Prevalence and impact of minority variant drug resistance mutations in primary HIV-1 infection.

To evaluate minority variant drug resistance mutations detected by the oligonucleotide ligation assay (OLA) but not consensus sequencing among subjects with primary HIV-1 infection.Observational, longitudinal cohort study. Consensus sequencing and OLA were performed on the first available specimens from 99 subjects enrolled after 1996. Survival analyses, adjusted for HIV-1 RNA levels at the start of antiretroviral (ARV) therapy, evaluated the time to virologic suppression (HIV-1 RNA<50 copies/mL) among subjects with minority variants conferring intermediate or high-level resistance.Consensus sequencing and OLA detected resistance mutations in 5% and 27% of subjects, respectively, in specimens obtained a median of 30 days after infection. Median time to virologic suppression was 110 (IQR 62-147) days for 63 treated subjects without detectable mutations, 84 (IQR 56-109) days for ten subjects with minority variant mutations treated with ≥3 active ARVs, and 104 (IQR 60-162) days for nine subjects with minority variant mutations treated with <3 active ARVs (p = .9). Compared to subjects without mutations, time to virologic suppression was similar for subjects with minority variant mutations treated with ≥3 active ARVs (aHR 1.2, 95% CI 0.6-2.4, p = .6) and subjects with minority variant mutations treated with <3 active ARVs (aHR 1.0, 95% CI 0.4-2.4, p = .9). Two subjects with drug resistance and two subjects without detectable resistance experienced virologic failure.Consensus sequencing significantly underestimated the prevalence of drug resistance mutations in ARV-naïve subjects with primary HIV-1 infection. Minority variants were not associated with impaired ARV response, possibly due to the small sample size. It is also possible that, with highly-potent ARVs, minority variant mutations may be relevant only at certain critical codons

HIV-1 drug resistance in ARV-naïve subjects with primary HIV-1 infection.

<p>ARV: antiretroviral; OLA: oligonucleotide ligation assay; PBMC: peripheral blood mononuclear cells.</p><p>+ = subjects with ≥1 mutation or mixture.</p><p>− = subjects without mutations or with indeterminate results.</p><p>Numbers represent subjects in whom HIV-1 drug resistance was/was not detected in plasma and PBMC specimens that had been obtained a median of 29 (IQR 19–66) and 31 (IQR 19–66) days after HIV-1 infection, respectively; all specimens were collected within six months of infection. McNemar's exact tests compare only subjects with discordant results (indicated in bold).</p

Time to suppression of plasma HIV-1 RNA levels among previously ARV-naïve subjects with and without minority variant drug resistance mutations.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028952#pone-0028952-g001" target="_blank">Figure 1:</a> The median time to virologic suppression (HIV-1 RNA<50 copies/mL) was 110 (IQR 62–147) days for 63 treated subjects without detectable mutations (solid line), 84 (IQR 56–109) days for 10 subjects with minority variant mutations treated with ≥3 active ARVs (dashed line), and 104 (60–162) days for nine subjects with minority variant mutations treated with <3 active ARVs (dotted line) (p = .9).</p

Characteristics of study subjects with primary HIV-1 infection evaluated for drug resistance mutations.

<p>OLA: oligonucleotide ligation assay; CS: consensus sequencing; IQR: interquartile range; NS: not significant at p = .05; ARV: antiretroviral; PI: protease inhibitor; NRTI: nucleoside reverse transcriptase inhibitor; NNRTI: non-nucleoside reverse transcriptase inhibitor therapy.</p><p>*differences between groups were not significant in analyses that were both unadjusted and adjusted for time from infection to the date of sampling.</p

HIV-1 drug resistance detected by consensus sequencing and OLA in ARV-naïve subjects and virologic response to ARV therapy.

<p>In this table, the subset of subjects who received antiretroviral (ARV) therapy are grouped based on whether they had drug resistance detected by consensus sequencing (Group I), drug resistance detected by OLA but who received at least three active ARV agents (Group II), or drug resistance detected by OLA who received fewer than three active agents (Group III). ARVs are highlighted in grey if subjects had mutations conferring at least intermediate level resistance to that ARV. K70R, L74V, T215F, and V82S/T were not detected in any treated subjects.</p><p>CS: consensus sequencing; OLA: oligonucleotide ligation assay; VL: viral load (HIV-1 RNA level); ARV: antiretroviral; VF: virologic failure; IDV: indinavir, HU: hydroxyurea, ABC: abacavir, EFV: efavirenz, NVP: nevirapine, r-: ritonavir-boosted, LPV: lopinavir, ATZ: atazanavir; DNS: did not suppress.</p>1<p>Log₁₀ copies/mL.</p>2<p>Antiretroviral medications were switched on day 5 due to side effects.</p>3<p>Subject #69234 subsequently discontinued medications two months later due to adherence difficulties.</p>4<p>OLA probes did not test for M41L and T215D.</p>5<p>OLA on PBMC for subject 56710 yielded indeterminate results for T215Y.</p>6<p>DNS: did not suppress prior to discontinuing ARVs or study censorship. Subjects #26973, 44378, and 78882 were followed for 104, 44, and 63 days, respectively, while receiving ARVs.</p

Patient Characteristics During Early Transmission of SARS-CoV-2, Palau, January 13–February 24, 2022

Palau had no reported evidence of COVID-19 community spread until January 2022. We chart reviewed hospitalized patients who had a positive SARS-CoV-2 test result during early community transmission. Booster vaccinations and early outpatient treatment decreased hospitalizations. Inadequate hospital infection control practices contributed to iatrogenic COVID-19 and preventable deaths