The first B/G intersubtype recombinant form of human immunodeficiency virus type 1 (HIV-1) identified in Germany was undetected or underquantitated by some commercial viral load assays

Abstract

The high level of genetic diversity of human immunodeficiency virus type 1 (HIV-1) and the continual emergence of recombinant forms have important implications not only for the global evolution of HIV but also for diagnosis, monitoring, and treatment strategies. The present study reports the first intersubtype B/G recombinant strain of HIV-1 in Germany. This strain is notable from a clinical perspective, since it was undetectable in the NucliSens HIV-1 QT assay (Organon Tecknika/bioMérieux) and was significantly underquantitated in the Monitor v1.5 test (Roche Molecular Systems) relative to the LCx HIV RNA Quantitative assay (Abbott Laboratories). Gag-encoded p24 (gag p24), pol-encoded integrase (pol IN), and env-encoded gp41 (env gp41) immunodominant region (IDR) sequences were characterized to establish group and subtype designation and to evaluate the degree of genetic diversity at primer and probe binding sites of the viral load assays. Phylogenetic analysis revealed that this virus is an intersubtype B/G recombinant strain. The gag p24 region is subtype G, env gp41 IDR is subtype B, and pol IN is a B/G chimera. Nucleotide mismatches within primer and probe-binding sites provided the molecular basis for differences in quantitation observed between viral load assays. Genetic diversity of HIV-1 continues to challenge the reliability of detection and quantitation by viral load assays.

Comparison of the RealTime HIV-1, COBAS TaqMan 48 v1.0, Easy Q v1.2, and Versant v3.0 assays for Determination of HIV-1 Viral Loads in a Cohort of Canadian Patients with Diverse HIV Subtype Infections

“…Only the Abbott Laboratories qRT-PCR HIV assay has successfully detected an HIV-1 group P infection (32). Limited clinical evaluations of currently available HIV-1 viral load assays have been performed with patients with diverse HIV subtype infections (11,15,19,33,36,38,40,41), but there have been several recent reports on the clinical impact of underquantification of group M, non-subtype B infections (10,14,44).…”

Minimal sequence variability of the region of HIV-1 integrase targeted by the Abbott RealTime HIV-1 viral load assay in clinical specimens with reduced susceptibility to raltegravir

“…Such evolution can be a challenge for the design of molecular diagnostic assays that rely on reactivity of synthetic primers and probes within the target sequence. Thus, numerous publications have described underestimation of plasma viral load in the setting of non-B subtypes, or in specimens that have divergent sequence in critical positions (Bolivar et al, 2009;Damond et al, 2007;Delaugerre et al, 2009;Foglieni et al, 2011;Holguin et al, 2008;Korn et al, 2009;Pyne et al, 2010;Rossotti et al, 2011;von Truchsess et al, 2006;Yotsumoto et al, 2011). Notwithstanding these observations, the Abbott RealTime HIV assay has performed well in studies with divergent sequences in critical positions and certain non-B subtypes (Swanson et al, 2006a(Swanson et al, ,b, 2007.…”

High frequency of antiviral drug resistance and non-B subtypes in HIV-1 patients failing antiviral therapy in Cuba

“…16 The high prevalence of subtype G in the gag/pol region (18% G and BG recombinants) is worrisome, as these genetic forms are often undetected or substantially underquantified by some commercial viral load assays. [17][18][19][20] Especially the NucliSens HIV-1 QT assay (Biomérieux, France), the first viral load assay ever available in Cuba and currently still in use, failed to detect subtype G. Occasional data analysis of the local cohort has indeed revealed discordances between worsening immunological and clinical outcome and undetectable viral loads in patients receiving ART (unpublished data).…”