Analysis scripts and supplementary files: Incidence of symptomatic and asymptomatic HIV-associated sensory neuropathy in tenofovir-exposed individuals

<b>Bibliometric information</b>Pillay P, Wadley AL, Cherry CL, Karstaedt AS, Kamerman PR. HIV-associated sensory neuropathy continues to be a problem in South Africans starting tenofovir-based antiretroviral treatment.<br><b>Abstract</b><i>Objectives:</i> HIV-associated sensory neuropathy (HIV-SN) is a common and often painful neurological condition associated with HIV-infection and its treatment. However, data on the incidence of HIV-SN in neuropathy-free individuals initiating combination antiretroviral therapies (cART) that do not contain the neurotoxic agent stavudine are lacking.<br><i>Design: </i>We investigated the six-month incidence of HIV-SN in ART naïve individuals initiating tenofovir (TDF)-based cART, and the clinical factors associated with the development of HIV-SN.<br><i>Methods:</i> 120 neuropathy-free and ART naïve individuals initiating cART at a single centre in Johannesburg, South Africa were enrolled. Participants were screened for HIV-SN at study enrolment and then approximately every two-months for a period of approximately six-months. Symptomatic HIV-SN was defined by the presence of at least one symptom (pain/burning, numbness, paraesthesias) and at least two clinical signs (reduced vibration sense, absent ankle reflexes or pin-prick hypoaesthesia). Asymptomatic HIV-SN required at least two clinical signs only.<br><i>Results: </i>Approximately 80% of the cohort completed three or more visits with the six-mopnth period. Eleven individuals developed asymptomatic HIV-SN and nine developed symptomatic HIV-SN, giving a six-month cumulative incidence of neuropathy of 140 cases per 1000 patients (95% CI: 80 - 210) at an incidence rate of 0.37 (95% CI: 0.2 - 0.5) per person year. Increasing height and a current tuberculosis (TB) infection were independently associated with the risk of developing HIV-SN (p &lt; 0.05).<br><i>Conclusions: </i>We found that within the first six months of starting cART, incident SN persists in the post-stavudine era, but tends to be asymptomatic.<b><br></b><b>Analysis outputs</b>The data required to run the scripts have not been included in the repo because study participants did not consent to public release of their data. However, the data are available on request from Peter Kamerman ([e-mail]), or by submitting an issue at: https://github.com/kamermanpr/hivsn-incidence/issues.<br>The outputs from all analysis scripts are located in the /outputs directory. The outputs are formatted as markdown and html. The markdown documents are intermediate outputs generated during the production of the html documents, and while they allow quick browsing of the analysis outputs on GitHub, MathJax formulae and tables are not formatted. <br>

**文献计量信息**
Pillay P、Wadley AL、Cherry CL、Karstaedt AS、Kamerman PR. HIV相关感觉神经病仍是接受替诺福韦类抗逆转录病毒治疗的南非患者面临的问题。

**摘要**
*研究目的：* HIV相关感觉神经病（HIV-associated sensory neuropathy, HIV-SN）是HIV感染及其治疗过程中常见且常伴随疼痛的神经系统疾病。然而，针对未使用神经毒性药物司他夫定（stavudine）的无神经病患者启动联合抗逆转录病毒治疗（combination antiretroviral therapies, cART）后，HIV-SN发病率的相关数据仍存在缺失。
*研究设计：* 本研究旨在探究初治艾滋病患者启动替诺福韦（tenofovir, TDF）类联合抗逆转录病毒治疗后，HIV-SN的6个月发病率，以及与HIV-SN发生相关的临床危险因素。
*研究方法：* 本研究纳入南非约翰内斯堡单中心的120名无神经病病史且未接受过抗逆转录病毒治疗、新启动cART的受试者。研究人员在受试者入组时即开展HIV-SN筛查，并在随后约6个月内每2个月左右复查一次。有症状HIV-SN的判定标准为：至少存在1项相关症状（疼痛/烧灼感、麻木、感觉异常），且至少存在2项临床体征（振动觉减退、踝反射消失或针刺觉减退）；无症状HIV-SN则仅要求至少存在2项临床体征。
*研究结果：* 约80%的受试者在6个月随访期内完成了3次及以上随访。其中11名受试者出现无症状HIV-SN，9名出现有症状HIV-SN，据此计算得出6个月累积神经病发病率为140例/1000名患者（95%置信区间：80~210），发病率为0.37（95%置信区间：0.2~0.5）例/人年。身高更高以及合并当前活动性结核（tuberculosis, TB）感染是HIV-SN发生的独立危险因素（p < 0.05）。
*研究结论：* 本研究发现，在停用司他夫定的治疗阶段，启动cART后的前6个月内仍会新发HIV-SN，但多数表现为无症状性。

**分析产出结果**
本研究未将脚本运行所需的原始数据存入代码仓库，原因在于研究受试者未同意将其个人数据公开共享。若有需求，可联系Peter Kamerman（邮箱：[e-mail]）或在以下网址提交议题申请获取数据：https://github.com/kamermanpr/hivsn-incidence/issues。所有分析脚本的产出结果均存储于/outputs目录下，格式为markdown与html。其中markdown文档为生成html文档过程中产生的中间产物，虽可在GitHub平台快速浏览分析结果，但无法正确渲染MathJax公式与表格。