{"doi":"10.1038/s41467-024-46261-4","title":"Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data","abstract":"With the recent onset of the SARS-CoV-2 pandemic, there has been great interest in interpreting the within-patient evolutionary dynamics of this virus. Indeed, the accurate identification of genomic regions experiencing positive selection, and the quantification of these selective effects, is of crucial importance for both evolutionary as well as clinical interpretation. With this goal, the recently published Gu et al. 1 work collected 2820 respiratory samples to investigate observed levels of within-patient synonymous relative to non-synonymous variation, and relied upon this comparison to assign genomic regions as evolving under purifying selection, neutrality, or positive selection. Specifically, they interpreted \\({\\pi }_{N}-{\\pi }_{S}\\) > 0 as being indicative of positive selection, ~0 as being indicative of neutrality, and <0 as being indicative of purifying selection (e.g., see Fig. 2 of Gu et al.). Using this criterion when performing sliding window analyses, the authors claimed that multiple genomic regions are experiencing positive selection. Crucially, the authors relied upon their selection inference derived from these \\(\\pi\\) -based comparisons to support conclusions regarding infection dynamics in vaccinated vs. unvaccinated patients, a focal point of their publication.","journal":"Nature Communications","year":2024,"id":454384,"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":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9481,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1058376,"name":"John W. Terbot","orcid":"0000-0002-8067-0674","position":1,"is_corresponding":false},{"id":7661,"name":"Jeffrey D. Jensen","orcid":"0000-0002-4786-8064","position":2,"is_corresponding":false},{"id":1039399,"name":"Vivak Soni","orcid":"0000-0002-9496-9562","position":0,"is_corresponding":true}],"reference_count":26,"raw_metadata":null,"created_at":"2026-07-19T02:03:07.923686Z","pmid":"38627371","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":[]}