Nal file 3: Figure S3. Hierarchical clustering analysis of single nucleotide polymorphisms
Nal file 3: Figure S3. Hierarchical clustering analysis of single nucleotide polymorphisms (SNPs) in all HIV1 coding regions plus the longterminal regions (LTRs). Dendograms were calculated using the Euclidian distance and Complete cluster methods with 1000 bootstrap iterations as described in Los Alamos HIV Sequence Database (http:// www.hiv.lanl.gov.content/sequence/HEATMAP/heatmap.html). Bootstrap values >60 are indicated by an asterisk. Green and grey blocks indicate the presence and absence of SNPs, respectively.Abbreviations HIV1: human immunodeficiency virus type 1; VNP: viremic nonprogressors; TP: typical progressor; RP: rapid progressor; LTNP: longterm nonprogressors; SNP: singlenucleotide polymorphism; HLA: human leukocyte antigen; CTL: cytotoxic T cell; PBMC: peripheral blood mononuclear cells; MOI: multiplicity of infection. Authors’ contributions JW and MEQM designed the study, collected and assembled the data, wrote and drafted the manuscript. RMG, LS, DS, JH, JW, and MP performed all cellWeber et al. AIDS Res Ther (2017) 14:Page 14 ofculture, molecular, and sequencing experiments. JW, MML, BR and MEQM contributed to the overall analysis of the data. All authors read and approved the final manuscript. Author details 1 Institute of Organic Chemistry and Biochemistry v.v.i., Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic. 2 University Hospital Translational Laboratory, University Hospitals Cleveland Medical Center, Cleveland, OH, USA. 3 Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, 10900 Euclid Avenue, Cleveland, OH PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28381880 441067288, USA. 4 Department of Pathology, Case Western Reserve University, Cleveland, OH, USA. Acknowledgements We thank Michelle Gallagher and the Case Western Reserve University/Uni versity Hospitals Center for AIDS Research (NIH P30 AI036219) for providing access to critical clinical information. Competing interests The authors declare that they have no competing interests. Availability of data and materials All near fulllength HIV1 genome sequences and raw deep sequencing reads generated in this study are available upon request. Ethics Blood samples from HIVinfected individuals were obtained with the written informed consent of each participant as described in IRB protocol AIDS 125, University Hospitals Cleveland Medical Center/Case Western Reserve University. Funding J.W. was supported by a research grant from the Ministry of Education, Youth and Sports of the Czech GW610742 web Republic (LK11207). M.E.QM was partially supported by research Grant NIHAI71747, the CWRU/UH Center for AIDS Research (P30 AI036219) and funding from University Hospitals Cleveland Medical Center (UHCMC) for the University Hospitals Translational Laboratory (UHTL). Received: 30 November 2016 Accepted: 15 March8.9. 10. 11. 12. 13. 14.15.16.17.18.19. References 1. Poorolajal J, Hooshmand E, Mahjub H, Esmailnasab N, Jenabi E. Survival rate of AIDS disease and mortality in HIVinfected patients: a meta analysis. Public Health. 2016;139:3?2. 2. Lackner AA, Lederman MM, Rodriguez B. HIV pathogenesis: the host. Cold Spring Harb Perspect Med. 2012;2(9):a007005. 3. Casado C, Colombo S, PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28242652 Rauch A, Martinez R, Gunthard HF, Garcia S, Rodriguez C, Del Romero J, Telenti A, LopezGalindez C. Host and viral genetic correlates of clinical definitions of HIV1 disease progression. PLoS ONE. 2010;5(6):e11079. 4. Okulicz JF, Marconi VC, Landrum ML, Wegner S, Weintrob A.