Central Nervous System Compartmentalization of HIV-1 Subtype C Variants Early and Late in Infection in Young Children

HIV-1 subtype B replication in the CNS can occur in CD4+ T cells or macrophages/microglia in adults. However, little is known about CNS infection in children or the ability of subtype C HIV-1 to evolve macrophage-tropic variants. In this study, we examined HIV-1 variants in ART-naïve children aged three years or younger to determine viral genotypes and phenotypes associated with HIV-1 subtype C pediatric CNS infection. We examined HIV-1 subtype C populations in blood and CSF of 43 Malawian children with neurodevelopmental delay or acute neurological symptoms. Using single genome amplification (SGA) and phylogenetic analysis of the full-length env gene, we defined four states: equilibrated virus in blood and CSF (n = 20, 47%), intermediate compartmentalization (n = 11, 25%), and two distinct types of compartmentalized CSF virus (n = 12, 28%). Older age and a higher CSF/blood viral load ratio were associated with compartmentalization, consistent with independent replication in the CNS. Cell tropism was assessed using pseudotyped reporter viruses to enter a cell line on which CD4 and CCR5 receptor expression can be differentially induced. In a subset of compartmentalized cases (n = 2, 17%), the CNS virus was able to infect cells with low CD4 surface expression, a hallmark of macrophage-tropic viruses, and intermediate compartmentalization early was associated with an intermediate CD4 entry phenotype. Transmission of multiple variants was observed for 5 children; in several cases, one variant was sequestered within the CNS, consistent with early stochastic colonization of the CNS by virus. Thus we hypothesize two pathways to compartmentalization: early stochastic sequestration in the CNS of one of multiple variants transmitted from mother to child, and emergence of compartmentalized variants later in infection, on average at age 13.5 months, and becoming fully apparent in the CSF by age 18 months. Overall, compartmentalized viral replication in the CNS occurred in half of children by year three.

成人中枢神经系统（central nervous system, CNS）内的B亚型人类免疫缺陷病毒1型（HIV-1 subtype B）可在CD4阳性T淋巴细胞（CD4+ T cells）或巨噬细胞/小胶质细胞中完成复制。但目前学界对儿童中枢神经系统的HIV感染情况，以及C亚型HIV-1演化出嗜巨噬细胞变异株的能力，仍知之甚少。
本研究针对3岁及以下未接受抗反转录病毒治疗（antiretroviral therapy, ART）的儿童，旨在明确与C亚型HIV-1儿童中枢神经系统感染相关的病毒基因型与表型。
我们对43名出现神经发育迟缓或急性神经系统症状的马拉维儿童的血液与脑脊液（cerebrospinal fluid, CSF）中的C亚型HIV-1病毒群体进行了检测。
通过单基因组扩增（single genome amplification, SGA）与全长env基因系统发育分析，我们将病毒群体划分为四类：血液与脑脊液内病毒种群平衡（n=20，占比47%）、中度区域化（n=11，占比25%），以及两种不同类型的脑脊液区域化病毒种群（n=12，占比28%）。
较高的患儿年龄与脑脊液/血液病毒载量比值与病毒区域化显著相关，这与中枢神经系统内存在独立病毒复制的现象相符。
我们采用可差异诱导CD4与CCR5受体表达的细胞系，以假型报告病毒感染实验评估病毒的细胞嗜性。
在17%的区域化病例亚组（n=2）中，中枢神经系统来源的病毒可感染CD4表面低表达的细胞——这是嗜巨噬细胞病毒的标志性特征；且早期中度区域化与中间型CD4入侵表型存在关联。
5名受试儿童观察到多变异株传播现象；在部分病例中，某一病毒变异株被隔离于中枢神经系统内，这与病毒早期随机定植中枢神经系统的假说一致。
据此我们提出两种导致病毒区域化的途径：一是母婴传播的多变异株中，某一株早期随机定植于中枢神经系统；二是感染后期出现区域化变异株，平均出现年龄为13.5个月，并在患儿18月龄时于脑脊液中完全显现。
总体而言，至受试儿童3岁时，约半数出现了中枢神经系统内的区域化病毒复制。