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. 2022 May 17;22(1):474.
doi: 10.1186/s12879-022-07453-9.

HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting

Jonah Omooja  1 , Nicholas Bbosa  2 , Dan Bugembe Lule  2 , Maria Nannyonjo  2 , Sandra Lunkuse  2 , Faridah Nassolo  2 , Stella Esther Nabirye  2 , Hamidah Namagembe Suubi  2 , Pontiano Kaleebu  2   3   4 , Deogratius Ssemwanga  5   6   7
Affiliations

HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting

Jonah Omooja et al. BMC Infect Dis. .

Abstract

Background: HIV-1 drug resistance genotyping is critical to the monitoring of antiretroviral treatment. Data on HIV-1 genotyping success rates of different laboratory specimen types from multiple sources is still scarce.

Methods: In this cross-sectional study, we determined the laboratory genotyping success rates (GSR) and assessed the correlates of genotyping failure of 6837 unpaired dried blood spot (DBS) and plasma specimens. Specimens from multiple studies in a resource-constrained setting were analysed in our laboratory between 2016 and 2019.

Results: We noted an overall GSR of 65.7% and specific overall GSR for DBS and plasma of 49.8% and 85.9% respectively. The correlates of genotyping failure were viral load (VL) < 10,000 copies/mL (aOR 0.3 95% CI: 0.24-0.38; p < 0.0001), lack of viral load testing prior to genotyping (OR 0.85 95% CI: 0.77-0.94; p = 0.002), use of DBS specimens (aOR 0.10 95% CI: 0.08-0.14; p < 0.0001) and specimens from routine clinical diagnosis (aOR 1.4 95% CI: 1.10-1.75; p = 0.005).

Conclusions: We report rapidly decreasing HIV-1 genotyping success rates between 2016 and 2019 with increased use of DBS specimens for genotyping and note decreasing median viral loads over the years. We recommend improvement in DBS handling, pre-genotyping viral load testing to screen samples to enhance genotyping success and the development of more sensitive assays with well-designed primers to genotype specimens with low or undetectable viral load, especially in this era where virological suppression rates are rising due to increased antiretroviral therapy roll-out.

Keywords: DBS; Genotypic resistance testing; HIV-1; Plasma; Resource-limited settings; Success rates.

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Conflict of interest statement

The authors have no competing interests to declare.

Figures

Fig. 1
Fig. 1
Trends in the median VLs of the specimen genotyped over the years. Median VLs were determined for all specimens analysed in each year. Overall median VLs for DBS and plasma, and General median VLs represent values obtained for specimens over the 4 years
Fig. 2
Fig. 2
Trends in the overall and genotyping success rates of DBS and plasma specimens from 2016 to 2019. Overall genotyping success rates (GSR) were obtained by analysing all specimens genotyped in the 4 years (2016–2019). The GSR was a proportion of specimens that yielded clean sequences (genotypes) with the denominator being the total number of specimens that we attempted to genotype in that year or in all the 4 years for the overall GSR (see Table 1 for denominator values). The analysis was also independently done for DBS and plasma specimens
Fig. 3
Fig. 3
Variations in genotyping success rates, number and proportion of DBS specimens genotyped with time. The proportion of DBS specimens represents the number of DBS specimens being the numerator and the denominator being the total number of specimens we attempted to genotype in a particular year (see Table 1). The overall genotyping success rates (GSR) decreased as both the number and proportion of DBS specimens we attempted to genotype increased from 2016 to 2019
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