PT  - JOURNAL ARTICLE
AU  - Shing Hei Zhan
AU  - Benjamin E. Deverman
AU  - Yujia Alina Chan
TI  - SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?
AID  - 10.1101/2020.05.01.073262
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.01.073262
4099  - http://biorxiv.org/content/early/2020/05/02/2020.05.01.073262.short
4100  - http://biorxiv.org/content/early/2020/05/02/2020.05.01.073262.full
AB  - In a side-by-side comparison of evolutionary dynamics between the 2019/2020 SARS-CoV-2 and the 2003 SARS-CoV, we were surprised to find that SARS-CoV-2 resembles SARS-CoV in the late phase of the 2003 epidemic after SARS-CoV had developed several advantageous adaptations for human transmission. Our observations suggest that by the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV. However, no precursors or branches of evolution stemming from a less human-adapted SARS-CoV-2-like virus have been detected. The sudden appearance of a highly infectious SARS-CoV-2 presents a major cause for concern that should motivate stronger international efforts to identify the source and prevent near future re-emergence. Any existing pools of SARS-CoV-2 progenitors would be particularly dangerous if similarly well adapted for human transmission. To look for clues regarding intermediate hosts, we analyze recent key findings relating to how SARS-CoV-2 could have evolved and adapted for human transmission, and examine the environmental samples from the Wuhan Huanan seafood market. Importantly, the market samples are genetically identical to human SARS-CoV-2 isolates and were therefore most likely from human sources. We conclude by describing and advocating for measured and effective approaches implemented in the 2002-2004 SARS outbreaks to identify lingering population(s) of progenitor virus.Competing Interest StatementShing Hei Zhan is a Co-founder and lead bioinformatics scientist at Fusion Genomics Corporation, which develops molecular diagnostic assays for infectious diseases.