An observational study of high‐ and low‐abundance anti‐retroviral resistance mutations among treatment‐naïve people living with HIV in New Zealand between 2012 and 2017

HIV resistance genotyping detects drug resistance mutations (DRM) in ≥20% of circulating virus within an infected individual (high‐abundance DRM). Deep sequencing also detects DRM in smaller viral subpopulations (low‐abundance DRM), although these are of uncertain importance. In this retrospective analysis of 292 treatment‐naïve patients, high‐abundance DRM were present in 30/292 (10%) patients, but only one (0.3%) had resistance to first‐line anti‐retrovirals. Low‐abundance DRM were present in 36/247 (15%) patients, but none who received anti‐retrovirals for which these were present had virologic failure. These findings demonstrate that starting first‐line therapy in treatment‐naïve patients need not be delayed while awaiting resistance testing.     

Long‐term follow up of HIV‐1‐infected Korean haemophiliacs,after infection from a common source of virus

In the early 1990s, 20 haemophiliacs (HPs) were infected with a common source of HIV‐1 viruses through the contaminated clotting factor IX. The aim of this study is to review 20 HPs infected with a common source of virus. The enrolled patients have been consecutively treated with Korean red ginseng (KRG), zidovudine (ZDV) or two‐drug therapy and highly active antiretroviral therapy (HAART). We determined full‐length pol gene over 20 years and human leukocyte antigen (HLA) class I with peripheral blood mononuclear cells and reviewed medical records. Eighteen HPs experienced various opportunistic infections or clinical manifestations. There were significant inverse correlations between the HLA prognostic score and the annual decrease in CD4+ T‐cell counts prior to HAART (AD) (P < 0.05) and the amount of KRG and the AD (P < 0.01). From 1998, the HPs had been treated with HAART. Each of the two patients died without and with HAART regimen respectively. At present, 16 HPs have been alive with HAART. Among the 16 HPs, 12 and 4 are on HAART‐plus‐KRG and HAART only respectively. Eleven HPs including 2 HPs with G‐to‐A hypermutations had revealed resistance mutations. Ten and two HPs have shown poor adherence and incomplete viral suppres‐sion on HAART respectively. Virological failure based on WHO guidelines was not observed on KRG‐plus‐HAART. Two HPs revealed additional resistance mutations against two classes on KRG‐plus‐HAART. As a nationwide study, we first report overall features on clinical course of Korean haemophiliacs. Further education on the importance of drug adherence is needed.     

Long‐term follow‐up of 11 protease inhibitor (PI)‐naïve and PI‐treated HIV‐infected patients harbouring virus with insertions in the HIV‐1 protease gene

Objectives

Amino acid insertions in the protease gene have been reported rarely, and mainly in patients receiving protease inhibitors (PIs). The aim of the study was to assess the long‐term viro‐immunological follow‐up of HIV‐infected patients harbouring virus with protease insertions.

Methods

Cases of virus exhibiting protease insertions were identified in routine resistance genotyping tests. Therapeutic, immunological and virological data were retrospectively collected.

Results

Eleven patients harbouring virus with a protease gene insertion were detected (prevalence 0.24%), including three PI‐naïve patients. The insertions were mainly located between codons 33 and 39 and associated with surrounding mutations (M36I/L and R41K). The three PI‐naïve patients were infected with an HIV‐1 non‐B subtype. Follow‐up of these PI‐naïve patients showed that the insert‐containing virus persisted for several years, was archived in HIV DNA, and displayed a reduced viral replicative capacity with no impact on resistance level. Of the eight PI‐experienced patients, 63% were infected with HIV‐1 subtype B; one had been antiretroviral‐free for 5 years and seven were heavily PI‐experienced (median duration of follow‐up 24 months; range 10–62 months). The protease insertion was selected under lopinavir in four patients and under darunavir in one, in the context of major PI‐resistance mutations, and following long‐term exposure to PIs. The insert‐containing virus persisted for a median of 32 months (range 12–62 months) and displayed no specific impact on phenotypic resistance level or viral replicative capacity.

Conclusion

Our data, obtained during long‐term follow‐up, show that insertions in the protease gene do not seem to have an impact on resistance level. This finding supports the recommendation of PI‐based regimens, although further work is required to confirm it.     

Long‐term (96‐week) follow‐up of antiretroviral‐naïve HIV‐infected patients treated with first‐line lopinavir/ritonavir monotherapy in the MONARK trial*

Background

The toxicities, cost and complexity of triple combinations warrant the search for other treatment options, such as boosted protease inhibitor (PI) monotherapy. MONotherapy AntiRetroviral Kaletra (MONARK) is the first randomized trial comparing lopinavir/ritonavir monotherapy to triple combination therapy with zidovudine/lamivudine and lopinavir/ritonavir in antiretroviral‐naïve patients.

Methods

A total of 136 antiretroviral‐naïve patients, with a CD4 cell count above 100 cells/μL and a plasma HIV RNA below 100 000 HIV‐1 RNA copies/mL, were randomized and dosed with either lopinavir/ritonavir monotherapy (n=83) or lopinavir/ritonavir+zidovudine/lamivudine (n=53). We focus here on patients in the lopinavir/ritonavir monotherapy arm followed to week 96. The intent‐to‐treat (ITT) analysis initially involved all patients randomized to lopinavir/ritonavir monotherapy (n=83), and then focused on patients who had an HIV RNA <50 copies/mL at week 48 (n=56).

Results

At week 96, 39 of 83 patients (47%) had HIV RNA <50 copies/mL, five of 83 had HIV RNA between 50 and 400 copies/mL, and three of 83 had HIV RNA >400 copies/mL. Focusing on the 56 patients with an HIV RNA <50 copies/mL at week 48, 38 of 56 patients (68%) had a sustained HIV RNA <50 copies/mL to week 96. To week 96, a total of 28 patients (34%) had discontinued the study treatment. In addition, the allocated treatment was changed for seven patients. PI‐associated resistance mutations were evident in five of 83 patients in the monotherapy arm from baseline to week 96.

Conclusion

By ITT analysis, 39 of the 83 patients initially randomized to lopinavir/ritonavir monotherapy had HIV RNA <50 copies/mL at week 96. The occurrence in some patients of low‐level viraemia (50–500 copies/mL) may increase the risk of drug resistance. First‐line lopinavir/ritonavir monotherapy cannot be systematically recommended.     

中国部分地区人免疫缺陷病毒耐药及其影响因素分析

目的分析吉林、黑龙江、河南、陕西、辽宁、内蒙古、云南7省人类免疫缺陷病毒(HIV)感染者耐药变异情况及其影响因素。方法2005年5月至9月将中国医科大学附属第一医院艾滋病研究所问卷调查的718例HIV感染者治疗和漏服情况,RT-PCR和套式PCR扩增HIVpol区基因,逆转录酶和蛋白酶基因序列,与国际HIV耐药数据库比对辨别耐药变异。结果治疗组HIV抑制情况显著好于未治疗感染者(P<0.01),但其耐药变异高于未治疗组(P<0.05);抗病毒治疗6个月以内组耐药突变率显著低于6个月以上组(P<0.01);依从性好的患者HIV耐药突变率明显低于依从性差的患者(P<0.05),HIV抑制情况明显优于依从性差的患者(P<0.05);D4T/3TC/NVP方案HIV抑制效果明显优于其他方案(P<0.01),HIV耐药突变率也较低(P<0.05)。结论随着抗病毒治疗时间延长,耐药突变率显著增高,服药依从性与耐药突变显著相关。一线治疗方案首选D4T/3TC/NVP。     

Transmitted drug-resistant HIV-1 in primary HIV-1 infection; incidence, evolution and impact on response to antiretroviral therapy

OBJECTIVES: The aim of the study was to determine the incidence and persistence of transmitted drug-resistant HIV-1 in an incident cohort between 2000 and 2004, and to investigate the impact of transmitted drug-resistant HIV-1 on the response to antiretroviral therapy (ART). METHODS: A prospective, nonrandomized study was carried out on 140 individuals identified with primary HIV-1 infection (PHI). PHI was defined as an HIV-positive antibody test with an HIV antibody-negative result in the prior 6 months (n = 69); positive HIV DNA in the absence of antibody (n = 30); an evolving titre positive HIV antibody test (n = 23), or an incident 'detuned' assay (B clade viruses only) (n = 18). Genotypic resistance testing was performed at baseline, following ART and annually over a 4-year period. RESULTS: The prevalence of transmitted drug-resistant HIV-1 infection between January 2000 and June 2004 was nine in 140 (6.0%) and the annual incidence was stable. Seven of these nine patients had a single point mutation conferring single-class drug resistance and the other two patients had multiple mutations conferring multiclass drug resistance (MDR). In eight of the nine cases, mutations conferring drug resistance persisted for more than 12 months off therapy. In contrast to transmitted MDR HIV-1, the virological response to initial ART and CD4 decline were comparable in those with wild-type virus, virus with 'polymorphisms' (secondary mutations) and virus with single drug-resistance mutations. CONCLUSIONS: The incidence of transmitted drug-resistant HIV remained stable and low over a 4-year period. Although MDR remains rare, its presence significantly affects the response to first-line ART, predisposes towards the accumulation of new resistance mutations and is associated with a more rapid CD4 decline.     

Hepatitis B e antigen‐suppressing mutations enhance the replication efficiency of adefovir‐resistant hepatitis B virus strains

Summary. Hepatitis B e antigen (HBeAg) negative hepatitis B virus (HBV) infections caused by precore (PC) or basal core promoter (BCP) mutations are associated with disease progression and complications. PC or BCP mutations may enhance the replication capacity of distinct drug‐resistance‐associated polymerase mutations, but their effect on adefovir‐resistant HBV mutants is unclear. Importantly, BCP mutations were an independent risk factor for virological breakthrough in lamivudine‐resistant patients treated with adefovir. We aimed at addressing the functional consequences of PC and BCP mutations on the replication and drug susceptibility of adefovir‐resistant HBV mutants. Therefore, HBV constructs with wild type (WT) or adefovir‐resistant rtN236T, rtA181V and rtA181T mutations, with or without concomitant PC or BCP mutations, were analysed in vitro using molecular assays. The adefovir‐resistant polymerase mutations rtN236T, rtA181V and rtA181T showed a drastically reduced viral replication compared with WT. Interestingly, additional PC or BCP mutations enhanced the reduced replication efficacy of adefovir‐resistant constructs and restored HBV replication to WT level. HBV rtA181T mutants displayed abolished hepatitis B surface antigen (HBsAg) secretion, owing to a sW172* stop codon in the overlapping envelope gene. All rtN236T‐ or rtA181V/T‐containing constructs, regardless of concomitant PC or BCP mutations, were resistant to adefovir, but remained susceptible to telbivudine, entecavir and tenofovir. In conclusion, adefovir drug resistance mutations reduced viral replication, which can be significantly increased by additional HBeAg‐suppressing PC or BCP mutations. Because increased HBV replication in HBeAg‐negative patients has been associated with an unfavourable clinical course, close monitoring appears indispensable during adefovir treatment in HBeAg‐negative patients.     

Totally drug‐resistant tuberculosis and adjunct therapies

The first cases of totally drug‐resistant (TDR) tuberculosis (TB) were reported in Italy 10 years ago; more recently, cases have also been reported in Iran, India and South Africa. Although there is no consensus on terminology, it is most commonly described as ‘resistance to all first‐ and second‐line drugs used to treat TB’. Mycobacterium tuberculosis (M.tb) acquires drug resistance mutations in a sequential fashion under suboptimal drug pressure due to monotherapy, inadequate dosing, treatment interruptions and drug interactions. The treatment of TDR‐TB includes antibiotics with disputed or minimal effectiveness against M.tb, and the fatality rate is high. Comorbidities such as diabetes and infection with human immunodeficiency virus further impact on TB treatment options and survival rates. Several new drug candidates with novel modes of action are under late‐stage clinical evaluation (e.g. delamanid, bedaquiline, SQ109 and sutezolid). ‘Repurposed’ antibiotics have also recently been included in the treatment of extensively drug resistant TB. However, because of mutations in M.tb, drugs will not provide a cure for TB in the long term. Adjunct TB therapies, including therapeutic vaccines, vitamin supplementation and/or repurposing of drugs targeting biologically and clinically relevant molecular pathways, may achieve better clinical outcomes in combination with standard chemotherapy. Here, we review broader perspectives of drug resistance in TB and potential adjunct treatment options.     

Prevalence and clinical characterization of patients with acute hepatitis B induced by lamivudine‐resistant strains

Background and Aims: Acute hepatitis caused by lamivudine (LMV)‐resistant strains has not been reported, and the clinical impact of LMV‐resistant strains on acute hepatitis is not known. The aim of this study was to investigate the molecular and clinical characteristics of patients with acute hepatitis B caused by LMV‐resistant strains. Methods: Forty‐five patients with acute hepatitis B were studied. Hepatitis B virus (HBV) subgenotypes and LMV‐resistance mutations were determined by direct sequencing of the preS and polymerase regions, respectively. Results: HBV subgenotypes A2 (n = 18), B1 (n = 1), B2 (n = 3), B3 (n = 2), C1 (n = 1), C2 (n = 19) and C6 (n = 1) were detected in patients with acute hepatitis. LMV‐resistance mutations were detected in two patients. LMV‐resistance mutations (L180M, M204I) were detected in a patient with subgenotype C2 who had acute self‐limited hepatitis. The other patient with LMV‐resistance mutations (L180M, M204V) was infected with subgenotype A2 and had severe hepatitis. Conclusion: LMV‐resistant strains are rare, but they are starting to be found in patients with acute hepatitis B. Surveillance for detecting drug‐resistant HBV strains would be important for clinical practice.     

Drug resistance profiles for the HIV integrase gene in patients failing raltegravir salvage therapy

Objectives

Recent data showed the selection of mutations in the integrase gene, mainly involving position 148 or 155, in patients displaying virological failure (VF) on raltegravir (RAL) therapy. Here, we describe the development of RAL resistance, in both plasmatic and cellular compartments, in three heavily pretreated HIV‐infected patients failing RAL‐containing regimens.

Methods

Three of 17 patients receiving RAL displayed VF. The entire integrase gene, isolated from plasma and peripheral blood mononuclear cells (PBMC), was sequenced. A clonal analysis was performed in one patient at the time of VF.

Results

At the time of VF, RAL‐resistance mutations were selected: (i) Q148R in patients 1 and 3; (ii) T66A and E92Q in patient 2. A gradual accumulation of new mutations was observed in all patients, including G140S, Q148H and N155H in patient 1, L74I in patient 2, and G140S in patient 3. Clonal analysis showed the coexistence, in patient 1, of the two common resistance pathways (mutations Q148R/H and N155H) found in distinct quasi‐species. In addition, RAL‐resistance mutations were detected in HIV DNA in all patients.

Conclusions

Having rapidly established, resistance to RAL evolves and diversifies, and is likely to impact the efficacy of subsequently used second‐generation integrase inhibitors. Moreover, RAL‐resistance mutations can be archived early in PBMC.     

NS3 protease polymorphisms and genetic barrier to drug resistance of distinct hepatitis C virus genotypes from worldwide treatment‐naïve subjects

Hepatitis C virus (HCV) NS3 protease inhibitors have been primarily designed against genotype 1, the one with the lowest response to dual therapy. However, less evidence of their efficacy on non‐1 genotypes is available, and any such information is mostly concentrated on genotypes 2‐4. This study evaluated HCV protease resistance profiles in the major six HCV genotypes and identified genetic barrier (GB) profiles to each available protease inhibitor across HCV strains from different locations worldwide. We obtained 15 099 HCV sequences from treatment‐naïve subjects retrieved at the Los Alamos HCV Sequence Database. The wild‐type codons of different HCV genotypes were used to analyse the smallest number of nucleotide substitution steps required for changing that codon to the closest one associated with drug resistance. The 36L and 175L RAVs were found as genetic signatures of genotypes 2‐5, while the 80K RAV was found in all genotype 5 sequences. Genotypes 4 and 6 showed a higher GB to RAV mutations conferring resistance to telaprevir, while genotypes 2‐5 presented baseline resistance to that drug, carrying the 36L mutation. Genotype 4 had a higher GB to simeprevir resistance, requiring three substitutions to acquire the 155K mutation. Subtype 1b showed a higher GB than subtype 1a to resistance for most PIs, with RAVs at codons 36 and 155. Geographic disparities were also found in frequencies of certain RAVs in genotypes 2 and 3. Under a scenario of unprecedented evolution of anti‐HCV direct‐acting agents, the genetic composition of the circulating HCV sequences should be evaluated worldwide to choose the most appropriate/feasible therapeutic schemes with the highest genetic barriers to resistance.     

HIV-1的耐药基因突变

人免疫缺陷病毒(HIV)耐药,是影响艾滋病抗病毒治疗效果的主要因素。随着抗病毒治疗的发展及新型靶点抗病毒药物的临床应用,已确定了200多个各种类型HIV耐药相关的基因突变,它们对于耐药及病毒的生物学特性产生不同程度的影响。该文对HIV的耐药基因突变,及其对耐药的作用和对复制适应性的影响进行了综述,并分析了今后耐药性研究应关注的重点。     

Successful optimization of antiretroviral regimens in treatment‐experienced people living with HIV undergoing liver transplantation

Modern antiretroviral therapy (ART) extends life expectancy for people living with HIV (PLWH). However, most older PLWH (≥50 years) “aged” with HIV and were exposed to historical HIV care practices and older, more toxic ART. In PLWH with exposure to older and multiple ART regimens, the drug interactions between ART frequently used in treatment‐experienced persons and commonly used immunosuppressants remain a significant challenge. However, the advent of newer ART classes (eg, integrase non‐strand transfer inhibitors) and more advanced HIV genetic resistance testing may allow optimization of ART regimens with minimal drug interactions. Here, we present a case series of three PLWH whose complicated ART interacted (or was at risk for interacting) with their post–liver transplant immunosuppression. After a review of their proviral DNA resistance testing, they successfully transitioned onto safer integrase non‐strand transfer inhibitor‐containing ART regimens without viral blips or evidence of organ rejection.