Complete genomic sequence and phylogenetic relatedness of hepatitis B virus isolates from Iran

Hepatitis B virus (HBV) is one of the main etiological agents of acute and chronic liver disease that is still a major public health problem in the world. Numerous HBV isolates have grouped into eight genotypes, A to H, based on the complete genome sequence. To date, no study has been carried out on the complete HBV genome sequence in Iran. The objective of this study was to investigate the complete genome sequence organization and phylogenetic analysis of the five HBV strains, which obtained from Iranian chronic infected patients. Results showed that Iranian strains were closely related to each other, with 97-100% nucleotide similarity. Phylogenetic analysis based on the complete genome sequences and the precore/core gene sequences revealed that all strains were of genotype D, sub-genotype D1 with bootstrap value 100 and 99%, respectively. The S gene encoded Arg122, Pro127, and Lys160 corresponding to subtype ayw2. Iranian HBV isolates had closely related with Turkish HBV strains. All strains had a nucleotide length of 3,182 base pair (bp) except IR-P4 strain, with a 3,185 bp in length and with a unique Phe89 insertion in the X gene. The intragenotypic divergence of the complete genome sequence of Iranian strains was 1.8% and the intergenotypic in genotype D was 3.8% and with the other genotypes was 7.9-15.4%. In conclusion, this study revealed that the HBV genotype D, sub-genotype D1, subtype ayw2 dominates in the Iranian infected patients. A single Phe89 insertion in the X gene of the one Iranian strain with an unforeseen length of 3185 bp was identified.     

Molecular epidemiology of hepatitis B virus in Iran

Hepatitis B virus (HBV) infection is a major cause of liver disease worldwide. Eight genotypes and 24 subgenotypes of HBV have been identified. The aim of this study was to determine the distribution of HBV genotypes, subgenotypes and subtypes, and to understand HBV genetic variability in the HBV genome circulating in Iranian provinces. Two hundred and forty-nine sera from HBV-infected patients living in 25 provinces of Iran were collected (2004–2007). A part of the HBV S / pol and whole BCP / C genes were amplified, sequenced and then subjected to phylogenetic, recombination and genetic variability analysis. Results revealed genotype D of HBV in all samples and subgenotypes  D1 (98.52%), D2 (0.74%) and D3 (0.74%) among Iranian patients living in different provinces of Iran. Subtypes  ayw2 (94.4%), ayw1 (2.8%), ayw3 (2%) and ayw4 (0.4%) were deduced, on the basis of HBV small surface antigen (HBsAg) amino acid sequences. The mean percentage intra-genotypic distance of S plus core regions was 2.8%; the mean percentage inter-genotypic distance of this region between Iranian strains and genotype D isolates was 3.1%; and this rate for other genotypes was 5.2–11.4%. Various rates of point mutations have been found within different HBV genes, e.g. HBsAg (17.2%), precore-G1896A (59.5%) and Basal core promoter (BCP) double mutations (49.2%), whereas no recombination was found. In conclusion, these results indicate that the only genotype circulating in the provinces of Iran is genotype D. There exist high genetic variabilities in the S / pol and BCP / C regions among the Iranian HBV isolates.     

Improved tracing of hepatitis B virus transmission chains by phylogenetic analysis based on C region sequences

An effective vaccine is available for the hepatitis B virus (HBV), which is a very contagious human pathogen. The prevalence of chronic HBV infection is very low in the Netherlands (<0.5%), and no universal vaccination is in place. Instead, a program of vaccination for targeted groups at high risk of HBV exposure has been implemented. Because transmission of HBV can occur by various routes, the effectiveness of this targeted vaccination strategy is difficult to assess. Molecular typing data for the surface protein encoding gene of HBV isolates, in combination with epidemiological data, provide some insight into the main transmission routes. Due to the low mutation rate of the HBV genome, many isolates have identical S region sequences, which hampers phylogenetic analysis and identification of transmission chains. The molecular epidemiological analysis of acute HBV isolates based on the surface and core protein encoding regions were compared. The nucleotide diversity found in the C region was statistically significant greater (1.5 times) than in the S region, and phylogenetic analysis based on the C region showed a higher resolution. C region analysis resulted in an almost 50% reduction of genotype A isolates with identical sequences. C region analysis also indicated that no long-chain transmission of genotype D strains is occurring in the Netherlands, as all genotype D isolates have unique C region sequences. Defining the goals of molecular typing of HBV isolates should precede the choice for phylogenetic analysis on the basis of either C or S region sequences.     

A nationwide molecular epidemiological study on hepatitis B virus in Indonesia: identification of two novel subgenotypes,B8 and C7

Upon phylogenetic analysis of a partial S gene sequence [396 nucleotides (nt)], 928 hepatitis B virus (HBV) strains obtained from 899 viremic subjects in 28 major cities on 15 islands of Indonesia in 1989–2007 segregated into four HBV genotypes. Genotype B was predominant (66%), followed by genotype C (26%), genotype D (7%), and genotype A (0.8%). Comparative and phylogenetic analyses of the 396-nt S gene sequence of 928 HBV isolates and whole genomic sequences of 25 selected HBV isolates revealed a total of 14 subgenotypes within genotypes A–D: two (A1 and A2) in genotype A (HBV/A), five (B2, B3, B5, B7, and a novel subgenotype, tentatively designated B8) in HBV/B, five (C1, C2, C5, C6, and another novel subgenotype, C7) in HBV/C, and two (D1 and D3) in HBV/D. The distribution of HBV genotypes/subgenotypes, including B8 and C7, seems to be associated with ethnological origins in Indonesia. The nucleotide sequence data reported in this study have been assigned DDBJ/EMBL/GenBank accession numbers AP011084–AP011108 for 25 entire HBV genomes and AB466339–AB467266 for 928 partial HBV sequences.     

Genotypes and phylogenetic characterization of hepatitis B and delta viruses in Egypt

Hepatitis B virus (HBV) and hepatitis D virus (HDV) sequences among HBV carriers from Egypt have not been evaluated sufficiently. The genotypes of HBV isolated from 105 serum samples from Egyptian carriers were determined. Four complete genomes and 11 entire preS1/S2/S genes were sequenced and evaluated. All serum samples were classified into HBV genotype D using serologic and genetic methods. The length of four complete nucleotide sequences was 3,182 bp. In all 15 samples, the common 33 nucleotides (11 amino acids) deletions in the preS1 region specific for HBV genotype D were observed. In the phylogenetic analysis based on the complete nucleotide sequences, all samples were clustered with the HBV isolates reported from previously Western and Mediterranean countries with nucleotide homology ranging from 96.0-98.0%. Of 75 HBsAg positive samples, anti-HDV was found in 15 (20%), and HDV RNA was detected in 9 of 15 (60%). The proportion of the patients with liver disease was higher in HBV carriers of anti-HDV positive with HDV RNA than in HBV carriers of anti-HDV positive without HDV RNA (P < 0.05). In the phylogenetic analysis based on the sequences in nucleotide position 853-1267 of HDV, nine samples were classified into HDV genotype I with the nucleotide homology ranging from 88.3-92.1% (mean; 90.5%) and clustered with HDV strains reported previously from Ethiopia, Somalia, Egypt, and Lebanon. These results indicate that HBV genotype D and HDV genotype I are most prevalent in Egypt, and HDV co-infection in HBV carriers is related to severity of liver disease.     

Hepatitis B virus genotypes in Mongols and Australian Aborigines

Hepatitis B virus (HBV) is spread worldwide. Seven genotypes, A-G, have been described, differing by more than 8% of the genome. In eastern Asia and Oceania genotypes B and C are predominant. However, little is known about genotypes in Mongolia and Australian aborigines. We analysed the preS and S regions of HBV from 9 Mongols and 5 Australian Aborigines. All Mongolian strains were of genotype D and were most similar to Central Asian sequences. All the Australian strains were genetically of serotype ayw3, and could not be reliably classified by the S region analysis, but placed on a separate branch. By preS analysis, they were however clearly of genotype C. The 6-7% nucleotide difference from published Asian genotype C sequences suggests that they diverged from Asian genotype C branch more than 1000 years ago.     

Hepatitis B virus genotype D strains from Estonia share sequence similarity with strains from Siberia and may specify ayw4

The genotypes and subtypes of 205 HBV isolates collected during 1989-2002 in Estonia and 14 other regions of the former USSR were determined by sequencing and phylogenetic analysis of the S gene. The in Europe prevailing genotypes, A and D, were also circulating in the whole territory of the former USSR including Estonia and accounted for 18.5 and 81% of the strains, respectively. All genotype A strains specified adw2, and a single genotype C strain specified adrq+. Most genotype D strains specified ayw3 and ayw2, although, three strains from Estonia and Siberia specified ayw4. Due to unique substitutions, Ser122 and Ala127, four strains could not be classified according to the subtype. One strain specifying ayw3 encoded Leu143 and Ala145 and was possibly an immune "escape" mutant. At phylogenetic analysis 93% of the Estonian genotype D strains belonged to a cluster specifying mainly ayw3 and were more similar to isolates from Siberia and the Far-East of Russia than to isolates originating from Central Russia which belonged to another cluster of strains specifying mainly ayw2. This pattern might be explained by part of the Estonian population, has roots east of European Russia, based on linguistic evidence. Eight dominant HBV strains represented by identical S gene sequences were identified, one within genotype A and seven within genotype D, three of which included isolates from Estonia and Siberia. Some of these strains were collected over a period of at least 13 years indicating there are genetically stable variants of HBV that remain conserved over decades.     

Comparison of genotypes C and D of the hepatitis B virus in Japan: a clinical and molecular biological study

The genotype-related differences between genotype C and genotype D of the hepatitis B virus (HBV) remain unknown. The relationship was studied between the HBV genotypes and their clinical features, paying special attention to genotypes C and D. Serum samples from 413 HBV carriers were genotyped using an enzyme immunoassay (EIA) and by restriction fragment length polymorphism. The nucleotide sequences at the basic core promoter (BCP) and precore (PreC) regions were analysed by direct sequencing. The full genome sequences of three HBV genotype D cases were also examined. Almost all carriers with HBV genotype D were asymptomatic carriers (84.2%). Genotype D was not found in patients with liver cirrhosis and hepatocellular carcinoma. In contrast, carriers with genotype C had mainly chronic liver disease (63.2%; P<0.001). The ratio of hepatitis B e antigen (HBeAg)/anti-HBe was significantly higher in genotype C than in genotype D in the young age-matched group (P<0.01). The mutation at BCP (T1762, A1764) was significantly lower in genotype D than in genotype C among HBeAg-negative patients (P<0.05). The HBV full-genome sequences are very similar to certain HBV genotype D sequences from Europe. In conclusion, genotype C was associated with chronic liver disease, whereas genotype D was related to asymptomatic carriers with earlier HBeAg seroconversion. Thus, the outcome of chronic HBV infection may be different in persons infected with HBV genotypes C and D.     

Hepatitis B virus genotyping, core promoter, and precore/core mutations among Afghan patients infected with hepatitis B: a preliminary report

In spite of hepatitis B virus (HBV) vaccination, HBV infection remains an important public health problem worldwide. Although the HBV genotype distribution has been determined in some parts of South Central Asia, no survey has been conducted to determine the HBV genotype in Afghanistan. Twelve Afghan patients infected with HBV living in Afghanistan were enrolled in this study. Partial HBsAg and basic core promoter, precore, and core (BCP/preC/C) regions were amplified and subjected for direct sequencing. In parallel, precore G1896A mutation was also determined by an amplification-created restriction site method. Results revealed HBV genotype D (95% bootstrap value), sub-genotype D1 (98% bootstrap value), and subtype ayw2 in all Afghan isolates. Afghan isolates clustered in a separate branch in the D1 sub-genotype called D1', while supported by 82% bootstrap value. The percentage of intra-genotypic distance among Afghan isolates was 1.05% and inter-genotypic distance with the other genotype D was 2.87% and with other genotypes was 7.50%-11.1%. The wild-type, mixed infection, and precore mutant were found in six, two, and four HBV isolates, respectively. The A1762T/G1764A BCP dual mutation was found in one isolate. Three isolates presented single mutation in the BCP dual mutation region, whereas two showed a novel G1764T mutation. In conclusion, this preliminary study revealed HBV genotype D, sub-genotype D1, and subtype ayw2 of HBV among hepatitis B infected patients from Afghanistan. Further investigation should be carried out.     

Clade analysis and surface antigen polymorphism of hepatitis B virus American genotypes

Eight genotypes (A-H) of hepatitis B virus (HBV) have been described, HBV genotypes F and H being autochthonous to America. HBV genotype F has been classified in four clusters. The objective of this study was to gain insight into the molecular epidemiology of HBV American genotypes, as well as to analyze the genotype-related polymorphism in some functional domains of the surface proteins. The sequences of the S region of 106 isolates genotype F and H were analyzed, out of which 47 isolates genotype F circulated in different Venezuelan populations. Most of the Venezuelan isolates genotype F were grouped in cluster III (n = 39) and 7 in cluster II. One isolate obtained from a blood donor could not be classified in any clade and harbored amino acid substitutions characteristic of a vaccine escape mutant (G145R) and a stop codon in the surface antigen. Amino acid analysis of the PreS and S gene products showed unique genetic characteristics in genotype F and H sequences in some important domains involved in the early steps of infection. Out of 30 available sequences, two complete genome sequences of HBV genotype F from Venezuela were obtained. Phylogenetic analysis of these complete genomes confirmed the presence of four clusters inside genotype F, differing in more than 4% nucleotide divergence. Our extended analysis showed that genotype F clades Ia, III, and IV exhibit a restricted geographic distribution (Central America, the North and the South of South America, respectively) while clades Ib and II are found in all the Americas except in the Northern South America and North America respectively.     

新疆居民HBV基因型的分布及其与临床表现关系的初步研究

目的 了解新疆地区乙肝患者HBV基因型的分布及其与临床表现的关系.方法 从2000余份血清中筛选出HBsAg阳性血清200份.利用巢式PCR法扩增血清中HBV DNA S基因进行测序并分型;统计分析基因型分布及与临床表现的关系.结果 新疆HBV有B、C、D三个基因型,其中B基因型10例（7.8%）,C基因型58例（45.7%）,D基因型59例（46.5%）.C基因型中汉族51例（87.9%）,D型中汉族27例（45.7%）,维吾尔族24例（40.7%）.结论 新疆地区HBV基因型以C、D型为主,少量为B型.C型以汉族为主,D型中汉族和维吾尔族占多数.C型与更严重的疾病及转归有关.     

新疆地区居民乙肝病毒基因型的初步研究

目的 初步确定新疆地区乙肝患者乙肝病毒基因型的基本情况.方法 对在新疆地区采集的2000余份血清中检测得到200份HBsAg阳性的血清,利用巢氏PCR法扩增其S基因并测序,用MEGA3软件将测序结果与GenBank中的HBV标准序列进行分析,构建并绘制系统发生树,分析基因型.结果 在200份样本中.127例(63.5%)成功检出基因型,其中B基因型10例(7.8%),C基因型58例(45.7%),D基因型59例(46.5%).结论 新疆地区HBV基因型以C、D型为主,少量为B型.     

Genotype,serotype, and phylogenetic characterization of the complete genome sequence of hepatitis B virus isolates from Malawian chronic carriers of the virus

Hepatitis B virus (HBV) genotypes have distinct geographical distribution. HBV sequences among hepatitis B carriers in Malawi have not been evaluated thus far. HBsAg serotype and genotype of HBV was determined in 20 serum samples from Malawian chronic HBV carriers, and two complete genomes and 13 entire pre-S2/S genes were sequenced directly. Genotype A HBV isolates were found in all of the samples, and serotype with adw2 and ayw2 were detected in three and 17 samples, respectively. In phylogenetic analyses, two complete genomes were classified into a subgroup A' that was described previously in South African isolates of the virus, and were separated from HBV isolates in Western countries with nucleotide differences ranging from 4.1-6.2%. The separation of subgroup A' was also evident in the tree topology of the entire pre-S1/S2, X and precore/core region, but not evident in the small-S region. The nucleotide divergences in subgroup A' were higher than those among genotype A without subgroup A' in the complete genomes as well as each of four open reading frames. All of the 13 pre-S2/S sequences were classified into the subgroup A', and clustered with known HBV isolates with ayw2 in carriers from South Africa and Zimbabwe. Three amino acids in the pre-S2/S gene were characteristic of subgroup A' with ayw2. In conclusion, unique HBV isolates of subgroup A' with ayw2 are prevalent in Malawi, and subgroup A' with a relatively higher nucleotide diversity may be a HBV isolate characteristic of the indigenous population of some African countries.     

Molecular epidemiological study of hepatitis B virus in blood donors from five Chinese blood centers

Although the genetic variability of hepatitis B virus (HBV) in HBV-infected patients has been extensively studied, reports on genotypes, subtypes and mutations in the S region of HBV strains from Chinese blood donors are limited. In this study, 245 blood samples from HBsAg-positive blood donors were collected from five geographically diverse blood centers in China. The S region of HBV was amplified, and the HBV genotype and subtype were determined. The amino acid sequences of the S region were aligned, and mutations related to the failure of immunization and HBsAg detection were determined. Of the 245 samples, 228 (93?%) were genotyped successfully. We found that genotypes B, C, D and A accounted for 58.8?%, 21.9?%, 6.6?% and 3.95?% of the isolates, respectively. The distribution of HBV antigen subtypes was as follows: adw (67.6?%), adr (23.3?%) and ayw (8.7?%). Mutations were present in 39 (17.1?%) of 228 samples in the major hydrophilic region (MHR) of the S region. This study demonstrated that HBV genotype/subtype B/adw was the most frequent strain circulating in HBV-infected Chinese blood donors, followed by C/adr. The occurrence of MHR mutants in HBV-infected blood donors and the potential failure to detect some of them in collected units poses a threat to transfusion safety.     

云南省乙型肝炎病毒基因型和血清型的流行状况分析

目的了解云南省人群中流行的乙型肝炎病毒（Hepatitis B virus,HBV）基因型和血清型分布情况。方法从参加健康体检的人群中筛查HBsAg阳性的血清标本,利用巢式PCR扩增HBVS基因片段,并对扩增产物进行序列测定,从GenBank中查获A～I基因型共27株HBV参考序列,构建HBVS基因系统发生树,以此确定其样本的基因型及血清型,并对结果进行统计分析。结果从2216名体检人员血清标本中筛查出39份HBsAg阳性的样本,HBV的s基因序列分型结果表明有4种基因型：c型占76．9％,B型占15．4％;D型占5．1％;I型占2．5％。血清分型结果为：adw2型占71．8％;adrq‘型占17．9％;ayr型占10．3％。所有adw2血清型标本均为c基因型。HBsAg、HBeAg双阳性标本中75％为c基因型／adw2血清亚型。结论云南省HBV感染人群中HBV基因型的分布以C型为主,血清型以adw2型为主。     

云南省乙型肝炎病毒基因型和血清型的流行状况分析

目的 了解云南省人群中流行的乙型肝炎病毒(Hepatitis B virus,HBV)基因型和血清型分布情况.方法 从参加健康体检的人群中筛查HBsAg阳性的血清标本,利用巢式PCR扩增HBV S基因片段,并对扩增产物进行序列测定.从GenBank中查获A～I基因型共27株HBV参考序列,构建HBV S基因系统发生树,以此确定其样本的基因型及血清型,并对结果进行统计分析.结果 从2216名体检人员血清标本中筛查出 39份HBsAg阳性的样本,HBV的S基因序列分型结果表明有4种基因型:C型占76.9%,B型占15.4%;D型占5.1%;I型占2.5%.血清分型结果为:adw2型占71.8%;adrq+型占17.9%;ayt型占10.3%.所有adw2血清型标本均为C基因型.HBsAg、HBeAg双阳性标本中75%为C基因型/adw2血清亚型.结论 云南省HBV感染人群中HBV基因型的分布以C型为主,血清型以adw2型为主.     

云南省乙型肝炎病毒基因型和血清型的流行状况分析

目的 了解云南省人群中流行的乙型肝炎病毒(Hepatitis B virus,HBV)基因型和血清型分布情况.方法 从参加健康体检的人群中筛查HBsAg阳性的血清标本,利用巢式PCR扩增HBV S基因片段,并对扩增产物进行序列测定.从GenBank中查获A～I基因型共27株HBV参考序列,构建HBV S基因系统发生树,以此确定其样本的基因型及血清型,并对结果进行统计分析.结果 从2216名体检人员血清标本中筛查出 39份HBsAg阳性的样本,HBV的S基因序列分型结果表明有4种基因型:C型占76.9%,B型占15.4%;D型占5.1%;I型占2.5%.血清分型结果为:adw2型占71.8%;adrq+型占17.9%;ayt型占10.3%.所有adw2血清型标本均为C基因型.HBsAg、HBeAg双阳性标本中75%为C基因型/adw2血清亚型.结论 云南省HBV感染人群中HBV基因型的分布以C型为主,血清型以adw2型为主.     

Another novel subgenotype of hepatitis B virus genotype C from papuans of Highland origin

Hepatitis B virus (HBV) genotypes and subtypes have been identified worldwide. As HBV genotypes/subtypes, the HBV subgenotypes seem to be associated with their geographical distribution and ethnic origin. A previous study showed the novel HBV subgenotype C6 based on the complete genome sequences of isolates in Papua, Indonesia. In the present study, further characterization of HBV in Jayapura (capital of Papua Province), particularly from native people of Papua originating from the highland (highland Papuans) and those from the lowland (lowland Papuans) were examined. Of 32 HBV isolates from both highland and lowland Papuan blood donors with HBsAg positive, part of the S gene and the core gene sequences were analyzed. Analyses of some isolates from highland Papuans were confirmed by the complete genome sequences. Most HBV isolates were classified into genotype C (78.1%), followed by genotype B (18.8%), and genotype D (3.1%). The subtype adr was predominant (71.9%), followed by adw2 (25.1%), and ayw2 (3.1%). As with previous findings, phylogenetic analyses revealed that most HBV isolates from Papuans, C/adr, belonged to subgenotype C6. Interestingly, some C/adr isolates from highland Papuans formed a distinct cluster from all reported subgenotypes of HBV/C, and they differed from HBV/C1-C10 by 4.2-7.2% over the complete genome. SimPlot analysis showed no evidence of recombination with HBV/C1-C10. The isolated life and closed social systems of highland Papuans, even though some have been moving to Jayapura, likely contribute to the formation of this unique cluster of infection with a novel subgenotype of HBV, named C11.     

2008-2009年北京分离的肠道病毒71型基因组3'末端序列分析

目的 了解2008-2009年北京分离的肠道病毒71型(EV71)基因组3'末端的基因特征(未包括多聚腺苷尾),探讨是否与病毒的致病性有关.方法 于2008-2009年手足口病流行期间采集来首都儿科研究所附属儿童医院就诊的普通手足口病患儿和合并重症神经系统并发症患儿的咽/鼻拭子或疱疹液标本.将标本接种Vero细胞进行肠道病毒分离,同时设计肠道病毒通用引物、EV71和柯萨奇病毒A组16型(CA16)特异性引物通过巢式RT-PCR对分离到的肠道病毒进行型别鉴定.对引起不同临床类型感染的10株EV71分离株的基因组3'末端进行序列测定和分析.结果 10株EV71的3'末端均包含1386 nt的3D、终止密码子TGA和81 nt的3'UTR,由3D核苷酸序列所推导的3D蛋白含462个氨基酸.10株EV71的3D和3'UTR核苷酸同源性分别为95.8%～99.6%和96.3%～100%,重症来源的4株毒株中有3株在3Dpol第140位和第263位同时出现了相同的氨基酸变异(R140K和I263V).10株EV71的3D与C4亚型代表株具有最高的核苷酸和氨基酸同源性,分别为92.7%～94.2%和96.8%～97.6%;在3'UTR与CA16/G10具有最高的核苷酸同源性(88.9%～91.4%).3D区的遗传进化分析表明10株EV71在亲缘关系上与C4亚型最密切,与CA16/G10较密切,而与EV71其他基因型和亚型较疏远.结论 基因组3'末端在EV71进化中可能有一定的作用.     

2008至2009年北京地区分离的肠道病毒71型全基因组序列分析

目的了解2008至2009年从北京地区手足口病（HFMD）患儿分离到的肠道病毒71型（EV71）全基因组序列特点（未包括多聚腺苷尾）,以探讨基因序列的改变是否与病毒的致病性有关。方法选取首都儿科研究所病毒研究室2008年分离到的5株EV71毒株和2009年分离到的4株EV71毒株,其中4株来源于重症HFMD患儿（伴高热、持续抽搐及意识丧失等中枢神经系统症状）,5株来源于轻症HFMD患儿。设计覆盖病毒全基因组的10对特异性引物,对9株EV71毒株进行RT-PCR扩增、全基因组序列测定和分析。结果 9株EV71毒株的全基因组长度为7406bp或7405bp,部分毒株在5′UTR存在1处1个碱基的缺失。9株EV71毒株的全基因组核苷酸和氨基酸同源性分别为96.3%～99.4%和98.2%～99.6%,在VP1区核苷酸和氨基酸同源性分别为96.9%～99.9%和98.3%～100.0%。重症HFMD来源的4株毒株中有3株在VP2蛋白第144位及3D聚合酶（3Dpol）第140和263位同时出现相同的氨基酸变异（T144S、R140K和I263V）,并且在5′UTR区第208和254位同时出现相同的碱基变异（G208A和A254G）。9株EV71毒株的全基因组与C4亚型毒株具有最高的核苷酸同源性,在VP1区为94.3%～95.5%;在3D及3′UTR区与CV-A16/G10的同源性（84.3%～85.0%和89.0%～91.5%）高于与EV71-B型、A型及C型（C1～3、C5）的同源性。VP1和3D基因的遗传进化分析显示,9株EV71毒株与C4亚型毒株属同一分支。结论 VP2蛋白第144位氨基酸突变（T→S）、3Dpol第140和263位氨基酸突变（R→K和I→V）及5′UTR区第254位碱基突变（A→G）可能与EV71感染后引起的不同临床症状有关。根据VP1核苷酸序列,2008至2009年北京地区流行的EV71属于C4亚型;非结构蛋白基因在EV71进化中可能有一定的作用。