Ji-Fu Wei

Rapidly increasing prevalence of HIV and syphilis and HIV-1 subtype characterization among men who have sex with men in Jiangsu, China.

Objectives: To investigate the prevalence of HIV, hepatitis B (HBV), hepatitis C (HCV), and syphilis among men who have sex with men (MSM) in 2 cities of Jiangsu, China, and to characterize the HIV-1 subtypes prevalent among this population. Methods: During September 2006 and July 2007, 296 and 173 MSM were recruited from Nanjing and Yangzhou, respectively. Sera samples were collected and tested for HIV, HBV, HCV, and syphilis infections. The nucleotide sequences of p17 and C2V3 regions were determined by RT-nested-PCR and sequencing. HIV-1 subtypes were characterized by phylogenetic analysis. Results: The prevalence of HIV, HBV, HCV, and syphilis infections among MSM was 5.8%, 11.1%, 0.7%, and 27.7%, respectively. The prevalence of HIV and syphilis was significantly higher in 2006–2007 than in 2003 (P ≤0.0013) in Jiangsu than in other regions of China (P ≤0.003). In contrast, there was no significant difference in HBV and HCV prevalence between present and 2003 studies (P >0.05). The phylogenetic tree of p17 showed that HIV-1 subtypes B, CRF01_AE, and CRF07_BC accounted for 35.7%, 35.7%, and 28.6%, respectively. The result of C2V3 showed that 45.5%, 36.4%, and 18.2% sequences belonged to HIV-1 subtype B, CRF01_AE, and BC recombinants, respectively. The subtype characterization in Jiangsu was significantly different from those in Beijing (P <0.05). Furthermore, Jiangsu HIV-1 B strains were different from majority of China B′ strains and originated from Beijing. Conclusions: The rapidly increasing prevalence and complex subtypes of HIV-1 suggest that effective prevention and intervention strategies are urgently needed for MSM in Jiangsu.

Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups.

BackgroundIt is believed that animal-to-human transmission of severe acute respiratory syndrome (SARS) coronavirus (CoV) is the cause of the SARS outbreak worldwide. The spike (S) protein is one of the best characterized proteins of SARS-CoV, which plays a key role in SARS-CoV overcoming species barrier and accomplishing interspecies transmission from animals to humans, suggesting that it may be the major target of selective pressure. However, the process of adaptive evolution of S protein and the exact positively selected sites associated with this process remain unknown.ResultsBy investigating the adaptive evolution of S protein, we identified twelve amino acid sites (75, 239, 244, 311, 479, 609, 613, 743, 765, 778, 1148, and 1163) in the S protein under positive selective pressure. Based on phylogenetic tree and epidemiological investigation, SARS outbreak was divided into three epidemic groups: 02–04 interspecies, 03-early-mid, and 03-late epidemic groups in the present study. Positive selection was detected in the first two groups, which represent the course of SARS-CoV interspecies transmission and of viral adaptation to human host, respectively. In contrast, purifying selection was detected in 03-late group. These indicate that S protein experiences variable positive selective pressures before reaching stabilization. A total of 25 sites in 02–04 interspecies epidemic group and 16 sites in 03-early-mid epidemic group were identified under positive selection. The identified sites were different between these two groups except for site 239, which suggests that positively selected sites are changeable between groups. Moreover, it was showed that a larger proportion (24%) of positively selected sites was located in receptor-binding domain (RBD) than in heptad repeat (HR)1-HR2 region in 02–04 interspecies epidemic group (p = 0.0208), and a greater percentage (25%) of these sites occurred in HR1–HR2 region than in RBD in 03-early-mid epidemic group (p = 0.0721). These suggest that functionally different domains of S protein may not experience same positive selection in each epidemic group. In addition, three specific replacements (F360S, T487S and L665S) were only found between 03-human SARS-CoVs and strains from 02–04 interspecies epidemic group, which reveals that selective sweep may also force the evolution of S genes before the jump of SARS-CoVs into human hosts. Since certain residues at these positively selected sites are associated with receptor recognition and/or membrane fusion, they are likely to be the crucial residues for animal-to-human transmission of SARS-CoVs, and subsequent adaptation to human hosts.ConclusionThe variation of positive selective pressures and positively selected sites are likely to contribute to the adaptive evolution of S protein from animals to humans.

Detection and identification of plasma bacterial and viral elements in HIV/AIDS patients in comparison to healthy adults

A low level of CD4+ lymphocyte cells makes end-stage HIV/AIDS patients highly susceptible to microbial infections. We have adopted the next generation sequencing method to identify the spectrum of bacterial plasma and viral elements that might be present in these patients. The HIV/AIDS plasma microbiome was dominated by bacterial elements in the taxonomical order Pseudomonadales, while healthy people carried fewer bacterial DNA in the plasma. We have found that many of the bacterial elements in HIV/AIDS plasma are similar to those of the microbes found in the human gut, suggesting potential acquisition of microbial elements from the gut. The HIV/AIDS and normal plasma DNA virome shared some similarities in the presence of common ubiquitous eukaryotic viruses. The normal DNA virome was mainly composed of viruses from Anelloviridae. In contrast, the HIV/AIDS DNA virome contained a large proportion of bacteriophages, endogenous retroviruses and a non-human virus. In addition, several sequences, which might belong to novel bacteria or endogenous retroviruses, were identified. Taken together, the use of high-throughput sequencing technology in unveiling microbial metagenomics may facilitate future research in combating HIV/AIDS and its associated microbial complications.

First detection of a novel HIV type 1 CRF01_AE/07_BC recombinant among an epidemiologically linked cohort of IDUs in Jiangsu, China.

Our recent study showed that almost equal proportions of B, CRFs_BC, and CRF01_AE were circulating among MSM in Jiangsu, suggesting that there is a very high likelihood of generating new intersubtypes/CRFs recombinants. Here, we report an epidemiologically linked cohort including 22 HIV-1-positive IDUs in Jiangsu. Fifteen blood samples were collected to investigate HIV-1 subtype characterization. The analyses of gag-RT regions showed that 14 of these samples belonged to CRF07_BC. Importantly, we detected, for the first time, a novel second-generation HIV-1 recombinant (07JSNJ001) between CRF01_AE and CRF07_BC. The analyses of the near full-length genomic sequence of 07JSNJ001 (GenBank accession number FJ238521) showed that 07JSNJ001 is composed of at least 10 interlaced CRF07_BC and CRF01_AE segments, quite distinct from any previously identified CRF and URF around the world. The detection of the CRF01_AE/CRF07_BC recombinant may be a harbinger of more new intersubtypes/CRFs recombinants occurring in Jiangsu Province.

IFN-λ inhibits HIV-1 integration and post-transcriptional events in vitro, but there is only limited in vivo repression of viral production.

The lambda interferons (IL-28a, 28b, and IL-29) inhibit the replication of many viruses, but their role in the inhibition of HIV-1 infection remains unclear. During this study, we monitored IL-29 production in HIV-1 infected individuals and analyzed the in vitro and in vivo inhibition of HIV-1 production. Prior treatment with IL-28a or IL-29 induced an antiviral state in cultured primary T-cells, which suppressed HIV-1 integration and post-transcriptional events. The antiviral factors MxA, OAS, and PKR were up-regulated. In HIV-1 infected patients, IL-29 level was increased along with the depletion of CD4⁺ T-cells in peripheral blood, while the elevated IL-29 did not show a significantly negative correlation with viral load. Further analysis of HIV-1 infected individuals showed that IL-29 was positively correlated with IFN-β and anti-inflammatory cytokine IL-10, and was negatively correlated with IFN-γ, which might suggest that IFN-λ participates in modulating antiviral immune responses during HIV-1 infection in vivo. Together, although IFN-λ impeded HIV-1 infection of T-cells in vitro, IFN-λ showed only limited in vivo repression of viral production. The modulation of IFN-λ on inflammatory factors might be worthy for further concentrating on for better understanding the host immune response during HIV-1 infection.

Predicted co-receptor tropism and sequence characteristics of China HIV-1 V3 loops: implications for the future usage of CCR5 antagonists and AIDS vaccine development

BACKGROUND The co-receptor tropism of any given HIV-1 isolate is closely associated with the progression of AIDS. Understanding the co-receptor tropism and genetic diversity of circulating HIV-1 strains is critical for AIDS treatment and vaccine development. METHODS All available China HIV-1 V3 sequences with known subtypes/circulating recombinant forms (CRFs) and transmission routes were retrieved from the Los Alamos HIV Sequence Database. HIV-1 co-receptor tropism was predicted using online tool HIV-1 PhenoPred. RESULTS All C/CRF07_BC/CRF08_BC strains appeared to use CCR5 for cell entry (R5 strains), while 61.1% of subtype B and 38.7% of CRF01_AE were also R5, indicating a higher prevalence of R5 (76.9%) than X4. The prevalence of R5 remained relatively stable over the different sample years regardless of C/CRF07_BC/CRF08_BC, B, or CRF01_AE subtypes. The co-receptor usage of HIV-1 appeared to be associated with the different subtypes, rather than transmission route. Furthermore, the V3 sequences of C/CRF07_BC/CRF08_BC were more genetically homogeneous relative to both subtypes B and CRF01_AE. CONCLUSIONS The higher prevalence of R5 and higher level of homogeneity of V3 sequences in C/CRF07_BC/CRF08_BC suggest that CCR5 antagonists will be promising drugs for future AIDS treatment in China, and that circulating R5 strains are valuable candidates for AIDS vaccine development.

Near full-length genome characterization of an HIV-1 CRF01_AE strain in Jiangsu, China: evidence of two independent introductions from Fujian.

The occurrence of a novel CRF01_AE-associated recombinant in Jiangsu implies the importance of characterizing full-length CRF01_AE genomic sequence from injecting drug users (IDUs). Here, we reported a near full-length CRF01_AE sequence 07JSWX045 obtained from a Jiangsu IDU, using a modified method. The sequence analyses of 07JSWX045 revealed several interesting findings. First, 07JSWX045 was phylogenetically close to CRF01_AE strains circulating among Jiangsu men who have sex with men (MSM), implying a recent common ancestor. Second, 07JSWX045 was not genetically associated with the CRF01_AE part of the new CRF01_AE/07_BC recombinant found in Jiangsu. Third, both 07JSWX045 and the CRF01_AE parent of CRF01/07 recombinant phylogenetically clustered with two different CRF01_AE subgroups circulating in Fujian, respectively. It suggests that at least two genetically independent CRF01_AE descendants are circulating in Jiangsu possibly via two independent introductions from Fujian. Fourth, two AZT resistance mutations in the RT gene were detected within patient JSWX045, who did not receive any antiviral therapy before sampling, providing valuable bioinformatics sites for investigating the epidemic origin and molecular properties of Jiangsu CRF01_AE strains. Furthermore, patient JSWX045 had two high-risk behaviors including injection drug use and heterosexual contact. He might have been initially infected with CRF01_AE via heterosexual contact, and then introduced this subtype to other people via injection drug use. Therefore, increasing concern is urgently needed for those persons who often have more than two high-risk behaviors.

Local Base Order Influences the Origin of ccr5 Deletions Mediated by DNA Slip Replication

CCR5 is a seven-transmembrane G-protein-coupled receptor that binds the CC-chemokines including RANTES, eotaxin, MIP-1α and β. CCR5 serves as an essential coreceptor for cell entry of R5 (macrophage-tropic, nonsyncytium-inducing) strains of HIV-1. To date, four deletions have been found in human and primate ccr5. There is little evidence, however, on how these deletion mutations occur. In the present study, we analyzed ccr5 sequences of both mutants and wild type and found that direct repeats flanked the breakpoints of the deletions, suggesting that these deletions resulted from slipped mispairing during DNA replication. Of particular interest was the location of these deletions in or near the regions with higher negative FORS-D values. High negative FORS-D values stand for high stem-loop potential determined by base order and influence mainly the formation of stem-loop structures. Therefore, the particular location of these deletions suggests that the local sequence of bases might be important in the initiation of deletions mediated by DNA slip replication in concert with direct repeats.

Evaluation of FORS-D Analysis: A Comparison with the Statistically Significant Stem-loop Potential

The stem-loop potential of a nucleic acid segment (expressed as a FONS value), decomposes into base composition-dependent and base order-dependent components. The latter, expressed as a FORS-D value, is derived by subtracting the value of the base composition-dependent component (FORS-M) from the FONS value. FORS-D analysis is the use of FORS-D values to estimate the potential of local base order to contribute to a stem-loop structure, and it has been used to investigate the relationship between stem-loop structure and other selective pressures on genomes. In the present study, we evaluated the reliability of FORS-D analysis by comparing it with statistically significant stem-loop potential, another robust method developed by Le and Maizel for examining stem-loop structure. We found that FORS-M values calculated using 10 randomized sequences are as reliable as those calculated using 100 randomized sequences. The resulting FORS-D values have a similar trend and distribution as statistically significant stem-loop potential, implying that FORS-D analysis is as reliable as the latter in measuring the distribution of base order-dependent stem-loop potential. Since the calculation of the FORS-M values is time consuming, the integrated program Bodslp developed by us will become a convenient tool for large-scale FORS-D analysis. The results also suggest that for some purposes the online program SigStb developed by Le and Maizel may be used as an alternative tool for FORS-D analysis.