Molecular epidemiological characteristics of HIV-1 strains isolated from newly diagnosed MSM subjects (2006-2010) in Beijing, China / 病毒学报

This study aims to analyze the molecular epidemiological characteristics of HIV-1 strains prevailing among men who have sex with men (MSM) in Beijing, China. The pol gene fragments from 250 newly diagnosed HIV-1-infected MSM individuals during 2006-2010 in Beijing were amplified by RT-nested PCR, sequenced, and phylogenetically analyzed. HIV-1 pol gene from 189 individuals were amplified and analyzed; 81 (42. 9%), 3 (1. 6%), 2 (1.0%), 88 (46. 6%), and 15 (7.9%) individuals were infected with HIV-1 subtypes B, B', C, CRF01_AE, and CRF07_BC, respectively. The subtypes B and CRF01_AE could both be grouped into two clusters, and CRFO7_BC strains shared high homology and were presumed to originate from a common ancestor. The HIV-1 circulating in MSM in Beijing had a lower genetic diversity than in heterosexuals. The HIV-1 epidemic (2006-2010) in MSM in Beijing was actually a rapid spread of HIV-1 CRF01 AE and B, or rather native strains of the two viruses.

Molecular-epidemiological characteristics of HIV-1 isolated from newly diagnosed female subjects in Beijing, 2006 - 2010 / 中华流行病学杂志

<p><b>OBJECTIVE</b>To analyze the molecular-epidemiological characteristics of HIV-1 strains prevailing among female people living with HIV in Beijing.</p><p><b>METHODS</b>Gag gene fragments from the 100 newly diagnosed female HIV-1 infections during 2006 to 2010 in Beijing were amplified, sequenced, and phylogenetically analyzed.</p><p><b>RESULTS</b>Eighty-two HIV-1 gag gene fragments were amplified and analyzed. 1 (1.22%), 1 (1.22%), 3 (3.66%), 23 (28.05%), 8 (9.76%), 2 (2.44%), 1 (1.22%), 18 (21.95%), 3 (3.66%), 1 (1.22%), 14 (17.07%), 4 (4.88%) and 3 (3.66%) individuals were infected with HIV-1 subtypes A1, A2, B, B', C, D, G, H, CRF01_AE, CRF02_AG, CRF07_BC, CRF08_BC and B'/C recombinants respectively.</p><p><b>CONCLUSION</b>The subtypes circulating in female HIV infections in Beijing were more diverse than in male and the proportions of B' and rare subtypes were relatively high. Surveillance programs on HIV-1 genetic diversity should be strengthened.</p>

Genetic characteristics of viral quasispecies of HIV-1 CRF07_BC among intravenous drug users / 病毒学报

To explore the genetic characteristics of viral quasispecies in HIV-1 CRF07_BC infections among intravenous drug users (IDU), the gp120 fragments of HIV-1 env gene were amplified from plasma samples collected from 6 CRF07_BC infected persons using single genome amplification and sequencing (SGA/ SGS) method, and 11 to 28 sequences were obtained from these samples, respectively, A neighbor-joining phylogenetic tree was reconstructed to describe the genetic characteristics of viral quasispecies. The Simplot, segments' phylogenetic trees and diversity plots based on average pairwise distance (APD) were used to identify the recombination events between quasispecies. The SGA sequences derived from single specimen formed a large monophyletic cluster in the neighbor-joining phylogenetic tree and showed the complex topologic structures of viral quasispecies. Of the 6 CRF07_BC infected patients, only one possessed the high genetic homogeneity, whereas the other five individuals showed high heterogeneity, with two to four subclusters inside the monophyletic cluster for each specimen. In addition, the recombinant events were identified among viral quasispecies from 3 cases. The results show SGA technique and phylogenetic analyses are useful tool to investigate the intrahost CRF07_BC gp120 complex quasispecies variation and high genetic diversity.

A new approach for sequencing virion genome of Chinese HIV-1 strains subtype B and BC from plasma / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>Although it was widely accepted that full-length HIV genome sequences is important in studying virus genetic evolution and variation as well as developing vaccine candidate, to directly sequencing HIV-1 genome of virion RNA remains as a challenge worldwide. Up to date, no published genomic sequences from virion RNA are available for Chinese prevalent HIV-1 strains due to the absence of specialized protocol and appropriate lab equipments. In this study we developed a straightforward approach for amplifying and sequencing HIV virion RNA from plasma by modifying published protocols and further confirmed it is suitable to process Chinese samples.</p><p><b>METHODS</b>The methods for viral RNA extraction and gene amplification was modified and optimized as could be widely used in most Chinese labs. Gene alignment of Chinese HIV-1 strains was employed for designing specialized primer sets for Thai-B and BC recombinant strains. Based on comprehensively consideration of high variable gene region and recombinant breakpoints in BC recombinant strains, a three-amplicon strategy (including 4.3-kb gag-pol, 2.9-kb pol-env and 2.7-kb env-nef) was developed. In addition, one amplicon (9 kb near full-length genome) was also used in 32 samples with varied viral loads. All amplicons were directly sequenced by DNA automated sequencer.</p><p><b>RESULTS</b>Twenty-five percent (8/32) amplification efficiency was achieved by the one-amplicon strategy and 65.6% (21/32) by three-amplicon strategy. For one amplicon strategy, none of complete near full-length genome sequences was obtained by DNA sequencing. For three-amplicon strategy, 75% sequences were achieved in DNA sequencing. Amplification efficiency but not sequencing efficiency was closely associated with viral loads.</p><p><b>CONCLUSION</b>Three-amplicon strategy covering all encoding regions of HIV-1 is suitable for Thai-B and BC recombinant strains and could be potentially employed in less-well equipped Chinese labs.</p>

Genetic characteristics of HIV-1 CRF01_AE strains circulating in Beijing / 中华流行病学杂志

Objective To analyze the genetic characteristics of HIV-1 CRF01_AE strains prevailing in Beijing. Methods Plasma samples were collected from the newly diagnosed HIV-1 individuals being reported during 2006 to 2008 in Beijing. Gag gene fragments were amplified from RNA template which were extracted from plasma by RT and nested PCR methods. 105 CRF01_AE sequences were analyzed by phylogcnetic methods and characterized through calculating the genetic distance and Entropy analysis. Results There were four main sub-clusters in the phylogenetic tree.We named them as sub-clusters Homo-Max ( 67 sequences ), Hetero( 6 sequences), Mix (8 sequences)and Homo-Min ( 18 sequences)respectively, based on the mode of transmission. It was found that no international reference strain was closely related to the sub-cluster Homo-Max, Hetero or Homo-Min,including 91 samples. The strains in sub-cluster Mix consisting 8 cases that were closely related to the strains identified in Thailand and Vietnam. Genetic distance analysis on gag genes showed that the diversity of sub-clusters Homo-Max and Homo-Min was obviously less than that of the sub-cluster Hetero or Mix. When compared with sub-cluster Mix, there were 37,29 and 11 significantly different nucleotides polymorphism compositions sites in sub-clusers Homo-Max Homo-Min and Hetero.Conclusion This was the first report describing that four main epidemic sub-clusters were existed in CRF01_AE strains prevailing in Beijing. The virus with sub-cluster Homo-Max was the dominant strain in this region with shorter period of circulation and higher proportion seen in the HIV-infected persons. The virus in sub-cluster Mix was highly homologic with the CRF01_AE strains from Thailand and Vietnam.

Genotypic drug-resistance of HIV-1 CRF01_AE in Zhejiang province, 2004-2007 / 中华流行病学杂志

Objective To study the genotypic drug-resistant mutation among treat-naive or treated patients infected with HIV-1 CRF01_AE in Zhejiang province during 2004-2007. Methods HIV-i pol amplicons (PR+RT) from 13 treated and 43 treat-naive patients were obtained by reverse transcription-polymerase chain reaction (RT-PCR). The sequences were analyzed for genotypic antiretroviral resistance through online tools (http://hivdb.stanford.edu). Results The median count of CD44+ T lymphocytes in 43treat-naive patients was 229 cells/mm3 and the median log10 viral load was 3.41. Some drug-resistant mutations were seen in these samples including amino acid 10, 46, 71, in the genes of protease (PR) and 103, 118, in the genes of reverse transcriptase (RT) whereas twenty-nine resistance mutations in the genes of PR and RT were obtained in the 13 treated patients (8/13, 61.5% ). The high prevalence of drug-resistant mutations was observed in patients who had been receiving HAART (hight active antiretroviral therapy). Among them, cross drug resistance was dominant. Correspondingly, the median counts of CD44+ T lymphocytes and the log10 viral load were 186 cells/mm3 and 3.91. Conclusion There was a low prevalence of genotypic drug-resistant mutations in treat-naive patients, but higher drug-resistant mutation in treated patients. More attention should be paid to the transmission of drug-resistant HIV strains and the antiretroviral therapy recipe should be adjusted correspondingly for the development of ART drugs, intervention as well as clinical therapy programs.

Unusual patterns of neural tube defects in a high risk region of northern China / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To study the prevalence of different types of neural tube defects (NTDs) in Luliang Prefecture, Shanxi province, where the prevalence of NTDs is unusually high and the correlation between NTDs prevalence and patterns.</p><p><b>METHODS</b>A surveillance population-based birth defects was performed in Luliang Prefecture, Shanxi province.</p><p><b>RESULTS</b>The results of our study showed that the prevalence of NTDs was 2-fold higher in Luliang Prefecture than in other areas of Shanxi province. Unusual patterns of NTDs were found, however, multiple NTDs were relatively common in Luliang Prefecture, accounting for over 13% of all NTDs cases in China.</p><p><b>CONCLUSION</b>The prevalence of NTDs is associated with its patterns.</p>

Recombinant expression of human influenza A virus nucleocapsid protein and its antigenicity analyses / 中华实验和临床病毒学杂志

<p><b>OBJECTIVE</b>To prepare anti-recombinant protein antibody from immunized mice with recombinant nucleocapsid protein (NP) of human influenza A3 (IFV-A3) virus expressed in prokaryotic cell, and to explore the feasibility of utilizing anti-recombinant protein antibody to detect influenza A virus.</p><p><b>METHODS</b>NP genes of human influenza A virus were analyzed with computer softwares of ClustalX, Antheprot, et al. to determine the antigenicity in conserved regions. Three different partial NP genes were harvested and cloned into pET-28(c) plasmid, the recombinant plasmids were induced to express partial NP segments in BL21 cells. The recombinant proteins were purified with Ni-agarose by affinity chromatography and immunized BALB/c mice. The polyclonal antisera harvested from mice were analyzed with Western Blot and immunohistochemistry assays to detect the reactions with IFV-A.</p><p><b>RESULTS</b>Three recombinant plasmids were expressed with high yield in BL21 cells, about 15-20 mg/L. Western Blot results indicated that the three prepared antisera (1:2000) positively reacted with NP from IFV-A3-infected cells. And immunohistochemistry assays suggested that anti-NP1, anti-NP2, anti-NP3 antisera positively reacted with IFV-A3 or IFV-A1-infected MDCK cells, with titers of 1:640 to 1:1280.</p><p><b>CONCLUSION</b>The recombinant NP of IFV-A3 would induce polyclonal antibodies with high titers in mice. The polyclonal antibodies would cross-react with IFV-A3 and IFV-A1. It is feasible to predict the antigenicity with systematical bioinformatics analyses and then induce anti-IFV antibodies with high dilutions, and it is possible to be utilized in the early detection and subtyping analyses of IFV-infections.</p>

Molecular characteristics of HIV-1 CRF01 _ AE strains in Zhejiang province / 中华流行病学杂志

<p><b>OBJECTIVE</b>Using molecular epidemiology method to characterize human immunodeficiency virus type 1 (HIV-1) subtype CRF01 _ AE strains being prevailed in Zhejiang province.</p><p><b>METHODS</b>Gag fragments of the HIV-1 strains were amplified by nested-polymerase chain reaction (nPCR) from the DNA extracted from whole blood of HIV-1 infected individuals in Zhejiang province. PCR products were sequenced and analyzed by phylogenetic method.</p><p><b>RESULTS</b>81 HIV-1 subtype CRF01 _ AE sequences were identified from the 192 samples that sequenced successfully. As one of the dominant subtypes in Zhejiang, CRF01 _ AE was transmitted mainly by heterosexual or homosexual contact in local residents. In migrants living in Zhejiang, CRF01 _ AE were transmitted mainly by heterosexual contact or injecting drug use. There were three main clusters in the phylogenetic tree which bootstrap value was larger than 60. We named the clusters with group MIX (47 sequences), group SEX (7 sequences) and group MSM (12 sequences) based on the transmission. Pairwise DNA distances in the gag region within the three groups and between CM240 were different (P = 0.000). Data through the analyses of deduced amino acid sequences from the three groups showed that several signature amino acid sites were distinct from the same positions of the subtype reference strains.</p><p><b>CONCLUSION</b>The CRF01 _ AE strain prevailing in Zhejiang province was from several sources, transmitted by more than three different transmission routes, and becoming the main subtypes circulating in homosexual population in this study. More attention needs to be paid to the epidemic characteristic of CRF01 _ AE.</p>

Correlation between birth defects and dietary nutrition status in a high incidence area of China / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To investigate the association between birth defects and dietary nutrient intake in a high risk area of China.</p><p><b>METHODS</b>A dietary survey was performed and serum folic acid was measured in women whose pregnancy was affected by neural tube defects (NTDs) or unaffected by any birth defects (BDs) in Zhongyang and Jiaokou Counties in Shanxi Province of China.</p><p><b>RESULTS</b>The local average consumption of foods including dark green vegetables, fruits, fat and meat, and nutrient intake (e.g., energy, protein, retinol, riboflavin, vitamin E, and selenium) were lower than the national average level. In women of childbearing age, these regions, the intake of nutrients was much lower than the recommended nutrient intake (9%-77%). The case-control dietary nutrition study of women whose pregnancy was affected by BDs (including NTDs and congenital heart defects) demonstrated that, in early pregnancy, adequate nutrition (i.e., eating meat, fresh vegetables, fruit more than once a week) was a protective factor, while eating germinated potatoes was a risk factor. The geometrical mean (p5-p95) of serum folic acid in women with NTD birth defects was 9.6 nmol/L (3.6, 23.03), which was significantly lower than that in normal women (14.03 nmol/L).</p><p><b>CONCLUSION</b>Women of childbearing age in the two counties of Shanxi Province, China, have a marked insufficient intake of some nutrients, especially folic acid, zinc, vitamins A and B12. This nutrient deficiency may be an important risk factor for the high prevalence of birth defects in these regions. Therefore, adequate dietary nutrition in early pregnancy can prevent BDs.</p>

Intrauterine infections and birth defects / 生物医学与环境科学（英文）

Intrauterine infection is an important cause of some birth defects worldwide. The most common pathogens include rubella virus, cytomegaloviurs, ureaplasma urealyticum, toxoplasma, etc. General information about these pathogens in epidemiology, consequence of birth defects, and the possible mechanisms in the progress of birth defects, and the interventions to prevent or treat these pathogens' infections are described. The infections caused by rubella virus, cytomegaloviurs, ureaplasma urealyticum, toxoplasma, etc. are common, yet they are proved to be fatal during the pregnant period, especially during the first trimester. These infections may cause sterility, abortion, stillbirth, low birth weight, and affect multiple organs that may induce loss of hearing and vision, even fetal deformity and the long-term effects. These pathogens' infections may influence the microenvironment of placenta, including levels of enzymes and cytokines, and affect chondriosome that may induce the progress of birth defect. Early diagnosis of infections during pregnancy should be strengthened. There are still many things to be settled, such as the molecular mechanisms of birth defects, the effective vaccines to certain pathogens. Birth defect researches in terms of etiology and the development of applicable and sensitive pathogen detection technology and methods are imperative.