Our study has some limitations

Our study has some limitations. While our study provides data from a diverse multi-country setting, we did not have a sufficient sample size to investigate whether the relationship of micronutrients and Clofarabine synthesis with CD4 recovery differed by country. We relied on measurement of deficiencies based on measurement in serum, which may not represent ‘true’ deficiency in an individual at the level of the tissue; however, serum samples are commonly used to measure micronutrient deficiency and are clinically relevant in most instances. Additionally, we investigated the effect of single deficiencies and did not explore the effects of concurrent deficiencies on CD4 recovery (e.g., both selenium and vitamin D deficiencies). We also had few cases of immunologic failure in our cohort (n = 14) and could not assess factors associated with immunologic failure. This may indicate that our clinical trial cohort is generally healthier than the population of individuals starting cART treatment in routine program settings. Therefore, we may have underestimated some associations. Further, small numbers of participants were deficient in some biomarkers, such as vitamin B12; thus our analysis was not powered to detect significant differences in CD4 count among B12 deficient and non-deficient participants. Other trace minerals, such as zinc and copper, which may be important in HIV immune reconstitution were not measured in this study because the parent study did not collect and store the samples in a way that was required to assess these appropriately. Despite these acknowledged limitations, we had a high quality dataset with robust longitudinal CD4 data allowing us to address CD4 recovery adequately over a two-year period.
Conflict of interest Thomas B Campbell has served on advisory boards for Gilead Sciences, ViiV and Theratechnologies. Amita Gupta and Rupak Shivakoti has received grant funding from Gilead Foundation. All authors declare no conflicts of interest. This work was supported by the National Institutes of Health, National Institute of Allergy and Infectious Diseases [UM1 AI069465, R01 AI080417]. RS was supported by National Institute of Child Health and Human Development [grant numbers K99 HD089753] of the National Institutes of Health. The parent study was supported by NIAID grants UM1 AI068634, UM1 AI068636 and UM1 AI106701. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The parent trial A5175 was also supported in part by Boehringer-Ingelheim, Bristol-Myers Squibb, Gilead Sciences, and GlaxoSmithKline. Funders had no role in study design, data collection, analysis, publication decision, or manuscript preparation.
Acknowledgements
Introduction Myasthenia gravis is a chronic autoimmune disease characterized by muscle fatigability and weakness. In the majority of patients pathogenic antibodies against the AChR can be detected. For a long time it has been known that myasthenia gravis is associated with pathologies of the thymic gland. Around 10–15% of patient do harbour a thymic tumour that is differentiated according to histology in rather epithelial or lymphocytic subtypes. Furthermore most patients with an early onset form of the disease show a thymic lymphoid hyperplasia, an enlargement of the thymus with histological signs of germinal centers (Gilhus and Verschuuren, 2015). Consequently, thymectomy is used for treatment of MG and it has been shown to provide a significant clinical benefit (Wolfe et al., 2016). This argues for an important role of the thymus not only in the pathogenesis but also in the maintenance of the disease. In patients with thymic hyperplasia, the thymus might be regarded as starting point of T cell activation where consecutive generation of germinal centers and production of pathogenic antibodies takes place (Weiss et al., 2013). In contrast, in MG associated thymoma the abnormal generation of T cells is regarded to be important for disease pathogenesis. As measured by T cell receptor excision circle (TREC) content, CD4+ and CD8+ T cell output into the peripheral blood has been observed to be increased in thymoma patients with MG (Buckley et al., 2001), whereas in thymoma patients without MG, CD4 TREC levels were comparable to healthy controls(Buckley et al., 2001). In contrast, the frequency of CD45RA+ CD62L+ naïve CD4+ T cells has been reported to be decreased in thymoma patients without MG, whereas thymoma patients with MG showed frequencies comparable to healthy controls (Strobel et al., 2002).