Timing the SARS-CoV-2 index case in Hubei province

[Infinity Blade]

Abstract

Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

A rather telling excerpt from this study.

Our results highlight the unpredictable dynamics that characterized the earliest days of the COVID-19 pandemic. The successful establishment of SARS-CoV-2 post-zoonosis was far from certain, as more than two-thirds of simulated epidemics quickly went extinct. It is highly probable that SARS-CoV-2 was circulating in Hubei province at low levels in early-November 2019 and possibly as early as October 2019, but not earlier. Nonetheless, the inferred prevalence of this virus was too low to permit its discovery and characterization for weeks or months. By the time COVID-19 was first identified, the virus had firmly established itself in Wuhan. This delay highlights the difficulty in surveillance for novel zoonotic pathogens with high transmissibility and moderate mortality rates.

science.sciencemag.org/content/early/2021/03/17/science.abf8003