Specialised Molecular Diagnostics |
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New Technologies and ApproachesThe Unit has extended the range of its activities as seen above. Project support has mainly been the detection of HIV-1 using DNA PCR in infants using a standard HIV PCR detection system. Similarly viral loads have been performed using standard technologies currently present in the laboratory. An important advance in the case of the viral loads is the utilisation of automation. To this end for example the COBAS Ampliprep and Cobas now segue to ensure full automation. There are advantages in settings with high specimen throughput. The Unit has participated in the stringent Viral Quality Assurance programme as well as the QCMD programme to ensure that this approach performs well. In addition, the laboratory continues to actively support the evaluation of new technologies and thus the Exavir viral load that is based on protease activity continues to be evaluated. An example of typical results of the Exavir viral load assay versus RNA amplification is presented in the form of a Bland Altman plot (see Figure One). The laboratory evaluation will lead to a field trial planned for 2005. Additional methodologies explored included the use of AMPLISCREEN (Roche) as a tool for the detection of acute/recent HIV infections. The approach is that of the use of optimal pool sizes (primary and secondary pools) in order to make the procedure practical. The work was performed in collaboration with Isaac Choge (AIDS Virus Research Unit). |
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 Mr. Moses Mashiloane setting up a CD4 count. |
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Contact us |
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For queries relating to specific tests, please contact E Cutler:Tel: +27 (011) 386 6439Fax" +27 (011) 386 6411 |
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 Mrs Ewaldé Cutler preparing viral load specimens. |
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Staff |
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| Prof AJ Puren, Deputy Director (Head of Unit) Hepatitis UnitDr Sheila Bowyer, Medical Scientist (Snr) II Nishi Prabdial-Sing, Medical Scientist (Snr) II HIV Molecular DiagnosticsEwaldé Cutler, Medical Scientist (Snr) II, Laboratory Supervisor Mariza Vos, Medical Scientist, Laboratory Quality Representative Deirdré Greyling, Medical Scientist Mark Goosen, Medical Scientist Elizabeth Botha, Medical Scientist Shirley Muvhulawa, Intern Medical Scientist Monalisa Kalimashe, Intern Medical Scientist Prinola Naicker, Intern Medical Scientist Wayne Howard, Medical Scientist Moses Mashiloane, Laboratory Assistant Thokozani Maseko, Laboratory Assistant Support StaffJosias Sekgobela, General Worker |
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Quality Assurance and Quality Control |
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Continued Collaboration with QCMDThe clinical sciences have been dramatically transformed by the rapid evolution of molecular diagnostic nucleic acid testing (NAT). One area where molecular diagnostics has had a significant influence is clinical virology. Technologies offer advances in viral NAT quantification for therapeutic monitoring, the determination of drug resistance and facilitated the discovery of new viruses (recently SARS, avian flu). NAT has the potential of faster, accurate and reliable diagnosis over conventional culture methods. From a quality assurance perspective there are concerns that the rate of molecular diagnostic innovations has meant that issues of QC are left behind while technology advances. Concerns have been raised about quality performance in the routine clinical setting and general lack of method standardization and acceptable QC practices. The quality concerns in molecular diagnostics include: assay sensitivity and specificity, contamination, clinical significance, variable isolation/amplification procedures, lack of robustness and standardisation, lack of appropriate control material, regulations and policies. These concerns will be applicable when considering the routine use of NAT in patient monitoring in ART programme in South Africa. We therefore propose that External Quality Assessment (EQA) be an integral part of the different laboratories quality management system (QMS) that will detect weak spots in performance as well as improve on the reliability and confidence when reporting results. An EQA programme allows comparison and benchmarking, education in good laboratory practise (GLP) and method utility. In addition, EQA provides reference where no international standards are available as well supports the validation & implementation of new methods for clinical use and helps to identify quality improvements. EQA thus complements internal QC as is a necessary part of the clinicalaccreditation process. Figure2 summarises the processes that lead to assay development and the place of an EQA programme in the quality cycle.  Fig 2. The place of EQA in the Quality Cycle QCMD Blood Borne Virus (BBV) EQA Programmes for 2004: South African Participating Laboratories (AJ Puren, NICD and Paul Wallace, QCMD)The NICD-QCMD ran an EQA programme during 2004. Eleven laboratories in total participated in the 2004 BBV (HBV, HCV, HIV) programmes and an additional HIV (DNA) pilot programme. The HIV DNA panel was an unique aspect of the programme and was specifically designed for South African participants. Table One outlines data that is useful in terms of, for example, technologies used for detection and data can be extracted for analysis purposes from a national perspective. Additional analyses include individual laboratory or group performance against world-wide performance. South Africa ranks 13th in terms of the numbers of programmes participated in. The NICD will take on more responsibilities for the 2005 programme as well as providing source material in order that panels become more relevant from a regional perspective. In addition, the NICD has made a presentation to the full executive board of the QCMD in 2004 with respect to the roles and functions of the NICD as a reference laboratory. |
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Publications |
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Recent publications |
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| Auvert B, Males S, Puren A, Taljaard D, Carael M, Williams B. Can highly active antiretroviral therapy reduce the spread of HIV? : A study in a township of South Africa. J Acquir Immune Defic Syndr 2004; 36: 613-21. Day JH, Grand AD, Fielding KL, Morris L, Moloi V. Charalambous S, Puren AJ, Chaisson RE, De Cock KM, Hayes RF, Churchyard GJ. Does tuberculosis increase HIV viral load? J. Infect Dis 2004; 190: 1677-84. Maila HT, Bowyer SM, Swanepoel R. Identification of a new strain of hepatitis E virus from an outbreak in Namibia in 1995. J. Gen Virol 2004; 85: 89-95. Masemola AM, Mashishi TN, Khoury G, Bredell H, Paximadis M, Mathebula T, Barkhan D, Puren AJ, Vardas E, Colvin M, Zijenah L, Katzenstein D, Musonda R, Allen S, Kumwenda N, Taha T, Gray G, McIntyre J, Abdool Karim S, Sheppard H, Gray CM. Novel and promiscuous CTL epitopes in conserved regions of Gag targeted by individuals with early subtype C HIV type 1 infection from southern Africa. J. Immunol 2004; 173: 4607-4617. Conferences and MeetingsDr Puren: Meeting at CDC on HIV diagnostics in Infants: the use of real time PCR, October 2004 Dr Puren: Board meeting of QCMD: the role of EQA in the molecular diagnostics lab, October 2004 |
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