Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients.
Human pegivirus (HPgV), formerly 'GB virus C' or 'hepatitis G virus', is a member of the genus Flavivirus (Flaviviridae) that has garnered significant attention due to its inhibition of HIV, including slowing disease progression and prolonging survival in HIV-infected patients. Currently, there are six proposed HPgV genotypes that have roughly distinct geographical distributions. Genotypes 2 and 3 are the most comprehensively characterized, whereas those genotypes occurring on the African continent, where HPgV prevalence is highest, are less well studied. Using deep sequencing methods, we identified complete coding HPgV sequences in four of 28 patients (14.3%) in rural Uganda, east Africa. One of these sequences corresponds to genotype 1 and is the first complete genome of this genotype from east Africa. The remaining three sequences correspond to genotype 5, a genotype that was previously considered exclusively South African. All four positive samples were collected within a geographical area of less than 25 km(2), showing that multiple HPgV genotypes co-circulate in this area. Analysis of intra-host viral genetic diversity revealed that total single-nucleotide polymorphism frequency was approximately tenfold lower in HPgV than in hepatitis C virus. Finally, one patient was co-infected with HPgV and HIV, which, in combination with the high prevalence of HIV, suggests that this region would be a useful locale to study the interactions and co-evolution of these viruses.
Department of Biology, McGill University, Montreal, QC, Canada.
Ria R
RR
Ghai
Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Samuel D
SD
Sibley
Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
Michael
M
Lauck
Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Jorge M
JM
Dinis
Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
Adam L
AL
Bailey
Department of Anthropology and McGill School of Environment, Montreal, QC, Canada, and Wildlife Conservation Society, NY, USA.
Colin A
CA
Chapman
Makerere University Biological Field Station, Fort Portal, Uganda.
Patrick
P
Omeja
Wisconsin National Primate Research Center, Madison, WI, USA.|Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Thomas C
TC
Friedrich
School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.|Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
David H
DH
O'Connor
Wisconsin National Primate Research Center, Madison, WI, USA.|Makerere University Biological Field Station, Fort Portal, Uganda.|Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Tony L
TL
Goldberg
D000293:Adolescent; D000328:Adult; D000818:Animals; D005260:Female; D018178:Flaviviridae Infections / Q000453:epidemiology* / Q000821:virology; D029407:GB virus C / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D015658:HIV Infections / Q000150:complications / Q000453:epidemiology / Q000821:virology; D006525:Hepatitis, Viral, Human / Q000453:epidemiology* / Q000821:virology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D012424:Rural Population / Q000706:statistics & numerical data*; D017422:Sequence Analysis, DNA; D014454:Uganda / Q000453:epidemiology; D055815:Young Adult