A pan-HIV strategy for complete genome sequencing

Journal of Clinical Microbiology

Volumn 54, Issue 4, 2016, Pages 868-882

  Berg, Michael G ^a   Yamaguchi, Julie ^a   Alessandri Gradt, Elodie ^b   Tell, Robert W ^a   Plantier, Jean Christophe ^b   Brennan, Catherine A ^a  

^a ABBOTT DIAGNOSTICS   (United States)

^b ROUEN UNIVERSITY HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; VIRUS CLASSIFICATION; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS LOAD; VIRUS MORPHOLOGY; VIRUS RECOMBINANT; VIRUS STRAIN; CAMEROON; CLASSIFICATION; DNA SEQUENCE; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; ISOLATION AND PURIFICATION; PHYLOGENY; PLASMA; PROCEDURES; VIROLOGY; VIRUS GENOME;

CAMEROON; GENOME, VIRAL; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV; HIV INFECTIONS; HUMANS; PHYLOGENY; PLASMA; SEQUENCE ANALYSIS, DNA;

EID: 84962615411     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02479-15     Document Type: Article

References (57)

1. Hemelaar J. 2013. Implications of HIV diversity for the HIV-1 pandemic. J Infect 66:391-400. http://dx.doi.org/10.1016/j.jinf.2012.10.026.
2. Korber B, Gaschen B, Yusim K, Thakallapally R, Kesmir C, Detours V. 2001. Evolutionary and immunological implications of contemporary HIV-1 variation. Br Med Bull 58:19-42. http://dx.doi.org/10.1093/bmb/58.1.19.
3. Brennan CA, Yamaguchi J, Devare SG, Foster GA, Stramer SL. 2010. Expanded evaluation of blood donors in the United States for human immunodeficiency virus type 1 non-B subtypes and antiretroviral drugresistant strains: 2005 through 2007. Transfusion 50:2707-2712. http://dx.doi.org/10.1111/j.1537-2995.2010.02767.x.
4. Pyne MT, Hackett J, Jr, Holzmayer V, Hillyard DR. 2013. Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States. J Clin Microbiol 51:2662-2669. http://dx.doi.org/10.1128/JCM.00880-13.
5. Semaille C, Barin F, Cazein F, Pillonel J, Lot F, Brand D, Plantier JC, Bernillon P, Le Vu S, Pinget R, Desenclos JC. 2007. Monitoring the dynamics of the HIV epidemic using assays for recent infection and serotyping among new HIV diagnoses: experience after 2 years in France. J Infect Dis 196:377-383. http://dx.doi.org/10.1086/519387.
6. Callegaro A, Di Filippo E, Astuti N, Ortega PA, Rizzi M, Farina C, Valenti D, Maggiolo F. 2014. Early clinical response and presence of viral resistant minority variants: A proof of concept study. J Int AIDS Soc 17: 19759. http://dx.doi.org/10.7448/IAS.17.4.19759.
7. Dudley DM, Chin EN, Bimber BN, Sanabani SS, Tarosso LF, Costa PR, Sauer MM, Kallas EG, O'Connor DH. 2012. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One 7:e36494. http://dx.doi.org/10.1371/journal.pone.0036494.
8. Ekici H, Rao SD, Sonnerborg A, Ramprasad VL, Gupta R, Neogi U. 2014. Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low-and middle-income countries. J Antimicrob Chemother 69:3349-3355. http://dx.doi.org/10.1093/jac/dku278.
9. Fisher RG, Smith DM, Murrell B, Slabbert R, Kirby BM, Edson C, Cotton MF, Haubrich RH, Kosakovsky Pond SL, Van Zyl GU. 2015. Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure. J Clin Virol 62:48-53. http://dx.doi.org/10.1016/j.jcv.2014.11.014.
10. Garcia-Diaz A, McCormick A, Booth C, Gonzalez D, Sayada C, Haque T, Johnson M, Webster D. 2014. Analysis of transmitted HIV-1 drug resistance using 454 ultra-deep-sequencing and the DeepChek-HIV system. J Int AIDS Soc 17:19752. http://dx.doi.org/10.7448/IAS.17.4.19752.
11. Archer J, Weber J, Henry K, Winner D, Gibson R, Lee L, Paxinos E, Arts EJ, Robertson DL, Mimms L, Quinones-Mateu ME. 2012. Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS One 7:e49602. http://dx.doi.org/10.1371/journal.pone.0049602.
12. Swenson LC, Daumer M, Paredes R. 2012. Next-generation sequencing to assess HIV tropism. Curr Opin HIV AIDS 7:478-485. http://dx.doi.org/10.1097/COH.0b013e328356e9da.
13. Giallonardo FD, Topfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, Daumer M, Beisel C, Rusert P, Trkola A, Gunthard HF, Roth V, Beerenwinkel N, Metzner KJ. 2014. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Res 42:e115. http://dx.doi.org/10.1093/nar/gku537.
14. Hughes AL, Becker EA, Lauck M, Karl JA, Braasch AT, O'Connor DH, O'Connor SL. 2012. SIV genome-wide pyrosequencing provides a comprehensive and unbiased view of variation within and outside CD8 T lymphocyte epitopes. PLoS One 7:e47818. http://dx.doi.org/10.1371/journal.pone.0047818.
15. Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptue L, Chiu CY, Brennan CA, Hackett J, Jr. 2015. Utility of metagenomic next-generation sequencing for characterization of HIV and human pegivirus diversity. PLoS One 10:e0141723. http://dx.doi.org/10.1371/journal.pone.0141723.
16. Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Gunthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM. 2012. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 8:e1002529. http://dx.doi.org/10.1371/journal.ppat.1002529.
17. Bimber BN, Dudley DM, Lauck M, Becker EA, Chin EN, Lank SM, Grunenwald HL, Caruccio NC, Maffitt M, Wilson NA, Reed JS, Sosman JM, Tarosso LF, Sanabani S, Kallas EG, Hughes AL, O'Connor DH. 2010. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J Virol 84: 12087-12092. http://dx.doi.org/10.1128/JVI.01378-10.
18. Hemelaar J. 2012. The origin and diversity of the HIV-1 pandemic. Trends Mol Med 18:182-192. http://dx.doi.org/10.1016/j.molmed.2011.12.001.
19. Li G, Piampongsant S, Faria NR, Voet A, Pineda-Pena AC, Khouri R, Lemey P, Vandamme AM, Theys K. 2015. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology 12: 18. http://dx.doi.org/10.1186/s12977-015-0148-6.
20. Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D, Kellam P. 2012. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J Clin Microbiol 50:3838-3844. http://dx.doi.org/10.1128/JCM.01516-12.
21. Brennan CA, Bodelle P, Coffey R, Devare SG, Golden A, Hackett J, Jr, Harris B, Holzmayer V, Luk KC, Schochetman G, Swanson P, Yamaguchi J, Vallari A, Ndembi N, Ngansop C, Makamche F, Mbanya D, Gurtler LG, Zekeng L, Kaptue L. 2008. The prevalence of diverse HIV-1 strains was stable in Cameroonian blood donors from 1996 to 2004. J Acquir Immune Defic Syndr 49:432-439. http://dx.doi.org/10.1097/QAI.0b013e31818a6561.
22. Chang M, Gottlieb GS, Dragavon JA, Cherne SL, Kenney DL, Hawes SE, Smith RA, Kiviat NB, Sow PS, Coombs RW. 2012. Validation for clinical use of a novel HIV-2 plasma RNA viral load assay using the Abbott m2000 platform. J Clin Virol 55:128-133. http://dx.doi.org/10.1016/j.jcv.2012.06.024.
23. Merck. 9 February 2016, accession date. Benzonase endonuclease: The smart solution for DNA removal. Merck, Darmstadt, Germany. https://www.bioneer.dk/files/Files/Benzonase1.pdf.
24. Law J, Jovel J, Patterson J, Ford G, O'Keefe S, Wang W, Meng B, Song D, Zhang Y, Tian Z, Wasilenko ST, Rahbari M, Mitchell T, Jordan T, Carpenter E, Mason AL, Wong GK. 2013. Identification of hepatotropic viruses from plasma using deep sequencing: A next generation diagnostic tool. PLoS One 8:e60595. http://dx.doi.org/10.1371/journal.pone.0060595.
25. Ray S. 9 February 2016, accession date. SCRoftware. http://sray.med.som.jhmi.edu/SCRoftware/.
26. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152-160.
27. Muzzey D, Evans EA, Lieber C. 2015. Understanding the basics of NGS: from mechanism to variant calling. Curr Genet Med Rep 3:158-165. http://dx.doi.org/10.1007/s40142-015-0076-8.
28. Chenchik A, Zhu Y, Diatchenko L, Li R, Hill J, Siebert P. 1998. Generation and use of high-quality cDNA from small amounts of total RNAbySMARTPCR, p 305-319. In Siebert P, Larrick J (ed), Gene cloning and analysis by RT-PCR. Biotechniques Books, Natick, M.A.
29. Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ. 2008. Viral genome sequencing by random priming methods. BMC Genomics 9:5. http://dx.doi.org/10.1186/1471-2164-9-5.
30. Hall RJ, Wang J, Todd AK, Bissielo AB, Yen S, Strydom H, Moore NE, Ren X, Huang QS, Carter PE, Peacey M. 2014. Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery. J Virol Methods 195:194-204. http://dx.doi.org/10.1016/j.jviromet.2013.08.035.
31. Ragupathy V, Gao F, Sanchez A, Schito M, Denny T, Busch M, Zhao J, Mbondji C, Vemula S, Hewlett I. 2015. PCR-free full genome characterization of diverse HIV-1 strains by Nextgen sequencing. Webcast. CROI 2015: Conf Retrovir Opportunistic Infect, Seattle, WA, 23 to 26 February 2015. http://www.croiwebcasts.org/st/themed?link-nav&linkc-sesstype.
32. Svraka S, Rosario K, Duizer E, van der Avoort H, Breitbart M, Koopmans M. 2010. Metagenomic sequencing for virus identification in a public-health setting. J Gen Virol 91:2846-2856. http://dx.doi.org/10.1099/vir.0.024612-0.
33. Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV. 2010. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One 5:e13564. http://dx.doi.org/10.1371/journal.pone.0013564.
34. Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. 2011. Accurate sampling and deep sequencing of the HIV-1 protease gene using a primer ID. Proc Natl Acad SciUSA108:20166-20171. http://dx.doi.org/10.1073/pnas.1110064108.
35. Danaviah S, Manasa J, Wilkinson E, Pillay S, Sibisi Z, Msweli S, Pillay D, de Oliveira T. 2015. Near full length HIV-1 sequencing to understand HIV phylodynamics in Africa in real time. Webcast. CROI 2015: Conf Retrovir Opportunistic Infect, Seattle, WA, 23 to 26 February 2015. http://www.croiwebcasts.org/st/themed?link-nav&linkc-sesstype.
36. Quinones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. 2014. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 61:9-19. http://dx.doi.org/10.1016/j.jcv.2014.06.013.
37. Greninger AL, Chen EC, Sittler T, Scheinerman A, Roubinian N, Yu G, Kim E, Pillai DR, Guyard C, Mazzulli T, Isa P, Arias CF, Hackett J, Schochetman G, Miller S, Tang P, Chiu CY. 2010. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One 5:e13381. http://dx.doi.org/10.1371/journal.pone.0013381.
38. Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martinez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Jr, Miller S, Chiu CY. 2014. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 24:1180-1192. http://dx.doi.org/10.1101/gr.171934.113.
39. Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL. 2008. The long march: A sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing. PLoS One 3:e3495. http://dx.doi.org/10.1371/journal.pone.0003495.
40. Li L, Deng X, Linsuwanon P, Bangsberg D, Bwana MB, Hunt P, Martin JN, Deeks SG, Delwart E. 2013. AIDS alters the commensal plasma virome. J Virol 87:10912-10915. http://dx.doi.org/10.1128/JVI.01839-13.
41. Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ. 2013. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res 41:e13. http://dx.doi.org/10.1093/nar/gks794.
42. Alfson KJ, Beadles MW, Griffiths A. 2014. A new approach to determining whole viral genomic sequences including termini using a single deep sequencing run. J Virol Methods 208:1-5. http://dx.doi.org/10.1016/j.jviromet.2014.07.023.
43. Logan G, Freimanis GL, King DJ, Valdazo-Gonzalez B, Bachanek-Bankowska K, Sanderson ND, Knowles NJ, King DP, Cottam EM. 2014. A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq. BMC Genomics 15:828. http://dx.doi.org/10.1186/1471-2164-15-828.
44. Wellenreuther R, Schupp I, Poustka A, Wiemann S. 2004. SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones. BMC Genomics 5:36. http://dx.doi.org/10.1186/1471-2164-5-36.
45. Bartolini B, Giombini E, Abbate I, Selleri M, Rozera G, Biagini T, Visco-Comandini U, Taibi C, Capobianchi MR. 2015. Near full length hepatitis C virus genome reconstruction by next generation sequencing based on genotype-independent amplification. Dig Liver Dis 47:608-612. http://dx.doi.org/10.1016/j.dld.2015.03.015.
46. Hara K, Rivera MM, Koh C, Sakiani S, Hoofnagle JH, Heller T. 2013. Important factors in reliable determination of hepatitis C virus genotype by use of the 5= untranslated region. J Clin Microbiol 51:1485-1489. http://dx.doi.org/10.1128/JCM.03344-12.
47. Zhu YY, Machleder EM, Chenchik A, Li R, Siebert PD. 2001. Reverse transcriptase template switching: A SMART approach for full-length cDNA library construction. Biotechniques 30:892-897.
48. Hedskog C, Doehle B, Chodavarapu K, Gontcharova V, Crespo Garcia J, De Knegt R, Drenth JP, McHutchison JG, Brainard D, Stamm LM, Miller MD, Svarovskaia E, Mo H. 2015. Characterization of hepatitis C virus intergenotypic recombinant strains and associated virological response to sofosbuvir/ribavirin. Hepatology 61:471-480. http://dx.doi.org/10.1002/hep.27361.
49. Donaldson EF, Harrington PR, O'Rear JJ, Naeger LK. 2015. Clinical evidence and bioinformatics characterization of potential hepatitisCvirus resistance pathways for sofosbuvir. Hepatology 61:56-65. http://dx.doi.org/10.1002/hep.27375.
50. Halfon P, Sarrazin C. 2012. Future treatment of chronic hepatitis C with direct acting antivirals: is resistance important? Liver Int 32(Suppl 1):S79-S87. http://dx.doi.org/10.1111/j.1478-3231.2011.02716.x.
51. Schneider MD, Sarrazin C. 2014. Antiviral therapy of hepatitis C in 2014: do we need resistance testing? Antiviral Res 105:64-71. http://dx.doi.org/10.1016/j.antiviral.2014.02.011.
52. Sullivan JC, De Meyer S, Bartels DJ, Dierynck I, Zhang EZ, Spanks J, Tigges AM, Ghys A, Dorrian J, Adda N, Martin EC, Beumont M, Jacobson IM, Sherman KE, Zeuzem S, Picchio G, Kieffer TL. 2013. Evolution of treatment-emergent resistant variants in telaprevir phase 3 clinical trials. Clin Infect Dis 57:221-229. http://dx.doi.org/10.1093/cid/cit226.
53. Hoper D, Hoffmann B, Beer M. 2011. A comprehensive deep sequencing strategy for full-length genomes of influenza A. PLoS One 6:e19075. http://dx.doi.org/10.1371/journal.pone.0019075.
54. Zhou B, Donnelly ME, Scholes DT, St George K, Hatta M, Kawaoka Y, Wentworth DE. 2009. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses. J Virol 83:10309-10313. http://dx.doi.org/10.1128/JVI.01109-09.
55. Gibson RM, Schmotzer CL, Quinones-Mateu ME. 2014. Nextgeneration sequencing to help monitor patients infected with HIV: ready for clinical use? Curr Infect Dis Rep 16:401. http://dx.doi.org/10.1007/s11908-014-0401-5.
56. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N. 2012. Application of next-generation sequencing technologies in virology. J Gen Virol 93:1853-1868. http://dx.doi.org/10.1099/vir.0.043182-0.
57. Taylor BS, Sobieszczyk ME, McCutchan FE, Hammer SM. 2008. The challenge of HIV-1 subtype diversity. N Engl J Med 358:1590-1602. http://dx.doi.org/10.1056/NEJMra0706737.