A12 Modeling residual HIV replication and the emergence of drug resistance on ART

Abstract There are conflicting reports regarding the presence of low-level HIV replication during suppressive antiretroviral therapy (ART). We simulated varying levels of replication and estimated the number of generations needed to obtain linked, drug resistance mutations to explore the effects of replication during ART. HIV replication was simulated with varying population sizes (10 to 3,000,000). Each population size was modeled ten times. Each genome was given a Poisson-distributed number of mutations according to its length and the average replication error rate (3.4 × 10−5 sub/nt/cycle). Simulations were run a maximum of 20,000 generations with endpoints defined as detection of a variant with resistance mutations to at least two ARVs. In all simulations, variants that were resistant to all three ARVs emerged in less than 20,000 generations. The time to emergence ranged from 148–16,156 generations in the various simulations, depending on the replicating population size (4.8 months to 44.3 years if the generation time is 1 day). Clinically detectable virologic failure can result from linkage of two mutations conferring resistance to two ARVs in a regimen. In our simulations, two linked mutations emerged in from 9 to 6,429 generations (9 days to 17.6 years). Our simulations suggest that in patients continually suppressed on ART for at least 10 years, the replicating population size would have to be less than ten, or virologic failure would have occurred from emergence of two ARV-resistant variants. Because most patients on ART do not experience virologic failure, our simulations suggest that any residual replicating population on ART is very small and thus not likely to either sustain or significantly contribute to the HIV reservoir.

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Stochastic Interplay between Mutation and Recombination during the Acquisition of Drug Resistance Mutations in Human Immunodeficiency Virus Type 1

Journal of Virology ◽

10.1128/jvi.79.21.13572-13578.2005 ◽

2005 ◽

Vol 79 (21) ◽

pp. 13572-13578 ◽

Cited By ~ 67

Author(s):

Christian L. Althaus ◽

Sebastian Bonhoeffer

Keyword(s):

Human Immunodeficiency Virus ◽

Drug Resistance ◽

Population Size ◽

Mutation Rate ◽

Population Genetic ◽

Resistance Mutations ◽

Effective Population ◽

Drug Resistance Mutations ◽

Immunodeficiency Virus ◽

Population Sizes

ABSTRACT The emergence of drug resistance mutations in human immunodeficiency virus (HIV) has been a major setback in the treatment of infected patients. Besides the high mutation rate, recombination has been conjectured to have an important impact on the emergence of drug resistance. Population genetic theory suggests that in populations limited in size recombination may facilitate the acquisition of beneficial mutations. The viral population in an infected patient may indeed represent such a population limited in size, since current estimates of the effective population size range from 500 to 105. To address the effects of limited population size, we therefore expand a previously described deterministic population genetic model of HIV replication by incorporating the stochastic processes that occur in finite populations of infected cells. Using parameter estimates from the literature, we simulate the evolution of drug-resistant viral strains. The simulations show that recombination has only a minor effect on the rate of acquisition of drug resistance mutations in populations with effective population sizes as small as 1,000, since in these populations, viral strains typically fix beneficial mutations sequentially. However, for intermediate effective population sizes (104 to 105), recombination can accelerate the evolution of drug resistance by up to 25%. Furthermore, a reduction in population size caused by drug therapy can be overcome by a higher viral mutation rate, leading to a faster evolution of drug resistance.

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Detectable viral load among HIV -1 positive pregnant women on ART (Option B +) in northern Tanzania: Baseline results from the HIVDR study

East Africa Science ◽

10.24248/easci-d-20-00009 ◽

2021 ◽

Vol 3 (1) ◽

pp. 44-50

Author(s):

Nicholaus Steven Mazuguni ◽

Festo Mazuguni ◽

Eva Prosper Muro

Keyword(s):

Drug Resistance ◽

Viral Load ◽

Virological Failure ◽

Virologic Failure ◽

Resistance Mutation ◽

Resistance Testing ◽

Resistance Mutations ◽

Drug Resistance Mutations ◽

Hiv 1 ◽

Level Resistance

Introduction: In Tanzania, the Ministry of Health, Community Development, Gender, Elderly and Children (MoHCDEC) has implemented the Option B+ as one of the strategies to facilitate achievement of elimination of mother to child transmission of HIV. To prevent emergence of drug resistance mutations early identification of option B+ failure is critical. The emergence of drug resistance mutation and subsequent treatment failure poses a major concern for HIV program in low- and middle-income resource settings where treatment options are limited. Methodology: We recruited treatment naïve, treatment experienced HIV-1 positive pregnant women and those who had prophylaxis in their previous pregnancy in Kilimanjaro, northern Tanzania August 2016 to February 2017. Whole blood (2ml) for biochemistry, viral load and drug resistance testing were taken at baseline. ARV drug resistance testing was done on women with VL ≥ 1000 copies/ml. We used descriptive statistic and logistic regression to determine the strength of association between virologic outcome (virologic failure) and independent predictors. Results: One hundred and forty eight (148) pregnant HIV-positive women were enrolled in the study with mean age of 29.82 years (SD=6.17) from August, 2016 to February, 2017. Virologic failure was demonstrated in 34 (23%) with viral load ≥ 1,000 copies/ml. Genotyping results were available from 26 women, mutations associated with ARV resistance were detected in 23.1% (n = 6/26). Among the six women with ARV resistance mutation 4(66.7%) had high level resistance and 2(33.3%) had low level resistance. Among the 26 samples genotyped 15(58%) viruses were subtype A, while eight were subtype C (31%) and three subtypes D (11%). The most dominant drug resistance mutations against the reverse transcriptase inhibitors for the women with high level resistance were K103N, Y188L, D67N, K70R, M184V, T215F, K219EQ, and the low-level resistance was E138A. The older age was associated with virological failure compared to those who were < 20 year of age. Conclusion: Viral load testing should be done on women who were already on antiretroviral treatment on their first antenatal visit to ensure early detection of virological failure and enable clinicians to take an appropriate course of action on their management. Educational intervention on adherence should be targeted at an early stage to women with virological failure during pregnancy to reduce the emergence of HIV-1 drug resistance mutations.

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Predictors of first-line antiretroviral therapy failure among adults and adolescents living with HIV/AIDS in a large prevention and treatment program in Nigeria

AIDS Research and Therapy ◽

10.1186/s12981-020-00317-9 ◽

2020 ◽

Vol 17 (1) ◽

Author(s):

Nicaise Ndembi ◽

Fati Murtala-Ibrahim ◽

Monday Tola ◽

Jibreel Jumare ◽

Ahmad Aliyu ◽

...

Keyword(s):

Drug Resistance ◽

Virologic Failure ◽

Resistance Mutations ◽

First Line ◽

Drug Resistance Mutations ◽

Entry Points ◽

The Mean ◽

Living With Hiv ◽

Hiv 1

Abstract Background A substantial number of persons living with HIV (PLWH) in Nigeria do not experience durable viral suppression on first-line antiretroviral therapy (ART). Understanding risk factors for first-line treatment failure informs patient monitoring practices and distribution of limited resources for second-line regimens. We determined predictors of immunologic and virologic failures in a large ART delivery program in Abuja, Nigeria. Methods A retrospective cohort study was conducted at the University of Abuja Teaching Hospital, a tertiary health care facility, using data from February 2005 to December 2014 in Abuja, Nigeria. All PLWH aged ≥ 15 years who initiated ART with at least 6-month follow-up and one CD4 measurement were included. Immunologic failure was defined as a CD4 decrease to or below pre-ART level or persistent CD4 < 100 cells per mm3 after 6 months on ART. Virologic failure (VF) was defined as two consecutive HIV-1 RNA levels > 1000 copies/mL after at least 6 months of ART and enhanced adherence counselling. HIV drug resistance (Sanger sequences) was analyzed using the Stanford HIV database algorithm and scored for resistance to common nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). Univariate and multivariate log binomial regression models were used to estimate relative risks (RRs) and 95% confidence intervals (CIs). Results Of 12,452 patients followed, a total of 5928 initiated ART with at least 6 months of follow-up and one CD4 measurement. The entry point for 3924 (66.2%) was through the program’s own voluntary counseling and testing (VCT) center, while 1310 (22.1%) were referred from an outside clinic/program, 332 (5.6%) in-patients, and 373 (6.3%) through other entry points including prevention of mother to child transmission (PMTCT) and transferred from other programs. The mean CD4 at enrollment in care was 268 ± 23.7 cells per mm3, and the mean HIV-1 RNA was 3.3 ± 1.3.log10 copies/mL. A total of 3468 (80.5%) received nevirapine (NVP) and 2260 (19.5%) received efavirenz (EFV)—based regimens. A total of 2140 (36.1%) received tenofovir (TDF); 2662 (44.9%) zidovudine (AZT); and 1126 (19.0%) stavudine (d4T). Among those receiving TDF, 45.0% also received emtricitabine (FTC). In a multivariate model, immunologic failure was more common among PLWH with female gender as compared to male [RR (95% CI) 1.22 (1.07–1.40)] and less common among those who entered care at the program’s VCT center as compared to other entry points [0.79 (0.64–0.91)], WHO stage 3/4 as compared to 1/2 [0.19 (0.16–0.22)], or CD4 200 + cells per mm3 as compared to lower [0.19 (0.16–0.22)]. Virologic failure was more common among PLWH who entered care at the program’s VCT center as compared to other entry points [RR (95% CI) 1.45 (1.11–1.91) and those with CD4 < 200 cells per mm3 at entry into care as compared to higher [1.71 (1.36–2.16)]. Of 198 patient-derived samples sequenced during virologic failure, 42 (21%) were wild-type; 145 (73%) carried NNRTI drug resistance mutations; 151 (76.3%) M184I/V; 29 (14.6%) had ≥ 3 TAMs, and 37 (18.7%) had K65R, of whom all were on TDF-containing first-line regimens. Conclusions In this cohort of Nigerian PLWH followed for a period of 9 years, immunologic criteria poorly predicted virologic failure. Furthermore, a subset of samples showed that patients failing ART for extended periods of time had HIV-1 strains harboring drug resistance mutations.

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Survival among antiretroviral-experienced HIV-2 patients experiencing virologic failure with drug resistance mutations in Cote d’Ivoire West Africa

PLoS ONE ◽

10.1371/journal.pone.0236642 ◽

2020 ◽

Vol 15 (8) ◽

pp. e0236642

Author(s):

Boris K. Tchounga ◽

Charlotte Charpentier ◽

Patrick A. Coffie ◽

François Dabis ◽

Diane Descamps ◽

...

Keyword(s):

Drug Resistance ◽

West Africa ◽

Cote D'ivoire ◽

Côte D’Ivoire ◽

Virologic Failure ◽

Resistance Mutations ◽

Cote D’Ivoire ◽

Drug Resistance Mutations ◽

Côte D'ivoire

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Assessment of Transmitted HIV-1 Drug Resistance Mutations Using Ultra- Deep Pyrosequencing in a Turkish Cohort

Current HIV Research ◽

10.2174/1570162x16666180910130112 ◽

2018 ◽

Vol 16 (3) ◽

pp. 216-221 ◽

Cited By ~ 3

Author(s):

Uluhan Sili ◽

Burak Aksu ◽

Aysun Tekin ◽

Ufuk Hasdemir ◽

Guner Soyletir ◽

...

Keyword(s):

Drug Resistance ◽

Virologic Failure ◽

Treatment Success ◽

Transmitted Drug Resistance ◽

Drug Resistant ◽

Resistance Mutations ◽

Drug Resistance Mutations ◽

Sensitivity Score ◽

Minority Variants ◽

Genotypic Sensitivity Score

Background: Antiretroviral treatment (ART) reduces morbidity and mortality caused by human immunodeficiency virus (HIV) infection; however, the emergence of drug-resistant strains poses an important obstacle to treatment success. Using conventional sequencing methods to determine antiretroviral resistance, mutations present in ≥20% of quasispecies can be identified, but drug-resistant minority variants can lead to virologic failure. Objective: We aimed to assess transmitted drug resistance mutations (TDRMs) within minority variants using ultra-deep pyrosequencing (UDPS). Method: Treatment-naive adult patients were included in this observational study. Surveillance TDRMs were classified as ≥20% or at minority variant level (≥2% – <20%). Genotypic sensitivity score calculated by using all pre-treatment drug resistance mutations (PDRMs) was also evaluated. Results: Thirty-six patients were analyzed. Any TDRM at ≥20% level was detected in 8.3% of the patients (n=3). This prevalence increased to 30.6% (n=11) with the inclusion of minority variants. All non-nucleoside reverse transcriptase inhibitor and protease inhibitor-related TDRMs were within minority variants. The genotypic sensitivity score of rilpivirine-based regimens was considerably diminished when minority variants were included in the PDRM analysis. Conclusion: UDPS was used for the first time to assess TDRM in a Turkish HIV cohort and uncovered several mutations hidden within minority variants. UDPS may be preferred to detect PDRMs for avoiding virologic failure with rilpivirine-based ART regimens.

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Persistence of Human Immunodeficiency Virus-1 Drug Resistance Mutations in Proviral Deoxyribonucleic Acid After Virologic Failure of Efavirenz-Containing Antiretroviral Regimens

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz034 ◽

2019 ◽

Vol 6 (3) ◽

Cited By ~ 1

Author(s):

Justin De La Cruz ◽

Saran Vardhanbhuti ◽

Malaya K Sahoo ◽

Robert Rovner ◽

Ronald J Bosch ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Drug Resistance ◽

Reverse Transcriptase ◽

Deoxyribonucleic Acid ◽

Mononuclear Cells ◽

Virologic Failure ◽

Resistance Mutations ◽

Proviral Dna ◽

Drug Resistance Mutations ◽

Immunodeficiency Virus

Abstract Background Efavirenz (EFV)-based regimens select broad drug resistance to nonnucleoside reverse-transcriptase inhibitors (NNRTIs), limiting the effectiveness of EFV and other NNRTIs. The duration, persistence, and decay of drug resistance mutations (DRMs) in the proviral reservoir is not well defined. Methods Participants with virologic failure of EFV-based regimens and drug-resistant viremia with the K103N mutation in plasma ribonucleic acid (RNA) were identified from AIDS Clinical Trials Group (ACTG) studies A364 and A5095. These individuals received a second-line, boosted protease inhibitor-based regimen with suppression of viremia for up to10 years during long-term follow-up (median = 3.6 years; interquartile range, 2.1–6.9 years). Proviral deoxyribonucleic acid (DNA) from cryopreserved peripheral blood mononuclear cells was sequenced to identify the persistence of DRM. Results Twenty-eight participants from ACTG 364 and ACTG 5095 were evaluated. Sanger sequencing of proviral DNA detected K103N as well as additional reverse-transcriptase inhibitor (RTI) mutations. Ultradeep sequencing confirmed persistence of K103N in 71% of participants with minimal decay over time. In an adjusted model including years since suppression, persistent proviral K103N was 2.6 times more likely (95% confidence interval, 1.0–6.4) per log10 higher human immunodeficiency virus RNA at EFV failure. Conclusions Persistence of RTI mutations in proviral DNA after virologic failure has implications for the effectiveness of future drug regimens and the recycling of RTI drugs.

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