Development and evaluation of a 28S rRNA gene-based nested PCR assay for P. falciparum and P. vivax

Pathogens and Global Health

Volumn 107, Issue 4, 2013, Pages 180-188

  Pakalapati, Deepak ^a   Garg, Shilpi ^a   Middha, Sheetal ^b   Acharya, Jyoti ^b   Subudhi, Amit K ^a   Boopathi, Arunachalam P ^b   Saxena, Vishal ^a   Kochar, Sanjay K ^b   Kochar, Dhanpat K ^c   Das, Ashis ^a  

^a BIRLA INSTITUTE OF TECHNOLOGY AND SCIENCE   (India)

^b S P MEDICAL COLLEGE   (India)

^c Kothari Medical and Research Institute ^*  (India)

Author keywords

28S rRNA gene; Malaria diagnosis; Nested PCR; Plasmodium detection; Surveillance tools

Indexed keywords

RNA 28S;

ARTICLE; CONTROLLED STUDY; CROSS REACTION; DIAGNOSTIC TEST ACCURACY STUDY; GENE SEQUENCE; HUMAN; LIMIT OF DETECTION; MALARIA; MICROSCOPY; MIXED INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARASITEMIA; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

COINFECTION; DNA PRIMERS; DNA, PROTOZOAN; GENES, RRNA; HUMANS; INDIA; MALARIA; MOLECULAR DIAGNOSTIC TECHNIQUES; PARASITOLOGY; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 28S; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 84879538907     PISSN: 20477724     EISSN: 20477732     Source Type: Journal    
DOI: 10.1179/2047773213Y.0000000090     Document Type: Article

References (45)

1. World Health Organization. World malaria report 2010. Geneva: World Health Organization. 2010.
2. World Health Organization. Severe falciparum malaria. Trans R Soc Trop Med Hyg. 2000;94:1-90.
3. Kochar DK, Das A, Kochar SK, Saxena V, Sirohi P, Garg S, et al. Severe Plasmodium vivax Malaria: a report on serial cases from Bikaner in northwestern India. Am J Trop Med Hyg. 2009;80(2):194-8.
4. Warhurst DC, Williams JE. ACP Broadsheet no 148. July 1996. Laboratory diagnosis of malaria. J Clin Pathol. 1996;49(7):533-8.
5. Beadle C, Long GW, McElroy PD, Hoffman SL, Weiss WR, Maret SM, et al. Diagnosis of malaria by detection of Plasmodium falciparum HRP-2 antigen with a rapid dipstick antigen-capture assay. Lancet. 1994;343(8897):564-8.
6. Palmer CJ, Lindo JF, Klaskala WI, Quesada JA, Kaminsky R, Baum MK, et al. Evaluation of the OptiMAL test for rapid diagnosis of Plasmodium vivax and Plasmodium falciparum malaria. J Clin Microbiol. 1998;36(1):203-6.
7. Snounou G, Viriyakosol S, Zhu X, Jarra W, Pinheiro L, do Rosario V, et al. High sensitivity of detection of human malaria parasites by the use of nested polymerase chain reaction. Mol Biochem Parasitol. 1993;61:315-20.
8. Oyedeji SI, Awobode HO, Monday GC, Kendjo E, Kremsner PG, Ku JF. Comparison of PCR-based detection of Plasmodium falciparum infections based on single and multicopy genes. Malar J. 2007;6(1):112.
9. Cunha MG, Medina TS, Oliveira SG, Marinho AN, Póvoa MM, Ribeiro-dos-Santos AKC. Development of a polymerase chain reaction (PCR) method based on amplification of mitochondrial DNA to detect Plasmodium falciparum and Plasmodium vivax. Acta Trop. 2009;111(1):35-8.
10. Tanomsing N, Imwong M, Theppabutr S, Pukrittayakamee S, Day NPJ, White NJ, et al. Accurate and sensitive detection of Plasmodium species in humans by use of the dihydrofolate reductase-thymidylate synthase linker region. J Clin Microbiol. 2010;48(10):3735-7.
11. Demas A, Oberstaller J, DeBarry J, Lucchi NW, Srinivasamoorthy G, Sumari D, et al. Applied genomics: data mining reveals species-specific malaria diagnostic targets more sensitive than 18S rRNA. J Clin Microbiol. 2011;49(7):2411-8.
12. Das A, Holloway B, Collins WE, Shama VP, Ghosh SK, Sinha S, et al. Species-specific 18S rRNA gene amplification for the detection of P. falciparum and P. vivax malaria parasites. Mol Cell Probes. 1995;9(3):161-5.
13. Poon LLM, Wong BWY, Ma EHT, Chan KH, Chow LMC, Abeyewickreme W, et al. Sensitive and inexpensive molecular test for falciparum malaria: detecting Plasmodium falciparum DNA directly from heat-treated blood by loop-mediated isothermal amplification. Clin Chem. 2006;52(2):303-6.
14. Mens P, Schoone G, Kager P, Schallig H. Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification. Malar J. 2006;5(1):80.
15. Rougemont M, Van Saanen M, Sahli R, Hinrikson HP, Bille J, Jaton K. Detection of four Plasmodium species in blood from humans by 18S rRNA gene subunit-based and species-specific real-time PCR assays. J Clin Microbiol. 2004;42(12):5636-43.
16. Veron V, Simon S, Carme B. Multiplex real-time PCR detection of P. falciparum, P. vivax and P. malariae in human blood samples. Exp Parasitol. 2009;121(4):346-51.
17. Sambrook J, MacCallum P, Russell D. Molecular cloning: A laboratory manual: CSHL Press; 2001.
18. Tjitra E, Suprianto S, Dyer M, Currie BJ, Anstey NM. Field evaluation of the ICT malaria P.f/P.v immunochromatographic test for detection of Plasmodium falciparum and Plasmodium vivax in patients with a presumptive clinical diagnosis of malaria in Eastern Indonesia. J Clin Microbiol. 1999;37(8):2412-7.
19. Roper C, Pearce R, Nair S, Sharp B, Nosten F, Anderson T. Intercontinental spread of pyrimethamine-resistant malaria. Science. 2004;305(5687):1124.
20. Dondorp AM, Nosten F, Yi P, Das D, Phyo AP, Tarning J, et al. Artemisinin resistance in Plasmodium falciparum malaria. N Engl J Med. 2009;361(5):455-67.
21. Yang Z, Li C, Miao M, Zhang Z, Sun X, Meng H, et al. Multidrug-resistant genotypes of Plasmodium falciparum, Myanmar. Emerg Infect Dis. 2011;17(3):498-501.
22. Kochar DK, Kochar SK, Agrawal R, Sabir M, Nayak K, Agrawal T, et al. The changing spectrum of severe falciparum malaria: a clinical study from Bikaner (northwest India). J Vector Borne Dis. 2006;43(3):104-8.
23. Kochar DK, Saxena V, Singh N, Kochar SK, Kumar SV, Das A. Plasmodium vivax malaria. Emerg Infect Dis. 2005(11):132-4.
24. Kochar DK, Pakalapati D, Kochar SK, Sirohi P, Khatri MP, Kochar A, et al. An unexpected cause of fever and seizures. Lancet. 2007;370(9590):908.
25. Alexandre MA, Ferreira CO, Siqueira AM, Magalhães BL, Mourão MP, Lacerda MV, et al. Severe Plasmodium vivax malaria, Brazilian Amazon. Emerg Infect Dis. 2010;16(10): 1611-4.
26. Makler MT, Palmer CJ, Ager AL. A review of practical techniques for the diagnosis of malaria. Ann Trop Med Parasitol. 1998;92:419-33.
27. van Spaendonk RML, Ramesar J, van Wigcheren A, Eling W, Beetsma AL, van Gemert GJ, et al. Functional equivalence of structurally distinct ribosomes in the malaria parasite, Plasmodium berghei. J Biol Chem. 276(25):22638-47.
28. Waters AP, Syin C, McCutchan TF. Developmental regulation of stage-specific ribosome populations in Plasmodium. Nature. 1989;342(6248):438-40.
29. Li J, Gutell R, Damberger S, Wirtz R, Kissinger J, Rogers M, et al. Regulation and trafficking of three distinct 18 S ribosomal RNAs during development of the malaria parasite. J Mol Biol. 1997;269:203-13.
30. Coleman R, Sattabongkot J, Promstaporm S, Maneechai N, Tippayachai B, Kengluecha A, et al. Comparison of PCR and microscopy for the detection of asymptomatic malaria in a Plasmodium falciparum/vivax endemic area in Thailand. Malar J. 2006;5(1):121.
31. Steenkeste N, Rogers WO, Okell L, Jeanne I, Incardona S, Duval L, et al. Sub-microscopic malaria cases and mixed malaria infection in a remote area of high malaria endemicity in Rattanakiri province, Cambodia: implication for malaria elimination. Malar J. 2010(9):108.
32. Kho WG, Chung JY, Sim EJ, Kim MY, Kim DW, Jongwutiwes S, et al. A multiplex polymerase chain reaction for a differential diagnosis of Plasmodium falciparum and Plasmodium vivax. Parasitol Int. 2003;52(3):229-36.
33. Lee MA, Tan CH, Aw LT, Tang CS, Singh M, Lee SH, et al. Real-time fluorescence-based PCR for detection of malaria parasites. J Clin Microbiol. 2002;40(11):4343-5.
34. Playford EG, Walker J. Evaluation of the ICT malaria P.f/P.v and the optimal rapid diagnostic tests for malaria in febrile returned travellers. J Clin Microbiol. 2002 2002;40(11):4166-71.
35. Farcas GA, Zhong KjY, Lovegrove FE, Graham CM, Kain KC. Evaluation of the Binax NOW (R) Ict test versus polymerase chain reaction and microscopy for the detection of malaria in returned travelers. Am J Trop Med Hyg. 2003;69(6):589-92.
36. Mayxay M, Pukrittayakamee S, Newton PN, White NJ. Mixedspecies malaria infections in humans. Trends Parasitol. 2004;20(5):233-40.
37. Genton B, D'Acremont V, Rare L, Baea K, Reeder JC, Alpers MP, et al. Plasmodium Vivax and mixed infections are associated with severe malaria in children: a prospective cohort study from Papua New Guinea. PLoS Med. 2008;5(6):e127.
38. Kochar DK, Das A, Kochar A, Middha S, Acharya J, Tanwar GS, et al. Thrombocytopenia in Plasmodium falciparum, Plasmodium vivax and mixed infection malaria: a study from Bikaner (Northwestern India). Platelets. 2010;21:623-7.
39. Tjitra E, Anstey NM, Sugiarto P, Warikar N, Kenangalem E, Karyana M, et al. Multidrug-resistant Plasmodium vivax associated with severe and fatal malaria: a prospective study in Papua, Indonesia. PLoS Med. 2008;5(6):e128.
40. Lyn P. Cerebral malaria and mixed falciparum-vivax infections. Ann Acad Med Singapore. 1987;16:310-2.
41. Luxemburger C, Ricci F, Nosten F, Raimond D, Bathet S, White NJ. The epidemiology of severe malaria in an area of low transmission in Thailand. Trans R Soc Trop Med Hyg. 1997;91(3):256-62.
42. Price RN, Simpson JA, Nosten F, Luxemburger C, Hkirjaroen L, ter Kuile F, et al. Factors contributing to anemia after uncomplicated falciparum malaria. Am J Trop Med Hyg. 2001;65(5):614-22.
43. Gupta B, Gupta P, Sharma A, Singh V, Dash AP, Das A. High proportion of mixed-species Plasmodium infections in India revealed by PCR diagnostic assay. Trop Med Int Health. 2010;15(7):819-24.
44. Polz MF, Cavanaugh CM. Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol. 1998;64(10): 3724-30.
45. Suzuki M, Giovannoni S. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol. 1996;62(2):625-30.