High Failure Rate of the ViroSeq HIV-1 Genotyping System for Drug Resistance Testing in Cameroon, a Country with Broad HIV-1 Genetic Diversity

Abstract

The ViroSeq HIV-1 genotyping system is used in many African countries for drug resistance testing. In this study, we used a panel of diverse HIV-1 group M isolates circulating in Cameroon to show that the performance of this assay can be altered by the sequence variation of non-B HIV-1 strains that predominate in African settings.

Investigation of HIV-1 Primary Drug Resistance Mutations in Antiretroviral Therapy-Naive Cases

“…Bu nedenle, çalışmamızda test kiti ile sonuç alınamadığı durumlarda B dışındaki diğer alttipleri de kapsayan alternatif primerleri içeren "in-house" yöntemiyle çalışılmıştır [9][10][11] . İncelenen .…”

“…Ticari test kiti ile sonuç alınamadığı durumlarda, farklı primer çiftlerinin kullanıldığı "in-house" yöntemi uygulandı [9][10][11] . Yöntemde, 'mini spin' kolon tekniği ile safl aştırılan plazma örneklerinde referans HxB2 suşunda 2248-3309.…”

HIV-1 Diversity and Its Implications in Diagnosis, Transmission, Disease Progression, and Antiretroviral Therapy

“…Several studies analyzed the performance of commercially available genotypic resistance assays and in-house methods in B and non-B strains (Aghokeng et al, 2011;Beddows et al, 2003;Fontaine et al, 2001;Jagodzinski et al, 2003;Maes et al, 2004). In commercial kits a greater degree of success was obtained when sequencing subtype B isolates compared to non-B isolates, and some studies report that alternative amplification/sequencing primers had to be used for some samples belonging to non-B subtypes.…”

“…As a result of sequencing problems, 18.5% of the samples had to be processed with in-house procedures. In Cameroon, where all groups of HIV-1 circulate, the sequencing efficiency of the ViroSeq assay was also evaluated (Aghokeng et al, 2011). The sequencing failures involved mainly the 5´end of the PR and the 3` end of the RT genes because of the high failure rate of primers A, D, F, and H. There was a high degree of polymorphism in non-B isolates in the areas for which these primers are designed.…”

Application of PCR Technologies to Humans, Animals, Plants and Pathogens from Central Africa

“…Scores of articles have used PCR methods to report findings related to the viral diversity of HIV in this region, emergence of new strains [85] and recombinant forms [86], emergence of resistance to antiretroviral drugs [87], and challenges encountered for the genotyping tests because of the broad diversity of HIV strains [88]. In this section we'll explain the usefulness of PCR in i) the identification of various HIV strains found in Central Africa, ii) the early diagnosis of HIV, especially in exposed infants, iii) the management of infected patients, iv) implementation research and finally, we'll underline the need of an African AIDS vaccine.…”