Antiretroviral resistance among HIV type 1-infected women first exposed to antiretrovirals during pregnancy: plasma versus PBMCs

Virological Outcomes Among Pregnant Women Receiving Antiretroviral Treatment in the Amhara Region, North West Ethiopia

Background

Globally, approximately 35 million people are infected with HIV infection. Sub-Saharan countries contributed 71% of global burden. Women are the most affected groups accounting for 51% of global infection and 90% of HIV infections in children (<15 years) are a result of mother to child transmission. In the absence of any intervention, mother-to-child transmission has been estimated to 30-40% that could occur at various periods like during pregnancy, delivery, and post-partum, via breastfeeding. For future generations to be born HIV-free, evidences on the level of viremia and contributing factors in pregnant mothers is important.

Objective

The objective of this study is to determine the magnitude of viral non-suppression rate among pregnant women and identify the risk factors associated with viral non-suppression.

Methods

A cross-sectional study was conducted from July 01, 2021 to June 30, 2022, in pregnant women who are on antiretroviral treatment and attending HIV viral load testing in Amhara region viral load testing sites, North West Ethiopia. Socio-demographic, clinical, and HIV-1 RNA viral load data were collected from the excel database. The data were analyzed in SPSS 23.0 statistical software.

Results

Overall viral non-suppression rate was 9.1%. In other words, the viral suppression rate was 90.9%. Pregnant women being at AIDS stages III and IV and with fair treatment adherence and suspected testers were statistically associated with increased viral non-suppression rate.

Conclusion

Relatively low viral non-suppression rate among pregnant mothers that had almost met the third 90 of UNAIDS target. But, still, some mothers received a non-suppressed viral replication specifically the odds of having a non-suppressed viral load was higher in pregnant women with poor treatment adherence and WHO Stage III and IV and suspected testers.

Treatment Experience and Repeat Pregnancy Impact the Effectiveness of Non-Nucleoside Reverse Transcription Inhibitor-Highly Active Antiretroviral Therapy for the Prevention of Mother to Child Transmission of Human Immunodeficiency Virus

Non-nucleoside reverse transcription inhibitor (NNRTI)-containing antiretroviral therapy (ART) for the prevention of mother to child transmission (PMTCT) of human immunodeficiency virus (HIV) has led to dramatic reductions in perinatal HIV infection in resource-constrained settings. Nonetheless, PMTCT programs are complicated by repeat pregnancies, in which long-term or repeat exposures to PMTCT regimens over time may lead to the acquisition of HIV drug resistance mutations, and consequent treatment failure. In this study, we retrospectively assessed the effectiveness of the NNRTI-based PMTCT protocol from 2008 to 2010 in The Bahamas National HIV/AIDS Program. We show that women who had been in repeat pregnancies and those who were already prescribed ART at conception were at increased risk of virologic failure, relative to treatment-inexperienced women and primigravida, respectively (AOR 3.1, 95% CI: 1.3-7.1, p = .008 and AOR 5.0, 95% CI: 1.8-14.1, p = .002). In addition, women undergoing treatment at conception were more likely to possess HIVDR mutations relative to treatment-naive women (AOR 447.1, 95% CI: 17.9-11,173.5, p = .001). Therefore, individual treatment history is a key metric determining the effectiveness of current and future PMTCT interventions. The implications of this to PMTCT programmatic success in light of the most recent WHO guidelines are discussed.

Prevalence of Drug Resistance Mutations in Protease, Reverse Transcriptase, and Integrase Genes of North Central Mexico HIV Isolates

This study set out to determine the frequency of antiretroviral drug resistance mutations in treatment-naive subjects of the north central Mexican state of San Luis Potosí. Mexican studies of antiretroviral drug resistance mutations have focused mainly on large metropolitan areas and border towns subjected to intense international migrations. This study set forth to describe the frequency of these mutations in a Mexican region less subjected to such migratory influences and more representative of smaller Mexican cities. Thirty-eight full-length pol sequences spanning the protease, reverse-transcriptase, and integrase-encoding regions were obtained from 42 treatment-naive human immunodeficiency virus (HIV)-infected subjects. Most exhibited subtype B homology, but CRF02_AG was also detected. Evidence of APOBEC3 hypermutation was seen in two samples. Calibrated population analysis revealed a surveillance drug resistance mutation prevalence of 4.9% for protease inhibitors, of 2.7% for nucleoside reverse transcriptase inhibitors, of 8.1% for non-nucleoside reverse transcriptase inhibitors, and an overall prevalence of 9.5%. This corresponds to an intermediate level of transmitted drug resistance according to the World Health Organization. The identification of integrase mutations suggests that transmitted drug mutations are being imported, as inhibitors targeting integrase have not been widely used in Mexico. Our results provide a greater understanding of HIV diversity in Mexico and highlight the way internal migrations allow HIV mutations and genetic features to permeate regions less subjected to international migrations. The implications of these findings will become more evident as Mexico hosts increased repatriations of migrants in the coming years.

HIV drug resistance mutations in proviral DNA from a community treatment program

Background

Drug resistance mutations archived in resting memory CD4+ cells may persist despite suppression of HIV RNA to <50 copies/ml. We sequenced pol gene from proviral DNA among viremic and suppressed patients to identify drug resistance mutations.

Methods

The Peninsula AIDS Research Cohort study enrolled and followed over 2 years 120 HIV infected patients from San Mateo and San Francisco Counties. HIV-1 pol genotyping by bulk sequencing was performed on 38 DNA and RNA from viremic patients and DNA only among 82 suppressed patients at baseline. Antiretroviral susceptibility was predicted by HIVDB.stanford.edu.

Results

Among 120 subjects, 81% were on antiretroviral therapy and had been treated for a median time of 7 years. Thirty-two viremic patients showed concordant RNA and DNA genotypes (84%); the discordant profiles were mainly observed in patients with low-level viremia. Among suppressed patients, 21 had drug resistance mutations in proviral DNA (26%) with potential resistance to one, two or three ARV classes in 16, 4 and 1 samples respectively.

Conclusions

The high level of genotype concordance between DNA and RNA in viremic patients suggested that DNA genotyping might be used to assess drug resistance in resource-limited settings, and further investigation of extracted DNA from dried blood spots is needed. Drug resistance mutations in proviral DNA in 26% of subjects with less than 50 copies/ml pose a risk for the transmission of drug resistant virus with virologic failure, treatment interruption or decreased adherence.

No clinically significant drug-resistance mutations in HIV-1 subtype C-infected women after discontinuation of NRTI-based or PI-based HAART for PMTCT in Botswana

Risk of developing drug resistance after stopping antiretroviral regimens to prevent mother-to-child HIV-1 transmission is unknown. The Mma Bana Study randomized treatment-naive pregnant women with CD4 ≥200 cells per cubic millimeter to receive either abacavir/zidovudine/lamivudine [triple nucleoside reverse transcriptase inhibitor (NRTI) arm] or lopinavir/ritonavir/zidovudine/lamivudine [protease inhibitor (PI) arm]. Drugs were discontinued after 6 months of breastfeeding. One month after discontinuation, 29 NRTI arm samples and 25 PI arm samples were successfully genotyped. No clinically significant antiretroviral resistance mutations were detected. Eight minor resistance mutations were found among 11 (20%) women (3 from NRTI arm and 8 from PI arm), occurring at similar frequencies to those reported in HIV-1 subtype C treatment-naive cohorts.

Low-abundance resistant mutations in HIV-1 subtype C antiretroviral therapy-naive individuals as revealed by pyrosequencing

Given the recent scale-up of antiretroviral therapy (ART) in sub-Saharan Africa, we sought to determine how often and at what levels do drug-resistant mutant variants exist in ART-naive HIV subtype C infected individuals. Samples from 10 ART-naive Zambian individuals were subjected to ultra-deep pyrosequencing (UDPS) to characterize the frequency of low-abundance drug resistance mutations in the pol gene. Low-abundance clinically relevant variants were detected for nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) in eight of the ten subjects. Intermediate to high-level resistance was predicted for the majority of NRTIs. Mutations conferring resistance to most first-line and some second-line therapy drugs were also observed. UDPS detected a number of additional major resistant mutations suggesting that these individuals may have an increased risk of virological failure after initiating ART. Moreover, the effectiveness of first-line and even some secondline ART may be compromised in this setting.

Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing

The evolution of drug resistance mutations in plasma samples is relatively well-characterized. However, the viral population and diversity in other body compartments such as peripheral blood mononuclear cells (PBMC) remains poorly understood. Previous studies have mostly focused on protease and reverse transcriptase drug resistance mutations (DRMs). In this study, we used 454 "deep" sequencing technology to observe and quantify longitudinally the prevalence of resistance mutations associated with the integrase inhibitor, raltegravir, in plasma versus PBMC samples from a San Francisco-based cohort. Four heavily treatment-experienced subjects were monitored in this study over a median of 1.2 years since the initiation of raltegravir-containing regimens. We observed a consistent discordance in the prevalence of DRMs, but not resistance pathway(s), in the plasma versus PBMC viral populations. In the final paired samples that were tested while the subjects were on a raltegravir-containing regimen, DRM prevalence reached 100% in plasma but remained 1% in PBMC on day 177 post-therapy in Subject 3180 (Q148H/G140S), 100% in plasma and 36% in PBMC on day 224 in Subject 3242 (N155H), 78% in plasma and 11-12% in PBMC on day 338 in Subject 3501 (Q148H/G140S), and 100% in plasma and 0% in PBMC on day 197 in Subject 3508 (Y143R). Furthermore, absolute sequence homology comparison between the two compartments revealed that 21% - 99% of PBMC sequences had no match in plasma, whereas 14% - 100% of plasma sequences had no match in PBMC. Overall, our observations suggested that plasma and PBMC hosted drastically different HIV-1 populations even after a prolonged exposure to raltegravir selection pressure.

Comparison of HIV-1 resistance profiles in plasma RNA versus PBMC DNA in heavily treated patients in Honduras, a resource-limited country

The World Health Organization currently does not recommend the use of dried blood spot specimens for drug resistance testing in patients undergoing antiretroviral therapy (ART). Therefore, HIV-1 resistance testing using peripheral blood mononuclear cells (PBMCs) may be of value in resource-limited settings. We compared genotypic resistance profiles in plasma and PBMCs from patients failing ART in two cities of Honduras (Tegucigalpa and San Pedro Sula), a resource-limited country. One hundred patients failing ART were randomly selected from a longitudinal patient monitoring cohort. Plasma and PBMC samples without patient identifier were used for genotypic resistance testing. Sequence data were analyzed, resistance profiles were determined and compared using Stanford HIV Drug Resistance Database algorithm. Specimens with concordant resistance profiles between the two compartments were 88% (95% CI: 80.3% - 94.5 %). Nine specimens (12%, 95% CI: 6.5% - 21.3%) had discordant resistance profiles of clinical significance. Logistic regression analyses indicated that patients on triple therapy were 17.24 times more likely to have concordant drug resistance profile than those on non-triple therapies (OR=17.24, 95% CI: 3.48, 83.33), while patients with increasing number of regimens and years on ART have a decreased rate of concordance (OR = 0.59, 95% CI: 0.32, 1.09 and OR = 0.62, 95% CI: 0.43, 0.88), respectively, than those with less number of regimens and years on ART. Our results show high level of concordance between plasma and PBMC resistance profiles, indicating the possibility of using PBMCs for drug resistance testing in resources-limited settings.

Selection of HIV resistance associated with antiretroviral therapy initiated due to pregnancy and suspended postpartum

OBJECTIVE

Compare the risk of HIV drug resistance in women stopping suppressive nelfinavir (NFV)-based or Nevirapine (NVP)-based antiretroviral therapy (ART) after pregnancy.

METHODS

Specimens collected after stopping ART were tested for drug resistance by an oligonucleotide ligation assay and consensus sequencing. When postpartum drug resistance was detected, specimens obtained at study entry and during ART were evaluated.

RESULTS

Sixteen of 38 women with ART-induced suppression of viral replication suspended ART postpartum. Resistance mutations were detected in 75% who stopped NFV-ART and in 50% who stopped NVP-ART. M184V, associated with Lamivudine resistance, was more frequent among those randomized to NFV-ART compared with NVP-ART (6 of 8 versus 1 of 8; P = 0.04), and nonnucleoside reverse transcriptase inhibitor resistance was detected in 4 of 8 stopping NVP-ART.

CONCLUSIONS

HIV drug resistance was frequently observed among women who stopped suppressive NVP-ART or NFV-ART postpartum. This suggests that NFV-ART may have suboptimal potency, that staggering discontinuation of NVP-ART may be warranted, and/or ART adherence may be lax in women who choose to stop ART postpartum.

HIV drug resistance and mother-to-child transmission of HIV

This article covers HIV drug resistance among pregnant women and the implications of transmission of resistant HIV to the infant. Resistance to antiretroviral drugs may be acquired or can emerge while HIV-infected pregnant women are on antiretroviral therapy, either before or during pregnancy. Resistance to antiretroviral drugs among HIV-infected infants may be acquired from the mother in utero or during the intrapartum period. Resistance may also emerge from exposure to antiretroviral drugs given to the infant for prophylaxis against HIV transmission. In settings where breastfeeding is practiced, ongoing transmission of HIV from breastfeeding may lead to transmission of resistant HIV from the mother. If the mother is taking antiretroviral drugs while breastfeeding, resistance to antiretroviral drugs may emerge in an HIV-infected infant from ingestion of antiretroviral drugs via breast milk. The magnitude and implications of antiretroviral resistance among HIV-infected pregnant women and HIV-infected infants are summarized.

High viral fitness during acute HIV-1 infection

Several clinical studies have shown that, relative to disease progression, HIV-1 isolates that are less fit are also less pathogenic. The aim of the present study was to investigate the relationship between viral fitness and control of viral load (VL) in acute and early HIV-1 infection. Samples were obtained from subjects participating in two clinical studies. In the PULSE study, antiretroviral therapy (ART) was initiated before, or no later than six months following seroconversion. Subjects then underwent multiple structured treatment interruptions (STIs). The PHAEDRA study enrolled and monitored a cohort of individuals with documented evidence of primary infection. The subset chosen were individuals identified no later than 12 months following seroconversion to HIV-1, who were not receiving ART. The relative fitness of primary isolates obtained from study participants was investigated ex vivo. Viral DNA production was quantified using a novel real time PCR assay. Following intermittent ART, the fitness of isolates obtained from 5 of 6 PULSE subjects decreased over time. In contrast, in the absence of ART the fitness of paired isolates obtained from 7 of 9 PHAEDRA subjects increased over time. However, viral fitness did not correlate with plasma VL. Most unexpected was the high relative fitness of isolates obtained at Baseline from PULSE subjects, before initiating ART. It is widely thought that the fitness of strains present during the acute phase is low relative to strains present during chronic HIV-1 infection, due to the bottleneck imposed upon transmission. The results of this study provide evidence that the relative fitness of strains present during acute HIV-1 infection may be higher than previously thought. Furthermore, that viral fitness may represent an important clinical parameter to be considered when deciding whether to initiate ART during early HIV-1 infection.

Short communication: antiretroviral therapy resistance mutations present in the HIV type 1 subtype C pol and env regions from therapy-naive patients in Zambia

The prevalence of antiretroviral therapy (ART) resistance mutations present in HIV-1 subtype C pol and env regions of the proviral DNA was analyzed and compared from therapy-naive individuals before (Cohort A) and after (Cohort B) the availability of free ART in Zambia. Mutations present in sequences published in a previous study from Zambian ART-naive individuals infected with subtype C were analyzed using current parameters for the classification of ART drug resistance and compared with Cohorts A and B. No statistically significant differences were observed when comparing mutations present in the pol and env of these cohorts. However, an increase in the number of minor, borderline, or partial resistance mutations as well as the presence of major resistance mutations were observed in Cohort B. These results suggest there is an increasing trend of drug resistance-associated mutations that could be a result of the availability of free ART in Zambia. Moreover, the high prevalence of resistance mutations observed for maraviroc and vicriviroc in both cohorts may suggest a limited efficacy of entry inhibitors on HIV-1 subtype C.

A review of nucleoside reverse transcriptase inhibitor use to prevent perinatal transmission of HIV

Worldwide, women comprise > 50% of all people living with HIV and the vast majority of these women are of childbearing age. In fact, a significant proportion of these women are identified as HIV-infected during pregnancy. Preventing perinatal transmission has been one of the greatest prevention successes of the HIV epidemic with < 2% of live births resulting in an HIV-infected infant. The strategic use of combination antiretroviral therapy has been a critical component of this reduction. With more antiretroviral agents available for HIV, the appropriate selection of therapy is often based on provider familiarity with the various agents. Although benefits of antiretroviral use in pregnancy tremendously outweigh the risks, concerns regarding short- and long-term toxicity in mothers and their children, in addition to the risk of the development of HIV resistance, remain subjects of discussion. The choice of antiretroviral 'backbone' is supported by extensive data showing efficacy in the prevention of HIV vertical transmission. Co-formulated zidovudine/lamivudine is the most commonly used combination in pregnancy. Long-term consequences of in utero exposure to antiretroviral agents are not fully understood. In this article, we review the data regarding nucleoside reverse transcriptase inhibitors with a focus on tenofovir.