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

Abstract

A histological specimen from the University of Kinshasa archives has been used to obtain HIV gene sequences dating back to the pre-AIDS era. From a lymph node biopsy taken in 1960 from an adult female in Léopoldville in the Belgian Congo (now Kinshasa, Democratic Republic of the Congo), sample 'DRC60' makes possible the first evolutionary analysis of pre-AIDS 'fossil' HIV-1 sequences, via comparison with the one other viral sequence from the period, from a plasma sample taken in 1959, also in Kinshasa. The analysis supports the idea that diversification of HIV-1 in west-central Africa occurred long before the recognized AIDS pandemic. Almost fifty years on, a major concern in HIV epidemiology is China. Here, HIV-1 infection was largely confined to high-risk groups but it is now breaking out into the general population. Lin Lu et al. report on efforts to contain the epidemic in Yunnan Province, where there has been a dramatic increase in sexual transmission of HIV. Newly isolated HIV genome sequences from a 1960 biopsy sample from Kinshasa are analysed in comparison with the viral sequence from 1959. The analysis presents supporting evidence that diversification of HIV-1 in west-Central Africa occurred long before the recognized AIDS pandemic. 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 before 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 them 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 most recent common ancestor of the M group to near the beginning of the twentieth 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 palaeovirological investigation of the evolutionary history of HIV-1 that is not accessible by other methods.