Implications of viral transmitted/founder (T/F) dynamics on vaccine development

References

• McCrone JT, Lauring AS. Genetic bottlenecks in intraspecies virus transmission. Curr Opin Virol. 2018 Feb;28:20–25. PubMed Central. doi:10.1016/j.coviro.2017.10.008.
   PubMed Web of Science ®Google Scholar
• Campo DS, Zhang J, Ramachandran S, Khudyakov Y. Transmissibility of intra-host hepatitis C virus variants. BMC Genomics. Dec 2017;18(Suppl 10). PubMed Central. doi:10.1186/s12864-017-4267-4.
   Web of Science ®Google Scholar
• Boeras DI, Hraber PT, Hurlston M, Evans-Strickfaden T, Bhattacharya T, Giorgi EE, Mulenga J, Karita E, Korber BT, Allen S, et al. Role of donor genital tract HIV-1 diversity in the transmission bottleneck. Proc Natl Acad Sci U S A. 2011 Nov;108(46):E1156–1163. PubMed. doi:10.1073/pnas.1103764108.
   PubMed Web of Science ®Google Scholar
• Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, et al. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog. Sept 2011;7 (9). PubMed Central. doi:10.1371/journal.ppat.1002209.
   PubMed Web of Science ®Google Scholar
• Shaw GM, Hunter E. HIV transmission. Cold Spring Harb Perspect Med. Nov 2012;2(11). PubMed. doi:10.1101/cshperspect.a006965.
   PubMed Web of Science ®Google Scholar
• Lin X-D, Wang W, Guo W-P, Zhang X-H, Xing J-G, Chen S-Z, Li M-H, Chen Y, Xu J, Plyusnin A, et al. Cross-species transmission in the speciation of the currently known murinae-associated hantaviruses. J Virol. 2012 Oct;86(20):11171–82. jvi.asm.org. doi:10.1128/JVI.00021-12.
   PubMed Web of Science ®Google Scholar
• Weiss RA, Hamilton W, Weiss RA, Wain–Hobson S. The leeuwenhoek lecture 2001. Animal origins of human infectious disease. Philos Trans R Soc London Ser B. 2001 June;356(1410):957–77. PubMed Central. doi:10.1098/rstb.2001.0838.
   PubMed Web of Science ®Google Scholar
• Klempner MS, Shapiro DS. Crossing the species barrier — one small step to man, one giant leap to mankind. N Engl J Med. 2004 Mar;350(12):1171–72. Taylor and Francis+NEJM. doi:10.1056/NEJMp048039.
   PubMed Web of Science ®Google Scholar
• Borucki MK, Chen-Harris H, Lao V, Vanier G, Wadford DA, Messenger S, Allen JE. Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission. PLoS Negl Trop Dis. Nov 2013;7(11). PubMed Central. doi:10.1371/journal.pntd.0002555.
   PubMed Web of Science ®Google Scholar
• Haynes BF, Shaw G, Korber B, Kelsoe G, Sodroski J, Hahn B, Borrow P, McMichael A. HIV-host interactions: implications for vaccine design. Cell Host Microbe. 2016 Mar;19(3):292–303. PubMed Central. doi:10.1016/j.chom.2016.02.002.
   PubMed Web of Science ®Google Scholar
• Barton NH. Natural selection and random genetic drift as causes of evolution on islands. Philos Trans R Soc Lond B Biol Sci. 1996 June;351(1341):785–94. discussion 795. PubMed. doi:10.1098/rstb.1996.0073.
   PubMed Web of Science ®Google Scholar
• Andersson S, Ellmer M, Jorgensen TH, Palmé A. Quantitative genetic effects of bottlenecks: experimental evidence from a wild plant species, nigella degenii. J Hered. 2010 June;101(3):298–307. PubMed. doi:10.1093/jhered/esp108.
   PubMed Web of Science ®Google Scholar
• Matute DR. The role of founder effects on the evolution of reproductive isolation. J Evol Biol. 2013;26(11):2299–311. Wiley Online Library. doi:10.1111/jeb.12246.
   PubMed Web of Science ®Google Scholar
• Forni D, Cagliani R, Clerici M, Sironi M. Molecular evolution of human coronavirus genomes. Trends Microbiol. 2017 Jan;25(1):35–48. ScienceDirect. doi:10.1016/j.tim.2016.09.001.
   PubMed Web of Science ®Google Scholar
• Lapa D, Garbuglia A, Capobianchi M, Del Porto P. Hepatitis C virus genetic variability, human immune response, and genome polymorphisms: which is the interplay? Cells. Apr 2019;8(4). PubMed Central. doi:10.3390/cells8040305.
   PubMed Web of Science ®Google Scholar
• Joseph SB, Swanstrom R, Kashuba AD, Cohen MS. Bottlenecks in HIV-1 transmission: insights from the study of founder viruses. Nat Rev Microbiol. 2015 July;13(7):414–25. PubMed Central. doi:10.1038/nrmicro3471.
   PubMed Web of Science ®Google Scholar
• Nicholson KG, Wood JM, Zambon M. Influenza. Lancet (London, England). 2003 Nov;362(9397):1733–45. PubMed. doi:10.1016/S0140-6736(03)14854-4.
   PubMed Web of Science ®Google Scholar
• Webster RG. Wet markets—a continuing source of severe acute respiratory syndrome and influenza? Lancet (London, England). 2004 Jan;363(9404):234–36. PubMed Central. doi:10.1016/S0140-6736(03)15329-9.
   PubMed Web of Science ®Google Scholar
• Gomaa MR, Kandeil A, Kayed AS, Elabd MA, Zaki SA, Abu Zeid D, El Rifay AS, Mousa AA, Farag MM, McKenzie PP, et al. Serological evidence of human infection with avian influenza A H7virus in Egyptian poultry growers. Plos One. 2016 June;11(6):e0155294. PLoS Journals. doi:10.1371/journal.pone.0155294.
   PubMed Web of Science ®Google Scholar
• Louz D, Bergmans HE, Loos BP, Hoeben RC. Cross‐species transfer of viruses: implications for the use of viral vectors in biomedical research, gene therapy and as live‐virus vaccines. J Gene Med. 2005 Oct;7(10):1263–74. PubMed Central. doi:10.1002/jgm.794.
   PubMed Web of Science ®Google Scholar
• Tang X, Li G, Vasilakis N, Zhang Y, Shi Z, Zhong Y, Wang L-F, Zhang S. Differential stepwise evolution of SARS coronavirus functional proteins in different host species. BMC Evol Biol. Mar 2009; 9. PubMed Central. doi:10.1186/1471-2148-9-52.
   PubMed Web of Science ®Google Scholar
• Bordería AV, Stapleford KA, Vignuzzi M. RNA virus population diversity: implications for inter-species transmission. Curr Opin Virol. 2011 Dec;1(6):643–48. ScienceDirect. doi:10.1016/j.coviro.2011.09.012.
   PubMed Web of Science ®Google Scholar
• Ayouba A, Akoua-Koffi C, Calvignac-Spencer S, Esteban A, Locatelli S, Li H, Li Y, Hahn BH, Delaporte E, Leendertz FH, et al. Evidence for continuing cross-species transmission of SIVsmm to humans: characterization of a new HIV-2 lineage in rural côte d’ivoire. AIDS (London, England). Sept 2013;27 (15). PubMed Central. doi:10.1097/01.aids.0000432443.22684.50.
   PubMed Web of Science ®Google Scholar
• Anthony SJ, Johnson CK, Greig DJ, Kramer S, Che X, Wells H, Hicks AL, Joly DO, Wolfe ND, Daszak P, et al. Global patterns in coronavirus diversity. Virus Evol. Jan 2017;3 (1). academic.oup.com. doi:10.1093/ve/vex012.
   PubMed Web of Science ®Google Scholar
• Korber B, Myers G. Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses. 1992 Sept;8(9):1549–60. PubMed. doi:10.1089/aid.1992.8.1549.
   PubMed Web of Science ®Google Scholar
• Sagar M, Laeyendecker O, Lee S, Gamiel J, Wawer M, Gray R, Serwadda D, Sewankambo N, Shepherd J, Toma J, et al. Selection of HIV variants with signature genotypic characteristics during heterosexual transmission. J Infect Dis. 2009 Feb;199(4):580–89. PubMed Central. doi:10.1086/596557.
   PubMed Web of Science ®Google Scholar
• Chohan B, Lang D, Sagar M, Korber B, Lavreys L, Richardson B, Overbaugh J. Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. J Virol. 2005 May;79(10):6528–31. PubMed Central. doi:10.1128/JVI.79.10.6528-6531.2005.
   PubMed Web of Science ®Google Scholar
• Ping L-H, Joseph SB, Anderson JA, Abrahams M-R, Salazar-Gonzalez JF, Kincer LP, Treurnicht FK, Arney L, Ojeda S, Zhang M, et al. Comparison of viral env proteins from acute and chronic infections with subtype C human immunodeficiency virus type 1 identifies differences in glycosylation and CCR5 utilization and suggests a new strategy for immunogen design. J Virol. 2013 July;87(13):7218–33. PubMed Central. doi:10.1128/JVI.03577-12.
   PubMed Web of Science ®Google Scholar
• Rathore U, Saha P, Kesavardhana S, Kumar AA, Datta R, Devanarayanan S, Das R, Mascola JR, Varadarajan R. Glycosylation of the core of the HIV-1 envelope subunit protein Gp120 is not required for native trimer formation or viral infectivity. J Biol Chem. 2017 June;292(24):10197–219. PubMed Central. doi:10.1074/jbc.M117.788919.
   PubMed Web of Science ®Google Scholar
• Parrish NF, Gao F, Li H, Giorgi EE, Barbian HJ, Parrish EH, Zajic L, Iyer SS, Decker JM, Kumar A, et al. Phenotypic properties of transmitted founder HIV-1. Proc Natl Acad Sci U S A. 2013 Apr;110(17):6626–33. PubMed Central. doi:10.1073/pnas.1304288110.
   PubMed Web of Science ®Google Scholar
• Astrakhantseva I, Campo DS, Araujo A, Teo CG, Khudyakov Y, Kamili S. Variation in physicochemical properties of the hypervariable region 1 during acute and chronic stages of hepatitis C virus infection. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), 2011. Semantic Scholar. doi:10.1109/BIBMW.2011.6112357
   Google Scholar
• D’Arienzo V, Moreau A, D’Alteroche L, Gissot V, Blanchard E, Gaudy-Graffin C, Roch E, Dubois F, Giraudeau B, Plantier JC, et al. Sequence and functional analysis of the envelope glycoproteins of hepatitis C virus variants selectively transmitted to a new host. J Virol. 2013 Dec;87(24):13609–18. jvi.asm.org. doi:10.1128/JVI.02119-13.
   PubMed Web of Science ®Google Scholar
• Li, Hui, et al. “Molecular Identification of Transmitted/Founder Hepatitis C Viruses and Their Progeny by Single Genome Sequencing.” Methods in Molecular Biology (Clifton, N.J.), vol. 1911, 2019, pp. 139–55. PubMed, doi:10.1007/978-1-4939-8976-8_9
   Google Scholar
• Regenmortel V, Marc HV. Development of a preventive HIV vaccine requires solving inverse problems which is unattainable by rational vaccine design. Front Immunol. 2018;8. Frontiers. doi:10.3389/fimmu.2017.02009.
   PubMed Web of Science ®Google Scholar
• Liao H-X, Tsao C-Y, Alam SM, Muldoon M, Vandergrift N, Ma B-J, Lu X, Sutherland LL, Scearce RM, Bowman C, et al. Antigenicity and immunogenicity of transmitted/ founder,consensus, and chronic envelope glycoproteins of human immunodeficiency virus type 1. J Virol. 2013 Apr;87(8):4185–201. jvi.asm.org. doi:10.1128/JVI.02297-12.
   PubMed Web of Science ®Google Scholar
• Burm R, Collignon L, Mesalam AA, Meuleman P. Animal models to study hepatitis C virus infection. Front Immunol. May 2018; 9. PubMed Central. doi:10.3389/fimmu.2018.01032.
   PubMed Web of Science ®Google Scholar
• Policicchio BB, Pandrea I, Apetrei C. Animal models for HIV cure research. Front Immunol. 2016;7. Frontiers. doi:10.3389/fimmu.2016.00012.
   PubMed Web of Science ®Google Scholar
• Chen G-W, Chang S-C, Mok C-K, Lo Y-L, Kung Y-N, Huang J-H, Shih Y-H, Wang J-Y, Chiang C, Chen C-J, et al. Genomic signatures of human versus avian influenza A viruses. Emerg Infect Dis. 2006 Sept;12(7):1353–60. PubMed Central. doi:10.3201/eid1209.060276.
   PubMed Web of Science ®Google Scholar
• Folgori A, Capone S, Ruggeri L, Meola A, Sporeno E, Ercole BB, Pezzanera M, Tafi R, Arcuri M, Fattori E, et al. A T-cell HCV vaccine eliciting effective immunity against heterologous virus challenge in chimpanzees. Nat Med. 2006 Feb;12(2):190–97. www.nature.com. doi:10.1038/nm1353.
   PubMed Web of Science ®Google Scholar