HIV-1 subtypes in Denmark.

The objective of this study was to investigate the presence of non-subtype B HIV-1 in Denmark. The C2-V3-C3 region of the env gene from proviral DNA obtained from patients suspected of being infected with non-subtype B virus was PCR-amplified and directly sequenced. The DNA sequences were aligned with full-length HIV-1 reference strains from each subtype and analysed using the phylogenetic package PHYLIP 3.1. The neighbour-joining method was used with 100 bootstraps. Of the 144 patients included in this study C2-V3-C3 sequences were obtained from 129 patients (90%). The phylogenetic analyses showed that virus from 49 patients (38%) was subtype A, 39 (30%) subtype C, 9 (7%) subtype D, 14 (11%) subtype CRF01_AE, 16 (12%) subtype B, 1 (1%) subtype F and 1 (1%) subtype J. This study demonstrates that almost all subtypes can be detected in Denmark; all non-subtype B infections could be traced to countries with a high prevalence of non-subtype B virus.

Molecular investigation of transmission of human immunodeficiency virus type 1 in a criminal case.

Very few criminal cases involving human immunodeficiency virus type 1 (HIV-1) transmission have been described. We report on an HIV-1 transmission case with a child being infected by an HIV-1-positive man. The objective was to determine through molecular epidemiology and phylogenetic analyses whether HIV-1 from the HIV-1-positive man could be the source of infection in the HIV-1-positive child, as claimed by the authorities. We conducted genetic analysis of three different parts of the HIV-1 genome (gag, pol, and env) by PCR, direct-sequencing, and phylogenetic analyses. We used maximum likelihood, maximum parsimony, and neighbor-joining methods for the phylogenetic analyses to investigate whether the sequences from the man and the child were related. We found that the viral sequences from the man and the child formed separate clusters in all of the phylogenetic analyses compared to the local controls. A unique amino acid deletion was identified in the C2-V3-C3 region of the env gene in the virus from the man and the child. These results were used in the criminal court to elucidate whether the virus from the man was related to the virus from the child. In summary, the results from the phylogenetic analyses, the sequence distances between the virus from the man and the virus from the child, and the identification of the unique molecular fingerprint in the env gene together indicated that the virus from the man and the virus from the child were epidemiologically linked.

Subtype-specific problems with qualitative Amplicor HIV-1 DNA PCR test.

BACKGROUND: commercial HIV-1 qualitative DNA PCR tests have the potential to detect virus in patients in whom antibody tests may be ineffective, such as patients with primary HIV infection and infants born to HIV seropositive mothers. However, the genetic diversity of HIV-1 raises concern about the ability of the PCR tests to detect all current subtypes. OBJECTIVES: to asses the sensitivity of the Amplicor HIV-1 test on 126 whole-blood samples representing seven different subtypes and to investigate the sensitivity when the standard assay was modified by including the primer pair SK145 and SKCC1B. RESULTS: of the 126 HIV-1 infected persons, 113 were tested positive and 13 were DNA PCR negative. On the basis of these results, the standard Amplicor HIV-1 test had a sensitivity of 90% in our cohort. In addition, 9% of the positive samples showed a low reactivity but above the cut-off of the assay. The standard assay yielded sensitivities of 100% for subtype B (n=16), D (n=9) and G (n=1), but only 83% for subtype A (n=41), 98% for subtype C (n=43), 79% for subtype E (n=14) and 0% for subtype F (n=2). All samples with low reactivity were non-B subtype. Eight of the DNA PCR negative samples, four subtype A, one C and three E were amplified with the modified Amplicor HIV-1 test with addition of SK145/SKCC1B primers. Using this modified protocol, six samples out of eight became positive. However, two samples (one A and one C) remained DNA PCR negative. CONCLUSION: this study confirms that the Amplicor HIV-1 test does not detect all subtypes with equivalent sensitivity and 10% of the samples, tested negative. Thus, it is preferable to add the SK145/SKCC1B primers to the standard test, where infection with non-B subtype is suspected.

No association of HIV-1 envelope (C2-V3-C3) sequence pattern with long-term nonprogression.

We previously identified a group of 10 long-term nonprogressors (LTNP) with HIV-1 infection. In this study, we have sequenced the envelope gene (C2-V3-C3) from the 10 LTNPs and from a control group of 9 people with rapidly progressing infection (RPI). The 19 individuals' CCR5 genotype and virus phenotype (i.e., syncytium-inducing/non-syncytium-inducing [SI/NSI]) were obtained from a previous study. A phylogenetic tree was constructed containing the 19 envelope sequences together with 42 local control env sequences obtained from other studies. Analysis of the phylogenetic tree did not reveal any relation between the envelope gene (C2-V3-C3) from LTNPs versus RPIs. When data from the CCR5 genotype and the virus phenotype were assembled in the phylogenetic tree, no significant clustering was observed. From alignment of the protein sequences, we found a possible N-glycan in position aa294 in env that was conserved in only 1 of 10 LTNPs; however, it was conserved in 6 of 9 RPIs. Our study could not demonstrate any association between LTNPs and the sequenced envelope gene segment (C2-V3-C3). This lack of association could be due to the relatively small sample size of the data set. Nor did we find any relation between the CCR5 genotype or the SI/NSI phenotype with the sequenced envelope genes from the 19 participants. The possible N-glycan position we have described is an interesting observation that may require further investigation.

Nosocomial HIV-transmission in an outpatient clinic detected by epidemiological and phylogenetic analyses.

OBJECTIVE: To determine if a case of HIV-infection in a patient (GP) with common variable immunodeficiency, and with no known risk factors for HIV-infection, could be due to horizontal nosocomial transmission. METHODS: For determination of time of transmission stored serum-samples from GP were analysed for HIV RNA content. Patient records were used to identify patients, who had received intravenous therapy on the same day as GP. Samples from GP and these possible source patients were identified and phylogenetic analyses of the env, gag and RT-encoding region of pol were performed. Furthermore, routines in conjunction with intravenous therapy were examined. RESULTS: We identified a patient (FDL) harbouring virus almost indistinguishable from the virus isolated from GP. The pairwise nucleotide distance between the C2-V3-C3 region of the env and gag sequences from the two patients were 1.9 and 0.9% respectively. In addition, GP harboured HIV RNA with a foscarnet resistance mutation further lending support to virus from the foscarnet-treated FDL being the source of the infection. Interestingly, GP experienced increases in immunoglobulin production after contracting the HIV-infection, and decreases after antiretroviral-induced viral suppression. A clinical procedure which, under stressful conditions, could lead to breaches in infection control measures was identified. The source of the infection was most likely a contaminated multidose vial. CONCLUSION: Through epidemiological and phylogenetic analyses a case of horizontal nosocomial HIV-transmission was disclosed. Identification of multidose vials as possible vehicles for horizontal nosocomial transmission recently led to the recommendation of restriction of the use of multidose vials, a recommendation supported by the present study. The study underlies the importance of a constant survey of infection control precautions.

Transmission of a minor variant of transcriptionally active HIV-1.

We investigated the genotypic variation of pro-viral human immunodeficiency virus type 1 (HIV-1) DNA in a virus donor-recipient pair by comparing sequences from the HIV-1 V3 region of the gp120 gene and the p17gag gene. We found that the transmitted virus was a minor variant in the donor's virus population in blood. Possible selection mechanisms within the host (neutralization by antibodies) were studied in order to investigate whether antibodies could explain the conserved HIV genotype found in the recipient. In conclusion, our data indicate that a minor variant of pro-viral transcriptionally active HIV-1 found in PBMC was transmitted from donor to recipient. Development of a homogeneous genotype regarding the V3 region (V3d-B1(1)) of pro-viral DNA in the recipient's PBMC and a partially homogeneous genotype regarding the HIV-RNA was possibly caused by an envelope associated selection that is not dependent upon neutralizing antibodies.

Comparisons of DNA-mediated immunization procedures directed against surface glycoproteins of human immunodeficiency virus type-1 and hepatitis B virus.

DNA vaccination methods were compared to examine the in vivo expression of HIV-1 gp160 and beta-galactosidase, and the resulting immune response. Beta-galactosidase plasmid showed expression rates of 2-5% of muscle fibers with or without pretreatments using bupivacaine or cardiotoxin facilitators 1 or 5 days earlier, respectively. In contrast, HIV gp160 expression was lower in untreated or bupivacaine-treated muscles, but was improved by pretreatment with cardiotoxin. Equal expression of beta-galactosidase and HIV gp160 was obtained using gene gun delivery to the epidermis. Unlike the i.m. in situ expression of gp160, the anti-HIV antibody response did not improve after muscle pretreatments but depended on the vaccination intervals. Gene gun delivery of pMN160 also resulted in a slow and low titered antibody response. In contrast, a single i.m. injection of plasmid encoding another viral envelope, HBsAg, resulted in earlier seroconversion to high titers without the need for pretreatments or boostings. Intradermal inoculation by gene gun using 100-fold less DNA resulted in the same anti-HBsAg antibody profile only after boostings. In contrast to the differences in antibody responses, a specific CTL response was obtained in all cases. Bupivacaine-treated muscles showed an extreme degree of edema with disruption of connective tissue (endo- and mesomysium) and was not well tolerated (4 of 19 mice died). Cardiotoxin created muscle necrosis and occasional (2 of 20 mice) development of fibrotic muscles. It is concluded that in vivo expression cannot be properly predicted using reporter gene experiments and that the resulting immune response does not follow directly with the expression rate. It is suggested that the antibody response may depend primarily on the nature of the antigen expressed rather than the DNA vaccination method. It is proposed that gene gun or i.m. injection be used without pretreatment in the case of DNA vaccination with plasmid encoding HIV MN gp160.

Chemokine receptor polymorphism and autologous neutralizing antibody response in long-term HIV-1 infection.

We have previously reported that slowly progressing HIV infection (SPI) was associated with the presence of contemporaneous autologous neutralizing antibodies. In contrast, a group of individuals with more rapidly progressing infection (RPI) generally lacked these antibodies. To understand the importance of autologous neutralizing antibodies in SPI more fully, we have now conducted a prospective study taking consecutive blood samples from the individuals with SPI (8 patients) and RPI (10 patients). Blood sampling in the group with SPI was done 110 and 123 months after the estimated seroconversion and at similar time points in the group with RPI. Virus isolation was attempted at both time points in both groups of individuals; crossed neutralization assays were set up with autologous virus. These confirmed our previous finding of significant autologous neutralizing titers in the group with SPI (geometric mean titer [GMT] 8.7 versus 1.6 in SPI and RPI, respectively; p = 0.0048). However, not all individuals with SPI possessed autologous neutralizing antibodies, indicating that other factors may be decisive for SPI. Furthermore, neutralizing antibody titers did not increase from early to late serum samples. Finally, late virus isolates from individuals with SPI generally remained sensitive to neutralization by early serum samples. Virus phenotype (SI/NSI) and CCR5 genotype was determined for all individuals. Neither showed significant correlation with SPI. However, all SPI individuals who were heterozygous for the CCR5 deletion were infected with virus of NSI phenotype. In contrast, all RPI individuals who were heterozygous for the CCR5 deletion were infected with virus of SI phenotype (p = .028). Thus, a beneficial effect of having a partly nonfunctional CCR5 coreceptor may depend on the viral SI/NSI phenotype.

Improved humoral and cellular immune responses against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the hepatitis B surface antigen.

The gp120-derived V3 loop of HIV-1 is involved in co-receptor interaction, it guides cell tropism, and contains an epitope for antibody neutralization. Thus, HIV-1 V3 is an attractive vaccine candidate. The V3 of the MN strain (MN V3) contains both B- and T-cell epitopes, including a known mouse H-2d-restricted cytotoxic T lymphocyte (CTL) epitope. In an attempt to improve the immunogenicity of V3 in DNA vaccines, a plasmid expressing MN V3 as a fusion protein with the highly immunogenic middle (pre-S2 + S) surface antigen of hepatitis B virus (HBsAg) was constructed. Epidermal inoculation by gene gun was used for genetic immunization in a mouse model. Antibody and CTL responses to MN V3 and HBsAg were measured and compared with the immune responses obtained after vaccination with plasmids encoding the complete HIV-1 MN gp160 and HBsAg (pre-S2 + S), respectively. DNA vaccination with the HIV MN gp160 envelope plasmid induced a slow and low titred anti-MN V3 antibody response at 12 weeks post-inoculation (p.i.) and a late appearing (7 weeks), weak and variable CTL response. In contrast, DNA vaccination with the HBsAg-encoding plasmid induced a rapid and high titred anti-HBsAg antibody response and a uniform strong anti-HBs CTL response already 1 week p.i. in all mice. DNA vaccination with the chimeric MN V3/HBsAg plasmid elicited humoral responses against both viruses within 3-6 weeks which peaked at 6-12 weeks and remained stable for at least 25 weeks. In addition, specific CTL responses were induced in all mice against both MN V3 and HBsAg already within the first 3 weeks, lasting at least 11 weeks. Thus, HBsAg acts as a 'genetic vaccine adjuvant' augmenting and accelerating the cellular and humoral immune response against the inserted MN V3 loop. Such chimeric HIV-HBsAg plasmid constructs may be useful in DNA immunizations as a 'carrier' of protein regions or minimal epitopes which are less exposed or poorly immunogenic.

Applications of vector fields to image processing.

We use rotational and curvature properties of vector fields to identify critical features of an image. Using vector analysis and dif-ferential geometry, we establish the properties needed, and then use these properties in three ways. First, our results make it theoretically possible to identify extremal edges of an intensity function f(x, y) of two variables by considering the gradient vector field V = ¿f. There is also enough information in ¿f to find regions of high curvature (i.e., high curvature of the level paths of f). For color images, we use the vector field V = (I, Q). In application, the image is partitioned into a grid of squares. On the boundary of each square, V/|V| is sampled, and these unit vectors are used as the tangents of a curve ¿. The rotation number (or topological degree) ¿(¿) and the average curvature f|¿¿| are computed for each square. Analysis of these numbers yields infor-mation on edges and curvature. Experimental results from both simu-lated and real data are described.

Finding edges in noisy scenes.

Edge detection in the presence of noise is a well-known problem. This paper examines an applications-motivated approach for solving the problem using novel techniques and presents a method developed by the authors that performs well on a large class of targets. ROC curves are used to compare this method with other well-known edge detection operators, with favorable results. A theoretical argument is presented that favors LMMSE filtering over median filtering in extremely noisy scenes. Simulated results of the research are presented.