Data from: 1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

The emergence of HIV-1 group M subtype B in North American men who have sex with men was a key turning point in the HIV/AIDS pandemic. Phylogenetic studies have suggested cryptic subtype B circulation in the United States (US) throughout the 1970s1, 2 and an even older presence in the Caribbean2. However, these temporal and geographical inferences, based upon partial HIV-1 genomes that postdate the recognition of AIDS in 1981, remain contentious3, 4 and the earliest movements of the virus within the US are unknown. We serologically screened >2,000 1970s serum samples and developed a highly sensitive approach for recovering viral RNA from degraded archival samples. Here, we report eight coding-complete genomes from US serum samples from 1978–1979—eight of the nine oldest HIV-1 group M genomes to date. This early, full-genome ‘snapshot’ reveals that the US HIV-1 epidemic exhibited extensive genetic diversity in the 1970s but also provides strong evidence for its emergence from a pre-existing Caribbean epidemic. Bayesian phylogenetic analyses estimate the jump to the US at around 1970 and place the ancestral US virus in New York City with 0.99 posterior probability support, strongly suggesting this was the crucial hub of early US HIV/AIDS diversification. Logistic growth coalescent models reveal epidemic doubling times of 0.86 and 1.12 years for the US and Caribbean, respectively, suggesting rapid early expansion in each location3. Comparisons with more recent data reveal many of these insights to be unattainable without archival, full-genome sequences. We also recovered the HIV-1 genome from the individual known as ‘Patient 0’ (ref. 5) and found neither biological nor historical evidence that he was the primary case in the US or for subtype B as a whole. We discuss the genesis and persistence of this belief in the light of these evolutionary insights.人类免疫缺陷病毒1型M组B亚型（HIV-1 group M subtype B）在北美男男性行为人群中的出现，是艾滋病（HIV/AIDS）大流行进程中的关键转折点。系统发育研究表明，20世纪70年代期间B亚型在美国（US）存在隐秘传播[1,2]，且在加勒比地区的流行时间更早[2]。然而，这些基于1981年艾滋病被发现之后的部分HIV-1基因组序列所做出的时间与地理推论仍存在争议[3,4]，且病毒在美国境内的最早传播路径仍不明确。本研究对2000余份20世纪70年代的血清样本进行了血清学筛查，并开发出一种可从降解存档样本中回收病毒RNA的高灵敏度方法。本研究报道了1978至1979年美国血清样本中的8个编码完整的基因组序列，这也是目前已知的9份最古老HIV-1 M组基因组中的8份。这一早期全基因组“快照”显示，20世纪70年代美国的HIV-1流行株已具备丰富的遗传多样性，同时也为其起源于当时已存在的加勒比地区流行株提供了有力证据。贝叶斯系统发育分析估算出病毒传入美国的时间约为1970年，且将美国病毒的祖先株定位于纽约市，后验概率支持率达0.99，有力表明这里是美国早期HIV/AIDS病毒多样化传播的核心枢纽。逻辑增长溯祖模型显示，美国与加勒比地区的流行株倍增时间分别为0.86年与1.12年，表明两地在早期均实现了快速的病毒扩散[3]。与近期数据的对比研究表明，若缺乏存档全基因组序列，诸多上述关键发现将无法获得。本研究还从被称为“零号患者（Patient 0）”的个体样本中获取了HIV-1基因组[5]，并未发现任何生物学与历史学证据表明他是美国乃至整个B亚型HIV-1流行的首例病例。本研究结合这些进化生物学视角，探讨了这一认知的起源与持续流传原因。