{"doi":"10.1016/j.chom.2022.01.005","title":"SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape","abstract":"Characterizing SARS-CoV-2 evolution in specific geographies may help predict properties of the variants that come from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from ancestral virus in a person with advanced HIV disease in South Africa; this person was infected prior to emergence of the Beta and Delta variants. We longitudinally tracked the evolved virus and tested it against self-plasma and convalescent plasma from ancestral, Beta, and Delta infections. Early virus was similar to ancestral, but it evolved a multitude of mutations found in Omicron and other variants. It showed substantial but incomplete Pfizer BNT162b2 escape, weak neutralization by self-plasma, and despite pre-dating Delta, it also showed extensive escape of Delta infection-elicited neutralization. This example is consistent with the notion that SARS-CoV-2 evolving in individual immune-compromised hosts, including those with advanced HIV disease, may gain immune escape of vaccines and enhanced escape of Delta immunity, and this has implications for vaccine breakthrough and reinfections.","journal":"Cell Host & Microbe","year":2022,"id":232202,"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":241,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.945,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":406977,"name":"Farina Karim","orcid":"0000-0001-9698-016X","position":1,"is_corresponding":false},{"id":584139,"name":"Gila Lustig","orcid":"0000-0002-8204-0182","position":2,"is_corresponding":false},{"id":287019,"name":"James Emmanuel San","orcid":null,"position":3,"is_corresponding":false},{"id":475192,"name":"Tandile Hermanus","orcid":"0000-0003-4734-1980","position":4,"is_corresponding":false},{"id":282134,"name":"Houriiyah Tegally","orcid":"0000-0002-7102-8540","position":5,"is_corresponding":false},{"id":805339,"name":"Jumari Snyman","orcid":"0000-0003-4647-8934","position":6,"is_corresponding":false},{"id":501393,"name":"Thandeka Moyo-Gwete","orcid":"0000-0002-4269-9281","position":7,"is_corresponding":false},{"id":282133,"name":"Eduan Wilkinson","orcid":"0000-0002-2503-9441","position":8,"is_corresponding":false},{"id":614567,"name":"Mallory Bernstein","orcid":"0000-0001-7498-2391","position":9,"is_corresponding":false},{"id":614565,"name":"Khadija Khan","orcid":"0000-0001-7565-7400","position":10,"is_corresponding":false},{"id":614528,"name":"Shi-Hsia Hwa","orcid":"0000-0002-5648-9808","position":11,"is_corresponding":false},{"id":616134,"name":"Sasha W. 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