Molecular epidemiology of chronic hepatitis B virus infection in Greece

Virological data on chronic hepatitis B virus (HBV) infection in Greece are limited. HBV genotypes, surface antigen (HBsAg) subtypes, and HBsAg “a” determinant mutations among patients infected chronically with HBV, were investigated. Serum samples from 135 HBsAg positive patients were tested. Serologic (HBsAg, anti‐HBs, HBeAg, and anti‐HBe), virologic (HBV‐DNA quantitation) and biochemical markers (serum alanine aminotransferase/ALT and aspartate aminotransferase/AST) were analyzed. HBV genotypes and HBsAg subtypes were determined by partial sequencing of the S gene. Genotyping was performed by using the National Center for Biotechnology Information online Genotyping tool and phylogenetic analysis. Nucleotide sequences were aligned pair wise with ClustalW and phylogenetic trees were constructed by the neighbor‐joining method. Sequences were also used to predict HBV HBsAg subtypes. In six patients (4%), simultaneous presence of HBsAg and anti‐HBs was determined, whereas 47 patients (35%) were HBeAg positive, 84 (62.5%) were anti‐HBe positive, and four patients (3%) were characterized by the simultaneous presence of HBeAg and anti‐HBe. Mean ALT was 238 IU/L (standard deviation = 576.84), and HBV‐DNA levels ranged from 1.02 × 10⁵ to 2.2 × 10⁷ IU/ml. Genotype D was predominant (98%), with viral groups D/ayw2 (73%) and D/ayw3 (27%). Group A/adw accounted for 1% of cases. Genotypes B and C were found exclusively in the Chinese immigrants (1%). Single or multiple point mutations were found in 35 cases (26%). Some of the most common mutations occurred at amino acid positions 129, 133, 134, 144, 145, including the “vaccine escape” mutation G145R. Mutations analysis revealed that amino acid substitutions did not affect detection by commercial immunoassays. J. Med. Virol. 83:245–252, 2011. © 2010 Wiley‐Liss, Inc.     

Molecular epidemiology of hepatitis C virus infection amongst intravenous drug users in rural communities

The prevalence of hepatitis C virus (HCV) infection amongst a group of intravenous drug users (IVDUs) resident in West Suffolk (East Anglia, England) was investigated and compared with the prevalence of infection with hepatitis B virus (HBV) and human immunodeficiency virus (HIV). In addition, both the level of HCV persistence, as defined by detection of viral RNA, and the HCV genotypes present in this population were determined. It was found that HCV antibodies were present in 59% of those tested; by comparison 22% had antibodies to HBV and 1% antibodies to HIV. HCV RNA was found in 44% of those with HCV antibody. HCV genotype 1 was the most prevalent within this population although both genotypes 2 and 3 were also represented. © 1995 Wiley-Liss, Inc.     

Molecular epidemiology of rotaviral infection in South Indian children with acute diarrhea from 1995-1996 to 1998-1999

The distribution of VP7 (G-) and VP4 (P-) genotypes among 126 rotavirus strains from South Indian children, < 5 years of age and with acute diarrhoea, presenting to a single hospital during the months to November and December, from 1995 to 1998, was studied. Multiplex hemi-nested G- and P-typing polymerase chain reactions determined 101 (80%) G types and 78 (61%) P types, respectively. In order of frequency, the commonest G types were G1, G4, G2, G9, G3, and G8, and P types were P1B[4], P1A[8], and P2A[6] and the most common G:P combinations were G1:P1A[8], G1:P1B[4], G2P1B[4] and G4:P1A[8]. G1, G2, and G4 types were seen in all years. The single G3 isolate was seen in 1998. The single G8 isolate and the 5 G9 isolates were seen in 1997, after a period of heavy rain. Sequence analysis showed that the G8 isolate was related most closely to the bovine strain A5, and the G9 strains were distinct from the nonpathogenic Indian isolate 116E and similar to G9s isolated in Mysore and the United Kingdom described previously.     

Genotypes and titers of hepatitis C virus for predicting response to interferon in patients with chronic hepatitis C

Interferon induces remission in about 50% of patients with chronic hepatitis C, but it is difficult to predict which patients will respond. Host and viral factors were evaluated for correlation with response to interferon in patients with chronic hepatitis C. Recombinant interferon alpha-2b with a total dose of 480-560 million units was given to 136 patients, of whom 74 (54%) responded. Genotypes of hepatitis C virus (HCV) in sera, I, II, III, IV, and V, were determined by poly-merase chain reaction (PCR) with type-specific primers. In 72 patients, pretreatment levels of HCV RNA were titrated by PCR in serial tenfold dilutions of RNA extracted from serum. Response to interferon occurred in 34 (40%) of 85 patients infected with HCV of genotype II, less frequently than in 22 (85%) of 26 with genotype III (P < 0.001) or in 7 (70%) of 10 with genotype IV. Of 51 patients with genotype II HCV, 6 of 8 (75%) with HCV RNA titers <10⁶ responded, more frequently than 4 of 43 (9%) with titers ≥ 10⁶ (P < 0.001). Responders were younger than non-responders (45.7 ± 11.7 vs. 50.3 ± 9.6 yr) and had received transfusions less frequently (26/74 or 35% vs. 37/62 or 60%, P < 0.01). Response to interferon correlated inversely with the severity of liver histopathology. These results indicate that response to interferon is influenced by HCV genotypes and pretreatment levels of HCV RNA in serum. © 1994 Wiley-Liss, Inc.     

Molecular epidemiology of the hepatitis C virus in Western Siberia

Western Siberia is the region with little information on the prevalence of hepatitis C virus (HCV) infection, genotypic diversity of HCV isolates and risk factors. A molecular epidemiological survey was conducted to clarify these issues. Four groups of volunteers were included in a cross-sectional study (n = 500 in each group): health care workers; daycare patients from a hospital for drug users, daycare patients from an AIDS prevention and control center; and persons admitted to a local general practice clinic for any reason (outpatients). The anti-HCV IgG prevalence was 4.6% in health care workers, 48.0% in a narcological center, 35.8% in AIDS center, and 5.6% in outpatients. HCV RNA was found in 79.3%-86.3% of seropositives. A total of 388 HCV isolates were genotyped by direct sequencing and phylogenetic analysis of the 5'-UTR and NS5B regions of HCV genome. The genotypes distribution was: 1b--50.3%, 2a--4.4%, 2c--0.3%, 3a--44.8%. One isolate (0.3%) could not be typed unambiguously. This genotypic diversity is intermediate between that of European Russia and China. Genotype 1 prevailed in an older age group (75% among 51-60 years old), and genotype 3 was most prevalent in young people (51.4% in 16-20 years old). A statistically significant (P < 0.05) increase in risk was found in intravenous drug users (odds ratio (OR) = 77.5), unemployed persons (OR = 16.3), persons having >4 sexual partners during lifetime (OR = 4.3), and male homosexuals (OR = 6.6).     

Molecular epidemiology of hepatitis C virus in Iran as reflected by phylogenetic analysis of the NS5B region

Hepatitis C virus (HCV) subtypes were determined in 125 Iranian patients by phylogenetic analysis within the NS5B or 5'-UTR/core regions. Subtypes 1a and 3a were predominant accounting for 47 and 36%, whereas 1b and 4 accounted for 8 and 7%. This subtype distribution differs from that of Turkey and Pakistan, where subtypes 1b and 3a dominate and also from neighbouring Arabic countries where subtype 4 is the prevalent genotype. The Iranian 1a and 3a strains formed subclusters in the dendrogram indicating that these subtypes are indigenous to Iran. In contrast, the 1b strains intermixed with strains derived worldwide. Subtype 1a was frequent in South Iran (70%), while 3a was more prevalent in North-West Iran (83%), a region with a high proportion of Turkish inhabitants. Patients infected by blood products had more frequently subtype 1a (57%), while younger drug users had more frequently subtype 3a (54%). Genotype 4 was over-represented among haemodialysis patients in Tehran. One strain, most similar to genotype 5, was highly divergent in the NS5B region and further analysis is needed to assess the systematic status of this strain. In half of the patients with unknown source of infection only the 5'-UTR could be amplified, most of which were from North-West Iran and from patients younger than those with unknown source of infection with typable strains, mean age 29 versus 43 years. In conclusion, the NS5B sequence data revealed population based subtype patterns in Iran, the further study of which may help to understand the molecular epidemiology of HCV in a low-endemic area.     

Serotyping and genotyping of hepatitis C virus (HCV) strains in chronic HCV infection

Hepatitis C virus (HCV) genotypes can be established by methods based on PCR typing and serological typing. The accuracy of these methods depends on their sensitivity and specificity. These should be compared with the reference method, direct sequencing, and analysis of viral genomes. Among the serologic methods recently developed, the performance of a new serotyping assay (RIBA HCV 3.0 SIA, Chiron corporation, Emeryville) was assessed using a panel of 147 well-characterized French isolates from chronic hepatitis C patients. Definitive genotypes of the isolates were established by direct sequencing in 5′ NC and in some cases in NS-5B. HCV serotypes 1, 2, and 3 were determined by measuring type specific antibodies to core and NS-4 derived peptide antigens. Of the 147 sera, serotypic-specific antibodies were detected in 136 (sensitivity, 92.5%). The specificity of the RIBA SIA HCV serotyping assay was 92.6% (including samples with mixed results); without these, the specificity was 80.1%. Analysis of the 28 discrepant samples showed that (1) a different serotype was found in 18 samples including five for genotype 1, three for genotype 2, two for genotype 3, five for genotype 4, and three for genotype 5, and that (2) ten patients showed a reactivity with mixed serotypes, one had circulating antibodies to type 1 or 2, and nine had circulating antibodies to type 1 or 3. In summary, except for genotypes 4 and 5, the results of the test were well correlated (85.7%) with those of direct sequence genotyping. The former test is rapid and does not require the strict HCV RNA storage and preservation conditions of the latter. This new method may thus be considered as an alternative for HCV typing. However, although it is convenient, its lower sensitivity compared to the molecular typing method and the discrepant results limit its routine use in a clinical context. J. Med. Virol. 52:391–395, 1997. © 1997 Wiley-Liss, Inc.     

Preimmunization epidemiology of hepatitis B virus infection in South African children.

The prevalence of hepatitis B surface antigen (HBsAg) was determined in a community-based, cross-sectional, age-stratified sample of children from 0 to 6 years of age (n = 2,299) from the Eastern Cape Province of South Africa. The purpose of the study was to investigate the epidemiology and the age of acquisition of hepatitis B virus (HBV) infection in children, thus providing a preimmunization baseline measure of this infection in the population targeted for HBV immunization in South Africa. Overall, 10.4% (95% CI, 9.2-11.7) of the children tested were HBsAg-positive. There was a high rate of positivity in the 0-6- and 7-12-month age groups at 8.1% (95% CI, 5.5-11.7) and 8.9% (95% CI, 6.1-12.7), respectively, suggesting a higher rate of early acquisition of this infection than previously reported in South Africa. The proportion of HBsAg-positive children increased significantly with increasing age (chi2trend = 5.9, df = 1, P = 0.02), reaching 15.7% in the 61-72-month age group. This is the highest rate of HBV infection reported in community-based children from South Africa, indicating a significant burden of this infection. The difference in HBsAg prevalence between urban and rural children was not statistically significant (chi2 = 0.32, df = 1, P = 0.57). There was also no difference in positivity between males (10.5%; 95% CI, 8.7-12.5) and females (9.8%; 95% CI, 8.1-11.7), (chi2 = 0.006, df = 1, P = 0.94). This study provides the most recent preimmunization, community-based baseline investigation of the epidemiology of HBV infection in children targeted for universal immunization in South Africa.     

深圳市HIV-1 E亚型感染毒株的分子流行病学分析

目的 了解人类免疫缺陷病毒１型Ｅ亚型毒株在深圳市不同人群中流行传播情况、流行时间和传播规律。方法 应用聚合酶链反应（ＰＣＲ）方法对１９９６年深圳市检出的３份人类免疫缺陷病毒１型（ＨＩＶ－１）感染者外周血单个核细胞样本进行扩增,获得ＨＩＶ－１膜蛋白（ｅｎｖ）基因片段,并对Ｃ２－Ｖ３及其邻区３５０～４５０个核苷酸序列进行测定和分析。结果 这３份血样为ＨＩＶ－１Ｅ亚型毒株感染（ｓｚ－Ｅ）,彼此间的基因离散率为２．６％;与Ａ－Ｅ国际参考亚型及国内部分地区流行的ＢＥ型代表株比较,ｓｚ－Ｅ与Ａ－Ｄ参考亚型共享序列及国内Ｂ亚型代表株间的基因离散率均大于２４％,而与主要代表泰国Ｅ亚型（Ｅｃｏｎ）间的基因离散率仅为６．２％。系统树分析显示,ｓｚ－Ｅ与Ｅｃｏｎ聚集在一起,远离其他国际亚型毒株序列。结论 ＨＩＶ－１Ｅ亚型在深圳的流行     

Molecular epidemiology of circulating measles virus in Ireland 2002–2007

The molecular characterization of measles virus (MeV) is a valuable epidemiological tool to monitor virus transmission and to discriminate between imported and endemic infection. There has been significant immigration into Ireland in recent years and many individuals originate from regions of high measles incidence. Ireland has had a number of outbreaks of MeV which appear attributable to sub‐optimal vaccine uptake and possibly imported strains as new genotypes have been identified in recent years. To ascertain any significant changes in circulating measles genotypes we investigated 65 confirmed measles cases between the years 2002 and 2007. The laboratory diagnosis of measles was confirmed by detection of measles‐specific IgM in oral fluid in conjunction with a real‐time polymerase chain reaction assay targeting the MeV hemagglutinin gene. Phylogenetic analysis based on the 3′ hypervariable region of the nucleoprotein gene was performed and three genotypes, all within measles clade D, were found to be circulating during this time period. In 2002 and 2003, genotype D8 (n = 2) was observed whereas genotype D7 was dominant in 2003 (n = 31). A distinct change in the circulating MeV genotype and increased genetic diversity was observed between 2004 and 2007. All cases were within genotype D4 (n = 32) but were phylogenetically distinct from each other. These data provide important epidemiologic baseline information on MeV in Ireland and facilitates detailed examination of measles transmission. J. Med. Virol. 81:125–129, 2009. © 2008 Wiley‐Liss, Inc.     

Molecular epidemiology of enterovirus outbreaks in Canada during 1991–1992: Identification of echovirus 30 and coxsackievirus B1 strains by amplicon sequencing

The relatedness of enteroviral isolates associated with two recent outbreaks in Canada was assessed using direct sequencing of amplicons derived from a large portion of the 5′ nontrans-lated region (NTR) of the viral genome. The amplicons of 60 echovirus 30 isolates originating from seven different provinces in 1991 were found to share 99% or greater sequence identity. Recent coxsackievirus B1 isolates characterised in the same manner were identical to each other. When the 5′ NTR sequence of these isolates was compared to prototype strains a difference of 11–15% in nucleotide composition was observed. These results indicate that the variability of nucleotide sequence found in 5′ NTRs can be utilized to identify rapidly enteroviral strains associated with particular outbreaks and distinguish them from other strains and serotypes. © 1994 Wiley-Liss, Inc.     

t(15;17)的变异型插入易位ins(17;15)(q21;q14q22)的细胞遗传学和分子遗传学研究

目的　报道 1例 t(15 ;17)的变异型插入易位 ins(17;15 ) (q2 1;q14 q2 2 )病例及其染色体涂染、逆转录 - PCR的研究结果。方法　骨髓细胞经直接法或 2 4 h培养和外周血单采白血病细胞培养 6天后制备染色体标本 ,以 R显带技术进行核型分析 ;以 15号和 17号整条染色体涂染探针进行染色体涂染 ;以逆转录 -PCR技术检测 PML - RARα和 RARα- PML融合基因的转录本。结果　该患者骨髓细胞和外周血白血病细胞染色体 R显带核型分析结果均提示 15 q-和 17q ;涂染研究证实 17号染色体长臂插入一段 15号染色体来源的染色体片段 ;逆转录 - PCR检出 PML- RARα融合基因短型转录本 ,未检出 RARα- PML 融合基因的转录本 ,符合 ins(17;15 )所致的遗传学改变。结论　染色体涂染和逆转录 - PCR技术是明确急性早幼粒细胞白血病患者涉及 15和 17号染色体插入易位的可靠手段。     

巢式RT-PCR检测甲肝疫苗的感染性滴度研究

目的 建立一种快速灵敏特异的检测甲肝疫苗滴度的巢式RT-PCR检测方法。方法 运用巢式RT-PCR法对甲肝疫苗病毒滴度进行检测，并与细胞培养ELISA检测法进行比较。结果 巢式RT-PCR灵敏度和特异性均与细胞培养ELISA检测法相似。结论 巢式RT-PCR是一种简便、快速、灵敏的甲肝病毒检测方法，用于疫苗的常规检测有较好前景。