Correction to: Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda (Scientific Reports, (2017), 7, 1, (11810), 10.1038/s41598-017-11814-9);Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda

Scientific Reports

Volumn 7, Issue 1, 2017, Pages

  Ruybal Pesántez, Shazia ^a,b   Tiedje, Kathryn E ^a,b   Tonkin Hill, Gerry ^c   Rask, Thomas S ^a,b   Kamya, Moses R ^d   Greenhouse, Bryan ^e   Dorsey, Grant ^e   Duffy, Michael F ^a   Day, Karen P ^a,b  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b NEW YORK UNIVERSITY   (United States)

^c WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^d MAKERERE UNIVERSITY COLLEGE OF HEALTH SCIENCES   (Uganda)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTOZOAL PROTEIN;

CHILD; CLINICAL TRIAL; FEMALE; GENETIC VARIATION; GENETICS; HUMAN; INFANT; MALARIA FALCIPARUM; MALE; MULTICENTER STUDY; PATHOGENICITY; PLASMODIUM FALCIPARUM; PRESCHOOL CHILD; TRANSMISSION; UGANDA;

CHILD; CHILD, PRESCHOOL; FEMALE; GENETIC VARIATION; HUMANS; INFANT; MALARIA, FALCIPARUM; MALE; PLASMODIUM FALCIPARUM; PROTOZOAN PROTEINS; UGANDA;

EID: 85029646750     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-024-72799-w     Document Type: Erratum

References (64)

1. Day, K. P. & Marsh, K. Naturally acquired immunity to Plasmodium falciparum. Immunol Today 12, 68-71 (1991).
2. Baruch, D. I. et al. Cloning the P. falciparum gene encoding Pf EMP1, a malarial variant antigen and adherence receptor on the surface of parasitized human erythrocytes. Cell 82, 77-87 (1995).
3. Smith, J. D. et al. Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes. Cell 82, 101-110 (1995).
4. Su, X. Z. et al. The large diverse gene family var encodes proteins involved in cytoadherence and antigenic variation of Plasmodium falciparum-infected erythrocytes. Cell 82, 89-100 (1995).
5. Scherf, A. et al. Antigenic variation in malaria: In situ switching, relaxed and mutually exclusive transcription of var genes during intra-erythrocytic development in Plasmodium falciparum. EMBO J 17, 5418-5426 (1998).
6. Voss, T. S. et al. A var gene promoter controls allelic exclusion of virulence genes in Plasmodium falciparum malaria. Nature 439, 1004-1008 (2006).
7. Dzikowski, R., Frank, M. & Deitsch, K. Mutually exclusive expression of virulence genes by malaria parasites is regulated independently of antigen production. PLoS Pathog 2, 0184-0194 (2006).
8. Smith, J. D., Subramanian, G., Gamain, B., Baruch, D. I. & Miller, L. H. Classification of adhesive domains in the Plasmodium falciparum Erythrocyte Membrane Protein 1 family. Mol Biochem Parasitol 110, 293-310 (2000).
9. Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498-511 (2002).
10. Lavstsen, T., Salanti, A., Jensen, A. T. R., Arnot, D. E. & Theander, T. G. Sequence Analysis of Coding and Non-Coding Regions. 14, 1-14 (2003).
11. Rask, T. S., Hansen, D. A., Theander, T. G., Pedersen, A. G. & Lavstsen, T. Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes-divide and conquer. PLoS Comput Biol 6 (2010).
12. Barry, A. E. et al. Population genomics of the immune evasion (var) genes of Plasmodium falciparum. PLoS Pathog 3, e34 (2007).
13. Chen, D. S. et al. A molecular epidemiological study of var gene diversity to characterize the reservoir of Plasmodium falciparum in humans in Africa. PLoS One 6, e16629 (2011).
14. Tessema, S. K. et al. Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area. Mol Ecol 24, 484-497 (2015).
15. Day, K. P. et al. Evidence of strain structure in Plasmodium falciparum var gene repertoires in children from Gabon, West Africa, doi:https://doi. org/10. 1073/pnas. 1613018114 (2017).
16. Kraemer, S. M. & Smith, J. D. A family affair: var genes, Pf EMP1 binding, and malaria disease. Curr Opin Microbiol 9, 374-80 (2006).
17. Kraemer, S. M. & Smith, J. D. Evidence for the importance of genetic structuring to the structural and functional specialization of the Plasmodium falciparum var gene family. Mol Microbiol 50, 1527-1538 (2003).
18. Salanti, A. et al. Selective upregulation of a single distinctly structured var gene in chondroitin sulphate A-adhering Plasmodium falciparum involved in pregnancy-associated malaria. Mol Microbiol 49, 179-191 (2003).
19. Kraemer, S. M. et al. Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates. BMC Genomics 8, 45 (2007).
20. Zilversmit, M. M. et al. Hypervariable antigen genes in malaria have ancient roots. BMC Evol Biol 13, 110 (2013).
21. Paul, R. E. et al. Mating patterns in malaria parasite populations of Papua New Guinea [see comments]. Science (80-) 269, 1709-1711 (1995).
22. Babiker, H. A. et al. Random mating in a natural population of the malaria parasite Plasmodium falciparum. Parasitology 109(Pt 4), 413-421 (1994).
23. Artzy-Randrup, Y. et al. Population structuring of multi-copy, antigen-encoding genes in plasmodium falciparum. Elife 2012, 1-17 (2012).
24. Buckee, C. O. & Recker, M. Evolution of the multi-domain structures of virulence genes in the human malaria parasite, Plasmodium falciparum. PLoS Comput Biol 8 (2012).
25. Claessens, A. et al. Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis. PLoS Genet 10 (2014).
26. Jensen, A. T. R. et al. Plasmodium falciparum associated with severe childhood malaria preferentially expresses Pf EMP1 encoded by group A var genes. J Exp Med 199, 1179-1190 (2004).
27. Kaestli, M. et al. Virulence of malaria is associated with differential expression of Plasmodium falciparum var gene subgroups in a case-control study. J Infect Dis 193, 1567-74 (2006).
28. Rottmann, M. et al. Differential expression of var gene groups is associated with morbidity caused by Plasmodium falciparum infection in Tanzanian children. Infect Immun 74, 3904-3911 (2006).
29. Kyriacou, H. M. et al. Differential var gene transcription in Plasmodium falciparum isolates from patients with cerebral malaria compared to hyperparasitaemia. Mol Biochem Parasitol 150, 211-218 (2006).
30. Normark, J. et al. Pf EMP1-DBL1alpha amino acid motifs in severe disease states of Plasmodium falciparum malaria. Proc Natl Acad Sci USA 104, 15835-40 (2007).
31. Warimwe, G. M. et al. Plasmodium falciparum var gene expression is modified by host immunity. Proc Natl Acad Sci USA 106, 21801-6 (2009).
32. Falk, N. et al. Analysis of Plasmodium falciparum var genes expressed in children from Papua New Guinea. J Infect Dis 200, 347-356 (2009).
33. Kalmbach, Y. et al. Differential var gene expression in children with malaria and antidromic effects on host gene expression. J Infect Dis 202, 313-317 (2010).
34. Warimwe, G. M. et al. Prognostic indicators of life-threatening malaria are associated with distinct parasite variant antigen profiles. Sci Transl Med 4, 129ra45-129ra45 (2012).
35. Scherf, A., Lopez-Rubio, J. J. & Riviere, L. Antigenic variation in Plasmodium falciparum. Annu Rev Microbiol 62, 445-470 (2008).
36. Dara, A. et al. New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali. Genome Med 9, 30 (2017).
37. Chao, A., Hwang, W. H., Chen, Y. C. & Kuo, C. Y. Estimating the number of shared species in two communities. Stat Sin 10, 227-246 (2000).
38. Chazdon, R. L., Colwell, R. K., Denslow, J. S. & Guariguata, M. R. Statistical methods for estimating species richness of woody regeneration in primary and secondary rainforests of noetheastern Costa Rica. For Biodivers Res Monit Model 20, 285-309 (1998).
39. Chao, A. Estimating the population size for capture-recapture data with unequal catchability. Biometrics 43, 783-791 (1987).
40. Burnham, K. P. & Overton, W. S. Robust Estimation of Population Size When Capture Probabilities Vary Among Animals. Ecology 60, 927-936 (1979).
41. Smith, E. P. & van Belle, G. Nonparametric Estimation of Species Richness. Biometrics 40, 119-129 (1984).
42. Palmer, M. W. Estimating Species Richness: The Second-Order Jackknife Reconsidered. Ecology 72, 1512-1513 (1991).
43. Greenwood, B., Marsh, K. & Snow, R. Why do some African children develop severe malaria Parasitol Today 7, 277-281 (1991).
44. Snow, R. W. & Marsh, K. New insights into the epidemiology of malaria relevant for disease control. 54, 293-309 (1998).
45. Daniels, R. et al. Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal. PLoS One 8, e60780 (2013).
46. Bull, P. C. et al. Plasmodium falciparum variant surface antigen expression patterns during malaria. PLoS Pathog 1, 0202-0213 (2005).
47. Bull, P. C. et al. Plasmodium falciparum antigenic variation. Mapping mosaic var gene sequences onto a network of shared, highly polymorphic sequence blocks. Mol Microbiol 68, 1519-1534 (2008).
48. Nielsen, M. A. et al. Plasmodium falciparum Variant Surface Antigen Expression Varies Between Isolates Causing Severe and Nonsevere Malaria and Is Modified by Acquired Immunity. J Immunol 168, 3444-3450 (2002).
49. Barry, A. E. et al. The Stability and Complexity of Antibody Responses to the Major Surface Antigen of Plasmodium falciparum Are Associated with Age in a Malaria Endemic Area. Mol Cell Proteomics 10, M111. 008326-M111. 008326 (2011).
50. Bengtsson, A. et al. A Novel Domain Cassette Identifies Plasmodium falciparum Pf EMP1 Proteins Binding ICAM-1 and Is a Target of Cross-Reactive, Adhesion-Inhibitory Antibodies. J Immunol 190, 240-249 (2013).
51. Buckee, C. O., Bull, P. C. & Gupta, S. Inferring malaria parasite population structure from serological networks. Proc Biol Sci 276, 477-485 (2009).
52. Hopkins, H. et al. Rapid diagnostic tests for malaria at sites of varying transmission intensity in Uganda. J Infect Dis 197, 510-8 (2008).
53. Roche. Using multiplex identifier (MID) adaptors for the GS FLX titanium chemistry-extended MID set. Tech Bull Genome Seq FLX Syst TCB No 005-2009 (2009).
54. Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J. & Knight, R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5, 235-237 (2008).
55. Cock, P. J. A. et al. Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11), 1422-1423 (2009).
56. Quince, C., Lanzen, A., Davenport, R. J. & Turnbaugh, P. J. Removing Noise From Pyrosequenced Amplicons (2011).
57. Rask, T. S., Petersen, B., Chen, D. S., Day, K. P. & Pedersen, A. G. Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data. BMC Bioinformatics 17, 176 (2016).
58. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
59. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection 27, 2194-2200 (2011).
60. Colwell, R. K. EstimateS: Statistical estimation of species richness and shared species from samples. Version 9. 1. Available at: http:// viceroy. eeb. uconn. edu/estimates/ (2006).
61. R Core Team. R: A language and environment for statistical computing (2015).
62. Chao, A. et al. Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies. Ecol Monogr 84, 45-67 (2014).
63. Colwell, R. K. & Coddington, J. A. Estimating terrestrial biodiversity through extrapolation. Philos Trans Biol Sci 345, 101-118 (1994).
64. Chao, A. & Lee, S.-M. Estimating the Number of Classes via Sample Coverage. Journal of the American Statistical Association 87, 210-217 (1992).