Dynamic analysis of genetic diversity of gag and env regions of HIV-1 CRF07_BC recombinant in intravenous drug users in Xinjiang Uvghur Autonomous Region, China

HIV-1 diversity in infected individuals in Suzhou and Suqian, China

Jiangsu is one province with severe HIV-1 epidemic in China. However, the molecular epidemiological characterizations of HIV-1 in many cities of Jiangsu remain unclear. A molecular epidemiological investigation was performed based on 38 HIV-positive samples collected from Suzhou and Suqian during 2011–2013. Five HIV-1 genomic fragments, p17, pol, vif-vpr, vpr-env, and C2V3 were amplified and sequenced from these samples. HIV-1 group M subtype of each sample was determined by phylogenetic analyses with the standard reference sequences. Among these infected individuals, 81.6 % (31/38) self-reported to be infected via sexual contacts, including 50.0 % (19/38) via heterosexual contact and 31.6 % (12/38) via homosexual contact. Among 34 samples with available pol or vif-env sequence, 19 (55.9 %) CRF01_AE, 7 (20.6 %) CRF07_BC, 3 (8.8 %) CRF08_BC, and 5 (14.7 %) inter-subtype recombinants were identified. No pure B, B′ and C subtypes were found in this cohort. The five recombinants contain one B/C, three CRF01/B and one CRF01/B/C recombinants. These results suggest that CRF01_AE was the most predominant HIV-1 group M subtype and CRF01_AE-involved recombinants were the major recombinant forms. Comparison showed that there was no obvious difference in HIV-1 group M subtype distribution between Jiangsu (including Suzhou and Suqian) and the surrounding provinces (e.g., Shanghai, Anhui, and Shandong). CRF01_AE and CRF07_BC were the top two predominant HIV-1 genotypes in Jiangsu, and less and/or no pure subtype B and C was currently circulating here. We predicted that more CRF01/CRF07 recombinants, but fewer B/C recombinants will be generated in Jiangsu in future.

Cross-neutralizing antibody profile of Chinese HIV-1-infected individuals and the viral envelope features from elite neutralizers

OBJECTIVE

Knowledge about the profile of neutralization responses and the viral envelope features of HIV-1-infected individuals in China may provide new insights for vaccine design against local viruses.

METHODS

Eight hundred sixty plasma samples from antiretroviral treatment-naive HIV-1-infected individuals in Xinjiang province (611) and Guangxi province (249), who had acquired infection over 3 years through intravenous drug use or sexual contact, were examined for their ability to neutralize diverse envelope-pseudoviruses of 5 subtypes. The sequence features of the envelopes from elite neutralizers were analyzed.

RESULTS

From Xinjiang and Guangxi, 29.1% and 5.2% of plasmas displayed intrasubtype cross neutralization against subtype B and subtype C, respectively. From Xinjiang, 10.6% of the plasmas displayed broad neutralization against the 3 subtypes, B, C, and CRF01_AE; whereas only 2.4% from Guangxi displayed broad neutralization. Envelopes from 6 elite neutralizers were obtained by single-genome amplification. The variations of their envelopes including the lengths, glycans, and net charges in V1, V2, and V4 regions were compared with those from CRF07_BC env sequences from the HIV Sequence Database. The Envs from 3 elite neutralizers displayed the sensitivities to the monoclonal broadly neutralizing antibodies such as PG9, PG16, and 4E10. Some unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers were found.

CONCLUSIONS

The neutralization profile of HIV-1-infected individuals in the 2 regions of China, where the HIV-1 subtypes are the representative in China, and the unique characteristics of the envelope glycoproteins from the Chinese elite neutralizers provide useful information for viral infection prevention and an insight for vaccine design against locally epidemic viruses.

A new migration map of HIV-1 CRF07_BC in China: analysis of sequences from 12 provinces over a decade

BACKGROUND

As one of prevalence HIV-1 strains in IDUs in Asia, the origination and full transmission map of CRF07_BC is of great interested and remains unclear. In the study, we collected 769 CRF07_BC derived sequences (including 45 sequences generated in our laboratory) from 12 provinces in China for reconstructing transmission map. Meanwhile, ample historic epidemic evidences were also reviewed to assist sequences analysis.

METHODOLOGY/PRINCIPAL FINDINGS

In the study, we collected 769 CRF07_BC derived sequences and identified 138 independent sequences from 12 provinces in China for subsequent phylogeographic tree analysis, Bayes Factor test and the estimation of state tMRCA. The analyses demonstrated that CRF07_BC was originated in 1993 in IDU in Yunnan province and then initially spread to Guangxi (eastern neighbor to Yunnan) in 1994, to Xinjiang (northwest) in 1995 and to Sichuan (northern neighbor to Yunnan) in 1996. The subsequent transmissions occurred from Yunnan to Liaoning (northeast) in 1997 and to Jiangsu in 1998. Interestingly, after the early introduction of CRF07_BC into Guangxi, Xinjiang and Sichuan, these three regions served as secondary epicenters for further spreading into Gansu, Ningxia, Qinghai, Beijing and Hunan during 1999-2001. These analyzed results are in accordance with early epidemic investigations.

CONCLUSIONS/SIGNIFICANCE

Our data not just reconstructed the migration map of CRF07_BC, but also firstly revealed the active roles of these secondary epicenters in the dynamic migration of CRF07_BC in China.

HIV epidemic in Asia: optimizing and expanding vaccine development

The recent evidence in Thailand for protection from acquisition of HIV through vaccination in a mostly heterosexual population has generated considerable hope. Building upon these results and the analysis of the correlates of risk remains among the highest priorities. Improved vaccine concepts including heterologous prime-boost regimens, improved proteins with potent adjuvants and new vectors expressing mosaic antigens may soon enter clinical development to assess vaccine efficacy in men who have sex with men. Identifying heterosexual populations with sufficient HIV incidence for the conduct of efficacy trials represents perhaps the main challenge in Asia. Fostering translational research efforts in Asian countries may benefit from the development of master strategic plans and program management processes.

Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity

Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution.

Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection

BACKGROUND

Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM) diversity assay to compare HIV diversity in adults with different stages of HIV infection. This assay provides a single numeric HRM score that reflects the level of genetic diversity of HIV in a sample from an infected individual.

METHODS

HIV diversity was measured in 203 adults: 20 with acute HIV infection (RNA positive, antibody negative), 116 with recent HIV infection (tested a median of 189 days after a previous negative HIV test, range 14-540 days), and 67 with non-recent HIV infection (HIV infected >2 years). HRM scores were generated for two regions in gag, one region in pol, and three regions in env.

RESULTS

Median HRM scores were higher in non-recent infection than in recent infection for all six regions tested. In multivariate models, higher HRM scores in three of the six regions were independently associated with non-recent HIV infection.

CONCLUSIONS

The HRM diversity assay provides a simple, scalable method for measuring HIV diversity. HRM scores, which reflect the genetic diversity in a viral population, may be useful biomarkers for evaluation of HIV incidence, particularly if multiple regions of the HIV genome are examined.

Phylogeographic analyses reveal a crucial role of Xinjiang in HIV-1 CRF07_BC and HCV 3a transmissions in Asia

Background

China faces an increasing prevalence of two HIV-1 circulating recombinant forms (CRFs) 07_BC and 08_BC. Both CRFs_BC were previously demonstrated to originate in Yunnan and spread to Liaoning from Yunnan via injection drug use (IDU) in China. Supposing it is true, we are unable to answer why only CRF07_BC, rather than both CRFs_BC together, was transmitted to Xinjiang.

Methodology/Principal Findings

We investigated the phylogeography of CRF07_BC and CRF08_BC using multiple HIV-1 genomic regions with Bayesian phylogeography method. Phylogenetic reconstructions showed that all CRF07_BC sequences were divided into two clades, Yunnan and Xinjiang, and all strains from other regions of mainland China clustered within the Xinjiang clade. Significant geographic diffusion links of Xinjiang with other regions (including Liaoning, Beijing, Jiangsu and Guangdong) were supported by Bayes factor tests. The temporal dynamics analyses showed that CRF07_BC spread from Xinjiang to Liaoning in 1996.10, and to Jiangsu in 2000.9. The analyses of CRF08_BC not only confirmed the previous conclusion on temporal and spatial dynamics of CRF08_BC, but also indicated that the CRF08_BC strains from Guangdong and Shanghai originated from Yunnan. The analyses of HCV 3a showed that it was introduced into Xinjiang in the early 1980s, and spread from Xinjiang to Yunnan in 1990.10 and to Jiangsu in 1999.2, and further from Yunnan to Guangxi in 1995.3. The temporal and spatial dynamics of HCV 3a were similar to some extent to that of HIV-1 CRF07_BC and/or CRF08_BC, suggesting a possible association in migration patterns between HCV and HIV-1 through IDU. In addition, HCV 3a spread from Xinjiang to Pakistan, implying a drug trafficking route linking them.

Conclusions/Significance

Xinjiang, as the most important transfer station for drug trafficking from Golden Crescent to other regions of China, plays a very crucial role in the transmission of viruses (e.g., HIV-1 and HCV) through IDU in Asia.

Association of HIV diversity and survival in HIV-infected Ugandan infants

BACKGROUND

The level of viral diversity in an HIV-infected individual can change during the course of HIV infection, reflecting mutagenesis during viral replication and selection of viral variants by immune and other selective pressures. Differences in the level of viral diversity in HIV-infected infants may reflect differences in viral dynamics, immune responses, or other factors that may also influence HIV disease progression. We used a novel high resolution melting (HRM) assay to measure HIV diversity in Ugandan infants and examined the relationship between diversity and survival through 5 years of age.

METHODS

Plasma samples were obtained from 31 HIV-infected infants (HIVNET 012 trial). The HRM assay was used to measure diversity in two regions in the gag gene (Gag1 and Gag2) and one region in the pol gene (Pol).

RESULTS

HRM scores in all three regions increased with age from 6-8 weeks to 12-18 months (for Gag1: P = 0.005; for Gag2: P = 0.006; for Pol: P = 0.016). Higher HRM scores at 6-8 weeks of age (scores above the 75(th) percentile) were associated with an increased risk of death by 5 years of age (for Pol: P = 0.005; for Gag1/Gag2 (mean of two scores): P = 0.003; for Gag1/Gag2/Pol (mean of three scores): P = 0.002). We did not find an association between HRM scores and other clinical and laboratory variables.

CONCLUSIONS

Genetic diversity in HIV gag and pol measured using the HRM assay was typically low near birth and increased over time. Higher HIV diversity in these regions at 6-8 weeks of age was associated with a significantly increased risk of death by 5 years of age.

Constraints on HIV-1 diversity from protein structure

The high rate of HIV-1 evolution contributes to immune escape, enables the virus to escape drug therapy, and may underlie the difficulty of producing an effective vaccine. Identifying constraints on HIV evolution is therefore of prime importance. To investigate this problem, we examined the relationships between sequence diversity, selection, and protein structure. We found that while there was an increase in sequence diversity over time, this variation had a tendency to be limited to specific structural regions. When individual sites were analyzed, there was, in contrast, substantial and widespread evolutionary constraint over gag and env. This constraint was present even in the highly variable envelope proteins. The evolutionary significance of an individual site is indicated by the change in selection pressure along the time course: increasing entropy indicates that the site is evolving predominantly in a more "clock"-like manner, low entropy values with no increase indicate a high degree of constraint, and high entropy values indicate a lack of constraint. Few sites display high degrees of turnover. Mapping these sites onto the three-dimensional protein structure, we found a significant difference between evolutionary rates for regions buried in the core of the protein and those on the surface. This constraint did not change over the time period analyzed and was not subtype dependent, as similar results were found for subtypes B and C. This link between sequence and structure not only demonstrates the limits of recent HIV-1 evolution but also highlights the origins of evolutionary constraint on viral change.

Review of HIV and HCV infection among drug users in China

PURPOSE OF REVIEW

Drug abuse has resulted in a huge public health and economic burden in China, especially the rapid spread of HIV/AIDS and hepatitis C virus (HCV) infection. Multiple HIV and HCV subtypes were detected among drug users in China, this study reviews the molecular distribution of HIV and HCV among injection drug users (IDUs) and explores new epidemiologic trends of HIV and HCV among drug users in China.

RECENT FINDINGS

The 2009 National Narcotic Control Commission report showed that the percentage of users of 'new-type drugs', including amphetamine-type stimulants (ATS: methamphetamine and MDMA/ecstasy) and ketamine, was about 27% of total drug users. The pooled data from published papers showed that CRF07BC was the predominant HIV-1 subtype, which accounted for 38.8%, and it was followed by AE, which accounted for 22.7% among HIV-positive IDUs. Following these, the CRF08BC, B' and C subtypes accounted for about 10.8%, 9.9% and 9.2%, respectively. Subtype 6a was the predominant HCV subtype, accounting for 36.7%, and subtypes 3b, 1a, 3a and 1b were the next most predominant subtypes.

SUMMARY

With the increase of 'new-type drugs' use and AE HIV-1 subtype infection among IDUs, the situation regarding HIV/AIDS and HCV infection has become complicated. More comprehensive prevention and intervention strategies should be instigated for the extensive high-risk populations in China.

Phenotypic and genotypic characterization of human immunodeficiency virus type 1 CRF07_BC strains circulating in the Xinjiang Province of China

Background

HIV-1 CRF07_BC recombinant previously circulated mainly among the intravenous drug users (IDUs) in Xinjiang province of China and is currently spreading in the entire country. The aim of this study is to characterize the genotypic and phenotypic properties of HIV-1 CRF07_BC isolates in comparison with those of the subtype B' (Thailand B) which is prevalent in the former plasma donors (FPDs) in China.

Results

Twelve HIV-1 CRF07_BC variants were isolated from the blood of the HIV-1-infected IDUs in Xinjiang province, and 20 subtype B' isolates were obtained from the FPDs in Anhui and Shanxi provinces of China. All the CRF07_BC viruses utilized CCR5 co-receptor, whereas 12 subtype B' viruses were R5-tropic, and the remaining B' isolates were dual (R5X4) tropic. CRF07_BC viruses had lower net charge value in the V3 loop and exhibited slower replication kinetics than subtype B' viruses. The number and location of the potential N-linked glycosylation sites in V1/V2 and the C2 region of the CRF07_BC viruses were significantly different from those of the subtype B' viruses.

Conclusion

The HIV-1 CRF07_BC recombinant strains with relatively lower net charges in the V3 loop exclusively utilize CCR5 co-receptor for infection and exhibit slow replication kinetics in the primary target cells, suggesting that CRF07_BC may be superior over B' and other HIV-1 subtypes in initiating infection in high-risk population. These findings have molecular implications for the adaptive evolution of HIV-1 circulating in China and the design of tailored therapeutic strategy for treatment of HIV-1 CRF07_BC infection.