Performance of two commercially available sequence‐based HIV‐1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes

Beddows, Simon; Galpin, S.; Kazmi, Shamim H.; Ashraf, Ambreen; Johargy, Ayman; Frater, John; White, Natalie C.; Braganza, Ruth; Clarke, John R.; McClure, Myra O.; Weber, Jonathan

doi:10.1002/jmv.10401

Cited by 43 publications

(23 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To date, the HIV subtype distribution in Poland was similar to that reported for Western 182 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 shown to be highly efficient for B clade sequencing, their detection thresholds for non-B variants is 240 lower [Beddows 2003]. Therefore, the possibility that some variants may have gone undetected 241 exists, however, only these detection methods were available.…”

supporting

confidence: 85%

Characteristics of HIV‐1 non‐B subtype infections in Northwest Poland

Parczewski¹,

Leszczyszyn-Pynka²,

Bander³

et al. 2010

Journal of Medical Virology

View full text Add to dashboard Cite

The number of non‐B subtype HIV‐1 infections in Europe has been increasing even though major regional differences have been observed. This trend was investigated in northwestern Poland using sequence and epidemiological data from a cohort of 102 HIV‐1‐infected patients from Szczecin, Poland. HIV‐1 subtypes were defined by phylogenetic analysis of viral reverse transcriptase‐ and protease‐partial coding regions, and results were compared with online subtyping by Standford and REGA tools. Subtype analysis using on‐line subtyping methods produced varying results if compared to phylogenesis, with concordant variant assignment obtained for 98% (100/102) of sequences by Stanford and 85% (87/102) by REGA. In the population studied, non‐B subtype infections comprised 21% of the infections and consisted of subtype D (57%, n = 12), CRF01_AE (19%, n = 4), A and C clades (9.5%, n = 2), and the CRF13_cpx recombinant isolate (4.8%, n = 1). Patients carrying non‐B subtypes were predominantly heterosexuals with high percentage (57%) of women observed in the group. All HIV‐1 non‐B women were Caucasian with majority (83%) of infections acquired in Poland; however, among 12 travelers included in the study a higher proportion of non‐B infections was noted (50%, P = 0.01). Moreover, lower baseline lymphocyte CD4 counts (P = 0.01), higher baseline HIV‐1 viremia (P = 0.08), and a more advanced stage of the disease (P = 0.03) were observed among individuals infected with non‐B subtypes. The data indicated that the proportion of HIV‐1 non‐B subtype infections was higher than previously reported in Poland consisting of a high subtype D prevalence. Furthermore, subtype D transmission occurred primarily between heterosexual Caucasian individuals from this region. J. Med. Virol. 82:1306–1313, 2010. © 2010 Wiley‐Liss, Inc.

show abstract

supporting

confidence: 85%

Characteristics of HIV‐1 non‐B subtype infections in Northwest Poland

Parczewski¹,

Leszczyszyn-Pynka²,

Bander³

et al. 2010

Journal of Medical Virology

View full text Add to dashboard Cite

show abstract

“…Our finding that version 1.5 of the TruGene assay enables non-B HIV-1 subtype viruses to be sequenced with a high success rate is consistent with previous studies examining the performance characteristics of this version of the assay (5,15,20). The primary difference between versions 1.0 and 1.5 of the TruGene HIV-1 genotyping assay is a modification to the RT-PCR primers (20).…”

Section: Discussionsupporting

confidence: 87%

Use of Sequence Data Generated in the Bayer TruGene Genotyping Assay To Recognize and Characterize Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains

Hirigoyen

Cartwright

2005

J Clin Microbiol

View full text Add to dashboard Cite

“…The two commercially available genotyping assays, the Viroseq HIV-1 genotyping system (Celera, Alameda CA) and the TruGene HIV-1 genotyping system (Siemans Medical Solutions Diagnostics, Tarrytown, NY), were designed and approved by the FDA for HIV-1 subtype B only. Although studies have indicated that these assays can be used for other HIV-1 group M subtypes, the reported sensitivities vary (2,10,11,29,33). The assay we report here and the one reported recently by Buckton et al (7) are the only assays that have directly addressed subtype-genotyping-efficiency issues.…”

Section: Discussionmentioning

confidence: 68%

Development and Application of a Broadly Sensitive Dried-Blood-Spot-Based Genotyping Assay for Global Surveillance of HIV-1 Drug Resistance

et al. 2010

View full text Add to dashboard Cite

As antiretroviral therapy (ART) is scaled up in resource-limited countries, surveillance for HIV drug resistance (DR) is vital to ensure sustained effectiveness of first-line ART. We have developed and applied a broadly sensitive dried-blood-spot (DBS)-based genotyping assay for surveillance of HIV-1 DR in international settings. In 2005 and 2006, 171 DBS samples were collected under field conditions from newly diagnosed HIV-1-infected individuals from Malawi ( n = 58), Tanzania ( n = 60), and China ( n =53). In addition, 30 DBS and 40 plasma specimens collected from ART patients in China and Cameroon, respectively, were also tested. Of the 171 DBS analyzed at the protease and RT regions, 149 (87.1%) could be genotyped, including 49 (81.7%) from Tanzania, 47 (88.7%) from China, and 53 (91.4%) from Malawi. Among the 70 ART patient samples analyzed, 100% (30/30) of the Chinese DBS and 90% (36/40) of the Cameroonian plasma specimens were genotyped, including 8 samples with a viral load of <400 copies/ml. The results of phylogenetic analyses indicated that the subtype, circulating recombinant form (CRF), and unique recombinant form (URF) distribution was as follows: 73 strains were subtype C (34%), 37 were subtype B (17.2%), 24 each were CRF01_AE or CRF02_AG (11.2% each), 22 were subtype A1 (10.2%), and 9 were unclassifiable (UC) (4.2%). The remaining samples were minor strains comprised of 6 that were CRF07_BC (2.8%), 5 that were CRF10_CD (2.3%), 3 each that were URF_A1C and CRF08_BC (1.4%), 2 each that were G, URF_BC, and URF_D/UC (0.9%), and 1 each that were subtype F1, subtype F2, and URF_A1D (0.5%). Our results indicate that this broadly sensitive genotyping assay can be used to genotype DBS collected from areas with diverse HIV-1 group M subtypes and CRFs. Thus, the assay is likely to become a useful screening tool in the global resistance surveillance and monitoring of HIV-1 where multiple subtypes and CRFs are found.

show abstract

Performance of two commercially available sequence‐based HIV‐1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes

Cited by 43 publications

References 9 publications

Characteristics of HIV‐1 non‐B subtype infections in Northwest Poland

Characteristics of HIV‐1 non‐B subtype infections in Northwest Poland

Use of Sequence Data Generated in the Bayer TruGene Genotyping Assay To Recognize and Characterize Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains

Development and Application of a Broadly Sensitive Dried-Blood-Spot-Based Genotyping Assay for Global Surveillance of HIV-1 Drug Resistance

Contact Info

Product

Resources

About