[1] B. Greenwood, “The contribution of vaccination to global health: past, present and future,” Philos. Trans. R. Soc. Lond., B, Biol. Sci., vol. 369, no. 1645, p. 20130433, 2014, doi: 10.1098/rstb.2013.0433.
[2] “World malaria report 2019.” https://www.who.int/publications-detail/world-malaria-report-2019 (accessed May 20, 2020).
[3] J. Healer, A. F. Cowman, D. C. Kaslow, and A. J. Birkett, “Vaccines to Accelerate Malaria Elimination and Eventual Eradication,” Cold Spring Harb Perspect Med, vol. 7, no. 9, Sep. 2017, doi: 10.1101/cshperspect.a025627.
[4] J. Langhorne, F. M. Ndungu, A.-M. Sponaas, and K. Marsh, “Immunity to malaria: more questions than answers,” Nat. Immunol., vol. 9, no. 7, Art. no. 7, Jul. 2008, doi: 10.1038/ni.f.205.
[5] T. L. Richie et al., “Progress with Plasmodium falciparum sporozoite (PfSPZ)-based malaria vaccines,” Vaccine, vol. 33, no. 52, pp. 7452–7461, Dec. 2015, doi: 10.1016/j.vaccine.2015.09.096.
[6] R. A. Seder et al., “Protection Against Malaria by Intravenous Immunization with a Nonreplicating Sporozoite Vaccine,” Science, vol. 341, no. 6152, pp. 1359–1365, Sep. 2013, doi: 10.1126/science.1241800.
[7] K. E. Lyke et al., “Attenuated PfSPZ Vaccine induces strain-transcending T cells and durable protection against heterologous controlled human malaria infection,” PNAS, vol. 114, no. 10, pp. 2711–2716, Mar. 2017, doi: 10.1073/pnas.1615324114.
[8] J. E. Epstein et al., “Live attenuated malaria vaccine designed to protect through hepatic CD8+ T cell immunity,” Science, vol. 334, no. 6055, Art. no. 6055, Oct. 2011, doi: 10.1126/science.1211548.
[9] S. A. Jongo et al., “Safety, Immunogenicity, and Protective Efficacy against Controlled Human Malaria Infection of Plasmodium falciparum Sporozoite Vaccine in Tanzanian Adults,” Am J Trop Med Hyg, vol. 99, no. 2, Art. no. 2, Aug. 2018, doi: 10.4269/ajtmh.17-1014.
[10] S. A. Jongo et al., “Safety and Differential Antibody and T-Cell Responses to the Plasmodium falciparum Sporozoite Malaria Vaccine, PfSPZ Vaccine, by Age in Tanzanian Adults, Adolescents, Children, and Infants,” Am. J. Trop. Med. Hyg., vol. 100, no. 6, pp. 1433–1444, 2019, doi: 10.4269/ajtmh.18-0835.
[11] A. Olotu et al., “Advancing Global Health through Development and Clinical Trials Partnerships: A Randomized, Placebo-Controlled, Double-Blind Assessment of Safety, Tolerability, and Immunogenicity of PfSPZ Vaccine for Malaria in Healthy Equatoguinean Men,” Am J Trop Med Hyg, vol. 98, no. 1, Art. no. 1, Jan. 2018, doi: 10.4269/ajtmh.17-0449.
[12] M. S. Sissoko et al., “Safety and efficacy of PfSPZ Vaccine against Plasmodium falciparum via direct venous inoculation in healthy malaria-exposed adults in Mali: a randomised, double-blind phase 1 trial,” The Lancet Infectious Diseases, vol. 17, no. 5, Art. no. 5, May 2017, doi: 10.1016/S1473-3099(17)30104-4.
[13] D. L. Hill et al., “Immune system development varies according to age, location, and anemia in African children,” Sci Transl Med, vol. 12, no. 529, Feb. 2020, doi: 10.1126/scitranslmed.aaw9522.
[14] G. de Bruyn, “Cofactors that may influence vaccine responses,” Current Opinion in HIV and AIDS, vol. 5, no. 5, pp. 404–408, Sep. 2010, doi: 10.1097/COH.0b013e32833d1fca.
[15] N. Lenz et al., “Antiviral Innate Immune Activation in HIV-Infected Adults Negatively Affects H1/IC31-Induced Vaccine-Specific Memory CD4+ T Cells.,” Clin Vaccine Immunol, vol. 22, no. 7, Art. no. 7, Jul. 2015, doi: 10.1128/CVI.00092-15.
[16] C. S. Rocha et al., “Subclinical Cytomegalovirus Infection Is Associated with Altered Host Immunity, Gut Microbiota, and Vaccine Responses,” Journal of Virology, vol. 92, no. 13, Art. no. 13, Jul. 2018, doi: 10.1128/JVI.00167-18.
[17] S. Rodriguez, M. Roussel, K. Tarte, and P. Amé-Thomas, “Impact of Chronic Viral Infection on T-Cell Dependent Humoral Immune Response,” Front Immunol, vol. 8, Oct. 2017, doi: 10.3389/fimmu.2017.01434.
[18] S. Singh and J. T. Blackard, “Human pegivirus (HPgV) infection in sub-Saharan Africa-A call for a renewed research agenda,” Rev. Med. Virol., vol. 27, no. 6, Art. no. 6, 2017, doi: 10.1002/rmv.1951.
[19] E. T. Chivero, N. Bhattarai, R. T. Rydze, M. A. Winters, M. Holodniy, and J. T. Stapleton, “Human pegivirus RNA is found in multiple blood mononuclear cells in vivo and serum-derived viral RNA-containing particles are infectious in vitro,” J. Gen. Virol., vol. 95, no. Pt 6, Art. no. Pt 6, Jun. 2014, doi: 10.1099/vir.0.063016-0.
[20] E. T. Chivero and J. T. Stapleton, “Tropism of human pegivirus (formerly known as GB virus C/hepatitis G virus) and host immunomodulation: insights into a highly successful viral infection,” J. Gen. Virol., vol. 96, no. Pt 7, Art. no. Pt 7, Jul. 2015, doi: 10.1099/vir.0.000086.
[21] J. Xiang et al., “Effect of coinfection with GB virus C on survival among patients with HIV infection.,” N Engl J Med, vol. 345, no. 10, Art. no. 10, Sep. 2001, doi: 10.1056/NEJMoa003364.
[22] G. Horemheb-Rubio et al., “High HPgV replication is associated with improved surrogate markers of HIV progression,” PLOS ONE, vol. 12, no. 9, Art. no. 9, Sep. 2017, doi: 10.1371/journal.pone.0184494.
[23] H. L. Tillmann et al., “Infection with GB virus C and reduced mortality among HIV-infected patients,” N. Engl. J. Med., vol. 345, no. 10, Art. no. 10, Sep. 2001, doi: 10.1056/NEJMoa010398.
[24] M. Lauck, A. L. Bailey, K. G. Andersen, T. L. Goldberg, P. C. Sabeti, and D. H. O’Connor, “GB Virus C Coinfections in West African Ebola Patients,” Journal of Virology, vol. 89, no. 4, Art. no. 4, Feb. 2015, doi: 10.1128/JVI.02752-14.
[25] R. T. Rydze, N. Bhattarai, and J. T. Stapleton, “GB virus C infection is associated with a reduced rate of reactivation of latent HIV and protection against activation-induced T-cell death,” Antivir Ther, vol. 17, no. 7, Art. no. 7, 2012, doi: 10.3851/IMP2309.
[26] J. T. Blackard et al., “Cytokine/chemokine expression associated with Human Pegivirus (HPgV) infection in women with HIV,” J Med Virol, vol. 89, no. 11, Art. no. 11, Nov. 2017, doi: 10.1002/jmv.24836.
[27] M. C. Lanteri et al., “Downregulation of Cytokines and Chemokines by GB Virus C After Transmission Via Blood Transfusion in HIV-Positive Blood Recipients,” J Infect Dis, vol. 211, no. 10, Art. no. 10, May 2015, doi: 10.1093/infdis/jiu660.
[28] G. Nunnari et al., “Slower progression of HIV-1 infection in persons with GB virus C co-infection correlates with an intact T-helper 1 cytokine profile,” Ann. Intern. Med., vol. 139, no. 1, Art. no. 1, Jul. 2003, doi: 10.7326/0003-4819-139-1-200307010-00009.
[29] S. A. Jongo et al., “Increase of dose associated with decrease in protection against controlled human malaria infection by PfSPZ Vaccine in Tanzanian adults,” Clin. Infect. Dis., Nov. 2019, doi: 10.1093/cid/ciz1152.
[30] Jongo et. al, “Immunogenicity and protective efficacy of radiation-attenuated and chemo-attenuated 4 PfSPZ vaccines in Equatoguinean adults (Jongo et al., manuscript in press).” .
[31] J. Hitchen, R. Sooknanan, and A. Khanna, “Rapid and Efficient Methods for Preparing Globin- and rRNA-Depleted Directional RNA-Seq Libraries,” J Biomol Tech, vol. 24, no. Suppl, pp. S43–S44, May 2013.
[32] S. Rampelli et al., “ViromeScan: a new tool for metagenomic viral community profiling,” BMC Genomics, vol. 17, p. 165, Mar. 2016, doi: 10.1186/s12864-016-2446-3.
[33] S. Flygare et al., “Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling,” Genome Biol., vol. 17, no. 1, p. 111, 26 2016, doi: 10.1186/s13059-016-0969-1.
[34] S. S. Tithi, F. O. Aylward, R. V. Jensen, and L. Zhang, “FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data,” PeerJ, vol. 6, p. e4227, Jan. 2018, doi: 10.7717/peerj.4227.
[35] B. Buchfink, C. Xie, and D. H. Huson, “Fast and sensitive protein alignment using DIAMOND,” Nat. Methods, vol. 12, no. 1, pp. 59–60, Jan. 2015, doi: 10.1038/nmeth.3176.
[36] G. J. Xu et al., “Viral immunology. Comprehensive serological profiling of human populations using a synthetic human virome,” Science, vol. 348, no. 6239, p. aaa0698, Jun. 2015, doi: 10.1126/science.aaa0698.
[37] A. Moustafa et al., “The blood DNA virome in 8,000 humans,” PLoS Pathog., vol. 13, no. 3, p. e1006292, 2017, doi: 10.1371/journal.ppat.1006292.
[38] M. Kearse et al., “Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data,” Bioinformatics, vol. 28, no. 12, pp. 1647–1649, Jun. 2012, doi: 10.1093/bioinformatics/bts199.
[39] M. Frankel et al., “Development of a high-throughput multiplexed real time RT-PCR assay for detection of human pegivirus 1 and 2,” Journal of Virological Methods, vol. 241, pp. 34–40, Mar. 2017, doi: 10.1016/j.jviromet.2016.12.013.
[40] S. Krähenbühl et al., “ELIMU-MDx: a web-based, open-source platform for storage, management and analysis of diagnostic qPCR data,” BioTechniques, vol. 68, no. 1, pp. 22–27, 2020, doi: 10.2144/btn-2019-0064.
[41] K. F. N’Guessan et al., “Human pegivirus (HPgV) infection in Ghanaians co-infected with human immunodeficiency virus (HIV) and hepatitis B virus (HBV),” Virus Genes, vol. 54, no. 3, Art. no. 3, Jun. 2018, doi: 10.1007/s11262-018-1555-2.
[42] I. E. Souza et al., “Effect of primer selection on estimates of GB virus C (GBV-C) prevalence and response to antiretroviral therapy for optimal testing for GBV-C viremia,” J. Clin. Microbiol., vol. 44, no. 9, Art. no. 9, Sep. 2006, doi: 10.1128/JCM.02663-05.
[43] P. Amelio et al., “HIV Infection Functionally Impairs Mycobacterium tuberculosis-specific CD4 and CD8 T-cell responses,” Journal of Virology, p. JVI.01728-18, Dec. 2018, doi: 10.1128/JVI.01728-18.
[44] A. D. Douglas et al., “Comparison of Modeling Methods to Determine Liver-to-blood Inocula and Parasite Multiplication Rates During Controlled Human Malaria Infection,” J Infect Dis, vol. 208, no. 2, pp. 340–345, Jul. 2013, doi: 10.1093/infdis/jit156.
[45] N. Segata et al., “Metagenomic biomarker discovery and explanation,” Genome Biol., vol. 12, no. 6, p. R60, Jun. 2011, doi: 10.1186/gb-2011-12-6-r60.
[46] A. Shibui et al., “Th17 cell-derived IL-17 is dispensable for B cell antibody production,” Cytokine, vol. 59, no. 1, pp. 108–114, Jul. 2012, doi: 10.1016/j.cyto.2012.03.018.
[47] S. L. Gallou, G. Caron, C. Delaloy, D. Rossille, K. Tarte, and T. Fest, “IL-2 Requirement for Human Plasma Cell Generation: Coupling Differentiation and Proliferation by Enhancing MAPK–ERK Signaling,” The Journal of Immunology, vol. 189, no. 1, pp. 161–173, Jul. 2012, doi: 10.4049/jimmunol.1200301.
[48] I. F. Hoffman et al., “The effect of Plasmodium falciparum malaria on HIV-1 RNA blood plasma concentration,” AIDS, vol. 13, no. 4, pp. 487–494, Mar. 1999, doi: 10.1097/00002030-199903110-00007.
[49] A. Reynaldi et al., “Impact of Plasmodium falciparum Coinfection on Longitudinal Epstein-Barr Virus Kinetics in Kenyan Children,” J Infect Dis, vol. 213, no. 6, Art. no. 6, Mar. 2016, doi: 10.1093/infdis/jiv525.
[50] G. Gentile and A. Micozzi, “Speculations on the clinical significance of asymptomatic viral infections,” Clinical Microbiology and Infection, vol. 22, no. 7, Art. no. 7, Jul. 2016, doi: 10.1016/j.cmi.2016.07.016.
[51] D. Bonsall et al., “Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR.,” Emerg Infect Dis, vol. 22, no. 4, Art. no. 4, Apr. 2016, doi: 10.3201/eid2204.151812.
[52] R. Schlaberg et al., “Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology,” J Infect Dis, vol. 215, no. 9, Art. no. 9, May 2017, doi: 10.1093/infdis/jix148.
[53] F. E. Chaer and H. M. E. Sahly, “Vaccination in the Adult Patient Infected with HIV: A Review of Vaccine Efficacy and Immunogenicity,” The American Journal of Medicine, vol. 132, no. 4, pp. 437–446, Apr. 2019, doi: 10.1016/j.amjmed.2018.12.011.
[54] A. S. Muerhoff, G. J. Dawson, and S. M. Desai, “A previously unrecognized sixth genotype of GB virus C revealed by analysis of 5′-untranslated region sequences,” Journal of Medical Virology, vol. 78, no. 1, Art. no. 1, 2006, doi: 10.1002/jmv.20510.
[55] Y. Feng et al., “A Novel Genotype of GB Virus C: Its Identification and Predominance among Injecting Drug Users in Yunnan, China,” PLOS ONE, vol. 6, no. 10, Art. no. 10, Oct. 2011, doi: 10.1371/journal.pone.0021151.
[56] C. Schwarze-Zander et al., “GB Virus C (GBV-C) Infection in Hepatitis C Virus (HCV)/HIV–Coinfected Patients Receiving HCV Treatment: Importance of the GBV-C Genotype,” J Infect Dis, vol. 194, no. 4, Art. no. 4, Aug. 2006, doi: 10.1086/505713.
[57] L. D. D. Mota et al., “Molecular and Clinical Profiles of Human Pegivirus Type 1 Infection in Individuals Living with HIV-1 in the Extreme South of Brazil,” Biomed Res Int, vol. 2019, Jun. 2019, doi: 10.1155/2019/8048670.
[58] M. T. M. Giret et al., “Prevalence, Incidence Density, and Genotype Distribution of GB Virus C Infection in a Cohort of Recently HIV-1-Infected Subjects in Sao Paulo, Brazil,” PLOS ONE, vol. 6, no. 4, Art. no. 4, Apr. 2011, doi: 10.1371/journal.pone.0018407.
[59] K. Stark, G. Poggensee, M. Höhne, U. Bienzle, I. Kiwelu, and E. Schreier, “Seroepidemiology of TT virus, GBC-C/HGV, and hepatitis viruses B, C, and E among women in a rural area of Tanzania,” J. Med. Virol., vol. 62, no. 4, Art. no. 4, Dec. 2000.
[60] C. Menéndez et al., “Molecular Evidence of Mother-to-Infant Transmission of Hepatitis G Virus among Women without Known Risk Factors for Parenteral Infections,” J Clin Microbiol, vol. 37, no. 7, pp. 2333–2336, Jul. 1999.
[61] D. B. Smith et al., “Discrimination of hepatitis G virus/GBV-C geographical variants by analysis of the 5’ non-coding region.,” Journal of General Virology, vol. 78, no. 7, Art. no. 7, 1997, doi: 10.1099/0022-1317-78-7-1533.
[62] Y. Tanaka et al., “African origin of GB virus C/hepatitis G virus 1,” FEBS Letters, vol. 423, no. 2, Art. no. 2, 1998, doi: 10.1016/S0014-5793(98)00083-0.
[63] H. F. Liu, J. J. Muyembe-Tamfum, K. Dahan, J. Desmyter, and P. Goubau, “High prevalence of GB virus C/hepatitis G virus in Kinshasa, Democratic Republic of Congo: a phylogenetic analysis,” J. Med. Virol., vol. 60, no. 2, Art. no. 2, Feb. 2000.
[64] R. Tuveri et al., “Prevalence and genetic variants of hepatitis GB-C/HG and TT viruses in Gabon, equatorial Africa,” Am. J. Trop. Med. Hyg., vol. 63, no. 3–4, Art. no. 3–4, Oct. 2000, doi: 10.4269/ajtmh.2000.63.192.
[65] K.-C. Luk et al., “Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity,” PLOS ONE, vol. 10, no. 11, Art. no. 11, Nov. 2015, doi: 10.1371/journal.pone.0141723.
[66] J. C. Iles et al., “Hepatitis C virus infections in the Democratic Republic of Congo exhibit a cohort effect,” Infection, Genetics and Evolution, vol. 19, pp. 386–394, Oct. 2013, doi: 10.1016/j.meegid.2013.01.021.
[67] Y. Vitrenko, I. Kostenko, K. Kulebyakina, and K. Sorochynska, “Prevalence of human pegivirus-1 and sequence variability of its E2 glycoprotein estimated from screening donors of fetal stem cell-containing material,” Virol. J., vol. 14, no. 1, p. 167, 31 2017, doi: 10.1186/s12985-017-0837-y.
[68] E. L. Mohr and J. T. Stapleton, “GB virus type C interactions with HIV: the role of envelope glycoproteins,” J. Viral Hepat., vol. 16, no. 11, pp. 757–768, Nov. 2009, doi: 10.1111/j.1365-2893.2009.01194.x.
[69] L. C. Borish and J. W. Steinke, “2. Cytokines and chemokines,” Journal of Allergy and Clinical Immunology, vol. 111, no. 2, Supplement 2, Art. no. 2, Supplement 2, Feb. 2003, doi: 10.1067/mai.2003.108.
[70] R. Domingo-Gonzalez, O. Prince, A. Cooper, and S. A. Khader, “Cytokines and Chemokines in Mycobacterium tuberculosis Infection,” Microbiology Spectrum, vol. 4, no. 5, Art. no. 5, Oct. 2016, doi: 10.1128/microbiolspec.TBTB2-0018-2016.
[71] U. Ateba-Ngoa et al., “Cytokine and chemokine profile of the innate and adaptive immune response of schistosoma haematobium and plasmodium falciparum single and co-infected school-aged children from an endemic area of Lambaréné, Gabon,” Malaria Journal, vol. 14, no. 1, Art. no. 1, Feb. 2015, doi: 10.1186/s12936-015-0608-4.
[72] S. H. Ross and D. A. Cantrell, “Signaling and Function of Interleukin-2 in T Lymphocytes,” Annu. Rev. Immunol., vol. 36, no. 1, Art. no. 1, Apr. 2018, doi: 10.1146/annurev-immunol-042617-053352.
[73] J. G. Pol, P. Caudana, J. Paillet, E. Piaggio, and G. Kroemer, “Effects of interleukin-2 in immunostimulation and immunosuppression,” J. Exp. Med., vol. 217, no. 1, Jan. 2020, doi: 10.1084/jem.20191247.
[74] A. Fama et al., “Human Pegivirus infection and lymphoma risk and prognosis: a North American study,” British Journal of Haematology, vol. 182, no. 5, Art. no. 5, 2018, doi: 10.1111/bjh.15416.
[75] T. Aoshi, S. Koyama, K. Kobiyama, S. Akira, and K. J. Ishii, “Innate and adaptive immune responses to viral infection and vaccination,” Current Opinion in Virology, vol. 1, no. 4, Art. no. 4, Oct. 2011, doi: 10.1016/j.coviro.2011.07.002.
[76] C. L. Baldwin et al., “Bovine T cells, B cells, and null cells are transformed by the protozoan parasite Theileria parva.,” Infect Immun, vol. 56, no. 2, Art. no. 2, Feb. 1988.
[77] J. T. Stapleton et al., “A Novel T Cell Evasion Mechanism in Persistent RNA Virus Infection,” Trans Am Clin Climatol Assoc, vol. 125, pp. 14–26, 2014.
[78] N. Bhattarai, J. H. McLinden, J. Xiang, T. M. Kaufman, and J. T. Stapleton, “GB Virus C Envelope Protein E2 Inhibits TCR-Induced IL-2 Production and Alters IL-2–Signaling Pathways,” The Journal of Immunology, vol. 189, no. 5, Art. no. 5, Sep. 2012, doi: 10.4049/jimmunol.1201324.
[79] E. Bettelli, M. Oukka, and V. K. Kuchroo, “TH-17 cells in the circle of immunity and autoimmunity,” Nature Immunology, vol. 8, no. 4, Art. no. 4, Apr. 2007, doi: 10.1038/ni0407-345.
[80] P. Meng et al., “Involvement of the Interleukin-23/Interleukin-17 Axis in Chronic Hepatitis C Virus Infection and Its Treatment Responses,” Int J Mol Sci, vol. 17, no. 7, Art. no. 7, Jul. 2016, doi: 10.3390/ijms17071070.
[81] F. Y. Yue, A. Merchant, C. M. Kovacs, M. Loutfy, D. Persad, and M. A. Ostrowski, “Virus-Specific Interleukin-17-Producing CD4+ T Cells Are Detectable in Early Human Immunodeficiency Virus Type 1 Infection,” Journal of Virology, vol. 82, no. 13, Art. no. 13, Jul. 2008, doi: 10.1128/JVI.02550-07.
[82] V. I. Avelino-Silva et al., “CD4/CD8 Ratio and KT Ratio Predict Yellow Fever Vaccine Immunogenicity in HIV-Infected Patients,” PLOS Neglected Tropical Diseases, vol. 10, no. 12, Art. no. 12, Dec. 2016, doi: 10.1371/journal.pntd.0005219.
[83] J. H. McLinden et al., “Yellow Fever Virus, but Not Zika Virus or Dengue Virus, Inhibits T-Cell Receptor–Mediated T-Cell Function by an RNA-Based Mechanism,” J Infect Dis, vol. 216, no. 9, Art. no. 9, Nov. 2017, doi: 10.1093/infdis/jix462.
[84] L. Rénia and S. M. Potter, “Co-infection of malaria with HIV: an immunological perspective,” Parasite Immunology, vol. 28, no. 11, Art. no. 11, 2006, doi: 10.1111/j.1365-3024.2006.00903.x.
[85] K. Rosenke et al., “Plasmodium Parasitemia Associated With Increased Survival in Ebola Virus–Infected Patients,” Clin Infect Dis, vol. 63, no. 8, Art. no. 8, Oct. 2016, doi: 10.1093/cid/ciw452.
[86] O. Ouwe-Missi-Oukem-Boyer et al., “Hepatitis C Virus Infection May Lead to Slower Emergence of P. falciparum in Blood,” PLoS One, vol. 6, no. 1, Art. no. 1, Jan. 2011, doi: 10.1371/journal.pone.0016034.