title: Detection and characterization of hepatitis A virus circulating in Egypt.
abstract: 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.
authors.affiliation: Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt. hazem.hamzanrc@gmail.com.
authors.forename: Hazem
authors.initials: H
authors.lastname: Hamza
authors.affiliation: Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
authors.forename: Dina Nadeem
authors.initials: DN
authors.lastname: Abd-Elshafy
authors.affiliation: Department of Biochemistry, Faculty of Agriculture, Cairo University, Cairo, Egypt.
authors.forename: Sayed A
authors.initials: SA
authors.lastname: Fayed
authors.affiliation: Immune and Biomarkers for Infection Laboratory, The Center of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt.
authors.forename: Mahmoud Mohamed
authors.initials: MM
authors.lastname: Bahgat
authors.affiliation: Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
authors.forename: Nagwa Abass
authors.initials: NA
authors.lastname: El-Esnawy
authors.affiliation: Department of Biochemistry, Faculty of Agriculture, Cairo University, Cairo, Egypt.
authors.forename: Emam
authors.initials: E
authors.lastname: Abdel-Mobdy
mesh_terms: D000595:Amino Acid Sequence; D004534:Egypt / Q000453:epidemiology; D015967:Gene Expression Regulation, Viral / Q000502:physiology; D005838:Genotype; D006506:Hepatitis A / Q000453:epidemiology* / Q000821:virology*; D030041:Hepatitis A virus / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D015678:Viral Structural Proteins / Q000235:genetics / Q000378:metabolism; D062065:Wastewater / Q000821:virology; D014871:Water Microbiology
chemical_list: D012367:RNA, Viral; D015678:Viral Structural Proteins; D062065:Wastewater; C096539:VP1 protein, hepatitis A virus