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BackgroundHuman pegivirus (HPgV) is structurally similar to hepatitis C virus (HCV) and was discovered 20 years ago. Its distribution, natural history and exact rule of this viral group in human hosts remain unclear. Our aim was to determine, by deep next-generation sequencing (NGS), the entire genome sequence of HPgV that was discovered in an Egyptian patient while analyzing HCV sequence from the same patient. We also inspected whether the co-infection of HCV and HPgV will affect the patient response to HCV viral treatment. To the best of our knowledge, this is the first report for a newly isolated HPgV in an Egyptian patient who is co-infected with HCV.Case presentationThe deep Next Generation Sequencing (NGS) technique was used to detect HCV sequence in hepatitis C patient’s plasma. The results revealed the presence of HPgV with HCV. This co-infection was confirmed using conventional PCR of the HPgV 5′ untranslated region. The patient was then subjected to direct-acting-antiviral treatment (DAA). At the end of the treatment, the patient showed a good response to the HCV treatment (i.e., no HCV-RNA was detected in the plasma), while the HPgV-RNA was still detected. Sequence alignment and phylogenetic analyses demonstrated that the detected HPgV was a novel isolate and was not previously published.ConclusionWe report a new variant of HPgV in a patient suffering from hepatitis C viral infection.

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Background: The new classification of Head and Neck Squamous Cell Carcinoma (HNSCC) according to their association with human papillomavirus (HPV) infection into HPV positive tumors with good prognosis and HPV negative tumors with poor prognosis has changed the treatment strategy of HNSCCs dramatically worldwide. However, data concerning HPV infection in HNSCCs patients is still limited and there are no studies regarding HPV genotypes in HNSCC among Egyptians. Therefore, the aim of the current study is to investigate the frequency of HPV and to detect the most prevalent HPV genotypes in the patients with oral cavity and oropharyngeal carcinoma from EgyptMethods: This cross sectional study was conducted from January 2016 to November 2017. Ninety-two oral brushing samples (76 oral cavity and 16 oropharynx) were collected by cytobrushing in CYTO-fast solution. HPV-DNA was subjected to two methods which are the: (1) HPV Direct Flow CHIP system for automatic detection and genotyping (2) conventional PCR for detection of HPV using consensus primers (MYO9/MYO11). SPSS software was used for statistical analysis.Results: Out of the 92 cases assessed, HPV DNA was present in three samples only (3/92; 3.3%) and the HPV66 genotype was the only genotype detected by HPV Direct Flow CHIP System.Conclusion: The Results of this study may (1) indicate that the HPV-associated HNSCC among Egyptian patients is very low and (2) highlight the presence of HPV66 genotype in these malignancies. Other studies from other countries in general and from different governorates in Egypt are still needed to determine the exact frequency of HPV infections in head and neck cancer.

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