背景:人类嗜T淋巴细胞病毒1型(HTLV-1)感染仍然是一个很大程度上被忽视的公共卫生问题,特别是在传染性和非传染性疾病负担较高的资源贫乏地区,例如,澳大利亚中部的一些偏远人群,估计有37%的成年人感染了HTLV-1。我们对HTLV-1感染的大部分理解来自对全球传播的亚型A(HTLV-1a)的研究,很少有分子研究报道,在印度太平洋和大洋洲地区主要使用南方-美拉尼西亚亚型C(HTLV-1c)。
结果:使用引物行走策略和直接测序,我们构建了来自澳大利亚中部22名使用HTLV-1c的原住民参与者的HTLV-1c基因组共有序列.与先前发表的HTLV-1a基因组相比,该C亚型前病毒gDNA的系统发育和成对分析显示出更高水平的基因组差异。虽然亚型之间的总体基因组同源性为92.5%,最低的核苷酸和氨基酸序列同一性发生在前病毒基因组编码调节基因的3末端附近,特别是重叠的HBZ(85.37%,77.46%,分别)和orf-I产品p12(82.00%,70.30%,分别)。引人注目的是,HTLV-1c基因组共有序列一致显示由HTLV-1Aorf-I编码的免疫调节蛋白p12/p8的翻译起始密码子缺陷。在许多受试者中检测到前病毒基因组中的缺失,特别是在结构方面,pol和env基因。同样,使用液滴数字PCR测定法,测量每个参考宿主基因组的gag和tax拷贝,我们定量地证实,前病毒在比gag更高的水平上保留了税收基因区域。
结论:我们对澳大利亚中部的HTLV-1c与较早的美拉尼西亚HTLV-1c序列进行的基因组分析,阐明关于全球传播的HTLV-1a的实质性差异。未来的研究应该解决这些基因组差异对感染的影响以及相关肺部疾病的区域独特频率。了解导致观察到的不同发病率的宿主和病毒亚型因素,对于在澳大利亚中部偏远的原住民社区中开发急需的治疗方法和疫苗策略至关重要。
BACKGROUND: Human T cell lymphotropic virus type 1 (HTLV-1) infection remains a largely neglected public health problem, particularly in resource-poor areas with high burden of communicable and non-communicable diseases, such as some remote populations in Central Australia where an estimated 37% of adults are infected with HTLV-1. Most of our understanding of HTLV-1 infection comes from studies of the globally spread subtype-A (HTLV-1a), with few molecular studies reported with the Austral-Melanesian subtype-C (HTLV-1c) predominant in the Indo-Pacific and Oceania regions.
RESULTS: Using a primer walking strategy and direct sequencing, we constructed HTLV-1c genomic consensus sequences from 22 First Nations participants living with HTLV-1c in Central Australia. Phylogenetic and pairwise analysis of this subtype-C proviral gDNA showed higher levels of genomic divergence in comparison to previously published HTLV-1a genomes. While the overall genomic homology between subtypes was 92.5%, the lowest nucleotide and amino acid sequence identity occurred near the 3\' end of the proviral genome coding regulatory genes, especially overlapping hbz (85.37%, 77.46%, respectively) and orf-I product p12 (82.00%, 70.30%, respectively). Strikingly, the HTLV-1c genomic consensus sequences uniformly showed a defective translation start codon for the immune regulatory proteins p12/p8 encoded by the HTLV-1A orf-I. Deletions in the proviral genome were detected in many subjects, particularly in the structural gag, pol and env genes. Similarly, using a droplet digital PCR assay measuring the copies of gag and tax per reference host genome, we quantitatively confirmed that provirus retains the tax gene region at higher levels than gag.
CONCLUSIONS: Our genomic analysis of HTLV-1c in Central Australia in conjunction with earlier Melanesian HTLV-1c sequences, elucidate substantial differences with respect to the globally spread HTLV-1a. Future studies should address the impact these genomic differences have on infection and the regionally distinctive frequency of associated pulmonary disease. Understanding the host and virus subtype factors which contribute to the differential morbidity observed, is crucial for the development of much needed therapeutics and vaccine strategies against this highly endemic infection in remote First Nations communities in Central Australia.