AIM To explore a rapid and easy sequencing method for hepatitis C virus (HCV) genome, and establish a new sequencing method in China. METHODS Polymerase Chain Reaction (PCR) was combined with DNA sequencing techn...AIM To explore a rapid and easy sequencing method for hepatitis C virus (HCV) genome, and establish a new sequencing method in China. METHODS Polymerase Chain Reaction (PCR) was combined with DNA sequencing technique. PCR products were purified by agarose gel electrophoresis, polyacrylamide gel electrophoresis (PAGE), Polyethylene glycol (PEG) respectively. Then in the presence of a 5′ labeling PCR primer, purified PCR products were directly sequenced. By this method, HCV NS5b cDNA from two HCV infected individuals (HC 42 and HC 49) were sequenced.展开更多
Hepatitis B virus(HBV)is a DNA virus with complex replication,and high replication and mutation rates,leading to a heterogeneous viral population.The population is comprised of genomes that are closely related,but not...Hepatitis B virus(HBV)is a DNA virus with complex replication,and high replication and mutation rates,leading to a heterogeneous viral population.The population is comprised of genomes that are closely related,but not identical;hence,HBV is considered a viral quasispecies.Quasispecies variability may be somewhat limited by the high degree of overlapping between the HBV coding regions,which is especially important in the P and S gene overlapping regions,but is less significant in the X and preCore/Core genes.Despite this restriction,several clinically and pathologically relevant variants have been characterized along the viral genome.Next-generation sequencing(NGS)approaches enable high-throughput analysis of thousands of clonally amplified regions and are powerful tools for characterizing genetic diversity in viral strains.In the present review,we update the information regarding HBV variability and present a summary of the various NGS approaches available for research in this virus.In addition,we provide an analysis of the clinical implications of HBV variants and their study by NGS.展开更多
Objectives: To investigate the relationship between HBV (hepatitis B virus) polymerase gene 180 and 204 sites mutation and lamivudine resistance. Methods: One hundred forty-one patients with lamivudine resistance afte...Objectives: To investigate the relationship between HBV (hepatitis B virus) polymerase gene 180 and 204 sites mutation and lamivudine resistance. Methods: One hundred forty-one patients with lamivudine resistance after lamivudine treatment and 60 chronic hepatitis B patients without lamivudine treatment were enrolled in this study. The serum HBV DNA mutation was analyzed by sequence detection via polymerase chain reaction (PCR). The sequences of the same patient were analyzed before and after lamivudine treatment. Results: One hundred and nine lamivudine resistance patients had HBV YMDD (tyrosine-methionine-aspartate-aspartate) mutation. Among them, 45 patients had rtL 180M/M204V mutation (41.28%), 28patients had rtL180M/M204I mutation (25.70%) and 36 patients had rtM204I mutation (33.02%). There were 6 patients with rtL180M mutation in 32 lamivudine resistance patients. Sixty chronic hepatitis patients without lamivudine treatment had no mutations. Conclusions: HBV mutations, which play an important role in lamivudine resistance usually locate at polymerase gene 204 site; 180 site mutation was also observed in these patients. Evaluation of the anti-virus therapy by surveillance of the two sites mutations is of importance.展开更多
Direct-acting antiviral agents(DAAs)for hepatitis C virus(HCV)infection are one of the major advances in its medical treatment.The HCV protease inhibitors boceprevir and telaprevir were the first approved DAAs in the ...Direct-acting antiviral agents(DAAs)for hepatitis C virus(HCV)infection are one of the major advances in its medical treatment.The HCV protease inhibitors boceprevir and telaprevir were the first approved DAAs in the United States,Europe,and Japan.When combined with peginterferon plus ribavirin,these agents increase sustained virologic response rates to70%-80%in treatment-na?ve patients and previoustreatment relapsers with chronic HCV genotype 1 infection.Without peginterferon plus ribavirin,DAA monotherapies increased DAA-resistance mutations.Several new DAAs for HCV are now in clinical development and are likely to be approved in the near future.However,it has been reported that the use of these drugs also led to the emergence of DAA-resistance mutations in certain cases.Furthermore,these mutations exhibit cross-resistance to multiple drugs.The prevalence of DAA-resistance mutations in HCV-infected patients who were not treated with DAAs is unknown,and it is as yet uncertain whether such variants are sensitive to DAAs.We performed a population sequence analysis to assess the frequency of such variants in the sera of HCV genotype 1-infected patients not treated with HCV protease inhibitors.Here,we reviewed the literature on resistance variants of HCV protease inhibitors in treatment na?ve patients with chronic HCV genotype 1,as well as our experience.展开更多
AIM To detect infection rate of GBV-C/HGV inhepatitis C patients,to determine the methodsof higher sensitivity and the primers of higherefficiency for GBV-C/HGV RNA detection and tostudy the dominant subtype and mutat...AIM To detect infection rate of GBV-C/HGV inhepatitis C patients,to determine the methodsof higher sensitivity and the primers of higherefficiency for GBV-C/HGV RNA detection and tostudy the dominant subtype and mutation ofGBV-C/HGV.METHODS Quantitative RT-PCR for detectionpf HCV RNA concentration in serum samples,RT-nested PCR with two sets of primers fordetection of GBV-C RNA,RT-PCR ELISA with twosets of primers for detection of HGV RNA,nucleotide sequence and putative amino acidsequence analysis.RESULTS The positive rates of GBV-C RNA atthe 5’-NCR and NS3 region in 211 serums amplesfrom the patients with HCV infection were 31.8%and 22.8% respectively.The positive rates ofHGV RNA at the 5’-NCR and NS5 region in thesame samples were 47.9% and 31.8%respectively.The total positive rate of GBV-C/HGV RNA was as high as 55.5%.HCV copynumbers in the patients without GBV-C/ HGVcoinfection were statistically higher than that inthe patients with GBV-C/ HGV coinfection(P【0.01).Frequent mutation of nucleotideresidue was present in the amplificationproducts.Frameshift mutation was found in twosamples with GBV-C NS3 region nucleotidesequences.All nucleotide sequences fromamplification products showed higher homologyto HGV genome than to GBV-C genome even though part of the sequences were amplifiedwith GBV-C primers.CONCLUSION A high frequency of GBV-C/ HGV coinfection existed in the hepatitis C patients. RT-PCR ELISA was more sensitive than RT-nested PCR for detection of GBV-C/ HGV RNA. The primers derived from the 5 -NCR was more efficient than those derived from the NS3 and NS5 regions. A reverse relationship was found to exist between HCV RNA concentration and GBV-C/ HGV infection frequency. HGV was the dominant subtype of the virus in the local area. The major mutations of GBV-C/ HGV genomes were random mutation of nucleotide residue.展开更多
To understand the clinical significance of sequence variations in the hypervariable region (HVR) of hepatitis C virus during infection Methods Eight patients with acute hepatitis C and 20 patients with chronic hepat...To understand the clinical significance of sequence variations in the hypervariable region (HVR) of hepatitis C virus during infection Methods Eight patients with acute hepatitis C and 20 patients with chronic hepatitis C were followed up for two years Blood samples were taken at intervals of six months for analysis of HCV HVR sequences by reverse transcription polymerase chain reaction (RT PCR) and direct sequencing methods Results HCV HVR sequences of the 28 patients changed in various degrees 92% of these nucleotide substitutions led to changes of corresponding amino acid sequences Only 8% of changed nucleotide were synonymous substitutions Of 27 amino acids variation of amino acid ranged from 1 to 20 (mean 8, 30%) The most common nucleotide substitution (62%) occurred in the first position of codon, 31% in the second and the rest in the third HVR variation rate was 0 89×10 1 per genome site per year in acute hepatitis C, compared with 2 31×10 1 per genome site per year in chronic hepatitis C ( P <0 05), but had no relation to HCV subtype Variation of HVR in the flare up type (ALT>150?μ/L) was much more than that in the quiescent type (ALT<100?μ/L) Conclusion Our results suggested that sequence variation of HVR during HCV chronic infection seems to be an adaptive response to HCV to evade the host immune pressure and might play a major role in the establishment of persistent infection as well as in the flare up of hepatitis展开更多
文摘AIM To explore a rapid and easy sequencing method for hepatitis C virus (HCV) genome, and establish a new sequencing method in China. METHODS Polymerase Chain Reaction (PCR) was combined with DNA sequencing technique. PCR products were purified by agarose gel electrophoresis, polyacrylamide gel electrophoresis (PAGE), Polyethylene glycol (PEG) respectively. Then in the presence of a 5′ labeling PCR primer, purified PCR products were directly sequenced. By this method, HCV NS5b cDNA from two HCV infected individuals (HC 42 and HC 49) were sequenced.
基金Supported by Instituto de Salud Carlos Ⅲ,grant PI12/1893cofinanced by the European Regional Development Fund(ERDF)Instituto Carlos Ⅲ of the Spanish Ministry of Health andC onsumer Affairs
文摘Hepatitis B virus(HBV)is a DNA virus with complex replication,and high replication and mutation rates,leading to a heterogeneous viral population.The population is comprised of genomes that are closely related,but not identical;hence,HBV is considered a viral quasispecies.Quasispecies variability may be somewhat limited by the high degree of overlapping between the HBV coding regions,which is especially important in the P and S gene overlapping regions,but is less significant in the X and preCore/Core genes.Despite this restriction,several clinically and pathologically relevant variants have been characterized along the viral genome.Next-generation sequencing(NGS)approaches enable high-throughput analysis of thousands of clonally amplified regions and are powerful tools for characterizing genetic diversity in viral strains.In the present review,we update the information regarding HBV variability and present a summary of the various NGS approaches available for research in this virus.In addition,we provide an analysis of the clinical implications of HBV variants and their study by NGS.
文摘Objectives: To investigate the relationship between HBV (hepatitis B virus) polymerase gene 180 and 204 sites mutation and lamivudine resistance. Methods: One hundred forty-one patients with lamivudine resistance after lamivudine treatment and 60 chronic hepatitis B patients without lamivudine treatment were enrolled in this study. The serum HBV DNA mutation was analyzed by sequence detection via polymerase chain reaction (PCR). The sequences of the same patient were analyzed before and after lamivudine treatment. Results: One hundred and nine lamivudine resistance patients had HBV YMDD (tyrosine-methionine-aspartate-aspartate) mutation. Among them, 45 patients had rtL 180M/M204V mutation (41.28%), 28patients had rtL180M/M204I mutation (25.70%) and 36 patients had rtM204I mutation (33.02%). There were 6 patients with rtL180M mutation in 32 lamivudine resistance patients. Sixty chronic hepatitis patients without lamivudine treatment had no mutations. Conclusions: HBV mutations, which play an important role in lamivudine resistance usually locate at polymerase gene 204 site; 180 site mutation was also observed in these patients. Evaluation of the anti-virus therapy by surveillance of the two sites mutations is of importance.
基金Supported by Grants from the Japan Society for Promotion of Science(JSPS)Scientific Research from the Ministry of Education,Culture,Sports,Science,and Technology of Japanand Grants from the Ministry of Health,Labour,and Welfare of Japan
文摘Direct-acting antiviral agents(DAAs)for hepatitis C virus(HCV)infection are one of the major advances in its medical treatment.The HCV protease inhibitors boceprevir and telaprevir were the first approved DAAs in the United States,Europe,and Japan.When combined with peginterferon plus ribavirin,these agents increase sustained virologic response rates to70%-80%in treatment-na?ve patients and previoustreatment relapsers with chronic HCV genotype 1 infection.Without peginterferon plus ribavirin,DAA monotherapies increased DAA-resistance mutations.Several new DAAs for HCV are now in clinical development and are likely to be approved in the near future.However,it has been reported that the use of these drugs also led to the emergence of DAA-resistance mutations in certain cases.Furthermore,these mutations exhibit cross-resistance to multiple drugs.The prevalence of DAA-resistance mutations in HCV-infected patients who were not treated with DAAs is unknown,and it is as yet uncertain whether such variants are sensitive to DAAs.We performed a population sequence analysis to assess the frequency of such variants in the sera of HCV genotype 1-infected patients not treated with HCV protease inhibitors.Here,we reviewed the literature on resistance variants of HCV protease inhibitors in treatment na?ve patients with chronic HCV genotype 1,as well as our experience.
文摘AIM To detect infection rate of GBV-C/HGV inhepatitis C patients,to determine the methodsof higher sensitivity and the primers of higherefficiency for GBV-C/HGV RNA detection and tostudy the dominant subtype and mutation ofGBV-C/HGV.METHODS Quantitative RT-PCR for detectionpf HCV RNA concentration in serum samples,RT-nested PCR with two sets of primers fordetection of GBV-C RNA,RT-PCR ELISA with twosets of primers for detection of HGV RNA,nucleotide sequence and putative amino acidsequence analysis.RESULTS The positive rates of GBV-C RNA atthe 5’-NCR and NS3 region in 211 serums amplesfrom the patients with HCV infection were 31.8%and 22.8% respectively.The positive rates ofHGV RNA at the 5’-NCR and NS5 region in thesame samples were 47.9% and 31.8%respectively.The total positive rate of GBV-C/HGV RNA was as high as 55.5%.HCV copynumbers in the patients without GBV-C/ HGVcoinfection were statistically higher than that inthe patients with GBV-C/ HGV coinfection(P【0.01).Frequent mutation of nucleotideresidue was present in the amplificationproducts.Frameshift mutation was found in twosamples with GBV-C NS3 region nucleotidesequences.All nucleotide sequences fromamplification products showed higher homologyto HGV genome than to GBV-C genome even though part of the sequences were amplifiedwith GBV-C primers.CONCLUSION A high frequency of GBV-C/ HGV coinfection existed in the hepatitis C patients. RT-PCR ELISA was more sensitive than RT-nested PCR for detection of GBV-C/ HGV RNA. The primers derived from the 5 -NCR was more efficient than those derived from the NS3 and NS5 regions. A reverse relationship was found to exist between HCV RNA concentration and GBV-C/ HGV infection frequency. HGV was the dominant subtype of the virus in the local area. The major mutations of GBV-C/ HGV genomes were random mutation of nucleotide residue.
基金ThisworkwassupportedbytheNationalNaturalScience FoundationofChina (No 395 0 0 0 6 7)
文摘To understand the clinical significance of sequence variations in the hypervariable region (HVR) of hepatitis C virus during infection Methods Eight patients with acute hepatitis C and 20 patients with chronic hepatitis C were followed up for two years Blood samples were taken at intervals of six months for analysis of HCV HVR sequences by reverse transcription polymerase chain reaction (RT PCR) and direct sequencing methods Results HCV HVR sequences of the 28 patients changed in various degrees 92% of these nucleotide substitutions led to changes of corresponding amino acid sequences Only 8% of changed nucleotide were synonymous substitutions Of 27 amino acids variation of amino acid ranged from 1 to 20 (mean 8, 30%) The most common nucleotide substitution (62%) occurred in the first position of codon, 31% in the second and the rest in the third HVR variation rate was 0 89×10 1 per genome site per year in acute hepatitis C, compared with 2 31×10 1 per genome site per year in chronic hepatitis C ( P <0 05), but had no relation to HCV subtype Variation of HVR in the flare up type (ALT>150?μ/L) was much more than that in the quiescent type (ALT<100?μ/L) Conclusion Our results suggested that sequence variation of HVR during HCV chronic infection seems to be an adaptive response to HCV to evade the host immune pressure and might play a major role in the establishment of persistent infection as well as in the flare up of hepatitis
