At present the origins of major human pathogens associated with hepatic disease are poorly understood. The absence of such information pertaining to the evolutionary history of hepatitis B virus (HBV) and hepatitis C virus (HCV) and its genetically related viruses impacts upon the development of vaccines and effective eradication strategies. Studies are currently limited by the absence of historical samples from which to date the emergence of human infections and therefore the evolution of human hepatic viruses relies on epidemiological studies and genetic analysis of contemporary virus populations worldwide. Approximately one third of the world’s population is infected with HBV, and despite the availability of a vaccine, the virus is attributed with over 1 million deaths per year through liver disease. HBV variants infecting humans show genetic and antigenic heterogeneity and are currently classified into 8 genotypes A-H with nucleotide divergence of between 9-13%. In addition to these variants, recombination has been detected between genotypes A and D, and B and C, which can generate novel variants. The past 10 years has seen the detection of HBV in chimpanzees, gorillas and other non-human primates (NHPs) at frequencies comparable to those observed in regions of endemic human HBV infection. Despite the genetic divergence between human and NHP HBV variants the detection of recombination between human genotype C and chimpanzee and gibbon variants suggests that HBV can share hosts in nature. The evolutionary process that may have given rise to the distinct species-specific variants of NHP HBV within overlapping geographical regions has not been reconciled, with evidence supporting both allopatric speciation and co-speciation. HCV a member of the Flaviviridae family currently infects approximately 3% of the world’s population and is one of the major causes of chronic liver disease, hepatocellular carcinoma and liver cirrhosis. Human pegivirus (HPgV) a member of the Pegivirus genus of the Flaviviridae family infects approximately 5% of the world’s population, although it is of unknown disease association. Very recently, several studies of wild rodent and bat populations have revealed much greater viral diversity of members of both Hepacivirus and Pegivirus genera. Homologues of HCV have been detected in a range of species including domestic dogs (canine hepacivirus [CHV]) and horses (non-primate hepaciviruses [NPHV]). Similarly, several new pegiviruses have been described in horses (equine pegivirus, [EPgV] and Theiler’s Disease Associated Virus [TDAV]), several species of rodents (rodent pegivirus [RPgV]), and further species of bats (bat pegivirus, [BPgV]). Despite the differences in pathogenicity between HCV and HPgV infections, they share similar genomic organisation and are capable of establishing persistent infections in humans. Studies into bat, horse and rodent homologs of HCV and HPgV have yet to determine disease associations, transmission routes and seroprevalence. Studies presented within this thesis broaden our understanding of the clinical presentations and host range of NPHV and EPgV. Screening to determine the level of active and past infection to both viruses provides novel insight into infection frequencies, host range, disease progression and examines the correlation between infections and the presence or absence of hepatic disease. Research examining HBV variants circulating in NHPs in Cameroon provides novel evidence for the occurrence of recombination and cross species transmission between NHP variants of HBV and examines the role these findings play in expanding our understanding of the evolution of HBV.

Human Pegivirus (HPgV; originally called GB virus C) is an RNA virus within the Pegivirus genus of the Flaviviridae that commonly causes persistent infection. Worldwide, approximately 750 million people are infected with HPgV. No causal association between HPgV and disease has been identified; however, several studies found an association between persistent HPgV infection and prolonged survival of HIV-infected individuals that appears to be related to a reduction in host immune activation. HPgV replicates well in vivo (>10 million genome copies/ml plasma) but grows poorly in vitro and systems to study this virus are limited. Consequently, mechanisms of viral persistence and host immune modulation remain poorly characterized, and the primary permissive cell type(s) has not yet been identified. The overall goals of my thesis were to characterize HPgV tropism, effects of HPgV infection on host immune response and mechanisms of viral persistence. Previous studies found HPgV RNA in T and B lymphocytes and ex vivo infected lymphocytes produce viral particles. To further characterize HPgV tropism, we quantified HPgV RNA in highly purified CD4+ and CD8+ T cells, including naïve, central memory, and effector memory populations, and in B cells (CD19+), NK cells (CD56+) cells and monocytes (CD14+) obtained from persistently infected humans using real time RT-PCR. Single genome sequencing was performed on virus within individual cell types to estimate genetic diversity among cell populations. HPgV RNA was present in CD4+ and CD8+ T lymphocytes (9 of 9 subjects), B lymphocytes (7 of 9), NK cells and monocytes (both 4 of 5). HPgV RNA levels were higher in naïve (CD45RA+) CD4+ cells than in central memory and effector memory cells (p<0.01). HPgV sequences were highly conserved between patients (0.117 ± 0.02 substitutions per site) and within subjects (0.006 ± 0.003 substitutions per site). The non-synonymous/synonymous substitution ratio was 0.07 suggesting low selective pressure. CFSE-labeled HPgV RNA-positive microvesicles (SEV) from serum delivered CFSE to uninfected monocytes, NK cells, T and B lymphocytes, and HPgV RNA was transferred to peripheral blood mononuclear cells (PBMCs) with evidence of subsequent viral replication. Thus, HPgV RNA-positive SEV may contribute to delivery of HPgV to PBMCs in vivo, explaining the apparent broad tropism of this persistent human RNA virus. Although HPgV infection reduces NK cell activation in HIV-infected individuals, the mechanism by which this occurs is not characterized. We studied HPgV effects on NK cell non-cytolytic function in HIV-infected people by measuring expression of IL-12 induced interferon gamma (IFNg) and cytolytic function by measuring K562 target-cell induced CD107a and granzyme B. IFNg expression was lower in HIV-HPgV co-infected subjects compared to HIV mono-infected subjects treated with combination antiretroviral therapy (p=0.02). In contrast, cytolytic NK cell functions were not affected by HPgV. Inhibition of IFNg was due to inhibition of tyrosine kinase (Tyk2) by HPgV envelope protein E2. HPgV positive human sera, extracellular vesicles containing E2 protein, recombinant E2 protein and synthetic E2 peptides containing a predicted Tyk2 interacting motif inhibited IL-12-mediated IFNg release by NK cells. Thus HPgV-E2 inhibits NK cell non-cytolytic functions. Inhibition of NK cell-induced proinflammatory/antiviral cytokines may contribute to both HPgV's ability to persist with high viral loads (>10 million genome copies/ml plasma) and reduce immune cell activation. Understanding mechanisms by which HPgV alters immune activation may contribute towards novel immunomodulatory therapies to treat HIV and inflammatory diseases.

O HPgV (Pegivirus Humano), conhecido anteriormente por GBV-C, causa infecção assintomática, persistente e com alta carga viral. Sendo o vírus de RNA sem patologia associada mais prevalente no mundo até os dias de hoje, os estudos in vitro ainda não foram capazes de mimetizar a replicação in vivo, permanecendo pouco esclarecidos vários aspectos de sua biologia. Estudos em macacos mostraram que os órgãos responsáveis pela maior replicação viral são o baço e a medula óssea, no entanto as células específicas permissíveis à infecção ainda não foram determinadas. Na década de 90, o HPgV ganhou notoriedade por diminuir os efeitos patológicos do HIV e aumentar a sobrevida de pacientes coinfectados HIV/HPgV, através da diminuição da ativação do sistema imune. Devido a essa característica, diversos estudos tentaram associar a presença de viremia a doenças hematológicas e um deles mostrou que a viremia de HPgV parece estar associada com o desenvolvimento de linfoma não- Hodgkin, porém muitas variáveis de confusão parecem influenciar esse resultado. Em conjunto, os dados mostram que o HPgV pode ter influência sobre a maturação e liberação de células progenitoras da medula óssea e, portanto, tornou-se primordial avaliar o impacto da viremia em pacientes com doenças hematológicas e definir o tropismo viral. Para tanto, o presente trabalho analisou a dinâmica de exposição à viremia de HPgV em pacientes submetidos ao transplante de células-tronco hematopoiéticas (HSCT), em cadáveres autopsiados pelo Sistema de Verificação de Óbitos da Capital de São Paulo (SVOC-SP) e em pacientes submetidos à cirurgia de artroplastia pelo Instituto de Ortopedia e Traumatologia (IOT) do HCSP. A carga viral de HPgV foi mensurada por qRT-PCR em Tempo Real levando em consideração valores adquiridos com um curva padrão desenvolvida para este trabalho. Para os pacientes HSCT, o efeito da presença de viremia antes e após o procedimento foi avaliada quanto aos principais desfechos do transplante: doença enxerto-hospedeiro aguda (aGVHD), recaída da doença hematológica primária e mortalidade. Para amostras SVOC e IOT, células específicas dos tecidos (cérebro, fígado, baço, linfonodo, medula óssea e sangue) foram avaliadas quanto à quantidade de RNA viral de polaridade positiva e negativa, a fim de quantificar a replicação e definir o tropismo do vírus. Os resultados mostraram que a prevalência de HPgV encontrada nos pacientes HSCT foi maior do que em estudos similares: 42% para as amostra pré- HSCT e 31% para as amostras pós-HSCT; porém, para as amostras SVOC, a prevalência foi menor do que o esperado: 1,2%. A presença de alta carga viral de HPgV em pacientes HSCT foi associada com aumento da taxa de incidência de aGVHD (95% CI 1,05-5,37, p=0,038). Dada a alta prevalência de HPgV na população brasileira, é essencial confirmar esse achado em outras coortes, de modo a determinar se o monitoramento do HPgV pode beneficiar o cuidado a esses pacientes. Nas amostras SVOC e IOT, a medula óssea apresentou maior número de populações celulares com replicação viral, com destaque para as células B progenitoras e para as células dendríticas. Porém, devido às condições da coleta e do processamento das amostras, o tipo celular permissível à infecção não pôde ser identificado com clareza, portanto fazendo-se necessária a coleta de um número maior de amostras SVOC / HPgV (Human Pegivirus), previously known as GBV-C, causes asymptomatic, persistent and high viral load infection. To date, it is the most prevalent RNA virus without associated pathologies in the world, yet in vitro studies have not yet been able to mimic the in vivo replication, consequently many aspects of its biology remaining unclear. Studies in non-humam primatas have shown that the organs responsible for the greatest viral replication are spleen and bone marrow, however the specific cells permissible for infection have not yet been determined. In the 1990s, HPgV gained notoriety by decreasing the pathological effects of HIV and increasing the survival of coinfected HIV/HPgV patients, by decreasing the activation of the immune system. Because of this characteristic, several studies have attempted to associate the presence of viremia with haematological diseases, and one has shown that HPgV appears to be associated with the development of non-Hodgkin\'s lymphoma, but many confounding variables still seems to influence this outcome. Together, the data show that HPgV may influence the maturation and release of bone marrow progenitor cells and therefore it has become crucial to evaluate the impact of HPgV viremia in patients with haematological diseases and to define viral tropism. Therefore, the present study analyzed the dynamics of HPgV viremia exposure in patients submitted to hematopoietic stem cell transplantation (HSCT), in cadavers autopsied by the São Paulo City Death Verification System (SVOC-SP) and in patients submitted to arthroplasty surgery by the Orthopedics and Traumatology Institute (IOT) of the Clinics Hospital of Sao Paulo. The HPgV was identified by real-time qRT-PCR and the viral load quantification was estimated by a standard curve developed for this work. For HSCT patients, the effect of viremia before and after the procedure was evaluated for the main transplant outcomes: acute graft vs host disease (aGVHD), relapse of primary haematological disease and mortality. For SVOC and IOT samples, tissue-specific cells (brain, liver, spleen, lymph node, bone marrow and blood) were evaluated for the amount of viral positive and negative RNA strains, in order to quantify replication and define virus tropism. The results showed that the prevalence of HPgV found in HSCT patients was higher than in similar studies: 42% for pre-HSCT samples and 31% for post-HSCT samples; however, for SVOC samples, the prevalence was lower than expected: 1.2%. The presence of high viral load of HPgV in HSCT patients was associated with an increase in the incidence rate of aGVHD (95% CI 1.05-5.37, p = 0.038). Given the high prevalence of HPgV in the Brazilian population, it is essential to confirm this finding in other cohorts, in order to determine if HPgV monitoring can improve the care of these patients. In the SVOC and IOT samples, the bone marrow presented a higher number of cell populations with viral replication, especially the progenitor B cells and the dendritic cells. However, due to the conditions of specimen collection and processing, the major permissible cell could not be clearly identified, thus making it necessary to collect a larger number of SVOC samples