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. 2022 Jul 14;54(8):1103–1116. doi: 10.1038/s41588-022-01113-z

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 5 — a, Analysis of the OAS1 haplotypes (14.13 kb, hg38:112,911,065-112,925,192) comprised of 7 markers. The color-coding indicates the ancestral status of specific alleles – human (ancestral or derived), archaic humans (Neandertal or Denisova lineages), and COVID-19 severity status (Non-risk/Risk). Haplotype frequencies are shown for hospitalized patients with COVID-19 of European and African ancestry from COVNET. NA, haplotype is not detected. Odds ratios (ORs) and 95% confidence intervals (95%CIs) are for comparison with the common Risk haplotype (also marked as ref); full results can be found in Supplementary Table 4. The Non-risk haplotypes differ from the Risk haplotype by the alleles of rs1131454 and rs10774671. The COVID-19 risk is associated with human-specific derived alleles rs1131454-A and rs10774671-A. Additionally, the Risk haplotype includes a Denisova-type fragment of derived alleles spanning rs1131476 to rs4766664. Human polymorphisms rs1131454, rs1131476, rs1051042, and rs2660 were also explored and found monomorphic in genomic sequences of 29 chimpanzees: Pan troglodytes verus (n = 24) and Pan troglodytes troglodytes (n = 5). Source⁸: European Nucleotide Archive https://www.ebi.ac.uk, accession numbers FM163403.1–FM163432.1. b, OAS1 haplotypes and phylogenetic tree. COVID-19 risk alleles rs1131454-A and rs10774671-A are human-specific and derived.