Clinical evaluation of a Hepatitis C Virus whole-genome sequencing pipeline for genotyping and resistance testing.

OBJECTIVES: We sought to evaluate clinically a hepatitis C virus (HCV) whole-genome, next-generation sequencing (NGS) pipeline that is agnostic to viral genotype. METHODS: Performance of the NGS pipeline was assessed through comparison of results with Sanger sequencing (SS) of partial HCV genomes. RESULTS: There was 98.7% (376/381) concordance for viral subtype between SS and NGS. The positive and negative per cent agreements for determination of resistance-associated substitutions were 97.8% (95% CI 92.5-99.4%) and 99.9% (95% CI 99.5-100.0%), respectively. The NGS pipeline was also able to detect novel subtypes, mixtures, recombinants, transiently occurring resistance mutations and distinguish re-infection with the same subtype from relapse. DISCUSSION: Particular scenarios where NGS may be used include settings without universal access to pan-genotypic antiviral regimens, those infected with a 'rare' subtype or who have been failed by first-line therapy, and in cases of suspected re-infection.

Mother to Infant Transmission of Hepatitis B Virus in the Face of Neonatal Immunization Is Not Necessarily Primary Vaccine Failure.

BACKGROUND: Surveillance programs undertaken in infants born to mothers with hepatitis B virus (HBV) provide an opportunity to analyze virological markers from the neonate and early infancy. These data inform on mechanisms of HBV transmission and how available interventions can be better used for control of HBV infections arising at the mother/child interface. METHODS: Retrospective analysis of HBV serological markers was undertaken in dried blood spots collected from infants born to mothers infected with HBV. In addition, molecular analysis was performed in newborn blood spot cards, collected after birth, from infants identified as infected with HBV despite receiving prophylaxis. RESULTS: Perinatal exposure could not account for all transmissions, with at least one-quarter (22%) of infants already infected in utero. All harbored a wild-type hepatitis B surface antigen (HBsAg), with identical sequences noted in the neonatal and early infancy samples. In contrast, in infants infected perinatally (43%), selection of viruses harboring amino acid changes in the HBsAg were common (80% of sequences) and divergent from the linked maternal sample. CONCLUSION: Currently considered to represent vaccine failure, it is likely that a proportion of HBV infections result from in utero acquisition. These infections are unlikely to be susceptible to postnatal prophylaxis, and current recommendations for maternal antiviral treatment may be too late to prevent transmission. Consideration should be given to the earlier use of antivirals during gestation to reduce the risk of intrauterine transmission together with completion of the immunization schedule also to reduce the perinatal risk of HBV transmission.

Hepatitis A outbreak associated with consumption of dates, England and Wales, January 2021 to April 2021.

We report a national hepatitis A virus (HAV) outbreak linked to the consumption of Medjool dates. Twenty-nine cases of three genetically related sequences have been identified. Epidemiological investigations identified a suspected product (adjusted odds ratio: 47.36; 95% confidence interval: 1.79-1,256.07; p = 0.021). Microbiological testing has confirmed the presence of HAV on dates recovered from two cases and the product has been recalled. Date consumption is currently likely to be increased in connection with Ramadan, with potential ongoing contamination risk.

Hepatitis A outbreak among men who have sex with men (MSM) in England, 2016-2018: The contribution of past and current vaccination policy and practice.

BACKGROUND: We report on an outbreak of hepatitis A among men who have sex with men (MSM) in England and its associated healthcare resource burden, the strategies used to control the outbreak and the role of past and current hepatitis A vaccination policy and practice in England. METHODS: National surveillance of hepatitis A, including reference laboratory confirmation and molecular sequencing, and a case questionnaire, was enhanced in 2017 to collect demographic and risk information, disease severity and healthcare utilisation. National Health Service (NHS) data was used to calculate associated healthcare costs. RESULTS: During the outbreak period (July 2016 to January 2018), 670 confirmed cases were identified in England, caused by three distinct viral strains. The public health response included raising public and professional awareness, reinforcing vaccine recommendations for MSM, contact tracing for post-exposure vaccination, and mass community vaccination where spill-over of infection into the general population occurred. Hepatitis A vaccine was centrally procured to ensure sexual health clinics in England could offer vaccination to MSM. Outbreak associated healthcare costs were estimated to be approximately £1,500,000. CONCLUSIONS: While MSM are at increased risk of hepatitis A infection, inconsistent implementation of MSM vaccination policy in previous years led to an increasingly susceptible MSM population. The large number of cases, hospital admission rate and public health actions contributed to a significant healthcare burden. Recommending hepatitis A vaccination for MSM and clarifying commissioning responsibilities is essential to prevent future outbreaks.

Improving preparedness to respond to cross-border hepatitis A outbreaks in the European Union/European Economic Area: towards comparable sequencing of hepatitis A virus.

IntroductionSequence-based typing of hepatitis A virus (HAV) is important for outbreak detection, investigation and surveillance. In 2013, sequencing was central to resolving a large European Union (EU)-wide outbreak related to frozen berries. However, as the sequenced HAV genome regions were only partly comparable between countries, results were not always conclusive.AimThe objective was to gather information on HAV surveillance and sequencing in EU/European Economic Area (EEA) countries to find ways to harmonise their procedures, for improvement of cross-border outbreak responses.MethodsIn 2014, the European Centre for Disease Prevention and Control (ECDC) conducted a survey on HAV surveillance practices in EU/EEA countries. The survey enquired whether a referral system for confirming primary diagnostics of hepatitis A existed as well as a central collection/storage of hepatitis A cases' samples for typing. Questions on HAV sequencing procedures were also asked. Based on the results, an expert consultation proposed harmonised procedures for cross-border outbreak response, in particular regarding sequencing. In 2016, a follow-up survey assessed uptake of suggested methods.ResultsOf 31 EU/EEA countries, 23 (2014) and 27 (2016) participated. Numbers of countries with central collection and storage of HAV positive samples and of those performing sequencing increased from 12 to 15 and 12 to 14 respectively in 2016, with all countries typing an overlapping fragment of 218 nt. However, variation existed in the sequenced genomic regions and their lengths.ConclusionsWhile HAV sequences in EU/EEA countries are comparable for surveillance, collaboration in sharing and comparing these can be further strengthened.

Risk behaviours of homeless people who inject drugs during an outbreak of hepatitis C, Northern Ireland, 2016-2017.

From July to August 2016, 4 homeless people who injected drugs (PWID) with acute or recent hepatitis C virus (HCV) infection were reported in Belfast. A multidisciplinary team including public health, homeless and addiction services undertook an investigation to identify risk behaviours and interrupt transmission chains. Recent HCV cases were defined as negative test within the previous year, or reported injecting for less than 1 year; acute cases had tested negative within the previous 6 months. Contacts in the injecting networks of cases were identified for testing. We undertook a cross-sectional survey using structured questionnaires to elicit risk behaviours for PWID and compare behaviours between self-reported hepatitis C positive and negative subjects. During the outbreak investigation until December 2017, 156 PWID were tested and 45 (29%) cases identified, including 7 (16%) recent and 13 (29%) acute infections. 68 PWID, including 12 cases, were interviewed. All respondents reported using heroin, with 76% injecting once or more daily. Sharing was reported for spoons (58%) and filters (53%), but also needles (27%) and syringes (29%). Hepatitis C positive individuals had higher odds to be injecting in public toilets (AOR 17, 95% CI 0.71-400, P < .05) when compared with hepatitis C negative individuals. Hepatitis C positive individuals were more likely to inject in public spaces, but all respondents indicated concerning risk behaviours. We recommend active surveillance with ongoing testing, expanding existing harm reduction programmes and access to bespoke services.

Oral fluid testing facilitates understanding of hepatitis A virus household transmission.

The public health response to sporadic hepatitis A virus (HAV) infection, hepatitis A, can be complex especially when the index case is a child and no obvious source is identified. Identifying an infection source may avoid mass immunisation within schools when transmission is found to have occurred within the household. Screening of asymptomatic contacts via venepuncture can be challenging and unacceptable, as a result non-invasive methods may facilitate public health intervention. Enzyme-linked immunoassays were developed to detect HAV immunoglobulin M (IgM) and immunoglobulin G (IgG) in oral fluid (ORF). A validation panel of ORF samples from 30 confirmed acute HAV infections were all reactive for HAV IgM and IgG when tested. A panel of 40 ORF samples from persons known to have been uninfected were all unreactive. Two hundred and eighty household contacts of 72 index cases were screened by ORF to identify HAV transmission within the family and factors associated with household transmission. Almost half of households (35/72) revealed evidence of recent infection, which was significantly associated with the presence of children ⩽11 years of age (odds ratio 9.84, 95% confidence interval: 2.74-35.37). These HAV IgM and IgG immunoassays are easy to perform, rapid and sensitive and have been integrated into national guidance on the management of hepatitis A cases.

Vaccination strategies for control of community outbreaks of hepatitis A: A comparison of two outbreaks in England.

In August 2015 two community outbreaks of hepatitis A virus (HAV) occurred in sub-urban communities in Northern England. Each was managed by an independent outbreak control team. In outbreak one, mass vaccination was deployed targeting a residential area and two schools, while in outbreak two, vaccination was reserved for household-type contacts of cases. The highest vaccination uptake was achieved in the school settings (82% and 95%). These case studies illustrate the range of approaches that can be used and the factors that influence decision-making in response to a hepatitis A community outbreak. Both outbreaks likely started from importation(s) of HAV by returning travellers and spread through extended social networks and the local community. Vaccination strategies were selected based on hypotheses about transmission pathways, which were informed by evidence from oral fluid (OF) testing of asymptomatic contacts. More evidence about the effectiveness of mass vaccination in community outbreaks of hepatitis A in low endemicity settings is needed. Hepatitis A guidelines should include recommendations for the use of mass vaccination and OF testing in outbreaks.

Hepatitis A outbreak disproportionately affecting men who have sex with men (MSM) in the European Union and European Economic Area, June 2016 to May 2017.

Between 1 June 2016 and 31 May 2017, 17 European Union (EU) and European Economic Area countries reported 4,096 cases associated with a multi-country hepatitis A (HA) outbreak. Molecular analysis identified three co-circulating hepatitis A virus (HAV) strains of genotype IA: VRD_521_2016, V16-25801 and RIVM-HAV16-090. We categorised cases as confirmed, probable or possible, according to the EU outbreak case definitions. Confirmed cases were infected with one of the three outbreak strains. We investigated case characteristics and strain-specific risk factors for transmission. A total of 1,400 (34%) cases were confirmed; VRD_521_2016 and RIVM-HAV16-090 accounted for 92% of these. Among confirmed cases with available epidemiological data, 92% (361/393) were unvaccinated, 43% (83/195) travelled to Spain during the incubation period and 84% (565/676) identified as men who have sex with men (MSM). Results depict an HA outbreak of multiple HAV strains, within a cross-European population, that was particularly driven by transmission between non-immune MSM engaging in high-risk sexual behaviour. The most effective preventive measure to curb this outbreak is HAV vaccination of MSM, supplemented by primary prevention campaigns that target the MSM population and promote protective sexual behaviour.

Two concurrent outbreaks of hepatitis A highlight the risk of infection for non-immune travellers to Morocco, January to June 2018.

From January to June 2018, two ongoing hepatitis A outbreaks affected travellers returning from Morocco and cases in Europe without travel history, resulting in 163 patients in eight European countries. Most interviewed travel-related cases were unaware of the hepatitis A risk in Morocco. Molecular analysis revealed two distinct hepatitis A virus (HAV) strains (subgenotype IA DK2018_231; subgenotype IB V18-16428). Vaccination recommendations should be emphasised to increase awareness among non-immune travellers to Morocco and HAV-endemic countries.

Hepatitis B Virus Immunization and Neonatal Acquisition of Persistent Infection in England and Wales.

Background: It is believed that between 2% and 5% of infants born to hepatitis B virus (HBV)-infected mothers at a high risk of perinatal transmission will become persistently infected despite immunization starting at birth. We investigated factors associated with breakthrough infections. Methods: Sixty-nine samples from HBV-infected infants born between 2003 and 2015 were tested for HBV serological and molecular markers. Sequencing and epitope phenotyping were used to investigate alterations in hepatitis B surface antigen (HBsAg) sequence and antigenicity in infants and in mothers known to have transmitted and not to have transmitted virus to their infants. Results: Vaccine/hepatitis B immune globulin uptake was complete in the majority of HBV-infected infants. A minority (8 [12%]) had detectable plasma antibody to HBsAg at 12 months. Twenty-five of 68 (37%) infants harbored a virus with amino acid changes in the HBsAg "a" determinant, of which 13 displayed altered HBsAg antigenicity. Viral load was 30-fold higher in maternal samples from those who transmitted. Conclusions: Our data provide evidence to suggest that immune selection drives change at mother-infant transmission, resulting in the alteration of HBsAg antigenicity. These changes may play a role in immunization failure, but other factors including viral load may be more important. Continued monitoring of vaccine efficacy is essential.

Outbreak of hepatitis A associated with men who have sex with men (MSM), England, July 2016 to January 2017.

Between July 2016 and January 2017, 37 confirmed cases of hepatitis A with two unique IA genotype strains primarily among men who have sex with men, were reported across eight areas in England and Northern Ireland. Epidemiological and laboratory investigations indicate that these strains may have been imported several times from Spain, with secondary sexual transmission in the United Kingdom. Local and national public health services are collaborating to control this ongoing outbreak.

International linkage of two food-borne hepatitis A clusters through traceback of mussels, the Netherlands, 2012.

This report describes an outbreak investigation starting with two closely related suspected food-borne clusters of Dutch hepatitis A cases, nine primary cases in total, with an unknown source in the Netherlands. The hepatitis A virus (HAV) genotype IA sequences of both clusters were highly similar (459/460 nt) and were not reported earlier. Food questionnaires and a case-control study revealed an association with consumption of mussels. Analysis of mussel supply chains identified the most likely production area. International enquiries led to identification of a cluster of patients near this production area with identical HAV sequences with onsets predating the first Dutch cluster of cases. The most likely source for this cluster was a case who returned from an endemic area in Central America, and a subsequent household cluster from which treated domestic sewage was discharged into the suspected mussel production area. Notably, mussels from this area were also consumed by a separate case in the United Kingdom sharing an identical strain with the second Dutch cluster. In conclusion, a small number of patients in a non-endemic area led to geographically dispersed hepatitis A outbreaks with food as vehicle. This link would have gone unnoticed without sequence analyses and international collaboration.

Molecular epidemiology of newly acquired hepatitis C infections in England 2008-2011: genotype, phylogeny and mutation analysis.

BACKGROUND: Analysis of laboratory testing data collected through the Sentinel Surveillance programme has provided a method for identifying individuals who have recently acquired their hepatitis C virus (HCV) infection. Access to samples from these individuals provided a rare opportunity to undertake molecular characterization studies. OBJECTIVES: To describe the epidemiology and genetic diversity of hepatitis C in recent seroconverter infections and to predict how this will impact on HCV treatment and control. STUDY DESIGN: One hundred and forty seven samples were available from individuals, identified to have recently acquired their HCV infection. Genotype determination with additional phylogenetic analysis was carried out on NS5B sequences. Analysis across the NS3 region investigated the presence of antiviral resistance mutations. Where possible, molecular data was linked to demographic and risk/behavioural factor information. RESULTS: The majority of new infections occurred in males with a mean age of 37 years. The most commonly observed genotypes were 1a (49%) and 3a (42%) and injecting drug use (58%) was the most common risk factor. Genotype distribution differed between persons who inject drugs and those with other risk factors suggesting two possible epidemics. Phylogenetic analysis indicated possible transmission networks within specific risk groups. Amino acid changes associated with antiviral resistance were noted in the NS3 region in some samples. CONCLUSIONS: Continued surveillance of linked molecular, virological, demographic and epidemiological information on recently acquired infections will contribute to understanding the on-going HCV epidemic in England.

Hepatitis C virus genotype 4 in England: diversity and demographic associations.

HCV strains belonging to genotype 4 may be gaining endemicity across Continental Europe but the extent of their spread in the United Kingdom is unknown. Sera referred from patients attending hospitals in England between 2004 through 2008 were characterised. A total of 243 sera carried HCV genotype 4. The most common subtypes were 4a (33%) and 4d (35%). Compared to patients infected by 4d, those infected by 4a were 20 times more likely to be Middle Eastern than English, and those infected by non-4a/4d were older, tended to be female, and 50 or 12 times more likely to be Middle Eastern or South Asian, respectively, than English. Persons infected by 4d tended to be English rather than Middle Eastern or South Asian. One group of 4d strains clustered with strains reported from persons in Europe engaged in male homosexual activity. Surveillance of trends in the importation and subsequent spread of HCV genotype 4 and its subtypes is advocated.

Acute hepatitis A in an elderly patient after care worker travel to high endemicity country.

Hepatitis A virus (HAV) is considered one of the most important vaccine-preventable diseases in travelers. HAV spreads from person to person via the fecal-oral route and gives rise to an estimated 1.4 million cases worldwide each year. In developing countries with poor sanitary conditions people tend to be infected during childhood and have few symptoms, whereas in developed countries with good sanitary conditions fewer people develop immunity during childhood. This leads to susceptible populations of adults, who are also more prone to severe complications. Here we describe two confirmed cases of hepatitis A associated with a nursing home. The index case was a care worker who had recently traveled to a high-endemicity country, and the second case was a resident at the nursing home where the index case worked. Both cases had an identical genotype IIIA strain, consistent with a transmission event. Current policy does not include a requirement for hepatitis A vaccine in care workers who travel to high endemicity countries despite the fact that infected care workers can potentially spread the disease to elderly patients and other groups at risk of severe complications from HAV infection. We suggest that employers should consider hepatitis A vaccine upon employment; particularly in care workers who plan to visit areas where HAV is known to be endemic.

Planning for the healthcare burden of hepatitis C infection: Hepatitis C genotypes identified in England, 2002-2007.

BACKGROUND: Identification of HCV genotype is a prerequisite for anti-viral treatment in England. Treatment length and sustained virological response rates vary by genotype. Therefore knowledge of circulating HCV genotypes is important for health-care providers. OBJECTIVES: To describe the HCV genotypes identified in English laboratories and to investigate changes over time; sub-analysis of young adults (15-24 years) to provide information on recently circulating genotypes. STUDY DESIGN: Data from the national reference laboratory and 19 English laboratories participating in the sentinel surveillance of hepatitis testing study were analysed. Multinomial regression was used to investigate trends in genotypes identified between 2002 and 2007. RESULTS: HCV genotypes were available for 18,031 individuals. The majority (89%) of people were genotypes 1 and 3; 3a was the single largest subtype. Half of people born between 1960 and 1989 were genotype 3a and the majority of South Asian people were genotype 3a. People born pre-1940 were nine times more likely to have genotype 1b than 3a. The proportion of 1b infections, relative to 3a, declined over time, but, after adjusting for birth cohort, this effect disappeared. There was no evidence of a relative change in 1a infections. CONCLUSIONS: This is the largest study of genotypes identified in England to date. Changes in genotypes over time were due to decreased genotyping of older individuals. As the population ages, the proportion of more difficult to treat genotypes may decline, leading to possible cost-savings for health-care providers, with a higher chance of achieving sustained virological response.

Outbreaks of hepatitis A in England and Wales associated with two co-circulating hepatitis A virus strains.

During 2002, an upsurge in frequency of hepatitis A outbreaks among injecting drug users was observed in England and Wales. As lack of risk factor information and the high mobility of the cases made linkage of outbreaks difficult, the relationship of nucleotide sequences in the VP1/2PA junction of the hepatitis A virus (HAV) genome amplified from serum of case-patients was investigated. A total of 204 HAV RNA positive sera obtained from a network of 23 laboratories were studied. Comparison of the sequences identified two principal strains: ES1 (n=95) belonging to type IB, and ES2 (n=72) to type IIIA. Of the remaining samples, 15 were type IA, 11 were type IB and 11 were type IIIA. ES1 predominated in Doncaster and other towns in Trent and northern England, and ES2 in the Midlands and southern England; the difference in geographical distribution between these two strains was significant (P<0.0001). In comparison to the sporadic cases, cases infected by either ES1 or ES2 tended to be younger, injecting drug users, people in contact with injecting drug users, or those with a history of incarceration in prisons or homelessness (P<0.0001). Cases infected by ES1 tended to be younger than those by ES2 (P<0.0001). The association of the outbreaks to two geographically restricted strains implicates two principal transmission pathways associated with injecting behavior. Identifying these routes may be conducive to preventing further outbreaks.

Hepatitis E in England and Wales.

In 2005, 329 cases of hepatitis E virus infection were confirmed in England and Wales; 33 were confirmed indigenous infections, and a further 67 were estimated to be indigenous infections. Hepatitis E should be considered in the investigation of patients with hepatitis even if they have no history of travel.