Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

Abstract

Human immunodeficiency virus type 1 (HIV-1) sequences that pre-date the recognition of AIDS are critical to defining the time of origin and the timescale of virus evolution1,2. A viral sequence from 1959 (ZR59) is the oldest known HIV-1 infection1. Other historically documented sequences, important calibration points to convert evolutionary distance into time, are lacking, however; ZR59 is the only one sampled prior to 1976. Here we report the amplification and characterization of viral sequences from a Bouin's-fixed paraffin-embedded lymph node biopsy specimen obtained in 1960 from an adult female in Léopoldville, Belgian Congo (now Kinshasa, Democratic Republic of the Congo [DRC]), and we use it to conduct the first comparative evolutionary genetic study of early pre-AIDS epidemic HIV-1 group M viruses. Phylogenetic analyses position this viral sequence (DRC60) closest to the ancestral node of subtype A (excluding A2). Relaxed molecular clock analyses incorporating DRC60 and ZR59 date the M group's most recent common ancestor near the beginning of the 20th century. The sizeable genetic distance between DRC60 and ZR59 directly demonstrates that diversification of HIV-1 in west-Central Africa occurred long before the recognized AIDS pandemic. The recovery of viral gene sequences from decades-old paraffin-embedded tissues opens the door to a detailed paleovirological investigation of the evolutionary history of HIV-1 that is not accessible by other methods.

Origin of the HIV-1 group O epidemic in western lowland gorillas

“…The most recent common ancestors of HIV-1 groups M and O are both estimated to have existed around 1920 (46,47), whereas the lower levels of diversity seen in group N, and especially in group P, indicate that they emerged more recently. Coalescent studies suggest that groups O and M underwent similar rates of exponential growth until about 1960, and only since then has the spread of group M far outstripped the spread of group O (47).…”

HIV Type 1polGene Diversity and Genotypic Antiretroviral Drug Resistance Mutations in Malabo, Equatorial Guinea

“…This has particularly been seen in the Democratic Republic of Congo (DRC), a country located in the heart of a region suspected to be an early epicenter of the global epidemic. 5,6 Less is known of the HIV diversity in Equatorial Guinea (GQ), a small relatively wealthy country in Western Equatorial Africa. Information on HIV diversity has mainly been derived from samples collected in 1999 or from immigrants in Spain.…”

A Clinical Perspective in Evolutionary Medicine: What We Wish We Had Learned in Medical School

“…No gerontologist should consider the aging process without appreciating the declining power of selection and tradeoffs between reproduction and longevity (Kirkwood 1997). Every epidemiologist and infectious disease specialist should be able to engage in "tree-thinking" (Baum et al 2005) and interpret the phylogenetic trees used to track the evolution of HIV (Woroby et al 2008) and the emergence of North American West Nile virus (McMullen et al 2011). It is beyond the scope of this article to detail these and many other important concepts and applications of evolutionary biology in medicine, and we hope that students will be inspired to explore them further.…”