HLA class I Sanger sequences data of Honduras HIV cohort

HLA polymorphisms represent the strongest genetic modifier of HIV disease progression. Diverse HLA distribution can lead to distinct HIV control landscapes at the population level. We aimed to describe HLA allele and haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency and the impact of these variants on HIV disease outcome. HLA class I (cI) loci were typed at 4-digit resolution, and CCR5 variants were determined in 402 HIV clade B-infected, ART-naïve individuals from Honduras. HLA LD were assessed using Fisher’s exact test. Using univariable and multivariable analyses we evaluated HLA associations with HIV pVL and CD4 counts. We did not find any effect on HIV control between CCR5 genotypes. Previously defined HLA associations were found: B*57:01/03, B*42:01, A*25:01 and C*12:03 (protective), and B*53:01 and A*68:01 (risk). Being consistent with our previous research in a Mesoamerican HIV cohort, Amerindian B*35:12 was associated to poor HIV control. Other HLA-HIV asso..., HLA class I loci (HLA-A, HLA-C and HLA-B) were resolved at second field resolution (i.e., subtype or protein level) using a previously described protocol. Briefly, a nested PCR with locus-specific primers were used to amplify a ~1000 bp region spanning exons 2 and 3. These PCR products were directly sequenced using a set of sequencing primers as previously described (Cotton LA, et al. 2012. HLA class I sequence-based typing using DNA recovered from frozen plasma. J Immunol Methods 382:40–47) on a 3730xl Genetic Analyzer (Applied Biosystems, Foster City). HLA subtypes were assigned using UType v7.1 RUO (Applied Biosystems) using the IPD-IMGT/HLA Database (release 3.31.0, 2018-01). Primer (allelic) and phase resolution ambiguities were resolved as previously explained (Valenzuela-Ponce H, et al. 2018. Novel HLA class I associations with HIV-1 control in a unique genetically admixed population. Sci Rep 8:17.)., , # HLA class I Sanger sequences data of Honduras HIV cohort

[https://doi.org/10.5061/dryad.x3ffbg7rc](https://doi.org/10.5061/dryad.x3ffbg7rc)

HLA Sanger sequences encompassing exons 2 and 3 of HLA-A, HLA-B and HLA-C loci of Honduras HIV cohort

## Description of the data and file structure

HLA class I loci *(HLA-A*, *HLA-C* and *HLA-B)* were resolved at second field resolution (i.e., subtype or protein level) using a previously described protocol (Valenzuela-Ponce H., et al. 2018. Novel HLA class I associations with HIV-1 control in a unique genetically admixed population. Sci Rep 8:17.). Briefly, a nested PCR with locus-specific primers were used to amplify a \~1000 bp region spanning exons 2 and 3. These PCR products were directly sequenced using a set of sequencing primers as previously described (Cotton LA, et al. 2012. HLA class I sequence-based typing using DNA recovered from frozen plasma. J Immunol Methods 382:40–47.) on a 3730xl Genetic Analyzer (Applied Biosystems, Foster C...