The origin of acquired immune deficiency syndrome: Darwinian or Lamarckian?

How did the ancestral HIV-1 group M retrovirus get to Leopoldville from southeastern Cameroon?

In previous papers in this journal, I have described and elaborated a hypothesis for the origin and evolution of a strain of HIV that has produced a lethal pandemic. Here I address the provocative question of how the ancestral HIV-1 group M retrovirus got to Leopoldville (Kinshasa, where the pandemic clearly spawned) from southeastern Cameroon (where the HIV-1 strains all seemed to originate from transfer of SIV(cpz) to humans). Consistent with the phylogenetic history of HIV-1 group M (e.g., by Korber et al.), I place the critical relocation of the ancestral HIV-1 in the timeframe 1920-1927. However, unlike other hypotheses, I believe that the ancestral retrovirus was already well adapted to humans and can be identified as HIV-1 Group M subtype A(pre)-1927. Based on documents from that time period (1920-1928), it can be shown that it was not unusual for native Africans to be brought as far as 500 miles for treatment at the Leopoldville clinic (national borders were no issue because health agencies had mandate to work throughout Cameroon and Congo-Brazzaville). Specifically, sleeping sickness (trypanosomiasis) was one of the diseases of most concern at the Leopoldville clinic; in the period 1926-1928 there was an outbreak of sleeping sickness in Cameroon; and one of the native African children in the pamaquine (plasmoquineTM) study that I believe selected for the major HIV-1 group M subgroups had trypanosomiasis. Thus, this child (or other patients/relatives from Cameroon) could have brought the ancestral HIV-1 group M retrovirus to the Leopoldville laboratory and spread it among the group of children who were undergoing treatment for malaria between February and August 1927. The diagnosis and monitoring of these protozoan diseases (trypanosomiasis and malaria) involved repetitive sampling of blood, which provides many opportunities for spreading the ancestral HIV-1 infection.

Mechanism and history of evolution of symbiotic HIV strains into lethal pandemic strains: the key event may have been a 1927 trial of pamaquine in Leopoldville (Kinshasa), Congo

In previous papers, I have rejected both the zoonosis and the serial transfer hypotheses of the origin and evolution of the current lethal pandemic strains of HIV. The hypothesis that fits the critical observations is that all the human and nonhuman primate species in central Africa (an area of hyper-endemic malaria) have shared (through inter-species transfers) a "primate T-cell retrovirus" (PTRV), which has adapted to each host species. This retrovirus is believed to assist primate T-cells attack the liver stage of the malaria infection. Each geographic region has a dominant primate host and a characteristic virus. Starting in 1955 and continuing into the late 1970s, chloroquine was provided by the WHO and used for prophylaxis against malaria. Chloroquine has a number of biochemical activities but two of the most important are blocking transcription of cellular genes and proviruses activated by NF-kappaB and blocking the glycosylation of surface proteins on viruses and cells. Concurrent with the development of resistance of the malaria parasite to chloroquine, HIV strains were quickly selected, which have enhanced transcription rates (by inclusion of multiple kappaB binding sites in their long terminal repeats by recombination) and enhanced infectivity (fusogenicity) (most likely by mutations in multiple viral genes that regulate glycosylation of Env). There also may have been mutations that enhanced activation of NF-kappaB in the host cell. These changes in the retrovirus genome were not manifest in effects of the HIV strains as long as the hosts were under the influence of chloroquine. But, when the virus infects people who are not protected by chloroquine, the virus multiplies more rapidly and is more communicable. Fortunately, most of these strains (i.e., HIV-2 groups, and HIV-1 O and HIV-1 N) self-regulate (i.e., infected cells kill infected cells) well enough that viral loads remain subdued and bystander cells of the immune system are not excessively attrited. In the case of HIV-1 group M, however, there is more going on. Following the work of Korber et al. on the phylogenetics of HIV-1 groups M, I reach the conclusion that the major subgroups giving rise to the worldwide pandemic, were founded in a 1927 clinical trial of pamaquine (plasmoquine) in Leopoldville (Kinshasa). This drug is much more toxic that chloroquine and appears to have strongly selected for resistance to apoptosis in infected cells, which allows these subgroups to attrite bystander cells leading to AIDS.

Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity

BACKGROUND

The routine use of drug resistance testing provides an abundant source of HIV-1 sequence data. However, it is not clear how reliable standard genotyping of these sequences is for describing HIV-1 genetic variation and for detecting novel genetic variants and epidemiological trends.

OBJECTIVES

To compare assignment of HIV-1 resistance test sequences to reference strains across commonly used genotyping protocols.

METHODS

Subtype assignments were compared across three standard genotyping protocols for 10 537 resistance test sequences, representing approximately one-fifth of all reported infections in the United Kingdom. Sequences that were inconsistently genotyped across methods, or that were unassigned by at least one method, were examined for evidence of recombination using sliding-window-based approaches.

RESULTS

Although agreement across methods was high for subtypes B, C and H, it was generally much lower (< 50%) for other subtypes. Disagreement between methods typically involved closely related, but epidemiologically distinct, groups or involved a significant proportion ( approximately 12%) of divergent sequences in which analysis revealed widespread evidence of recombination and a remarkable diversity of unusual recombinant forms.

CONCLUSIONS

With frequent long-distance transfer of viral strains and widespread recombination between them, genetic and epidemiological relationships within HIV-1 are becoming increasingly complex. Current methods of subtype assignment vary in their ability to identify novel genetic variants and to distinguish epidemiologically distinct strains. Capturing meaningful epidemiological information from resistance test data will require a critical understanding of the methodologies used in order to appreciate the possible sources of error and misclassification.

Importance and detection of virus reservoirs and compartments of HIV infection

Current therapies for treating HIV-1 infection are capable of suppressing virus load in blood to undetectable levels, and result in marked clinical improvement. Despite this suppression, HIV-1 infection persists and virus load quickly rebounds when therapy is interrupted. The origin of the rebounding virus is unknown, but is thought to result from continuing viral replication in anatomic or cellular compartments, and the release of virus from latent infection in reservoirs.

Investigating the origin of AIDS: some ethical dimensions

The theory that AIDS originated from contaminated polio vaccines raises a number of challenging issues with ethical dimensions. The Journal of Medical Ethics dealt with a submission about the theory a decade ago; subsequent developments have raised further issues. Four areas of contention are addressed: whether the theory should be investigated; whether anyone should be blamed; whether defamation actions are appropriate, and whether the scientific community has a responsibility to examine unorthodox theories.

An investigation of error sources and their impact in estimating the time to the most recent ancestor of spatially and temporally distributed HIV sequences

This is an investigation of significant error sources and their impact in estimating the time to the most recent common ancestor (MRCA) of spatially and temporally distributed human immunodeficiency virus (HIV) sequences. We simulate an HIV epidemic under a range of assumptions with known time to the MRCA (tMRCA). We then apply a range of baseline (known) evolutionary models to generate sequence data. We next estimate or assume one of several misspecified models and use the chosen model to estimate the time to the MRCA. Random effects and the extent of model misspecification determine the magnitude of error sources that could include: neglected heterogeneity in substitution rates across lineages and DNA sites; uncertainty in HIV isolation times; uncertain magnitude and type of population subdivision; uncertain impacts of host/viral transmission dynamics, and unavoidable model estimation errors. Our results suggest that confidence intervals will rarely have the nominal coverage probability for tMRCA. Neglected effects lead to errors that are unaccounted for in most analyses, resulting in optimistically narrow confidence intervals (CI). Using real HIV sequences having approximately known isolation times and locations, we present possible confidence intervals for several sets of assumptions. In general, we cannot be certain how much to broaden a stated confidence interval for tMRCA. However, we describe the impact of candidate error sources on CI width. We also determine which error sources have the most impact on CI width and demonstrate that the standard bootstrap method will underestimate the CI width.