Daily Sampling of an HIV-1 Patient with Slowly Progressing Disease Displays Persistence of Multiple env Subpopulations Consistent with Neutrality

The molecular evolution of HIV-1 is characterized by frequent substitutions, indels and recombination events. In addition, a HIV-1 population may adapt through frequency changes of its variants. To reveal such population dynamics we analyzed HIV-1 subpopulation frequencies in an untreated patient with stable, low plasma HIV-1 RNA levels and close to normal CD4+ T-cell levels. The patient was intensively sampled during a 32-day period as well as approximately 1.5 years before and after this period (days −664, 1, 2, 3, 11, 18, 25, 32 and 522). 77 sequences of HIV-1 env (approximately 3100 nucleotides) were obtained from plasma by limiting dilution with 7–11 sequences per time point, except day −664. Phylogenetic analysis using maximum likelihood methods showed that the sequences clustered in six distinct subpopulations. We devised a method that took into account the relatively coarse sampling of the population. Data from days 1 through 32 were consistent with constant within-patient subpopulation frequencies. However, over longer time periods, i.e. between days 1…32 and 522, there were significant changes in subpopulation frequencies, which were consistent with evolutionarily neutral fluctuations. We found no clear signal of natural selection within the subpopulations over the study period, but positive selection was evident on the long branches that connected the subpopulations, which corresponds to >3 years as the subpopulations already were established when we started the study. Thus, selective forces may have been involved when the subpopulations were established. Genetic drift within subpopulations caused by de novo substitutions could be resolved after approximately one month. Overall, we conclude that subpopulation frequencies within this patient changed significantly over a time period of 1.5 years, but that this does not imply directional or balancing selection. We show that the short-term evolution we study here is likely representative for many patients of slow and normal disease progression

Significance of HIV-1 genetic subtypes

The human immunodeficiency virus type 1 (HIV-1) displays high genetic variability. Phylogenetic studies have shown that a majority of HIV-1 sequences cluster into one large group called M (major), whereas a few are clearly distinct, group O (outlier) and group N (non-M-non-O). Group M sequences are further subdivided into at least nine genetic subtypes, A through H and J. Inter-subtype recombinants also exist. The geographical distribution of different subtypes varies. Subtype B dominates in Europe and North America. All subtypes have been described in Africa, but subtypes A, C and D dominates. Subtype C is probably the most prevalent subtype world-wide. This thesis was based on a prospective follow-up of all patients at Danderyd Hospital who were known or suspected to be infected with a virus of African origin. A majority of the study subjects were African immigrants who were infected before their arrival to Sweden. The subtype of the viruses was determined by phylogenetic analysis of DNA sequences corresponding to the V3 domain of the env gene. We found that almost all known subtypes (A, B, C, D, G, H and AE) were represented at Danderyd Hospital. A majority of the infections had occurred in Africa, but some transmissions of non-B-subtypes in Sweden were also documented. Subtype B, which dominates among Swedish HIV-1 infected homosexual men and i.v. drug users, was rare among the study subjects who mainly were heterosexually infected. Furthermore, we found that two patients from Zaire were infected with an earlier not described subtype. These viruses are now prototypes for a new subtype called subtype J. Plasma virus load is an important predictor of clinical prognosis. We found that two of three first generation assays for plasma HIV-1 RNA quantification failed to accurately quantify some subtypes e.g. subtype A. This finding limits the use of these assays in many parts of the world. In a later study, we found that newer versions of one of the assays more reliably quantified a majority of samples from all subtypes. Virus entry into cells requires interactions with the CD4 receptor and certain chemokine coreceptors. We investigated if coreceptor usage differs between genetic subtypes of HIV-1, We found that the ability to infect via the CXCR4 coreceptor predicted a rapid/high, SI virus phenotype for all subtypes. However, CXCR4-positive isolates were rare in subtype C, indicating subtypespecific differences in biological properties. Finally, we compared the rate of disease progression in patients infected with subtypes A through D by analysis of the rate of CD4 cell decline, plasma HIV-1 RNA levels and clinical status. Disease progression among ethnic Africans and ethnic Swedes was also compared. We found that neither genetic subtype of the virus nor the ethnicity of the host was found to significantly influence disease progression. This suggests that the difference in biological phenotype of subtype C isolates does not translate into differences in disease progression. 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

High Levels of Chronic Immune Activation in the T-Cell Compartments of Patients Coinfected with Hepatitis C Virus and Human Immunodeficiency Virus Type 1 and on Highly Active Antiretroviral Therapy Are Reverted by Alpha Interferon and Ribavirin Treatment ▿

Chronic immune activation is a driver of human immunodeficiency virus type 1 (HIV-1) disease progression. Here, we describe that subjects with chronic hepatitis C virus (HCV)/HIV-1 coinfection display sharply elevated immune activation as determined by CD38 expression in T cells. This occurs, despite effective antiretroviral therapy, in both CD8 and CD4 T cells and is more pronounced than in the appropriate monoinfected control groups. Interestingly, the suppression of HCV by pegylated alpha interferon and ribavirin treatment reduces activation. High HCV loads and elevated levels of chronic immune activation may contribute to the high rates of viral disease progression observed in HCV/HIV-1-coinfected patients