Smith T F, Srinivasan A, Schochetman G, Marcus M, Myers G
MBCRR Dana-Farber Cancer Institute, Harvard University, Boston, Massachusetts 02115.
Nature. 1988 Jun 9;333(6173):573-5. doi: 10.1038/333573a0.
Knowledge of the phylogenetic history of the human immunodeficiency viruses (HIV-1 and HIV-2) is important for our understanding of the epidemiology of AIDS, the disease caused by these viruses. Reconstruction of the evolutionary tree is hampered, however, by two problems. One is the high variation in nucleotide sequence between the known HIV isolates which can create formidable difficulties in identifying homologous genomic sites that may be used in a molecular phylogenetic reconstruction. Another impediment has been the lack of unequivocal time calibration points: there is only a sparse 'fossil record' for HIV and limited historical epidemiological data. We have largely overcome these difficulties by: (1) a thorough optimal-sequence alignment analysis; (2) the inclusion of sequences of an early (1976) HIV-1 isolate, a recent (1986) HIV-2 isolate and two simian immunodeficiency viruses (SIV) along with five other HIV-1 isolates; and (3) the reconstruction of a minimum-length evolutionary tree based on the envelope-gene variable positions. We conclude that HIV-1 may have evolved from its common ancestor with HIV-2 as recently as 40 years ago.
了解人类免疫缺陷病毒（HIV - 1和HIV - 2）的系统发育史对于我们理解由这些病毒引起的艾滋病的流行病学至关重要。然而，进化树的重建受到两个问题的阻碍。一个问题是已知HIV分离株之间核苷酸序列的高度变异，这可能在识别可用于分子系统发育重建的同源基因组位点时造成巨大困难。另一个障碍是缺乏明确的时间校准点：HIV只有稀疏的“化石记录”且历史流行病学数据有限。我们通过以下方式在很大程度上克服了这些困难：（1）进行全面的最优序列比对分析；（2）纳入一株早期（1976年）HIV - 1分离株、一株近期（1986年）HIV - 2分离株以及两种猴免疫缺陷病毒（SIV）的序列，以及另外五株HIV - 1分离株；（3）基于包膜基因可变位点重建最小长度进化树。我们得出结论，HIV - 1可能在距今仅40年前就与其HIV - 2的共同祖先分道扬镳。
