Enrichment of intersubtype HIV-1 recombinants in a dual infection system using HIV-1 strain-specific siRNAs

Retrovirology

Volumn 8, Issue , 2011, Pages

  Gao, Yong ^a   Abreha, Measho ^a   Nelson, Kenneth N ^a   Baird, Heather ^a   Dudley, Dawn M ^a   Abraha, Awet ^a   Arts, Eric J ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; VIRUS ENVELOPE PROTEIN; VIRUS ENVELOPE PROTEIN A; VIRUS ENVELOPE PROTEIN D;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; ENRICHMENT CULTURE; GENETIC CONSERVATION; HUMAN IMMUNODEFICIENCY VIRUS 1; MIXED INFECTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PROGENY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; VIRUS GENE; VIRUS INHIBITION; VIRUS RECOMBINANT; VIRUS RECOMBINATION; VIRUS STRAIN; ANTIVIRAL RESISTANCE; GENETIC RECOMBINATION; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; SEQUENCE ALIGNMENT; VIROLOGY; VIRUS REPLICATION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

BASE SEQUENCE; DRUG RESISTANCE, VIRAL; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; RECOMBINATION, GENETIC; RNA, SMALL INTERFERING; SEQUENCE ALIGNMENT; VIRUS REPLICATION;

EID: 78651309101     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-8-5     Document Type: Article

References (42)

1. Vogt PK. Genetically stable reassortment of markers during mixed infection with avian tumor viruses. Virology 1971, 46:947-952. 10.1016/0042-6822(71)90093-6, 4332983.
2. Beemon K, Duesberg P, Vogt P. Evidence for crossing-over between avian tumor viruses based on analysis of viral RNAs. Proc Natl Acad Sci USA 1974, 71:4254-4258. 10.1073/pnas.71.10.4254, 434370, 4372615.
3. Hu WS, Temin HM. Genetic consequences of packaging two RNA genomes in one retroviral particle: pseudodiploidy and high rate of genetic recombination. Proc Natl Acad Sci USA 1990, 87:1556-1560. 10.1073/pnas.87.4.1556, 53514, 2304918.
4. Jung A, Maier R, Vartanian JP, Bocharov G, Jung V, Fischer U, Meese E, Wain-Hobson S, Meyerhans A. Multiply infected spleen cells in HIV patients. Nature (London) 2002, 418:144.
5. Wain-Hobson S, Renoux-Elbe C, Vartanian JP, Meyerhans A. Network analysis of human and simian immunodeficiency virus sequence sets reveals massive recombination resulting in shorter pathways. J Gen Virol 2003, 84:885-895. 10.1099/vir.0.18894-0, 12655089.
6. Peeters M. Recombinant HIV sequences: Their role in the global epidemic. Human Retroviruses and AIDS 2000 2000, I-39-I-54. Los Alamos, NM: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Kuiken C, Foley B, Hahn B, Korber B, McCutchan F, Marx P.
7. Quinones-Mateu ME, Arts EJ. Recombination in human immunodeficiency virus type-1 (HIV-1): Update and implications. AIDS Rev 1998, 2:89-100.
8. Tebit DM, Nankya I, Arts EJ, Gao Y. HIV diversity, recombination and disease progression: how does fitness "fit" into the puzzle?. AIDS Rev 2007, 9:75-87.
9. Kuiken C, Leitner T, Foley B, Hahn BH, Marx P, McCutchan FE, et al. HIV-1 sequence compendium 2009, Los Alamos: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory.
10. Arien KK, Vanham G, Arts EJ. Is HIV-1 evolving to a less virulent form in humans?. Nat Rev Microbiol 2007, 5:141-151. 10.1038/nrmicro1594, 17203103.
11. Onafuwa-Nuga A, Telesnitsky A. The remarkable frequency of human immunodeficiency virus type 1 genetic recombination. Microbiol Mol Biol Rev 2009, 73:451-80. Table., 10.1128/MMBR.00012-09, 2738136, 19721086.
12. Baird HA, Galetto R, Gao Y, Simon-Loriere E, Abreha M, Archer J, Fan J, Robertson DL, Arts EJ, Negroni M. Sequence determinants of breakpoint location during HIV-1 intersubtype recombination. Nucleic Acids Res 2006, 34:5203-5216. 10.1093/nar/gkl669, 1636437, 17003055.
13. Baird HA, Gao Y, Galetto R, Lalonde M, Anthony RM, Giacomoni V, Abreha M, Destefano JJ, Negroni M, Arts EJ. Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination. Retrovirology 2006, 3:91. 10.1186/1742-4690-3-91, 1764423, 17164002.
14. Galetto R, Giacomoni V, Veron M, Negroni M. Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle. J Biol Chem 2006, 281:2711-20. 10.1074/jbc.M505457200, 16291743.
15. Rhodes T, Wargo H, Hu WS. High rates of human immunodeficiency virus type 1 recombination: near-random segregation of markers one kilobase apart in one round of viral replication. J Virol 2003, 77:11193-11200. 10.1128/JVI.77.20.11193-11200.2003, 224990, 14512567.
16. Chin MP, Rhodes TD, Chen J, Fu W, Hu WS. Identification of a major restriction in HIV-1 intersubtype recombination. Proc Natl Acad Sci USA 2005, 102:9002-9007. 10.1073/pnas.0502522102, 1157039, 15956186.
17. Quinones-Mateu ME, Gao Y, Ball SC, Marozsan AJ, Abraha A, Arts EJ. In vitro intersubtype recombinants of human immunodeficiency virus type 1: comparison to recent and circulating in vivo recombinant forms. J Virol 2002, 76:9600-9613. 10.1128/JVI.76.19.9600-9613.2002, 136488, 12208939.
18. Moutouh L, Corbeil J, Richman DD. Recombination leads to the rapid emergence of HIV-1 dually resistant mutants under selective drug pressure. Proc Natl Acad Sci USA 1996, 93:6106-6111. 10.1073/pnas.93.12.6106, 39197, 8650227.
19. Quan Y, Liang C, Brenner BG, Wainberg MA. Multidrug-resistant variants of HIV type 1 (HIV-1) can exist in cells as defective quasispecies and be rescued by superinfection with other defective HIV-1 variants. J Infect Dis 2009, 200:1479-1483. 10.1086/606117, 19758098.
20. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature (London) 1998, 391:806-811.
21. Zamore PD, Tuschl T, Sharp PA, Bartel DP. RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000, 101:25-33. 10.1016/S0092-8674(00)80620-0, 10778853.
22. Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature (London) 2001, 409:363-366.
23. Gao Y, Lobritz MA, Roth J, Abreha M, Nelson KN, Nankya I, Moore-Dudley DM, Abraha A, Gerson SL, Arts EJ. Targets of small interfering RNA restriction during human immunodeficiency virus type 1 replication. J Virol 2008, 82:2938-2951. 10.1128/JVI.02126-07, 2259002, 18199654.
24. Jacque JM, Triques K, Stevenson M. Modulation of HIV-1 replication by RNA interference. Nature (London) 2002, 418:435-438.
25. Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A, Salvaterra P, Rossi J. Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 2002, 20:500-505.
26. de FA, Vornlocher HP, Maraganore J, Lieberman J. Interfering with disease: a progress report on siRNA-based therapeutics. Nat Rev Drug Discov 2007, 6:443-453. 10.1038/nrd2310, 17541417.
27. Das AT, Brummelkamp TR, Westerhout EM, Vink M, Madiredjo M, Bernards R, Berkhout B. Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J Virol 2004, 78:2601-2605. 10.1128/JVI.78.5.2601-2605.2004, 369246, 14963165.
28. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
29. Gao Y, Paxinos E, Galovich J, Troyer R, Baird H, Abreha M, Kityo C, Mugyenyi P, Petropoulos C, Arts EJ. Characterization of a subtype D human immunodeficiency virus type 1 isolate that was obtained from an untreated individual and that is highly resistant to nonnucleoside reverse transcriptase inhibitors. J Virol 2004, 78:5390-5401. 10.1128/JVI.78.10.5390-5401.2004, 400369, 15113918.
30. Mansky LM, Temin HM. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase 1. J Virol 1995, 69:5087-5094. 189326, 7541846.
31. Powell RL, Urbanski MM, Burda S, Kinge T, Nyambi PN. High frequency of HIV-1 dual infections among HIV-positive individuals in Cameroon, West Central Africa. J Acquir Immune Defic Syndr 2009, 50:84-92. 10.1097/QAI.0b013e31818d5a40, 19295338.
32. Kozaczynska K, Cornelissen M, Reiss P, Zorgdrager F, van der Kuyl AC. HIV-1 sequence evolution in vivo after superinfection with three viral strains. Retrovirology 2007, 4:59. 10.1186/1742-4690-4-59, 2020475, 17716368.
33. Herbinger KH, Gerhardt M, Piyasirisilp S, Mloka D, Arroyo MA, Hoffmann O, Maboko L, Birx DL, Mmbando D, McCutchan FE, Hoelscher M. Frequency of HIV type 1 dual infection and HIV diversity: analysis of low- and high-risk populations in Mbeya Region, Tanzania. AIDS Res Hum Retroviruses 2006, 22:599-606. 10.1089/aid.2006.22.599, 16831083.
34. Hu DJ, Subbarao S, Vanichseni S, Mock PA, Ramos A, Nguyen L, Chaowanachan T, Griensven F, Choopanya K, Mastro TD, Tappero JW. Frequency of HIV-1 dual subtype infections, including intersubtype superinfections, among injection drug users in Bangkok, Thailand. AIDS 2005, 19:303-308.
35. Artenstein AW, VanCott TC, Mascola JR, Carr JK, Hegerich PA, Gaywee J, et al. Dual infection with human immunodeficiency virus type 1 of distinct envelope subtypes in humans. J Infect Dis 1995, 171:805-810.
36. Levy DN, Aldrovandi GM, Kutsch O, Shaw GM. Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci USA 2004, 101:4204-4209. 10.1073/pnas.0306764101, 384719, 15010526.
37. Simon-Loriere E, Galetto R, Hamoudi M, Archer J, Lefeuvre P, Martin DP, Robertson DL, Negroni M. Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus. PLoS Pathog 2009, 5:e1000418. 10.1371/journal.ppat.1000418, 2671596, 19424420.
38. Archer J, Pinney JW, Fan J, Simon-Loriere E, Arts EJ, Negroni M, Robertson DL. Identifying the important HIV-1 recombination breakpoints. PLoS Comput Biol 2008, 4:e1000178. 10.1371/journal.pcbi.1000178, 2522274, 18787691.
39. Dang Q, Chen J, Unutmaz D, Coffin JM, Pathak VK, Powell D, KewalRamani VN, Maldarelli F, Hu WS. Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways. Proc Natl Acad Sci USA 2004, 101:632-637. 10.1073/pnas.0307636100, 327199, 14707263.
40. Westerhout EM, ter BO, Berkhout B. The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference. Retrovirology 2006, 3:57. 10.1186/1742-4690-3-57, 1569866, 16948865.
41. Reed LJ, Muench H, . (Eds) A simple method of estimating fifty percent endpoints. Am J Hyg 1938, 27:493-497. (Eds).
42. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882. 10.1093/nar/25.24.4876, 147148, 9396791.