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Contents
SUMMARY ...................................................................................................................................... 6
BACKGROUND ............................................................................................................................... 9
MEMBERS OF THE JOINT INTERNATIONAL TEAM AND METHODS OF WORK ................ 12
MAIN FINDINGS........................................................................................................................... 16
EPIDEMIOLOGY ........................................................................................................................... 16
Surveillance data – morbidity ...................................................................................................... 16
Surveillance data – mortality ....................................................................................................... 30
Review of Stored Biological Samples Testing ............................................................................. 50
Summary and recommendations .................................................................................................. 53
References .................................................................................................................................. 56
MOLECULAR EPIDEMIOLOGY .................................................................................................. 58
Background on molecular epidemiology ...................................................................................... 58
Approach .................................................................................................................................... 61
Overview of global databases of SARS-CoV-2 ............................................................................ 61
Overview of the sequences of early cases, global overview .......................................................... 67
Zoonotic origins of SARS-CoV-2 ................................................................................................ 82
Genomic sequencing data of SARS-CoV-2 viruses in naturally infected animals ......................... 85
Summaries and perspectives ........................................................................................................ 87
References .................................................................................................................................. 88
ANIMAL AND ENVIRONMENT STUDIES ................................................................................. 92
Introduction ................................................................................................................................ 92
Methods ...................................................................................................................................... 93
Results ........................................................................................................................................ 94
Conclusions .............................................................................................................................. 108
Recommendations ..................................................................................................................... 109
References ................................................................................................................................ 110
POSSIBLE PATHWAYS OF EMERGENCE ................................................................................ 111
Direct zoonotic transmission ..................................................................................................... 112
Introduction through intermediate host followed by zoonotic transmission ................................. 114
Introduction through the cold/food chain ................................................................................... 116
Introduction through a laboratory incident ................................................................................. 118
References ................................................................................................................................ 120
CONCLUDING REMARKS ......................................................................................................... 120