HLA-G 3'-UTR SNP and 14-bp deletion polymorphisms in Portuguese and Guinea-Bissau populations

In the HLA-G locus, the 3'-untranslated region (3'-UTR) begins in the mid exon 6, and ends in exon 8. The occurrence of a 14-bp deletion within exon 8, the only mutation known until now in the 3'-UTR, has been considered a risk factor for disease and allograft rejection. To describe the polymorphism within this region, direct sequencing analysis was performed on 120 DNA samples from Portugal and Guinea-Bissau. Results indicate that exon 8 is less conserved than the coding exons. Nine single nucleotide polymorphisms and the previously described 14-bp deletion were found within exon 8 of both populations. Molecular diversity was higher in the Guinean samples than in the Portuguese; however, little differentiation was found among the populations, suggesting that local selection on exon 8 sequence variation is absent. The screening for sequence motifs suggests that polymorphism on this region may be involved in HLA-G post-transcriptional regulation and, therefore, in phenotype variation.

Two Distinct Introductions of the West Nile Virus in Portugal Disclosed by Phylogenetic Analysis of Genomic Sequences

In this report, we describe genomic sequencing and analysis of different West Nile virus strains isolated from mosquitoes in the south of Portugal (Alentejo and Algarve) at two different time points (1971 and 2004, respectively). Phylogenetic analysis indicated different origins for the two recorded introductions of WNV in our country, with strains segregating in different sub-clades within lineage 1a. PTRoxo (isolated in 1971) was found to be very similar to an Egyptian WNV strain isolated in 1951, while the viruses isolated in 2004 formed a statistically well-supported group with WNV strains isolated over the last decade in countries lining the Mediterranean (Morocco, Italy, and France). Analyses of the putative amino acid sequences showed all the main expected features described for viral mature proteins except for the absence of the N-glycosylation site in the envelope glycoprotein of PTRoxo, which may be reflected as attenuated neurovirulence and neuroinvasive phenotypes.

Genetic analysis of HIV type 2 from Ghana and Guinea-Bissau, West Africa

The phylogenetic variability of part of the long terminal repeat (LTR) region of HIV-2 strains isolated in 1995 from five individuals residing in Bissau, the capital city of Guinea-Bissau, and collected from seven persons from Kumasi, Ghana in 1996-1997, was analyzed. All Guinean samples and all but one Ghanaian sample clustered with HIV-2 subtype A. One Ghanaian sample (14%) was classified as HIV-2 subtype B. This study adds to previous reports on HIV-2 subtype distribution in West Africa indicating local prevalence of HIV-2 subtype B in Ivory Coast and neighboring Ghana.

Follow-up study of intrahost HIV type 2 variability reveals discontinuous evolution of C2V3 sequences

Sequence change dynamics in the highly polymorphic C2V3 region of the envelope glycoprotein gp105 coding sequence of HIV-2 was studied for two HIV-2 seropositive Guinean individuals over a 5-year period. Proviral DNA was amplified by PCR from uncultured peripheral blood mononuclear cells (PBMC), cloned, and sequenced. Amino acid sequence alignment and phylogenetic analysis showed distinct viral populations for the three collected samples (1992, 1995, and 1997) for both individuals. A discontinuous replacement of sequences suggests activation of latent viruses present in reservoirs, a process that has been documented for the HIV-1 infection but unreported so far for HIV-2. The nucleotide sequences presented in this work have been assigned accession numbers AJ400276 to AJ400319.

Longstanding presence of HIV-2 infection in Guinea-Bissau (West Africa)

We have retrospectively studied the seroprevalence of the human immunodeficiency virus (HIV) in Guinea-Bissau in a sample of sera collected from the whole country in 1980. We tested a total of 1248 individuals and found 11 individuals who were seropositive for HIV-2 but there were no HIV-1 seropositive samples. The mean age of the HIV-2 seropositive people was significantly higher than the age of the seronegative individuals. In the different areas surveyed, the HIV-2 seroprevalence ranged from 0 to 2.5%. A central region of the country, grossly centred in the capital city of Bissau, presented the highest prevalence of HIV-2 seropositivity (>2%), which contrasts with its virtual absence from the more remote rural areas located near the borders with the neighbouring countries. The overall seroprevalence found for HIV-2 in this study is 0.9% (1.8%, when considering the adult seroprevalence only), which proves that the virus was definitely circulating in Guinea-Bissau at the beginning of the 1980s.

Genetic variability of human immunodeficiency virus type 2 C2V3 region within and between individuals from Bissau, Guinea-Bissau, West Africa

The V3 loop of both HIV-1 and HIV-2 is characterized by a high degree of genetic variation. To investigate the spectrum of HIV-2 variability in nature we have focused on the C2V3 region of Env and analyzed 108 viral sequences obtained from uncultured peripheral blood mononuclear cells obtained from 16 HIV-2-seropositive individuals from Bissau (Guinea-Bissau). The estimated values of genetic divergence between individuals were higher than those calculated from sequence information collected in a single individual. We have also found that the sequences surrounding the V3 loop contribute significantly to the overall genetic diversity of the C2V3 region of HIV-2 gp105, while the V3 loop itself seems to be rather conserved. Phylogenetic analysis demonstrated that all the individuals enrolled in this study were infected with HIV-2 subtype A viruses.

Genetic characterization of HIV type 1 and type 2 from Bissau, Guinea-Bissau (West Africa)

Previous studies from Guinea-Bissau (West Africa) have demonstrated a unique epidemiology with respect to both HIV-1 and HIV-2 infection. In order to evaluate the prevalence and dynamics of HIV-1 and HIV-2 subtypes in Bissau, the capital city of Guinea-Bissau, a cross-sectional study was set up using serological and molecular techniques. Plasma samples from 103 individuals were screened for HIV-1 and HIV-2 antibodies by ELISA and Western-blot. Seropositive results were confirmed by PCR amplification of proviral sequences in primary peripheral blood mononuclear cells (PBMC) with env and LTR primer sets for HIV-2 and env, LTR and pol primers for HIV-1. A total of 38/103 individuals were HIV-seroreactive (four HIV-1, 15 HIV-2, 19 HIV-1/HIV-2). A total of eight out of 19 dually seropositive specimens showed double PCR amplification of HIV-1 and HIV-2 proviral sequences, accounting for 21% of the infected individuals. In the remaining 11 individuals either HIV-2 or HIV-1 sequences were detected, the majority (n=9) amplifying only HIV-2. These screening data demonstrate a high discrepancy between serology and PCR results for dually seroreactive samples, Western-blot giving an overestimation of double infection. Additionally, HIV-1 strains were subtyped by heteroduplex mobility assay (HMA) on the basis of gp120 sequences. Subtyping of HIV-2 was carried out by DNA sequencing and phylogenetic analysis of env V3 molecular clones. For both HIV-1 and HIV-2 strains circulating in Bissau, our results indicate dominance of subtype A.

Improved detection of HIV-2 proviral DNA in dually seroreactive individuals by PCR

OBJECTIVE

To improve the detection rate of HIV-2 proviral DNA in primary uncultured peripheral blood mononuclear cells (PBMC) of HIV-2-seroreactive and HIV-1-HIV-2 dually seroreactive individuals.

MATERIALS AND METHODS

Two newly designed HIV-2 PCR primer pairs in the long terminal repeat (LTR) gag and gag-pol regions and a previously described env and LTR HIV-2 PCR primer pairs were tested on samples from 66 confirmed HIV-2-seropositive individuals (The Gambia, 40; Côte d'Ivoire, 17; Guinea-Bissau, nine), 209 dually seroreactive individuals (The Gambia, 82; Côte d'Ivoire, 127), 24 genetically characterized isolated HIV-1 strains (group M subtypes A-H and group O), one simian immunodeficiency virus (SIV) strain cpz, 10 HIV-2 isolates (subtype A, B and unidentified), two SIVsm isolates, and 10 seronegative samples.

RESULTS

All HIV-2 primers evaluated showed 100% specificity since there was no amplification observed with 24 HIV-1, one SIVcpz and 10 seronegative samples. One single copy of the HIV-2 genome could be detected with all outer primer pairs as well as all inner primer pairs on one PCR round used. Sensitivity of primers (at least one of the four primer pairs was positive) to HIV-2-seropositive samples was 100% (all nine) in Guinea-Bissau, 71% (12/17) in Côte d'Ivoire, 100% (all 20) in Gambian AIDS patients, and 85% (17/20) in Gambian pregnant women. Doubling the PBMC of dually seroreactive individuals from 7.5 x 10(4) to 1.5 x 10(5) in the PCR revealed the presence of both HIV-1 and 2 proviral DNA in 72% (92/127) in Côte d'Ivoire and 72% (59/82) in The Gambia. By doubling the number of PBMC, HIV-2 detection in dually seroreactive individuals by PCR was increased from 65 to 77% in Côte d'Ivoire and from 67 to 83% in The Gambia.

CONCLUSIONS

The use of 1.5 x 10(5) primary uncultured PBMC and the newly designed HIV-2 primer pairs allowed us to document the highest percentage (72%) ever reported of HIV-1-HIV-2 dual infections amongst HIV-1-HIV-2 dually seroreactive individuals in Côte d'Ivoire and The Gambia. Improved detection of HIV-2 proviral DNA, rather than exposure to both viruses, infection with only one virus, or infection with a unique third virus containing epitopes common to both HIV-1 and HIV-2, contributes to a more accurate monitoring of the prevalence of HIV-1-HIV-2 dual infections.

Active replication of hepatitis B virus (HBV) in HIV type 1 and in HIV type 2 infected patients

To evaluate the effect of concurrent infection by HIV on HBV infection or immunity, we have studied a group of 66 HIV1+ symptomatic Caucasian patients and another of 38 African HIV2+ asymptomatic individuals, concerning their HBV status: serological markers of infection and presence of HBV-DNA in serum, the last taken as sign of hepatitis B virus active replication, were monitored. HIV+ groups were compared with seronegative controls, adequately matched for age, sex and ethnological background. HBV DNA was found in 7.6% of HIV1+ Caucasian patients and 3.2% of seronegative controls; in African HIV2+ individuals 2.6% were also HBV DNA+, a percentage close to that found in HIV2 seronegative controls (2.9%). No correlation was found between HIV infection and HBV active replication. Immunodepression that follows HIV infection over time may be compatible with a degree of T cell function capable of avoiding reinfection with or reactivation of HBV, even in symptomatic stages of acquired immunodeficiency syndrome. Our findings are relevant to the choice of preventive strategies in populations at risk for HIV and HBV infection.

Construction and characterization of an absolute deletion mutant of Escherichia coli ribonuclease II

The degradation of mRNA plays a central role in the control of protein synthesis. In Escherichia coli, the rnb gene encodes ribonuclease II (RNase II), one of the two main exonucleases involved in mRNA decay. We have constructed strain CMA201, in which the rnb promoter region and the gene were deleted from the chromosome and replaced by a tetr cassette. This is the first rnb absolute deletion mutant that shows the complete absence of rnb-specific mRNA. This strain has growth characteristics similar to the wild-type, even though it has no RNase II activity, and it should be useful in studies of mRNA metabolism.