First full-length genomic sequence of a hepatitis A virus isolated in Argentina shows recombination between subgenotypes IA and IB

Novel strategy for whole-genome sequencing of hepatitis A virus using NGS illumina technology and phylogenetic comparison with partial VP1/2A genomic region

Molecular epidemiology of hepatitis A virus (HAV) plays a critical role in identifying outbreak origin and conducting surveillance. Although it is mostly carried out using short partial VP1/2A genomic sequences, utilizing whole-genome sequences (WGS) provides more accurate and robust information. We developed an amplicon-based next-generation sequencing (NGS) strategy to obtain complete HAV genomes utilizing the COVIDSeq Test (Illumina). Twenty-five primer pairs were designed and used to amplify partial genomic fragments (400 bp) that comprise the entire HAV genome sequence from previously HAV positive serum and stool samples from Argentina. The DNA library was prepared using the Illumina COVIDSeq Test and sequenced in a MiSeq equipment. Phylogenetic analyses were performed with IQ-Tree using WGS and VP1/2A partial sequences of 1084pb and 422pb. Eleven samples were amplified and sequenced, with coverage between 79.3 and 100% (> 90% in 9 samples). Although phylogenetic analyses of partial sequences allowed genotype and subgenotype identification, WGS analyses yielded more accurate and reliable results for the phylogeny (phylogenetic definition). The amplicon-based NGS WGS tool developed by adapting the COVIDSeq test to HAV proved to be efficient. The study of partial VP1/2A regions (mainly the 1084 bp fragment) would constitute useful alternatives for outbreak investigation and surveillance when WGS could not be performed.

Viral Hepatitis: Host Immune Interaction, Pathogenesis and New Therapeutic Strategies

Viral hepatitis is a major cause of liver illness worldwide. Despite advances in the understanding of these infections, the pathogenesis of hepatitis remains a complex process driven by intricate interactions between hepatitis viruses and host cells at the molecular level. This paper will examine in detail the dynamics of these host-pathogen interactions, highlighting the key mechanisms that regulate virus entry into the hepatocyte, their replication, evasion of immune responses, and induction of hepatocellular damage. The unique strategies employed by different hepatitis viruses, such as hepatitis B, C, D, and E viruses, to exploit metabolic and cell signaling pathways to their advantage will be discussed. At the same time, the innate and adaptive immune responses put in place by the host to counter viral infection will be analyzed. Special attention will be paid to genetic, epigenetic, and environmental factors that modulate individual susceptibility to different forms of viral hepatitis. In addition, this work will highlight the latest findings on the mechanisms of viral persistence leading to the chronic hepatitis state and the potential implications for the development of new therapeutic strategies. Fully understanding the complex host-pathogen interactions in viral hepatitis is crucial to identifying new therapeutic targets, developing more effective approaches for treatment, and shedding light on the mechanisms underlying progression to more advanced stages of liver damage.

Genotyping and Molecular Diagnosis of Hepatitis A Virus in Human Clinical Samples Using Multiplex PCR-Based Next-Generation Sequencing

Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based NGS. HAV whole-genome sequence of one sample was obtained by conventional Sanger sequencing. The HAV strains demonstrated a geographic cluster with sub-genotype IA strains in the Republic of Korea. The phylogenetic pattern of HAV viral protein (VP) 3 region showed no phylogenetic conflict between the whole-genome and partial-genome sequences. The VP3 region in serum and stool samples showed sensitive detection of HAV with differences of quantification that did not exceed <10 copies/μL than the consensus VP4 region using quantitative PCR (qPCR). In conclusion, multiplex PCR-based NGS was implemented to define HAV genotypes using nearly whole-genome sequences obtained directly from hepatitis A patients. The VP3 region might be a potential candidate for tracking the genotypic origin of emerging HAV outbreaks. VP3-specific qPCR was developed for the molecular diagnosis of HAV infection. This study may be useful to predict for the disease management and subsequent development of hepatitis A infection at high risk of severe illness.

First evidence for continuous circulation of hepatitis A virus subgenotype IIA in Central Africa

Although a high seroprevalence of antibodies against hepatitis A virus (HAV) has been estimated in Central Africa, the current status of both HAV infections and seroprevalence of anti-HAV antibodies remains unclear due to a paucity of surveillance data available. We conducted a serological survey during 2015-2017 in Gabon, Central Africa, and confirmed a high seroprevalence of anti-HAV antibodies in all age groups. To identify the currently circulating HAV strains and to reveal the epidemiological and genetic characteristics of the virus, we conducted molecular surveillance in a total of 1007 patients presenting febrile illness. Through HAV detection and sequencing, we identified subgenotype IIA (HAV-IIA) infections in the country throughout the year. A significant prevalence trend emerged in the young child population, presenting several infection peaks which appeared to be unrelated to dry or rainy seasons. Whole-genome sequencing and phylogenetic analyses revealed local HAV-IIA evolutionary events in Central Africa, indicating the circulation of HAV-IIA strains of a region-specific lineage. Recombination analysis of complete genome sequences revealed potential recombination events in Gabonese HAV strains. Interestingly, Gabonese HAV-IIA possibly acquired the 5'-untranslated region (5'-UTR) of the rare subgenotype HAV-IIB in recent years, suggesting the present existence of HAV-IIB in Central Africa. These findings indicate a currently stable HAV-IIA circulation in Gabon, with a high risk of infections in children aged under 5 years. Our findings will enhance the understanding of the current status of HAV infections in Central Africa and provide new insight into the molecular epidemiology and evolution of HAV genotype II.

Genomic Sequence of the WHO International Standard for Hepatitis A Virus RNA

The World Health Organization (WHO) international standard for hepatitis A virus (HAV) RNA nucleic acid assays was characterized by complete genome sequencing. The entire coding sequence and noncoding regions were assigned HAV genotype IB. This information will aid the design, development, and evaluation of HAV RNA amplification assays.

Detection and characterization of hepatitis A virus circulating in Egypt

Hepatitis A virus (HAV) still poses a considerable problem worldwide. In the current study, hepatitis A virus was recovered from wastewater samples collected from three wastewater treatment plants over one year. Using RT-PCR, HAV was detected in 43 out of 68 samples (63.2%) representing both inlet and outlet. Eleven positive samples were subjected to sequencing targeting the VP1-2A junction region. Phylogenetic analysis revealed that all samples belonged to subgenotype IB with few substitutions at the amino acid level. The complete sequence of one isolate (HAV/Egy/BI-11/2015) showed that the similarity at the amino acid level was not reflected at the nucleotide level. However, the deduced amino acid sequence derived from the complete nucleotide sequence showed distinct substitutions in the 2B, 2C, and 3A regions. Recombination analysis revealed a recombination event between X75215 (subgenotype IA) and AF268396 (subgenotype IB) involving a portion of the 2B nonstructural protein coding region (nucleotides 3757-3868) assuming the herein characterized sequence an actual recombinant. Despite the role of recombination in picornaviruses evolution, its involvement in HAV evolution has rarely been reported, and this may be due to the limited available complete HAV sequences. To our knowledge, this represents the first characterized complete sequence of an Egyptian isolate and the described recombination event provides an important update on the circulating HAV strains in Egypt.

Evidence of the circulation of hepatitis A virus, subgenotype IA, in environmental samples from Antioquia, Colombia

INTRODUCTION

Hepatitis A virus (HAV) is an important pathogen, typically transmitted via the faecal-oral route. The epidemiology of the infection is directly related to drinking water access and adequate disposal of sewage water. 

OBJECTIVE

To determine the presence and identify the genotype of HAV in environmental samples from eight municipalities and two villages in Antioquia, northwestern Colombia. 

MATERIALS AND METHODS

Three serial samplings were done between December, 2012, and April, 2014. Water samples were obtained from drinking water plants prior to treatment, as well as from the main reserve of wastewater in each municipality included in the study. Viral concentrations for the two types of sample sources were determined by filtration/tangential ultrafiltration and polyethyleneglycol plus flocculation with skimmed milk, respectively. Total ARN was subsequently obtained from each sample and the VP3-VP1 region amplified for detection of the viral genome. The genotype was determined by amplification of the VP1-2B region. 

RESULTS

The HAV genome was detected in samples from drinking water plants at Puerto Berrío, Frontino and Nutibara, and in wastewater samples from the municipalities of Arboletes, Zaragoza and Venecia. HAV subgenotype IA was identified using phylogenetic analysis. 

CONCLUSION

In this study, HAV was identified in 6.6% of the samples from drinking water plants and 13.3% of wastewater samples. This is the first report of HAV subgenotype IA circulating in environmental samples from Antioquia.

Hepatitis A virus subgenotyping based on RT-qPCR assays

Background

The hepatitis A virus (HAV) is the most frequent cause of viral hepatitis worldwide and is recognized as one of the most widespread foodborne pathogens. HAV genotypes and subtypes differ in their geographic distribution and the incidence of HAV infection varies considerably among countries, and is particularly high in areas with poor sanitation and hygiene. Phylogenetic analyses are traditionally used in clinical microbiology for tracing the geographic origin of HAV strains. In food microbiology, this approach is complicated by the low contamination levels of food samples. To date, real-time reverse-transcription PCR has been one of the most promising detection methods due to its sensitivity, specificity and ability to deliver quantitative data in food samples, but it does not provide HAV subtyping information.

Results

Six subtype-specific RT-qPCR assays were developed for human HAV. The limit of detection of HAV was 50 genome copies/assay for subtype IIB, 500 genome copies assay for IA, IB, IIA and IIIB and 5000 genome copies/assay for IIIA. The specificity of the assays was evaluated by testing reference isolates and in vitro HAV RNA transcripts. No significant cross reactivity was observed. Subtyping results concordant with sequencing analysis were obtained from 34/35 clinical samples. Co-infection with a minor strain of a different subtype was suggested in 5 cases and a recombinant event in one case.

Conclusions

These RT-qPCR assays may be particularly useful for accurately tracing HAV in low-level contaminated samples such as food matrices but also to allow co-infection identification in human samples.

Evidence of hepatitis A virus circulation in central Argentina: seroprevalence and environmental surveillance

BACKGROUND

Hepatitis A virus (HAV) has shown intermediate endemicity in Argentina, but notification of clinical cases has decreased since the introduction of the vaccine in 2005.

OBJECTIVES

In order to get insight into the local circulation of this virus after four years of the official introduction of the vaccine, the aims of this study were to provide information on HAV immune status of the adult population of Córdoba city and to conduct environmental surveillance of HAV in sewage and river samples in the same region.

STUDY DESIGN

The prevalence of anti-HAV was determined by EIA in 416 samples of people (without prior vaccination) from Córdoba city (2009-2010). Spline regression models were estimated under generalized additive models. Environmental surveillance was conducted in river and sewage samples collected in the same period. Viral detection was performed by RT-Nested PCR of the 5'UTR.

RESULTS

In Córdoba, the global prevalence of anti-HAV was 73.5%. It increased with age (p<0.0001) and it was associated with the low-income population (OR: 1.14; 95% CI 1.05-1.25). This prevalence decreased in younger age groups, especially in the high-income population. Environmental monitoring revealed the presence of HAV (IA) in 20.8% and 16.1% of wastewater and river samples, respectively.

CONCLUSIONS

As a consequence of a decrease in HAV circulation due to improvements in immunization, socio-economic and hygienic conditions, young adults are becoming increasingly susceptible to HAV infections. Environmental monitoring demonstrated that HAV circulates in the local population; therefore, health care systems should consider the implementation of preventive measures for susceptible adults in order to reduce the risk of HAV infection.

Analysis of the circulation of hepatitis A virus in Argentina since vaccine introduction

Hepatitis A virus (HAV) has shown intermediate endemicity in Argentina, but its incidence has decreased since vaccine introduction in 2005. Environmental surveillance was conducted in five rivers from Argentina from 2005 to 2012, complementing clinical information. HAV detection decreased since 2005, although its circulation continues, maintaining viral diversity but not undergoing antigenic drift. Most sequences belonged to subgenotype IA, closely related to Argentinean clinical sequences, but one belonged to proposed subgenotype IC, previously undetected in the country. Environmental surveillance might contribute to monitoring the single-dose vaccination schedule, representing not only strains causing disease but also the circulating population and the viral introductions.