Low prevalence of doravirine-associated resistance mutations among polish human immunodeficiency-1 (HIV-1)–infected patients

Introduction Doravirine (DOR) is a novel non-nucleoside reverse transcriptase inhibitor (NNRTI) that retains activity against common NNRTI resistance mutations. In this study, we aimed to investigate the prevalence of DOR resistance mutations compared with that of resistance mutations for other NNRTIs among HIV-1-infected treatment‐experienced and -naïve patients from Poland. Methods Resistance to DOR and other NNRTIs was assessed in two datasets: 1760 antiretroviral treatment-naïve HIV-1 patients and 200 treatment‐experienced patients. All 1960 sequences were derived from the patients using bulk sequencing. For resistance analyses, Stanford HIV drug resistance database scores were used. Results Overall, DOR resistance was present in 32 patients (1.62%), of whom 13 (0.74%) were naïve and 19 (9.50%) were treatment-experienced. The most common DOR resistance mutations observed among the naïve patients were A98G and K101E (0.2% each), and those among cART-experienced patients were L100I (2.0%), K101E, V108I, H221Y, and P225H (1.5% each). Furthermore, among the naïve patients, less common resistance to DOR (0.7%) compared with that to nevirapine (NVP) (2.1%; p = 0.0013) and rilpivirine (5.40%; p < 0.0001) was observed. For sequences obtained from treatment-experienced patients, the frequency of resistance to DOR (9.5%) was lower than that for efavirenz (25.5%; p < 0.0001) and NVP (26.0%; p < 0.0001). Conclusions The frequency of transmitted drug resistance to DOR is low, allowing for effective treatment of antiretroviral treatment-naïve patients and rapid treatment initiation. In cART-experienced patients, this agent remains an attractive NNRTI option with a higher genetic barrier to resistance.

Emergence of Letermovir-resistant HCMV UL56 mutant during rescue treatment in a liver transplant recipient with ganciclovir-resistant infection HCMV: a case report

Background Human Cytomegalovirus (HCMV) still represents a crucial concern in solid organ transplant recipients (SOTRs) and the use of antiviral therapy are limited by side effects and the selection of viral mutations conferring antiviral drug resistance. Case presentation Here we reported the case of an HCMV seronegative patient with common variable immunodeficiency (CVID), multiple hepatic adenomatosis, hepatopulmonary syndrome and portal hypertension who received a liver transplant from an HCMV seropositive donor. The patient was treated with Valganciclovir (vGCV) and then IV Ganciclovir (GCV) at 5 week post-transplant for uncontrolled HCMV DNAemia. However, since mutation A594V in UL97 gene conferring resistance to ganciclovir was reported, GCV therapy was interrupted. Due to the high toxicity of Foscarnet (FOS) and Cidofovir (CDV), Letermovir (LMV) monotherapy at the dosage of 480 mg per day was administered, with a gradual viral load reduction. However, a relapse of HCMV DNAemia revealed the presence of mutation C325Y in HCMV UL56 gene conferring resistance to LMV. Conclusions In conclusion, even if LMV is an effective and favorable safety molecule it might have a lower genetic barrier to resistance. A warning on the use of LMV monotherapy as rescue treatments for HCMV GCV-resistant infections in transplant recipients is warranted.

Dolutegravir Reported Adverse Drug Reactions: A Systematic Review Protocol

Background: Until recently, the first-line regimen for the management of Human Immunodeficiency Virus (HIV) was Tenofovir (TDF)-Emtricitabine (FTC) and Efavirenz (EFV). However, the use of EFV has now been limited due to adverse neurosensory effects and a low genetic barrier to resistance. This regimen has been replaced by the Dolutegravir (DTG)-based regimen since DTG has a high genetic barrier to resistance. Studies have reported a higher risk of Immune Reconstitution Inflammatory Syndrome (IRIS), weight gain, insomnia, and neural tube defects amongst people who received DTG. This review aims to assess the adverse drug reaction (ADR) profile of Dolutegravir by identifying and classifying Dolutegravir-associated adverse drug reactions.Methods: Studies will be identified from an electronic database search. Studies that are potentially eligible will be selected through screening. Two team members will independently screen all citations, full-text articles, and abstract data; conflicts will be resolved through discussion. The (PRISMA-P) flow diagram that outlines all phases of screening and reasons for exclusion will be used during the selection process. After the selection of the final study sample, a data extraction form will be used as a collection tool. The data will be entered into Cochrane Collaboration Review Manager (RevMan 5.2) for storage and management. All the evidence gathered will be assessed for bias through the use of the Risk of Bias tool RoB 2.0 of Cochrane Collaboration. Reported ADRs will then be classified. We will also provide data for the effect of different demographic factors on ADRs as well as the effects of co-administration of DTG with other drugs on ADRs. We will additionally provide information on how Dolutegravir use in different regimens affects the ADRs. Results from the review will be summarized quantitatively through meta-analysis. A forest plot will be used to present results from the meta-analysis. Conclusion: A review of existing studies will aid in establishing the safety profile of this drug. This review will make significant contributions to healthcare practice. It will aid in improving prescribers' and dispensers’ knowledge of the drug. Additionally, it will also aid in patient education of the potential ADRs to DTG.Systematic review registration DOI: doi.org/10.17605/OSF.IO/Z9YAF

Human Immunodeficiency Virus (HIV) Drug Resistance: A Global Narrative Review

Background: Antiretroviral Therapy (ART) has significantly improved Human Immunodeficiency Virus (HIV) patients’ survival rates. However, the emergence of HIV Drug Resistance (HIVDR) has markedly reduced the effectiveness of Antiretroviral Therapy (ART). Aim: This narrative review was conducted to review published studies on HIV drug resistance and its consequences. Materials and methods: A literature search for this narrative review was carried out and the following databases were used PubMed, Google Scholar, and The Lancet. The cited articles were published from 1999 to 2021. The keywords used in the search of literature included ‘Antiretroviral therapy’, ‘resistance’, and ‘Human Immunodeficiency Virus drug resistance’, ‘HIV’, ‘HIV drug resistance’, ‘HIV vaccines’, and the Boolean word ‘AND’. Results: There is a high prevalence of HIV drug resistance globally that has been associated with some factors such as older age, non-adherence to treatment, long treatment duration, lower cell count and high viral load. HIV drug resistance may lead to treatment failure, prolongation of the time required to achieve viral suppression and leads to increased mortality. Increasing access to viral load monitoring can help mitigate HIV drug resistance. Conclusion: HIV drug resistance is a global threat to public health and has been associated with increased morbidity and mortality. Therefore, there is a need for more research to be carried out and various strategies like the use of antiretrovirals with a high genetic barrier to resistance need to be put in place to prevent further spread resistance. HIVDR must be monitored frequently taking into consideration the geographic variability. There is an urgent need for the development of anti-HIV vaccines that will help to prevent further transmission and spread of HIV.

Using machine learning and big data to explore the drug resistance landscape in HIV

Drug resistance mutations (DRMs) appear in HIV under treatment pressure. DRMs are commonly transmitted to naive patients. The standard approach to reveal new DRMs is to test for significant frequency differences of mutations between treated and naive patients. However, we then consider each mutation individually and cannot hope to study interactions between several mutations. Here, we aim to leverage the ever-growing quantity of high-quality sequence data and machine learning methods to study such interactions (i.e. epistasis), as well as try to find new DRMs. We trained classifiers to discriminate between Reverse Transcriptase Inhibitor (RTI)-experienced and RTI-naive samples on a large HIV-1 reverse transcriptase (RT) sequence dataset from the UK (n ≈ 55, 000), using all observed mutations as binary representation features. To assess the robustness of our findings, our classifiers were evaluated on independent data sets, both from the UK and Africa. Important representation features for each classifier were then extracted as potential DRMs. To find novel DRMs, we repeated this process by removing either features or samples associated to known DRMs. When keeping all known resistance signal, we detected sufficiently prevalent known DRMs, thus validating the approach. When removing features corresponding to known DRMs, our classifiers retained some prediction accuracy, and six new mutations significantly associated with resistance were identified. These six mutations have a low genetic barrier, are correlated to known DRMs, and are spatially close to either the RT active site or the regulatory binding pocket. When removing both known DRM features and sequences containing at least one known DRM, our classifiers lose all prediction accuracy. These results likely indicate that all mutations directly conferring resistance have been found, and that our newly discovered DRMs are accessory or compensatory mutations. Moreover, apart from the accessory nature of the relationships we found, we did not find any significant signal of further, more subtle epistasis combining several mutations which individually do not seem to confer any resistance.

High genetic barrier to escape from human polyclonal SARS-CoV-2 neutralizing antibodies

The number and variability of the neutralizing epitopes targeted by polyclonal antibodies in SARS-CoV-2 convalescent and vaccinated individuals are key determinants of neutralization breadth and, consequently, the genetic barrier to viral escape. Using chimeric viruses and antibody-selected viral mutants, we show that multiple neutralizing epitopes, within and outside the viral receptor binding domain (RBD), are variably targeted by polyclonal plasma antibodies and coincide with sequences that are enriched for diversity in natural SARS-CoV-2 populations. By combining plasma-selected spike substitutions, we generated synthetic polymutant spike proteins that resisted polyclonal antibody neutralization to a similar degree as currently circulating variants of concern (VOC). Importantly, by aggregating VOC-associated and plasma-selected spike substitutions into a single polymutant spike protein, we show that 20 naturally occurring mutations in SARS-CoV-2 spike are sufficient to confer near-complete resistance to the polyclonal neutralizing antibodies generated by convalescents and mRNA vaccine recipients. Strikingly however, plasma from individuals who had been infected and subsequently received mRNA vaccination, neutralized this highly resistant SARS-CoV-2 polymutant, and also neutralized diverse sarbecoviruses. Thus, optimally elicited human polyclonal antibodies against SARS-CoV-2 should be resilient to substantial future SARS-CoV-2 variation and may confer protection against future sarbecovirus pandemics.

Selection of Human Cytomegalovirus Mutants with Resistance against PDGFRα-Derived Entry Inhibitors

The human cytomegalovirus (HCMV) infects fibroblasts via an interaction of its envelope glycoprotein gO with the cellular platelet-derived growth factor receptor alpha (PDGFRα), and soluble derivatives of this receptor can inhibit viral entry. We aimed to select mutants with resistance against PDGFRα-Fc and the PDGFRα-derived peptides GT40 and IK40 to gain insight into the underlying mechanisms and determine the genetic barrier to resistance. An error-prone variant of strain AD169 was propagated in the presence of inhibitors, cell cultures were monitored weekly for signs of increased viral growth, and selected viruses were tested regarding their sensitivity to the inhibitor. Resistant virus was analyzed by DNA sequencing, candidate mutations were transferred into AD169 clone pHB5 by seamless mutagenesis, and reconstituted virus was again tested for loss of sensitivity by dose-response analyses. An S48Y mutation in gO was identified that conferred a three-fold loss of sensitivity against PDGFRα-Fc, a combination of mutations in gO, gH, gB and gN reduced sensitivity to GT40 by factor 4, and no loss of sensitivity occurred with IK40. The resistance-conferring mutations support the notion that PDGFRα-Fc and GT40 perturb the interaction of gO with its receptor, but the relatively weak effect indicates a high genetic barrier to resistance.

Population Genetic Structure of Raccoons as a Consequence of Multiple Introductions and Range Expansion in the Boso Peninsula, Japan

Raccoon (Procyon lotor) is a globally introduced invasive carnivore. Although controlling feral raccoon populations is important to reduce serious threats to local ecosystems, raccoons are not under rigid population control in Europe and Japan. We examined the D-loop and nuclear microsatellite regions to identify spatially explicit and feasible management units for effective population control and further range expansion retardation. Through the identification of five mitochondrial DNA haplotypes and three nuclear genetic groups, we identified at least three independent introductions, range expansion, and subsequent genetic admixture in the Boso Peninsula. Admitting that the currently recognizable two genetic clusters can be treated as different management units, these management units will soon fuse to a single but large population to which the effective population control will no longer be applicable due to the absence of a genetic barrier between southern and northern Chiba Prefecture.

Interaction analysis of statistically enriched mutations identified in Cameroon recombinant subtype CRF02_AG that can influence the development of Dolutegravir drug resistance mutations

Background The Integrase (IN) strand transfer inhibitor (INSTI), Dolutegravir (DTG), has been given the green light to form part of first-line combination antiretroviral therapy (cART) by the World Health Organization (WHO). DTG containing regimens have shown a high genetic barrier against HIV-1 isolates carrying specific resistance mutations when compared with other class of regimens. Methods We evaluated the HIV-1 CRF02_AG IN gene sequences from Cameroon for the presence of resistance-associated mutations (RAMs) against INSTIs and naturally occurring polymorphisms (NOPs), using study sequences (n = 20) and (n = 287) sequences data derived from HIV Los Alamos National Laboratory database. The possible impact of NOPs on protein structure caused by HIV-1 CRF02_AG variations was addressed within the context of a 3D model of the HIV-1 IN complex and interaction analysis was performed using PyMol to validate DTG binding to the Wild type and seven mutant structures. Results We observed 12.8% (37/287) sequences to contain RAMs, with only 1.0% (3/287) of the sequences having major INSTI RAMs: T66A, Q148H, R263K and N155H. Of these,11.8% (34/287) of the sequences contained five different IN accessory mutations; namely Q95K, T97A, G149A, E157Q and D232N. NOPs occurred at a frequency of 66% on the central core domain (CCD) position, 44% on the C-terminal domain (CTD) position and 35% of the N-terminal domain (NTD) position. The interaction analysis revealed that DTG bound to DNA, 2MG ions and DDE motif residues for T66A, T97A, Q148H, N155H and R263K comparable to the WT structure. Except for accessory mutant structure E157Q, only one MG contact was made with DTG, while DTG had no MG ion contacts and no DDE motif residue contacts for structure D232N. Conclusions Our analysis indicated that all RAM’s that resulted in a change in the number of interactions with encompassing residues does not affect DTG binding, while accessory mutations E157Q and D232N could affect DTG binding leading to possible DTG resistance. However, further experimental validation is required to validate the in silico findings of our study.