This is the accepted version of the paper.This version of the publication may differ from the final published version. Permanent repository link:

Despite concerted efforts over the past 2 decades at developing new diagnostics, drugs, and vaccines with expanding pipelines, tuberculosis remains a global emergency. Several novel diagnostic technologies show promise of better point-of-care rapid tests for tuberculosis including nucleic acid-based amplification tests, imaging, and breath analysis of volatile organic compounds. Advances in new and repurposed drugs for use in multidrug-resistant (MDR) or extensively drug-resistant (XDR) tuberculosis have focused on development of several new drug regimens and their evaluation in clinical trials and now influence World Health Organization guidelines. Since the failure of the MVA85A vaccine 2 years ago, there have been no new tuberculosis vaccine candidates entering clinical testing. The current status quo of the lengthy treatment duration and poor treatment outcomes associated with MDR/XDR tuberculosis and with comorbidity of tuberculosis with human immunodeficiency virus and noncommunicable diseases is unacceptable. New innovations and political and funder commitment for early rapid diagnosis, shortening duration of therapy, improving treatment outcomes, and prevention are urgently required.

Five years into the crisis, some progress has been made in disease surveillance, but governance and coordination problems, variable immunization coverage, and the dynamic and indiscriminate nature of the conflict continue to pose a serious threat to population health in Syria and surrounding countries. The risk of major cross-border communicable disease outbreaks is high, and challenges for health in a post-conflict Syria are formidable.

Previous studies have found an association between a single-nucleotide polymorphism 35 kb upstream of the HLA-C locus (؊35 SNP), HLA-C expression, and HIV-1 set point viral loads. We show that the difference in HLA-C expression across ؊35 SNP genotypes can be attributed primarily to the very low expression of a single allelic product, HLA-Cw7, which is a common HLA type. We suggest that association of the ؊35 SNP and HIV-1 load manifests as a result of linkage disequilibrium of this polymorphism with both favorable and unfavorable HLA-C and -B alleles.Infection with HIV-1 involves a complex interplay between virus and host. After the acute phase of infection, an equilibrium is reached between HIV-1 and the immune system, resulting in the decline of HIV-1 RNA levels to the widely variable viral set point, a known (though imperfect) predictor of time to progression to AIDS (36, 37). The early appearance of HIV-1-specific CD8 T cells and their rapid selection of escape mutants during the initial decline of viremia in primary infection imply that this T-cell response plays a central role in resolution of primary viremia and the long-term suppression of viral replication (21, 34).The major histocompatibility complex (MHC), located on chromosome 6, contains the HLA class I and II genes, which are the most polymorphic loci in humans (9). HLA class I molecules play a significant role in the immune response against HIV-1 by presenting viral peptides to CD8 T cells (adaptive immunity) and by serving as ligands for killer cell immunoglobulin-like receptors (KIRs) expressed on natural killer (NK) cells (innate immunity). The central role of the MHC region in HIV-1 control was highlighted by a recent genomewide association study of variants that influence the control of viral set point (17, 18). In Caucasian cohorts, two single-nucleotide polymorphisms (SNPs) were identified that associated with the HIV-1 set point, and a third was associated with disease progression. All three SNPs were located in the MHC region on chromosome 6. These findings have been replicated with other independent Caucasian cohorts (10, 15, 31, 53, 55).One minor allelic variant of an SNP (rs2395029) associated with lower viral set points is located in the HLA complex P5 (HCP5) gene and is a tag for HLA-B*5701 (17), which is associated with slow disease progression (2, 9, 25, 40, 42). The second most significant polymorphism (rs9264942), accounting for 6.5% of the variation in viral set point (18), is located 35 kb upstream of the HLA-C gene (Ϫ35 SNP), with the minor allele (C) associating with a lower set point than the major allele (T). The Ϫ35 SNP is also present in African-American populations but does not correlate with viral set point (47, 49), which suggests that the Ϫ35 SNP is a marker for another polymorphism and is not the causal SNP. Although HLA-B*5701 is in linkage disequilibrium with the Ϫ35 SNP, both associate independently with the viral load set point (17,18).The Ϫ35 C variant was associated with higher HLA-C mRNA expression in Epstein...