福建省HIV-1流行毒株基因分型与流行特征分析

目的了解HIV-I流行株在福建省感染人群中的基因亚型分布及流行特征。方法随机抽取福建省2003-2005年发现的70例HIV感染者血样，提取前病毒DNA进行体外扩增，获得核心蛋白（gag）、包膜蛋白（env）及pol区基因的核酸片段，并对各基因区核苷酸序列进行测定和序列分析。结果选取46份流行病学资料以及不同基因区域序列资料完整的样本进入亚型分析，结果显示目标人群中存在B、C2种亚型以及CRF07-BC、CRF08-BC、CRF01-AE3种流行重组型，以及国内未见报道的B／F重组毒株、A1／D重组毒株等，其中以CRF01-AE重组毒株为主，占69．56％。基因亚型的流行特征分析显示，本省感染的HIV患者中以CRF01-AE重组型占多数，可能的新型重组型全部分布于境外感染者中；在性接触传播的感染者（71．74％）中呈现多种亚型分布的特征；随着时间变化福建省HIV感染者的亚型分布发生变化。结论福建省HIV-I亚型分布众多，各亚型在不同感染地分布不平衡，性乱人群中的亚型分布较为复杂，从总的亚型流行特征来看，HIV-1在我省有流行加快的趋势。     

出入境人群HIV-1型env C2-V3区段基因序列分析和亚型研究

目的 了解出入境人群艾滋病病毒Ⅰ型(HIV-1)感染者毒株基因亚型分布及流行特征.方法 收集2001年以来上海口岸HIV抗体检测确认阳性的血样标本,提取前病毒DNA,使用套式聚合酶链反应进行体外扩增,获得包膜蛋白区基因(env)的核酸片段,测定其序列和进行亚型分析.结果 获得20例标本的亚型分析结果,共检出8个亚型,包括B亚型7例,CRF02-AG 3例,C亚型3例,CRF01-AE 2例,A亚型2例,B、CRF07-BC和CRF08-BC亚型各1例.上海口岸HIV-1毒株亚型分布于11个国家和地区,主要流行B亚型.结论 上海口岸流行的HIV-1毒株复杂多样,出入境人员是我国HIV毒株输入的主要渠道,流行毒株以性接触传播为主.     

MSM人群急性HIV-1感染者病毒亚型分析

目的研究2007-2009年男男性行为人群（MSM）艾滋病病毒-1型（HIV-1）的基因亚型,以监测MSM人群HIV病毒株的最新流行情况。方法采集95例MSM急性HIV-1感染者的外周全血,从外周全血浓缩白细胞中提取脱氧核糖核酸（DNA）,用巢式聚合酶链反应（Nested-PCR）对HIV-1的前病毒DNA进行扩增,然后检测并分析PCR扩增产物的核苷酸序列,确定病毒的基因亚型。结果 95例感染者平均年龄为（35.02±9.15）岁,其中20～50岁的青壮年45例（94.74%）,未婚51例（53.68%）,大专或大学及以上文化程度者30例（占31.58%）。感染者中共发现CRF01_AE亚型、B亚型、BC重组亚型（包括CRF07_BC和CRF08_BC）及C亚型4种亚型。其中CRF01_AE重组亚型56例（占58.95%）,B亚型28例（占29.47%）,BC重组亚型10例（占10.53%）,C亚型1例（1.05%）。结论 MSM人群急性HIV-1感染者年轻化,文化程度普遍偏低。小样本流行病学调查显示,急性HIV-1感染者中有CRF01_AE亚型、B亚型、BC重组亚型及C亚型4种亚型病毒株流行,CRF01_AE亚型为MSM人群的主要亚型。     

浦东新区MSM HIV-1分子流行病学的研究

目的了解上海市浦东新区近年来男男性行为人群(MSM)中,未经抗病毒治疗的艾滋病病毒1型(HIV-1)抗体阳性者,其HIV-1亚型分布和原发性耐药特征,监测该地区MSM HIV-1毒株的最新流行情况,为当前该区制定艾滋病防治策略提供科学依据。方法选取2011年至2014年4月份期间确认的MSM HIV-1感染者血浆标本70份,应用巢式反转录聚合酶链反应(RT-PCR)扩增pol基因,并对扩增产物进行测序,用Mega 6.0软件将测序结果与各亚型国际参考株比对,根据系统进化树分析确定基因亚型及其特征以及耐药情况。结果获62份pol区基因全序列片段,得到CRF01-AE、CRF07_BC、01B(CRF01_AE与B重组亚型)和B四种亚型。分布显示:CRF01-AE占58.06%(36/62),CRF07_BC占30.65%(19/62),01B占6.45%(4/62),B占4.84%(3/62)。离散率显示:CRF01-AE亚型的平均离散率为(2.1±0.2)%(n=36),CRF07-BC亚型的平均离散率也为(2.1±0.2)%(n=19),B亚型的平均离散率为(5.7±0.6)%(n=3),01B重组亚型的平均离散率为(6.3±.0.6)%(n=4)。耐药特征:62例中有7例分别产生了对核苷类反转录酶抑制剂(NRTIs)、非核苷类反转录酶抑制剂(NNRTIs)及蛋白酶类抑制剂(PIs)的耐药突变,其中2例产生了低度耐药,4例具有潜在的耐药特点。结论上海市浦东新区2011年至2014年4月间,MSM新确证HIV-1感染者中,基因亚型呈多元化趋势,以CRF01-AE和CRF07-BC为主,并已形成了浦东新区范围内的局部流行趋势,新的01B重组毒株已在浦东新区开始出现;HIV-1原发耐药株的传播尚处于低度流行水平,密切监视其流行趋势已显十分必要。     

浙江省2003-2005年HIV-1感染者分子流行病学研究

目的掌握浙江省2003-2005年新发现感染者艾滋病病毒Ⅰ型(HIV-1)毒株基因亚型分布和变异情况。方法对2003-2005年浙江省境内检测新发现的HIV-1感染者进行一般流行病学调查并采集血样,提取前病毒DNA,使用套式聚合酶链反应对gag基因区进行扩增并测定其序列。结果采集143份血样,112份扩增阳性,检出CRF01-AE亚型43例,CRF07-BC 37例,CRF08-BC 11例,B亚型20例,CRF02-AG 1例。CRF01-AE分布在11个市中的9个市,主要存在于异性性途径感染者中(53.5%),并已成为外省籍注射吸毒感染者的主要构成(44.8%)。CRF01-AE和CRF07-BC的亚型组内平均离散率在静脉吸毒感染者和性传播感染者中比较,差异有统计学意义。结论浙江省2003-2005年新检出感染者HIV-1毒株呈现多重组型别特征,CRF01-AE成为分布最广的类别,呈现扩大流行的趋势。HIV-1在性乱人群之间的传播要比在注射吸毒人群复杂,变异更大。     

运用系统进化分析技术研究全国献血人群HIV感染特征

目的了解献血人群中艾滋病病毒(HIV)感染者的病毒亚型分布及流行毒株特征,为无偿献血者的招募、健康征询提供科学数据。方法对来自全国13个省市献血人群中的HIV阳性样本进行分子流行病学调查。对pol区基因进行扩增和测序。基于系统进化分析技术构建贝叶斯(BI)和最大似然(ML)系统树,确定毒株亚型,并针对亚型地理分布进行统计分析。结果来自全国13个省市的115例HIV阳性献血者标本中,成功扩增并获得pol区基因序列89例,发现HIV-1基因亚型9种,其中,亚型CRF01_AE和CRF07_BC所占比例最高,分别占46.1%(41/89)和37.1%(33/89);亚型CRF08_BC、B分别占2.2%(2/89)、5.6%(5/89);其他亚型CRF65_CPX、CRF55_01B、CRF59_01B、CRF68_01B、CRF62_BC各占1.1%(1/89)。系统进化进一步分析显示,所占比例最高的是CRF01_AE中的Cluster 4和Cluster 5亚簇以及CRF07_BC中的msm亚簇,所占比例分别达到23.6%(21/89)、21.3%(19/89)和33.7%(30/89),这3个均是全国男男性行为者(MSM)传播途径中的主要流行亚簇。结论全国献血途径检测出的HIV-1基因型呈现复杂的多样性特征,尤其在MSM传播HIV感染者中占绝对优势毒株的CRF01_AE(C4和C5簇)和CRF07_BC-msm簇也是本次在献血人群中发现的主要流行毒株。     

江西省HIV-1基因序列流行特征分析

目的对江西省艾滋病病毒1型(HIV1)感染者进行基因亚型分析,了解HIV1的流行情况、亚型种类、毒株来源及其变异特征等,为政府部门预防控制决策提供技术资料。方法传统流行病学与分子流行病学相结合,对江西省27例HIV1感染者进行流行病学相关因素分析和基因序列、系统进化树分析。结果江西省HIV1感染人群中流行的毒株主要为HIV1CRF01AE,占6897%(20/29),其次为泰国B(B’)、CRF07BC、C三种亚型。序列分析表明,20份样品与泰国代表株相近,与CRF01AETH90CM240平均基因距离为947±271;3份样品与我国BC重组代表株相近,与BC重组代表株(CRF07BCCN97C54A)平均基因距离为566±241;3份样品与BCNRL42相近,与代表株BCNRL42平均基因距离为502±103;1份样品与印度代表株(CIN95IN21068)相近,基因距离为1299。而与已知的其它亚型国际参考株间的平均基因距离都在20%以上。系统进化树分析表明,27份样品与其相应的亚型共享序列聚集在一起,并远离其它国际参考株。吸毒人群中几乎全为HIV1CRF01AE,组内基因距离293±140(n=13),经性传播的四种亚型均有。结论目前江西省HIV1感染者中流行毒株为CRF01AE、CRF07BC、泰国B(B′)、C四种亚型,以CRF01AE为主。CRF01AE主要在吸毒人群中传播,局部爆发或流行时间大约有2年半左右,江西省HIV流行已     

福建省HIV-1新型独特重组毒株的鉴定分析

目的了解福建省1型艾滋病病毒(HIV-1)新型重组毒株的出现和传播情况,为艾滋病防治提供有针对性的科学依据。方法对2015年福建省HIV-1分子流行病学调查发现的未明确分型样本进行流行病学特征分析,分三段nested-聚合酶链反应扩增,获得HIV-1近全长基因片段序列。利用MEGA构建系统进化树,Simplot进行重组断点分析,最后通过Recombinant Drawing工具绘制重组镶嵌模式图。结果福建省56份未明确分型样本主要来自沿海经济较发达地区,且集中在文化程度较低的青壮年男性人群,主要以性传播为主。亚型分析显示,其中38份为CRF01-AE/CRF07-BC混合亚型,9份为01B/01-AE/07-BC混合亚型,9份为CRF55-01B/CRF07-BC混合亚型。对3株HIV-1近全长基因序列进行重组分析显示:XM03025是以CRF07-BC为骨架,在1916-2186bp、2786-5526bp、8726-8776bp、9216-9366bp处分别插入4个CRF01-AE的片段;XM03050是以CRF07-BC为骨架,在4916-6256bp处插入1个CRF01-AE片段;而XM06004是以CRF01-AE为骨架,在6490-6680bp、6920-8290bp、8950-9190bp处分别插入3个CRF07-BC片段。经鉴定该三株为新的独特重组型毒株。结论福建省已出现新的独特型重组毒株,并有可能在局部传播流行;应密切监测其流行趋势变化,并积极采取精准干预加以防控。     

武汉市HIV-1相关基因序列分析及亚型分布

目的研究武汉市HIV感染人群中的HIV毒株的亚型分布特点和流行规律。方法采集武汉市60名已被确认为HIV-1感染者的抗凝全血样品,提取前病毒DNA,用巢式聚合酶链反应方法（nested-PCR）扩增病毒膜蛋白env基因的C2-V5区及gag基因的部分区段,对PCR纯化产物直接测序,并应用GCG软件对序列进行分析。结果通过PCR扩增得到60份样品的结果,其中env基因序列45份、gag基因序列52份。依据env和gag区基因序列,与HIV-1各个亚型国际参考株比较,通过系统进化分析,最后确定武汉市样品分属5个亚型,分别为HIV-1B亚型中的泰国B（B’）亚型32份,流行重组型CRF07-BC12份,流行重组型CRF01-AE9份,A亚型1份和C亚型6份。结论武汉市存在多种HIV-1亚型,应加强对HIV-1毒株亚型变异的监测,及时调整防治策略。     

广州市男男性行为者HIV-1分子流行病学研究

目的了解广州市男男性行为人群（MSM）中,人类免疫缺陷病毒Ⅰ型（HIV-1）亚型流行状况和基因变异特征。方法从2006～2007年广州市发现的、全部19份经男男性传播感染的HIV-1阳性血清样本,应用套式聚合酶链式反应（Nested—PCR）分别扩增gag和fitly区基因,并测定、分析序列。结果被成功扩增的有17份样本,获得13份env基因序列和17份gag基因序列。经系统进化树分析,11份（64．71％）为CRF01_AE,2份（11．76％）为CRF07_BC,4份（23．53％）为B。各亚型组内基因离散率：在env区,CRF01_AE为（8．27±0．93）,CRF07_BC为（11．04±1．72）,B为（16．65±1．78）;在gag区,CRF01_AE为（5．36±0．68）,CRF07_BC为（4．29±1．14）,B为（11．75±1.35）。V3环顶端四肽分析显示：8份CRF01_AE和2份CRF07_BC V3环顶端四肽均为GPGQ;3份B亚型中2份为GPGR,1份为GWGR。根据V3环关键氨基酸推测辅助受体使用情况,结果显示：所有样本均被预测使用CCR5辅助受体。结论广州市MSM人群HIV-1感染者中,至少存在CRF01_AE、CRF07_BC 2种重组亚型和B亚型的流行,且大部分流行株可能为使用CCR5辅助受体的巨嗜细胞嗜性／NSI毒株。     

2018年至2019年浙江省绍兴市新确证人类免疫缺陷病毒1型感染者的分子传播网络特征分析

目的:分析浙江省绍兴市新确证人类免疫缺陷病毒1型(human immunodeficiency virus type 1,HIV-1)感染者传播关系的分子网络特征,为疫情流行趋势和防治提供依据。方法:纳入2018年8月至2019年12月绍兴市新确证未经抗病毒治疗的423份HIV-1感染/艾滋病病例血液样本,获得375份...     

Importation of multiple HIV type 1 strains into West Papua, Indonesia (Irian Jaya).

HIV-1 from 16 sexually transmitted disease clinic patients in Timika, West Papua, Indonesia was amplified by RT-PCR and subtyped by a combination of envelope and gag region heteroduplex mobility analysis (HMA) and direct PCR DNA sequencing. HMA showed the presence of 14 subtype E (CRF01_AE) and 2 subtype B HIV-1. Phylogenetic analysis of a 540-bp V3-V4 region of gp120 showed that 9 of 10 CRF01_AE variants clustered tightly with a median distance of 1.3% (range, 0.5 to 2.2%) whereas 1 CRF01_AE variant diverged significantly from the others (median distance, 10.7%; range, 10.1 to 11.8%). One subtype B virus envelope was typical of United States/European strains whereas the other appeared to be related to Thai subtype B' variants. These results reflect the independent introduction of multiple HIV-1 strains into West Papua, with the rapid spread in the majority of infected patients tested of a single strain of HIV-1E (CRF01_AE).     

Characterization of complete HIV type 1 genomes from non-B subtype infections in U.S. military personnel

Infections with non-B HIV-1 subtypes are rare in the United States, but comprise a significant percentage of infections among U.S. military personnel. Risk behavior while on overseas deployment correlates with non-B infection in this population. Extensive genetic characterization will be required to define HIV-1 diversity, and to effectively evaluate requirements for HIV-1 vaccines and other prevention strategies in this group. From 1997 to 2000, 520 recent seroconverters, identified through routine HIV-1 testing in the U.S. active military force, volunteered for a prospective study. V3 loop serology or partial genome sequencing identified 28 non- B subtype infections; 14 were studied by full genome sequencing and phylogenetic analysis. Five strains were CRF01_AE. Four of these clustered with CM240 from Thailand, and one clustered with African CRF01_AE. Four strains were CRF02_AG, prevalent in West and West Central Africa. Two strains were subtype C. One strain was a unique recombinant between CRF01_AE and subtype B, and another was a complex unique recombinant between subtype A and D. The final strain was a member of a complex circulating recombinant first identified in Senegal, CRF09_cpx, incorporating subtypes A, F, G, and an unclassified genome. This diversity of non-B subtype HIV-1 strains, encompassing three globally prevalent non-B strains and including rare or even possibly unique strains, illustrates the breadth of U.S. military exposure while deployed and sets the bar higher for breadth of cross-subtype protection to be afforded by an HIV-1 vaccine.     

The lack of epidemiological link between the HIV type 1 infections in Hong Kong and Mainland China

Blood samples were collected from 139 newly reported HIV-1 infections in Hong Kong over a 3-year period between 1999 and 2001, representing 22.8% of all reported cases. A majority of the patients were male (85.6%), Chinese (74%), and adult (97.1%) and acquired HIV-1 through sexual transmission (88.2%). The B and CRF01_AE were the major subtypes detected--49.6% and 44.6%, respectively. Over time, the frequency of CRF01_AE subtype increased, the B subtype decreased, and new subtypes of C (4) 2.8%, B' (1) 0.7%, and CRF07_BC (3) 2.2% emerged. The CRF01_AE subtype was commoner in female, Chinese, heterosexuals, and injection drug users whereas B subtype was commoner in male, white, and people with homosexual/bisexual contacts. There was no common source of infection from the analysis except a discernible cluster of Vietnamese injection drug users with the CRF01_AE subtype. The molecular findings did not suggest an epidemiological link between HIV infection in Hong Kong and Mainland China. Hong Kong's longstanding and extensive methadone treatment network may have contributed to the phenomenon.     

The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002

CRF01_AE and subtype B have dominated the HIV-1 epidemic in Thailand since 1989. We reported a new circulating recombinant form of HIV-1, CRF15_01B, as well as other unique CRF01_AE/B recombinants among prevalent HIV infections in Thailand. We sought to study this challenging molecular picture through assessment of subtypes among recent HIV-1 seroconverters in northern Thai drug users. A total of 847 HIV-1 seronegative drug users (342 IDU and 505 non-IDU) were enrolled, from 1999 to 2002, in a prospective study; 39 HIV-1 incident cases were identified and characteristics were collected. The overall HIV-1 incidence rate was 2.54/100PY, but it was 10.0/100PY among male IDU. HIV was strongly associated with injection history; 38 of 39 seroconverters gave a history of IDU. A near full-length genome of HIV-1 was recovered by PCR amplification and sequenced from peripheral mononuclear cell extracted DNA of 38 seroconverters. Phylogenetic analysis revealed that 33 (86.8%) were CRF01_AE and 5 (13.2%) were CRF01_AE/B recombinants. These recombinants had different structure but shared some common breakpoints, indicating an ongoing recombination process. Recombinant infection increased with year of sampling (0 to 57.1%). The molecular epidemiology of HIV-1 among drug users in northern Thailand has thus entered a new era. CRF01_AE remains predominant while pure subtype B is becoming rare, and now a substantial component of the epidemic. These findings support the need for CRF01_AE and subtype B components in clade-matched vaccine strategies for Thai phase III trials. Ongoing molecular surveillance of circulating HIV-1 strains is imperative for the evaluation of HIV vaccine efficacy.     

A new circulating recombinant form,CRF15_01B,reinforces the linkage between IDU and heterosexual epidemics in Thailand

HIV-1 subtype B and CRF01_AE have been in circulation in Thailand and Southeast Asia for more than a decade. Initially separated by risk group, the two strains are increasingly intermixed, and two recombinant strains of essentially reciprocal structure have been recently reported. Here we identify additional CRF_01B recombinants and provide the evidence that HIV-1 strains now pass freely between the two high-risk populations. HIV isolates that showed discordance between CRF01_AE and subtype B in multi-region genotyping assays were selected for the study. They were drawn from 3 different cohorts in Thailand representing different risk behaviors and demographic characteristics: a drug user cohort in the north, a family planning clinic attendee cohort in the southeast, and a cohort study of the mucosal virology and immunology of HIV-1 infection in Thailand. The DNA from these isolates was PCR amplified to recover the full HIV-1 genome and subjected to sequencing and phylogenetic analysis. We establish that one particular CRF_01B recombinant, with the external envelope of subtype B and the rest of the genome from CRF01_AE, is circulating widely in Thailand. Termed CRF15_01B (also referred to as CRF15), the strain was primarily heterosexually transmitted, although injecting drug use (IDU) also played a role. In aggregate data from the studies, CRF15 constituted 1.7% of all HIV-1 infections (95% confidence interval 0.5-4.4%) and was dispersed widely in the country. The previously separate heterosexual and IDU epidemics have apparently been bridged by a new CRF. The entry of CRF15 into the mainstream of the epidemic signals new complexity in the long stable molecular picture in Thailand. These recombinants must be considered in ongoing or projected efficacy evaluations of HIV-1 vaccines and antiviral therapies.     

Emergence of a New HIV Type 1 CRF01_AE Variant in Guangxi, Southern China

Abstract The distribution of HIV-1 subtypes and genetic characterization of CRF01_AE in Guangxi, southern China were identified. The distribution of HIV-1 genotypes based on gag, pol, and partial env sequences (n=349) was as follows: CRF01_AE (66.5%), CRF08_BC (19.2%), CRF07_BC (7.2%), URF (4.6%), subtype B (1.7%), and subtype B' (0.9%). CRF01_AE predominated in all geographic regions and risk populations and there were multiple introductions of CRF01_AE strains in Guangxi. We found a peculiar CRF01_AE monophyletic lineage distinct from other CRF01_AE viruses, and we designated it "CRF01_AE-v" for convenience. CRF01_AE-v circulating in both heterosexuals and injecting drug users (IDUs) had accounted for 39.7% of CRF01_AE. It showed a selective advantage in the Guangxi population and formed its own characteristic compared with all the CRF01_AE references. Our results suggested that CRF01_AE-v was a new variant of CRF01_AE and it might lead to a new epidemic in Guangxi.