Identifying and quantifying genotypes in polyclonal infections due to single species

Emerging Infectious Diseases

Volumn 12, Issue 3, 2006, Pages 475-482

  Colborn, James M ^a,d   Koita, Ousmane A ^b   Cissé, Ousmane ^b   Bagayoko, Mamadou W ^b   Guthrie, Edward J ^c   Krogstad, Donald J ^a  

^a TULANE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

^b UNIVERSITY OF BAMAKO   (Mali)

^c AGILENT TECHNOLOGIES   (United States)

^d TULANE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; ALLOTYPE; ARTICLE; BLOOD SAMPLING; CAPILLARY ELECTROPHORESIS; CONTROLLED STUDY; GENE AMPLIFICATION; GENOTYPE; HUMAN; INFECTION; PLASMODIUM FALCIPARUM; PROTOZOAL INFECTION; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY;

EID: 33644532850     PISSN: 10806040     EISSN: 10806059     Source Type: Journal    
DOI: 10.3201/eid1203.05057     Document Type: Article

References (40)

1. Janini LM, Tanuri A, Schechter M, Pweralta JM, Vicente AC, Dela Torre N, et al. Horizontal and vertical transmission of human immunodeficiency virus type 1 dual infections caused by viruses of subtypes B and C. J Infect Dis. 1998;177:227-31.
2. Rayfield MA, Downing RG, Baggs J, Hu DJ, Pieniazek D, Luo C-C, et al. A molecular epidemiologic survey of HIV in Uganda. AIDS. 1998;12:521-7.
3. Tuveri R, Rothschild C, Pol S, Reijasse D, Persico T, Gazengel C, et al. Hepatitis C virus genotypes in French hemophiliacs: kinetics and reappraisal. J Med Virol. 1997;51:36-41.
4. Walling DW, Shebib N, Weaver SC, Nichols CM, Flaitz CM, Webster-Cyriaque J. The molecular epidemiology and evolution of Epstein-Barr virus: sequence variation and genetic recombination in the latent membrane protein-1 gene. J Infect Dis. 1999;179:763-74.
5. Loroño-Pino MA, Cropp CB, Farfán JA, Vorndam AV, Rodríguez-Angulo EM, Rosado-Paredes EP, et al. Common occurrence of concurrent infections by multiple dengue virus serotypes. Am J Trop Med Hyg. 1999;61:725-30.
6. Warren RM, Victor TC, Streicher EM, Richardson M, Beyers N, Gey van Pittius N, et al. Patients with active tuberculosis often have different strains in the same sputum specimen. Am J Respir Crit Care Med. 2004;169:610-4.
7. Pavlic M, Allerberger F, Dierich MP, Prodinger WM. Simultaneous infection with two drug-susceptible Mycobacterium tuberculosis strains in an immunocompetent host. J Clin Microbiol. 1999;37:4156-7.
8. Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP. Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques. 1997;22:134-8.
9. Halford WP, Falco VC, Gebhardt BM, Carr DJ. The inherent quantitative capacity of the reverse transcription-polymerase chain reaction. Anal Biochem. 1999;266:181-91.
10. Trager W, Jensen JB. Human malaria parasites in continuous culture. Science. 1976;193:673-5.
11. Campbell CC, Collins WE, Milhous WK, Roberts JM, Armstead A. Adaptation of the Indochina I/CDC strain of Plasmodium falciparum to the squirrel monkey (Saimiri sciureus). Am J Trop Med Hyg. 1986;35:472-5.
12. Teklehaimanot A, Nguyen-Dinh P, Collins WE, Barber AM, Campbell CC. Evaluation of sporontocidal compounds using gametocytes produced in vitro. Am J Trop Med Hyg. 1985;34:429-4.
13. del Portillo HA, Nussenzweig RS, Enea V. Circumsporozoite gene of Plasmodium falciparum strain from Thailand. Mol Biochem Parasitol. 1987;24:289-4.
14. Miller LH, Roberts T, Shahabuddin M, McCutchan TF. Analysis of sequence diversity in the P. falciparum merozoite surface protein-1 (MSP-1). Mol Biochem Parasitol. 1993;59:1-14.
15. Davis CL, Field D, Metzgar D, Saiz R, Morin PA, Smith IL, et al. Numerous length polymorphisms at short tandem repeats in human cytomegalovirus. J Virol. 1999;73:6265-70.
16. Shurtleff AC, Beasley DWC, Chen JJY, Ni H, Suderman MT, Wang H, et al. Genetic variation in the 3? non-coding region of dengue viruses. Virology. 2001;187:75-87.
17. Bryant JE, Vasconcelos PFC, Rijnbrand RCA, Mutebi JP, Higgs S, Barrett ADT: Size heterogeneity in the 3? noncoding region of South American isolates of yellow fever virus. J Virol. 2005;79:3807-21.
18. Starcich BR, Hahn BH, Shaw G, McNeely PD, Medrow S, Wolf H, et al. Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell. 1986;45:637-48.
19. Delwart E, Magierowska M, Royz M, Foley B, Peddada L, Smith R, et al. Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection. AIDS. 2002;16:189-95.
20. Mokrousov I, Narvaskaya O, Limeschenko E, Otten T, Vyshnevskiy B. Novel IS6110 insertion sites in the direct repeat locus of Mycobacterium tuberculosis clinical strains from the St. Petersburg area of Russia and evolutionary and epidemiological considerations. J Clin Microbiol. 2002;40:1504-7.
21. Frothingham R, Meeker-O'Connell WA. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology. 1998;144:1189-96.
22. de la Salmonière Y-OLG, Kim CC, Tsolaki AG, Pym AS, Siegrist MS, Small PM. High-throughput method for detecting genomic deletion polymorphisms. J Clin Microbiol. 2004;42:2913-8.
23. Gierczynski R, Kaluzewski S, Rakin A, Jagielski M, Zasada A, Jakubczak A, et al. Intriguing diversity of Bacillus anthracis in eastern Poland - the molecular echoes of the past outbreaks. FEMS Microbiol Lett. 2004;239:235-40.
24. Hoffmaster AR, Fitzgerald CC, Ribot E, Mayer LW, Popovic T. Molecular subtyping of Bacillus anthracis and the 2001 bioterrorism-associated anthrax outbreak, United States. Emerg Infect Dis. 2002;8:1111-6.
25. Pourcel C, Andrè-Mazeaud F, Neubauer H, Ramisse F, Vergnaud G. Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis. BMC Microbiol. 2004;4:22.
26. Massung RF, Loparev VN, Knight JC, Totmenin AV, Chizhikov VE, Parsons JM, et al. Terminal region sequence variations in variola virus DNA. Virology. 1996;221:291-300.
27. Massung RF, Esposito JJ, Liu L-I, Qi J, Utterback TR, Knight JC, et al. Potential virulence determinants in terminal regions of variola smallpox virus genome. Nature. 1993;366:748-51.
28. de la Puente-Redondo VA, del Blanco NG, Gutiérrez-Martín CB, García-Peña FJ, Rodriguez Ferri EF. Comparison of different PCR approaches for typing of Franciscella tularensis strains. J Clin Microbiol. 2000;38:1016-22.
29. Farlow J, Smith KL, Wong J, Abrams M, Lytle M, Keim P. Francisella tularensis strain typing using multiple-locus variable-number tandem repeat analysis. J Clin Microbiol. 2001;39:3186-92.
30. Nachamkin I, Panaro NJ, Li M, Ung H, Yuen PK, Kricka LJ, et al. Agilent 2100 bioanalyzer for restriction fragment length polymorphism analysis of the Campylobacter jejuni flagellin gene. J Clin Microbiol. 2001;39:754-7.
31. Snounou G, Farnert A. Genotyping of Plasmodium falciparum parasites by PCR: msp1, msp2 and glurp. In: Ljungström I, Perlmann H, Schlichtherle M, Scherf A, Washlgren M, editors. Methods in malaria research. 4th ed. Manassas (VA): Malaria Research and Reference Resource Center and American Type Culture; 2004. p. 221-5. Available from http://www.malaria.mr4.org/Protocol_Book/ Methods_In_Malaria_Research.pdf.
32. Willmore C, Holden JA, Zhou L, Tripp S, Witwer CT, Layfield LJ. Detection of c-kit activating mutations in gastrointestinal stromal tumors by high-resolution amplicons melting analysis. Am J Clin Pathol. 2004;122:206-16.
33. Ye P, Parra EJ, Sosnoski DM, Hiester K, Underhill PA, Shriver MD. Melting curve SNP (McSNP) genotyping: a useful approach for diallelic genotyping in forensic science. J Forensic Sci. 2002;47:593-600.
34. Witt H, Landt O. Rapid detection of the Wilson's disease H1069Q mutation by melting curve analysis with the LightCycler. Clin Chem Lab Med. 2001;39:953-5.
35. Pals G, Young C, Mao HS, Worsham MJ. Detection of a single base substitution in a single cell using the LightCycler. J Biochem Biophys Methods. 2001;47:121-9.
36. Hill MD, Lorenzo E, Kumar A. Changes in the human immunodeficiency virus V3 region that correspond with disease progression: a meta-analysis. Virus Res. 2004;106:27-33.
37. Daniels RS, Wilson P, Patel D, Longhurst H, Patterson S, et al. Analysis of full-length HIV type 1 env genes indicates differences between the virus infecting T cells and dendritic cells in peripheral blood of infected patients. AIDS Res Hum Retroviruses. 2004;20:409-13.
38. Jensen MA, van't Wout AB. Predicting HIV-1 coreceptor usage with sequence analysis. AIDS Rev. 2003;5:104-12.
39. Zeuzem S. Hepatitis C virus: kinetics and quasispecies evolution during anti-viral therapy. Forum. 2000;10:32-42.
40. Iwasa Y, Michor F, Nowak MA. Virus evolution within patients increases pathogenicity. J Theoret Biol. 2005;232:17-26.