In the last decade, next-generation sequencing (NGS) technology, which is characterized by being high-throughput, rapid, sensitive, and accurate, has developed rapidly. Main components of NGS are platforms: 454 sequencing; illumina sequencing; ion torrent sequencing; SOLID sequencing. NGS is used widely for the human immunodeficiency virus (HIV)-1. In this review, we focus on applications of the dynamics of HIV-1 quasispecies.
Animals ; HIV Infections ; virology ; HIV-1 ; classification ; genetics ; isolation & purification ; High-Throughput Nucleotide Sequencing ; methods ; Humans

OBJECTIVETo study the distribution of human immunodeficiency virus-1 (HIV-1) genotypes in Hubei province.

METHODSEpidemiological survey was carried out to HIV-1 carriers who were identified in Hubei province. HIV-1 env V3-V4, gag P17/24 and the first exon of tat region were amplified by nested-polymerase chain reaction(nPCR) .The sequences were determined, and phylogenetic analyses were then performed.

RESULTS4 HIV-1 strains or circulating recombinant forms (CRFs) were identified in Hubei province with subtype B' the predominant which covered 5 kinds of populations including former blood donors, blood receivers, spouses of the infected people, sex workers and their clients, homosexuals, mainly distributed in the areas with many former blood donors. CRF08-BC and CRF01-AE were found distributed in economically more developed cities or southern area of the province, and the major transmission routes was through sexual contact. Only 1 patient, an injecting drug user, was identified having subtype C.

CONCLUSIONSubtype B' was the main epidemic subtypes in Hubei province while CRF08-BC, CRF01-AE and subtype C were also circulating in the province, indicating the transmission of the disease might to become more complex.

China ; epidemiology ; HIV Infections ; epidemiology ; HIV-1 ; classification ; Humans ; Molecular Epidemiology ; Phylogeny ; RNA, Viral ; genetics ; Sequence Analysis, RNA

OBJECTIVEIn order to evaluate the distribution of genetic subtypes and epidemiological feature of HIV-1 circulating strains in Fujian province.

METHODSBlood samples and epidemiological data were collected from 104 newly infected patients who were distinguished by BED-CEIA methodology, during 2011-2012. Viral sequences(n = 81) of HIV-1 gag, env, and pol segments were amplified by nested PCR.

RESULTSSubtypes B and four Circulating Recombinant Forms, (CRF01_AE, CRF07_BC, CRF08_BC and CRF55_01B) were found in the samples, CRF01_AE(45.68%)and CRF07_BC(35.80%) were the two main HIV-1 strains in Fujian province. Compared with previous data, the proportion of CRF07_BC rose significantly while it gradually decreased in CRF01_AE. Heterosexual contact was still the principal transmission route in Fujian province, but the number of infection among men-who-have-sex-with- men grew rapidly.

CONCLUSIONResults from this study suggested that different subtypes of HIV-1 strain existed in Fujian province. The distribution of subtypes and the mode of transmission were changing with the progress of epidemic. Dynamic monitoring of the molecular epidemiology trends of HIV-1 infection should be enhanced.

Adult ; China ; epidemiology ; Female ; Genotype ; HIV Infections ; epidemiology ; HIV-1 ; classification ; genetics ; Humans ; Male ; Molecular Epidemiology ; Young Adult

OBJECTIVETo analyze the geographical distribution and risk factors of HIV-1 subtypes in Yunnan province.

METHODSBlood samples from 1319 HIV positives were collected in Yunnan Province from 2001 to 2006. The nested polymerase chain reaction was used to amplify the gag (p24)-protease fragments from RNA extracted from plasma or sera. The sequences were used for subtype determination by phylogenetic tree analysis.

RESULTSAmong 1319 samples studied, the subtypes has been successfully obtained from 644 samples that were constituted of seven subtypes: CRF08_BC, CRF07_BC, CRF07/08_BC, CRF01_AE, C, B' and URFB/C. C/CRF07_BC/CRF08_BC were distributed in the whole province, but CRF01_AE were mainly distributed in the boarding areas with Myanmar such as Dehong, Baoshan, Xishuangbanna and Puer. Moreover, injecting drugs users accounted for 61.6% (270/438) among C/CRF07_BC/CRF08_BC infections, while only 8.5% (15/177) among CRF01_AE infections.

CONCLUSIONOur data indicated that at least seven subtypes were identified in Yunnan province, the relationship between subtypes and transmission routes were analyzed, and the geographic difference of subtypes was also observed.

China ; DNA, Viral ; Genotype ; HIV Infections ; transmission ; virology ; HIV-1 ; classification ; isolation & purification ; Humans ; Sequence Analysis, DNA

OBJECTIVETo analyze the genome mutations of HIV-1 gag, pol and env genes from HIV-infected paid blood donors in rural central China.

METHODSDNA was extracted from peripheral blood mononuclear cells, gag (p17-p24), pol (PR-RT), env (C2-V5) genes were amplified by nested polymerase chain reaction (PCR), purified products were sequenced, and sequence data was analyzed by MEGA5.0 soft wares.

RESULTSTwenty-three samples were subtype B, two samples were recombinant of subtype B and subtype C, one sample was recombinant of subtype CRF01_AE and subtype B. PI major resistance mutations were not found in the PR region. M184V, K101E and G190A were detected in the RT region, respectively.

CONCLUSIONSubtype B was the major HIV circulating genetic forms in this area. Most strains were sensitive to high active anti-retroviral therapy (HARRT). 91.7% V3 loop tip motifs of X4-tropic strains was GPGR. It showed that GPGR might be associated with accelerate disease progression to AIDS.

Blood Donors ; Drug Resistance, Viral ; genetics ; Genes, pol ; Genotype ; HIV-1 ; classification ; genetics ; Humans ; Phylogeny

OBJECTIVEUsing heteroduplex mobility assay (HMA) to subtype human immunodeficiency virus type 1 (HIV-1) for the purpose of understanding HIV-1 subtype epidemic in Fujian province.

METHODSDNA fragments of HIV-1 env gene were amplified from peripheral blood mononuclear cell (PBMC) cocultures of HIV-1 infected individuals by nested polymerase chain reaction (PCR). Heteroduplexs were formed through hybridizing PCR products from the samples and reference plasmid. According to the mobility of heteroduplexs in polyacrylamide gel electrophoresis, HIV-1 subtype from that sample was characterized and further confirmed by nucleotide sequencing analysis.

RESULTSThirteen of 15 (86.67%) samples were successfully subtyped by HMA, except 2 failures. Subtype E and B took up 80% (12/15) and 6.67% (1/15) respectively. Results indicated a high concordance between HMA and nucleotide sequencing analysis and concordance rate was 86.67% (13/15).

CONCLUSIONSSubtype E appeared to be the major epidemic strain of HIV-1 in Fujian. HMA showed the characteristics of fastness, easiness, economic and with high specificity, and can be used in the surviellance for the epidemic strain of HIV-1.

Genotype ; HIV-1 ; classification ; genetics ; Heteroduplex Analysis ; methods ; Polymerase Chain Reaction

Base Sequence ; Drug Resistance, Viral ; HIV Long Terminal Repeat ; HIV-1 ; classification ; drug effects ; genetics ; Humans ; Molecular Sequence Data ; Phylogeny ; Receptors, HIV ; physiology

OBJECTIVETo identify subtypes of human immunodeficiency virus 1 (HIV-1) strains and their distribution, infection sources, and the trends of HIV infection in Jiangsu province.

METHODSAnticongulated bloods from 46 infected persons were collected to separate previrus DNA. HIV-1 env genes were then amplified by nested-PCR and sequenced for their C2-V3 region so as to identify subtypes. The analysis of consensus sequence, genetic distance and phylogenetic tree were conducted with GCG software.

RESULTSBy the end of 2001, there had been six subtypes of HIV-1 strains identified in Jiangsu province: A, B, B', C, D and E. The predominant subtypes were C (accounting for 40.48%) and B' (accounting for 38.10%). Subtype C accounted for 86.67% among injecting DUs while subtype B' accounted for 91.67% among commercial blood donors and receivers.

CONCLUSIONSubtype B'among commercial blood donors was brought to Jiangsu from neighboring provinces. The outbreak of HIV-1 infection among local DUs was caused by subtype C from Xinjiang province. Findings from HIV/AIDS molecular epidemiologic study suggest that it is challenging for Jiangsu to treat patients, apply vaccine, prevent and control AIDS in the future.

China ; epidemiology ; Genes, env ; genetics ; HIV Infections ; blood ; epidemiology ; HIV Seroprevalence ; HIV-1 ; classification ; genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA

To investigate HIV-1 subtype distribution and prevalence of HIV-1 drug resistance in Liuzhou and Nanning, a total of 304 HIV-infected subjects or AIDS patients from Liuzhou and Nanning were recruited. Whole blood was withdrawn from a peripheral vein of each subject. HIV RNA were extracted from plasma, and subjected to PCR amplification targeting HIV pol gene fragment and DNA sequencing. Sequences obtained were subtyped by phylogenetic analysis. Two subtypes, CRF01_AE and CRF07_BC, were found in subjects from Liuzhou, accounting for 75.2% and 24.8%, respectively. Subtype CRF01 AE, CRFO8_BC, B, and C were found in subjects from Nanning. CRF01_AE and CRF08 BC were still the dominant strains in Nanning, accounting for 85.8% and 11.5%, respectively. Sequences were also analyzed for drug resistance mutations, and rates of drug resistance were calculated. The rate of drug resistance was 3.3% in ART-naive subjects from Liuzhou, and 8.7% in the ART-experienced. For patients from Nanning, the rate was 1.4% in ART-naive subjects, and 27.5% in ART-experienced subjects.
Anti-HIV Agents ; pharmacology ; China ; epidemiology ; Drug Resistance, Viral ; Genotype ; HIV Infections ; epidemiology ; virology ; HIV-1 ; classification ; drug effects ; genetics ; isolation & purification ; Humans ; Molecular Sequence Data ; Phylogeny

To obtain the pure and soluble P51 antigen of HIV-1 strain CN54, we transformed the Escherichia. coli strain BL21 codonplus-RIL with recombinant plasmid pTHioHisA51 which carries a gene encoding the Polymerase (Pol) P51 antigen of HIV-1 CN54 formerly, and induced protein expression by IPTG. We purified the recombinant protein with Chelating Sepharose FF-Ni and DEAE-Sepharose FF column chromatography, then renatured the recombinant protein by dialyzation. Purified protein was identified by Western blotting. We labeled and coated antigen P51 in a dual-antigen sandwich system, and tested it with serum samples from HIV-infected individuals. The results showed that P51 was expressed as inclusion body, and represented about 50% of total cellular protein. After purification and renaturation, the purity of P51 was up to 95%. Western blotting and sandwich ELISA demonstrated that recombinant P51 had good anti-HIV antibody specificity and sensitivity. The results suggested that recombinant HIV-1 P51 can be prepared as diagnostic reagent, and provides valuable support for HIV-1 detection and vaccine research.
Escherichia coli ; genetics ; metabolism ; HIV Antibodies ; blood ; immunology ; HIV Infections ; immunology ; virology ; HIV Reverse Transcriptase ; biosynthesis ; genetics ; immunology ; HIV-1 ; classification ; immunology ; Humans ; Protein Renaturation ; Recombinant Proteins ; biosynthesis ; genetics ; immunology ; Sensitivity and Specificity