Identification of numerous hepatitis C virus genotypes in Montreal, Canada.
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ABSTRACT:
SUBMITTER: Bernier L
PROVIDER: S-EPMC229409 | biostudies-other | 1996 Nov
REPOSITORIES: biostudies-other
Publications
Identification of numerous hepatitis C virus genotypes in Montreal, Canada.
Bernier L L Willems B B Delage G G Murphy D G DG
Journal of clinical microbiology 19961101 11
Hepatitis C virus genotypes were determined for 358 viremic individuals in Montreal, Canada, by restriction endonuclease analysis of PCR products and phylogenetic analysis of core gene sequences. Types 1, 2, and 3 occurred in 62.8, 14.2, and 13.7%, respectively; types 4 and 5 were found in 3.9 and 4.5%, respectively; and genotypes 6a and 7c and a novel genotype each occurred in 0.3%. Types 4, 6, and 7 and the novel genotype were mostly from persons who had immigrated to Canada. ...[more]
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Project description:ObjectiveThe prevalence and distribution of hepatitis B virus (HBV) genotypes in Canada is not known. Genotypic analysis may contribute to a better understanding of HBV strain distribution and transmission risk.MethodsHBV surface antigen (HBsAg) positive samples of acute (n = 152) and chronic (n = 1533) HBV submitted for strain analysis or reference genotype testing between 2006 and 2012 were analyzed. The HBsAg coding region was amplified to determine the HBV genotype by INNO-LiPA assay or sequence analysis. Single and multivariate analyses were used to describe genotypes' associations with known demographic and behavioral risk factors for 126 linked cases of acute HBV.ResultsNine genotypes were detected (A to I), including mixed infections. Genotype C (HBV/C) dominated within chronic infections while HBV/D and A prevailed among acute HBV cases. History of incarceration and residing with a chronic HBV carrier or injection drug user were the most frequently reported risks for acute HBV infection. Over time, HBV/A increased among both acute and chronic infections, and HBV/C and HBV/D decreased among chronic infections.ConclusionChronic and acute HBV genotypes in Canada differ in the relative distribution and their associations with known risk factors, suggesting different routes of transmission and clinical progression of infection.
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Project description:The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term "recombino-subgenotype". Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term "immigro-subgenotype" to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.
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Project description:Hepatitis C virus (HCV) mainly replicates in the cytoplasm, where it easily establishes persistent infection, resulting in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Due to its high rate of mutation, HCV forms viral quasispecies, categorized based on the highly variable regions in the envelope protein and nonstructural 5A protein. HCV possesses seven major genotypes, among which genotype 1 is the most prevalent globally. The distribution of HCV genotypes varies based on geography, and each genotype has a different sensitivity to interferon treatment. Recently-developed direct-acting antivirals (DAAs), which target viral proteases or polymerases, mediate drastically better antiviral effects than previous therapeutics. Although treatment with DAAs has led to the development of drug-resistant HCV mutants, the most recently approved DAAs show improved pan-genomic activity, with a higher barrier to viral resistance.
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Project description:Background & objectivesInfection by hepatitis B virus (HBV) results in acute or chronic hepatitis. Based on sequence differences of eight per cent or more, HBV is divided into 10 genotypes (A to J) and 35 sub-genotypes. Molecular characterization of the circulating HBV genome has helped in understanding the epidemiology and its clinical importance. Spiti valley in Himachal Pradesh, which shares its border with Tibet, is one of the most HBV prevalent areas in India. Since information about the circulating genotype/s of HBV in this area is limited, this study was conducted to identify the circulating HBV genotypes.MethodsThe surface and partial reverse transcriptase gene regions were sequenced using 14 hepatitis B surface antigen-positive samples.ResultsOut of the 14 hepatitis B surface antigen-positive samples 11 sample gave quality sequence for further analysis. All the 11 samples belonged to subtype ayw2. The phylogenetic and recombination analysis revealed that five out of 11 samples were of genotype CD1 and the rest six were of genotype D3.Interpretation & conclusionsThe CD1 recombinant sub-genotype might have immigrated during past or present transcontinental migration between the adjacent countries. Further studies using full-genome sequencing and high sample size will be helpful to understand this epidemiology and to combat the high prevalence of HBV in the area.
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Project description:Hepatitis E (HEV) is an emerging cause of viral hepatitis worldwide. Swine carrying hepatitis E genotype 3 (HEV-3) are responsible for the majority of chronic viral hepatitis cases in developed countries. Recently, genotype 7 (HEV-7), isolated from a dromedary camel in the United Arab Emirates, was also associated with chronic viral hepatitis in a transplant recipient. In Israel, chronic HEV infection has not yet been reported, although HEV seroprevalence in humans is ~10%. Camels and swine are >65% seropositive. Here we report on the isolation and characterization of HEV from local camels and swine. Sera from camels (n = 142), feces from swine (n = 18) and blood from patients suspected of hepatitis E (n = 101) were collected during 2017-2020 and used to detect and characterize HEV sequences. HEV-3 isolated from local swine and the camel-derived HEV-7 sequence were highly similar to HEV-3f and HEV-7 sequences (88.2% and 86.4%, respectively) related to viral hepatitis. The deduced amino acid sequences of both isolates were also highly conserved (>98%). Two patients were HEV-RNA positive; acute HEV-1 infection could be confirmed in one of them. The absence of any reported HEV-3 and HEV-7 infection in humans remains puzzling, especially considering the reported seroprevalence rates, the similarity between HEV sequences related to chronic hepatitis and the HEV genotypes identified in swine and camels in Israel.
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Project description:The hepatitis C virus (HCV) exhibits global genotypic diversity. HCV genotyping plays an important role in epidemiological studies and clinical management. Herein, we report the results of HCV genotype and subtype detection in a large number of clinical samples, as performed by an independent laboratory in China. In total, four HCV genotypes and 18 subtypes were identified among 32 030 patients from 29 provinces and municipalities in China. Five dominant subtypes were detected from 98.84% of the samples: 1b (n=16 713, 52.18%), 2a (n=9188, 28.69%), 3b (n=2261, 7.06%), 6a (n=2052, 6.41%) and 3a (n=1479, 4.62%). Twelve rare subtypes were detected, of which four (that is, 6b, 6j, 6q and 6r) are reported for the first time in the Chinese population. Genotypes 4, 5 and 7 were not detected. Mixed infections of the dominant subtypes were found in a small portion of samples (n=65, 0.203%), in the following combinations: 1b-2a, 1b-3b, 1b-6a, 3a-3b, 1b-3a and 2a-6a. No mixed infections with rare subtypes were found. Males, compared with females, showed higher HCV subtype diversity, a lower percentage of HCV1b and 2a and a higher percentage of rare subtypes and mixed infections. Our analyses revealed the comprehensive distribution patterns of HCV genotypes in the general population of mainland China. HCV genotypic patterns were differentially distributed on the basis of geography, sex and age.
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Project description:OBJECTIVE:To understand the oral healthcare experiences of humanitarian migrants in Montreal and their perceptions of ways to improve access to oral healthcare. METHODS:We used focused ethnography informed by a public health model of the dental care process. The adapted McGill Illness Narrative Interview (MINI) guided interviews of a purposeful sample of humanitarian migrants who received or needed dental care in Montreal. Each interview (50-60 min) was audio-recorded for verbatim transcription. Observation of dental care episodes occurred during mobile dental clinics in underserved communities over the same period (2015-2016). Data analysis combined deductive codes from the theoretical frameworks and inductive codes from interview transcripts and field notes to inform themes. RESULTS:We interviewed 25 participants (13 refugees and 12 asylum seekers) from 10 countries, who had been in Canada for a range of 1 month to 5 years. The dental care experiences of participants included delayed consultation, proximity to dental clinics, quality care, limited treatment choices, high cost, and long waiting times. A more inclusive healthcare policy, lower fees, integration of dental care into public insurance, and creation of community dental clinics were proposed strategies to improve access to dental care. CONCLUSION:Humanitarian migrants in this study experienced inadequate oral healthcare. Their lived experiences help us to identify gaps in the provision of oral healthcare services, and suggestions of participants have great potential to improve access to oral healthcare.
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Project description:Hepatitis E virus (HEV) is a major cause of viral hepatitis globally. Zoonotic HEV is an important cause of chronic hepatitis in immunocompromised patients. The rapid identification of novel HEV variants and accumulating sequence information has prompted significant changes in taxonomy of the family Hepeviridae. This family includes two genera: Orthohepevirus, which infects terrestrial vertebrates, and Piscihepevirus, which infects fish. Within Orthohepevirus, there are four species, A-D, with widely differing host range. Orthohepevirus A contains the HEV variants infecting humans and its significance continues to expand with new clinical information. We now recognize eight genotypes within Orthohepevirus A: HEV1 and HEV2, restricted to humans; HEV3, which circulates among humans, swine, rabbits, deer and mongooses; HEV4, which circulates between humans and swine; HEV5 and HEV6, which are found in wild boars; and HEV7 and HEV8, which were recently identified in dromedary and Bactrian camels, respectively. HEV7 is an example of a novel genotype that was found to have significance to human health shortly after discovery. In this review, we summarize recent developments in HEV molecular taxonomy, epidemiology and evolution and describe the discovery of novel camel HEV genotypes as an illustrative example of the changes in this field.
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Project description:BackgroundIn industrialized areas of the world, including Europe, Hepatitis E Virus (HEV) is considered an emerging pathogen. In fact, autochthonous cases caused by HEV genotype 3 (HEV-3) are increasingly reported. Several studies described the human HEV-3 subtypes and strains circulating in West Europe countries; in contrast, very little is known about the HEV strains responsible for acute hepatitis E in countries of East Europe/Balkans, such as Bulgaria.Methods and findingsAnti-HEV IgM positive serum samples (n = 103) from acute hepatitis cases (2013-2015) from all over Bulgaria were analysed for HEV RNA by Real-Time PCR. Viremia was detected in 90/103 samples. A fragment of the viral genome (ORF-2 region) was amplified by nested PCR from 76/90 viremic samples, leading to a sequence in 64 of them. Genotyping by phylogenetic analysis with standard reference sequences showed HEV-1 in 1/64 cases, HEV-3 in 63/64. Subtyping of HEV-3 sequences showed 3e (39/63, 62%), 3f (n = 15/63, 24%) and 3c (n = 8/63, 13%) subtypes; in one case the sequence subtype was uncertain and classified as 3hi. In the phylogenetic tree, most 3e sequences grouped in two well distinct clusters (A and B), each one with very low intragroup genetic distances. In contrast, 3f and 3c were interspersed with reference sequences and showed lower tendency to cluster and/or higher intragroup distances. Geographically, while 3f and 3c were scattered throughout the country, 3e was restricted to the South-West area, with most cases in two towns about 40 kilometres apart from each other.ConclusionsMost acute hepatitis E cases in Bulgaria are caused by HEV-3, subtypes 3e, 3f and 3c. Circulation of 3e appears quite different from 3f and 3c, with 3e restricted to the South-West area while 3f and 3c diffused over the country. The factors underlying the observed molecular and geographical differences remain to be investigated.
| S-EPMC5991722 | biostudies-literature