COVIPENDIUM Information available to support the development of medical countermeasures and interventions against COVID-19 Cite as: Martine DENIS, Valerie VANDEWEERD, Rein VERBEEKE, Anne LAUDISOIT, Tristan REID, Emma HOBBS, Laure WYNANTS & Diane VAN DER VLIET. (2020). COVIPENDIUM: information available to support the development of medical countermeasures and interventions against COVID-19 (Version 2020-08-18). Transdisciplinary Insights. This document is conceived as a living document, updated on a weekly basis. You can find its latest version at: https://rega.kuleuven.be/if/corona_covid-19. The COVIPENDIUM is based on open-access publications (scientific journals and preprint databases, communications by WHO and OIE, health authorities and companies) in English language. Please note that the present version has not been submitted to any peer-review process. Any comment / addition that can help improve the contents of this review will be most welcome. 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Authors: Martine Denis, Valerie Vandeweerd, Rein Verbeke, Anne Laudisoit, Tristan Reid, Emma Hobbs, Laure Wynants, Diane Van der Vliet COVIPENDIUM version: 18 AUG 2020 Transdisciplinary Insights - Living Paper | 1 Contents List of abbreviations .......................................................................................................................................................... 9 Introduction .................................................................................................................................................................... 10 The virus .......................................................................................................................................................................... 10 Coronaviruses ............................................................................................................................................................. 10 SARS-CoV-2 is a betacoronavirus ................................................................................................................................ 11 Genome structure ....................................................................................................................................................... 12 Origin of the virus ....................................................................................................................................................... 13 Multiple reasons to rule out a laboratory origin .................................................................................................... 15 Sequence diversity among isolates ............................................................................................................................. 16 Sequence homology of the S gene .............................................................................................................................. 18 Structure of S and interactions with the ACE2 receptor ............................................................................................. 18 Other SARS-CoV-2 genes and proteins ....................................................................................................................... 20 Immunity to SARS-CoV-2 infection ................................................................................................................................. 20 Epitope predictions ..................................................................................................................................................... 20 Observations in COVID-19 patients ............................................................................................................................ 21 Comparisons between symptomatic and asymptomatic subjects ......................................................................... 21 Antibody response .................................................................................................................................................. 22 Cellular responses ................................................................................................................................................... 24 Immunity to other coronaviruses and cross-reactivity ............................................................................................... 26 Cross-reactivity of antibodies ................................................................................................................................. 26 Cross reactive T cells ............................................................................................................................................... 27 Innate immunity .......................................................................................................................................................... 27 Immune evasion mechanisms ..................................................................................................................................... 28 RNAi ......................................................................................................................................................................... 28 Clinical disease ................................................................................................................................................................ 28 Initial observations in Wuhan ..................................................................................................................................... 28 Incubation period ........................................................................................................................................................ 28 Description of clinical disease ..................................................................................................................................... 29 Clinical disease in China .......................................................................................................................................... 29 Clinical disease outside China ................................................................................................................................. 32 Non-respiratory symptoms ..................................................................................................................................... 33 Clinical imaging ........................................................................................................................................................... 35 Authors: Martine Denis, Valerie Vandeweerd, Rein Verbeke, Anne Laudisoit, Tristan Reid, Emma Hobbs, Laure Wynants, Diane Van der Vliet COVIPENDIUM version: 18 AUG 2020 Transdisciplinary Insights - Living Paper | 2 Chest computed tomography ................................................................................................................................. 35 Lung ultrasound ...................................................................................................................................................... 38 Laboratory finding & biomarkers ................................................................................................................................ 38 Virus load ................................................................................................................................................................ 38 Cell counts ............................................................................................................................................................... 40 Biochemistry ........................................................................................................................................................... 41 Coagulation parameters.......................................................................................................................................... 42 Time from illness onset to death ................................................................................................................................ 43 Case fatality rate ......................................................................................................................................................... 43 Case fatality rate in China ....................................................................................................................................... 43 Case fatality rate outside China .............................................................................................................................. 45 Special populations ..................................................................................................................................................... 46 Elderly ..................................................................................................................................................................... 46 Haemodialysis patients ........................................................................................................................................... 46 Cancer patients ....................................................................................................................................................... 46 Immunocompromised patients .............................................................................................................................