Cross-clade immune responses to Gag p24 in patients infected with different HIV-1 subtypes and correlation with HLA class I and II alleles.

Individuals infected with different subtypes of HIV-1 (A, B, C, D, CRF01_AE and CRF02_AG) were analyzed for their antigen-specific immune response with respect to their HLA genetics. The p24 Gag protein was selected for analysis, since previous studies of the same cohort of patients had shown that almost 80% of these individuals responded to Gag peptides of subtypes A, B and/or C. A large number of Gag antigen-specific responses were recorded. Both previously recognized as well as new epitopes were identified, assumed to bind HLA classes I and/or II. Fifteen individuals showed class I cellular responses to T cell epitopes irrespective of the infecting virus subtype. For five individuals infected with subtypes A, B, D and CRF02_AG, new T cell epitopes are described. Responses related to the patient's class I alleles are frequent, and several new putative class II responses were found.

Significance of HIV-1 genetic subtypes.

HIV is the most significant new pathogen that emerged during the twentieth century. Since the recognition of AIDS in 1981, HIV has caused a worldwide epidemic. HIV-1 mutates extensively and shows high genetic diversity and thereby poses significant challenges for effective surveillance and disease control. At the beginning of the 1990s phylogenetic analyses of HIV-1 sequences from different sources of the world epidemic revealed that HIV-1 can be divided into different clades or subtypes. However, most of the knowledge from that time was based on information from western countries, where subtype B predominated. Important questions were raised about the possibility that genetic and phenotypic differences in HIV-1 may affect transmissibility, infectivity and pathogenicity, in addition to responses to therapy and vaccines. On this basis this study was initiated in 1994, and presented as a thesis in 1999. This paper gives an overview of the results from this thesis (based on 6 original papers) and the conclusions drawn. In summary, determination of the genetic subtype of HIV-1 probably has little value for routine clinical care of individual patients, but provides a powerful tool for monitoring changes in local and global transmission patterns.

Cross-reactive T-helper responses in patients infected with different subtypes of human immunodeficiency virus type 1.

Immunization with a recombinant glycoprotein 160 envelope immunogen derived from a virus of genetic subtype B induced strong specific T-helper cell responses in asymptomatic human immunodeficiency virus (HIV) carriers infected with subtypes B to G. This indicates that the HIV-specific T-helper immunity, which is the basis for development of antibodies and cytotoxic T lymphocytes, can be improved by both homologous and heterologous antigens. It also suggests that a particular immunogen can be effective against many different HIV strains.

Characterization of subtype A HIV-1 from Africa by full genome sequencing.

OBJECTIVE: To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been sequenced in their entirety. METHODS: Nine HIV-1-seropositive patients from Africa living in Sweden contributed peripheral blood mononuclear cells (PBMC) for this study. Sequencing of the C2-V3 region of env had shown them to be subtype A. DNA from virus cultures was used for the amplification of virtually full-length proviral sequences, and the resulting fragment was sequenced. RESULTS: Six of the nine viral isolates were subtype A throughout the genome, or non-recombinant, and all of these were from east Africa. One virus from the Ivory Coast had the AG(IbNG) genetic form, a recombinant form common in west Africa. Two of the isolates were novel recombinants: one was an A/C recombinant and the other was A/D. Analysis of gag reveals three subclusters within the A subtype: one containing the AG(IbNG) subtype viruses, one containing the AE(CM240) viruses and one containing the non-recombinant A viruses. These genetic clusters have different geographical distributions in Africa. CONCLUSION: The prevailing view of HIV-1 subtype A forming a uniform band across the center of sub-Saharan Africa needs revision. In all probability, the most common subtype in west Africa and west central Africa is the AG recombinant, AG(IbNG), whereas in east central Africa it is the non-recombinant subtype A.

Assay of plasma samples representing different HIV-1 genetic subtypes: an evaluation of new versions of the amplicor HIV-1 monitor assay.

Quantification of plasma HIV-1 RNA levels has rapidly become the main tool for monitoring disease progression and treatment. However, some first-generation assays do not accurately quantify all HIV-1 subtypes. This study compares the first-generation and two newer prototype Amplicor HIV-1 Monitor assays (Roche Diagnostic Systems) in terms of their performance in quantifying HIV-1 RNA in stored plasma samples from 101 individuals infected with various genetic subtypes of HIV-1 (28 subtype A, 18 B, 26 C, 20 D, 2 E, 3 G, 2 H, and 2 J). The HIV-1 subtype had previously been determined by direct sequencing of the V3 domain of the env gene. The results from the three assays agreed for subtypes B and C, as well as for most subtype D samples. In contrast, the first-generation assay reported significantly lower plasma HIV-1 RNA levels than did the two newer versions of the assay for most subtype A, E, G, and H samples. There were no differences in mean plasma HIV-1 RNA levels between individuals infected with subtypes A, B, C, and D if the results from the two newer test versions were used, and if an adjustment was made between subtypes for differences in CD4 count. Thus, this study confirms that the first-generation assay does not accurately quantify HIV-1 RNA levels in many individuals infected with subtype A, E, G, and H. These problems appeared to have been greatly reduced in the two new prototype versions.

Similar rate of disease progression among individuals infected with HIV-1 genetic subtypes A-D.

OBJECTIVE: HIV-1 is characterized by a high degree of genetic variation and can be divided into at least 10 distinct genetic subtypes. The purpose of this study was to investigate whether the rate of disease progression shows subtype-specific differences. DESIGN: The investigation was divided into two parts; one study in which 49 ethnic Africans were compared with 49 ethnic Swedes irrespective of the subtype of the infecting virus, and a second study in which 126 individuals infected with different genetic subtypes (28 with subtype A, 59 with subtype B, 21 with subtype C and 18 with subtype D) were compared. METHODS: CD4 cell counts, the rate of CD4 cell decline, plasma HIV-1 RNA levels, clinical status and antiviral treatment were prospectively and retrospectively recorded. The HIV-1 subtype had previously been determined by direct sequencing of the V3 domain of the env gene. RESULTS: There were no significant differences in the rate of CD4 cell decline or clinical disease progression between Africans and Swedes over an observation period of 2 years. Similarly, there were no differences in the rate of CD4 cell decline, clinical progression or plasma HIV-1 RNA levels between individuals infected with subtypes A, B, C or D over a mean observation period of 44 months. CONCLUSION: Neither the genetic subtype of the virus nor the ethnicity of the host appear to be major determinants of disease progression.

Differences in chemokine coreceptor usage between genetic subtypes of HIV-1.

HIV-1 uses chemokine coreceptors for cell entry. CXCR4 is the major coreceptor for T-cell-line-adapted isolates and CCR5 for non-T-cell-line-adapted isolates. This study investigated if coreceptor usage differs between genetic subtypes of HIV-1. Eighty-one primary isolates representing nine different genetic subtypes (A-J, except I) were tested on U87.CD4 glioma cells stably expressing chemokine receptor CCR1, CCR2b, CCR3, CCR5, or CXCR4. Coreceptor usage was compared to biological phenotype of the isolates (rapid/high, syncytium-inducing or slow/low, non-syncytium-inducing) and to clinical and immunological status of the study subjects. CXCR4 usage was perfectly correlated to the biological phenotype for all subtypes; all of 26 isolates with rapid/high phenotype and none of 55 isolates with slow/low phenotype could infect the CXCR4 expressing cell line. Importantly, the CXCR4-positive, rapid/high phenotype was underrepresented among subtype C isolates. Furthermore, dual tropism for CXCR4 and CCR5 was not found among subtype D isolates. Uni- and multivariate analyses indicated that these subtype-specific differences in coreceptor usage were not due to differences in clinical status, CD4 counts, or treatment. This study shows that CXCR4 usage determines the biological phenotype for all subtypes, but that there appear to exist subtype-dependent differences in frequency of usage of certain coreceptors. This opens up the possibility that genetic subtypes may differ in important biological properties such as virulence, tissue tropism, and transmissibility.

Drug susceptibility of subtypes A,B,C,D, and E human immunodeficiency virus type 1 primary isolates.

We determined the susceptibility to antiviral drugs of clinical isolates of human immunodeficiency virus type 1 (HIV-1) subtypes A, B, C, D, and E. Isolates from treated and untreated patients were tested for sensitivity to zidovudine (ZDV), lamivudine (3TC), didanosine (ddI), nevirapine (NVP), foscarnet (PFA), and ritonavir (RNV). The susceptibility to these different drugs was broadly similar between the different subtypes of HIV-1. Isolates of subtype D showed a tendency toward slightly lower susceptibility to all the antiviral drugs, which could be related to the rapid growth characteristics of these isolates.

Subtype-specific problems with quantification of plasma HIV-1 RNA.

OBJECTIVE: To determine whether two commercial assays for quantification of plasma HIV-1 RNA levels detect different genetic subtypes of HIV-1 with equal efficiency. DESIGN: Blind testing of stored plasma samples from 95 individuals infected with different genetic subtypes of HIV-1 (27 subtype A, 24 B, 18 C, 18 D, two E, two G, two H, and two J). The HIV-1 subtype had previously been determined by direct sequencing of the V3 domain of the env gene. METHODS: One plasma sample from each individual was tested once by the Roche HIV monitor assay and once by the Organon nucleic acid sequence-based amplification (NASBA) HIV-1 RNA quantitative assay, according to the manufacturers' recommendations. Information about CD4+ lymphocyte counts and antiretroviral treatment was available. RESULTS: The results from the two assays were strongly correlated with each other for subtypes B, C and D, but not for subtype A because many samples had RNA levels close to or below the lower detection limit of the assays. Thus, 15 out of 27 (56%) subtype A samples were negative by the HIV monitor assay and 12 (44%) were negative by the NASBA assay. These frequently occurring negative results among subtype-A-infected individuals were not due to better immunological status, more aggressive antiretroviral treatment, or differences in sample storage conditions. CONCLUSIONS: The HIV monitor assay and, possibly to slightly lesser degree, the NASBA assay appear unable to accurately quantify HIV-1 RNA levels in plasma samples from many subtype-A-infected individuals. These problems are likely to be due to primer mismatches and they limit the possibility of using these assays for routine monitoring of HIV-1-infected individuals in many parts of the world.

Most HIV-1 genetic subtypes have entered Sweden.

OBJECTIVE: The aim of this study was to document which genetic subtypes of HIV-1 have entered Sweden and to study transmission patterns of these virus variants. PATIENTS: All HIV-1 infected individuals at Danderyds Hospital, Stockholm, Sweden, who were suspected of carrying a virus of African origin were prospectively included in the study. The study subjects originated from 15 different African countries. METHODS: The V3 domain of the HIV-1 envelope was directly sequenced from uncultured peripheral blood mononuclear cells from 75 individuals included in the study. Phylogenetic analyses were used to determine genetic subtype and to study transmission patterns. RESULTS: The virus strains carried by the study subjects belonged to six established subtypes of HIV-1 (27A, 4B, 18C, 18D, 2G, 2H). Two individuals from Zaire carried a subtype, which had not been classified previously, provisionally named subtype 1. Eleven transmissions of non-subtype B strains in Sweden were documented. CONCLUSIONS: This study shows that most genetic HIV-1 subtypes have entered Sweden despite the relatively low prevalence of HIV infection in the country. Thus, the complete dominance of subtype-B infections which was seen during the early phase of the HIV-1 epidemic in Europe and the US has been broken in Sweden.

Interferon-alpha 2b treatment in hepatitis B carriers. Effect on hepatitis B virus DNA levels in children infected with different genotypes.

Eleven hepatitis B virus (HBV) carrier children, infected with genotypes A-D, were treated with interferon-alpha. Two children had a sustained loss of hepatitis B e-antigen and HBV DNA. They were infected with the non-Asian genotypes A and D, and had low HBV DNA and high ALT levels in serum before treatment. However, HBV DNA titres decreased during treatment also in children infected with the East-Asian genotypes B and C.

Vertical transmission of hepatitis C virus infection.

Vertical transmission of hepatitis C virus (HCV) was studied in 58 infants of 55 mothers (3 sets of twins). HCV RNA analyses by the polymerase chain reaction (PCR) and alanine aminotransferase (ALT) were performed on consecutive blood samples from birth to 18 months of age (0, 3, 9 and 18 months). Data on factors possibly influencing mother-to-infant transmission of HCV, such as concomitant human immunodeficiency virus (HIV) and hepatitis B virus infection during pregnancy, maternal HCV RNA status at delivery, mode of delivery, prematurity and breastfeeding habits were collected. In addition, 6 older siblings (age 4-10 years) of the infants were tested once for anti-HCV. Of the 55 mothers 52 (95%) had a history of intravenous drug use (IVDU). Two mothers were HIV positive. 40/54 (75%) tested mothers were HCV RNA positive. 16 (27%) infants were delivered by Caesarean section, and 50 (86%) infants were breastfed. All infants were HCV RNA negative on all occasions and anti-HCV negative at the age of 18 months. Maternally acquired anti-HCV antibodies disappeared and were not detected by 9 months in 78%. One of the 6 older siblings was anti-HCV and HCV RNA positive. We conclude that the risk of vertical HCV transmission is low in infants of HCV-positive/HIV-negative mothers, and that breastfeeding seems to be safe in this group.

Branhamella catarrhalis septicemia in an immunocompetent adult.

A 68-year-old man with otitis media developed signs of disseminated intravasal coagulation (DIC) and shock. Beta-lactamase positive Branhamella catarrhalis grew in all blood cultures and in secretion from the middle ear. The patient was immunocompetent and previously healthy. Severe B. catarrhalis septicemia has so far mainly been described in immunocompromised patients, mostly children, but this report shows that it may occasionally occur in immunocompetent adults.