It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). W... more It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). We tested for association between HCV phylogeny and reported injecting relationships using longitudinal data from a social network design study. People who inject drugs were recruited from street drug markets in Melbourne, Australia. Interviews and blood tests took place three monthly (during 2005–2008), with participants asked to nominate up to five injecting partners at each interview. The HCV core region of individual isolates was then sequenced and phylogenetic trees were constructed. Genetic clusters were identified using bootstrapping (cut-off: 70%). An adjusted Jaccard similarity coefficient was used to measure the association between the reported injecting relationships and relationships defined by clustering in the phylogenetic analysis (statistical significance assessed using the quadratic assignment procedure). 402 participants consented to participate; 244 HCV infections were ...
BackgroundHepatitis E virus (HEV) is a common cause of acute viral hepatitis with significant mor... more BackgroundHepatitis E virus (HEV) is a common cause of acute viral hepatitis with significant morbidity and mortality, particularly in pregnant women. There are four major genotypes which can cause disease in humans. Genotypes 1 and 2 are usually associated with outbreaks and spread via facal/oral route or contaminated water. Genotypes 3 and 4 are zoonotic and usually associated with handling of pigs or consumption of contaminated pork. The strains circulating in Australia have never been characterized.Rationale/AimsThe aims for this project are to identify the HEV genotypes found in Australia and link them to possible sources of transmission by phylogenetic analysis.Materials and MethodsBetween 2015 and 2020, 91 HEV isolates were sequenced and genotyped using an in-house PCR. Sixty-six of these were also sequenced by using the international HEVnet primers. Genotypes were determined using the BLASTn program. Relatedness to other strains in Australia was determined by phylogenetic an...
Background: We aimed to characterize the natural history of hepatitis C virus (HCV) reinfection a... more Background: We aimed to characterize the natural history of hepatitis C virus (HCV) reinfection and spontaneous clearance following reinfection (reclearance), including predictors of HCV reclearance. Methods: Data were synthesised from nine prospective cohorts evaluating HCV infection outcomes among people who inject drugs (InC 3 study). Participants with primary HCV infection were classified as achieving viral suppression if they had at least one subsequent negative HCV RNA test. Those with a positive HCV RNA test following viral suppression were investigated for reinfection. Viral sequence analysis was used to identify reinfection (heterologous virus with no subsequent detection of the original viral strain). Results: Among 591 participants with acute primary HCV infection, 118 were investigated for reinfection. Twenty-eight participants were reinfected (12.3/100 person-years, 95%CI: 8.5-17.8). Peak HCV RNA was lower in reinfection than primary infection (p=0.011). The reclearance proportion at six months after reinfection was 52% (95%CI: 33-73%). Adjusting for study site, females with IFNL4 (formerly IFNL3 and IL28B) rs12979860-CC genotype were more likely to reclear (HR:4.16, 95%CI: 1.24-13.94, p=0.021). Conclusions: Sex and IFNL4 genotype are associated with spontaneous clearance after reinfection.
To analyse the immune correlates in a setting of recurrent exposure to hepatitis C virus (HCV), w... more To analyse the immune correlates in a setting of recurrent exposure to hepatitis C virus (HCV), we studied T CD8 responses in injecting drug users (IDUs) with different disease outcomes. Ex vivo HCV-specific T CD8 responses assessed by interferon-γ (IFN γ ...
... James J. Giovannoni Erick N. Noensie Diane M. Ruezinsky. ... Fruit from both mutants fails ... more ... James J. Giovannoni Erick N. Noensie Diane M. Ruezinsky. ... Fruit from both mutants fails to synthesize climacteric ethylene or accumulate the red carotenoid lycopene, characteristic of ripe tomatoes, in addition to being deficient in softening and remaining resistant to microbial ...
BackgroundThe hepatitis C virus (HCV) causes significant morbidity and mortality worldwide, and i... more BackgroundThe hepatitis C virus (HCV) causes significant morbidity and mortality worldwide, and is highly prevalent among injecting drug users (IDUs). Whether initial HCV infection and clearance provides protection from reinfection has not been established, but is an important question for vaccine development.
A retrospective cohort study was established of injecting drug users (IDUs) to assess evidence fo... more A retrospective cohort study was established of injecting drug users (IDUs) to assess evidence for hepatitis C virus (HCV) protective immunity through a comparison of incidence of initial HCV infection and HCV reinfection. Incidence of initial HCV infection was determined among HCV seronegative IDUs, and HCV reinfection determined among IDUs with newly acquired HCV infection, HCV viraemia and subsequent HCV RNA clearance. Serum was available for HCV RNA analysis from stored samples taken at the time of prior blood-borne virus screening. Potential HCV reinfection was defined as a positive HCV RNA following at least one negative HCV RNA. Incidence of initial HCV infection was 17/100 person-years (95% CI, 14-20/100 person-years). The incidence of potential HCV reinfection was 42/100 person-years (95% CI, 25-61/100 personyears), and after excluding cases without a change in HCV genotype and less than three consecutive HCV RNA negative assessment, incidence of reinfection was 31/100 personyears (95% CI, 17-62/100 person-years). Following adjustment for HCV risk behaviour variables the incidence rate ratio of HCV reinfection to initial infection was 1.11 (P ¼ 0.8). Several cases of HCV reinfection appear to have developed persistent infection.
Background. A large outbreak of hepatitis A affected individuals in several Australian states in ... more Background. A large outbreak of hepatitis A affected individuals in several Australian states in 2009, resulting in a 2-fold increase in cases reported to state health departments compared with 2008. Two peaks of infection occurred (April-May and September-November), with surveillance data suggesting locally acquired infections from a widely distributed food product. Methods. Two case-control studies were completed. Intensive product trace-back and food sampling was undertaken. Genotyping was conducted on virus isolates from patient serum and food samples. Control measures included prophylaxis for close contacts, public health warnings, an order by the chief health officer under the Victorian Food Act 1984, and trade-level recalls on implicated batches of semidried tomatoes. Results. A multijurisdictional case-control study in April-May found an association between illness and consumption of semidried tomatoes (odds ratio [OR], 3.0; 95% CI 1.4-6.7). A second case-control study conducted in Victoria in October-November also implicated semidried tomatoes as being associated with illness (OR, 10.3; 95% CI, 4.7-22.7). Hepatitis A RNA was detected in 22 samples of semidried tomatoes. Hepatitis A virus genotype IB was identified in 144 of 153 (94%) patients tested from 2009, and partial sequence analysis showed complete identity with an isolate found in a sample of semidried tomatoes. Conclusions. The results of both case-control studies and food testing implicated the novel vehicle of semidried tomatoes as the cause of this hepatitis A outbreak. The outbreak was extensive and sustained despite public health interventions, the design and implementation of which were complicated by limitations in food testing capability and complex supply chains.
Background: Detectable HCV-specific cellular immune responses in HCV antibody and RNA negative pe... more Background: Detectable HCV-specific cellular immune responses in HCV antibody and RNA negative people who inject drugs (PWID) raise the question of whether some are resistant to HCV infection. Immune responses from people who have been exposed to hepatitis C virus (HCV) and remain anti-HCV negative are of interest for HCV vaccine development; however, limited research addresses this area. Objectives: In a cohort of HCV antibody and RNA negative PWID, we assessed whether the presence of HCV-specific IFN-γ responses or genetic associations provide any evidence of protection from HCV infection. Patients and Methods: One hundred and ninety-eight participants were examined longitudinally for clinical, behavioral, social, environmental and genetic characteristics (IFNL3 genotype [formally IL-28B] and HLA type). Sixty-one of the 198 participants were HCV antibody and RNA negative, with 53 able to be examined longitudinally for HCV-specific IFN-γ ELISpot T cell responses. Results: Ten of the 53 HCV antibody and RNA negative participants had detectable HCV-specific IFN-γ responses at baseline (18%). The magnitude of IFN-γ responses averaged 131 +/-96 SFC/10 6 PBMC and the breadth was mean 1 +/-1 pool positive. The specificity of responses were mainly directed to E2, NS4b and NS5b. Participants with (10) and without (43) HCV-specific IFN-γ responses did not differ in behavioral, clinical or genetic characteristics (P > 0.05). There was a larger proportion sharing needles (with 70%, without 49%, P = 0.320) and a higher incidence of HCV (with 35.1 per 100 py, 95% CI 14.6, 84.4, without 16.0 per 100 py, 95% CI 7.2, 35.6, P = 0.212) in those with IFN-γ responses, although not statistically significant. Half the participants with baseline IFN-γ responses became HCV RNA positive (5/10), with one of these participants spontaneously clearing HCV. The spontaneous clearer had high magnitude and broad Th1 responses, favorable IFNL3 genotype and favorable HLA types. Conclusions: This study demonstrated the detection of HCV-specific IFN-γ responses in HCV antibody and RNA negative individuals, with a tendency for HCV-specific IFN-γ responses to be associated with HCV exposure. The potential role of HCV-specific IFN-γ responses in those who remained HCV RNA negative is of value for the development of novel HCV therapeutics.
It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). W... more It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). We tested for association between HCV phylogeny and reported injecting relationships using longitudinal data from a social network design study. People who inject drugs were recruited from street drug markets in Melbourne, Australia. Interviews and blood tests took place three monthly (during 2005-2008), with participants asked to nominate up to five injecting partners at each interview. The HCV core region of individual isolates was then sequenced and phylogenetic trees were constructed. Genetic clusters were identified using bootstrapping (cut-off: 70%). An adjusted Jaccard similarity coefficient was used to measure the association between the reported injecting relationships and relationships defined by clustering in the phylogenetic analysis (statistical significance assessed using the quadratic assignment procedure). 402 participants consented to participate; 244 HCV infections were observed in 238 individuals. 26 genetic clusters were identified, with 2-7 infections per cluster. Newly acquired infection (AOR = 2.03, 95% CI: 1.04-3.96, p = 0.037, and HCV genotype 3 (vs. genotype 1, AOR = 2.72, 95% CI: 1.48-4.99) were independent predictors of being in a cluster. 54% of participants whose infections were part of a cluster in the phylogenetic analysis reported injecting with at least one other participant in that cluster during the study. Overall, 16% of participants who were infected at study entry and 40% of participants with newly acquired infections had molecular evidence of related infections with at least one injecting partner. Likely transmission clusters identified in phylogenetic analysis correlated with reported injecting relationships (adjusted Jaccard coefficient: 0.300; p,0.001). This is the first study to show that HCV phylogeny is associated with the injecting network, highlighting the importance of the injecting network in HCV transmission.
POSTERS performed using a non-targeted multiple platform methodology combining ultrahigh performa... more POSTERS performed using a non-targeted multiple platform methodology combining ultrahigh performance liquid chromatography/tandem mass spectrometry (UHPLC/MS) and gas chromatography/mass spectrometry (GC/MS). Metabolites were identified by automated comparison of ion features to a reference of chemical standard entries. Welch's two-sample t-tests were used to identify biochemicals that differed significantly between HCV infected and un-infected cells. Results: A total of 250 metabolites were detected and quantified, of which 73 were differentially regulated. At the 24-hour time point, there was a significant increase in a number of metabolites involved in nucleotide synthesis and RNA replication. NAD levels were also significantly increased along with several amino acids. A number of lipid metabolic pathways were disrupted by HCV infection, resulting in an increase in cholesterol and sphingolipid levels, altered phospholipid metabolism and a possible disruption in mitochondrial fatty acid transport. Fluctuations in methylthioadenosine (MTA) levels were also noted, along with alterations in the glutathione synthesis pathway. Conclusions: These results suggest that elevated metabolism and altered energy status are associated with early HCV infection. These findings also provide new information on the effect HCV infection has on the disruption of lipid metabolism.
It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). W... more It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). We tested for association between HCV phylogeny and reported injecting relationships using longitudinal data from a social network design study. People who inject drugs were recruited from street drug markets in Melbourne, Australia. Interviews and blood tests took place three monthly (during 2005–2008), with participants asked to nominate up to five injecting partners at each interview. The HCV core region of individual isolates was then sequenced and phylogenetic trees were constructed. Genetic clusters were identified using bootstrapping (cut-off: 70%). An adjusted Jaccard similarity coefficient was used to measure the association between the reported injecting relationships and relationships defined by clustering in the phylogenetic analysis (statistical significance assessed using the quadratic assignment procedure). 402 participants consented to participate; 244 HCV infections were ...
BackgroundHepatitis E virus (HEV) is a common cause of acute viral hepatitis with significant mor... more BackgroundHepatitis E virus (HEV) is a common cause of acute viral hepatitis with significant morbidity and mortality, particularly in pregnant women. There are four major genotypes which can cause disease in humans. Genotypes 1 and 2 are usually associated with outbreaks and spread via facal/oral route or contaminated water. Genotypes 3 and 4 are zoonotic and usually associated with handling of pigs or consumption of contaminated pork. The strains circulating in Australia have never been characterized.Rationale/AimsThe aims for this project are to identify the HEV genotypes found in Australia and link them to possible sources of transmission by phylogenetic analysis.Materials and MethodsBetween 2015 and 2020, 91 HEV isolates were sequenced and genotyped using an in-house PCR. Sixty-six of these were also sequenced by using the international HEVnet primers. Genotypes were determined using the BLASTn program. Relatedness to other strains in Australia was determined by phylogenetic an...
Background: We aimed to characterize the natural history of hepatitis C virus (HCV) reinfection a... more Background: We aimed to characterize the natural history of hepatitis C virus (HCV) reinfection and spontaneous clearance following reinfection (reclearance), including predictors of HCV reclearance. Methods: Data were synthesised from nine prospective cohorts evaluating HCV infection outcomes among people who inject drugs (InC 3 study). Participants with primary HCV infection were classified as achieving viral suppression if they had at least one subsequent negative HCV RNA test. Those with a positive HCV RNA test following viral suppression were investigated for reinfection. Viral sequence analysis was used to identify reinfection (heterologous virus with no subsequent detection of the original viral strain). Results: Among 591 participants with acute primary HCV infection, 118 were investigated for reinfection. Twenty-eight participants were reinfected (12.3/100 person-years, 95%CI: 8.5-17.8). Peak HCV RNA was lower in reinfection than primary infection (p=0.011). The reclearance proportion at six months after reinfection was 52% (95%CI: 33-73%). Adjusting for study site, females with IFNL4 (formerly IFNL3 and IL28B) rs12979860-CC genotype were more likely to reclear (HR:4.16, 95%CI: 1.24-13.94, p=0.021). Conclusions: Sex and IFNL4 genotype are associated with spontaneous clearance after reinfection.
To analyse the immune correlates in a setting of recurrent exposure to hepatitis C virus (HCV), w... more To analyse the immune correlates in a setting of recurrent exposure to hepatitis C virus (HCV), we studied T CD8 responses in injecting drug users (IDUs) with different disease outcomes. Ex vivo HCV-specific T CD8 responses assessed by interferon-γ (IFN γ ...
... James J. Giovannoni Erick N. Noensie Diane M. Ruezinsky. ... Fruit from both mutants fails ... more ... James J. Giovannoni Erick N. Noensie Diane M. Ruezinsky. ... Fruit from both mutants fails to synthesize climacteric ethylene or accumulate the red carotenoid lycopene, characteristic of ripe tomatoes, in addition to being deficient in softening and remaining resistant to microbial ...
BackgroundThe hepatitis C virus (HCV) causes significant morbidity and mortality worldwide, and i... more BackgroundThe hepatitis C virus (HCV) causes significant morbidity and mortality worldwide, and is highly prevalent among injecting drug users (IDUs). Whether initial HCV infection and clearance provides protection from reinfection has not been established, but is an important question for vaccine development.
A retrospective cohort study was established of injecting drug users (IDUs) to assess evidence fo... more A retrospective cohort study was established of injecting drug users (IDUs) to assess evidence for hepatitis C virus (HCV) protective immunity through a comparison of incidence of initial HCV infection and HCV reinfection. Incidence of initial HCV infection was determined among HCV seronegative IDUs, and HCV reinfection determined among IDUs with newly acquired HCV infection, HCV viraemia and subsequent HCV RNA clearance. Serum was available for HCV RNA analysis from stored samples taken at the time of prior blood-borne virus screening. Potential HCV reinfection was defined as a positive HCV RNA following at least one negative HCV RNA. Incidence of initial HCV infection was 17/100 person-years (95% CI, 14-20/100 person-years). The incidence of potential HCV reinfection was 42/100 person-years (95% CI, 25-61/100 personyears), and after excluding cases without a change in HCV genotype and less than three consecutive HCV RNA negative assessment, incidence of reinfection was 31/100 personyears (95% CI, 17-62/100 person-years). Following adjustment for HCV risk behaviour variables the incidence rate ratio of HCV reinfection to initial infection was 1.11 (P ¼ 0.8). Several cases of HCV reinfection appear to have developed persistent infection.
Background. A large outbreak of hepatitis A affected individuals in several Australian states in ... more Background. A large outbreak of hepatitis A affected individuals in several Australian states in 2009, resulting in a 2-fold increase in cases reported to state health departments compared with 2008. Two peaks of infection occurred (April-May and September-November), with surveillance data suggesting locally acquired infections from a widely distributed food product. Methods. Two case-control studies were completed. Intensive product trace-back and food sampling was undertaken. Genotyping was conducted on virus isolates from patient serum and food samples. Control measures included prophylaxis for close contacts, public health warnings, an order by the chief health officer under the Victorian Food Act 1984, and trade-level recalls on implicated batches of semidried tomatoes. Results. A multijurisdictional case-control study in April-May found an association between illness and consumption of semidried tomatoes (odds ratio [OR], 3.0; 95% CI 1.4-6.7). A second case-control study conducted in Victoria in October-November also implicated semidried tomatoes as being associated with illness (OR, 10.3; 95% CI, 4.7-22.7). Hepatitis A RNA was detected in 22 samples of semidried tomatoes. Hepatitis A virus genotype IB was identified in 144 of 153 (94%) patients tested from 2009, and partial sequence analysis showed complete identity with an isolate found in a sample of semidried tomatoes. Conclusions. The results of both case-control studies and food testing implicated the novel vehicle of semidried tomatoes as the cause of this hepatitis A outbreak. The outbreak was extensive and sustained despite public health interventions, the design and implementation of which were complicated by limitations in food testing capability and complex supply chains.
Background: Detectable HCV-specific cellular immune responses in HCV antibody and RNA negative pe... more Background: Detectable HCV-specific cellular immune responses in HCV antibody and RNA negative people who inject drugs (PWID) raise the question of whether some are resistant to HCV infection. Immune responses from people who have been exposed to hepatitis C virus (HCV) and remain anti-HCV negative are of interest for HCV vaccine development; however, limited research addresses this area. Objectives: In a cohort of HCV antibody and RNA negative PWID, we assessed whether the presence of HCV-specific IFN-γ responses or genetic associations provide any evidence of protection from HCV infection. Patients and Methods: One hundred and ninety-eight participants were examined longitudinally for clinical, behavioral, social, environmental and genetic characteristics (IFNL3 genotype [formally IL-28B] and HLA type). Sixty-one of the 198 participants were HCV antibody and RNA negative, with 53 able to be examined longitudinally for HCV-specific IFN-γ ELISpot T cell responses. Results: Ten of the 53 HCV antibody and RNA negative participants had detectable HCV-specific IFN-γ responses at baseline (18%). The magnitude of IFN-γ responses averaged 131 +/-96 SFC/10 6 PBMC and the breadth was mean 1 +/-1 pool positive. The specificity of responses were mainly directed to E2, NS4b and NS5b. Participants with (10) and without (43) HCV-specific IFN-γ responses did not differ in behavioral, clinical or genetic characteristics (P > 0.05). There was a larger proportion sharing needles (with 70%, without 49%, P = 0.320) and a higher incidence of HCV (with 35.1 per 100 py, 95% CI 14.6, 84.4, without 16.0 per 100 py, 95% CI 7.2, 35.6, P = 0.212) in those with IFN-γ responses, although not statistically significant. Half the participants with baseline IFN-γ responses became HCV RNA positive (5/10), with one of these participants spontaneously clearing HCV. The spontaneous clearer had high magnitude and broad Th1 responses, favorable IFNL3 genotype and favorable HLA types. Conclusions: This study demonstrated the detection of HCV-specific IFN-γ responses in HCV antibody and RNA negative individuals, with a tendency for HCV-specific IFN-γ responses to be associated with HCV exposure. The potential role of HCV-specific IFN-γ responses in those who remained HCV RNA negative is of value for the development of novel HCV therapeutics.
It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). W... more It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). We tested for association between HCV phylogeny and reported injecting relationships using longitudinal data from a social network design study. People who inject drugs were recruited from street drug markets in Melbourne, Australia. Interviews and blood tests took place three monthly (during 2005-2008), with participants asked to nominate up to five injecting partners at each interview. The HCV core region of individual isolates was then sequenced and phylogenetic trees were constructed. Genetic clusters were identified using bootstrapping (cut-off: 70%). An adjusted Jaccard similarity coefficient was used to measure the association between the reported injecting relationships and relationships defined by clustering in the phylogenetic analysis (statistical significance assessed using the quadratic assignment procedure). 402 participants consented to participate; 244 HCV infections were observed in 238 individuals. 26 genetic clusters were identified, with 2-7 infections per cluster. Newly acquired infection (AOR = 2.03, 95% CI: 1.04-3.96, p = 0.037, and HCV genotype 3 (vs. genotype 1, AOR = 2.72, 95% CI: 1.48-4.99) were independent predictors of being in a cluster. 54% of participants whose infections were part of a cluster in the phylogenetic analysis reported injecting with at least one other participant in that cluster during the study. Overall, 16% of participants who were infected at study entry and 40% of participants with newly acquired infections had molecular evidence of related infections with at least one injecting partner. Likely transmission clusters identified in phylogenetic analysis correlated with reported injecting relationships (adjusted Jaccard coefficient: 0.300; p,0.001). This is the first study to show that HCV phylogeny is associated with the injecting network, highlighting the importance of the injecting network in HCV transmission.
POSTERS performed using a non-targeted multiple platform methodology combining ultrahigh performa... more POSTERS performed using a non-targeted multiple platform methodology combining ultrahigh performance liquid chromatography/tandem mass spectrometry (UHPLC/MS) and gas chromatography/mass spectrometry (GC/MS). Metabolites were identified by automated comparison of ion features to a reference of chemical standard entries. Welch's two-sample t-tests were used to identify biochemicals that differed significantly between HCV infected and un-infected cells. Results: A total of 250 metabolites were detected and quantified, of which 73 were differentially regulated. At the 24-hour time point, there was a significant increase in a number of metabolites involved in nucleotide synthesis and RNA replication. NAD levels were also significantly increased along with several amino acids. A number of lipid metabolic pathways were disrupted by HCV infection, resulting in an increase in cholesterol and sphingolipid levels, altered phospholipid metabolism and a possible disruption in mitochondrial fatty acid transport. Fluctuations in methylthioadenosine (MTA) levels were also noted, along with alterations in the glutathione synthesis pathway. Conclusions: These results suggest that elevated metabolism and altered energy status are associated with early HCV infection. These findings also provide new information on the effect HCV infection has on the disruption of lipid metabolism.
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