Factors associated with a low HIV reservoir in patients with prolonged suppressive antiretroviral therapy.

OBJECTIVES: The relevance of low-level HIV DNA in patients who have undergone prolonged therapy is not well understood. The objective of this study was to determine factors that influence the establishment of low-level HIV DNA in long-term treated patients (excluding treatment since acute infection). METHODS: This was a cross-sectional study involving 243 patients receiving highly active antiretroviral therapy (HAART) for ≥6 months (median: 9 years of treatment) with plasma HIV RNA <50 copies/mL at the study timepoint, for whom total DNA measurements were performed. Patients treated since early acute infection or receiving cancer chemotherapeutic/immunosuppressive agents were excluded from the study. RESULTS: Overall, the median HIV DNA was 372 copies/10(6) peripheral blood mononuclear cells (PBMCs). Forty-seven patients had levels of HIV DNA below the limit of detection and 58 patients had low-level HIV DNA (<100 copies/10(6) PBMCs). In multivariate analysis, a low total HIV DNA in HAART-treated patients was clearly associated with a low HIV RNA pre-therapeutic viral load (P < 0.0001), regardless of the cut-off used. CONCLUSIONS: These results may be helpful to identify candidates for future trials aiming at a functional cure of HIV infection, since low total HIV DNA levels will most likely be a prerequisite of successful immunological control of HIV replication.

Molecular characterization of herpes simplex virus 2 strains by analysis of microsatellite polymorphism.

The complete 154-kbp linear double-stranded genomic DNA sequence of herpes simplex virus 2 (HSV-2), consisting of two extended regions of unique sequences bounded by a pair of inverted repeat elements, was published in 1998 and since then has been widely employed in a wide range of studies. Throughout the HSV-2 genome are scattered 150 microsatellites (also referred to as short tandem repeats) of 1- to 6-nucleotide motifs, mainly distributed in noncoding regions. Microsatellites are considered reliable markers for genetic mapping to differentiate herpesvirus strains, as shown for cytomegalovirus and HSV-1. The aim of this work was to characterize 12 polymorphic microsatellites within the HSV-2 genome by use of 3 multiplex PCR assays in combination with length polymorphism analysis for the rapid genetic differentiation of 56 HSV-2 clinical isolates and 2 HSV-2 laboratory strains (gHSV-2 and MS). This new system was applied to a specific new HSV-2 variant recently identified in HIV-1-infected patients originating from West Africa. Our results confirm that microsatellite polymorphism analysis is an accurate tool for studying the epidemiology of HSV-2 infections.

Frequency of amino acid changes associated with resistance to attachment inhibitor BMS-626529 in R5- and X4-tropic HIV-1 subtype B.

OBJECTIVES: Resistance to attachment inhibitor BMS-626529, which inhibits the binding of HIV to CD4, involves mutations in the HIV-1 gp120 gene. There is a lack of information on the primary resistance of HIV-1 subtype B to attachment inhibitors, so we decided to investigate. METHODS: Sequences from 109 attachment-inhibitor-naive patients infected with HIV-1 subtype B were analysed for the presence of previously described in vivo resistance mutations associated with attachment inhibitor BMS-626529 and tropism determination. RESULTS: The M426L substitution associated with a reduced efficacy of the attachment inhibitor BMS-626529 was present at 7.3%. There was no difference in mutation distribution according to virus tropism (R5 or X4). CONCLUSIONS: The attachment inhibitor BMS-626529 is suitable for most patients infected with HIV-1 subtype B.

HIV-1 genome is often defective in PBMCs and rectal tissues after long-term HAART as a result of APOBEC3 editing and correlates with the size of reservoirs.

OBJECTIVES: Precise characterization of viruses present in reservoirs in long-term pretreated patients will be a major issue to consider in the context of viral eradication. We assessed the frequency of defective viruses present in cellular reservoirs. METHODS: Peripheral blood mononuclear cells (PBMCs) and rectal biopsy samples were compared between five patients on successful long-term highly active antiretroviral therapy (HAART) (>7 years without blips) and five untreated patients. Molecular cloning and sequencing of the reverse transcriptase region were used to detect the presence of and quantify in-frame stop codons in HIV quasi-species. The relationship between the size of the reservoir and the frequency of defective genomes was assessed. RESULTS: Defective genomes were systematically detected in all patients on long-term HAART in both compartments (PBMCs and rectal tissues), with a higher level of defective genomes per sample compared with PBMCs of untreated patients. A high level of defective genomes was correlated with a small size of HIV proviral DNA. Regarding the nucleotide context, guanine (G) to adenine (A) substitution at tryptophan positions was responsible for the appearance of 89% of all in-frame stop codons in the context of G-to-A hypermutation, likely reflecting APOBEC3 footprints on the viral genome. CONCLUSIONS: We propose a scenario whereby defective genomes accumulate during HAART treatment, eventually reaching a viral extinction threshold. In the context of viral eradication, measurement of the relative amounts of defective and non-defective viruses (by molecular cloning and ultradeep sequencing) should be used as a new criterion for eradicating HIV.

Genetic analysis and putative role in resistance to antivirals of the human cytomegalovirus DNA polymerase UL44 processivity factor.

BACKGROUND: The human cytomegalovirus (HCMV) DNA polymerase is composed of the UL54 catalytic subunit and the UL44 accessory protein. UL44 increases the processivity of polymerase along the DNA template during replication and, incidentally, is a substrate for the UL97 phosphotransferase. The molecular mechanisms of HCMV resistance to antiviral drugs interfering with viral DNA synthesis reported so far only rely on the presence of amino acid changes within the UL97 and UL54 viral enzymes. We aimed to describe the natural polymorphism of UL44 and to analyse the changes of its amino acids potentially associated with HCMV resistance to antivirals. METHODS: The full-length UL44 gene sequence was compared to that of four reference strains (including the AD169 strain) and 43 clinical strains from patients who had not received any previous anti-HCMV treatment, and 25 blood samples from 15 HCMV-infected patients experiencing therapeutic failure and exhibiting genotypic traits of HCMV resistance to antivirals. RESULTS: Overall, seven different amino acid changes associated with natural polymorphisms were identified among the 433 residues of the UL44 protein, occurring at a frequency of 2.1% for five of them and 10.6% for the double change G296S+L319I. The analysis of the HCMV strains exhibiting genotypic resistance to antivirals did not show any changes in UL44 that had significant association with resistance mutations of UL97 and/or UL54. CONCLUSIONS: UL44 processivity factor exhibits a very low polymorphism that does not concern the assumed functional domains of the protein. From this preliminary study, UL44 does not seem to be involved in HCMV resistance to antivirals.

Rapid determination of antiviral drug susceptibility of herpes simplex virus types 1 and 2 by real-time PCR.

An antiviral drug susceptibility assay of herpes simplex virus (HSV) was developed using real-time PCR quantification of intracellular viral DNA load. The number of HSV DNA copies within Vero cells after 24 h infection was strongly correlated with the number of plaques obtained after 72 h infection. Antiviral drug susceptibility of HSV was determined after virus growth for 24h by measuring the reduction of intracellular HSV DNA in the presence of increasing concentrations of either acyclovir (ACV) or foscarnet (PFA). This assay required neither preliminary titration of infectious stock nor follow-up of cytopathic effect. The 50% inhibitory concentrations (IC50s) obtained with 27 isolates of HSV types 1 and 2 by using this test were significantly correlated with those obtained in parallel with plaque reduction assay taken as the reference method (r=0.91, p<0.0001 and r=0.51, p=0.009 for ACV and PFA, respectively). The threshold real-time PCR IC50s for ACV and PFA resistance did not differ according to HSV type and were determined to be 1.0 and 100 microM, respectively. The real-time PCR susceptibility assay reported here is rapid, reproducible, applicable for HSV-1 as well as HSV-2, and suitable for automation.

Management of multidrug-resistant CMV infection in immunocompromised patients: case report of a heart-transplant recipient and review of the literature.

Cytomegalovirus (CMV) remains a leading cause of morbidity after solid organ transplantation. The efficiency of antivirals for the treatment of CMV infections may be hampered because of the emergence of CMV resistance to antivirals. The development of CMV multidrug resistance, which remains uncommon but does occur, constitutes a clinically challenging complication and may contribute to difficult therapeutic management and adverse clinical outcome. We report here the observation of the emergence of a multidrug-resistant CMV infection in a heart-transplant recipient and review the literature on similar cases to identify the potential strategies for the successful management of CMV multidrug resistance among immunocompromised patients.

HIV and antiretroviral drug distribution in plasma and fat tissue of HIV-infected patients with lipodystrophy.

OBJECTIVE: To determine HIV and antiretroviral drug distribution in plasma and fat tissue of HIV-infected patients with lipodystrophy. METHODS: Twenty-three consecutive HIV-infected patients (median age, 43 years; male:female ratio, 18:5; median CD4 cell count, 419 x 10(6)/l) undergoing Coleman's lipostructure were enrolled prospectively in this study. HIV-1 RNA and plasma concentration of antiretroviral drugs were determined blindly in plasma and adipocyte lysate samples. HIV-1 proviral DNA was detected by nested PCR in fresh frozen adipocytes. RESULTS: Mean plasma HIV-1 RNA was significantly higher than that in adipocyte lysate samples (this was below the limit of detection in all patients tested). HIV-1 proviral DNA was positive in two out of 18 adipocyte samples with a level between 2 and 5 copies; the distribution seemed to be specific and comparable within each therapeutic class--protease inhibitors (PI) or non-nucleoside reverse transcriptase inhibitors (NNRTI). NNRTI concentrations in adipocyte lysates were approximately 100-fold higher than those of PI. Efavirenz may accumulate in fat tissue as a function of treatment duration. CONCLUSION: Our results suggest that HIV does not replicate and does not integrate its genome in fat tissue in patients with fat redistribution abnormalities. In patients with effective nadir plasma concentrations of PI and NNRTI, determination of concentration in adipocyte lysates suggests that PI may diffuse in fat tissue with the same pattern of distribution for all structurally related components tested. NNRTI present a high affinity for fat tissue and may accumulate in this compartment.

Quantification of Kaposi's sarcoma-associated herpesvirus in blood, oral mucosa, and saliva in patients with Kaposi's sarcoma.

The aims of this study were to measure Kaposi's sarcoma-associated herpesvirus (KSHV) load in oral mucosa and blood and to determine their relationship with clinical activity of KS in both AIDS-Kaposi's sarcoma (KS) and HIV-unrelated KS patients. Among AIDS patients, KSHV viral load in peripheral blood mononuclear cells (PBMCs) was higher in patients with active KS than in patients with KS in complete remission. In HIV-unrelated KS patients, KSHV viral load in PBMCs was not correlated with clinical stage. Thus, monitoring KSHV viral load in PBMCs could be useful, particularly in the context of HIV infection. In patients with HIV-unrelated KS, KSHV viral load in oral compartments can be very high even in patients with nonactive KS, implying that patients with nonactive KS are still a potential source of transmission of KSHV through oral contact.

Human cytomegalovirus (CMV) susceptibility to currently approved antiviral drugs does not impact on CMV terminase complex polymorphism.

Currently approved anti-human cytomegalovirus (CMV) drugs, all targeting the viral DNA polymerase, are associated with significant toxicities and emergence of drug resistance. In this context, CMV terminase complex constitutes a promising target for novel antiviral compounds. In this study, we describe the low natural polymorphism (interstrain identity >97.7% at both nucleotide and amino acid levels) of the terminase subunits pUL56 and pUL89, and the portal protein pUL104, among 63 CMV clinical strains, and we show that the CMV resistance profile to current DNA polymerase inhibitors has no impact on the natural polymorphism of CMV terminase complex. These results support the idea that both CMV clinical strains exhibiting either susceptibility or resistance to current CMV DNA polymerase inhibitors are comparably sensitive to novel inhibitors of CMV terminase complex, such as letermovir.

Polymorphism of gp41 glycoprotein might influence the progression to disease in HIV-1 infection.

We analysed the impact of envelope glycoprotein gp41 polymorphism on the persistence of long-term nonprogressor (LTNP) status in 59 HIV-1-infected individuals over a period of time exceeding 6 years. The presence of a leucine at the codon 830, instead of the predominant isoleucine residue, was significantly associated with nonprogression, independently of the presence of two particular classes of antigp41 antibodies (antigp41 IgG2 and anti-SWSNKS peptide) previously reported as markers of LTNP status.

Surveillance of herpes simplex virus resistance to antivirals: a 4-year survey.

Herpes simplex virus (HSV) resistance to antivirals constitutes a therapeutic challenge, especially among immunocompromised patients. This observational survey on HSV resistance to antivirals was conducted retrospectively over a 4-year period (2008-2012). A total of 211 HSV-positive clinical samples (94 HSV-1 and 117 HSV-2) recovered from 139 patients (11 immunocompetent patients, 85 immunocompromised patients, and 43 patients with unknown immune status) with suspected HSV drug-resistance were analyzed for acyclovir and foscarnet susceptibility. Antiviral resistance testing consisted in a two-step procedure including a first-step genotypic assay, based on UL23 (thymidine kinase, TK) and UL30 (Pol) gene sequencing, and a second-step phenotypic assay (i.e., plaque reduction assay) performed when unpreviously described mutations were detected. As a whole, susceptibility and resistance to antivirals were evidenced for 58 (30.7%) and 86 (45.5%) HSV, respectively, whereas antiviral profile remained undetermined for 45 (23.8%) HSV. The prevalence of drug resistance was significantly higher among HSV-2 isolates than among HSV-1 isolates (53.8% vs. 34.9%; p=0.012). The majority (i.e., 79.7%) of cases of ACV resistance conferred by TK mutations resulted from UL23 gene frameshift reading. Apart from the changes surely related to natural polymorphism or drug-resistance, 91 unpreviously reported mutations were identified in TK and Pol, including 51 potential natural polymorphisms, 22 mutations likely conferring resistance to antivirals, and 18 mutations of unclear significance.

Transmitted antiretroviral drug resistance in newly HIV-infected and untreated patients in Ségou and Bamako, Mali.

The WHO recommends regular surveillance for transmitted antiretroviral drug-resistant viruses in HIV antiretroviral treatment (ART)-naive patients in resource-limited settings. This study aimed to assess the prevalence of mutations associated with resistance in ART-naive patients newly diagnosed with HIV in Bamako and Ségou in Mali. HIV-positive patients who never received ART were recruited in Bamako and Ségou, Mali. The reverse transcriptase (RT) and protease (PR) genes of these patients were sequenced by the "ViroSeq" method. Analysis and interpretation of the resistance were made according to the WHO 2009 list of drug resistance mutations. In all, 51/54 (94.4%) sample patients were sequenced. The median age (IQR) of our patients was 24 (22-27) years and the median CD4 count was 380 (340-456) cells/mm(3). The predominant subtype was recombinant HIV-1 CRF02_AG (66.7%) followed by CRF06_cpx (12%) and CRF09_cpx (4%). Four patients had mutations associated with resistance, giving an overall prevalence of resistance estimated at 7.9%. There were two (4%) patients with nucleoside reverse transcriptase inhibitor (NRTI) mutations (one M184V and one T215Y), two (4%) with non-NRTI mutations (two K103N), and one (2%) with a protease inhibitor mutation (one I54V). The prevalence of primary resistance in newly infected patients in Mali is moderate (7.9%). This indicates that the standard NNRTI-based first-line regimen used in Mali is suboptimal for some patients. This study should be done regularly to inform clinical practice.

Genotypic characterization of herpes simplex virus DNA polymerase UL42 processivity factor.

The herpes simplex virus (HSV) DNA polymerase is composed of the UL30 catalytic subunit and the UL42 processivity factor. The UL42 subunit increases the processivity of the polymerase along the DNA template during replication. The molecular mechanisms of HSV resistance to drugs interfering with viral DNA synthesis reported so far mainly rely on modifications of the viral thymidine kinase and DNA polymerase. We aimed to extensively describe the genetic variations of HSV UL42 processivity factor and to evaluate its potential involvement in resistance to antivirals. The full-length UL42 gene sequence of HSV was investigated among two laboratory strains (KOS and gHSV-2), 94 drug-sensitive clinical isolates and 25 phenotypically ACV-resistant clinical isolates. This work provided extensive data about natural variability of UL42 processivity factor among both HSV-1 and HSV-2 strains and showed that this viral protein is highly conserved among HSV strains, with a weaker variability for HSV-2. The analysis of 25 HSV clinical isolates exhibiting ACV-resistance documented most of the previously reported mutations related to UL42 natural polymorphism in addition to some unpreviously described polymorphisms. Surprisingly, a single-base deletion in UL42 gene sequence leading to a frameshift in the C-terminal region was identified among 3 HSV clinical isolates. From this preliminary study, UL42 processivity factor did not seem to be likely involved in HSV resistance to antivirals.

Clinical and microbiological evaluation of travel-associated respiratory tract infections in travelers returning from countries affected by pandemic A(H1N1) 2009 influenza.

BACKGROUND: Although acute respiratory tract infections (RTI) have been recognized as a significant cause of illness in returning travelers, few studies have specifically evaluated the etiologies of RTI in this population. METHODS: This prospective investigation evaluated travelers returning from countries with endemic influenza A(H1N1) 2009, and who were seen in our department at the onset of the outbreak (April-July 2009). Patients were included if they presented with signs of RTI that occurred during travel or less than 7 days after return from overseas travel. Patients were evaluated for microbial agents with RespiFinder plus assay, and throat culture according to clinical presentation. RESULTS: A total of 113 travelers (M/F ratio 1.2:1; mean age 39 y) were included. They were mainly tourists (n = 50; 44.2%) mostly returning from North America (n = 65; 58%) and Mexico (n = 21; 18.5%). The median duration of travel was 23 days (range 2-540 d). The median lag time between return and onset of illness was 0.2 days (range 10 d prior to 7 d after). The main clinical presentation of RTI was influenza-like illness (n = 76; 67.3%). Among the 99 microbiologically evaluated patients, a pathogen was found by polymerase chain reaction (PCR) or throat culture in 65 patients (65.6%). The main etiological agents were influenza A(H1N1) 2009 (18%), influenza viruses (14%), and rhinovirus (20%). A univariate analysis was unable to show variables associated with influenza A(H1N1) 2009, whereas rhinorrhea was associated with viruses other than influenza (p = 0.04). CONCLUSION: Despite the A(H1N1) 2009 influenza pandemic, rhinovirus and other influenza viruses were also frequent causes of RTI in overseas travelers. Real-time reverse transcription-PCR and nasopharyngeal swab cultures are useful diagnostic tools for evaluating travelers with RTI.

Use of the Roche LightCycler 480 system in a routine laboratory setting for molecular diagnosis of opportunistic viral infections: Evaluation on whole blood specimens and proficiency panels.

The Roche LightCycler 480 (LC480) system was evaluated for quantitative molecular diagnosis of opportunistic viral infections caused by human cytomegalovirus (HCMV), Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6) and BK virus (BKV), in comparison with "in-house" real-time PCR assays. A total of 253 whole blood specimens obtained from transplant recipients were tested. Both the "in-house" and the LC480 methods were highly correlated (Spearman correlation coefficient Rho>or=0.85; p<0.0001) with an excellent overall qualitative agreement (90.5%) and no significant quantitative difference between both techniques for the four viruses tested. The accuracy of the LC480 protocols were confirmed further by the results obtained with the 44 samples from the Quality Control for Molecular Diagnosis (QCMD) 2008 proficiency panel. The LC480 system constitutes a suitable and versatile real-time PCR platform in a routine laboratory setting for the diagnosis and monitoring of opportunistic viral infections in transplant recipients, by measuring HCMV, EBV, HHV-6, and BKV loads in whole blood samples.

Nucleoside reverse transcriptase inhibitor-sparing regimen (nonnucleoside reverse transcriptase inhibitor + protease inhibitor) was more likely associated with resistance comparing to nonnucleoside reverse transcriptase inhibitor or protease inhibitor + nucleoside reverse transcriptase inhibitor in the randomized ANRS 121 trial.

The use of nonnucleoside reverse transcriptase inhibitor (NNRTI) + protease inhibitor regimen for the treatment of antiretroviral-naive patients was less successful than classical nucleoside reverse transcriptase inhibitor (NRTI) based regimen and associated with more resistance for protease inhibitors and NNRTIs. The selection for NNRTI resistance was particularly observed in patients with high viral load (>100 000 copies/ml) and low efavirenz trough levels (<1100 ng/ml). Contrary to the results observed in trials evaluating mono or dual protease inhibitors strategies, gag gene mutations were not involved in the low efficacy of this strategy. The NNRTI + protease inhibitor strategy should not be recommended as an antiretroviral first-line regimen, particularly in patients with high viral load at baseline.

Risk factors for selection of the L74I reverse transcriptase mutation in human immunodeficiency virus type 1-infected patients.

We analyzed 3,475 human immunodeficiency virus sequences and 241 therapeutic histories. The L74I mutation was carried by 7% of viruses. L74I was strongly associated with T215F, K70R, and V75M/S/T/A mutations and increased with the number of thymidine analog mutations. It seemed to be linked to the use of abacavir or efavirenz.