Frequencies and dynamics of HIV variants characterized by NGS exhibiting ART-associated DRM

Frequency and dynamics of drug resistance mutations (DRM) in treatment naïve HIV-infected men-who-have-sex-with-men (MSM) were studied longitudinally. Data were collected from 10 (ten) HIV-infected individuals (P) studied longitudinally from early/acute-to-chronic HIV infection stages involving up to 5 years of follow-up. HIV-polymerase gene was amplified by PCR and further used for HIV subtype characterization and genotypic antiretroviral therapy (ART) resistance testing. HIV-genotypic ART resistance testing was performed using next-generation sequencing (NGS) by MiSeq (Illumina) on clinical samples.
Consecutive samplings from each individual were numbered (p1.1; p1.2; p1.3, etc.).
The spreadsheet shows major drug-associated resistance mutations (DRM) defined according to Stanford University database (https://hivdb.stanford.edu/hivseq/by-mutations/). The analyzed region spanned up to 34 DRM positions. The frequencies of DRM were determined considering as valid those positions having ≥ 1000 reads of depth (red values are those that were discarded). Taking into consideration the frequency for each codon, the aminoacid were classified as "major" (highest frequency), and "second" or "tertiary" according to its frequency.
These codon sites were classified into 5 categories according to the nature of the detected substitution, as follows:
(i) “Wild type” (WT): the most abundant triplet was the only one with more than 0.01 of abundance and the encoded aminoacid was associated with susceptibility to treatment (non-colored rows);
(ii) “Major Drug Resistance Mutation” (Major DRM): either the dominant or the secondary variant encoded a treatment resistance aminoacid (violet rows);
(iii) “Stop”: the secondary variant encoded a stop codon or non-sense mutation (dark gray rows);
(iv) “Synonymous mutation Wild Type” (smWT): both the dominant and the secondary variant encoded the same susceptibility associated aminoacid (blue rows); and
(v) “Unknown”: either the dominant or the secondary variant encoded an aminoacid with an unknown impact on the resistance profile (yellow rows).
Among HIV-1 therapy-naïve MSM longitudinally studied, the frequency of DRM was low and mostly circumscribed to minority variants detected at acute/early stages of infection. At intra-patient, their frequency decreases as the infection progresses to chronicity. This information should be useful when considering the still controversial HIV baseline genotypic antiretroviral resistance testing implementation before starting HIV treatment.