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Increasing age and presence of co-morbidities are reported risk factors for severe disease and mortality, along with autoimmune diseases (ADs) and immunosuppressive treatments such as haematopoietic stem cell transplantation (HSCT), which are also associated with adverse outcomes. We review the impact of the pandemic on specific groups of patients with neurological, rheumatological, and gastroenterological indications, along with the challenges delivering HSCT in adult and pediatric populations. Moving forward, we developed consensus-based guidelines and recommendations for best practice and quality of patient care in order to support clinicians, scientists, and their multidisciplinary teams, as well as patients and their carers. These guidelines aim to support national and international organizations related to autoimmune diseases and local clinical teams delivering HSCT. Areas of unmet need and future research questions are also highlighted. The waves of the COVID-19 pandemic are predicted to be followed by an \u201cendemic\u201d phase and therefore an ongoing risk within a \u201cnew normality\u201d. These recommendations reflect currently available evidence, coupled with expert opinion, and will be revised according to necessary modifications in practice.<\/jats:p>","DOI":"10.1038\/s41409-021-01326-6","type":"journal-article","created":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T18:02:47Z","timestamp":1621879367000},"page":"1493-1508","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["Hematopoietic stem cell transplantation for autoimmune diseases in the time of COVID-19: EBMT guidelines and 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JAS declares honoraria for speaking at educational events supported by Jazz, Gilead, Janssen, Mallinckrodt, Actelion, an advisory board by MEDAC, and is a member of IDMC for a trial supported by Kiadis Pharma. TA declares travel grants from Neovii and study support from Amgen. PAM discloses travel support and speaker honoraria from unrestricted educational activities organized by Novartis, Bayer HealthCare, Bayer Pharma, Biogen Idec, Merck-Serono, and Sanofi Aventis. He also discloses consulting to Magenta Therapeutics and Jasper Therapeutics. PL reports grants and other from MSD, outside the submitted work. The other authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"This review, guideline and recommendations, and registry data analysis were approved, led, and supported by the Autoimmune Diseases Working Party (ADWP) and have been endorsed by the Pediatric (PWP) and Infectious Disease Working Parties (IDWP), Nurses Group (NG) of the European Society for Blood and Marrow Transplantation (EBMT), and the Joint Accreditation Committee of the International Society for Cellular Therapy (ISCT) and EBMT (JACIE).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval"}}]}}