昆明市静脉注射吸毒人群丙型肝炎病毒基因型分析

目的 研究云南省昆明市静脉注射吸毒人群(IDUs)中丙型肝炎病毒(HCV)基因型的流行特点。方法 2014年4－7月在昆明市连续收集276份IDUs的血浆,其中199份样品为HCV抗体阳性,提取RNA后用巢式PCR对E1E2基因和NS5B基因的部分片段进行扩增。扩增产物经基因序列测定,所得序列通过构建系统进化树确定HCV的分子亚型。结果 结合2 个基因片段,共有125份样品获得了分型结果,3b为主要的亚型,占48.8%(61/125);其他亚型按照比例依次为3a(30.4%,38/125)、6n(14.4%,18/125)、6a(3.2%,4/125)和1b(3.2%,4/125)。各HCV亚型按性别、婚姻、民族和HIV-1抗体是否阳性差异无统计学意义,按年龄分布差异有统计学意义,45岁以下组亚型多样化。分别计算不同亚型在E1E2和NS5B基因区的基因距离,结果显示3a、3b和6a亚型的基因距离大于1b和6n亚型的基因距离。3a、3b、6a 3种亚型中3b亚型毒株的基因距离大于3a亚型毒株。结论 昆明市IDUs人群中HCV存在5种亚型,3b和3a是主要毒株且在该人群中具有较长的流行时间。     

德宏傣族景颇族自治州2016年HIV/HCV合并感染者HCV分子传播簇分析

目的 了解HIV/HCV合并感染者中HCV主要亚型的流行分布特征,探讨HCV主要亚型分子传播簇及其影响因素。方法 利用全国艾滋病综合防治信息系统收集2016年新报告德宏傣族景颇族自治州（德宏州）HIV/AIDS病例共1 112例,筛选出HIV/HCV合并感染且血浆量≥ 200 μl的318份样本,采用巢式PCR法扩增HCV的CE1和NS5B基因片段,采用ChromasPro 1.5和BioEdit 7.0.9.0软件进行序列比对和基因型分析,采用Mega 7.0软件建立系统进化树和分子传播网络构建。结果 HIV/HCV合并感染且满足HCV基因亚型检测要求的样本有267份。HCV基因亚型呈多样化,主要有3b、6n、6u、1a、3a和其他亚型,构成比分别为32.6%（87/267）、18.4%（49/267）、15.7%（42/267）、13.1%（35/267）、11.2%（30/267）和9.0%（24/267）。1a、3a、3b、6n和6u亚型分子传播簇的总成簇率为39.1%（95/243）,1a的成簇率最高,为71.4%（25/35）。多因素logistic回归分析结果显示,除傣族和景颇族外的其他民族（与汉族相比,OR=0.17,95% CI：0.04~0.71）、已婚有配偶（与未婚相比,OR=0.42,95% CI：0.18~0.94）,6n与3a亚型（与3b亚型相比,OR=0.34,95% CI：0.12~0.95;OR=0.22,95% CI：0.05~0.93）较难形成传播簇;6u和1a亚型（与3b亚型相比,OR=3.10,95% CI：1.21~7.94;OR=4.00,95% CI：1.32~12.11）较易形成传播簇。结论 德宏州HIV/HCV合并感染者的民族、婚姻状况、HCV基因亚型是HCV分子传播簇形成的关联因素。     

武汉市美沙酮门诊治疗者丙型肝炎病毒基因分型

目的 探讨武汉市美沙酮门诊治疗者丙型肝炎病毒(HCV)及不同基因型感染状况.方法 用酶标记免疫(ELISA)法检测抗-HCV抗体,在86份抗-HCV抗体阳性的血清标本中,分别提取HCV RNA,通过逆转录巢式聚合酶链反应(RT-nested PCR)扩增C基因的羧基至E1基因的氨基端长度为474 bp的片段,测定其核苷酸序列,与GenBank中已知的HCV序列进行系谱分析,确定HCV基因型.结果 武汉市美沙酮门诊332名治疗者中抗-HCV IgG阳性率为94.3%;其中86份血清的HCV序列通过系谱显示6a型71例,占82.5%;3b 7例,占8.2%;1a 5例,占5.8%;1b 3例,占3.5%.结论 武汉市美沙酮门诊入组的吸毒者HCV感染以6a型为优势株,其次为3b,吸毒者中HCV感染率较高,且基因亚型呈现多样性.     

中国丙型肝炎病毒基因型分布

目的分析中国丙型肝炎病毒(HCV)基因型的分布及变化趋势。方法计算机检索1994年以来中国医院知识库(CHKD),1998年以来万方数据资源系统、中国生物医学文献数据库(CBMDisc)以及PubMed数据库,并结合文献追溯方法,收集国内HCV基因分型的相关文献。相同HCV亚型分别按地区、研究时间、人群分组,并进行简单数量合并,计算百分比。结果共纳人文献140篇(共168条记录)。不同地区HCV基因型存在差异,其中北方地区基因型较单一,以1b和2a型为主;南方地区HCV基因型种类较多,以1b型为主,2a,3a,3b及6a型各自占较大比例。早期HCV基因型较单一,随着时间推移,1b及2a亚型逐渐减少,而3a,3b及6a亚型逐年增加,亚型类型逐年增多。有偿献血人群lb,2a亚型所占比例较高;吸毒人群HCV基因亚型较多,3型(3a,3b亚型)及6a亚型所占比例较大,且有逐渐向普通人群扩散趋势。结论中国流行最广泛的HCV基因亚型为1b及2a,且分布地区差异较大,并随时间的推移,基因型分布产生较大变化。     

2014―2018年广西柳州市HCV的基因型和1b亚型NS5B区的序列特征

目的  分析2014―2018年广西柳州市丙型肝炎病毒（hepatitis C virus,HCV）的基因型分布和HCV 1b亚型NS5B区的序列特征。 方法  收集慢性丙型病毒性肝炎患者血清,提取HCV RNA,反转录后用巢式PCR扩增NS5B区序列,测序后构建进化树分析HCV基因型和基因亲缘关系。用聚类分析法对比HCV 1b本地群、非本地群和参照株NS5B区基因和蛋白序列的差异。 结果  广西柳州市HCV流行的基因型包括1a、1b、2a/c、3a、3b、6a、6c/d和未分型（NT）,分别占3.39%、43.01%、0.42%、13.98%、6.99%、28.81%、3.18%和0.21%;HCV 1b亚型中61.6%的病毒与各参照株进化距离均较远,其比例在2014―2018年分别占HCV 1b亚型的69.8%、78.6%、43.3%、47.6%和59.6%;该群HCV的NS5B基因有15个经常性突变位点,可导致NS5B蛋白I2682V和S2755N发生经常性变异。 结论  广西柳州市HCV流行的主导基因型依次为1b、6a和3a;HCV 1b亚型中的大部分属于本地亲缘性群,该群HCV的NS5B蛋白存在特征性的变异位点并可能影响直接抗病毒药的作用。     

云南边境地区禽流感H5N1亚型病毒NS基因进化分析

目的 阐明云南边境地区禽流感H5N1亚型病毒NSl、NS2基因变异特征及遗传进化关系。方法 在云南边境地区采集境外家禽和野生鸟类棉拭子样品,经H5N1亚型特异性多重RT-PCR检测,阳性样品对病毒NS基因进行扩增,克隆Z至pMDl8一T载体测序,获得NSl、NS2基因序列,并与已知参考毒株序列进行序列比对及系统发育分析。结果 自1240份样品中检出H5N]亚型阳性样品71份,阳性率为5．72％;30份代表性阳性样品病毒NS基因测序获得17种序列,存在3个不同进化(亚)分支(I一1、I一2、Ⅱ);NSl／NS2基因与病毒血凝素(HA)基因呈现不同进化关系;NSl蛋白涉及核定位信号区、RNA结合区、效应区及其他致病性相关的关键性氨基酸位点存在替代或突变。结论 云南边境地区H5N1亚型病毒NSl／NS2基因具有遗传差异,2010年以来NS基因进化分支I一2、Ⅱ已成为当地流行的优势毒株。     

白银市美沙酮门诊吸毒人群丙肝感染状况及影响因素分析

目的了解白银市美沙酮门诊吸毒人群丙型肝炎病毒（HCV）的感染状况及影响因素。方法用SPSS13.0对白银市588名吸毒者监测资料进行统计分析,比较丙肝阳性吸毒者与阴性吸毒者之间的差异,分析吸毒人群感染丙肝的可能影响因素。结果吸毒人群HCV阳性率为13.9%,HCV抗体阳性吸毒者中曾经注射吸毒的比例为40.0%,HCV抗体阴性吸毒者中曾经注射吸毒的比例为9.0%,与配偶或性伴发生性行为时未使用安全套的比例为70.1%。结论曾经注射吸毒、不安全性行为是吸毒人群感染和传播丙肝的重要因素。     

DRD2基因多态性与美沙酮维持治疗剂量的关联性研究

目的 探讨DRD2基因的3个单核苷酸多态性位点（rs1800497、rs6275以及rs1799978）与美沙酮维持治疗剂量之间的关联。方法 采用病例对照研究的方法,使用Quanto软件估算样本量至少180人。实际共纳入美沙酮维持治疗者257人,其中低剂量对照组89人,高剂量病例组168人。收集研究对象的一般情况、既往吸毒状况以及服药状况等信息,并对其进行DRD2基因分型,以探讨DRD2基因的多态性与美沙酮维持治疗剂量的关联性。结果 DRD2基因rs6275位点基因型在不同美沙酮维持治疗剂量组间的分布差异有统计学意义,TC基因携带者相比于TT基因携带者（OR=0.338,95% CI：0.115~0.986）,TC+CC基因型携带者相比于TT基因型携带者（OR=0.352,95% CI：0.127~0.975）可能需要更低的美沙酮维持治疗剂量。尚未发现rs6275位点的等位基因,rs1800497位点、rs1799978位点的等位基因以及各遗传模型下的基因型在不同美沙酮治疗剂量组间分布的差异有统计学意义。结论 DRD2基因rs6275位点与美沙酮维持治疗剂量有关联。尚未发现rs1800497位点、rs1799978位点与美沙酮维持治疗剂量有关联。     

志贺菌中成簇规律间隔短回文重复序列的分子分布特征

目的 探索志贺菌中成簇规律间隔短回文重复序列(CRISPR)的分布。方法 共选择志贺菌分离株52株, 其中河南41株, 江西6株, 北京5株。利用PCR扩增志贺菌的4个CRISPR位点(S1、S2、S3、S4), 产物送测序, 分析CRISPR的重复序列和间隔序列。结果 志贺菌的4个CRISPR位点阳性率分别为33. 69%(S1)、50.00%(S2)、82.69%(S3)和73.08%(S4);S1和S3包括2种亚型, S2有3种亚型, S4包括4种亚型。2004年前分离的河南分离株中检出S1位点, 2004年后分离的菌株中均未检出该位点;S2、S3和S4在两组的分布没有差异。结论 志贺菌各CRISPR位点含有不同亚型, 河南分离株S1的分布与细菌分离时间有关, 而S2、S3 及S4和分离时间无关。     

2016-2017年中国丙型肝炎哨点监测分析

目的 监测中国丙型肝炎（丙肝）哨点5类人群HCV感染率,为评估丙肝的流行趋势和评价防控效果提供数据。方法 全国31个省（自治区、直辖市）设立87个国家级丙肝哨点,对无偿献血者、单位体检者、医院侵入性诊疗患者、血液透析患者以及计划生育门诊就诊者5类哨点人群进行监测,了解HCV感染状况。2016、2017年4-6月以重复横断面调查方法,对5类哨点人群开展丙肝监测,同时采集血样进行HCV抗体检测。结果 2016年86个哨点（1个哨点未能开展调查）完成了监测,监测人数115 841人,HCV总阳性检出率为0.38%（442/115 841,95% CI：0.23%~0.53%）。2017年87个哨点完成了监测,监测人数120 486人,HCV总阳性检出率为0.37%（449/120 486,95% CI：0.23%~0.52%）。2016、2017年丙肝哨点监测人群中,血液透析患者的HCV抗体阳性率分别为4.46%（223/5 005,95% CI：2.18%~6.73%）和4.39%（216/4 919,95% CI：2.29%~6.50%）,医院侵入性诊疗患者的HCV抗体阳性率分别为0.85%（44/5 200,95% CI：0.27%~1.42%）和0.70%（36/5 150,95% CI：0.15%~1.24%）,无偿献血者、单位体检者和计划生育门诊就诊者3类人群的HCV抗体阳性率均≤ 0.25%,5类监测人群HCV抗体阳性率比较,差异有统计学意义（2016年,F=23.091,P<0.001;2017年,F=20.181,P<0.001）。结论 5类监测人群HCV抗体阳性率存在明显差异,血液透析患者HCV抗体阳性率最高,其次为医院侵入性诊疗患者HCV抗体阳性率,其他3类监测人群的HCV抗体阳性率维持在较低水平。     

HCV dispersal patterns among intravenous drug users (IDUs) in Athens metropolitan area

BackgroundMost of the HCV transmission the recent years in Greece was among IDUs. Our aim was to estimate the prevalence of HCV genotypes and to investigate the patterns of HCV dispersal among IDUs in Athens using current state of the art molecular epidemiology methods.MethodsHCV sequences were determined from 238 HIV-negative IDUs collected on the basis of the “ARISTOTLE” prevention program carried out in Athens between 2012 and 2013. Phylogenetic trees were inferred on HCV sequences isolated from IDUs in Athens for the most prevalent HCV clades (subtypes 1a and 3a). Phylogenetic analysis was performed by Neighbor-Joining and Bayesian methods using GTR + G as nucleotide substitution model. HCV dispersal patterns were estimated using as references, all globally available HCV sequences for subtypes 1a and 3a.ResultsThe prevalence of HCV subtypes was: 3a (59.2%), 1a (21.9%), 4 (13.0%), 1b (5.4%) and 2 (0.5%). Phylogenetic analyses revealed that most sequences (63.5%) οf subtypes 1a and 3a fell within IDU-specific monophyletic groups. The proportion of sequences in monophyletic clades was similar for subtype 3a (62.9%) and 1a (65.3%). For the latter group, monophyletic clades were smaller in size. Multivariable logistic regression analyses showed that monophyletic clustering was marginally associated recent onset of injecting ([AOR] = 1.44; 95% CI (0.97–2.13), p = 0.068).ConclusionsThe high proportions of HCV sequences within IDU-specific monophyletic clusters suggest that transmissions occurred locally among IDUs in Greece. The numerous clusters for both 1a and 3a provide evidence that both sub-epidemics were the result of multiple introductions among the IDUs. Higher regional clustering was probably associated with a more recent onset of drug use.     

Epidemic history of major genotypes of hepatitis C virus in Uruguay

Worldwide, more than 170 million people are chronically infected with the hepatitis C virus (HCV) and every year die more than 350,000 people from HCV-related liver diseases. Recently, HCV was reclassified into seven major genotypes and 67 subtypes. Some subtypes as 1a, 1b and 3a, have become epidemic as a result of the new parenteral transmission routes and are responsible for most HCV infections in Western countries. HCV 1a subtype have been sub-categorized into two separate sub clades. Recent studies based on the analysis of NS5B genome region, reveal that HCV epidemics in Argentina and Brazil are characterized by multiple introductions events of subtypes 1a, 1b and 3a, followed by subsequent local dispersion. There is no data about HCV genotypes circulating in Uruguay and their evolutionary and demographic history. To this end, a total of 153 HCV NS5B gene sequences were obtained from Uruguayan patients between 2005 and 2011. 86 (56%) sequences grouped with subtype 1a, 40 (26%) with subtype 3a and 27 (18%) with subtype 1b. Furthermore, subtype 1a sequences were distributed among both clades, 1 (n = 62, 72%) and 2 (n = 24, 28%). Four local HCV clades were found: UY-1a(I), UY-1a(II), UY-1a(III) and UY-3a; comprising a 39% of all HCV viruses analyzed in this study. HCV epidemic in Uruguay has been driving by multiple introductions of subtypes 1a, 1b and 3a and by local dissemination of a few country-specific strains. The evolutionary and demographic history of the major Uruguayan HCV clade UY-1a(I) was reconstructed under two different molecular clock rate models and displayed an epidemic history characterized by an initial phase of rapid expansion followed by a more recent reduction of growth rate since 2000–2005. This is the first comprehensive study about the molecular epidemiology and epidemic history of HCV in Uruguay.     

HCV resistance-associated substitutions following direct-acting antiviral therapy failure – Real-life data from Poland

BackgroundThis study analysed the NS3 and NS5A mutation frequencies, persistence and drug susceptibility in a cohort of real-life patients, with failed hepatitis C virus (HCV) therapy following directly acting antiviral (DAA) treatment.MethodsNS3/NS5A Sanger sequences from 105 patients infected with HCV genotype (G) 1a (6,5.7%), G1b (94,89.5%), G3a (4,3.8%), and G4 (1,1.0%) post DAA treatment failure were analysed. NS3 and NS5A resistance-associated substitutions (RASs) were identified using the geno2pheno algorithm and associated with clinical variables. Time trends were examined using logistic regression.ResultsNS5A RAS were found in 87.9% of sequences derived from patients exposed to this class of agents, whereas NS3 RAS was found in 59.1% of HCV protease-exposed subjects. The frequency of the NS3 RAS increased with fibrosis stage, from 40.0% among F0/F1 individuals to 81.8% among patients with liver cirrhosis (F4, p = 0.094). NS5A mutation frequencies were 7.6% for 28A/V/M, 10.6% for 30 K/Q/R, 42.4% for 31I/F/M/V, and 75.8% for 93H. For NS3, the most common RASs were 56F–23.7%, 168A/E/I/Y/T/V–14.0%, and 117H–5.4%. Susceptibility to glecaprevir/pibrentasvir, velpatasvir/voxlaprevir, and elbasvir/grazoprevir was retained in 92.9%, 43.4%, and, 25.3% of patients, respectively. The frequency of NS3 RAS decreased with time elapsed from failure to sampling (p = 0.034 for trend). NS5A RAS frequency remained stable over the 24-months.ConclusionsFollowing DAA treatment failure, NS5A and NS3 RASs were common with increasing frequency among patients with advanced liver disease. In most cases, despite the presence of RASs, susceptibility to DAA combinations with higher genetic barrier was retained.     

Epidemic history of Hepatitis C virus in Brazil

Hepatitis C virus (HCV) subtypes 1a, 1b and 3a are the most prevalent strains in Brazil, but very little is known about the epidemic history of these subtypes in the country. A total of 231 HCV NS5B gene sequences (subtype 1a = 89, subtype 1b = 56, and subtype 3a = 86) isolated in Brazil between 1995 and 2007 were analyzed in the present study. Sequences (328-pb) were subjected to phylogenetic analyses and statistical tests of phylogenetic mixing by sampling location and risk group. Our results revealed important variations in the pattern of HCV transmission among subtypes. Transmission of subtype 1a was characterized by dissemination of one major Brazilian lineage with a random virus exchange between different geographical regions but not between IDU and non-IDU populations. Transmission of subtype 1b was characterized by concurrent dissemination of multiple HCV lineages with a restricted virus exchange between country regions and risk groups. Transmission of subtype 3a was characterized by simultaneous spreading of multiple HCV lineages and random phylogenetic mixing by risk group and sampling location. Epidemic histories of major subtypes 1a, 1b and 3a Brazilian clades were estimated using a Bayesian coalescent approach. Our results indicate that all major HCV Brazilian clades probably start to circulate in the country during the second half of the 20th century and displayed roughly similar epidemic histories characterized by an initial phase of exponential expansion and by reduction of growth rates since 1980–1995. This suggests that the expansion of HCV may have been effectively controlled in Brazil.     

上海市浦东新区食源性小肠结肠炎耶尔森菌耐药及分子流行病学特征

目的 了解上海市浦东新区食源性小肠结肠炎耶尔森菌耐药及分子流行病学特征。方法 2012-2016年主动、定点采集上海市浦东新区4类流通生鲜食品,使用冷增菌方法分离小肠结肠炎耶尔森菌,并分析菌株生物型、血清型、毒力基因型、耐药性和PFGE分子型别。结果 共采集食品3 900份（禽类590份、畜类1 074份、水产品1 488份、蔬菜748份）,其中111份（2.8%）检出小肠结肠炎耶尔森菌。禽类制品（5.3%,31/590）和畜类制品（4.5%,48/1 074）的检出率高于水产品（1.6%,24/1 488）和蔬菜制品（1.1%,8/748）。分离株以生物1A型（95.5%）和O：8血清型（42.3%）为主,且分离数与年总分离数呈正相关。所有菌株均缺失4种（ail、ystA、yadA和virF）产毒株标记的毒力基因,76株（68.5%）ystB基因阳性（其中35株属于1A/O：8/ystB）。分离株对氨苄西林（74.8%）和阿莫西林/克拉维酸（70.3%）的耐药率最高,对头孢西丁不敏感率超过50.0%;未发现三代头孢菌素或氟喹诺酮类抗菌药物耐药株,38.7%（43/111）的菌株为多重耐药。O：8和O：5血清型菌株分别存在44和18种PFGE分子型别。结论 上海市浦东新区食源性小肠结肠炎耶尔森菌暴露风险以禽类制品和畜类制品为主,优势菌型为1A/O：8/ystB,虽无典型产毒株特征但仍有潜在致病力。菌株耐药率处于较低水平但存在多重耐药株,PFGE分子型别提示菌株呈高度遗传多样性。     

格卡瑞韦/哌仑他韦治疗HCV/HIV合并感染患者的临床研究

目的 分析格卡瑞韦/哌仑他韦治疗丙型肝炎病毒(HCV)/人类免疫缺陷病毒(HIV)合并感染患者的临床效果和安全性, 以期为临床治疗提供科学依据。 方法 选择2021年1月—2022年1月凉山州布拖县某医院收治的89例HCV/HIV合并感染无肝硬化的初治患者, 均予以8周的格卡瑞韦/哌仑他韦治疗, 随访12周。观察并记录治疗结束时的病毒学应答率、治疗结束12周后的持续病毒性应答率(SVR12)及不良反应发生情况。 结果 89例HCV/HIV合并感染无肝硬化的初治患者多为中青年已婚男性(79例, 88.8%), HIV感染主要经性接触传播(62例, 69.7%) 和静脉注射毒品传播(27例, 30.3%)。HCV基因型最常见的是基因1b型(33例, 37.1%) 和基因3b型(25例, 28.1%)。全部患者均顺利完成8周治疗, 且治疗结束时HCV RNA载量均低于检测值下限(＜25 IU/mL)。其中, 8例患者未能完成随访, 余81例(100%)患者均获得持续病毒学应答。患者观察期间均未出现严重不良反应, 但有11例患者发生轻度不良反应。 结论 格卡瑞韦/哌仑他韦8周方案治疗基因1、3、6型HCV/HIV合并感染无肝硬化的初治患者SVR12达100%, 且安全性和耐受性均较好, 可以作为此类患者临床治疗的优先选择。     

深圳市啮齿动物感染汉坦病毒的基因特征研究

目的 研究深圳市啮齿动物所携带的汉坦病毒分子流行病学特征,分析汉坦病毒基因型别。方法 采用笼日法布点捕鼠,收集鼠肺标本后研磨提取RNA。运用实时荧光PCR方法进行分型检测,进一步采用反转录-巢式PCR扩增部分M片段G2区和S片段核苷酸序列,并进行同源性和系统进化树分析。结果 共捕获200只鼠类动物,包含褐家鼠189只、黄胸鼠9只和小家鼠2只。汉坦病毒检出率为21.0%（42/200）,均为汉城病毒,其中宝安区鼠肺检出率最高,达45.7%（χ²=25.60,P<0.05）。从阳性鼠肺标本中分别扩增出25条汉坦病毒M片段G2区和S片段序列,核苷酸同源性分别为95.3%~100.0%和97.6%~100.0%,与来自广州市的参考序列核苷酸相似性较高。系统进化树显示此次研究深圳市鼠类动物所携带的汉坦病毒均为汉城病毒的S2亚型。氨基酸突变位点分析发现,在S基因编码的核衣壳蛋白中存在1个位点突变,为BA-111第973位由丙氨酸（Ala）变为苏氨酸（Thr）。结论 深圳市鼠类动物所携带的汉坦病毒为汉城病毒的S2亚型,与深圳市历年以及周边省市汉坦病毒代表病毒毒株相比变异不大。     

163例ECMO治疗患者医院感染情况及其危险因素

目的 了解接受体外膜肺氧合(ECMO)支持治疗患者术后相关医院感染情况及其危险因素.方法 回顾性收集某院2013年1月—2019年12月应用ECMO支持治疗患者的病历资料,统计、分析ECMO术后医院感染情况及其危险因素.结果 163例ECMO支持治疗患者中,39例发生ECMO术后医院感染,感染发病率为23.93％.以下...     

Identification of Indian sub-continent as hotspot for HCV genotype 3a origin by Bayesian evolutionary reconstruction

BackgroundRecent emphasis in Hepatitis C virus (HCV) evolutionary biology has focused on analysis using Core, E1/E2 and/or NS5b regions, with limited appreciation of full length genome. While HCV genotypes have been described as endemic in the Indian subcontinent, there has been no confirmation at the molecular evolutionary level of these genotypes. We have attempted here to determine the status of Indian HCV genotype 3a sequences in relation to similar genotypes from other parts of the world.MethodsCloning, sequencing and molecular characterization was performed on 9 Indian sequences and comparative analyses were performed with 46 sequences from other countries. Evolutionary-rate and molecular-clock hypothesis testing was addressed by Bayesian MCMC.ResultsGenetic analysis of full length genome revealed two hypervariable regions (HVR) in E2 region – HVR496 and HVR576, with a variable 5–8 amino-acid insertion sequence and a putative N-glycosylation site. Phylogenetic analysis revealed a divergence resulting in 2 distinct clades: clade-1 represented by HCV 3a subtype and clade-2 represented by other 3 subtype genomes. Clade-2 shows earlier divergence than clade-1. Analysis revealed that genotype 3a genomes from India roots out first (∼99 years ago) in clade1. Bayesian skyline plot analysis revealed an increase in effective number of infections from 1940s to 1990s, followed by a gradual decrease after 2000.ConclusionsGenotype 3a sequences appear to have originated in India and later dispersed to United Kingdom around mid 1940s, most likely around the time of Indian independence and World War II.