes for vertical transmission. Cell Host Microbe 20:155–166. https://doi.org/10.1016/j.chom.2016.07.002
Tang H, Hammack C, Ogden SC, Wen Z, Qian X, Li Y, Yao B, Shin J, Zhang F, Lee EM, Christian KM, Didier RA, Jin P, Song H, Ming G (2016) Zika virus infects human cortical neural progenitors and attenuates their growth. Cell Stem Cell 18:587–590. https://doi.org/10.1016/j.stem.2016.02.016
Yun S-I, Song B-H, Frank J, Julander J, Olsen A, Polejaeva I, Davies C, White K, Lee Y-M (2018) Functional genomics and immunologic tools: the impact of viral and host genetic variations on the outcome of Zika virus infection. Viruses 10:422. https://doi.org/10.3390/v10080422
Zhang F, Hammack C, Ogden SC, Cheng Y, Lee EM, Wen Z, Qian X, Nguyen HN, Li Y, Yao B, Xu M, Xu T, Chen L, Wang Z, Feng H, Huang W-K, Yoon K, Shan C, Huang L, Qin Z, Christian KM, Shi P-Y, Xu M, Xia M, Zheng W, Wu H, Song H, Tang H, Ming G-L, Jin P (2016) Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. Nucleic Acids Res 44:8610–8620. https://doi.org/10.1093/nar/gkw765
Funding
This work was supported by the Brazilian funding agencies, Coordenação de Aperfeiçoamento Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Edital MCTIC/FNDCT-CNPq/MEC-CAPES/MS-Decit/No 14/2016, project 440763/2016-9, and Ministry of Health.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
All authors are part of The Brazilian ZIKV Translational Research Taskforce
Electronic supplementary material
Supplementary Table 1
contain all the metadata. (CSV 3794 kb)
Supplementary Table 2
contain all papers published used to create the ZIKAVID. (XLSX 19 kb)
Rights and permissions
About this article
Cite this article
Rosa, R.L., Santi, L., Berger, M. et al. ZIKAVID—Zika virus infection database: a new platform to analyze the molecular impact of Zika virus infection. J. Neurovirol. 26, 77–83 (2020). https://doi.org/10.1007/s13365-019-00799-y
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13365-019-00799-y