Review on the molecular epidemiology of sexually acquired hepatitis C virus infection in the Asia‐Pacific region

Chan, Chin Pok; Uemura, Haruka; Kwan, Tsz Ho; Wong, Ngai Sze; Oka, Shinichi; Chan, David Yiu Leung; Lee, Shui Shan

doi:10.1002/jia2.25618

Cited by 5 publications

(6 citation statements)

References 40 publications

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“…While HIV-1 epidemiology is the predominant niche for distance-based molecular transmission analyses, other rapidly evolving viruses, especially HCV, have also been analyzed with these approaches(Bartlett et al, 2017). Unlike HIV-1, there is considerably less work on how to choose an appropriate distance threshold, further complicated by the use of different genes to build networks (see Chan et al (2020) for a comprehensive summary). Two commonly seen methods exist: use some measure of intra-host variation (obtained by deep sequencing) as a lower bound for the threshold, or tune D to obtain some desired network property, e.g., the maximal number of clusters.…”

Section: Resultsmentioning

confidence: 99%

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Auto-Tune: Selecting the Distance Threshold for Inferring Hiv Transmission Clusters

Weaver,

Dávila-Conn,

et al. 2024

Preprint

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Molecular surveillance of viral pathogens and inference of transmission networks from genomic data play an increasingly important role in public health efforts, especially for HIV-1. For many methods, the genetic distance threshold used to connect sequences in the transmission network is a key parameter informing the properties of inferred networks. Using a distance threshold that is too high can result in a network with many spurious links, making it difficult to interpret. Conversely, a distance threshold that is too low can result in a network with too few links, which may not capture key insights into clusters of public health concern. Published research using the HIV-TRACE software package frequently uses the default threshold of 0.015 substitutions/site for HIV pol gene sequences, but in many cases, investigators heuristically select other threshold parameters to better capture the underlying dynamics of the epidemic they are studying. Here, we present a general heuristic scoring approach for tuning a distance threshold adaptively, which seeks to prevent the formation of giant clusters. We prioritize the ratio of the sizes of the largest and the second largest cluster, maximizing the number of clusters present in the network. We apply our scoring heuristic to outbreaks with different characteristics, such as regional or temporal variability, and demonstrate the utility of using the scoring mechanism's suggested distance threshold to identify clusters exhibiting risk factors that would have otherwise been more difficult to identify. For example, while we found that a 0.015 substitutions/site distance threshold is typical for US-like epidemics, recent outbreaks like the CRF07\_BC subtype among men who have sex with men (MSM) in China have been found to have a lower optimal threshold of 0.005 to better capture the transition from injected drug use (IDU) to MSM as the primary risk factor. Alternatively, in communities surrounding Lake Victoria in Uganda, where there has been sustained heterosexual transmission for many years, we found that a larger distance threshold is necessary to capture a more risk factor-diverse population with sparse sampling over a longer period of time. Such identification may allow for more informed intervention action by respective public health officials.

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Section: Resultsmentioning

confidence: 99%

“…Unlike HIV-1, there is considerably less work on how to choose an appropriate distance threshold, further complicated by the use of different genes to build networks (see Chan et al (2020) for a comprehensive summary).…”

Section: E Comparisons With Published Hiv-1 Molecular Epidemiology St...mentioning

confidence: 99%

Auto-Tune: Selecting the Distance Threshold for Inferring Hiv Transmission Clusters

Weaver,

Dávila-Conn,

et al. 2024

Preprint

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“…Emergence of HCV, not just HIV, in the MSM community in the past decade is a cause for concern. The detection of unique HIV subtypes and HCV genotypes associated with MSM suggested the presence of a founder effect in the community (14). From the results of latent class analysis, HIV/HCV co-infected patients could be classified into four classes, two of which were composed of MSM.…”

Section: Discussionmentioning

confidence: 99%

“…It could be argued that drug-injecting MSM were the bridge between the two viral communities (14). However, the distinct genotype distributions among risk groups could only be explained by founder effect (25,26).…”

Section: Discussionmentioning

confidence: 99%

Hepatitis C Co-infection in People Living With HIV—Epidemiologic Differences Between Men Who Have Sex With Men MSM and Non-MSM

Kwan

Wong²,

Wong³

et al. 2022

Front. Public Health

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People living with human immunodeficiency virus (PLHIV) constitute a unique group at higher risk of hepatitis C virus (HCV) co-infection. In light of the diverse profiles of PLHIV, we differentiated between men who have sex with men (MSM) and non-MSM in the characterization of the epidemiologic features of HIV/HCV co-infection. Clinical data of HCV co-infection patients from the HIV specialist clinic in Hong Kong were retrospectively collected in conjunction with their HIV subtypes and HCV genotypes. Logistic regression models were used to identify factors associated with HIV/HCV co-infection in MSM. Survival analysis was performed to compare the time lag between HIV and HCV diagnoses between two groups. Latent class analysis was conducted to describe the features of different classes of co-infections. Four classes of HIV/HCV co-infections were identified: local MSM acquiring HCV after HIV diagnosis, local MSM with HIV/HCV co-diagnoses, local non-MSM, and non-local non-MSM. Accounting for over half of the co-infections, MSM were more likely to be younger, local residents, and associated with HCV genotype 3, compared to genotypes 1 and 6 in non-MSM. Overall, MSM had higher odds of achieving HIV viral suppression and co-diagnosing with a sexually transmitted infection at HCV diagnosis, and having a longer time lag between HIV and HCV diagnoses. Drug injection accounted for a majority of non-MSM HCV infection. There were distinctive epidemiologic differences between MSM and non-MSM co-infected with HIV and HCV, the characteristics of which could inform intervention strategies for achieving HCV micro-elimination.

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“…The highest prevalence of G3 in Western Europe is Norway (50%), England (47%), and Finland (43%) with 10% in North America (22% in Canada) with 26.9% in South America[ 3 - 5 ]. However, the greatest burden of G3 is in South and Central Asia with 71.6% of HCV infections being of this genotype which is very common in Pakistan and India[ 2 , 6 - 8 ].…”

Section: Introductionmentioning

confidence: 99%

Risk factors for hepatocellular carcinoma associated with hepatitis C genotype 3 infection: A systematic review

Farooq,

James,

Abbott

et al. 2024

World J Gastrointest Oncol

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BACKGROUND Hepatitis C virus (HCV) is a blood-borne virus which globally affects around 79 million people and is associated with high morbidity and mortality. Chronic infection leads to cirrhosis in a large proportion of patients and often causes hepatocellular carcinoma (HCC) in people with cirrhosis. Of the 6 HCV genotypes (G1-G6), genotype-3 accounts for 17.9% of infections. HCV genotype-3 responds least well to directly-acting antivirals and patients with genotype-3 infection are at increased risk of HCC even if they do not have cirrhosis. AIM To systematically review and critically appraise all risk factors for HCC secondary to HCV-G3 in all settings. Consequently, we studied possible risk factors for HCC due to HCV-G3 in the literature from 1946 to 2023. METHODS This systematic review aimed to synthesise existing and published studies of risk factors for HCC secondary to HCV genotype-3 and evaluate their strengths and limitations. We searched Web of Science, Medline, EMBASE, and CENTRAL for publications reporting risk factors for HCC due to HCV genotype-3 in all settings, 1946-2023. RESULTS Four thousand one hundred and forty-four records were identified from the four databases with 260 records removed as duplicates. Three thousand eight hundred and eighty-four records were screened with 3514 excluded. Three hundred and seventy-one full-texts were assessed for eligibility with seven studies included for analysis. Of the seven studies, three studies were retrospective case-control trials, two retrospective cohort studies, one a prospective cohort study and one a cross-sectional study design. All were based in hospital settings with four in Pakistan, two in South Korea and one in the United States. The total number of participants were 9621 of which 167 developed HCC (1.7%). All seven studies found cirrhosis to be a risk factor for HCC secondary to HCV genotype-3 followed by higher age (five-studies), with two studies each showing male sex, high alpha feto-protein, directly-acting antivirals treatment and achievement of sustained virologic response as risk factors for developing HCC. CONCLUSION Although, studies have shown that HCV genotype-3 infection is an independent risk factor for end-stage liver disease, HCC, and liver-related death, there is a lack of evidence for specific risk factors for HCC secondary to HCV genotype-3. Only cirrhosis and age have demonstrated an association; however, the number of studies is very small, and more research is required to investigate risk factors for HCC secondary to HCV genotype-3.

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Review on the molecular epidemiology of sexually acquired hepatitis C virus infection in the Asia‐Pacific region

Cited by 5 publications

References 40 publications

Auto-Tune: Selecting the Distance Threshold for Inferring Hiv Transmission Clusters

Auto-Tune: Selecting the Distance Threshold for Inferring Hiv Transmission Clusters

Hepatitis C Co-infection in People Living With HIV—Epidemiologic Differences Between Men Who Have Sex With Men MSM and Non-MSM

Risk factors for hepatocellular carcinoma associated with hepatitis C genotype 3 infection: A systematic review

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