{"doi":"10.1016/j.epidem.2025.100846","title":"Robust phylodynamic inference and model specification for HIV transmission dynamics","abstract":"The robustness and statistical efficiency of phylodynamic models have been tested by many investigators. However, little attention has been given to model specification and inductive bias that can occur if the model is misspecified or provides an overly simplistic representation of the evolutionary process. Here, we carried out a study involving the simulation of HIV epidemics using a complex model and calibrated to men who have sex with men from San Diego, USA. We then used this epidemic trajectory to simulate genealogies, sequence alignments equivalent to HIV partial pol gene and the complete genome. We proceeded to estimate migration rates using a simplistic representation of the epidemiological model by testing model-based phylodynamics and phylogeographic methods. We observed that even though there were some biases on the estimates using a simplistic representation of the epidemiological model, we were still able to estimate the migration rates depending on the method and sample size used in the analyses. • Simple structured coalescent models could recover migration rates whilst adjusting for nonlinear epidemiological dynamics. • Inductive bias can occur if the model is misspecified, but a small bias was observed for a sample size of ≥ 1000 sequences. • We were able to estimate migration rates using alignments equivalent to the partial pol gene or the complete HIV genome. • The estimation of a higher migration rate was more accurate than the estimation of a lower migration rate. • The phylogeographic model in BEAST to estimate migration rates was not scalable for datasets of 600 or more sequences.","journal":"Epidemics","year":2025,"id":570593,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9507,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":300754,"name":"Sanjay R. Mehta","orcid":"0000-0002-2028-8158","position":1,"is_corresponding":false},{"id":69651,"name":"Susan J. Little","orcid":"0000-0002-7645-9737","position":2,"is_corresponding":false},{"id":458962,"name":"Erik Volz","orcid":"0000-0001-6268-8937","position":3,"is_corresponding":false},{"id":1476166,"name":"Fabrícia F. Nascimento","orcid":"0000-0001-9426-6835","position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":null,"created_at":"2026-07-19T02:57:11.713851Z","pmid":"40683077","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}