Genetic diversity of HIV-1 subtype F from Brazil: failure of HIV-1 viral load testing based on molecular biology amplification methods

Mercado, João Marcos M.; Dio, R Di; Pradal, Mario G.

doi:10.1097/00002030-199910220-00032

Cited by 3 publications

(1 citation statement)

References 5 publications

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“…Variability not only makes it difficult for the immune system to identify the virus but it also facilitates the rapid viral immune escape. The high level of genetic diversity has important implications in screening, diagnostic testing, disease monitoring and treatment outcomes [6][7][8][9][10][11][12][13][14]. Questions have been raised on whether diversity may also affect viral transmissibility and pathogenicity [15][16][17][18][19][20].…”

Section: Hiv-1 Genetic Diversitymentioning

confidence: 99%

HIV Diversity and Classification, Role in Transmission

Duri¹,

Stray‐Pedersen²,

Müller³

2013

AID

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The hallmark of HIV-1 is its extensive genetic diversity that emanates mainly from high mutations. Phylogenetically, HIV can be classified into geographically confined groups, types, subtypes and circulating recombinant forms (CRFs) that are however subject to change over time. HIV genetic diversity may partially explain the observed heterogeneity in HIV prevalence and has also been reported to impact on viral transmissibility and differential rates of disease progression. The aim of this review is to present a simple overview of the principles and concepts of HIV diversity and classification. Tracking the presence of new HIV strains is not only important for surveillance purposes but is also critical in facilitating personalized targeted therapy as well as forming the basis for development of the much anticipated effective vaccines against this scourge.

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Section: Hiv-1 Genetic Diversitymentioning

confidence: 99%

HIV Diversity and Classification, Role in Transmission

Duri¹,

Stray‐Pedersen²,

Müller³

2013

AID

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Intersubtype BF Recombinants of HIV-1 in a Population of Injecting Drug Users in Argentina

Espinosa¹,

Vignoles²,

Carrillo³

et al. 2004

JAIDS Journal of Acquired Immune Deficiency Syndromes

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The presence of recombinant intersubtypes of HIV-1 in Argentina has been reported since the mid-1990s. In this study, sequences of a region of the gag, pol, and vpu genes of HIV-1 were analyzed in samples of 21 injection drug users (IDUs) residing in the suburbs of the city of Buenos Aires. Genomic characterization and identification of recombination sites were made comparing the 3 regions with reference isolation sequences of subtypes B, F, C, A, and B/F recombinants: CRF12_BF and non-CRF12_BF sequences. Subtype assignment of the analyzed segments was phylogenetically confirmed. All the samples turned out to be BF recombinants in at least 1 of the 3 studied genes. Twelve samples (57%) had the same pattern as the Argentinean CRF12_BF, whereas in the rest, the pattern differed in at least 1 of the 3 genes. The relation of these fragments to the CRF12_BF was phylogenetically verified. These results indicate the predominance of BF recombinants and the presence of a high percentage of sequences closely related to the CRF12_BF in the IDU population in Argentina and suggest a possible association between viral variants and the transmission route.

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Multicenter Study of the LCx® HIV RNA Quantitative Assay – a New Competitive Reverse Transcriptase-PCR which Targets pol Genomic Region of HIV-1 for the Measurement of Type B, Non-Type B and Group O HIV-1 RNA

Troonen¹,

Grey²,

Michel³

2002

Clinical Chemistry and Laboratory Medicine

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Performance characteristics of the Abbott LCx HIV RNA Quantitative Assay (LCx HIV) were established in a multicenter study comparing it with the manual (Amplicor v1.5) and automated (Cobas) ultra-sensitive Roche Amplicor HIV-1 Monitor v1.5, the Bayer Quantiplex HIV RNA 3.0 (bDNA v3.0), and the Organon NucliSens HIV QT 2.0 (NucliSens). Within-run precision of LCx HIV assessed in clinical specimens was SD log10 0.210 at approximately 50 copies/ml, and log10 0.133 at approximately 400 copies/ml. Total precision in a reconstituted type B HIV-1 RNA panel was SD log10 0.380 at 100 copies/ml, and SD log10 0.180 at 1000 copies/ml. Type B HIV-1 RNA sensitivity (1 ml input) assessed at a 50%, 75% and 95% detection rate ranged from 29 to 41, 54 to 75 and 94 to 176 copies/ml, respectively. Overall specificity in HIV seronegative individuals was 99.78%. Linear regression indicated close assay correlations and agreements for measurement of type B HIV-1 RNA. Pearson's correlations and (Log10LCx=aLog10x + b) linear regressions were 0.91 (y=0.892 Log10Amplicor + 0.595), 0.93 (y=0.827 Log10Cobas + 0.969), 0.93 (y=0.951 Log10bDNA + 0.550), and 0.79 (y=0.834 Log10NucliSens + 0.911). LCx HIV was least affected by the genetic variability of HIV-1. LCx HIV detected 99% of non-type B HIV-1 group M samples (subtypes A-G), Amplicor v1.5 detected 96%, and bDNA v3.0 detected 99%. The assays detected 10/11, 1/11 and 8/11, respectively of the HIV-1 group O samples. LCx HIV vs. Amplicor/bDNA Spearman's rank correlations for quantification of non-type B HIV-1 RNA were 0.76/0.84 (A), 0.93/0.93 (C), 0.73/0.99 (D), 0.86/0.98 (E), and 0.40/0.83 (group O). LCx HIV assays consistently detect and quantify type B, non-type B and group O HIV-1 RNA.

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Genetic diversity of HIV-1 subtype F from Brazil: failure of HIV-1 viral load testing based on molecular biology amplification methods

Cited by 3 publications

References 5 publications

HIV Diversity and Classification, Role in Transmission

HIV Diversity and Classification, Role in Transmission

Intersubtype BF Recombinants of HIV-1 in a Population of Injecting Drug Users in Argentina

Multicenter Study of the LCx® HIV RNA Quantitative Assay – a New Competitive Reverse Transcriptase-PCR which Targets pol Genomic Region of HIV-1 for the Measurement of Type B, Non-Type B and Group O HIV-1 RNA

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