我国主要HIV-1流行株耐药基因型检测方法的研究

目的 研究针对中国主要HIV-1流行株优化的实验室自建耐药基因型实验室自建检测方法( in-house)的扩增效果及检测敏感度.方法 选取中国主要流行亚型的B、CRF07 _BC、CRF01_AE亚型各10份样本,这些样本为2007 -2009年本实验室采集采自河南、新疆、湖南三地已接受抗病毒治疗患者的样本,并已确定亚型.选用生物梅里埃公司的Nuclisens Easy Q方法对选取的30份样本的病毒载量平行进行3次病毒载量检测,取平均值作为载量数值.对每份样本用HIV阴性血浆进行5个浓度的梯度稀释,稀释为＞ 1000、401～1000、101 ～400、50 ～100和＜50拷贝/ml 5个浓度梯度.提取核酸后,进行RT-PCR和巢式PCR扩增,对扩增结果进行统计扩增结果,确定每种亚型的扩增效果和最低检测限.随机选取12份样本的初浓度和最低浓度进行测序,对测序结果进行耐药结果分析和序列一致性分析.结果 所选样本的病毒载量介于2.03×102 ～5.92×104拷贝/ml之间.自建的In-house法对载量50 ～1000拷贝/ml范围的样本仍可达到较高的扩增效果(86％).样本稀释前后耐药位点相似,序列一致性在97％以上,在低病毒载量时优势病毒株的检测则更敏感.结论 自建的实验室方法的灵敏度较高,对低病毒载量水平的样本仍有较高的扩增效果.     

广西HIV-1重组毒株env区快速基因分型方法的建立

目的建立一种快速简便的基因分型方法，对广西HIV-1重组毒株env基因区进行亚型鉴定。方法从HIV阳性样品中提取核酸，使用HIV-1M组通用引物对env区进行第一轮扩增，第二轮则使用分别检测B′/C或C亚型和CRF01-AE亚型的二套特异性引物放入同一反应管中进行扩增，根据不同亚型扩增的目的带位置不同来判断亚型。将通用引物扩增出的所有样本均进行基因测序和系统树分析以验证结果。结果50份样本中，经基因测序和系统树分析证实CRF08-BC样本3份（6％），CRF01-AE样本43份（86％），4份（8％）样本无法确定亚型。经亚型特异性引物PCR法检测得出B′/C或C亚型样本3份（100％），CRF01-AE样本39份（90．7％），灵敏度为91．3％，特异度为100％。两种方法检测结果经差异性检验显示X^2=2．25，P〉0.05，差异无统计学意义，结果一致者占92％。与基因分析结果吻合。重复实验显示CRF08-BC平均重复性为100％（10／10），CRF01．AE为93．8％（61／65）。结论该方法是一种简便、快速、低成本，具有高度灵敏性和特异性的HIV-1毒株env基因区分型法，能够直接对广西HIV-1 CRF01-AE重组毒株进行鉴定。     

使用多重巢式PCR对我国HIV-1主要流行株亚型鉴定方法的建立

目的 建立一套新的亚型鉴定方法，仅仅使用巢式PCR，一次扩增，即可对我国HIV-1主要流行株B、C和CRF01-AE进行亚型鉴定。方法 从HIV阳性样本中提取核酸，使用能覆盖HIV-1型M组gag区的引物进行第一轮扩增，第二轮扩增则使用分别检测B、C、CRF01-AE亚型的三套特异性引物进行扩增，三套引物放在同一个反应管中。反应产物经琼脂糖电泳后观察，不同亚型的位置不同，以此来判断亚型。另外设计一套引物，专门检测我国重组株CRF07-BC和CRF08-BC。所有样品均经过基因测序、系统进化树分析，以进行结果验证。结果 在检测的119份样品中，经基因测序和系统进化树分析证实B亚型样品43份(欧美B11份，泰国B32份)，C、CRF01-AE、A和D亚型样品分别为54份、17份、3份和2份。其中C亚型的样品，有52份属于CRF07-BC和CRF08-BC。而经过上述多重巢式PCR方法检测到的B亚型样品为35份(81．4％)，C亚型46份(85．2％)和CRF01-AE13份(76．5％)。另外，检测CRF07-BC和CRF08-BC重组株的引物特异性地检测到43份(82．7％)样品。上述结果与基因分析结果吻合，各个亚型之间无交叉，一种亚型的特异性引物只对该亚型有反应，而对其他亚型无反应，特异性达到100％。虽然有时会有非特异扩增带，但一般不影响结果判断。结论 我们建立了一套简单快速的H1V-1亚型鉴定方法，不需基因测序，即可检测我国主要流行株B、C、CRF01-AE、CRF07-BC和CRF08-BC。该方法具有高度特异性和敏感性，可以作为初筛方法在我国及其他国家HIV-1实验室推广使用。     

广西地区HIV合并结核感染及其他因素对HIV复制影响的研究

目的 分析合并结核( tuberculosis,TB)感染及其他因素对广西地区HIV感染者病毒复制的影响.方法 2010年4月至2010年9月间在广西招募到未接受抗病毒治疗、CD4+T细胞数＜350个/μl的HIV/TB感染者61例,单纯HIV感染者34例.收集人口学、流行病学、临床信息,测定HIV病毒载量.结果 HIV/TB双重感染者与单纯HIV感染者血浆病毒载量差异无统计学意义[ (5.05±0.93) lg拷贝/ml vs (5.06±0.76) lg拷贝/ml,P=0.94].二元logistic回归分析显示,CRF01_AE亚型较其他亚型HIV感染者血浆病毒复制水平高,OR=8.07 (95％CI 1.07～61.20,P=0.04).年龄、感染途径、CD4+T细胞数,是否合并结核分枝杆菌(MTB)感染及TB临床类型对病毒复制水平的影响均不明显.结论 广西地区CD4+T细胞数较低的HIV感染者中,合并结核感染对病毒复制影响不明显;CRF01_AE亚型HIV-1病毒复制水平较高,在监测和治疗过程中需加强关注.     

先天性HCMV感染新生儿尿液中病毒载量与疾病严重度的关系探讨

目的探讨新生儿尿液中人巨细胞病毒（HCMV）病毒载量与先天性感染的关系及与HCMV所致疾病严重程度的关系。方法采集98例经PCR方法确诊的有症状及无症状的先天性HCMV感染新生儿尿液标本,用实时荧光定量PCR法（FQ—PCR）检测尿液中巨细胞病毒载量。结果98例先天性HCMV感染的新生儿中85例在出生后有临床症状（86％）。无症状感染和有症状感染的新生儿尿液中平均HCMV病毒载量分别是1．4×10^5拷贝／ml和3．1×10^6拷贝／ml,P〈0．01,差异有统计学意义。结论先天性HCMV感染的新生儿中无症状感染者尿液中病毒载量显著低于有症状感染者,提示病毒载量与疾病严重程度相关。     

2006年北京市外来人口中HIV-1感染者流行毒株gag基因序列测定和亚型分析

目的了解北京市外来人口中HIV-1亚型的特点和流行规律。方法随机采集北京市2006年外来人口中新确证HIV-1感染者的抗凝全血标本80份，分离血浆，提取病毒RNA，用套式聚合酶链反应扩增病毒gag基因，并进行序列测定和亚型分析。结果系统进化分析确定北京市外来人口HIV-1毒株属于8个亚型，分别为B亚型4份，泰国B亚型15份，C亚型1份，CRF01-AE亚型5份，CRF02-AG亚型1份，CRF07-BC亚型29份，CRF08-BC亚型3份，CRFl5—01B亚型1份。结论北京市外来人口中己存在8种HIV-1亚型和流行重组型，应该加强对HIV-1亚型变异的监测。     

河南省某市HIV感染者基因型耐药横断面调查

目的了解河南省某市HIV耐药毒株在HIV／AIDS患者中的情况。方法采集2011年河南省某市150份HIV／AIDS患者血清,提取RNA,逆转录及巢式PCR扩增HIV-1pol基因区。所得序列构建系统进化树分析亚型;并利用StanfordHIVDrugResistanceDatabase分析HIV基因耐药相关突变和耐药情况。结果150份样本中34份测序阳性,其中未接受抗病毒治疗样本9份,接受抗病毒治疗样本25份;B＋亚型占94．1％。测序阳性样本的基因突变率为58．8％,其中未接受抗病毒治疗的突变率为5．9％,接受抗病毒治疗的突变率为52．9％。结论接受抗病毒治疗的耐药样本中出现了对反转录酶抑制剂不同程度的耐药及多药耐药,说明仍需加强耐药监测及管理,尽量减少耐药株的产生,并根据耐药检测结果及时调整治疗方案。     

水中诺如病毒富集及定量检测研究

目的评估MCE—PEG富集法（混合硝酸纤维素膜第一次富集和PEG沉淀第二次富集）对水中诺如病毒的富集效果及检测灵敏度。为水源性诺如病毒胃肠炎疫情暴发的确定提供有效的实验室检测方法。方法把含有诺如病毒的粪便加入纯净水中,用MCE．PEG方法富集后,荧光PCR绝对定量检测富集前后水的病毒浓度．评估该方法的病毒回收率。同时梯度稀释粪便悬液,分别加入纯净水中,评估该方法的灵敏度。结果经过混合硝酸纤维素膜第一次富集后待滤水被浓缩100倍,病毒平均回收率为56．12％,灵敏度是待滤水中病毒浓度为10拷贝μl。PEG沉淀第二次富集后,浓缩倍数为1000倍,病毒平均回收率为42．47％,灵敏度是待滤水中病毒浓度为1拷贝／μl。结论MCE—PEG富集法操作简单、材料价格实惠、易于购买、病毒回收率及灵敏度较高。可望进一步优化后广泛应用于不同水中病毒富集浓缩检测,为水源性诺如病毒胃肠炎疫情暴发的确定提供了有效的实验室检测方法。     

北京市2016年新确证未治疗HIV感染者传播性耐药突变研究

目的 分析北京市2016年新确证HIV感染者HIV病毒pol基因传播性耐药突变特征.方法 利用一步法逆转录PCR和巢式PCR扩增感染者体内HIV病毒的pol基因,并对扩增产物进行测序.对得到的序列信息进行分析,分别获得病毒的亚型分布、耐药突变类型和构成.结果 2016年北京市新确证HIV感染者传播性耐药突变比例为4.2％.712名感染者中,CRF01_AE亚型为主要流行亚型,占49.3％,CRF07_BC亚型占28.8％,B亚型占10.3％.结论 与往年的研究相比,北京市未治疗的HIV感染者耐药率有所下降,总体上属于低水平的HIV耐药流行.     

实时荧光定量RT-PCR监测恒河猴体内人/猴免疫缺陷病毒载量在传代过程中的变化

目的为分析中国SHIV/猕猴AIDS模型的病毒载量变化趋势,建立一种实时、灵敏、特异的针对人/猴免疫缺陷病毒的定量检测方法。方法体外转录制备RNA标准品,利用TaqManEZRT-PCR试剂盒的反应体系和针对SHIVgag保守区91个碱基的TaqMan探针和引物,建立一步法实时荧光定量RT-PCR。提取126份来自SHIV-CN97001感染恒河猴血浆病毒RNA并定量检测。结果利用梯度稀释的RNA标准品对反应体系进行优化,标准曲线下限达到2×102拷贝/ml,相关性(r>0.99)及重复性(CV=4.14%)均能达到测定要求。病毒载量的检测结果表明SHIV-CN97001在猴体内传代过程中病毒载量有先升后降的趋势,病毒载量通常在接种病毒或感染猴的全血后第14天达到高峰。血浆载量可达到105~106拷贝/ml。结论成功地建立了一步法定量SHIVRNA的实时荧光定量RT-PCR,为SHIV/恒河猴AIDS模型的建立与应用提供了灵敏的病毒载量检测方法。SHIV-CN97001的体内繁殖能力在猴体内传代过程中有所增强。     

Detection of HIV-1 antiretroviral resistance from patients with persistently low but detectable viraemia

We modified the Abbott diagnostics HIV-1 Viroseq version 2 assay trade mark in order to detect the presence of HIV-1 drug resistance mutations in patients with viraemia below 1000 copies/ml of plasma. One hundred and forty-four patients with a detectable HIV-1 plasma viral load below 1000 copies/ml were selected and HIV-1 genetic analysis carried out using a modification of the Abbott Diagnostics Viroseq 2.0 assay trade mark. The procedure differs from the standard protocol in that a nested PCR amplification step was introduced. The oligonucleotide primers for the first round of PCR were those supplied in the RT-PCR module of the kit. The nested PCR primers were primers A and H taken from the sequencing module. One hundred and twenty-eight out of 144 (89%) plasma samples with an HIV-1 viral load of less than 1000 copies/ml (ranging from 54 to 992 copies) were successfully sequenced. HIV-1 genotypes were obtained from 68 out of 81 (84%) samples with a viral load of greater than 50 but less than 300 copies/ml and 60/63 (95%) of samples with a viral load of greater than 300 but less than 1000 copies/ml. Serial dilution of a sample with a high viral load did not affect the detection of resistance mutations. Multiple sequencing of samples with low viral load did not result in detection of additional mutations, although, in one sample the K103N mutation was detected in 3/6 replicates while wild-type was detected in 2/6 and a mixture of wild-type/mutant in 1/6. Samples from patients infected with both clade B and non-B clades of HIV-1 could be genotyped at low copy number. Modification of the Abbott Viroseq assay allows reproducible sequencing of the HIV-1 genome from patients with low, but detectable, plasma virus burden.     

一种简易的HIV-1病毒载量定量筛查方法的建立

目的 建立一种基于RT-PCR法的简易的HIV-1感染者或艾滋病患者血浆病毒载量筛查方法.方法 在广西南宁市采集18例HIV-1感染者和18例阴性对照者血液标本,提取RNA,以引物LTR-1/LTR-2对待测样本进行PCR扩增,获得Ct值.同时,应用Nuclisens EasyQ HIV-1 v1.2法作为对照对这些样本进行病毒载量检测.对Ct值与病毒载量之间进行相关性分析,获得相应的回归方程.结果 待测样本中HIV-1感染者Ct值在29.103～31.610个循环之间,阴性对照者未能扩增出产物.RT-PCR法Ct值与Nuclisens EasyQ HIV-1 v1.2法检测出的病毒载量对数值之间具有良好的线性关系（r=-0.51,P=0.03）,回归方程为logY（viral road）=57.55-1.56＆#215;（Ct value）.结论 所建立的HIV-1病毒载量RT-PCR检测方法操作简单,价格便宜,与商业化试剂盒具有较好的一致性,可用于HIV-1感染定量筛查.     

Improved quantitative PCR protocols for adenovirus and CMV with an internal inhibition control system and automated nucleic acid isolation

With the establishment of routine virus load (DNAemia) screening for Human adenovirus (HAdV) and Cytomegalovirus (CMV) in post-transplant care quality standards for quantitative PCR-assays are increasing. Established real-time PCR assays were improved with a fully automated DNA-extraction and with a competitive internal control DNA packaged into a lambda phage which serves as an extraction and amplification control in each sample. HAdV and CMV DNA were detected and quantified simultaneously in various types of diagnostic samples like blood, feces or respiratory tract materials. Inhibition was observed in 0.33-0.66% of over 14,000 diagnostic samples, an infrequent but nevertheless not negligible event, which is observed mainly in stool samples. CMV viral load in broncho-alveolar lavage fluid (BALF) ranged between positive but below the quantitation limit of 1,000 copies/ml up to 1.8 × 10(7) copies/ml with a median of 6.0 × 10(3) copies/ml. Forty-one (4.7%) BALF samples had a viral load above 5.0 × 10(5) copies/ml, which was proposed as a threshold for the diagnosis of pneumonia. HAdV viral loads ranged between positive but below the quantitation limit of 1,000 copies/ml to a very high concentration of 1.3 × 10(11) copies/ml in stool and BALF samples. A HAdV-DNAemia of >10(4) copies/ml was found only in patients with stool viral load of above 10(5) copies/ml. These data support the hypothesis that quantitation in diagnostic materials other than blood may give valuable diagnostic information and that further evaluation of this approach is reasonable.     

Modifications and substitutions of the RNA extraction module in the ViroSeq HIV-1 genotyping system version 2: effects on sensitivity and complexity of the assay

Genotypic testing for HIV-1 resistance to anti-retroviral drugs has become accepted widely as a routine method to guide anti-retroviral therapy. However, implementation into routine high-throughput laboratory diagnosis is difficult due to the complexity of the assay. A commercially available assay is the ViroSeq HIV-1 Genotyping System (Applied Biosystems, Weiterstadt, Germany). We modified and substituted the RNA extraction module to optimize the proportion of samples amplified successfully as follows: 1 ml plasma was concentrated by ultracentrifugation and extracted according to the manufacturer's instructions (Kit), by substituting the lysis buffer (Roche, Roche Diagnostics GmbH, Mannheim, Germany), and by using the QIAamp Viral RNA Kit (Qiagen GmbH, Hilden, Germany) with elution volumes of 60 (Q60) or 50 micro l (Q50). Overall Q50 showed a higher success rate (97%) than the other extraction modules used (range 88-91%). In samples with a viral load range of 1,000-4,999 copies/ml, Q50 was superior (95 vs. 65% to 83%), while in samples with a viral load range of 5,000-9,999 copies/ml or those with 10,000 or more copies/ml, the success rate of the extraction procedures showed no significant differences. In 18 samples, which were negative using the Kit or Roche extraction, Q60 resulted in 7/18 positive results; in addition the Q50 was successful in amplifying 7/10 of the Q60 negative samples. When investigating samples with a measurable viral load of less than 1,000 copies/ml or lower, Q50 had the highest success rate with 80% compared to the other procedures (33-63%). A statistically significant new cut-off could be defined for Q50 at a value of 250 copies/ml. The results showed clearly that the ViroSeq System is suitable for analyzing the HIV-1 genotype over a wide range of viral loads but could be improved significantly when substituting the RNA extraction module with Q50 without using a nested PCR protocol. This is of great importance as it avoids further time- and cost-intensive steps.     

A genotypic assay for the amplification and sequencing of integrase from diverse HIV-1 group M subtypes

Recently, the Food and Drug Administration (FDA) of the USA approved the first integrase inhibitor for inclusion in treatment regimens of HIV-1 patients failing their current regimens with multi-drug resistant strains. However, treatment failure has been observed during integrase inhibitor-containing therapy. Several mutational pathways have been described with signature mutations at integrase positions 66, 92, 148 and 155. Therefore, a genotypic assay for the amplification and sequencing of HIV-1 integrase was developed. The assay displayed a detection limit of 10 HIV-1 III(B) RNA copies/ml plasma. As the HIV-1 pandemic is characterised by a large genetic diversity, the new assay was evaluated on a panel of 74 genetically divergent samples belonging to the following genetic forms A, B, C, D, F, G, J, CRF01-AE, CRF02-AG, CRFF03-AB, CRF12-BF and CRF13-cpx. Their viral load ranged from 178 until >500,000 RNA copies/ml. The amplification and sequencing was successful for 70 samples (a success rate of 95%). The four failures were most probably due to low viral load or poor quality of RNA and not to subtype issues. Some of the sequences obtained from integrase inhibitor-na?ve patients displayed polymorphisms at integrase positions associated with resistance: 74IV, 138D, 151I, 157Q and 163AE. The relevance of these polymorphisms in the absence of the signature mutations remains unclear.