AE Subtype Research Articles

Transmission cluster and network of HIV-1 CRF01_AE strain in China, 1996-2014

Objective: To understand the transmission patterns and risk factors of HIV-1 strain CRF01_AE subtypes in China, and to provide guidance for the implementation of precise intervention. Methods: A total of 2 094 CRF01_AE pol sequences were collected in 19 provinces in China between 1996 and 2014. Phylogenetic tree was constructed by PhyML 3.0 software to select the transmission clusters. Transmission network was constructed by Cytoscape 3.6.0, which was further used for exploring of the major risk factors. Results: Of the 2 094 sequences, 12.18% (255/2 094) were in clusters. A total of 82 transmission clusters were identified. The numbers of clusters and contained sequences in intra-provincial transmission (61, 173) were significantly more than those in inter-provincial transmission (21, 82). The ratio of transmission clustering in MSM increased over time from 2.41% (2/83) during 1996-2008 to 23.61% (72/305) during 2013-2014, showing a significant upward trend (χ(2)=27.800, df=1, P=0.000). The proportion of MSM with inter-provincial transmission clusters were higher than those with intra-provincial transmission clusters, which increased from 0.67% (2/297) during 1996-2008 to 6.36%(30/472) during 2013-2014, showing a significant upward trend (χ(2)=20.276, df=1, P=0.000). The transmission rate in homosexuals of the inter-transmission clusters (86.59%, 71/82) was higher than that of intra-provincial transmission clusters (56.65%, 98/173), and the difference was statistically significant (χ(2)=22.792, P=0.000). The proportion of inter-provincial transmission clusters with more than 2 transmission routes (33.33%, 7/21) was higher than that of intra-provincial clusters (13.11%, 8/61), and the difference was statistically significant (χ(2)=4.273, P=0.039). Results from the transmission network analysis indicated that the proportion of high risk population (degree≥4) with inter-provincial transmission clusters (51.22%, 42/82) was significantly higher than that with intra-provincial transmission clusters (26.59%, 46/173), and the difference was statistically significant (χ(2)=14.932, P=0.000). Inter-provincial clusters were mainly detected in and and MSM. Conclusions: Complex transmission networks were found for HIV-1 CRF01_AE strains in the mainland of China. Inter-provincial transmission clusters increased rapidly, MSM played an important role in the wide spread of the strain. More researches in transmission networks are needed to guide the precision intervention.

Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations

Human immunodeficiency virus type 1 protease is essential for virus replication and maturation and has been considered as one of the important drug target for the antiretroviral treatment of HIV infection. The majority of HIV infections are caused due to non-B subtypes in developing countries. Subtype AE is spreading rapidly and infecting huge population worldwide. Understanding the interdependence of active and non-active site mutations in conferring drug resistance is crucial for the development effective inhibitors in subtype AE protease. In this work, we have investigated the mechanism of resistance against indinavir (IDV) due to therapy selected active site mutation V82F, non-active site mutations PF82V and their cooperative effects PV82F in subtype AE-protease using molecular dynamics simulations and binding free energy calculations. The simulations suggested all the three complexes lead to decrease in binding affinity of IDV, whereas the PF82V complex resulted in an enhanced binding affinity compared to V82F and PV82F complexes. Large positional deviation of IDV was observed in V82F complex. The preservation of hydrogen bonds of IDV with active site Asp25/Asp25′ and flap residue Ile50/50′ via a water molecule is crucial for effective binding. Owing to the close contact of 80s loop with Ile50′ and Asp25, the alteration between residues Thr80 and Val82, further induces conformational change thereby resulting in loss of interactions between IDV and the residues in the active site cavity, leading to drug resistance. Our present study shed light on the effect of active, non-active site mutations and their cooperative effects in AE protease.Communicated by Ramaswamy H. Sarma

Prevalence of HIV-1 Drug Resistance among Patients with Antiretroviral Therapy Failure in Sichuan, China, 2010-2016.

Antiretroviral therapy (ART) has been introduced recently and has significantly impacted morbidity and mortality, but can also engender drug resistance. To identify the prevalence of HIV-1 drug resistance (HIVDR) among patients with antiretroviral therapy failure in Sichuan during the period from 2010 to 2016, we carried out a longitudinal study in Sichuan, a province with the highest HIV/AIDS prevalence in China. The data and blood samples were collected from HIV/AIDS patients who received ART for more than half a year. Overall 5,512 sequences were completed from 7,059 ART-failure patients, and 2,499 individuals were identified as drug resistant. Among those with HIVDR mutations identified, 25.37% were against non-nucleoside reverse transcriptase inhibitors (NNRTIs), and 1.60% was against nucleoside reverse transcriptase inhibitors (NRTIs). NRTI-resistant drugs were mainly lamivudine (3TC) (57.77%) and emtricitabine (FTC), while NNRTI-resistant drugs were mainly nevirapine (NVP) (91.13%) and efavirenz (EFV) (72.81%). The most common recombination subtypes of HIV-1 in sequenced samples were CRF07_BC (circulating recombinant form, CRF) (41.42%), followed by CRF01_AE (40.77%). Moreover, drug resistance rate increased with the prolongation of treatment time (χ2 = 14.758, P < 0.05). The overall prevalence of acquired drug resistance in HIV-1 infected patients in Sichuan was 5.47%, which has remained relatively stable from 2010 to 2016. HIV-1 CRF01_AE and CRF07_BC subtypes were the main epidemic strains, and the possibility of resistance was higher in CRF01_AE subtypes. The current study highlights the importance of acquired drug resistance surveillance over a long period.

Characterization of a New HIV-1 CRF01_AE/B Recombinant Virus Form Among Men Who Have Sex with Men in Shanghai, China.

To date, there are 16 types of CRF01_AE/B circulating recombinant forms identified, and most of them are distributed in Asian countries such as China, Malaysia, and Singapore. Previous HIV molecular epidemiological surveys showed that CRF01_AE (27.6%) and B (9.6%) subtypes are predominant strains in mainland of China. At the same time, the HIV-1 virus spreads faster in the men who have sex with men (MSM) population than in other risk groups. In Shanghai district, ∼66.0% of newly reported cases were infected through homosexual transmission. In this study, we report a novel recombinant strain of CRF01_AE/B. The near full-length genome phylogenetic tree showed that the strain clustered with the CRF01_AE reference sequence and placed in the peripheral position within the branch of the CRF01_AE strain. Subregional evolutionary results indicated that the CRF01_AE subtype was derived from cluster 4 of CRF01_AE, which is mainly distributed in northern China. The subtype B was correlated with the U.S./Europe B, which are widely prevalent in the Chinese MSM population. In recent years, a large number of recombinant forms between CRF01_AE and B strains are continuously emerging in China. Therefore, understanding the current epidemic recombinant forms will have significant implications for prevention and treatment of HIV/AIDS.

Molecular Antiretroviral Resistance Markers of Human Immunodeficiency Virus-1 of CRF01_AE Subtype in Bali, Indonesia.

Background: Molecular epidemiological study of human immunodeficiency virus drug-resistant (HIVDR) markers is challenging in areas where the dominant subtype is non-B.Objective: Here we provide molecular data for HIVDR in the CRF01_AE subtype in Bali, Indonesia.Method: Seventy patients were enrolled in this study and grouped into treatment failure and treatment naïve groups. The full-length pol gene was amplified using nested reverse transcriptase polymerase chain reaction and the product was then sequenced. The readable sequence was then subjected to Stan-ford HIV Drug Resistance Database genotyping.Results: We found that clinical classification was in accordance with the presence of HIVDR markers in the pol gene. Independent of therapy history, the treatment failure group showed resistance markers against nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase in-hibitors (NNRTI), ranging from 72%–100% of patients. Only a small proportion of naïve patients harbored HIV with drug resistance markers to NNRTI. No protease inhibitor-resistant marker was found in either patient group. Molecular marker mutations, which were found in more than 50% of treatment failure patients, were M184V (100%), T215A/Y/F (88.2%), D67N/G (76.5%), and M41L (58.8%).Conclusion: The protocol used in this study to determine genetic markers of HIVDR based on sub-type B can be applied for the rapid determination of resistance of the CRF01_AE subtype. All patients with progressive clinical signs and increased viral load should be recommended to undergo second-line treatment of the ARV regimen.

Analisis Subtipe HIV-1 dan Faktor Penyebarannya pada Penderita HIV di RS. Yowari Kabupaten Jayapura, Papua

Acquaired immunodeficiency Syndrome (AIDS) is a symptoms caused by infection with Human Immuno-deficiency Virus (HIV). There are two types of HIV genetically distinguished as HIV-1 and HIV-2 subtype. Subtypes of HIV-1 globally have different distribution in state, where geographical factors could affected to the subtype differences. Papua is one of the provinces that have high case of HIV/AIDS. High number of people with HIV/AIDS in Papua caused by new regional area expansion and mobilization of the population in province and district area. This study was aimed to identify the sub type HIV-1 and the risk factors that correlated in the transmission of HIV-1 type. The research study was performed by cross-sectional design. There were 36 HIV patient sample respondent willing to participate in research and they were sign inform consent. Subtype HIV-1 identification was performed by used Nested-PCR, sequencing, and BLAST to found subtype HIV-1. The interview method used a questionnaires to found of  the risk factors  related to subtype HIV-1. The results of research showed that HIV-1 subtype found in people with HIV in Yowari hospital is CRF01_AE subtype (31 respondent) and subtype B ( 5 respondent). Chi-squre and Fisher exact test analysis of risk factors that influence the spread of HIV-1 subtype showed a non significant results. The research study concluded sub-type HIV-1 in patients is CRF01_AE and subtype B and  there were not correlated risk factors with HIV-1 subtype.Key words: HIV/AIDS , type HIV-1 , CRF01_AE , Sub type-B, RS Yowari.

SEKUENS TERAWETKAN TERKAIT HIV-1

Human Immunodeficiency Virus-1 (HIV-1) have the high levels of genetic variability (molecular variation) related to the mechanismof deletions, insertions, and especially as a recombination. The recombination between subgroups and their inter subtype HIV-1 producesa new virus strain causing a certain infection. Until now there were about 40 circulating recombinant form (CRF) and 100 uniquerecombinant forms (URF) worldwide. Various HIV-1 molecular variation cause pitfalls HIV detection due to the difficulty test designed todetect all HIV-1 strains. The purpose of this study was to know the determination of the molecular variation that can identify the HIV-1genome sequences which are conserved from local isolates of West Sumatera. The method used is a descriptive study on samples of patientssuspected of being infected by HIV-1 based on the antibody screening results using rapid HIV-1 test in the laboratory of Clinical Pathologyat Dr. M. Djamil Hospital Padang. The RNA isolation and amplification by RT-PCR was performed at the Microbiology Department,Faculty of Medicine of UGM. The amplicons were sequenced using the Sanger method and analyzed by Clustal W with sequence datafrom the HIV its database. The major subtypes of HIV-1 isolates derived from local West Sumatra is AE/B with four (4) isolates (57.1%),followed by subtype AE, 2 isolates (28.6%) and B, 1 isolates (14.3%). Most of the molecular variation in this study related to thesubstitution of one base followed by deletions and insertions. The protease showed a wide variation, which consists of 20–37 substitutionsand 1–3 deletions. p24 is a highly conserved gene, followed by gp120 and vpu. Based on this study, it can be concluded that the isolatesof HIV-1 recombination is the biggest proportion with conserved region found at p24 of protein group of the gag.

Characterization of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B′/C (CRF96_cpx), in Yunnan, China

Currently, complex HIV-1 recombinations among the B', C, and CRF01_AE genotypes have frequently arisen in Yunnan, China. A novel HIV-1 complex circulating recombinant form (CRF) consisting of B', C, and CRF01_AE (CRF96_cpx) was recently characterized from three epidemiologically unlinked individuals. Two strains of them were isolated from the injecting drug users in this study, the remaining one strain (JL. RL01) was obtained from a previous report in Jilin province. Phylogenetic analysis based on near full-length genome revealed that CRF96_cpx formed a distinct monophyletic cluster supported by a high bootstrap value of 100%, distantly related to all known HIV-1 subtypes/CRFs. CRF96_cpx had a CRF01_AE backbone with three subtype B' and C segments inserted, respectively, in the gag and pol region. Furthermore, subregion tree analysis showed that CRF01_AE backbone and subtype B segment inserted originated from a Thai-CRF01_AE lineage, whereas subtype C fragment inserted was from an India C lineage. They are different from previously documented CRF01_AE/B/C forms in its distinct backbone, inserted fragment size, and breakpoints. This highlighted the importance of continual monitoring of genetic diversity and complexity of HIV-1 strains in Yunnan, China.

HIV-1 subtype CRF01_AE and B differ in utilization of low levels of CCR5, Maraviroc susceptibility and potential N-glycosylation sites

HIV subtypes not only predominate in different geographical regions but also differ in key phenotypic characteristics. To determine if genotypic and/or phenotypic differences in the Envelope (Env) glycoprotein can explain subtype related differences, we cloned 37 full length Envs from Subtype B and AE HIV infected individuals from Singapore. Our data demonstrates that CRF01_AE Envs have lower Potential N Glycosylation Sites and higher risk of ×4 development. Phenotypically, CRF01_AE were less infectious than subtype B Envs in cells expressing low levels of CCR5. Moreover, the Maraviroc IC50 was higher for subtype B Envs and correlated with infectivity in low CCR5 expressing cells as well as PNGS. Specifically, the glycosylation site N301 in the V3 loop was seen less frequently in AE subtype and CXCR4 topic viruses. CRF01_AE differs from B subtype in terms of CCR5 usage and Maraviroc susceptibility which may have implications for HIV pathogenesis and virus evolution.

Amplification of the Gp41 gene for detection of mutations conferring resistance to HIV-1 fusion inhibitors on genotypic assay

Fusion inhibitors have potential for future use in HIV control programs in Indonesia, so the capacity to test resistance to such drugs needs to be developed. Resistance-detection with a genotypic assay began with amplification of the target gene, gp41. Based on the sequence of the two most common HIV subtypes in Indonesia, AE and B, a primer pair was designed. Plasma samples containing both subtypes were extracted to obtain HIV RNA. Using PCR, the primer pair was used to produce the amplification product, the identity of which was checked based on length under electrophoresis. Eleven plasma samples were included in this study. One-step PCR using the primer pair was able to amplify gp41 from 54.5% of the samples, and an unspecific amplification product was seen in 1.1% of the samples. Amplification failed in 36.4% of the samples, which may be due to an inappropriate primer sequence. It was also found that the optimal annealing temperature for producing the single expected band was 57.2 °C. With one-step PCR, the designed primer pair amplified the HIV-1 gp41 gene from subtypes AE and B. However, further research should be done to determine the conditions that will increase the sensitivity and specificity of the amplification process.

Drug Resistance Mechanism of L10F, L10F/N88S and L90M mutations in CRF01_AE HIV-1 protease: Molecular dynamics simulations and binding free energy calculations

HIV-1 protease plays a crucial role in viral replication and maturation, which makes it one of the most attractive targets for anti-retroviral therapy. The majority of HIV infections in developing countries are due to non-B subtype. Subtype AE is spreading rapidly and infecting huge population worldwide. The mutations in the active site of subtype AE directly impair the interactions with the inhibitor. The non-active site mutations influence the binding of the inhibitor indirectly and their resistance mechanism is not well understood. It is important to design new effective inhibitors that combat drug resistance in subtype AE protease. In this work, we examined the effect of non active site mutations L10F, L10F/N88S and L90M with nelfinavir using molecular dynamics simulation and binding free energy calculations. The simulations suggested that the L10F and L10F/N88S mutants decrease the binding affinity of nelfinavir, whereas the L90M mutant increases the binding affinity. The formation of hydrogen bonds between nelfinavir and Asp30 is crucial for effective binding. The benzamide moiety of nelfinavir shows large positional deviation in L10F and L10F/N88S complexes and the L10F/N88S mutation changes the hydrogen bond between the side chain atoms of 30th residue and the 88th residue. Consequently the hydrogen bond interaction between Asp30 and nelfinavir are destroyed leading to drug resistance. Our present study shed light on the resistance mechanism of the strongly linked mutation L10F/N88S observed experimentally in AE subtype.

HIV-1 CRF01_AE strain is associated with faster HIV/AIDS progression in Jiangsu Province, China

The goal of this study was to assess risk factors associated with HIV/AIDS progression. Between May 2007 and December 2014, 114 subjects were enrolled in Wuxi City and examined every 6 months. The pol gene sequence was amplified to ascertain the HIV-1 subtype. A Cox proportional hazards regression model was used to estimate the factors associated with HIV/AIDS progression. The median follow-up time for all 114 subjects was 26.70 months (IQR: 18.50–41.47), while the median progression time of the 38 progressed subjects was 24.80 months (IQR: 14.13–34.38). Overall, the CRF01_AE subtype was correlated with a significant risk of accelerated progression compared to non-CRF01_AE subtypes (HR = 3.14, 95%CI: 1.39–7.08, P = 0.006). In addition, a lower CD4 count (350–499) at baseline was associated with a risk of accelerated HIV/AIDS progression compared to higher CD4 count (≥500) (HR = 4.38, 95%CI: 1.95–9.82, P < 0.001). Furthermore, interaction analyses showed that HIV-1 subtypes interacted multiplicatively with transmission routes or CD4 count at baseline to contribute to HIV/AIDS progression (P = 0.023 and P < 0.001, respectively). In conclusion, the CRF01_AE subtype and a lower CD4 count at baseline tend to be associated with the faster progression of HIV/AIDS. Understanding the factors affecting HIV/AIDS progression is crucial for developing personalized management and clinical counselling strategies.

Subtypes and Risk Behaviors Among Incident HIV Cases in the Bangkok Men Who Have Sex with Men Cohort Study, Thailand, 2006-2014.

HIV-1 incidence and prevalence remain high among men who have sex with men (MSM), and transgender women (TGW), in Thailand. To examine the link between epidemiologic factors and HIV-1 subtype transmission among Thai MSM, we compared covariates of infection with HIV CRF01_AE and other HIV strains among participants in the Bangkok MSM Cohort Study (BMCS). The BMCS was an observational cohort study of Thai MSM and TGW with up to 60 months of follow-up at 4 monthly intervals. Participants underwent HIV/sexually transmitted infections testing and provided behavioral data at each visit. Infecting viral strain was characterized by gene sequencing and/or multiregion hybridization assay. We correlated behavioral/clinical variables with infecting strain using Cox proportional hazards. Among a total of 1372 HIV seronegative enrolled participants with 4,192 person-years of follow-up, we identified 215 seroconverters between April 2006 and December 2014, with 177 infected with CRF01_AE and 38 with non-CRF01_AE subtype. Age 18-21 years (adjusted hazard ratio [AHR] 2.2, 95% confidence interval [CI]: 1.4-3.5), age 22-29 (AHR 1.6, 95% CI: 1.1-2.3), living alone (AHR 1.5, 95% CI: 1.1-2.1), drug use (AHR 2.2, 95% CI: 1.4-3.5), intermittent condom use (AHR 1.7, 95% CI: 1.3-2.3), any receptive anal intercourse (AHR 1.7, 95% CI: 1.2-2.4), group sex (AHR 1.5, 95% CI: 1.1-2.2), anti-herpes simplex virus type 1 (AHR 1.5, 95% CI: 1.1-2.1), and Treponema pallidum antibody positivity (AHR 2.5, 95% CI: 1.4-4.4) were associated with CRF01_AE infection. Age 18-21 years (AHR 5.1, 95% CI: 1.6-16.5), age 22-29 (AHR 3.6, 95% CI: 1.3-10.4), drug use (AHR 3.1, 95% CI: 1.3-7.5), group sex (AHR 2.4, 95% CI: 1.1-5.0), and hepatitis B virus surface antigen (AHR 3.6, 95% CI: 1.3-10.2) were associated with non-CRF01_AE infection. We observed several significant biological and behavioral correlates of infection with CRF01_AE and other HIV strains among Thai MSM. Divergence in correlates by strain may indicate differences in HIV transmission epidemiology between CRF01_AE and other strains. These differences could reflect founder effects, transmission within networks distinguished by specific risk factors, and possibly biological differences between HIV strains.

Multi-layered Gag-specific immunodominant responses contribute to improved viral control in the CRF01_AE subtype of HIV-1-infected MSM subjects.

BackgroundThe purpose of this study was to characterize specific cytotoxic T-cell (CTL) responses in men who have sex with men (MSM) subjects infected with the human immunodeficiency virus type 1 (HIV-1) CRF01_AE subtype during the first year of infection and impacts on viral control and evolution.ResultsFifteen HIV-1 primary infected cases were recruited from Liaoning MSM prospective cohort. CTL responses to Gag, Pol and Nef proteins at 3 month and 1 year post infection were detected with Gamma interferon enzyme-linked immunospot (ELISPOT) assay using optimized consensus overlapping peptides, as well as the viral quasispecies sequences from the synchronous plasma. Gag and Nef proteins were the main targets of CTL responses during the first year of HIV-1 infection, and this was evident from the data after adjusting for the length of amino acids by dividing the amino acids number of the corresponding protein and multiplying by 100. Additionally, relative magnitudes of Gag at both 3 months and 1 year post infection were significantly negatively correlated with the viral set point (p = 0.002, r = −0.726; p = 0.025, r = −0.574). While the relative magnitude of Nef at 1 year post infection were significantly positively correlated with viral set point (p = 0.004, r = 0.697). Subjects with multi-layered Gag immunodominant responses during the first year of infection had significantly lower viral set points than subjects without such responses (p = 0.002).ConclusionMulti-layered Gag immunodominant responses during the first year of infection were correlated with viral control, which provides a theoretical basis for vaccine design targeting MSM subjects with the CRF01_AE subtype.Electronic supplementary materialThe online version of this article (doi:10.1186/s12865-016-0166-8) contains supplementary material, which is available to authorized users.

HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China.

ObjectiveDetermine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF).Methods29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels.ResultsDS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×104 c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1–4% and 24 (60%) at levels of 5–19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS.ConclusionsDS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects.

Geographic distribution and characteristics of genotype A hepatitis B virus infection in acute and chronic hepatitis B patients in Japan.

The prevalence of sexually transmitted acute infections of the genotype A hepatitis B virus (HBV) has been increasing in Japan. Genotype A HBV is associated with an increased risk of HBV progression to chronic infection after acute hepatitis B (AHB) in adults. A nationwide survey was conducted to evaluate the geographic distribution, clinical, and virologic characteristics of genotype A AHB and chronic hepatitis B (CHB) in Japan. Five hundred seventy AHB patients were recruited between 2005 and 2010, and 3682 CHB patients were recruited between 2010 and 2011. HBV genotypes were determined for 552 and 3619 AHB and CHB patients, respectively. Clinical characteristics were compared among different genotypes in AHB and CHB patients. Genomic characteristics of HBV genotype A were examined by molecular evolutionary analysis. Hepatitis B virus genotype A was the predominant genotype for AHB between 2005 and 2010. Phylogenetic analysis showed that all strains in the AHB patients with genotype A were classified into subtype Ae. Among CHB patients, the occurrence of genotype A was 4.1%, and genotype A was spreading in young adults. In genotype A CHB patients, early stage liver diseases were predominant, although liver diseases progressed to cirrhosis or hepatocellular carcinoma in some patients. The distribution of HBV genotypes is quite different between AHB and CHB in Japanese patients. Genotype A infection is spreading in young adults of Japanese CHB patients. Sequences derived from Japanese AHB patients were identical to or closely resembled the sequences derived from other Japanese AHB patients.

Longitudinal Trends in Western Australian HIV-1 Sequence Diversity and Viral Transmission Networks and Their Influence on Clinical Parameters: 2000–2014

We examined baseline HIV-1 protease and reverse transcriptase sequences and HIV clinical parameters from 1,021 consecutive patients (814 male, 207 female) through the Royal Perth Hospital HIV service to investigate HIV-1 subtype diversity and local phylogenetic networks from 2000 to 2014. HIV-1 subtype B virus sequences were demonstrated in 619 (61%) of cases, with increasing non-B HIV-1 subtypes from 23.2% (2000-2003) to 48% (2008-2011) and 43% (2012-2014) (p < 0.001), including the CRF01_AE subtype [6.6% (2000-2003) to 21.5% (2008-2011)] and HIV-1 C subtype [9.5% (2000-2003) to 20.2% (2008-2011)]. More HIV-1 B subtypes were assigned to phylogenetic clusters compared to non-B subtypes (34% vs. 18%; p < 0.001), with larger clusters identified (cluster size >2: 135/211; 64% vs. 13/69; 19%; p = 0.001), including one cluster of 53 HIV-1 B subtype sequences that evolved from 2008 to 2014. Non-B subtype HIV-1 was associated with lower baseline CD4 T cell count (p = 0.005) but not plasma HIV-1 RNA levels (p = 0.31), suggesting relatively delayed diagnosis. Baseline viral load was strongly associated with calendar time [mean 18,620 copies/ml in 2000-2003; 75,858 copies/ml in 2012-2014 (p < 0.001)], and was also associated with larger phylogenetic clusters (size >2) in adjusted analyses (p = 0.03). This study identifies a number of temporal trends over the past 15 years, including an increasing prevalence of non-B subtype HIV-1 that highlights the growing influence of migration and travel on the Australian HIV-1 epidemic and the associated increased role of heterosexual HIV-1 transmission in this context. At the same time, these data indicate that local transmission within predominantly male networks remains a challenging issue for HIV-1 prevention.

Drug-resistance characteristics of CRF01_AE and CRF07_BC subtypes of HIV-1 strains in Sichuan province

To investigate the drug resistance of HIV patients to the HIV-1 CRF01_AE and CRF07_BC strains in Sichuan province during 2010 to 2013. 1.5 ml of plasma were collected from AIDS patients who had been receiving anti-retroviral treatment for over 6 months but still had a HIV-1 virus load of over 1 000 copies/ml from January 1, 2010 to December 31, 2013 in Sichuan province. Genetic analysis of the HIV-1 pol gene was performed using self-established method, and patients with a positive drug-resistant HIV-1 pol gene mutation were included. HIV-1 poly gene was successfully sequenced for a total of 1 213 patients. Drug resistance of different HIV-1 strains was compared with χ2 test or Fisher exact test. 558 cases (46.0%) of the 1 213 successfully sequenced patients were infected by HIV-1-strains with drug-resistant mutations, including 327 cases (58.6%) infected by CRF01_AE strain, 126 (22.6%) by CRF07_BC strain, 46 (8.2%) by CRF08_BC strain, 33 (5.9%) by B strain, 4 (0.7%) by C strain, 1 (0.2%) by CRF02_AG strain, and 21 (3.8%) by unidentified strains. Drug-resistant mutation analysis revealed that L33, F116, L74, Q151, and T69 resistance mutations occurred only in the CRF01_AE strain, while A71, K43, and Q58 resistance mutations occurred only in the CRF07_BC strain; in nuclear nucleoside reverse transcriptase inhibitors (NRTIs) and non nucleoside reverse transcriptase inhibitors (NNRTIs), CRF01_AE subtype strains showed highly resistant rate were higher than CRF07_BC, CRF08_BC and B subtype strains, with the differences were statistically significant (P<0.05). The drug-resistant HIV-1 strains in Sichuan mainly included the CRF01_AE and CRF07_BC strains, which had different resistance mutations.

Short Communication: The Distribution of Potential N-Linked Glycosylation Sites in Gp120 Differs Among Major HIV-1 Subtypes Circulating in China.

CRF01_AE shows an obvious sexual transmission advantage over other major HIV-1 subtypes circulating in China. Previous studies showed that the presence or absence of potential N-linked glycosylation sites (PNGSs) in variable loops might affect HIV-1 transmission; it is therefore of interest to compare the distribution of potential PNGSs on envelopes of different subtypes circulating in China. Compared to CRF07_BC, CRF08_BC, B, and B' subtypes isolated in China, CRF01_AE subtypes isolated from both China and outside China had significantly fewer PNGSs in total and in V2/V4, while they had significantly more PNGSs in V5. HIV-1 subtype CRF01_AE has a unique PNGS distribution pattern in Gp120, which may contribute to its advantage in sexual transmission in China.

Retraction Note to: An infectious molecular clone in early infection with HIV-1 subtype CRF01_AE strains: construction and biological properties.

Our aim was to construct infectious molecular clones of the CRF01_AE subtype in the primary infection phase of an acute HIV-1 infections in people screened from MSM populations, as well as continue preliminary research on this virus and its biological properties pertaining to deriving viruses. Walking sequencing was performed on a half-molecular clone with target fragment inserted. Western Blot was used to detect protein expression in HIV-1 infected 293T cells. Sequence analysis of HIV-1 genomic clones showed full-length HIV-1 genomic clones without frame shift mutation or termination codon. HIV-1 p24 antigens generated from 08-IMC were slightly greater than those from infectious molecular clones pNL4-3 3 and 93JP-NH1, but without statistical difference (all P > 0.05). The relative light units of 08-ISO was higher than those of 08-IMC, but no significant difference was observed (all P > 0.05). 08-IMC-driven virus was linked to lower replication kinetics. The replication levels of pNL4-3 and 08-ISO were significantly higher than the 08-IMC replication level but close to NH1 replication level (all P < 0.05). 08-IMC could infect the cells expressing CCR5 and be replicated in the CCR5-expressing cells with a positive percentage of 24.3 %, 08-ISO may use CCR5-using macrophage-tropic isolates as coreceptor, while pNL4-3 viruses with T cell tropisms utilize the CXCR4 co-receptor. Our study showed that the infectious molecular clones of viruses in the primary infection phase have a close relationship with the major prevalent CRF01_AE strains and have high homology with the viral RNA in plasma.