*4.3. Analyses*

The Fisher's Exact Test was used to compare the proportion of each mutation in sequences from patients receiving boosted versus unboosted atazanavir, from patients who were previously ART-naïve versus ART-experienced, and from patients according to whether they had subtype B versus non-subtype B sequences. The Wilcoxon Rank Sum Test was used to compare the median number of mutations between two groups. The Holm's method was used to control for the familywise error rate for multiple hypothesis testing [53].

A binomial regression model was used to examine the relationship between the year of ART initiation and the presence or absence of PI-associated DRMs. To assess the association of covariates with the presence or absence of PI-associated DRMs, a multivariate generalized linear mixed logistic regression analysis was performed using the R package lme4. To account for study heterogeneity, study was included in the model as a random effect.

To identify the patterns of covariation among DRMs and NP-TSMs, we calculated Jaccard similarity coefficients and their standard Z scores for all pair of mutations [54]. To capture conditional dependency among the significantly co-occurring mutation pairs, defined as those pairs that had Jaccard similarity coefficient *p* < 0.01, we constructed a Bayesian network with a hill-climbing search using the R package bnlearn [55] and created a directed edge network graph using the R package visNetwork [56]. To learn the structure of the Bayesian network of core mutations associated with atazanavir, we excluded sequences containing more than four DRMs in this analysis.

For each sequence containing one or more DRMs, we determined the level of predicted resistance to atazanavir and the levels of predicted cross resistance to lopinavir/r and darunavir/r using the HIVDB drug resistance interpretation system.

### *4.4. Accession Numbers*

Sequences in this study had been submitted to GenBank (accession numbers ON058287- ON058987).

**Supplementary Materials:** The following supporting information can be downloaded at https: //www.mdpi.com/article/10.3390/pathogens11050546/s1, Text S1: The EuResist Network Study Group; Table S1: The complete set of 1497 one-per-person HIV-1 group M protease sequences from persons receiving atazanavir; Table S2: Nonpolymorphic PI treatment-selected mutations (NP-TSMs) occurring in ≥1 sequences from patients receiving boosted or unboosted atazanavir (ATV) as their first PI; Table S3: Studies in PubMed containing sequences from previously PI-naïve patients receiving boosted or unboosted atazanavir (ATV) for which the sequences were not available.

**Author Contributions:** Conceptualization, R.W.S.; Methodology, S.-Y.R. and R.W.S.; Validation, S.-Y.R., R.W.S. and M.Z.; Formal Analysis, S.-Y.R.; Resources, M.B., O.T., A.B.A., A.S. and D.K.; Data Curation, G.D.T., A.J.B. and S.-Y.R.; Writing—Original Draft Preparation, S.-Y.R. and R.W.S.; Writing—Review and Editing, S.-Y.R., O.T., D.K., A.B.A., M.Z. and R.W.S.; Visualization, S.-Y.R.; Funding Acquisition, R.W.S. All authors have read and agreed to the published version of the manuscript.

**Funding:** S.-Y.R., A.J.B. and R.W.S. were supported in part by the National Institute of Allergy and Infectious Diseases (NIAID) of the National Institute of Health (NIH) (award number AI136618). The work of O.T. and D.K. was supported by the Russian Science Foundation Grant No. 19-75-10097. A.B.A. received funding from Fundação para a Ciência e Tecnologia through projects PTDC/SAU-INF/31990/2017 (INTEGRIV) and PTDC/SAU-PUB/4018/2021 (MARVEL). G.D.T. was supported by EuResist Network GEIE.

**Institutional Review Board Statement:** The Stanford University review board approved this study (IRB-13900; approved on 30 June 2021).

**Informed Consent Statement:** Patient consent was waived by the IRB because the study involved the analysis of anonymized data that had already been collected.

**Data Availability Statement:** Datasets used in the present study are available in Tables 1 and S1.

**Conflicts of Interest:** A.S. received research grants from Gilead Sciences, and personal fees for advisory boards from Gilead Sciences, MSD, and ViiV Healthcare, all outside the present work. M.Z. received research grants from Gilead Sciences, MSD, Theratechnologies and ViiV Healthcare and personal fees for advisory boards from Gilead Sciences, Janssen-Cilag, MSD, Theratechnologies and ViiV Healthcare, all outside the present work. The funder had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
