Hepatitis C virus transmission during colonoscopy evidenced by phylogenetic analysis

Acute hepatitis due to the hepatitisC virus: Where are the transmission occurring?

OBJECTIVE

To know the transmission patterns of the acute infection by the hepatitisC virus at a time when we are close to its elimination.

PATIENTS AND METHODS

A prospective descriptive clinical-epidemiological study of cases of acute HCV infection diagnosed between 2016 and 2020 was carried out in a reference hospital in the island of Gran Canaria.

RESULTS

Twenty-two cases of acute HCV were diagnosed (10 primary infections and 12 reinfections). There was an increase in the incidence from 0.6 in 2016 and 2017 to 2.3 cases per 100,000 inhabitants in 2020. The median age was 46years. From these, 77.3% were men and 68.2% were HIV-positive. According to the risk factors, 54.5% had high-risk sexual practices, 83.3% were men who had sex with men (70% with a concomitant STI), 31.8% were drug users, 9.1% were women with neuropsychiatric disorders, and one woman (4.5%) had a previous surgical intervention. There were thirteen patients (40.9%) who presented symptoms and eleven out of the thirteen patients who were asymptomatic were HIV-positive.

CONCLUSIONS

An increase in incidence was observed in the last years of the study and the main route of infection was high-risk sexual practice, mainly in men who have sex with men and who are HIV positive. Cases related to unsafe sex in other non-HIV groups are probably under-diagnosed. Microelimination strategies may not be sufficient to diagnose these cases, so in order to achieve elimination of the HCV the best strategy would be a population-based screening.

Reuse of Biopsy Forceps may be Associated with Risk of Transmission of HCV in Egyptian Patients Undergoing Gastrointestinal Endoscopy

BACKGROUND AND AIMS

Hepatitis viruses are not transmitted via gastrointestinal endoscopy except if there are any mistakes in sterilization and disinfection of the endoscope that disrupt the infection control measures. So we aimed to measure the risk of transmitting HCV by GI endoscopy at department of Tropical Medicine and infectious Diseases, in a major University hospital in Egypt.

METHODS

Our study was conducted on four hundred patients with exclusion of those with HCV, HBV, and/or HIV positive antibodies. An ethical committee approval and a given consent were taken prior to enrollment on the study. Our patients are grouped into the following; 100 patients undergoing upper GI endoscopy without biopsy as group I; 100 patients undergoing upper GI endoscopy with biopsy as group II; 100 patients undergoing lower GI endoscopy without biopsy as group III and 100 patients undergoing lower GI endoscopy with biopsy as group IV. HCV antibodies were done 3 months after endoscopy with exclusion of other risks of HCV infection by a detailed questionnaire.

RESULTS

Only one case was reported positive after 3 months of procedure; it was after colonoscopy with biopsy using reusable forceps.

CONCLUSIONS

Strict infection control measures of the GI endoscopes despite being effective in preventing HCV transmission, the reuse of disinfected biopsy forceps may be associated with a risk of transmission. So, we recommend using disposable forceps for every patient to omit the risk of HCV transmission during endoscopy.

Hepatitis C virus transmission in a Dutch haemodialysis unit: detailed outbreak investigation using NS5A gene sequencing

BACKGROUND

Haemodialysis is a risk factor for hepatitis C virus (HCV) transmission. Two patients receiving haemodialysis in a Dutch dialysis unit in The Hague were found to seroconvert to HCV in December 2016 after the yearly routine control for blood-borne viruses. Following the presumed time of infection, three chronically infected HCV patients were identified as possible index cases.

AIM

To confirm inter-patient transmission and to identify the source.

METHODS

Molecular investigation and review of medical records were performed.

FINDINGS

Both of the incident cases and one of the three possible index cases were demonstrated to be infected with HCV genotype 2b based on 5'UTR sequencing. Epidemiological relatedness between these viruses was further investigated by sequencing of the NS5A region. Phylogenetic analysis clearly identified the incident cases and the index case to represent a cluster distinct from unrelated controls with HCV genotype 2b. Detailed review of the medical records identified two possible incidents that might have resulted in the HCV transmission cases: contamination of the venous pressure-sensing port due to high venous pressures or incomplete compliance with infection control precautions of the unit staff during handling of two incidents, that occurred at the same time in a single haemodialysis session with the index patient as well as both incident cases present.

CONCLUSION

This study demonstrates that detailed incident recording in combination with state-of-the-art molecular investigations such as sequencing of the NS5A region resulted in unravelling a set of two HCV transmissions that occurred at a haemodialysis unit.

Forensic application of phylogenetic analyses - Exploration of suspected HIV-1 transmission case

Transmission of human immunodeficiency virus (HIV) between individuals may have important legal implications and therefore may come to require forensic investigation based upon phylogenetic analysis. In criminal trials results of phylogenetic analyses have been used as evidence of responsibility for HIV transmission. In Serbia, as in many countries worldwide, exposure and deliberate transmission of HIV are criminalized. We present the results of applying state of the art phylogenetic analyses, based on pol and env genetic sequences, in exploration of suspected HIV transmission among three subjects: a man and two women, with presumed assumption of transmission direction from one woman to a man. Phylogenetic methods included relevant neighbor-joining (NJ), maximum likelihood (ML) and Bayesian methods of phylogenetic trees reconstruction and hypothesis testing, that has been shown to be the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals. End-point limiting-dilution PCR (EPLD-PCR) assay, generating the minimum of 10 sequences per genetic region per subject, was performed to assess HIV quasispecies distribution and to explore the direction of HIV transmission between three subjects. Phylogenetic analysis revealed that the viral sequences from the three subjects were more genetically related to each other than to other strains circulating in the same area with the similar epidemiological profile, forming strongly supported transmission chain, which could be in favour of a priori hypothesis of one of the women infecting the man. However, in the EPLD based phylogenetic trees for both pol and env genetic region, viral sequences of one subject (man) were paraphyletic to those of two other subjects (women), implying the direction of transmission opposite to the a priori assumption. The dated tree in our analysis confirmed the clustering pattern of query sequences. Still, in the context of unsampled sequences and inherent limitations of the applied methods, we cannot unambiguously prove that HIV-1 transmission occurred directly between two individuals. Further exploration of the known and suspected transmission cases is needed in order to define methodologies and establish their reliability.

Next Generation Sequencing-Based Investigation of Potential Patient-to-Patient Hepatitis C Virus Transmission during Hemodialytic Treatment

We investigated potential patient-to-patient transmission of hepatitis C virus (HCV) in two hemodialysis centers in Beijing, China. Approximately 8.25% (32/388) hemodialysis patients were HCV antibody positive, and 4.90% (19/388) were HCV RNA-positive, which consisted of 2a genotype (1/19) and 1b genotypes (18/19). Using next generation sequencing (NGS) approach, MiSeq platform, we sequenced HCV, targeting hypervariable region 1 (263 base-pairs) of genotype 1b specimens and obtained 18 to 243 unique HCV variants. Analysis of phylogenetic tree, viral epidemiology signature pattern (VESP) and Shannon entropy indicated no obvious HCV similarity for most HCV infections but limited HCV variants from Patient 31 (P31) were closer with respect to evolutionary relationship with Patient 24 (P24). However, it was unlikely that HCV was transmitted directly from P24 to P31 in the hemodialysis center. Otherwise, their genetic distance (3.92%-8.92%), would have been much less. Moreover, P31 was infected less than two years before specimen collection, and other external high risk factors existed for these two patients. Thus, our data indicated no evidence of patient-to-patient transmission of HCV in the two hemodialysis centers, suggesting that current HCV infection control measures are effective.

Phylogenetic Exploration of Nosocomial Transmission Chains of 2009 Influenza A/H1N1 among Children Admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011

Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events.

The Influence of Hepatitis C Virus Genetic Region on Phylogenetic Clustering Analysis

Sequencing is important for understanding the molecular epidemiology and viral evolution of hepatitis C virus (HCV) infection. To date, there is little standardisation among sequencing protocols, in-part due to the high genetic diversity that is observed within HCV. This study aimed to develop a novel, practical sequencing protocol that covered both conserved and variable regions of the viral genome and assess the influence of each subregion, sequence concatenation and unrelated reference sequences on phylogenetic clustering analysis. The Core to the hypervariable region 1 (HVR1) of envelope-2 (E2) and non-structural-5B (NS5B) regions of the HCV genome were amplified and sequenced from participants from the Australian Trial in Acute Hepatitis C (ATAHC), a prospective study of the natural history and treatment of recent HCV infection. Phylogenetic trees were constructed using a general time-reversible substitution model and sensitivity analyses were completed for every subregion. Pairwise distance, genetic distance and bootstrap support were computed to assess the impact of HCV region on clustering results as measured by the identification and percentage of participants falling within all clusters, cluster size, average patristic distance, and bootstrap value. The Robinson-Foulds metrics was also used to compare phylogenetic trees among the different HCV regions. Our results demonstrated that the genomic region of HCV analysed influenced phylogenetic tree topology and clustering results. The HCV Core region alone was not suitable for clustering analysis; NS5B concatenation, the inclusion of reference sequences and removal of HVR1 all influenced clustering outcome. The Core-E2 region, which represented the highest genetic diversity and longest sequence length in this study, provides an ideal method for clustering analysis to address a range of molecular epidemiological questions.

Epidemiology of hepatitis C in Europe

The advent of potent and safe direct-acting antivirals against the hepatitis C virus has the potential of fulfilling the dream of eliminating this infection and its impact on global public health. However, even if effective drugs are at hand, most patients remain unaware of their infection, which may be recognized only in late stages when dire complications have occurred. Europe is not spared by this scourge, with its estimated 19,000,000 persons infected, and knowledge of the epidemiology of HCV and its drivers is a critical tool in fighting this virus. A thorough review is provided on the extent of the HCV epidemic across Europe, with a discussion of the most important subgroups affected, and of the risk factors of infection, both traditional and new.

Chernobyl-Related Cancer and Precancerous Lesions: Incidence Increase vs. Late Diagnostics

The reported incidence of thyroid cancer in children and adolescents in Soviet Union before the Chernobyl accident was lower than in other developed countries. This is not clearly recognizable from the literature because comparisons of the high incidence figures 4 years after the accident and later have been made with those from the first years after the accident, when the registered incidence had already started to increase. Considering the low pre-accident registered incidence, there was an accumulated pool of undiagnosed thyroid tumors before the accident. The percentage of more advanced cancers, larger in size and less differentiated, was higher after the accident, when the pool of neglected cancers was diagnosed due to the screening and improved diagnostics. Some of these advanced tumors found by screening were interpreted as aggressive radiogenic cancers. The same tendency might be true also for other cancers, e.g. renal cell carcinoma. Furthermore, the screening-effect, false-positivity and registration of non-exposed patients as Chernobyl victims has obviously contributed to the registered incidence increase of malignancy.