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Correlation between Sequencing Results from Liquid Plasma and Dried Plasma Spot (DPS) for Determination of HIV Type 1 Non-B Subtypes

DOI: 10.4236/oalib.1102922, PP. 1-7

Subject Areas: HIV

Keywords: Sequencing, Liquid Plasma, Dried Plasma Spot, HIV-1 Non-B, Kinshasa

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Abstract

Background: The blotting paper is an alternative to the collection of blood in the tubes for analysis, especially in the field of Human Immunodeficiency Virus infection. This technique allows to easily send the collected samples to specialized laboratories while limiting the stresses of storage and transport. Objective: The objective of this study was to compare the results of sequencing performed on liquid plasma and Dried Plasma Spot (DPS) for the variants of HIV-1 non-B. Methodology: Fifty subjects diagnosed positive for HIV Type 1 using the Rapid Screening Tests voluntarily participated in this study. Two hundred microliters of plasma are deposited on blotting paper Whatman 903 and 500 μl in a micro tube. RNA was extracted from 140 μl of plasma fluid and from a piece of DPS of 5 mm of diameter using the QIAamp RNA Mini Kit QIAGEN. After extraction, the Viral Load (VL) was performed on each sample of liquid plasma. A Reverse Transcription PCR and Nested PCR were used to amplify the regions of interest on the Protease and Reverse Transcriptase for subsequent sequencing. Results: Protease and Reverse Transcriptase were amplified and sequenced respectively for 44 (88%) and 48 (96%) with the liquid plasma samples and 40 (80%) and 45 (90%) with the DPS. The results of Viral Loads were in the range of 2.5 log10 and 6.5 log10. The results of sequencing are comparable for plasma samples and DPS. The correlation coefficient (R2) between the two methods is good (R2 = 0.903, p < 0.001). Conclusion: Liquid Plasma and Dried Plasma Spot give highly correlated results for sequencing strains of HIV type 1 non-B.

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Kamangu, E. N. , Chatté, A. , Vaira, D. , Mol, P. D. , Mvumbi, G. L. , Kalala, R. L. and Hayette, M. (2017). Correlation between Sequencing Results from Liquid Plasma and Dried Plasma Spot (DPS) for Determination of HIV Type 1 Non-B Subtypes. Open Access Library Journal, 4, e2922. doi: http://dx.doi.org/10.4236/oalib.1102922.

References

[1]  Robertson, D.L., Anderson, J.P., Bradac, J.A., Carr, J.K., Foley, B., Funkhouser, R.K., Gao, F., Hahn, B.H., Kalish, M.L., Kuiken, C., Learn, G.H., Leitner, T., McCutchan, F., Osmanov, S., Peeters, M., Pieniazek, D., Salminen, M., Sharp, P.M., Wolinsky, S. and Korber, B. (2000) HIV Type 1 Nomenclature Proposal. Science, 288, 55-56.
https://doi.org/10.1126/science.288.5463.55d
[2]  Papathanasopoulos, M.A., Hunt, G.M. and Tiemessen, C.T. (2003) Evolution and Diversity of HIV Type 1 in Africa: A Review. Virus Genes, 26, 151-163.
https://doi.org/10.1023/A:1023435429841
[3]  Hemelaar, J., Gouws, E., Ghys, P.D. and Osmanov, S. (2006) Global and Regional Distribution of HIV Type 1 Genetic Subtypes and Recombinants in 2004. AIDS, 20, W13-W23.
https://doi.org/10.1097/01.aids.0000247564.73009.bc
[4]  Mei, J.V., Alenxander, J.R., Adam, B.W. and Hannon, W.H. (2001) Use of Filter Paper for Collection and Analysis of Human Whole Blood Specimens. Journal of Nutrition, 131, 1631S-1636S.
[5]  Chatté, A., Kamangu, E., Mahamat, M.A., Tchoumbou, B., Vaira, D. and Moutschen, M. (2013) Use of Dried Blood Spot to Improve the Diagnosis and Management of HIV in Resource-Limited Settings. World Journal of AIDS, 3, 251-256.
https://doi.org/10.4236/wja.2013.33033
[6]  Dachraoui, R., Brand, D., Brunet, S., Barin, F. and Plantier, J.C. (2008) RNA Amplification of the HIV-1 Pol and Env Regions on Dried Serum and Plasma Spots. HIV Medicine, 9, 557-561.
https://doi.org/10.1111/j.1468-1293.2008.00604.x
[7]  Hamers, R.L., Smit, P.W., Stevens, W., Schuurman, R. and Rinke de Wit, T.F. (2009) Dried Fluid Spots for HIV Type 1 Viral Load and Resistance Genotyping: A Systematic Review. Antiviral Therapy, 14, 619-629.
[8]  Monleau, M., Montavon, C., Laurent, C., Segondy, M., Montes, B., Delaporte, E., Boillot, F. and Peeters, M. (2009) Evaluation of Different RNA Extraction Methods and Storage Conditions of Dried Plasma and Blood Spots for Human Immunodeficiency Virus Type 1 RNA Quantification and PCR Amplification for Drug Resistance Testing. Journal of Clinical Microbiology, 47, 1107-1118.
https://doi.org/10.1128/JCM.02255-08
[9]  Andreotti, M., Pirillo, M., Guidotti, G., Ceffa, S., Paturzo, G., Germano, P., Luhanga, R., Chimwaza, D., Mancini, M.G., Marazzi, M.C., Vella, S., Palombi, L. and Giuliano, M. (2010) Correlation between HIV-1 Viral Load Quantification in Plasma, Dried Blood Spots and Dried Plasma Spots Using the Roche COBAS TaqMan Assay. Journal of Clinical Virology, 47, 4-7.
https://doi.org/10.1016/j.jcv.2009.11.006
[10]  Kamangu, N.E., Mayemba, C., Mbikayi, S., Ndarabu, A., Kalala, L.R., Mvumbi, L.G. and Vaira, D. (2014) Implementation of a Classic Nested PCR DNA for HIV Diagnosis in Kinshasa. International Journal of Collaborative Research on Internal Medicine and Public Health, 6, 145-151.
[11]  (2010) QIAGEN: QIAamp RNA Mini and Blood Mini Handbook. 3rd Edition, 27-29.
[12]  Kamangu, N.E., Chatte, A., Boreux, R., Kalala, L.R., Mvumbi, L.G., De Mol, P., Vaira, D. and Hayette, M.P. (2015) Implementation of an In-House Quantitative Real-Time PCR for Determination of HIV Viral Load in Kinshasa. Open Access Library Journal, 1: e0855.
https://doi.org/10.4236/oalib.1100855
[13]  Kamangu, N.E., Chatté, A., Susin, F., Boreux, R., Kalala, L.R., Mvumbi, L.G., De Mol, P., Vaira, D. and Hayette, M.P. (2015) Genetic Diversity and Antiretroviral Drug Resistance among Drug-Naive HIV Type 1 Infected Patients attending Clinics in Kinshasa, Democratic Republic of Congo. Journal of HIV and AIDS, 1, 1-6.
[14]  Tang, W.M., Liu, F.T. and Shafer, W.R. (2012) The HIVdb System for HIV-1 Genotypic Resistance Interpretation. Intervirology, 55, 98-101.
https://doi.org/10.1159/000331998
[15]  Hamers, R.L., Smit, P.W., Stevens, W., Schurman, R. and Rinke de Wit, T.F. (2009) Dried Fluid Spots for HIV Type 1 Viral Load and Resistance Genotyping: A Systematic Review. Antiviral Therapy, 14, 619-629.
[16]  Masciotra, S., Garrido, C., Youngpairoj, A.S., Mc Nulty, A., Zahonero, N.Z., Corral, A., Heneine, W., de Mendoza, C. and Garcia-Lerma, J.G. (2007) High Concordance between HIV-1 Drug Resistance Genotypes Generated from Plasma and Dried Blood Spots in Antiretroviral-Experienced Patients. AIDS, 21, 2503-2511.
https://doi.org/10.1097/QAD.0b013e3281c618db
[17]  Fransen, K., Zhong, P., Beenhouwer, H., Carpels, G., Peeters, M., Louwagie, J., Jassens, W., Piot, P. and Van, G. (1994) Design and Evaluation of New, Highly Sensitive and Specific Primers for Polymerase Chain Reaction Detection of HIV-1 Infected Primary Lymphocytes. Molecular and Cellular Probes, 8, 317-322.
https://doi.org/10.1006/mcpr.1994.1043
[18]  Taylor, B.S., Sobieszczyk, M.E., McCutchan, F.E. and Hammer, S.M. (2008) The Challenge of HIV-1 Subtype Diversity. The New England Journal of Medicine, 358, 1590-1602.
https://doi.org/10.1056/NEJMra0706737

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