A general method to eliminate laboratory induced recombinants during massive, parallel sequencing of cDNA library

Virology Journal

Volumn 12, Issue 1, 2015, Pages

  Waugh, Caryll ^a,b   Cromer, Deborah ^c   Grimm, Andrew ^c   Chopra, Abha ^d   Mallal, Simon ^d   Davenport, Miles ^c   Mak, Johnson ^a,b  

^a DEAKIN UNIVERSITY   (Australia)

^b CSIRO   (Australia)

^c UNIVERSITY OF NEW SOUTH WALES   (Australia)

^d MURDOCH UNIVERSITY   (Australia)

Author keywords

HIV; Mutation rate; Recombination rate; Transfection

Indexed keywords

COMPLEMENTARY DNA; PLASMID DNA; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE; RNA POLYMERASE; VIRUS RNA;

ACCURACY; ANALYTIC METHOD; ARTICLE; ARTIFACT; CHIMERA; DNA LIBRARY; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; NONHUMAN; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; CELL LINE; GENE LIBRARY; GENETIC REASSORTMENT; GENETICS; HIGH THROUGHPUT SEQUENCING; HIV INFECTIONS; HUMAN IMMUNODEFICIENCY VIRUS 1; PROCEDURES; STANDARDS; VIROLOGY;

RNA VIRUSES;

ARTIFACTS; CELL LINE; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV INFECTIONS; HIV-1; HUMANS; POLYMERASE CHAIN REACTION; REASSORTANT VIRUSES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TRANSFECTION;

EID: 84927934980     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/s12985-015-0280-x     Document Type: Article

References (21)

1. Smyth RP, Schlub TE, Grimm A, Venturi V, Chopra A, Mallal S, et al. Reducing chimera formation during PCR amplification to ensure accurate genotyping. Gene. 2010;469(1-2):45-51.
2. Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Kunzli-Gontarczyk M, et al. Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination. PLoS One. 2013;8(9):e74249.
3. Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, et al. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology. 2013;10:18.
4. Dudley DM, Chin EN, Bimber BN, Sanabani SS, Tarosso LF, Costa PR, et al. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One. 2012;7(5):e36494.
5. Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, et al. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol. 2012;86(11):6231-7.
6. Avidor B, Girshengorn S, Matus N, Talio H, Achsanov S, Zeldis I, et al. Evaluation of a benchtop HIV ultradeep pyrosequencing drug resistance assay in the clinical laboratory. J Clin Microbiol. 2013;51(3):880-6.
7. Schlub TE, Smyth RP, Grimm AJ, Mak J, Davenport MP. Accurately measuring recombination between closely related HIV-1 genomes. PLoS Comput Biol. 2010;6(4):e1000766.
8. Kucherlapati RS, Eves EM, Song KY, Morse BS, Smithies O. Homologous recombination between plasmids in mammalian cells can be enhanced by treatment of input DNA. Proc Natl Acad Sci U S A. 1984;81(10):3153-7.
9. Wake CT, Vernaleone F, Wilson JH. Topological requirements for homologous recombination among DNA molecules transfected into mammalian cells. Mol Cell Biol. 1985;5(8):2080-9.
10. Rauth S, Song KY, Ayares D, Wallace L, Moore PD, Kucherlapati R. Transfection and homologous recombination involving single-stranded DNA substrates in mammalian cells and nuclear extracts. Proc Natl Acad Sci U S A. 1986;83(15):5587-91.
11. Sprengel R, Varmus HE, Ganem D. Homologous recombination between hepadnaviral genomes following in vivo DNA transfection: implications for studies of viral infectivity. Virology. 1987;159(2):454-6.
12. Coffin JM. Structure, replication, and recombination of retrovirus genomes: some unifying hypotheses. J Gen Virol. 1979;42(1):1-26.
13. Hwang CK, Svarovskaia ES, Pathak VK. Dynamic copy choice: steady state between murine leukemia virus polymerase and polymerase-dependent RNase H activity determines frequency of in vivo template switching. Proc Natl Acad Sci U S A. 2001;98(21):12209-14.
14. Levy DN, Aldrovandi GM, Kutsch O, Shaw GM. Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci U S A. 2004;101(12):4204-9.
15. Dapp MJ, Clouser CL, Patterson S, Mansky LM. 5-Azacytidine can induce lethal mutagenesis in human immunodeficiency virus type 1. J Virol. 2009;83(22):11950-8.
16. Dapp MJ, Heineman RH, Mansky LM. Interrelationship between HIV-1 fitness and mutation rate. J Mol Biol. 2013;425(1):41-53.
17. Nguyen LA, Kim DH, Daly MB, Allan KC, Kim B. Host SAMHD1 protein promotes HIV-1 recombination in macrophages. J Biol Chem. 2014;289(5):2489-96.
18. Chen J, Nikolaitchik O, Singh J, Wright A, Bencsics CE, Coffin JM, et al. High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis. Proc Natl Acad Sci U S A. 2009;106(32):13535-40.
19. Englund G, Theodore TS, Freed EO, Engelman A, Martin MA. Integration is required for productive infection of monocyte-derived macrophages by human immunodeficiency virus type 1. J Virol. 1995;69(5):3216-9.
20. Schlub TE, Grimm AJ, Smyth RP, Cromer D, Chopra A, Mallal S, et al. Fifteen to twenty percent of HIV substitution mutations are associated with recombination. J Virol. 2014;88(7):3837-49.
21. Smyth RP, Schlub TE, Grimm AJ, Waugh C, Ellenberg P, Chopra A, et al. Identifying recombination hot spots in the HIV-1 genome. J Virol. 2014;88(5):2891-902.