title: A novel primer set for improved direct gene sequencing of human bocavirus genotype-1 from clinical samples.
abstract: Human bocavirus genotype (HBoV-1) is a parvovirus associated with respiratory tract infections in children with different degrees of severity. The current study intended to improve the direct gene sequencing of the HBoV-1 using a newly developed primer set. Screening the presence of human bocavirus infection among in-patients children suffering from lower respiratory tract infections was another aim of the current study. Nasopharyngeal swab samples from in-patients children suffering from lower respiratory tract infections were examined. The real-time polymerase chain reaction was used for the initial screening as a highly sensitive method to detect the HBoV. Genotyping of real-time positive samples was attempted by direct sequencing of PCR amplicons using NP, VP1/2 and the newly developed VP/NC primers. HBoV-1 was present in 56.8% of the examined children. The newly developed primer set successfully amplified all real-time PCR positive samples, however, the other primer pairs did not reliably detect real-time PCR positive samples. The gene sequences of the detected HBoV-1 showed conserved sequences to each other with a low rate of discrepancies. The high rate of infection and the similarity between the detected strains strongly suggest nosocomial infections.
authors.affiliation: Microbiology Department, College of Medicine, Taif University, Al-Taif 21944, Saudi Arabia; Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt. Electronic address: asa@tu.edu.sa.
authors.forename: Ahmed S
authors.initials: AS
authors.lastname: Abdel-Moneim
authors.affiliation: Clinical Pathology Department, National Cancer Institute, Cairo University, Giza, Egypt.
authors.forename: Mahmoud M
authors.initials: MM
authors.lastname: Kamel
authors.affiliation: Department of Paediatrics, Faculty of Medicine, Cairo University, Giza, Egypt.
authors.forename: Dina H
authors.initials: DH
authors.lastname: Hamed
authors.affiliation: Clinical Pathology Department, National Cancer Institute, Cairo University, Giza, Egypt.
authors.forename: Safaa S
authors.initials: SS
authors.lastname: Hassan
authors.affiliation: Clinical Pathology Department, Faculty of Medicine, Cairo University, Giza, Egypt.
authors.forename: May S
authors.initials: MS
authors.lastname: Soliman
authors.affiliation: Zoology Department, College of Science, King Saud University, Saudi Arabia, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
authors.forename: Saleh A
authors.initials: SA
authors.lastname: Al-Quraishy
authors.affiliation: Clinical Pathology Department, Faculty of Medicine, Cairo University, Giza, Egypt.
authors.forename: Amani A
authors.initials: AA
authors.lastname: El Kholy
mesh_terms: D002675:Child, Preschool; D003428:Cross Infection / Q000821:virology; D017931:DNA Primers; D004534:Egypt; D005260:Female; D005838:Genotype; D056661:Human bocavirus / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007223:Infant; D008297:Male; D009305:Nasopharynx / Q000821:virology; D010322:Parvoviridae Infections / Q000821:virology*; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D012141:Respiratory Tract Infections / Q000821:virology; D017422:Sequence Analysis, DNA / Q000379:methods; D019562:Viral Load
chemical_list: D017931:DNA Primers
keywords: Egypt; Genotyping; Human bocavirus; Nosocomial infection; Respiratory tract infection in children