Hepatitis C virus subtypes circulating among intravenous drug users in Lisbon, Portugal.

Hepatitis C virus (HCV) infects 2-3% of the world population and intravenous drug consumption is the leading cause of transmission in industrialized countries. The unavailability of data on the molecular epidemiology of HCV infection in Portugal prompted the study of HCV subtypes circulating among intravenous drug users residing in the Lisbon metropolitan area and sampled about 10 years apart (1998-2000 and 2008-2009). Partial coding sequences for E1 and/or NS5B were obtained from 124 individuals with HCV viremia, both mono-infected and co-infected with HIV.

Natural polymorphisms of HIV type 2 pol sequences from drug-naive individuals.

Until today, the susceptibility of human immunodeficiency virus type 2 (HIV-2) to protease and nucleosidic reverse-transcriptase inhibitors (PI and NRTI, respectively) has not been clearly documented. In this report we studied HIV-2 proviral sequences (n = 30) from drug-naive patients. Our results revealed that several amino acid positions in the protease and reverse transcriptase coding sequence harbored residues that have been associated with drug resistance in HIV-1-infected patients.

Genetic characterization of human immunodeficiency virus type 1 from Beira, Mozambique.

In this report, we examined the genetic diversity of HIV-1 strains circulating in the city of Beira, the second largest metropolitan area in Mozambique. A total of 131 blood samples, collected between August and October 2003 from antiretroviral-naïve individuals, were characterized with a combined approach consisting of heteroduplex mobility assay (HMA) subtyping for gag (n=74) and/or env (n=117) genes, and DNA sequence analysis of proviral env (C2V3C3, n=52), LTR (n=30) and/or pol (n=43) genomic regions. Aside from the identification, by bootscanning analysis, of a viral strain with a C/A1 mosaic C2V3C3 structure, classified as subtype A by env HMA, phylogenetic inference studies of the sequence data demonstrated the circulation of genetically diverse subtype C viruses, predominantly of the R5 type.

Genetic analysis of human immunodeficiency virus type 1 nef in Portugal: subtyping, identification of mosaic genes, and amino acid sequence variability.

Extending our previous genetic characterization of human immunodeficiency virus type 1 (HIV-1) strains circulating in Portugal, we here report the first phylogenetic and putative amino acid sequence variability analyses of nef accessory gene. Viral sequences (n = 53) were amplified by nested PCR from proviral DNA purified from peripheral blood mononuclear cells of HIV-1 infected individuals (n = 49). Phylogenetic inference analysis demonstrated a distribution of the viral sequences between subtypes A (sub-subtype A1), B, D, F (sub-subtype F1), G, H, and J, with subtypes G and B accounting altogether for more than half of the genotypes found.

Prevalence and partial characterization of genotypes of the human TT virus infecting Portuguese individuals.

The prevalence and genotype distribution of human TT viruses (TTV) were analyzed in 312 Portuguese individuals. Detection of TTV DNA was carried out by polymerase chain reaction (PCR) through the combined use of N22 and UTR-specific primers and revealed a prevalence of infection of 74%. Detection of TTV DNA was not statistically associated to the use of intravenous drugs, infection with HBV, HCV, HIV-1, HIV-1 viral load or CD4 cell count (in HIV-1 infected individuals).

Spreading of HIV-1 subtype G and envB/gagG recombinant strains among injecting drug users in Lisbon, Portugal.

We have evaluated the genetic diversity of HIV-1 strains infecting injecting drug users (IDUs) in Lisbon, Portugal. Heteroduplex mobility assay and/or phylogenetic analysis revealed that env (C2V3C3 or gp41) subtype B is present in 63.7% of the 135 viral samples studied, followed by subtypes G (23.

Molecular epidemiology of HIV type 1 infection in Portugal: high prevalence of non-B subtypes.

In this study, we have investigated the diversity of current HIV-1 strains circulating in the metropolitan area of Lisbon, Portugal. A total of 217 HIV-1-positive blood samples, collected between October 1998 and December 2000, was genetically characterized in the gp120 C2V3C3 region (n = 205) or part of the gp41 N-terminal segment (n = 12) by heteroduplex mobility assay (HMA) and/or DNA sequencing. The HMA subtyping efficiency (number of samples unambiguously subtyped by HMA divided by the total number of samples subtyped) was 65.