HIV-1 Variants Research Articles

Assessing the person-centered care framework and assessment tool (PCC-AT) in HIV treatment settings in Ghana: A pilot study protocol.

Evidence suggests that person-centered care (PCC) has the potential to overcome inequities in access to HIV services, support quality care that is responsive to diverse needs while increasing efficiencies and resilience of the health system. Despite emerging evidence on the effectiveness of PCC, there is limited information available on how to assess it in diverse clinical settings. This work builds upon a systematic literature review published elsewhere by this study team to develop a PCC framework for HIV treatment service delivery. The PCC framework informed the development of the PCC assessment tool (PCC-AT) to assess the degree to which PCC activities are operationalized in diverse HIV treatment settings. The study objectives are to assess: (1) content validity of the PCC framework; (2) PCC-AT score consistency and reliability between health facility staff and clients; and (3) PCC-AT feasibility in HIV treatment settings. The study team will pilot the PCC-AT among staff in five health facilities and conduct subsequent focus group discussions (FGDs) to determine PCC-AT feasibility. Key informant interviews (KIIs) with clients will explore content validity among PLHIV relative to each subdomain of the PCC-AT and provide a basis to compare score concordance. Quantitative data among health facility staff will examine how many and which cadres participated in the PCC-AT pilot and FGD, years of experience, gender, and the time required to complete the PCC-AT. Information on clients will include total time accessing treatment at the study health facility, years since diagnosis, age and gender. Qualitative data analysis, using descriptive coding with NVivo or a similar software, will be drawn from transcripts from the PCC-AT pilots, FGDs and KIIs. PCC assessment is a novel approach that aims to help health facilities assess and strengthen their ability to deliver PCC services to improve client outcomes.

Navigating Latency-Inducing Viral Infections: Therapeutic Targeting and Nanoparticle Utilization.

The investigation into viral latency illuminates its pivotal role in the survival strategies of diverse viruses, including herpesviruses, HIV, and HPV. This underscores the delicate balance between dormancy and the potential for reactivation. The study explores the intricate mechanisms governing viral latency, encompassing episomal and proviral forms, and their integration with the host's genetic material. This integration provides resilience against cellular defenses, substantially impacting the host-pathogen dynamic, especially in the context of HIV, with implications for clinical outcomes. Addressing the challenge of eradicating latent reservoirs, this review underscores the potential of epigenetic and genetic interventions. It highlights the use of innovative nanocarriers like nanoparticles and liposomes for delivering latency-reversing agents. The precision in delivery, capacity to navigate biological barriers, and sustained drug release by these nanocarriers present a promising strategy to enhance therapeutic efficacy. The review further explores nanotechnology's integration in combating latent viral infections, leveraging nanoparticle-based platforms for drug delivery, gene editing, and vaccination. Advances in lipid-based nanocarriers, polymeric nanoparticles, and inorganic nanoparticles are discussed, illustrating their potential for targeted, efficient, and multifunctional antiviral therapy. By merging a deep understanding of viral latency's molecular underpinnings with nanotechnology's transformative capabilities, this review underscores the promise of novel therapeutic interventions. These interventions have great potential for managing persistent viral infections, heralding a new era in the fight against diseases such as neuroHIV/AIDS, herpes, and HPV.

Evaluating the validity and reliability of the Tswana adaptation of the MOS-HIV tool for health-related quality of life among HIV Sub-populations in Botswana: A study protocol.

The lack of culturally and contextually appropriate adaptations of health-related quality of life (HRQoL) tools hinders HIV patient outcomes. This study aims to assess the validity and reliability of a Tswana version of the Medical Outcome Survey-HIV (MOS-HIV) tool among diverse HIV sub-populations in Botswana. In terms of the methodology the study will comprise of several steps. Firstly, forward and back-translation of the original U.S. English MOS-HIV tool into Setswana, followed by the review of the translated tool. Phase 1 will evaluate content, construct validity, and reliability of the newly developed tool among HIV outpatients at Gaborone Infectious Diseases Clinics (IDCC). A Cronbach's alpha coefficient >0.7 across the 35 items and 11 dimensions of the MOS-HIV tool will indicate internal consistency reliability. Phase 2 will employ the use of logistic regression models to identify predictors of poor HRQoL among randomly selected IDCC sites, both in urban and rural centers. Phase 3 will investigate predictors of poor HRQoL among inpatients receiving treatment for HIV-associated cryptococcal meningitis (CM) using longitudinal data analysis methods. Ethical approval has been obtained from the University of Botswana, Walter Sisulu University, Human Research and Development Unit, Ministry of Health, and Princess Marina Hospital. Prospective participants will provide written informed consent, with proxy consent explored when feasible. Voluntary participation and confidentiality will be ensured during data collection and analysis. Data will be securely stored under lock-and-key. Dissemination of study findings will adhere to strict privacy protocols, avoiding the sharing of personal identifiers.

Identification of CD38, CD97, and CD278 on the HIV surface using a novel flow virometry screening assay

While numerous cellular proteins in the HIV envelope are known to alter virus infection, methodology to rapidly phenotype the virion surface in a high throughput, single virion manner is lacking. Thus, many human proteins may exist on the virion surface that remain undescribed. Herein, we developed a novel flow virometry screening assay to discover new proteins on the surface of HIV particles. By screening a CD4+ T cell line and its progeny virions, along with four HIV isolates produced in primary cells, we discovered 59 new candidate proteins in the HIV envelope that were consistently detected across diverse HIV isolates. Among these discoveries, CD38, CD97, and CD278 were consistently present at high levels on virions when using orthogonal techniques to corroborate flow virometry results. This study yields new discoveries about virus biology and demonstrates the utility and feasibility of a novel flow virometry assay to phenotype individual virions.

Comprehensive Genetic Characterization of Four Novel HIV-1 Circulating Recombinant Forms (CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx): Insights from Molecular Epidemiology in Cyprus.

Molecular investigations of the HIV-1 pol region (2253-5250 in the HXB2 genome) were conducted on sequences obtained from 331 individuals infected with HIV-1 in Cyprus between 2017 and 2021. This study unveiled four distinct HIV-1 putative transmission clusters, encompassing 19 previously unidentified HIV-1 recombinants. These recombinants, each comprising eight, three, four, and four sequences, respectively, did not align with previously established Circulating Recombinant Forms (CRFs). To characterize these novel HIV-1 recombinants, near-full-length genome sequences were successfully obtained for 16 of the 19 recombinants (790-8795 in the HXB2 genome) using an in-house-developed RT-PCR assay. Phylogenetic analyses, employing MEGAX and Cluster-Picker, along with confirmatory neighbor-joining tree analyses of subregions, were conducted to identify distinct clusters and determine subtypes. The uniqueness of the HIV-1 recombinants was evident in their exclusive clustering within generated maximum likelihood trees. Recombination analyses highlighted the distinct chimeric nature of these recombinants, with consistent mosaic patterns observed across all sequences within each of the four putative transmission clusters. Conclusive genetic characterization identified four novel HIV-1 CRFs: CRF129_56G, CRF130_A1B, CRF131_A1B, and CRF138_cpx. CRF129_56G exhibited two recombination breakpoints and three fragments of subtypes CRF56_cpx and G. Both CRF130_A1B and CRF131_A1B featured seven recombination breakpoints and eight fragments of subtypes A1 and B. CRF138_cpx displayed five recombination breakpoints and six fragments of subtypes CRF22_01A1 and F2, along with an unclassified fragment. Additional BLAST analyses identified a Unique Recombinant Form (URF) of CRF138_cpx with three additional recombination sites, involving subtype F2, a fragment of unknown subtype origin, and CRF138_cpx. Post-identification, all putative transmission clusters remained active, with CRF130_A1B, CRF131_A1B, and CRF138_cpx clusters exhibiting further growth. Furthermore, international connections were identified through BLAST analyses, linking one sequence from the USA to the CRF130_A1B strain, and three sequences from Belgium and Cameroon to the CRF138_cpx strain. This study contributes valuable insights into the dynamic landscape of HIV-1 diversity and transmission patterns, emphasizing the need for ongoing molecular surveillance and global collaboration in tracking emerging viral variants.

The Association of HIV-1 Neutralization in Aviremic Children and Adults with Time to ART Initiation and CD4+/CD8+ Ratios.

Broadly neutralizing antibodies (bnAbs) bind and neutralize diverse HIV isolates and demonstrate protective effects in primate models and humans against specific isolates. To develop an effective HIV vaccine, it is widely believed that inducing these antibodies is crucial. However, the high somatic hypermutation in bnAbs and the limited affinity of HIV Env proteins for bnAb germline precursors suggest that extended antigen exposure is necessary for their production. Consequently, HIV vaccine research is exploring complex sequential vaccination strategies to guide the immune response through maturation stages. In this context, the exploration of the factors linked to the generation of these antibodies across diverse age groups becomes critical. In this study, we assessed the anti-HIV-1 neutralization potency and breadth in 108 aviremic adults and 109 aviremic children under 15 years of age who were receiving ART. We used a previously described minipanel of recombinant viruses and investigated the factors associated with neutralization in these individuals. We identified individuals in both groups who were capable of neutralizing viruses from three different subtypes, with greater cross-neutralization observed in the adult group (49.0% vs. 9.2%). In both groups, we observed an inverse association between neutralization breadth and the CD4+/CD8+ ratio, as well as a direct association with the time to ART initiation. However, we found no association with time post-infection, cumulative ART duration, or CD8+ cell levels. The present study demonstrates that children receiving antiretroviral therapy generate broadly neutralizing responses to HIV-1, albeit with lower magnitude compared to adults. We also observed that neutralization breadth is associated with CD4+/CD8+ levels and time to treatment initiation in both children and adults living with HIV-1. Our interpretation of these results is that a delay in ART initiation could have prolonged the antigenic stimulation associated with viral replication and thus facilitate the capacity to elicit long-lasting broadly neutralizing responses. These results corroborate prior findings that show that HIV-1-neutralizing responses can persist for years, even at low antigen levels, implying an HIV-1 vaccine may induce lasting neutralizing antibody response.

Rapid HIV-1 genotyping assay for the detection of capsid mutations.

Human immunodeficiency virus (HIV) capsid is one of the most recent viral proteins successfully targeted for the development of antiretrovirals. Lenacapavir is a first in class HIV-1 capsid inhibitor that was recently approved for the treatment of highly treatment-experienced people with HIV in combination with other anti-HIV drugs. Owing to the novelty of the viral target, methods to characterize the potential resistance-associated mutations present in capsid upon treatment failure have not been fully established yet. Here, we describe a rapid and simple method to amplify capsid fragments and to determine their sequence from various clinical samples including diverse HIV-1 subtypes. These methods could easily be implemented in laboratories, including hospital laboratories often caring for this patient population.

Performance characteristics of Allele-Specific PCR (ASPCR) in detecting drug resistance mutations among non-B HIV-1 Variants

Allele-Specific Polymerase Chain Reaction (ASPCR) is an affordable point-mutation assay whose validation could improve the detection of HIV-1 drug resistance mutations (DRMs) in resource-limited settings (RLS). We assessed the performance of ASPCR onforty-four non-B HIV-1 plasma samples from patients who were ARV treated in failure in N’Djamena-Chad. Viral RNA was reverse-transcribed and amplified using LightCycler® FastStart DNA MasterPLUS SYBR Green I. Detection of six major DRMs (K70R, K103N, Y181C, M184V, T215F, T215Y) was evaluated on Roche LightCycler®480 automated system (with dilutions 0.01–100%). ASPCR-results were compared to Sanger-sequencing (gold-standard). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02–0.28 vs. 0.12–0.37), K103N (0.08–0.42 vs. 0.12–0.37), Y181C (0.12–0.39 vs. 0.31–0.37), M184V (0.13–0.39 vs. 0.23–0.42), T215F (0.05–0.43 vs. 0.04–0.45) and T215Y (0.13–0.41 vs. 0.19–0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02–0.28 vs. 0.12–0.37), K103N (0.08–0.42 vs. 0.12–0.37), Y181C (0.12–0.39 vs. 0.31–0.37), M184V (0.13–0.39 vs. 0.23–0.42), T215F (0.05–0.43 vs. 0.04–0.45) and T215Y (0.13–0.41 vs. 0.19–0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). ASPCR appears more efficient for detecting DRMs on diverse HIV-1 non-B circulating in RLS like Chad.

Transmitted Drug Resistance and HIV Diversity Among Adolescents Newly Diagnosed With HIV in Spain.

Virological characterization of newly HIV-diagnosed adolescents could help to improve their specific needs. The objective was to describe the transmitted drug resistance mutations (TDR) and its transmission by clusters in this population in Spain. TDR to retrotranscriptase and protease inhibitors included in the WHO TDR list 2009 implemented in the Calibrated Population Resistance tool v8.0 (Stanford) were studied in HIV pol sequences from all HIV-diagnosed adolescents (12-19-year-old) enrolled during 2004-2019 period in the Spanish pediatric and adult (CoRISpe-CoRIS) cohorts. The found TDR were compared with the provided by the Stanford algorithm v9.0 2021. HIV-1 variants and transmission clusters were also studied. Among 410 HIV-1 adolescents diagnosed, 141 (34.4%) had available ART-naive sequences. They were mostly male (81.6%), Spanish (55.3%) and with behavioral risk (92.2%), mainly male-to-male sexual contact (63.1%). TDR prevalence was significantly higher by Stanford versus WHO list (18.4% vs. 7.1%; P = 0.004). The most prevalent TDR by the WHO list was K103N (3.6%) and by Stanford E138A (6.6%), both at retrotranscriptase. E138A, related to rilpivirine/etravirine resistance, was absent in the WHO list. One in 4 adolescents carried HIV-1 non-B variants. We described 5 transmission clusters, and 2 carried TDR mutations. Our data suggest a high TDR prevalence in adolescents with a new HIV diagnosis in Spain, similar to adults, 2 active TDR transmission clusters, and the need for the WHO TDR list update. These findings could have implications for the options of the recently available rilpivirine-related long-acting treatment and in first-line regimen election.

HIV-1 envelope diversity and sensitivity to broadly neutralizing antibodies across stages of acute HIV-1 infection.

We studied the relationship between viral diversity and susceptibility to broadly neutralizing antibodies (bNAbs) in longitudinal plasma and peripheral blood mononuclear cells from 89 people with HIV who initiated antiretroviral therapy (ART) during acute and early HIV-1 infection (AEHI). HIV-1 diversity and predicted bNAb susceptibility were comparable across AEHI. Diversity evolution was not observed during ART, suggesting (pro)viruses at initiation or during treatment may identify individuals with susceptible virus for bNAb interventional trials.

Features of Tat Protein in HIV-1 Sub-Subtype A6 Variants Circulating in the Moscow Region, Russia.

Tat, the trans-activator of transcription, is a multifunctional HIV-1 protein that can induce chronic inflammation and the development of somatic diseases in HIV-infected patients. Natural polymorphisms in Tat can impact the propagation of the inflammatory signal. Currently, Tat is considered an object for creating new therapeutic agents. Therefore, the identification of Tat protein features in various HIV-1 variants is a relevant task. The purpose of the study was to characterize the genetic variations of Tat-A6 in virus variants circulating in the Moscow Region. The authors analyzed 252 clinical samples from people living with HIV (PLWH) with different stages of HIV infection. Nested PCR for two fragments (tat1, tat2) with subsequent sequencing, subtyping, and statistical analysis was conducted. The authors received 252 sequences for tat1 and 189 for tat2. HIV-1 sub-subtype A6 was identified in 250 samples. The received results indicated the features of Tat1-A6 in variants of viruses circulating in the Moscow Region. In PLWH with different stages of HIV infection, C31S in Tat1-A6 was detected with different occurrence rates. It was demonstrated that Tat2-A6, instead of a functional significant 78RGD80 motif, had a 78QRD80 motif. Herewith, G79R in Tat2-A6 was defined as characteristic amino acid substitution for sub-subtype A6. Tat2-A6 in variants of viruses circulating in the Moscow Region demonstrated high conservatism.

V3 tip determinants of susceptibility to inhibition by CD4-mimetic compounds in natural clade A human immunodeficiency virus (HIV-1) envelope glycoproteins.

CD4-mimetic compounds (CD4mcs) are small-molecule inhibitors of human immunodeficiency virus (HIV-1) entry into host cells. CD4mcs target a pocket on the viral envelope glycoprotein (Env) spike that is used for binding to the receptor, CD4, and is highly conserved among HIV-1 strains. Nonetheless, naturally occurring HIV-1 strains exhibit a wide range of sensitivities to CD4mcs. Our study identifies changes distant from the binding pocket that can influence the susceptibility of natural HIV-1 strains to the antiviral effects of multiple CD4mcs. We relate the antiviral potency of the CD4mc against this panel of HIV-1 variants to the ability of the CD4mc to activate entry-related changes in Env conformation prematurely. These findings will guide efforts to improve the potency and breadth of CD4mcs against natural HIV-1 variants.

HIV-1 subtype diversity and immuno-virological outcomes among adolescents failing antiretroviral therapy in Cameroon: A cohort study.

We sought to evaluate the variability of HIV-1 and its effect on immuno-virological response among adolescents living with perinatally acquired HIV (APHI). A cohort study was conducted from 2018-2020 among 311 APHI receiving antiretroviral therapy (ART) in Cameroon. Sequencing of protease and reverse transcriptase regions was performed for participants experiencing virological failure, VF, (Plasma viral load, PVL ≥ 1000 RNA copies/ml). HIV-1 subtypes were inferred by phylogeny; immuno-virological responses were monitored at 3-time points (T1-T3). Cox regression modeling was used to estimate adjusted hazard ratios (aHRs) of progression to: CD4 < 250, and PVL > 5log10, adjusted for acquired drug resistance, gender, ART line, adherence, and duration on treatment; p < 0.05 was considered statistically significant. Of the 141 participants in VF enrolled, the male-female ratio was 1:1; mean age was 15 (±3) years; and median [IQR] duration on ART was 51 [46-60] months. In all phases, 17 viral clades were found with a predominant CRF02_AG (58.2%, 59.4%, and 58.3%). From T1-T3 respectively, there was an increasing CD4 count (213 [154-313], 366 [309-469], and 438 [364-569] cells/mm3) and decline log10 PVL (5.23, 4.43, and 4.43), similar across subtypes. Among participants with CRF02_AG infection, duration of treatment was significantly associated with both rates of progression to CD4 < 250, and PVL > 5log10, aHR = 0.02 (0.001-0.52), and aHR = 0.05 (0.01-0.47) respectively. Moreover, four potential new HIV-1 recombinants were identified (CRF02_AG/02D, CRF02_AG/02A1F2, D/CRF02_AG, and AF2/CRF02_AG), indicating a wide viral diversity. Among APHI in settings like Cameroon, there is a wide genetic diversity of HIV-1, driven by CRF02_AG and with potential novel clades due to ongoing recombination events. Duration of treatment significantly reduces the risk of disease progression.

The role of HIV-1 polymorphism in the pathogenesis of the disease

High genetic variability is one of the defining HIV-1 properties. It contributes to the appearance of drug resistance and to the formation of various HIV variants. In the world, the different variants of HIV-1 are distributed unevenly. In Russia there are circulating unique virus variants which are characteristic for our country and some countries of the former USSR and which are difference from HIV-1 variants circulating in other countries of the world. For many years, the studies aimed on the analysis of the influence of various HIV-1 variants on pathogenesis have been conducted. Within the framework of these studies, the polymorphism mutations in different subtypes and recombinant forms have been detected. Currently the main objects of antiretroviral therapy are HIV-1 structural proteins, mainly enzyme proteins, thus polymorphic mutations in which could affect the degree of virus sensitivity to antiretroviral therapy. Non-structural HIV-1 proteins are involved in virus replication and virus protection from the host immune system, enter the bloodstream and tissues, causing the development of inflammation. The polymorphic mutations in non-structural proteins could affect the degree of HIV infection progression and the development of concomitant somatic diseases. Today, nonstructural proteins are considered as objects for the creation of therapeutic agents, thus the identification of polymorphic mutations in nonstructural proteins in different HIV-1 variants is a basis for such developments. Thus, the study of polymorphism of both structural and non-structural HIV-1 proteins is a promising area of research in the future.

Genetic diversity of HIV-1 at the current stage of the epidemic in the Russian Federation: an increase in the prevalence of recombinant forms

The aim of the study: assessment of genetic diversity and prevalence of recombinant forms of HIV-1 at the current stage of the epidemic in the Russian Federation.Materials and methods. The study used collections of blood and its components obtained from 3178 HIV-infected patients of federal and regional «Centers for the Prevention and Control of AIDS» in the period from 2011 to 2020. Next, the extraction of proviral DNA or HIV-1 viral RNA was carried out, followed by amplification of the pol gene region and sequencing of the ampli fication products. Then, the obtained nucleotide sequences were analyzed to determine their subtype and the prevalence of recombinant forms of the virus was estimated.Results and discussion. It was found that sub-subtype A6 remains the dominant (82.9%) genetic variant of HIV-1 at the current stage of the epidemic in the Russian Federation. The second most common was subtype B — 7.14%. The share of each of the recombinant forms of HIV-1 — CRF02_AG and CRF03_AB accounted for about 1% of all analyzed samples, CRF63_02A6 — about 3.59%. In addition to circulating recombinant forms of HIV-1, 87 unique recombinants (2.74%) were identified. A significant (p&lt;0.001) increase in the frequency of occurrence of HIV-1 recombinant forms of over time was revealed. The largest proportion of recombinant forms of HIV-1 was detected in the Siberian (35.83%) and Northwestern (15.98%) federal districts, the smallest — in the Volga (1.99%) and Ural (2.36%) federal districts.Conclusion. The results obtained indicate the growing genetic diversity of HIV-1 in the Russian Federation, along with the spread of HIV infection beyond vulnerable groups, as well as an increase in the frequency of occurrence of recombinant forms of HIV-1 over time and their involvement in the epidemic process.

Genetic profile of HIV-1 in the Republic Sakha, Yakutia

Aim. To perform molecular-genetic analysis of HIV-1 variants circulation in the Republic Sakha (Yakutia) and analysis of drug resistance mutations.Materials and methods. 123 patients diagnosed with HIV infection were examined. Mutations of drug resistance were detected via sequencing of amplified fragments of pol gene that is coding protease and a part of reverse transcriptase of HIV-1 using «Amplisens® HIV-Resist-Seq» test-system. Phylogenetic analysis was performed with software MEGA version 7.0.Results and discussion. Sub-subtype A6 that is prevalent in the Russian Federation was revealed most frequently (78.0%) in the examined group. Subtype B was detected in four cases (3.3%). Isolated cases of infection due to subtypes C, G and subsubtype A7 were revealed. Recombinant forms of the virus were found in 16.2% of the patients (n=20). Drug resistance mutations were revealed in 65 patients (52.8%) that were undergoing antiretroviral therapy (ART) which dictates a necessity of changing ART drugs.Conclusion. The results of the research state changes in the genetic profile of HIV-1 variants that were circulating during the last years in the Republic Sakha (Yakutia).

Fostemsavir resistance-associated polymorphisms in HIV-1 subtype C in a large cohort of treatment-naïve and treatment-experienced individuals in Botswana.

There are limited data on the prevalence of fostemsavir (FTR) resistance-associated polymorphisms in people with HIV in Botswana. We sought to determine the prevalence of FTR resistance-associated polymorphisms in HIV-1 subtype C sequences from antiretroviral therapy (ART)-naïve and ART-experienced individuals in Botswana. Previously reported FTR resistance-associated polymorphisms from literature were surveyed from HIV-1C proviral sequences generated from a large HIV-1 population-based cohort enrolled between 2013 and 2018. Sequences from ART-naïve and ART-experienced individuals were included in the analysis. A total of 6,078 participants with gp120 sequences were included in this study, and 6,030 (99.2%) had known ART status; 1,282 (21.3%) were from ART-naïve individuals, while 4,748 (78.7%) were from individuals on ART at study enrollment. Viral load (VL) data were available for 4,739 (99.8%) ART-experienced individuals, of whom 4,526 (95.5%) were suppressed and 213 (4.5%) had virologic failure (VF) (VL >400). Among those with VF and ART naive, the overall prevalence of FTR resistance was 13.3% (95% CI 11.6%-15.1%) and did not differ between ART-experienced with VF individuals (29/213, 13.6%) and ART-naïve individuals (170/1,282, 13.3%) (P-value = 0.9). The most predominant mutations (prevalence ≥1.0%) were M434I (9.8%), M475I (5.9%), and M426L (1.1%). The overall prevalence of FTR polymorphisms was similar in both ART-naïve and ART-experienced individuals with VF in a setting with no prior FTR exposure. We recommend further studies on the phenotypic impact of these polymorphisms to guide how to monitor for FTR resistance. (This study has been registered at ClinicalTrials.gov under registration no. NCT01965470.) IMPORTANCE Fostemsavir (FTR) is a newly licensed antiretroviral drug that has been shown to have activity against HIV-1. The mechanism of action of FTR is different from all currently available antiretrovirals (ARVs), and as such, it offers hope for HIV-1 suppression in those people with HIV (PWH) who harbor HIV-1 variants with drug resistance mutations to currently used ARVs. Using 6,030 HIV-1 sequences covering the HIV-1 envelope from PWH in Botswana who are antiretroviral therapy (ART) naïve as well as those who are failing ART, we explored the sequences for FTR resistance-associated polymorphisms. We found the prevalence of FTR polymorphisms to be similar in both ART-naïve and ART-experienced individuals with VF in this setting, with no prior FTR exposure. Further studies on the phenotypic impact of these polymorphisms are warranted to guide how to monitor for FTR resistance.

Transmitted drug resistance and subtype patterns of viruses from reported new HIV diagnoses in Germany, 2017–2020

BackgroundThe transmission of resistant HIV variants jeopardizes the effective use of antiretrovirals for therapy and prophylaxis. Molecular surveillance of new HIV diagnoses with a focus on prevalence and type of resistance associated mutations and the subtype of circulating viruses is mandatory.MethodFrom 2017 to 2020, 11,527 new HIV diagnoses were reported in Germany to the Robert Koch Institute (RKI). Protease (PR) and reverse-transcriptase (RT) sequences were obtained from 4559 (39.6%) cases, and PR, RT and integrase (IN) sequences were obtained from 3097 (26.9%) cases. The sequences were analyzed with data from the national HIV reports.ResultsAmong all cases in the analysis, the proportion of primary resistance was 4.3% for nucleoside reverse-transcriptase inhibitors (NRTIs), 9.2% for non-NRTI (NNRTIs), 3.3% for protease inhibitors (PIs) and 1.4% for integrase inhibitors (INIs). Dual-class resistance was highest for NRTIs/NNRTIs with 1.2%. There was no trend in the proportion of viruses resistant to drug classes. Most individual key mutations associated with relevant resistance had a prevalence below 1% including K65R (0.1%) and M184V (0.6%). A notable exception was K103NS, with a prevalence of 2.9% and a significant increase (pTrend=0.024) during 2017–2020. In this period, diagnoses of infections with HIV-1 subtype B were the most common at 58.7%, but its prevalence was declining (pTrend=0.049) while the frequency of minority subtypes (each < 1%) increased (pTrend=0.007). Subtype B was highest (75.6%) in men who have sex with men (MSM) and lowest in reported heterosexual transmissions (HETs, 22.6%).ConclusionThe percentage of primary resistance was high but at a stable level. A genotypic determination of resistance is therefore still required before the start of therapy. The subtype diversity of circulating HIV-1 is increasing.

An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting

The existence of broadly cross-reactive antibodies that can neutralize diverse HIV-1 isolates (bnAbs) has been appreciated for more than a decade. Many high-resolution structures of bnAbs, typically with one or two well-characterized HIV-1 Env glycoprotein trimers, have been reported. However, an understanding of how such antibodies grapple with variability in their antigenic targets across diverse viral isolates has remained elusive. To achieve such an understanding requires first characterizing the extent of structural and antigenic variation embodied in Env, and then identifying how a bnAb overcomes that variation at a structural level. Here, using hydrogen/deuterium-exchange mass spectrometry (HDX-MS) and quantitative measurements of antibody binding kinetics, we show that variation in structural ordering in the V1/V2 apex of Env across a globally representative panel of HIV-1 isolates has a marked effect on antibody association rates and affinities. We also report cryo-EM reconstructions of the apex-targeting PGT145 bnAb bound to two divergent Env that exhibit different degrees of structural dynamics throughout the trimer structures. Parallel HDX-MS experiments demonstrate that PGT145 bnAb has an exquisitely focused footprint at the trimer apex where binding did not yield allosteric changes throughout the rest of the structure. These results demonstrate that structural dynamics are a cryptic determinant of antigenicity, and mature antibodies that have achieved breadth and potency in some cases are able to achieve their broad cross-reactivity by “threading the needle” and binding in a highly focused fashion, thus evading and overcoming the variable properties found in Env from divergent isolates.

HIV Drug Resistance Mutations and Subtype Profiles among Pregnant Women of Ho Chi Minh City, South Vietnam.

According to the latest data released by UNAIDS, the global number of people living with HIV (PLHIV) in 2021 was 38.4 million, with 1.5 million new HIV infections. In different countries, a significant proportion of these cases occur in the adult fertile population aged 15-49 years. According to UNAIDS, Vietnam had a national HIV prevalence of 0.3% of the total population at the end of 2019, with approximately 230,000 PLHIV. The most effective way to prevent mother-to-child transmission of HIV is ART to reduce maternal viral load. HIV-infected pregnant women should undergo monthly monitoring, especially before the expected date of delivery. The aim of our work was to analyze subtypic structure and drug-resistant variants of HIV in pregnant women in Ho Chi Minh City. The study material was blood plasma samples from HIV-infected pregnant women: 31 women showed virological failure of ART, and 30 women had not previously received therapy. HIV-1 genotyping and mutation detection were performed based on analysis of the nucleotide sequences of the pol gene region. More than 98% of sequences genotyped as HIV-1 sub-subtype CRF01_AE. When assessing the occurrence of drug resistance mutations, genetic resistance to any drug was detected in 74.41% (95% CI: 62.71-85.54%) of patients. These included resistance mutations to protease inhibitors in 60.66% (95% CI: 47.31-72.93%) of patients, to NRTIs in 8.20% (95% CI: 2.72-18.10%), and to NNRTIs in 44.26% (95% CI: 31.55-57.52%). Mutations associated with NRTI (2) and NNRTI (8) resistance as well as PI mutations (12), including minor ones, were identified. The high prevalence of drug resistance mutations found in this study among pregnant women, both in therapeutically naive individuals and in patients with virological failure of ART, indicates that currently used regimens in Vietnam are insufficient to prevent vertical HIV infection.