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

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.
Adult ; China ; epidemiology ; Epidemics ; Genetic Variation ; HIV Infections ; diagnosis ; epidemiology ; virology ; HIV-1 ; classification ; genetics ; isolation & purification ; Homosexuality, Male ; statistics & numerical data ; Humans ; Male ; Middle Aged ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Young Adult

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.
Adult ; Drug Users ; Female ; HIV Infections ; virology ; HIV-1 ; classification ; genetics ; isolation & purification ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Substance Abuse, Intravenous ; virology ; Young Adult

To investigate the subtype distribution of human immunodeficiency virus-1(HIV-1) infection among men who have sex with men (MSM) in Zhengzhou, Henan Province, forty blood samples were collected from HIV-1 carriers, who acknowledged to have sex with men. The complete gag gene was amplified by RT-PCR and nested-PCR and sequenced. All sequences were edited by BioEdit and subtyped by genotyping software. Phylogenetic analysis of gag gene were then performed using the MEGA 3.1 software, the gene distances were calculated by Distance program. There were three different HIV-1 subtypes including B, CRF01-AE and CRF07-BC present among twenty four MSMs in Zhengzhou. Genotyping results showed that 33.33% (8/24) were B, 41.67% (10/24) were CRF01-AE and 25% (6/24) were CRF07-BC, and subtype CRF01-AE had become the most prevalent HIV-1 subtype in Zhengzhou, Henan province. In conclusion, recombinant HIV-1 strains are circulating in Henan province and the epidemiology is complicated.
Adult ; China ; HIV-1 ; classification ; genetics ; isolation & purification ; Homosexuality, Male ; Humans ; Male ; Middle Aged ; Phylogeny ; Sequence Analysis, DNA ; Young Adult ; gag Gene Products, Human Immunodeficiency Virus ; genetics

OBJECTIVETo study the prevalent status of CRF01_AE strains of recombinant HIV-1 in Shenzhen and their source of infection in order to predict the epidemic trend and evolution.

METHODSA total of 489 samples of HIV-1 positive plasma were collected from 1992 to 2008 in Shenzhen. HIV-1 Env genes were amplified by nested-PCR from RNA. Subtype analysis were performed on the nucleotide sequence data. CRF01_AE sequences were analyzed by phylogenetic methods and characterized by calculating the genetic distance.

RESULTSA total of 300 CRF01_AE strain sequences were amplified, accounting for 64.5% of all genotyped samples of all the 465 samples. The CRF01_AE strains of recombinant in 1992 - 1999, 2000 - 2005 and 2006 - 2008 accounted for 56.8% (21/37), 68.4% (78/114) and 64.0% (201/314) of genotyped samples, respectively. And in these three periods of times, 52.4% (11/21), 43.6% (34/78) and 45.8% (92/201) were heterosexually acquired adults; 4.8% (1/21), 0.0% (0/78) and 22.4% (45/201) were homosexually acquired adults; 19.0% (4/21), 51.3% (40/78), 30.8% (62/210) were intravenous drug users, respectively.Phylogenetic tree analysis revealed that HIV samples from different period of time showed distinct aggregation in time and transmission as well as cross infection. The gene divergence rate of CRF01_AE strains in the three different periods of time were (8.783 ± 4.717)%, (11.054 ± 7.141)%, and (13.218 ± 4.080)%, respectively.

CONCLUSIONCRF01_AE is the major epidemic strains in Shenzhen, which is transmitted through heterosexual contact, MSM and intravenous drug users. The gene variation increased gradually as time goes by.

Acquired Immunodeficiency Syndrome ; epidemiology ; virology ; China ; epidemiology ; Evolution, Molecular ; Female ; Genotype ; HIV-1 ; classification ; genetics ; isolation & purification ; Humans ; Male ; Molecular Epidemiology ; Polymerase Chain Reaction ; Recombination, Genetic

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 investigate the subtype distribution and sequence characteristics of HIV-1 strains prevalent in Beijing during 2007 and to analyze the relationship between distribution of HIV-1 subtypes and transmission routes, we collected the anti-conglutinated whole blood samples from HIV-1 newly infected individuals in Beijing during 2007 and separated plasma specimens from the aamples. RNAs were extracted and the gag genes from the various samples were amplified by RT-PCR and nest-PCR. The PCR products were sequenced directly and phylogenetic analyses of gag genes were performed using the MEGA2 software. Among 200 HIV-1 plasma samples,161 gag HIV-1 gene fragments were amplified and analyzed. Seven HIV-1 subtypes or circulating recombinant forms (CRFs) of HIV-1 including A1 (1 strains), B (35 strains), Thai B (19 strains), C (3 strains), CRF01_AE (49 strains), CRF07_BC (51 strains), CRF08_BC (3 strain) were identified circulating in Beijing. The gene divergences inside the subtypes were different, with 7.7%, 6.5%, 6.7%, 6.7%, 5.5%, 4.3%, 5.8%, in subtype A1, B, Thai B, C, CRF01_AE, CRF07_BC, CRF08_BC, respectively. Subtypes CRF07_BC and CRF01_AE were predominant in Beijing account for 31.7% and 30.4% among samples. Seven HIV-1 subtypes exist in Beijing and the surveillance of HIV-1 gene variation should be paid more attention.
Adolescent ; Adult ; China ; epidemiology ; Genotype ; HIV Infections ; epidemiology ; virology ; HIV-1 ; classification ; genetics ; isolation & purification ; Humans ; Male ; Middle Aged ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Young Adult ; gag Gene Products, Human Immunodeficiency Virus ; genetics

PURPOSE: To study the epidemic characteristics, transmission sources and routes of various subtypes of human immunodeficiency virus type 1 (HIV-1) and sequence variations in Henan, central China. To provide theoretical foundation for Acquired Immune Deficiency Syndrome (AIDS) prevention strategy in this region where the primary HIV transmission route was through former paid blood donation. MATERIALS AND METHODS: HIV-1 gene env and gag were amplified by nested polymerase chain reaction (PCR) from uncultured peripheral blood mononuclear cells (PBMCs) obtained from 1,287 HIV-1 confirmed samples in Henan. RESULTS: Among 1,287 samples, 5 HIV-1 strains were found including subtypes B' (95.9%), C (0.47%) and recombinant subtypes CRF 07_BC (1.09%), CRF 08_BC (1.79%) and CRF 01_AE (0.78%). Phylogenetic tree analysis found that 1,234 Henan subtype B' were closely related to those commonly found in Thailand, and were distantly related to other international subtypes. The dominant strain in former blood plasma donors (FPDs) was subtype B', and the dominant strains in sexual transmission were subtype B' and BC. Among HIV patients who were most likely infected through routes other than paid blood donation, the percentage of non-B' subtypes was much higher than those of FPD. CONCLUSION: These findings suggest that the prevailing strain of HIV-1 in Henan is subtype B', similar to the B' subtype found in Thailand. In addition, for the first time we found subtypes C and recombinant subtypes CRF07_BC, CRF08_BC and CRF01_AE in this region. Indicating that the subtype feature of HIV-1 became more complicated than before in central China.
Acquired Immunodeficiency Syndrome/prevention & control ; Blood Donors ; China/epidemiology ; HIV Infections/*epidemiology/transmission/virology ; HIV-1/classification/*genetics/isolation & purification ; Humans ; Phylogeny ; Prevalence ; Thailand

OBJECTIVETo study the epidemic status of human immunodeficiency virus type 1 (HIV-1) subtypes and sequence variations in Henan province and to explore their epidemic characteristics and transmission sources and routes.

METHODSHIV-1 env gene was amplified by nested PRC from uncultured peripheral blood mononuclear cells (PBMCs) obtained from 1157 HIV-1 carriers confirmed in Henan from 2005 to 2006. The C2-V3 region (about 350450 bp) of HIV-1 env was sequenced.

RESULTSOf 1157 samples, there were 4 HIV-1 strains including subtype B', C and recombinant subtype BC and AE, accounting for 96.456% (1116/1157), 0.346% (4/1157), 2.593% (30/1157) and 0.605% (7/1157), respectively. In comparison with the sequences of the international strains of RL42, C.95in21068, 07BC.CN.97.C54A and 01AE.TH.90.CM240, the genetic divergence was (8.971 +/- 3.182)%, (5.109 +/- 0.112)%, (3.568 +/- 0.254)% and (4.775 +/- 0.128)%, respectively. The phylogenetic tree analysis showed that 1116 Henan B' strain was closely related to those of Thailand B' and was far different from other international subtypes. The major transmit route in subtype B' strain was mainly found among former blood donators, while sexual transmission was the major route for BC spreading. For AE, the major transmission was sex and blood transfusion, and sex was defined as the major route for C.

CONCLUSIONThere are four HIV-1 strains including subtype B', C and recombinant subtype BC and AE identified in Henan province currently, and the dominant subtype B' is closely related to HIV-1 strains of Thailand B'. While, for non-B' subtype, there exists the aggregating phenomenon in some local areas. Therefore, it is necessary to attach importance and to strengthen the HIV test and surveillance on migrant populations.

Adolescent ; Adult ; Base Sequence ; China ; DNA, Viral ; Female ; HIV-1 ; classification ; genetics ; isolation & purification ; Humans ; Male ; Middle Aged ; Polymerase Chain Reaction ; Protein Isoforms ; Sequence Analysis, Protein ; Viral Proteins

OBJECTIVEUsing molecular epidemiology method to characterize human immunodeficiency virus type 1 (HIV-1) subtype CRF01 _ AE strains being prevailed in Zhejiang province.

METHODSGag 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.

RESULTS81 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.

CONCLUSIONThe 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.

Adolescent ; Adult ; Child ; Child, Preschool ; China ; epidemiology ; Female ; HIV Infections ; epidemiology ; virology ; HIV-1 ; classification ; genetics ; isolation & purification ; Humans ; Male ; Middle Aged ; Molecular Epidemiology ; methods ; Phylogeny ; Young Adult