bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human single-chain antibodies that neutralize homologous and heterologous strains and clades of influenza a virus subtype H5N1
Authors: Maneewatch Santi , Thanongsaksrikul Jeeraphong , Songserm Thaweesak , Thueng-In Kanyarat , Kulkeaw Kasem , Thathaisong Umaporn , Srimanote Potjanee , Tongtawe Pongsri , Tapchaisri Pramuan , Chaicumpa Wanpen 
Published: April 2022

Background Human antibodies that interfere with the biological activity of haemagglutinins (HAs) of influenza viruses have high potential as an antiviral agent. Methods Human single-chain antibody fragments (HuScFv) to recombinant and native HAs of the influenza virus H5N1 subtype were produced using a human antibody phage display library with the intention to increase the therapeutic arsenal against this highly pathogenic virus. Results The HuScFv inhibited HA activity and neutralized infectivity of both homologous and heterologous strains and clades of the H5N1 subtype in Madin–Darby canine kidney cell cultures. Intraperitoneally injected HuScFv also mediated immunotherapeutic protection in mice that were intranasally challenged with highly pathogenic H5N1 viruses belonging to different strains and clades. Conclusions Our data indicate that it might be worth pursuing these HuScFv further for future consideration as candidates for influenza intervention and treatment.
Mutations in the thumb–connection and RNase H domain of HIV type-1 reverse transcriptase of antiretroviral treatment-experienced patients
Authors: Waters Joshua M , O'Neal Wesley , White Kirsten L , Wakeford Charles , Lansdon Eric B , Harris Jeanette , Svarovskaia Evguenia S , Miller Michael D , Borroto-Esoda Katyna 
Published: April 2022

Background Antiretroviral therapy that targets HIV type-1 (HIV-1) reverse transcriptase (RT) can be linked to mutations in the thumb–connection (amino acids [AA] 241–426) and RNase H (AA 427–560) domains, which could affect drug resistance. Methods Genotypical and statistical analyses were performed on HIV-1 RT from 100 antiretroviral treatment-naive and 248 antiretroviral treatment-experienced patients, the majority of whom were infected with HIV-1 subtype B. The RT region was analysed in three parts: the polymerase (AA 1–240), thumb–connection (AA 241–426) and RNase H (AA 427–560) domains. Results The polymerase domain had statistically significant changes between the two groups at 24 AA positions that are known resistance sites. Within the thumb–connection domain, R284 and N348 had statistically significant changes between the groups ( P=0.007 and P≤0.001, respectively). In treatment-experienced patients, 17.3% had R284K, whereas 24.5% had N348I substitutions. Both R284 and N348 were 100% conserved in treatment-naive patients. Within the RNase H domain, only K451 showed a statistically significant change ( P≤0.001), with K451R present in 11% of treatment-experienced patients but remaining 100% conserved among treatment-naive patients. Conclusions RT mutations at three positions outside of the polymerase region were associated with antiretroviral therapy: R284K, N348I and K451R. Both R284K and K451R interact with the phosphate backbone of the template or primer in HIV-1 RT crystal structures and could potentially influence the positioning of the primer strand, thus affecting polymerization, the efficiency of nucleoside reverse transcriptase inhibitor excision and/or RNase H activity.
Identification of nonsense mutations in hepatitis B virus S gene in patients with hepatocellular carcinoma developed after lamivudine therapy
Authors: Lai Ming-Wei , Huang Shiu-Feng , Hsu Chao-Wei , Chang Mei-Hui , Liaw Yun-Fan , Yeh Chau-Ting 
Published: April 2022

Background Lamivudine is widely used in patients with chronic hepatitis B virus (HBV) infection. In cirrhotic patients, long-term lamivudine therapy significantly reduced the risk of hepatocellular carcinoma (HCC). However, in a small but substantial portion of patients, HCC still developed despite lamivudine therapy. Prolonged usage of lamivudine led to mutations in the polymerase gene, where concurrent nonsense mutations in the HBV S gene occasionally occurred. The significance of such mutations in hepatocarcinogenesis remains elusive. Here, we aimed to understand the oncogenicity of HBV pre-S/S nonsense mutations identified in patients with HCC that developed after lamivudine therapy. Methods Of 141 consecutive hepatitis B surface antigen-positive HCC patients, 8 developed HCC after receiving lamivudine therapy. The HBV pre-S/S sequences in their serum and tissue samples were analysed. A sex-and age-matched group of HCC patients who never received lamivudine therapy were included as controls. Site- directed mutagenesis experiments were performed to generate identified pre-S/S nonsense mutations in expression vectors for tumourigenicity analysis. Results Seven of eight patients in the lamivudine-treated group harboured nonsense mutations in the S gene compared with none in the control group ( P<0.001). Site- directed mutagenesis and transient transfection experiments revealed that these mutants could transactivate oncogene promoters. NIH3T3 cells stably expressing sL21*, sW156* and sW172* pre-S/S mutants had increased tumourigenicity in nude mice. Conclusions HCCs developed in lamivudine-treated patients who frequently carried nonsense mutations in the S gene. Such pre-S/S mutants are potentially oncogenic and might counteract the effect of lamivudine in preventing hepatocarcinogenesis.
CD4+ T-cell percentage is an independent predictor of clinical progression in AIDS-free antiretroviral-naive patients with CD4+ T-cell counts >200 cells/mm3
Authors: Guiguet Marguerite , Kendjo Eric , Carcelain Guislaine , Abgrall Sophie , Mary-Krause Murielle , Tattevin Pierre , Yazdanpanah Yazdan , Costagliola Dominique , Duval Xavier 
Published: April 2022

Background The aim of this study was to evaluate the clinical prognostic value of the CD4+ T-cell percentage (%CD4), the CD4+/CD8+ T-cell ratio or the CD8+ T-cell count, in addition to the CD4+ T-cell count and viral load (VL) in antiretroviral-naive HIV- infected patients with CD4+ T-cell counts >200 cells/ mm3. Methods Antiretroviral-naive patients ( n=9,740) who were AIDS-free and had a CD4+ T-cell count >200 cells/ mm3 at their first visit after January 1997 were followed-up until treatment initiation or clinical progression (mean follow- up 17 months and 13,660 person-years). Poisson regression was used for statistical analyses. Results Progression to AIDS-defining events (ADEs), serious ADEs and death occurred in 228 patients (crude rate 1.69 per 100 person-years), 105 patients (0.77 per 100 person-years) and 67 patients (0.49 per 100 person-years), respectively. Regarding progression to ADE, the data fit was improved when the model also included the %CD4 (Akaike's information criteria [AIC] 2,049) and, to a lesser extent, the CD4+/CD8+ T-cell ratio (AIC 2,053), in addition to CD4+ T-cell count and VL (AIC 2,056). After adjustment for VL and baseline characteristics, patients with CD4+ T-cell counts of 350–500 cells/mm3 and %CD4<15% had an estimated incidence of ADE of 3 per 100 person-years, similar to that in patients with CD4+ T-cell counts of 200–350 cells/mm3 and %CD4>15%. The %CD4 was also significantly associated with the risk of serious ADE. By contrast, %CD4, CD4+/CD8+ T-cell ratio or CD8+ T-cell count had no additional prognostic value for the risk of death. Conclusions In antiretroviral-naive HIV-infected patients with CD4+ T-cell counts >200 cells/mm3, the %CD4 was predictive of the risk of clinical progression independently of CD4+ T-cell count and VL.
Long-term hepatitis C internal ribosome entry site-dependent gene expression mediated by phage φC31 integrase in mouse model
Authors: Sun Zhidong , Wang Yi , Fu Qiuxia , Zhou Yong , Jia Shuaizheng , Du Juan , Peng Jianchun , Wang Yingli , Yang Shuhua , Zhan Linsheng 
Published: April 2022

Background The lack of a robust small animal model for hepatitis C virus (HCV) has hindered the development of novel drugs, including internal ribosome entry site (IRES) inhibitors. Phage φC31 integrase has emerged as a potent tool for achieving long-term gene expression in vivo. This study utilized φC31 integrase to develop a stable, reproducible and easily accessible HCV IRES mouse model. Methods φC31 integrase plasmid and the reporter vector, HCV-IRES–luciferase expression cassette (containing an attB site), was codelivered to murine livers using high pressure tail vein injection. HCV IRES-dependent translation refected by luciferase expression was accurately monitored in vivo by bioluminescence imaging. Genomic integration of the transgene was confirmed by partial hepatectomy and nested PCR. An HCV IRES-targeted short hairpin RNA (shRNA) expression plasmid, sh184, was hydrodynamically transfected into mouse liver to study its inhibition efficacy in vivo. Results φC31 integrase mediated intramolecular recombination between wild-type attB and attP sites in mice. The expression of luciferase was stable after 30 days post-transfection and remained so for 300 days only in the livers of mice that were coinjected with the integrase-encoding plasmid. Luciferase levels reduced dramatically after hydrodynamic transfection of sh184. Conclusions These results indicate that this mouse model provides a powerful tool for accurate and long-term evaluation of potential anti-IRES compounds in vivo.
Clinical and Virological Responses to Clevudine Therapy in Chronic Hepatitis B Patients: Results at 1 Year of an Open-Labelled Prospective Study
Authors: Ko Soon Young , Kwon So Young , Choe Won Hyeok , Kim Byung Kook , Kim Kyun-Hwan , Lee Chang Hong 
Published: April 2022

Background A previous clinical study of oral clevudine monotherapy for 24 weeks demonstrated that it has potent sustained antiviral effects without inducing drug resistance. The aim of this study was to evaluate the antiviral effects and safety of clevudine monotherapy for 12 months. Methods In this open-labelled prospective study, 45 treatment-naive chronic hepatitis B patients treated with 30 mg clevudine once daily for 12 months were monitored at baseline and at 3-month intervals during treatment. Results At baseline, the mean age of patients was 42 years, 32 were hepatitis B e antigen (HBeAg)-positive and 15 had liver cirrhosis. After 12 months of clevudine therapy, the mean serum hepatitis B virus (HBV) DNA level in HBeAg-positive patients had decreased by 4.6 log10 IU/ ml. Serum HBV DNA was undetectable in 68.7% of patients. HBeAg loss or seroconversion was observed in five patients (15.6%) and serum alanine aminotransferase (ALT) level had normalized after 12 months of treatment in 75% of patients. In all 13 HBeAg-negative patients, serum HBV DNA level was undetectable after 12 months of therapy and ALT level was normal in 61.5% of patients. Viral breakthrough occurred in one patient after 9 months of clevudine treatment. This patient had an HBV polymerase mutation, rtM204I. There were no serious adverse events. Conclusions One-year clevudine therapy is effective for suppressing serum HBV DNA level and for normalization of ALT level. Viral breakthrough associated with the rtM204I mutation in the HBV polymerase gene occurs during long-term clevudine treatment.
Virological response at 4 weeks to predict outcome of hepatitis C treatment with pegylated interferon and ribavirin
Authors: Martinot-Peignoux Michelle , Maylin Sarah , Moucari Rami , Ripault Marie-Pierre , Boyer Nathalie , Cardoso Ana-Carolina , Giuily Nathalie , Castelnau Corinne , Pouteau Michèle , Stern Christiane , Aupérin Anne , Bedossa Pierre , Asselah Tarik , Marcellin Patrick 
Published: April 2022

Background Viral kinetics during therapy provides information on how to individualize treatment. To determine the benefit of assessing positive predictive values (PPVs) and negative predictive values (NPVs) of rapid virological responses (RVRs) and early virological responses (EVRs), on-treatment outcomes in chronic hepatitis C patients were examined. Methods A total of 408 patients (221 treatment-naive) treated with pegylated interferon-α2b and ribavirin were included. Hepatitis C virus (HCV) RNA was measured at baseline, 4 weeks and 12 weeks. RVR was defined as undetectable HCV RNA at 4 weeks and EVR as ≥2 log10 decrease in HCV RNA at 12 weeks. The additive value of RVR on predicting sustained virological response (SVR) was assessed with receiver operating characteristic (ROC) curves. Results SVR, RVR and EVR were observed in 46%, 23% and 78% of patients, respectively. PPVs of RVR were 96%, 100% and 100% in treatment-naive patients, relapsers and non-responders, respectively. NPVs of failure to achieve EVR were 97%, 75% and 91%, in treatment- naive patients, relapsers and non-responders, respectively. At 4 weeks, patients with RVR had the highest probability to achieve SVR (odds ratio 44.98 in the entire population and 32.95 in treatment-naive patients). ROC curves showed the area under the ROC curve to be 0.758 versus 0.832 in the entire population and 0.795 versus 0.858 in treatment-naive patients at baseline versus week 4, respectively. Conclusions RVR is a strong predictor of SVR (PPV>96%) and failure to achieve EVR is a strong predictor of non-SVR (NPV>75%), independent of patients’ pretreatment status. Added to baseline characteristics, RVR increased the accuracy to predict SVR. The combination of RVR and EVR provided complementary information, and thus provides a key opportunity to individualize treatment and improve the benefit/risk ratio of therapy.
The effects of HIV type-1 viral suppression and non-viral factors on quantitative proteinuria in the highly active antiretroviral therapy era
Authors: Gupta Samir K , Smurzynski Marlene , Franceschini Nora , Bosch Ronald J , Szczech Lynda A , Kalayjian Robert C ,   for the AIDS Clinical Trials Group Longitudinal Linked Randomized Trials Study Team
Published: April 2022

Background Proteinuria is associated with progressive renal disease and overall mortality in HIV-infected patients; however, the prevalence and correlates of quantitative pro-teinuria in the highly active antiretroviral therapy era are unknown. Methods Spot urine protein to creatinine (P/Cr) ratios, an accepted measure of quantitative daily proteinuria, were measured annually since 2002 in participants of the AIDS Clinical Trials Group Longitudinal Linked Randomized Trials cohort. We used linear regression models with general estimating equations to identify factors associated with the abnormal P/Cr thresholds of ≥0.2 and ≥1.0. Results Of the 2,857 participants (most of whom were receiving antiretroviral therapy) analysed, 16% and 3% had P/Cr levels ≥0.2 and ≥1.0, respectively, at first measurement. P/Cr levels did not change during a median follow-up of 3 years (interquartile range 2–4). Factors associated with P/Cr≥0.2 at any measurement included greater age, lower glomerular filtration rate, female sex, antiretroviral therapy prior to entry into parent randomized trial, HIV type-1 RNA level ≥400 copies/ ml, lower CD4+ T-cell count and history of hypertension, diabetes or hepatitis C coinfection (all P<0.04). Black race and higher non-high-density lipoprotein cholesterol levels were associated with P/Cr levels ≥1.0, but not with P/ Cr levels ≥0.2. Hepatitis B coinfection and current use of adefovir, indinavir and tenofovir were not associated with either of the P/Cr thresholds. Conclusions Both HIV-1 and non-HIV-1-related factors are associated with abnormal levels of proteinuria and identify those who are at a greater risk of worse clinical outcomes. Several of these factors are differentially associated with lower and higher proteinuria thresholds.
Immunological and mutagenic actions of ribavirin monotherapy preceding combination therapy with interferon for patients with chronic hepatitis C
Authors: Ogawa Koji , Hige Shuhei , Nakanishi Mitsuru , Yamamoto Yoshiya , Chuma Makoto , Nagasaka Atsushi , Asaka Masahiro 
Published: April 2022

Background We aimed to investigate the effects of ribavirin on hepatitis C virus (HCV). Immunological and virological effects were analysed in patients undergoing treatment with ribavirin monotherapy prior to the initiation of combination therapy with interferon-α. Methods A total of 25 patients with chronic HCV infection were enrolled in this study. All patients received ribavirin for 4 weeks during monotherapy; subsequently, interferon-α2b was additionally given as combined therapy. Patients were divided into two groups according to virological response. A rapid viral responder (RVR) was defined as a patient in whom HCV RNA became undetectable within 4 weeks after combination therapy. The changes of the T-helper (Th)1/Th2 subset of peripheral blood CD4+ T-cells, serum cytokine levels and the alignment of the interferon sensitivity- determining region (ISDR) during ribavirin monotherapy were analysed by flow cytometry, ELISAs and sequencing methods. Results A total of 17 patients were classed as RVR. In the RVR group, the mean ±sd serum alanine aminotransferase levels significantly decreased (before treatment 103 ±92 IU/l and after treatment 57 ±46 IU/l; P<0.05) during ribavirin monotherapy. The mean ±sd Th1/Th2 ratio significantly increased (before treatment 13.9 ±5.1 and after treatment 16.7 ±6.2; P<0.05), but did not change in the non-RVR group. The levels of Th2 cytokines (interleukin-10 and soluble CD30) significantly decreased, especially in the RVR group. The mean ±sd mutation rates of ISDR at the nucleotide level increased in the RVR group (before treatment 2.6 ±0.9 sites/clone and after treatment 3.9 ±1.6 sites/clone; P<0.05), but did not change in the non-RVR group. Conclusions Ribavirin administration might increase the efficacy of interferon therapy for patients with chronic hepatitis C by stimulating the host immune system and promoting HCV gene mutation.
In vivo selection by enfuvirtide of HIV type-1 env quasispecies with optimal potential for phenotypic expression of HR1 mutations
Authors: Goubard Armelle , Clavel François , Mammano Fabrizio , Labrosse Béatrice 
Published: April 2022

Background HIV type-1 (HIV-1) resistance to enfuvirtide (ENF) is mediated by mutations in the HR1 domain of gp41. We have previously shown that some of these mutations are selected in the context of env backgrounds that are not dominant before exposure to ENF, suggesting that particular env environments could facilitate phenotypic expression of HR1-mediated ENF resistance. Methods Envelope clones, representing the viral quasispecies present in the longitudinal follow-up of a patient who failed ENF-based salvage therapy, were tested for ENF susceptibility and Env-related replicative capacity. ENF resistance mutations in HR1 were introduced or back-mutated in representative clones to evaluate their phenotypic effect in different genetic contexts. Results The ENF resistance levels produced by the introduction of mutation V38A in pretherapeutic env sequences were significantly lower than those of env clones harvested after viral escape, and in which V38A was naturally selected. Back-mutation of V38A from these clones resulted in a strong loss in ENF resistance, but these clones retained significant residual resistance, again strongly suggesting the role of determinants outside of HR1 in HIV-1 resistance to ENF. By contrast with changes in resistance, addition or removal of HR1 mutations in env clones had little effect on viral replicative capacity. Conclusions The development of ENF resistance in vivo is a concerted coevolutionary process whereby HR1 mutations are selected within env variants that permit their optimal phenotypic expression.
Transmitted antiretroviral drug resistance among acute and recent HIV infections in North Carolina from 1998 to 2007
Authors: Hurt Christopher B , McCoy Sandra I , Kuruc JoAnn , Nelson Julie AE , Kerkau Melissa , Fiscus Susan , McGee Kara , Sebastian Joseph , Leone Peter , Pilcher Christopher , Hicks Charles , Eron Joseph 
Published: April 2022

Background Transmitted drug resistance (TDR) limits antiretroviral options and thus complicates the management of HIV-positive patients. HIV disproportionately affects the southern US, but available national estimates of TDR prevalence principally reflect large metropolitan centres outside this region. Methods The Duke/UNC Acute HIV Program has collected data on acute or recent HIV infections (ARHI) in North Carolina since 1998. Acute infections represent antibody-negative, RNA-positive patients. Recent infection was determined by history of HIV testing or concordance between detuned ELISA and antibody avidity assays. Genotypic sequence data from the earliest collected pretreatment plasma samples were analysed with the Stanford HIV Database and screened for surveillance drug resistance mutations (SDRMs). Results A total of 253 individuals with ARHI between May 1998 and May 2007 had complete genotypic sequence data for analysis; 39.5% were acute infections, 78.7% were male, 64.8% were non-White and 53.8% were men who have sex with men. The overall prevalence of TDR was 17.8%, with SDRMs for non-nucleoside/ nucleotide reverse transcriptase inhibitors (NNRTIs) in 9.5% of the cohort. Mutations for nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) were detected in 7.5% and for protease inhibitors (PIs) in 3.2%. K103N was the most common mutation (7.5%). Thymidine analogue mutations were found in 4.7% of samples; the most common PI SDRM was L90M (2.4%). Dual- or triple-class antiretroviral resistance was rare, encountered in only six (2.4%) samples. Conclusions The prevalence of TDR in North Carolina is similar to estimates from the US metropolitan areas. These findings have implications for initial regimen selection and secondary prevention efforts outside of large, metropolitan HIV epicentres.
Variability of reverse transcriptase and overlapping S gene in hepatitis B virus isolates from untreated and lamivudine-resistant chronic hepatitis B patients
Authors: Pollicino Teresa , Isgrò Graziella , Di Stefano Rosa , Ferraro Donatella , Maimone Sergio , Brancatelli Santa , Squadrito Giovanni , Marco Vito Di , Craxì Antonio , Raimondo Giovanni 
Published: April 2022

Background The high degree of diversity of the hepatitis B virus (HBV) quasispecies in chronically infected individuals raises the possibility that HBV genetic variants favouring resistance to nucleoside/nucleotide analogues (NAs) might pre-exist to treatment. The aim of this study was to investigate the genetic variability of the entire HBV reverse transcriptase (RT) domain and of the overlapping S gene in a large series of untreated hepatitis B surface antigen carriers and in lamivudine (3TC)-resistant patients. Methods Sequencing analysis of the entire HBV RT domain of isolates from 100 untreated (treatment- naive group) and 59 3TC-resistant (3TC-resistant group) consecutive patients with chronic hepatitis B was performed. Results In the treatment-naive group, primary mutations known to cause resistance to NAs were not detected, but variably combined secondary/compensatory mutations were found in 46 (46%) patients. Moreover, four patients carried mutations that modified the S protein antigenicity. In the 3TC-resistant group, besides the primary 3TC-resistant mutations, various combinations of primary and secondary mutations conferring resistance to other NAs were detected in 41/59 (69.5%) patients. Importantly, the RT mutations induced by 3TC provoked stop codons in the overlapping S gene in two patients and modified the S protein antigenicity in another nine. Conclusions This study shows that HBV mutants associated with resistance to NAs might already be present as the major infecting population in untreated patients, and that variants emerging under 3TC might also carry mutations favouring resistance to other NAs and/or potentially altering the S protein immunoreactivity.