Whole-genome sequencing of human Pegivirus variant from an Egyptian patient co-infected with hepatitis C virus: a case report

Abstract

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.

Persistent Human Pegivirus Infection across Two Pregnancies without Evidence of Vertical Transmission

“…Several genotypes of HPgV-1 have been identified world-wide by genome sequencing (3,6,12,50,51). HPgV-1 genotyping in our subject showed high homology to HPgV-1 genotype 2 and remained remarkably unchanged over the 4-year interval between the collections of samples.…”

“…HPgV has two structural proteins (E1 and E2), two predicted proteins of undetermined function (X and p* protein), and six non-structural (NS) proteins (1)(2)(3)(4). To date, seven genotypes of HPgV-1 (species Pegivirus C, formerly GBV-C) have been classified, along with many variants (1,5,6), which vary in their distribution across the globe.…”

A Case of Persistent Human Pegivirus Infection in Two Separate Pregnancies of a Woman

“…Several genotypes of HPgV-1 have been identified world-wide by genome sequencing [ 3 , 6 , 12 , 56 , 57 ]. HPgV-1 genotyping in our subject showed high homology to HPgV-1 genotype 2.…”

“…HPgV has two structural proteins (E1 and E2), two predicted proteins of undetermined function (X and p* protein), and six non-structural (NS) proteins [ 1 , 2 , 3 , 4 ]. To date, seven genotypes of HPgV-1 (species Pegivirus C , formerly GBV-C) have been classified, along with many variants [ 1 , 5 , 6 ], which vary in their distributions across the globe.…”

“…Antibodies directed toward the envelope HPgV glycoprotein E2, which is thought to be the immunodominant antigenic site, are detected as viremia is cleared [ 18 ]. While the pathogenicity of this virus remains unclear, HPgV-1 has a propensity to co-infect individuals with other viral infections, particularly human immunodeficiency virus (HIV) [ 19 , 20 ] and HCV [ 6 , 21 ]. HPgV interferes with the pathogenicity of HIV [ 22 ] and slows disease progression [ 7 , 9 , 19 , 23 , 24 ].…”