Underestimation of HIV Type 1 Drug Resistance Mutations: Results from the ENVA-2 Genotyping Proficiency Program

Abstract

Current recommendations indicate the use of HIV-1 drug resistance genotyping in the treatment of HIV-1 infection, primarily on treatment failure, and in specific instances also before the initiation of therapy. As such, HIV-1 genotyping is becoming a standard of care parameter in HIV-1 treatment monitoring and a rapidly increasing number of laboratories now use this technology routinely. A study of proficiency, using the ENVA-2 panel, was performed to evaluate the current HIV-1 resistance genotyping quality in 34 laboratories from different parts of the world. The results demonstrated extensive interlaboratory variation in the quality of genotyping and a significant underestimation of resistance mutations, even in samples expressing pure mutant genotype. The level of variation could not be attributed to the sequencing technology used and was therefore considered to be laboratory associated. The direct clinical consequences of this may be inadequate treatment of HIV-1-infected individuals and a more rapid exhaustion of therapeutic options for the patients. Drug resistance mutations are frequently missed. Therefore, quality control programs are urgently needed. Until these are widely implemented, clinicians must consider this issue and interpret the reported genotyping results with caution.

Global Proficiency Study of Human Papillomavirus Genotyping

“…Complete genomes of HPV cloned into plasmid vectors had been provided to Lund University by the respective proprietors with written approval for their use in this proficiency panel: Ethel-Michele de Villiers (HPV types 6,11,16,18, and 45), Gérard Orth (HPV types 33, 39, 66, and 68), Saul Silverstein (HPV type 51), Attila Lörincz (HPV types 31, 35, and 56), Wayne Lancaster (HPV type 52), and Toshihiko Matsukura (HPV types 58 and 59). The agreements allowed distribution of the plasmids only for the performance of this WHO proficiency study.…”

“…Purified plasmids containing cloned genomic DNAs for HPV types 6,11,16,18,31,33,35,39,45,51,52,56,58,59, 66, and 68 were diluted to a stock concentration of 10 8 genome equivalents/l in TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0) to be used for preparation of 43 samples. Human placenta DNA (Sigma-Aldrich; no.…”

“…At the WHO meeting held in Geneva, Switzerland, from 15 to 17 August 2005, an expert group recommended the establishment of a global HPV laboratory network (HPV LabNet) to contribute to improving the quality of laboratory services for effective surveillance and HPV vaccination impact monitoring. Major activities within the HPV LabNet include the development of international standard reagents and standard operating procedures (SOPs) and the development of internationally comparable quality assurance methods (5, 26).International proficiency panels are already widely used for several microorganisms, including hepatitis A, B, and C viruses; herpes simplex virus (HSV); and human immunodeficiency virus (HIV) (15,18,24). As there is no natural source of biological material that could be used to generate type-specific HPV international standards (ISs), the first WHO international collaborative study of the detection of HPV DNA examined the feasibility of using recombinant HPV DNA plasmids as standards, focusing on HPV16 and HPV18 (13).…”

“…International proficiency panels are already widely used for several microorganisms, including hepatitis A, B, and C viruses; herpes simplex virus (HSV); and human immunodeficiency virus (HIV) (15,18,24). As there is no natural source of biological material that could be used to generate type-specific HPV international standards (ISs), the first WHO international collaborative study of the detection of HPV DNA examined the feasibility of using recombinant HPV DNA plasmids as standards, focusing on HPV16 and HPV18 (13).…”

Development of a Novel Codon-Specific Polymerase Chain Reaction for the Detection of CXCR4-Utilizing HIV Type 1 Subtype B

“…6 In addition, consensus genotypes can be indeterminate when subpopulations are variable at the codons of interest, or when insertions or deletions cause overlapping reading frames; both are common in the HIV-1 envelope. Next-generation sequencing may prove to be the best method of detection, as it is not only sensitive, but can also give a fairly accurate estimation of the percent X4 in a population.…”