A new study published online today in Nature reports the identification of the second-oldest known HIV-1 sequence. The sequence was recovered from a stored lymph tissue sample taken at a hospital in Kinshasa in 1960. The authors, led by Michael Worobey, were able to sequence around 5% of the HIV-1 genome and their analyses suggest that the virus began to spread and diversify in Africa around the turn of the century. The authors speculate that the growth of cities like Leopoldville facilitated an increase in transmission and the ultimate spread of HIV-1 across the globe. Due to the many potential pitfalls associated with attempting to recover viral sequences from ancient samples, the work was confirmed by an independent laboratory, and the long lag time between the submission of the paper to Nature and publication also suggests that a great deal of rigor went into assuring the paper's reviewers that the findings were accurate. In a news article for Science, Jon Cohen provides some additional background, noting that the tissue sample came from a 28-year old woman and was part of a group of samples taken from individuals with illnesses that had defied diagnosis, including lymph node abnormalities. Many more such samples are available for study, and Michael Worobey hopes to continue shedding light on HIV-1's early spread into the human population.
Nature 455, 661-664 (2 October 2008)
doi:10.1038/nature07390
Received 21 May 2008; Accepted 8 September 2008
Letter
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
Michael Worobey, Marlea Gemmel, Dirk E. Teuwen, Tamara Haselkorn, Kevin Kunstman, Michael Bunce, Jean-Jacques Muyembe, Jean-Marie M. Kabongo, Raphaël M. Kalengayi, Eric Van Marck, M. Thomas P. Gilbert & Steven M. Wolinsky
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.
Accompanying commentary:
Nature 455, 605-606 (2 October 2008)
doi:10.1038/455605a
Published online 1 October 2008
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Paul M. Sharp & Beatrice H. Hahn
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